NEMO specifically recognizes K63‐linked poly‐ubiquitin chains through a new bipartite ubiquitin‐binding domain

An important property of NEMO, the core element of the IKK complex involved in NF‐κB activation, resides in its ability to specifically recognize poly‐ubiquitin chains. A small domain called NOA/UBAN has been suggested to be responsible for this property. We recently demonstrated that the C‐terminal Zinc Finger (ZF) of NEMO is also able to bind ubiquitin. We show here by ZF swapping and mutagenesis that this represents its only function. While neither NOA nor ZF shows any preference for K63‐linked chains, we demonstrate that together they form a bipartite high‐affinity K63‐specific ubiquitin‐binding domain. A similar domain can be found in two other proteins, Optineurin and ABIN2, and can be freely exchanged with that of NEMO without interfering with its activity. This suggests that the main function of the C‐terminal half of NEMO is to specifically bind K63‐linked poly‐ubiquitin chains. We also demonstrate that the recently described binding of NEMO to linear poly‐ubiquitin chains is dependent on the NOA alone and does not require the presence of the ZF.     

Roadsides provide refuge for orchids: characteristic of the surrounding landscape

Seminatural habitats are declining throughout the world; thus, the role of small anthropogenic habitats in the preservation of plants is becoming increasingly appreciated. Here, we surveyed the orchid flora of roadside verges in five Central European countries (Austria, Hungary, Romania, Slovakia, and Slovenia) and tested how the surrounding landscape matrix affects the overall number of species and individuals, and also different functional groups of orchids. We found more than 2,000 individuals of 27 orchid species during our surveys. According to our results, the increasing coverage of agricultural and urban areas negatively affects both the number of orchid species and individuals on roadsides. Our study further suggests that differences in the surrounding habitats affect which species are found on roadsides, since the increasing coverage of grasslands or forested areas around orchid occurrences had a significant positive effect on the number of grassland or forest‐dwelling species and individuals, respectively. Most variance in orchid numerosity and diversity was explained by the cover of the suitable habitat types of the respective taxa in the surrounding landscape of the sampling points. This highlights the importance of roadsides acting as refugia for numerous species and valuable plant communities as well as in supporting biodiversity in general.     

Parameter estimation for discretely observed linear birth‐and‐death processes

Birth‐and‐death processes are widely used to model the development of biological populations. Although they are relatively simple models, their parameters can be challenging to estimate, as the likelihood can become numerically unstable when data arise from the most common sampling schemes, such as annual population censuses. A further difficulty arises when the discrete observations are not equi‐spaced, for example, when census data are unavailable for some years. We present two approaches to estimating the birth, death, and growth rates of a discretely observed linear birth‐and‐death process: via an embedded Galton‐Watson process and by maximizing a saddlepoint approximation to the likelihood. We study asymptotic properties of the estimators, compare them on numerical examples, and apply the methodology to data on monitored populations.     

晋西黄土区典型乔灌木短期水分利用效率对环境因子的响应

为明确晋西黄土区植物的水分利用规律及对半干旱区的适应策略, 提高黄土地区植被建设效益, 该研究对该地区典型乔灌木短期水分利用效率随环境因子的变化进行了探究。以典型乔木油松(Pinus tabuliformis)、刺槐(Robinia pseudoacacia)及其林下灌木黄刺玫(Rosa xanthina)、杠柳(Periploca sepium)为研究对象, 测定叶片可溶性糖稳定碳同位素比值(δ¹³C_leaf)与枝条渗出液稳定碳同位素比值(δ¹³C_branch), 使用δ¹³C_leaf推导计算7-10月叶片尺度下植物短期水分利用效率(WUE_leaf)变化趋势, 使用δ¹³C_branch明确植物光合作用后分馏情况, 确定半干旱区植物在生长季的水分变化规律对环境因子变化的响应。结果表明: (1) 7-10月4种植物δ¹³C_leaf总体呈现降低趋势, δ¹³C_branch呈现先升高后降低趋势。δ¹³C_leaf在种间和生活型中均存在差异。具体表现为: 灌木>乔木, 常绿乔木(油松) >落叶乔木(刺槐)。研究过程中未发现明显的碳同位素在光合作用后发生分馏的情况。(2) 4种植物WUE_leaf在7-8月保持稳定, 9-10月逐渐升高。21.5 ℃、0.9 kPa、52.4%分别为WUE_leaf随温度(T_a)、饱和水汽压差(VPD)、相对湿度(RH)变化的突变点, 突变点之后4种植物WUE_leaf均表现出稳定的变化趋势, 不再随T_a、VPD、RH升高而降低。(3) WUE_leaf与T_a、RH、VPD之间存在显著负相关关系, T_a通过非气孔因素, 即酶的作用改变光合速率, 引起WUE_leaf变化。RH、VPD等水分因子则通过改变气孔开度, 影响蒸腾, 进而改变WUE_leaf。随着土壤含水量(SWC)的升高, WUE_leaf呈现先升高后降低的趋势。油松林和刺槐林在SWC分别达到15%-18%、13%-14%时, WUE_leaf达到最高值。经过混合线性模型(LMM)分析得到, 油松和刺槐WUE_leaf主导环境因子分别为RH和VPD, 黄刺玫和杠柳WUE_leaf主导环境因子均为T_a。该研究得到了黄土地区典型乔灌木生长季水分利用效率变化的规律和主要环境影响因子, 明确了黄土地区植物对气候因子变化的适应机制。     

LEC–BiFC: a new method for rapid assay of protein interaction

Abstract

Protein–protein interactions play fundamental roles in most biological processes. Bimolecular fluorescence complementation (BiFC) is a promising method for its simplicity and direct visualization of protein–protein interactions in cells. This method, however, is limited by background fluorescence that appears without specific interaction between the proteins. We report here a point mutation (V150L) in one Venus BiFC fragment that efficiently decreases background fluorescence of BiFC assay. Furthermore, by combining this modified BiFC and linear expression cassette (LEC), we develop a simple and rapid method (LEC–BiFC) for protein interaction analysis that is demonstrated by a case study of the interaction between Bcl–X_L and Bak BH3 peptide. The total analysis procedure can be completed in two days for screening tens of mutants. LEC–BiFC can be applied easily in any lab equipped with a fluorescence microscope.     

The past,present and future of thermophilous Cyperus polystachyos Rottb. (Cyperaceae) on the island of Ischia (southern Italy)

Cyperus polystachyos is a hygrophilous, thermophilous and heliophilous plant with a punctiform distribution in southern Italy, where it is almost exclusively found on Ischia, an island in the Bay of Naples characterized by widespread volcanic hydrothermal activity. This species is a native of tropical and subtropical areas and there is evidence for ancient isolation events in the creation of its current distribution pattern. We have studied the historical literature available for this plant since 1800 and collected temporal and spatial presence data of this species in order to develop a habitat suitability map based on a GIS approach and using a multiple linear regression model. Moreover, we have used univariate and multivariate statistical analysis. The results show the importance of the environmental mosaic around fumaroles to preserve the species; urbanization and geothermal energy use of fumaroles in the past and the combination of abandonment of the typical agricultural system and the natural occurrence of reforestation in the present are the main causes of the decline in the number of populations.     

Prediction of HIV-1 protease inhibitory activity of 4-hydroxy-5,6-dihydropyran-2-ones: QSAR study

Inhibition of human immunodeficiency virus 1 (HIV-1) protease is an important strategy for the treatment of HIV and acquired immune deficiency syndrome (AIDS). Therefore, HIV-1 protease inhibitory activity of dihydropyranone derivatives has been analyzed with different physico-chemical parameters. In the present work, QSAR studies were performed on a series of 4-hydroxy-5,6-dihydropyran-2-ones to explore the physico-chemical parameters responsible for their HIV-1 protease inhibitory activity. Physico-chemical parameters were calculated using WIN CAChe 6.1. Stepwise multiple linear regression analysis was performed to derive QSAR models which were further evaluated for statistical significance and predictive power by internal and external validation. The selected best QSAR model was having correlation coefficient (R)?=?0.875 and cross-validated squared correlation coefficient (Q²)?=?0.707. The developed significant QSAR model indicates that hydrophobicity of whole molecule and the substituent present at sixth position of dihydropyranones play an important role in the HIV-1 protease inhibitory activities of 4-hydroxy-5,6-dihydropyran-2-ones.     

Driving factors of a vegetation shift from Scots pine to pubescent oak in dry Alpine forests

An increasing number of studies have reported on forest declines and vegetation shifts triggered by drought. In the Swiss Rhone valley (Valais), one of the driest inner‐Alpine regions, the species composition in low elevation forests is changing: The sub‐boreal Scots pine (Pinus sylvestris L.) dominating the dry forests is showing high mortality rates. Concurrently the sub‐Mediterranean pubescent oak (Quercus pubescens Willd.) has locally increased in abundance. However, it remains unclear whether this local change in species composition is part of a larger‐scale vegetation shift. To study variability in mortality and regeneration in these dry forests we analysed data from the Swiss national forest inventory (NFI) on a regular grid between 1983 and 2003, and combined it with annual mortality data from a monitoring site. Pine mortality was found to be highest at low elevation (below 1000 m a.s.l.). Annual variation in pine mortality was correlated with a drought index computed for the summer months prior to observed tree death. A generalized linear mixed‐effects model indicated for the NFI data increased pine mortality on dryer sites with high stand competition, particularly for small‐diameter trees. Pine regeneration was low in comparison to its occurrence in the overstorey, whereas oak regeneration was comparably abundant. Although both species regenerated well at dry sites, pine regeneration was favoured at cooler sites at higher altitude and oak regeneration was more frequent at warmer sites, indicating a higher adaptation potential of oaks under future warming. Our results thus suggest that an extended shift in species composition is actually occurring in the pine forests in the Valais. The main driving factors are found to be climatic variability, particularly drought, and variability in stand structure and topography. Thus, pine forests at low elevations are developing into oak forests with unknown consequences for these ecosystems and their goods and services.