Conservation implications of past and present nesting habitat selection of the endangered Osprey Pandion haliaetus population of the Canary Islands

We studied nesting habitat selection of the endangered non‐migratory Osprey Pandion haliaetus population of the Canary Islands and evaluated the effect of human expansion in recent decades. Compared with randomly selected potential nest‐sites, Osprey nests were more frequently found on taller, southwest‐facing cliffs, characterized by lower human pressure and closer to Yellow‐legged Gull Larus michahellis colonies and Barbary Falcon Falco pelegrinoides breeding sites. Furthermore, changes in some breeding habitat features have been detected in recent decades. According to our predictive models, large areas of suitable habitat are available but unoccupied in the Canaries, and human activities are probably limiting the settlement and dispersion of new pairs.     

CTCF, cohesin, and histone variants: connecting the genome

During the last decades our view of the genome organization has changed. We moved from a linear view to a looped view of the genome. It is now well established that inter- and intra-connections occur between chromosomes and play a major role in gene regulations. These interconnections are mainly orchestrated by the CTCF protein, which is also known as the "master weaver" of the genome. Recent advances in sequencing and genome-wide studies revealed that CTCF binds to DNA at thousands of sites within the human genome, providing the possibility to form thousands of genomic connection hubs. Strikingly, two histone variants, namely H2A.Z and H3.3, strongly co-localize at CTCF binding sites. In this article, we will review the recent advances in CTCF biology and discuss the role of histone variants H2A.Z and H3.3 at CTCF binding sites.     

Drought-induced tree growth decline in the desert margins of Northwestern China

Water deficiency is the primary limiting factor for tree growth in arid and semi-arid areas. Droughts associated with rising temperatures have increased in severity and frequency globally over the past few decades, making the trees in the drought-prone sites first be affected by water shortages. However, our understanding of tree growth status in these areas, and of their response to drought, is currently insufficient; especially in the context of global warming. Here, we studied 94 Chinese pine (Pinus tabulaeformis) and 86 spruce (Picea crassifolia) trees from different altitudes [2,100–2400 m above sea level (a.s.l.)] distributed at the desert margins of Northwestern China to explore tree growth and drought response from multiple perspectives using dendroecological approaches. Significant growth decline, across all tree species and altitudes, was detected in response to an interdecadal trend towards a drier climate. Moreover, the extent of tree growth decline, the proportion of affected trees, and the degree of moisture dependence have all tended to increase in each sample site, most likely due to enhanced drought severity and duration in recent decades. The more sensitive and susceptible trees were found at lower elevations (drier sites) and may signify a higher vulnerability to heating-induced drought stress. Tree resistance to drought showed strong negative correlation with drought severity across all sample sites. However, the connection between post-drought tree resilience and drought intensity is weak, perhaps because the samples were all collected from living trees, while those that had died were not sampled. The priority for future work should be to combine surviving and dead trees simultaneously, thus achieving a more representative view of tree resilience to drought; this will improve our knowledge of forest dynamics and even ecosystem succession in these vulnerable and sensitive environments.     

Organization of glycosaminoglycan sulfation in the biosynthesis of proteochondroitin sulfate and proteodermatan sulfate

Although the intermediates for sulfation of proteochondroitin and proteodermatan have been known for several decades, organizational aspects of this formation have not been clearly defined. Work in several laboratories, including our own, have indicated a pattern which strongly suggests that sulfation ordinarily takes place together with glycosaminoglycan polymerization in the same Golgi sites, and with close relationship to aspects of polymer elongation, polymer modification and polymer termination. the organization of sulfation together with polymerization may be a major factor controlling the location, type, and degree of sulfation, which in turn may direct specific functions of these proteoglycans.     

Following the RAD6 pathway

Errol Friedberg suggested that I write a biographical account of the work carried out in my lab for the Historical Reflections section of the DNA Repair. Although I started out studying meiotic recombination, I have spent much of the last four and a half decades focused on trying to understand the mechanism underlying induced mutagenesis, which led me into what was eventually called DNA damage tolerance, the process that facilitates the resumption of replication when replicases are stalled at sites of DNA template damage. The following account highlights some of our work that contributed to an understanding of the mechanisms underlying these activities, carried out by the RAD6 pathway, my main preoccupation over this period.     

Ribosomal antibiotics

In spite of decades of research, our understanding of the principles of antibiotic binding to the ribosome and the mechanisms of drug action remains only fragmentary. Recent progress in biochemical and genetic studies of some "old" and new antibiotics and the availability of high-resolution structures of the ribosome subunits allows mapping the antibiotic-binding sites at atomic resolution. In this review, interaction of three groups of antibiotics with the ribosome and the mechanisms of the drug action are discussed, considering the data used to map the binding sites of the new macrolide derivatives, ketolides, a novel clinically important antibiotic linezolid, and a still experimental drug evernimicin.     

Setting the stage: host invasion by HIV

For more than two decades, HIV has infected millions of people worldwide each year through mucosal transmission. Our knowledge of how HIV secures a foothold at both the molecular and cellular levels has been expanded by recent investigations that have applied new technologies and used improved techniques to isolate ex vivo human tissue and generate in vitro cellular models, as well as more relevant in vivo animal challenge systems. Here, we review the current concepts of the immediate events that follow viral exposure at genital mucosal sites where most documented transmissions occur. Furthermore, we discuss the gaps in our knowledge that are relevant to future studies, which will shape strategies for effective HIV prevention.     

Phenotypic shifts in urban areas in the tropical lizard Anolis cristatellus

Urbanization is an increasingly important dimension of global change, and urban areas likely impose significant natural selection on the species that reside within them. Although many species of plants and animals can survive in urban areas, so far relatively little research has investigated whether such populations have adapted (in an evolutionary sense) to their newfound milieu. Even less of this work has taken place in tropical regions, many of which have experienced dramatic growth and intensification of urbanization in recent decades. In the present study, we focus on the neotropical lizard, Anolis cristatellus. We tested whether lizard ecology and morphology differ between urban and natural areas in three of the most populous municipalities on the island of Puerto Rico. We found that environmental conditions including temperature, humidity, and substrate availability differ dramatically between neighboring urban and natural areas. We also found that lizards in urban areas use artificial substrates a large proportion of the time, and that these substrates tend to be broader than substrates in natural forest. Finally, our morphological data showed that lizards in urban areas have longer limbs relative to their body size, as well as more subdigital scales called lamellae, when compared to lizards from nearby forested habitats. This shift in phenotype is exactly in the direction predicted based on habitat differences between our urban and natural study sites, combined with our results on how substrates are being used by lizards in these areas. Findings from a common‐garden rearing experiment using individuals from one of our three pairs of populations provide evidence that trait differences between urban and natural sites may be genetically based. Taken together, our data suggest that anoles in urban areas are under significant differential natural selection and may be evolutionarily adapting to their human‐modified environments.     

Climate Change Increases Drought Stress of Juniper Trees in the Mountains of Central Asia

Assessments of climate change impacts on forests and their vitality are essential for semi-arid environments such as Central Asia, where the mountain regions belong to the globally important biodiversity hotspots. Alterations in species distribution or drought-induced tree mortality might not only result in a loss of biodiversity but also in a loss of other ecosystem services. Here, we evaluate spatial trends and patterns of the growth-climate relationship in a tree-ring network comprising 33 juniper sites from the northern Pamir-Alay and Tien Shan mountain ranges in eastern Uzbekistan and across Kyrgyzstan for the common period 1935–2011. Junipers growing at lower elevations are sensitive to summer drought, which has increased in intensity during the studied period. At higher elevations, juniper growth, previously favored by warm summer temperatures, has in the recent few decades become negatively affected by increasing summer aridity. Moreover, response shifts are observed during all seasons. Rising temperatures and alterations in precipitation patterns during the past eight decades can account for the observed increase in drought stress of junipers at all altitudes. The implications of our findings are vital for the application of adequate long-term measures of ecosystem conservation, but also for paleo-climatic approaches and coupled climate-vegetation model simulations for Central Asia.     

Vegetation Dynamics on an Abandoned Vacuum-Mined Peatland: 5 Years of Monitoring

We studied from 1998 to 2002 the fine-scale vegetation dynamics of a poorly regenerated vacuum-mined bog located in southern Quebec. We selected mined sites that have been abandoned for 14 years and monitored the vascular and non-vascular plants, and some hydrological characteristics. We focussed our study on the monitoring of cotton-grass (Eriophorum vaginatum L.) tussocks. Major changes in the plant cover were observed during the five-year period, such as a decrease (26–31%) in the number of cotton-grass tussocks and an increase in the ericaceous shrub cover. The water table level (lower than 40 cm below the soil surface) and frost heaving appear to be the main factors explaining the failure of cotton-grass and of other typical bog plant species to colonize abandoned mined surfaces. The ericaceous shrub cover, although increasing, was still sparse even after two decades of abandonment, and it may take several additional decades before a complete shrub cover establishes itself. While the natural revegetation process of this vacuum-mined bog is still dynamic after two decades of abandonment, there is no evidence to suggest that vegetation assemblages will eventually resemble those of undisturbed peatlands.     

Site fertility drives temporal turnover of vegetation at high latitudes

Experimental evidence shows that site fertility is a key modulator underlying plant community changes under climate change. Communities on fertile sites, with species having fast dynamics, have been found to react more strongly to climate change than communities on infertile sites with slow dynamics. However, it is still unclear whether this generally applies to high‐latitude plant communities in natural environments at broad spatial scales. We tested a hypothesis that vegetation of fertile sites experiences greater changes over several decades and thus would be more responsive under contemporary climate change compared to infertile sites that are expected to show more resistance. We resurveyed understorey communities (vascular plants, bryophytes, and lichens) of four infertile and four fertile forest sites along a latitudinal bioclimatic gradient. Sites had remained outside direct human disturbance. We analyzed the magnitude of temporal community turnover, changes in the abundances of plant morphological groups and strategy classes, and changes in species diversity. In agreement with our hypothesis, temporal turnover of communities was consistently greater on fertile sites compared to infertile sites. However, our results suggest that the larger turnover of fertile communities is not primarily related to the direct effects of climatic warming. Furthermore, community changes in both fertile and infertile sites showed remarkable variation in terms of shares of plant functional groups and strategy classes and measures of species diversity. This further emphasizes the essential role of baseline environmental conditions and nonclimatic drivers underlying vegetation changes. Our results show that site fertility is a key determinant of the overall rate of high‐latitude vegetation changes but the composition of plant communities in different ecological contexts is variously impacted by nonclimatic drivers over time.     

Efficiency of nutrient management in controlling eutrophication of running waters in the Middle Danube Basin

Nutrient emission dropped significantly during the last two decades in the Danube Basin. To assess the effect of reduced nutrient loads on the trophic status of running waters, this regional study analyzed the relationships between nutrients (P and N) and suspended chlorophyll (Chl) using long-term monitoring data in Hungary. Including the upstream catchments of trans-boundary rivers, the study covered an approximate area of 400,000 km², equivalent to the half of the entire Danube catchment. Decadal median Chl was unrelated to P and N concentrations in the whole data set and weakly related to total P (TP) at natural-moderately polluted (N-MP) sites, which were distinguished from highly polluted (HP) sites by using cutoff values for chloride, chemical oxygen demand and TP. At both the N-MP sites and most of the HP sites, Chl increased with channel length. This indicated that water residence time was a more important determinant of Chl than nutrients. Nutrient concentrations showed a significant downward trend in time at half of our sites. With a nearly equal frequency, a parallel trend might or might not occur in Chl. The apparent efficiency of nutrient management was expressed as the quotient of the slopes of linear trends in Chl and nutrients. At sites within 150 km from source, this efficiency was marginal. In larger rivers, efficiency improved steeply. The highest efficiency was observed in the downstream reach of the Danube (upstream length >1,300 km) where P availability might frequently limit algal growth. The results suggest that eutrophication management in rivers should be based on Chl response functions, rather than universal nutrient criteria. Four Chl response classes were identified based on the observed longitudinal P and Chl gradients.     

Predicting the Spatial Distribution of Wolf (Canis lupus) Breeding Areas in a Mountainous Region of Central Italy

Wolves (Canis lupus) in Italy represent a relict west European population. They are classified as vulnerable by IUCN, though have increased in number and expanded their range in recent decades. Here we use 17 years of monitoring data (from 1993 to 2010) collected in a mountainous region of central Italy (Arezzo, Tuscany) in an ecological niche-based model (MaxEnt) to characterize breeding sites (i.e. the areas where pups were raised) within home ranges, as detected from play-back responses. From a suite of variables related to topography, habitat and human disturbance we found that elevation and distance to protected areas were most important in explaining the locality of wolf responses. Rendezvous sites (family play-back response sites) typically occurred between 800 and 1200 m a.s.l., inside protected areas, and were usually located along mountain chains distant from human settlements and roads. In these areas human disturbance is low and the densities of ungulates are typically high. Over recent years, rendezvous sites have occurred closer to urban areas as the wolf population has continued to expand, despite the consequent human disturbance. This suggests that undisturbed landscapes may be reaching their carrying capacity for wolves. This, in turn, may lead to the potential for increased human-wolf interactions in future. Applying our model, both within and beyond the species’ current range, we identify sites both within the current range and also further afield, that the species could occupy in future. Our work underlines the importance of the present protected areas network in facilitating the recolonisation by wolves. Our projections of suitability of sites for future establishment as the population continues to expand could inform planning to minimize future wolf-human conflicts.     

RNA-protein interactions in the Escherichia coli ribosome.

Over the last two decades essentially three different approaches have been used to study the topography of RNA-protein interactions in the ribosome. These are: (a) the analysis of binding sites for individual ribosomal proteins or groups of proteins on the RNA; (b) the determination of protein footprint sites on the RNA by the application of higher order structure analytical techniques; and (c) the localisation of RNA-protein cross-link sites on the RNA. This article compares and contrasts the types of data that the three different approaches provide, and gives a brief and highly simplified summary of the results that have been obtained for both the 16S and 23S ribosomal RNA from E coli.     

过去二十年贵州黑叶猴分布与种群动态及致危因子分析(英文)

本文通过整理相关文献与政府报告数据并结合我们在贵州的最新调查与监测数据,总结过去20年间黑叶猴在贵州的分布、种群变动及其所面临的主要威胁,并在此基础上提出相关的保护管理建议。贵州黑叶猴野生种群在过去20年间增长了约10%～20%:从20世纪90年代的约109群1000只增加到现在的约132～137群1160～1200只。但同期黑叶猴已从5个原有的分布点绝迹,现仅存于大沙河、柏箐、麻阳河、宽阔水和野钟等5个保护区,总面积约912km2。现有的5个隔离分布点保存有全球黑叶猴野生种群(1800～2000)的约62%,是黑叶猴物种保存的最关键地区,并应该给于保护管理的优先考虑。偷猎压力在贵州相对较小:在过去的20年间仅有3次偷猎的官方记录。黑叶猴在贵州所面临的主要威胁是栖息地的丧失与退化。其主要表现形式有:以农作物和烟草种植为目的的耕地扩大,以做饭、取暖以及烟叶烘烤为目的的薪材需求,以及家畜(主要是山羊)的过度放牧。     

Change within and among forest communities: the influence of historic disturbance,environmental gradients,and community attributes

Understanding how ecological communities change over time is critical for biodiversity conservation, but few long‐term studies directly address decadal‐scale changes in both the within‐ and among‐community components of diversity. In this study, we use a network of permanent forest vegetation plots, established in Great Smoky Mountains National Park (USA) in 1978, to examine the factors that influence change in community composition within and among communities. In 2007, we resampled 15 plots that were logged in the late 1920s and 15 plots that had no documented history of intensive human disturbance. We found that understory species richness decreased by an average of 4.3 species over the 30‐yr study period in the logged plots, but remained relatively unchanged in the unlogged plots. In addition, tree density decreased by an average of 145 stems ha^?1 in the logged plots, but was relatively stable in the unlogged plots. However, we found that historic logging had no effect on within‐community understory or tree compositional turnover during this time period. Instead, sites at lower elevations and sites with lower understory biomass in 1978 had higher understory compositional turnover than did sites at higher elevations and sites with higher understory biomass. In addition, sites with lower soil cation exchange capacity (CEC) and with lower tree basal area in 1978 had higher tree compositional turnover than did sites with higher soil CEC and higher tree basal area. Among‐community similarity was unchanged from 1978 to 2007 for both the logged and unlogged plots. Overall, our results indicate that human disturbance can affect plant communities for decades, but the extent of temporal change in community composition may nevertheless depend more on environmental gradients and community attributes.     

Ribosomal Antibiotics

In spite of decades of research, our understanding of the principles of antibiotic binding to the ribosome and the mechanisms of drug action remains only fragmentary. Recent progress in biochemical and genetic studies of some old and new antibiotics and the availability of high-resolution structures of the ribosome subunits allows mapping the antibiotic-binding sites at atomic resolution. In this review, interaction of three groups of antibiotics with the ribosome and the mechanisms of the drug action are discussed, considering the data used to map the binding sites of the new macrolide derivatives, ketolides, a novel clinically important antibiotic linezolid, and a still experimental drug evernimicin.     

Permafrost thaw induces short-term increase in vegetation productivity in northwestern Canada

Over the past several decades, various trends in vegetation productivity, from increases to decreases, have been observed throughout Arctic–Boreal ecosystems. While some of this variation can be explained by recent climate warming and increased disturbance, very little is known about the impacts of permafrost thaw on productivity across diverse vegetation communities. Active layer thickness data from 135 permafrost monitoring sites along a 10° latitudinal transect of the Northwest Territories, Canada, paired with a Landsat time series of normalized difference vegetation index from 1984 to 2019, were used to quantify the impacts of changing permafrost conditions on vegetation productivity. We found that active layer thickness contributed to the observed variation in vegetation productivity in recent decades in the northwestern Arctic–Boreal, with the highest rates of greening occurring at sites where the near-surface permafrost recently had thawed. However, the greening associated with permafrost thaw was not sustained after prolonged periods of thaw and appeared to diminish after the thaw front extended outside the plants' rooting zone. Highest rates of greening were found at the mid-transect sites, between 62.4° N and 65.2° N, suggesting that more southernly sites may have already surpassed the period of beneficial permafrost thaw, while more northern sites may have yet to reach a level of thaw that supports enhanced vegetation productivity. These results indicate that the response of vegetation productivity to permafrost thaw is highly dependent on the extent of active layer thickening and that increases in productivity may not continue in the coming decades.     

The influence of land use on the sedimentation of the river delta in the Kyrönjoki drainage basin

Sediment surface samples (0–2 cm) from 66 sites, and longer cores (up to 540 cm) from 9 sites in the estuary of the river Kyrönjoki, Western Finland, were analysed for organic content, P, Fe, Mn, Pb, Cd, Cu and Zn. One core was dated on the basis of annual laminations.Chemical analyses of the cores showed that organic matter and heavy metal content have increased in recent decades. The heavy metal content was clearly lower than in areas polluted by industry. The sedimentation rate in the delta increased between the 1930s and 1950. It decreased in the 1960s, and has been below 1930s levels since 1970. The sedimentation rates of organic matter were fairly stable all through the period measured, even though the organic content increased.The increase in organic matter and the heavy metal content of the sediment in recent decades is evidently due to the increased intensity of agriculture, forestry and peat harvesting in the drainage basin. Drainage of peatlands in particular has increased erosion and the organic sediment load of the river. Reservoir building after 1970 has decreased the sedimentation rates in the delta.