A model of restriction endonuclease MvaI in complex with DNA: a template for interpretation of experimental data and a guide for specificity engineering

R.MvaI is a Type II restriction enzyme (REase), which specifically recognizes the pentanucleotide DNA sequence 5'-CCWGG-3' (W indicates A or T). It belongs to a family of enzymes, which recognize related sequences, including 5'-CCSGG-3' (S indicates G or C) in the case of R.BcnI, or 5'-CCNGG-3' (where N indicates any nucleoside) in the case of R.ScrFI. REases from this family hydrolyze the phosphodiester bond in the DNA between the 2nd and 3rd base in both strands, thereby generating a double strand break with 5'-protruding single nucleotides. So far, no crystal structures of REases with similar cleavage patterns have been solved. Characterization of sequence-structure-function relationships in this family would facilitate understanding of evolution of sequence specificity among REases and could aid in engineering of enzymes with new specificities. However, sequences of R.MvaI or its homologs show no significant similarity to any proteins with known structures, thus precluding straightforward comparative modeling. We used a fold recognition approach to identify a remote relationship between R.MvaI and the structure of DNA repair enzyme MutH, which belongs to the PD-(D/E)XK superfamily together with many other REases. We constructed a homology model of R.MvaI and used it to predict functionally important amino acid residues and the mode of interaction with the DNA. In particular, we predict that only one active site of R.MvaI interacts with the DNA target at a time, and the cleavage of both strands (5'-CCAGG-3' and 5'-CCTGG-3') is achieved by two independent catalytic events. The model is in good agreement with the available experimental data and will serve as a template for further analyses of R.MvaI, R.BcnI, R.ScrFI and other related enzymes.     

Radio-telemetric monitoring of dispersing stag beetles: implications for conservation

Migratory movements of the endangered stag beetles Lucanus cervus (18 males, 38 females) were monitored radio-telemetrically for three reproductive periods (2003–2005). The aim of the study was to estimate the migratory range of free-ranging individuals as a measure of connectivity among neighbouring populations for future conservation measures. Miniature transmitters of c . 350 mg (battery life: 10–15 days) were attached externally to the pronotum. Transmitter/beetle mass ratio was 12.8% on average (7.1–28.0%). Male dispersal behaviour consisted of frequent flights directed to sites with reproductive females and rarely of on-ground movement. Total displacement distance recorded was up to 2065 m, the maximum distance of a single flight being 1720 m. Flights always began at elevated structures such as trees and shrubs and took place in an air temperature range of 11–27°C. Within this range, temperature did not influence flight distance. Female dispersal behaviour consisted mostly of a single flight, followed by mating and consequent ground movements towards oviposition sites. Total displacement distance recorded was up to 762.6 m, the maximum distance of a single flight being 701 m. Climatic constraints of flights were the same as in males. Modelling the dispersal behaviour suggests that about 1% of males are capable of maintaining gene flux among nest sites within a radius of about 3 km. However, the colonization of new nest sites depends on the dispersal ability of females and amounts to less than 1 km. Thus, isolated populations (distance to the next population greater than 3 km) have an increased probability of local extinction.     

陕西省植被覆盖时空变化及其对极端气候的响应

基于2001—2018年MODIS NDVI数据,从生态分区视角分析陕西省归一化植被指数(NDVI)的时空变化特征,并结合该地区31个气象站点日值数据,探讨NDVI对极端气温和极端降水指数的响应特征。结果表明：(1)陕西省及其各生态区的NDVI变化均显著上升,整体呈南高北低的分布特点,其中秦巴山地落叶与阔叶林生态区(IV)NDVI值最高为0.86,陕北北部典型草原生态区(I)NDVI值最低为0.38。(2)年际尺度上,陕西省NDVI与极端气温暖极值(暖夜日数)和极端降水指数总体呈显著正相关(P<0.05),在陕西省北部NDVI变化主要受极端降水的影响,南部则对极端气温的敏感度更高。(3)多年月尺度上,各生态区NDVI对极端气温冷极值(最低气温、日最低气温的极低值和日最高气温的极低值)和极端气温暖极值(最高气温、日最低气温的极高值和日最高气温的极高值)存在明显的滞后性,滞后时间多为3个月;与极端降水指数(单日最大降水量和连续5日最大降水量)的滞后时间为2个月,说明陕西省内NDVI对极端气候的响应具有显著的滞后效应。     

A narrowing gyre? The Lega Nord and the shifting balance of Italian immigration policy

This article reflects on the relations between xenophobic parties and immigration policy in Italy. It argues that the salience of the Northern League (Lega Nord), the instability of the Italian party system and the recent transformation of Italy from an emigration country to an immigration country all contribute to Italy's difficulty in achieving a coherent immigration policy. Since the first comprehensive immigration policy emerged in 1998 with the Turco-Napolitano law, there have been six changes of government, with frequent oscillation between centre-right and centre-left coalitions. While the effects of these oscillations, particularly of the centre-right's effort to restrict immigrants’ rights and entry possibilities, have been dampened by the Italian courts and the European Union, it is still problematic to speak of an Italian model. Drawing on Carvalho's book, this article will address the effects of the Lega on creating and maintaining this policy imbalance.     

Systemic lupus erythematosus: molecular cloning and analysis of 22 individual recombinant monoclonal kappa light chains specifically hydrolyzing human myelin basic protein

Antibodies hydrolyzing myelin basic protein (MBP) can play an important role in the pathogenesis of multiple sclerosis (MS) and systemic lupus erythematosus (SLE). An immunoglobulin light chain phagemid library derived from peripheral blood lymphocytes of patients with SLE was used. Small pools of phage particles displaying light chains with different affinities for MBP were isolated by affinity chromatography on MBP‐Sepharose, and the fraction eluted with 0.5 M NaCl was used for preparation of individual monoclonal light chains (MLChs, 26–27 kDa). Seventy‐two of 440 individual colonies were randomly chosen, expressed in Escherichia coli in a soluble form, and MLChs were purified by metal chelating chromatography. Twenty‐two of 72 MLChs have high affinity and efficiently hydrolyze only MBP (not other control proteins) demonstrating various pH optima in a 5.7–9.0 range and different substrate specificity in the hydrolysis of four different MBP oligopeptides. Four MLChs demonstrated serine protease‐like and three thiol protease‐like activities, while 11 MLChs were metalloproteases. The activity of three MLChs was inhibited by both phenylmethylsulfonyl fluoride (PMSF) and Ethylenediaminetetraacetic acid (EDTA), two other by EDTA and iodoacetamide, and one by PMSF, EDTA, and iodoacetamide. The ratio of relative activity in the presence of Ca²⁺, Mg²⁺_, Mn²⁺, Ni²⁺, Zn²⁺, Cu²⁺, and Co²⁺ was individual for each of 22 MLCh preparations. It is the first examples of human MLChs, which probably can possess two or even three different proteolytic activities. These observations suggest an extreme diversity of anti‐MBP abzymes in SLE patients. The immune systems of individual SLE patients can generate a variety of anti‐MBP abzymes, which can attack MBP of myelin‐proteolipid sheath of axons and play an important role in MS and SLE pathogenesis. Copyright © 2015 John Wiley & Sons, Ltd.     

Light pollution alters the phenology of dawn and dusk singing in common European songbirds

Artificial night lighting is expanding globally, but its ecological consequences remain little understood. Animals often use changes in day length as a cue to time seasonal behaviour. Artificial night lighting may influence the perception of day length, and may thus affect both circadian and circannual rhythms. Over a 3.5 month period, from winter to breeding, we recorded daily singing activity of six common songbird species in 12 woodland sites, half of which were affected by street lighting. We previously reported on analyses suggesting that artificial night lighting affects the daily timing of singing in five species. The main aim of this study was to investigate whether the presence of artificial night lighting is also associated with the seasonal occurrence of dawn and dusk singing. We found that in four species dawn and dusk singing developed earlier in the year at sites exposed to light pollution. We also examined the effects of weather conditions and found that rain and low temperatures negatively affected the occurrence of dawn and dusk singing. Our results support the hypothesis that artificial night lighting alters natural seasonal rhythms, independently of other effects of urbanization. The fitness consequences of the observed changes in seasonal timing of behaviour remain unknown.     

Environmental variation and population responses to global change

Species' responses to environmental changes such as global warming are affected not only by trends in mean conditions, but also by natural and human‐induced environmental fluctuations. Methods are needed to predict how such environmental variation affects ecological and evolutionary processes, in order to design effective strategies to conserve biodiversity under global change. Here, we review recent theoretical and empirical studies to assess: (1) how populations respond to changes in environmental variance, and (2) how environmental variance affects population responses to changes in mean conditions. Contrary to frequent claims, empirical studies show that increases in environmental variance can increase as well as decrease long‐term population growth rates. Moreover, environmental variance can alter and even reverse the effects of changes in the mean environment, such that even if environmental variance remains constant, omitting it from population models compromises their ability to predict species' responses to changes in mean conditions. Drawing on theory relating these effects of environmental variance to the curvatures of population growth responses to the environment, we outline how species' traits such as phylogenetic history and body mass could be used to predict their responses to global change under future environmental variability.     

Cold truths: how winter drives responses of terrestrial organisms to climate change

Winter is a key driver of individual performance, community composition, and ecological interactions in terrestrial habitats. Although climate change research tends to focus on performance in the growing season, climate change is also modifying winter conditions rapidly. Changes to winter temperatures, the variability of winter conditions, and winter snow cover can interact to induce cold injury, alter energy and water balance, advance or retard phenology, and modify community interactions. Species vary in their susceptibility to these winter drivers, hampering efforts to predict biological responses to climate change. Existing frameworks for predicting the impacts of climate change do not incorporate the complexity of organismal responses to winter. Here, we synthesise organismal responses to winter climate change, and use this synthesis to build a framework to predict exposure and sensitivity to negative impacts. This framework can be used to estimate the vulnerability of species to winter climate change. We describe the importance of relationships between winter conditions and performance during the growing season in determining fitness, and demonstrate how summer and winter processes are linked. Incorporating winter into current models will require concerted effort from theoreticians and empiricists, and the expansion of current growing‐season studies to incorporate winter.