An evaluation of a novel estimator of linkage disequilibrium

The analysis of systems involving many loci is important in population and quantitative genetics. An important problem is the study of linkage disequilibrium (LD), a concept relevant in genome-enabled prediction of quantitative traits and in exploration of marker–phenotype associations. This article introduces a new estimator of a LD parameter (ρ²) that is much easier to compute than a maximum likelihood (or Bayesian) estimate of a tetra-choric correlation. We examined the conjecture that the sampling distribution of the estimator of ρ² could be less frequency dependent than that of the estimator of r², a widely used metric for assessing LD. This was done via an empirical evaluation of LD in 806 Holstein–Friesian cattle using 771 single-nucleotide polymorphism (SNP) markers and of HapMap III data on 21 991 SNPs (chromosome 3) observed in 88 unrelated individuals from Tuscany. Also, 1600 haplotypes over a region of 1 Mb simulated under the coalescent were used to estimate LD using the two measures. Subsequently, a simulation study compared the new estimator with that of r² using several scenarios of LD and allelic frequencies. From these studies, it is concluded that ρ² provides a useful metric for the study of LD as the distribution of its estimator is less frequency dependent than that of the standard estimator of r².     

基于集合经验模态分解去趋势的水分利用效率对气候变化响应的高程分异——以“21世纪海上丝绸之路”沿线省份为例

水分利用效率(WUE)是表征陆地碳-水循环耦合关系的重要指标，但其对气候变化响应的高程分异仍不清楚。通过集合经验模态分解(EEMD)去趋势和偏相关方法，以"21世纪海上丝绸之路"沿线省份为研究区，揭示WUE对气候变化的响应及其随高程的分异。研究结果表明：(1)研究区内WUE多年均值由中心向南北递减。不同植被类型的WUE多年均值由高到低依次为：常绿针叶林、混交林、常绿阔叶林、稀树灌木草地、耕地和城市建设用地。(2)51.11%的区域表现出均温与WUE的正相关；而81.46%地区表明温差的扩大会使得WUE增加；有近一半的研究区表明最高温的升高有利于提高WUE，而最低温的作用则相反；有67.99%的区域表明降水增多反而会导致WUE的减少。(3)在大多数土地覆盖类型，日温差和最低温主要与WUE呈正相关，而最高温和降水主要与WUE呈负相关。在常绿针叶林、耕地和城市建设用地，日均温与WUE呈负相关。在其他三种植被类型下则呈正相关。(4)在低海拔地区，均温与WUE呈负相关而在中高海拔地区则转变为正相关关系。而最高温则正好相反。降水与WUE的负相关关系系数随高度的增加而不断加强，而温差和最低温与WUE的正相关关系也随高度的增加而剧烈波动增强。     

Validation of chemical speciation model of inorganic arsenic in river waters with mobilisation processes

Abstract

The thermodynamic model of inorganic arsenic (acid–base, complexation, precipitation and redox equilibria) was validated with results obtained in arsenic mobilisation processes taking place in several river sediment samples of the Basque Country (North of Spain). Natural waters in contact with the sediment were collected at each sampling point, together with the sediment samples. These waters were analysed and then used as the extractant in the mobilisation studies. Considering pH, redox potential and total concentration values of the main cations and anions, the stoichiometric equilibrium constant were computed for each river water situation. The activity coefficient values of the inorganic arsenic species were estimated by means of the Modified Bromley Methodology (MBM). Both water and sediment for each sampling site were used in the mobility experiments, and the results were compared with the theoretical predictions of the thermodynamic model extrapolated to the chemical conditions of the sampling point. Moreover, a correlation analysis was also performed taking into account all the data and sampling sites; these results were also discussed and compared with the theoretical speciation obtained from the basic model of inorganic arsenic.     

基于MODIS NDVI的长江中游区域植被动态及与气候因子的关系

基于1999-2015年的MODIS NDVI时间序列遥感数据，应用趋势分析、变异系数、重标极差分析和偏相关分析等方法，分析了长江中游的植被时空变化特征及其与气象因子的关系。结果表明，长江中游地区NDVI均值总体上呈上升趋势（从0.72增加到0.80）。从空间分布来看，NDVI低值区域（0.1-0.5）占1.40%，高值区域（>0.7）占87.15%；NDVI空间格局呈"西高东低、北高南低"的分布特征，低值区域表现为以三省省会城市为中心向外辐射。Hurst指数显示，研究区大部分区域（60.54%）的NDVI变化趋势具有不确定性，持续性改善区域（34.78%）主要分布在西部山地区，持续性退化区域（3.26%）主要分布在人类活动频繁的较发达城市区域。在年际尺度上，研究区NDVI与各气象因子关系均不显著；月际尺度上，NDVI与降水、相对湿度和日照时数显著相关，降水和日照时数有明显的时滞性。区域内NDVI动态趋势以不确定性发展为主，城市群周边NDVI呈现持续退化的区域应该引起关注。     

Analysis of homodimeric avian and human galectins by two methods based on fluorescence spectroscopy: Different structural alterations upon oxidation and ligand binding

Spectroscopic monitoring is applied to detect structural alterations for homodimeric adhesion/growth-regulatory galectins. Mammalian galectin-1 and the avian ortholog CG-1B, due to their distinct patterns of cysteine positioning, can undergo oxidation. When monitoring tryptophan fluorescence anisotropy comparatively, an indicator of structural changes affecting rotational diffusion, segmental motion and/or fluorescence life time, reductions are seen in both cases upon oxidation. The decrease was especially marked for the human protein, more than 2-fold compared to the avian lectin. Using this approach to analyze binding of lactose, equilibrium and kinetic binding constants of both proteins were similar. This result is corroborated by fluorescence correlation spectroscopy with labeled proteins. Of note, the diffusion constant of CG-1B increased by 5.6% in the presence of lactose, as has been seen for the human protein. When processing the other two homodimeric avian galectins (CG-1A, CG-2) accordingly it was revealed that sequence homology does not translate into identical behavior. The diffusion constant of CG-1A was not affected, a slight decrease (−3.8%) was observed for CG-2. Obviously, alterations induced by oxidation and responses to ligand binding are different between these closely related proteins. Methodologically, the two spectroscopic techniques are proven to be sensitive and robust sensors for detecting intergalectin differences.     

Gas phase infrared spectra via the phase integration quasi-classical method

We apply the recently developed phase integration method (PIM) (Monteferrante et al. Mol Phys. 2011;109:3015–3027) to the calculation of infrared spectra of gas phase molecules. The PIM combines a generalised Monte Carlo sampling of the exact thermal density of the system with classical molecular dynamics to obtain approximate time quantum correlation functions. To describe the molecules, we adopt very simple analytical potentials that have, however, proved interesting, and surprisingly challenging, benchmarks for approximate quantum dynamical schemes. We show that, in contrast with two other commonly applied methods, our spectra do not exhibit spurious features or unphysical shifts depending on the temperature. Identifying the positions of the peaks requires only a few tens of trajectories, while an accurate evaluation of the relative intensities of the peaks is computationally more demanding.     

A quantitative validation of fluorophore-labelled cell-permeable peptide conjugates: fluorophore and cargo dependence of import

Cell-permeable peptides were evaluated for a quantitatively controlled import of small molecules. The dependence of the import efficiency on the fluorophore, on the position of the fluorophore as well as on the nature of the cargo were addressed. Cellular uptake was quantitated by flow cytometry and fluorescence correlation microscopy (FCM). Fluorophores with different spectral characteristics, covering the whole visible spectral range, were selected in order to enable the simultaneous detection of several cell-permeable peptide constructs. The transcytosis sequences were based either on the sequence of the Antennapedia homeodomain protein (AntpHD)-derived penetratin peptide or the Kaposi fibroblast growth factor (FGF)-derived membrane translocating sequence (MTS)-peptide. In general, the AntpHD-derived peptides had a three- to fourfold higher import efficiency than the MTS-derived peptides. In spite of the very different physicochemical characteristics of the fluorophores, the import efficiencies for analogues labelled at different positions within the sequence of the import peptides showed a strong positive correlation. However, even for peptide cargos of very similar size, pronounced differences in import efficiency were observed. The use of cell-permeable peptide/cargo constructs for intracellular analyses of structure-function relationships therefore requires the determination of the intracellular concentrations for each construct individually.     

Heterozygosity is linked to the costs of immunity in nestling great tits (Parus major)

There is growing evidence that heterozygosity–fitness correlations (HFCs) are more pronounced under harsh conditions. Empirical evidence suggests a mediating effect of parasite infestation on the occurrence of HFCs. Parasites have the potential to mediate HFCs not only by generally causing high stress levels but also by inducing resource allocation tradeoffs between the necessary investments in immunity and other costly functions. To investigate the relative importance of these two mechanisms, we manipulated growth conditions of great tit nestlings by brood size manipulation, which modifies nestling competition, and simultaneously infested broods with ectoparasites. We investigated under which treatment conditions HFCs arise and, second, whether heterozygosity is linked to tradeoff decisions between immunity and growth. We classified microsatellites as neutral or presumed functional and analyzed these effects separately. Neutral heterozygosity was positively related to the immune response to a novel antigen in parasite‐free nests, but not in infested nests. For nestlings with lower heterozygosity levels, the investments in immunity under parasite pressure came at the expenses of reduced feather growth, survival, and female body condition. Functional heterozygosity was negatively related to nestling immune response regardless of the growth conditions. These contrasting effects of functional and neutral markers might indicate different underlying mechanisms causing the HFCs. Our results confirm the importance of considering marker functionality in HFC studies and indicate that parasites mediate HFCs by influencing the costs of immune defense rather than by a general increase in environmental harshness levels.