When the going gets tough: behavioural type-dependent space use in the sleepy lizard changes as the season dries

Understanding space use remains a major challenge for animal ecology, with implications for species interactions, disease spread, and conservation. Behavioural type (BT) may shape the space use of individuals within animal populations. Bolder or more aggressive individuals tend to be more exploratory and disperse further. Yet, to date we have limited knowledge on how space use other than dispersal depends on BT. To address this question we studied BT-dependent space-use patterns of sleepy lizards (Tiliqua rugosa) in southern Australia. We combined high-resolution global positioning system (GPS) tracking of 72 free-ranging lizards with repeated behavioural assays, and with a survey of the spatial distributions of their food and refuge resources. Bayesian generalized linear mixed models (GLMM) showed that lizards responded to the spatial distribution of resources at the neighbourhood scale and to the intensity of space use by other conspecifics (showing apparent conspecific avoidance). BT (especially aggressiveness) affected space use by lizards and their response to ecological and social factors, in a seasonally dependent manner. Many of these effects and interactions were stronger later in the season when food became scarce and environmental conditions got tougher. For example, refuge and food availability became more important later in the season and unaggressive lizards were more responsive to these predictors. These findings highlight a commonly overlooked source of heterogeneity in animal space use and improve our mechanistic understanding of processes leading to behaviourally driven disease dynamics and social structure.     

Cross‐Reactivity of Polyclonal Antibodies against Canavalia ensiformis (Jack Bean) Urease and Helicobacter pylori Urease Subunit A Fragments

Overlapping decapeptide fragments of H. pylori urease subunit A (UreA) were synthesized and tested with polyclonal antibodies against Canavalia ensiformis (Jack bean) urease. The linear epitopes of UreA identified using the dot blot method were then examined using epitope mapping. For this purpose, series of overlapping fragments of UreA, frameshifted ± four amino acid residues were synthesized. Most of the UreA epitopes which reacted with the Jack bean urease polyclonal antibodies had been recognized in previous studies by monoclonal antibodies against H. pylori urease. Fragments 11 – 24, 21 – 33, and 31 – 42 were able to interact with the Jack bean urease antibodies, giving stable immunological complexes. However, the lack of recognition by these antibodies of all the components in the peptide map strongly suggests that a non‐continuous (nonlinear) epitope is located on the N‐terminal domain of UreA.     

There Is No Need To Be Normal: Generalized Linear Models of Natural Variation

Both ecological field studies and attempts to extrapolate from laboratory experiments to natural populations generally encounter the high degree of natural variability and chaotic behavior that typify natural ecosystems. Regardless of this variability and non-normal distribution, most statistical models of natural systems use normal error which assumes independence between the variance and mean. However, environmental data are often random or clustered and are better described by probability distributions which have more realistic variance to mean relationships. Until recently statistical software packages modeled only with normal error and researchers had to assume approximate normality on the original or transformed scale of measurement and had to live with the consequences of often incorrectly assuming independence between the variance and mean. Recent developments in statistical software allow researchers to use generalized linear models (GLMs) and analysis can now proceed with probability distributions from the exponential family which more realistically describe natural conditions: binomial (even distribution with variance less than mean), Poisson (random distribution with variance equal mean), negative binomial (clustered distribution with variance greater than mean). GLMs fit parameters on the original scale of measurement and eliminate the need for obfuscating transformations, reduce bias for proportions with unequal sample size, and provide realistic estimates of variance which can increase power of tests. Because GLMs permit modeling according to the non-normal behavior of natural systems and obviate the need for normality assumptions, they will likely become a widely used tool for analyzing toxicity data. To demonstrate the broad-scale utility of GLMs, we present several examples where the use of GLMs improved the statistical power of field and laboratory studies to document the rapid ecological recovery of Prince William Sound following the Exxon Valdez oil spill.     

The walk is never random: subtle landscape effects shape gene flow in a continuous white-tailed deer population in the Midwestern United States

One of the pervasive challenges in landscape genetics is detecting gene flow patterns within continuous populations of highly mobile wildlife. Understanding population genetic structure within a continuous population can give insights into social structure, movement across the landscape and contact between populations, which influence ecological interactions, reproductive dynamics or pathogen transmission. We investigated the genetic structure of a large population of deer spanning the area of Wisconsin and Illinois, USA, affected by chronic wasting disease. We combined multiscale investigation, landscape genetic techniques and spatial statistical modelling to address the complex questions of landscape factors influencing population structure. We sampled over 2000 deer and used spatial autocorrelation and a spatial principal components analysis to describe the population genetic structure. We evaluated landscape effects on this pattern using a spatial autoregressive model within a model selection framework to test alternative hypotheses about gene flow. We found high levels of genetic connectivity, with gradients of variation across the large continuous population of white-tailed deer. At the fine scale, spatial clustering of related animals was correlated with the amount and arrangement of forested habitat. At the broader scale, impediments to dispersal were important to shaping genetic connectivity within the population. We found significant barrier effects of individual state and interstate highways and rivers. Our results offer an important understanding of deer biology and movement that will help inform the management of this species in an area where overabundance and disease spread are primary concerns.     

Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies

We have compared the predictions of ligand‐binding affinities from several methods based on end‐point molecular dynamics simulations and continuum solvation, that is, methods related to MM/PBSA (molecular mechanics combined with Poisson–Boltzmann and surface area solvation). Two continuum‐solvation models were considered, viz., the Poisson–Boltzmann (PB) and generalised Born (GB) approaches. The nonelectrostatic energies were also obtained in two different ways, viz., either from the sum of the bonded, van der Waals, nonpolar solvation energies, and entropy terms (as in MM/PBSA), or from the scaled protein–ligand van der Waals interaction energy (as in the linear interaction energy approach, LIE). Three different approaches to calculate electrostatic energies were tested, viz., the sum of electrostatic interaction energies and polar solvation energies, obtained either from a single simulation of the complex or from three independent simulations of the complex, the free protein, and the free ligand, or the linear‐response approximation (LRA). Moreover, we investigated the effect of scaling the electrostatic interactions by an effective internal dielectric constant of the protein (?_int). All these methods were tested on the binding of seven biotin analogues to avidin and nine 3‐amidinobenzyl‐1H‐indole‐2‐carboxamide inhibitors to factor Xa. For avidin, the best results were obtained with a combination of the LIE nonelectrostatic energies with the MM+GB electrostatic energies from a single simulation, using ?_int = 4. For fXa, standard MM/GBSA, based on one simulation and using ?_int = 4–10 gave the best result. The optimum internal dielectric constant seems to be slightly higher with PB than with GB solvation. © Proteins 2012; © 2012 Wiley Periodicals, Inc.     

FbpA — A bacterial transferrin with more to offer

Background

Gram negative bacteria require iron for growth and virulence. It has been shown that certain pathogenic bacteria such as Neisseria gonorrhoeae possess a periplasmic protein called ferric binding protein (FbpA), which is a node in the transport of iron from the cell exterior to the cytosol.

Scope of review

The relevant literature is reviewed which establishes the molecular mechanism of FbpA mediated iron transport across the periplasm to the inner membrane.

Major conclusions

Here we establish that FbpA may be considered a bacterial transferrin on structural and functional grounds. Data are presented which suggest a continuum whereby FbpA may be considered as a naked iron carrier, as well as a Fe–chelate carrier, and finally a member of the larger family of periplasmic binding proteins.

General significance

An investigation of the molecular mechanisms of action of FbpA as a member of the transferrin super family enhances our understanding of bacterial mechanisms for acquisition of the essential nutrient iron, as well as the modes of action of human transferrin, and may provide approaches to the control of pathogenic diseases. This article is part of a Special Issue entitled Transferrins: Molecular mechanisms of iron transport and disorders.     

几何形态测量学方法在小哺乳动物化石分类鉴定中的应用——4种(鼠平)类化石大样本的个案研究

小哺乳动物化石在晚新生代生物地层学和生物年代学研究中具有重要作用,尤其是筛洗法在古生物调查中得到广泛应用后,通常可以采集到数量可观的标本,使得其地位较大型哺乳动物化石更加彰显.因此,小哺乳动物化石标本的分类鉴定也成了一项十分关键的工作.然而,传统形态学方法在对大量标本进行分类鉴定时,往往容易受主观因素影响而将不稳定的细微性状变异作为依据建立新种,或者忽视一些肉眼难于察觉的形态学差异而将两个甚至多个类群合并到一起,导致基于形态学的化石分类鉴定随意性增加,失去客观性.此外,对于不具鉴定意义的非关键性单个牙齿,很难凭借肉眼或显微镜观察进行区分.针对这些问题,本文选取了安徽繁昌人字洞早更新世早期三种(鼠平)类甘肃模鼠Mimomys gansunicus,郑氏异模鼠Heteromimomys zhengi和繁昌维蓝尼鼠Hllanyia fanchangensis的1284件臼齿并以早上新世内蒙古比例克的比例克模鼠Mimomys bilikeensis的163件臼齿作为参考,采用几何形态测量学方法在各个臼齿咬合面上分别选取了7～14个同源landmark对咬合面的形态特征进行了线性判别分析,建立了针对这4个种的臼齿咬合面形态差异判别函数.分析结果表明,根据这些landmark所提供的形态差异信息,人字洞的1284件臼齿标本中的确存在3个可以明显区分且形态学性状稳定的类群,先前的分类鉴定得到了验证.与之不同地点不同时代的比例克模鼠也可以很好区分.因此,建立在大样本基础上的这4种(鼠平)类臼齿咬合面同源形态特征的判别函数可以用来描述这些种类较为稳定的形态特征差异,并用来作为今后对样本较少的标本进行分类鉴定时的判别依据.因为几何形态测量学的方法不仅可以对二维的离散landmark数据以及重要形态学特征的轮廓线进行分析,甚至还可以扩展至三维空间,所以上述方法对于较为容易获得大样本标本的小哺乳物化石分类鉴定具有普遍意义.     

线性回归法复原化石标本中的残缺数据(英文)

基于多元统计分析中对样本完整性的要求,为了在分析中不抛弃大量不完整的化石标本或者不大大减少变量,创建了一种恢复标本残缺数据的方法。本方法基于线性回归理论,假设同类标本个体之间的区别仅仅是大小的区别,形状的区别可以忽略不计,因此,在同类标本中,可以用一件标本的已知测量数据预测另一件标本的残缺测量数据。在多件标本的情况下,对某件标本的某个残缺数据的预测结果是用其他标本分别进行预测所得值的加权平均,加权系数的选取与每件标本的保存完好程度相关。用现生马属头骨及肢骨标本做的数据试验证明,该方法具有良好的稳定性,对标本的种类、数量及残缺值的多少均不敏感,对于尺寸较大的标本或数值较大的数据的预测效果要比对尺寸较小的标本或数值较小的数据的预测效果要好。与传统的线性回归方法的不同之处在于,本方法利用的是样本(即标本)间的线性相关性,传统方法利用的是变量(即测量项)间的线性相关性。在通常情况下,样本间的线性相关程度要优于变量间的线性相关程度。本方法简单实用,在对化石标本进行统计分析,特别是多元统计分析中具有良好的应用前景。     

粳稻糙米钙含量QTL分析

以'十和田'为轮回亲本,'丽粳2号'为供体,培育出糙米钙含量近等基因系下的重组近交系261个BC_5F_6株系,采用BSA法从遍布水稻12条染色体上的600对SSR引物中筛选到1个与糙米钙含量有关联的SSR标记RM5536.进一步据其在水稻染色体上的位置,结合PCR找到了与糙米钙含量有关的3个SSR标记(RM5794、RM5362和RM12178).用MAPMAKER/EXP3.0软件做出了这4个标记的连锁群,最后采用混合线性模型找到了糙米钙含量QTL位点.QTL分析结果显示:该位点位于1号染色体引物RM12178和RM5362之间,贡献率为9.62%,为新发现的糙米钙含量QTL位点,暂命名为qBRCA-1.并发现与糙米锶含量有关的QTL位点,其位于标记RM5362和RM5794之间,贡献率为3.93%.同时本试验首次从分子水平上验证了偏相关比简单相关更准确解释元素间的相关性.