BAmSA: Visualising transmembrane regions in protein complexes using biotinylated amphipols and electron microscopy

Membrane protein (MP) complexes play key roles in all living cells. Their structural characterisation is hampered by difficulties in purifying and crystallising them. Recent progress in electron microscopy (EM) have revolutionised the field, not only by providing higher-resolution structures for previously characterised MPs but also by yielding first glimpses into the structure of larger and more challenging complexes, such as bacterial secretion systems. However, the resolution of pioneering EM structures may be difficult and their interpretation requires clues regarding the overall organisation of the complexes. In this context, we present BAmSA, a new method for localising transmembrane (TM) regions in MP complexes, using a general procedure that allows tagging them without resorting to neither genetic nor chemical modification. Labels bound to TM regions can be visualised directly on raw negative-stain EM images, on class averages, or on three-dimensional reconstructions, providing a novel strategy to explore the organisation of MP complexes.     

Local cryostimulation acutely preserves maximum isometric handgrip strength following fatigue in young women

Several types of cryostimulation have been recently proposed to rapidly lower skin temperature therefore gaining a possible neuro/muscular recovery after strenuous exercise or, more generally, in sports. Local cryostimulation may be a viable and relatively portable tool to obtain physiological benefits in previously-efforted muscular districts. However, cohesive and standardized cryo-exposure protocols are lacking as well as the righteous procedure to efficaciously combine duration, treatments and temperature in relation to desirable effects on muscular strength. In this randomized-controlled study, fifty young women were tested for maximum isometric handgrip strength, before and after exhausting contractions.Following the fatiguing protocol, the intervention group (cryo, n = 25, 24.7 ± 2.5 years, BMI 21.7 ± 1.8 kg/m²) underwent a 6-min local cryostimulation (−160 °C) on the extensor-flexor muscles of the dominant arm, while control-matched peers sat rested in a thermo-neutral room (22 ± 0.5 °C). Handgrip tests were repeated at baseline (T0), after cryostimulation (T1), and 15 min after T1 (T2). Throughout the protocol, the AUC of the strength performance was significantly higher in the cryo- compared to control group (P = 0.006). In particular, following fatigue and cryostimulation, the cryo group preserved higher strength at T1 with respect to controls (26.8 ± 2.8 vs 23.9 ± 2.8 kg, Bonferroni's post-hoc, P < 0.01). Likewise, ventral and dorsal temperature, recorded with a thermal camera, were lower in cryo- than control group (P < 0.0001).In conclusion, a brief session of local cryostimulation may acutely preserve maximal isometric force in young women following a fatiguing protocol. These findings may have implications in orchestrating strategies of district muscular recovery.     

Managing for multiple species: greater sage-grouse and sagebrush songbirds

Human activity has altered 33–50% of Earth's surface, including temperate grasslands and sagebrush rangelands, resulting in a loss of biodiversity. By promoting habitat for sensitive or wide-ranging species, less exigent species may be protected in an umbrella effect. The greater sage-grouse (Centrocercus urophasianus; sage-grouse) has been proposed as an umbrella for other sagebrush-obligate species because it has an extensive range that overlaps with many other species, it is sensitive to anthropogenic activity, it requires resources over large landscapes, and its habitat needs are known. The efficacy of the umbrella concept, however, is often assumed and rarely tested. Therefore, we surveyed sage-grouse pellet occurrence and sagebrush-associated songbird abundance in northwest Colorado, USA, to determine the amount of habitat overlap between sage-grouse and 4 songbirds (Brewer's sparrow [Spizella breweri], sage thrasher [Oreoscoptes montanus], sagebrush sparrow [Artemisiospiza nevadensis]), and green-tailed towhee [Pipilo chlorurus]). During May and June 2013–2015, we conducted standard point count breeding surveys for songbirds and counted sage-grouse pellets within 300 10-m radius plots. We modeled songbird abundance and sage-grouse pellet occurrence with multi-scaled environmental features, such as sagebrush cover and bare ground. To evaluate sage-grouse as an umbrella for sagebrush-associated passerines, we determined the correlation between probability of sage-grouse pellet occurrence and model-predicted songbird densities per sampling plot. We then classified the sage-grouse probability of occurrence as high (probability >0.5) and low (probability ≤0.5) and mapped model-predicted surfaces for each species in our study area. We determined average songbird density in areas of high and low probability of sage-grouse occurrence. Sagebrush cover at intermediate scales was an important predictor for all species, and ground cover was important for all species except sage thrashers. Areas with a higher probability of sage-grouse occurrence also contained higher densities of Brewer's sparrows, green-tailed towhees, and sage thrashers, but predicted sagebrush sparrow densities were lower in these areas. In northwest Colorado, sage-grouse may be an effective umbrella for Brewer's sparrows, green-tailed towhees, and sage thrashers, but sage-grouse habitat does not appear to capture areas that support high sagebrush sparrow densities. A multi-species focus may be the best management and conservation strategy for several species of concern, especially those with conflicting habitat requirements. © The Wildlife Society, 2019     

Testing and interpreting the shared space‐environment fraction in variation partitioning analyses of ecological data

Variation partitioning analyses combined with spatial predictors (Moran's eigenvector maps, MEM) are commonly used in ecology to test the fractions of species abundance variation purely explained by environment and space. However, while these pure fractions can be tested using a classical residuals permutation procedure, no specific method has been developed to test the shared space‐environment fraction (SSEF). Yet, the SSEF is expected to encompass a major driver of community assembly, that is, an induced spatial dependence effect (ISD; i.e. the reflection of a spatially structured habitat filter on a species distribution). A reliable test of this fraction is therefore crucial to properly test the presence of an ISD on ecological data. To bridge the gap, we propose to test the SSEF through spatially‐constrained null models: torus‐translations, and Moran spectral randomisations. We investigated the type I error rate and statistical power of our method based on two real environmental datasets and simulations of tree distributions. Ten types of tree distribution displaying contrasted aggregation properties were simulated, and their abundances were sampled in 153 regularly‐distributed 20 × 20 m quadrats. The SSEF was tested for 1000 simulated tree distributions either unrelated to the environment, or filtered by environmental variables displaying contrasting spatial structures. The method proposed provided a correct type I error rate (< 0.05). The statistical power was high (> 0.9) when abundances were filtered by an environmental variable structured at broad scale. However, the spatial resolution allowed by the sampling design limited the power of the method when using a fine‐scale filtering variable. This highlighted that an ISD can be properly detected providing that the spatial pattern of the filtering process is correctly captured by the sampling design of the study. An R function to apply the SSEF testing method is provided and detailed in a tutorial.     

Response of Net Ecosystem Productivity of Three Boreal Forest Stands to Drought

In 2001–03, continuous eddy covariance measurements of carbon dioxide (CO₂) flux were made above mature boreal aspen, black spruce, and jack pine forests in Saskatchewan, Canada, prior to and during a 3−year drought. During the 1st drought year, ecosystem respiration (R) was reduced at the aspen site due to the drying of surface soil layers. Gross ecosystem photosynthesis (GEP) increased as a result of a warm spring and a slow decrease of deep soil moisture. These conditions resulted in the highest annual net ecosystem productivity (NEP) in the 9 years of flux measurements at this site. During 2002 and 2003, a reduction of 6% and 34% in NEP, respectively, compared to 2000 was observed as the result of reductions in both R and GEP, indicating a conservative response to the drought. Although the drought affected most of western Canada, there was considerable spatial variability in summer rainfall over the 100−km extent of the study area; summer rainfalls in 2001 and 2002 at the two conifer sites minimized the impact of the drought. In 2003, however, precipitation was similarly low at all three sites. Due to low topographic position and consequent poor drainage at the black spruce site and the coarse soil with low water-holding capacity at the jack pine site almost no reduction in R, GEP, and NEP was observed at these two sites. This study shows that the impact of drought on carbon sequestration by boreal forest ecosystems strongly depends on rainfall distribution, soil characteristics, topography, and the presence of vegetation that is well adapted to these conditions.     

Fish–environment Associations in the Coastal Waters of Andros Island, The Bahamas

Synopsis We surveyed fish communities and corresponding environmental conditions at three broadly similar coastal sites of eastern Andros Island, The Bahamas over a summer–winter–summer sequence to assess the relationship between detailed environmental features and fish species patterns. Environmental variables included covers of various benthic flora components, benthic flora diversity, floral canopy height, micro-crustacean diversity and density, water temperature, extent of destructive land-use and extent of invasion by human-introduced exotic terrestrial plants. Correspondence analysis (CA) indicated that spatial (site) differences in environmental characteristics were greater than temporal (seasonal) differences. Detrended canonical correspondence analysis (DCCA) was used to assess the strength of relationships between the environmental characteristics and the distribution patterns of 25 fish species. Environmental features deemed to be most important in influencing fish species patterns included benthic flora canopy height, extent of invasion by exotic terrestrial plants, cover of Batophora oerstedii, cover of Thalassia testudinum, turf cover, water temperature, micro-crustacean diversity, and micro-crustacean density. Based upon similarities in distribution patterns, fish species formed four clusters which, ultimately, reflected similarities in species’ feeding habits and preferences for habitats that likely maximize foraging success. We conclude that fish distribution patterns are related to environmental characteristics, and that anthropogenic coastal activity, by influencing coastal benthic characteristics, may influence the distribution and abundances of fish species in coastal habitats.     

Quantifying Littoral Vertical Habitat Structure and Fish Community Associations using Underwater Visual Census

Synopsis We developed and tested a new visual census technique to quantify the importance of vertical habitat structure on the associated fish assemblages in the littoral zone of a freshwater lake. We demonstrated that the primary environmental gradient, accounting for the most variation in the species data, represented a temporal gradient of seasonal characteristics. The secondary environmental gradient was related to the vertical structure at the sampling locations, showing the importance of the vertical component of the environment on fish community structure. Characterizing the vertical component at different resolutions provided different interpretations. The primary difference was the strength of influence of woody material on community structure. Woody material had a stronger influence on community structure throughout the water column when a single vertical unit defined the fish data. The appropriateness of defining the data by either multiple vertical strata or by a single vertical one would be dependent on the objectives of the study, as neither approach was found to explain substantially more variation in the species data. The current study demonstrates that fish are closely associated with particular elements of habitat structure in the littoral zone, even in the absence of major piscivorous predators. We provide a novel study quantifying the vertical multiple habitat structures and habitat use by fish in the water column of a freshwater lake. The new vertical visual census technique can be used to more comprehensively sample the three-dimensional environment of lake littoral zones, and quantify the fish–habitat spatial relationships across a range of abiotic and biotic habitat features.     

Comparative floral morphometrics in day-flowering, night-flowering and self-pollinated Caryophylloideae (Agrostemma, Dianthus, Saponaria, Silene, and Vaccaria)

Morphological variation of flowers with different pollination modes was studied in 53 species representing five genera (Agrostemma, Dianthus, Saponaria, Silene s.l., Vaccaria) of the subfamily Caryophylloideae. All species were classified a priori as either diurnal, nocturnal, or selfing. Canonical discriminant analysis (CDA) of 13 floral characters revealed significant correlations between floral morphometry and pollination modes. A CDA of taxonomical groups represented with more than three species (Dianthus, and subgroups of Silene s.l.: Lychnis, Silene s.str., and Viscaria), revealed that the discrimination between these four taxa, based on the same floral characters, is also well supported. Main factors for the discrimination of the species with different pollination modes were characters that (a) define nectar accessibility (calyx length, calyx tooth length), (b) are related to the positioning of anthers and stigmatic areas in relation to pollinators and (c) are important for the visual attractiveness of flowers (plate width). The functional distance between the nectar source (anthophore base) and contact zone with pollinators (style tips), given as the sum of anthophore length, ovary length, and style length (hence called AOS-complex) is better correlated with the calyx length than the single characters. Further, the total AOS-complex length differs significantly between pollination modes suggesting that these characters form a functionally linked complex that is related to the pollen placement on, and stigma contact with, the pollinator's body. However, the contribution of anthophore and style length to the total AOS-complex differed significantly between Silene s.l. and other taxa indicating that the taxonomic groups follow different evolutionary ways for the construction of the functionally linked AOS-complex.     

自然保护区管理效果影响因素

自然保护区的管理效果是保护区管理工作能力的重要考核指标。由于管理基础、管理机制和管理行为的不同,对保护区的管理效果产生影响的因素也有差异。为了剖析保护区管理过程中各项管理要素对管理效果产生影响情况及其重要程度,从林业系统中选取154个国家级自然保护区进行问卷调查,从26项管理要素中得到14项能体现管理有效性的关键评价指标,在此基础上。利用X^2检验的方法,分析这些关键评价指标与保护区的管理效果之间的关系,为今后的管理工作提供参考依据。经过研究,自然保护区管理效果的3个指标（保护状况E1、保护区控制E2、对当地社区经济效益的影响E3）中,目前E1在各个保护区中的管理效果得分中最高,这说明维护保护区的保护状况仍是各个保护区最为重视的工作目标;而保护区管理有效性评价指标中各个因子对于管理效果有不同的影响结果。在这些管理评价指标中,宣传项目是唯一对保护区管理效果中的3个指标都有影响的因素,并对E1这一管理效果因素影响最大,而管理监督评价和旅游管理与收费则是分别对E2、E3的影响最大。通过分析,将会更加明确保护区的管理因素中各个指标的重要性,通过对采取合理的方式,最终可以提高保护区的管理效果。     

Linkage disequilibrium between a melanin-based colour polymorphism and tail length in the barn owl

A linkage disequilibrium between sexually selected and life history traits can be explained by three mutually non-exclusive mechanisms. Genes coding for two traits may be located close on the same chromosome, genes responsible for variation in one of the trait may pleiotropically alter the other, and non-random pairing with respect to two traits may generate a non-physical linkage disequilibrium between their genes. Knowledge of which of these three mechanisms is responsible for a covariation between two traits is of interest to understand why differently ornamented individuals differ in several phenotypic aspects. In Switzerland, barn owls Tyto alba mate randomly with respect to a colour polymorphism generating a large range of variants between reddish-brown and white, males being lighter coloured than females. Several studies have shown that plumage coloration is not neutral with respect to some life history components. To test whether coloration is genetically associated with body size, partial cross-fostering experiments were performed by exchanging some hatchlings between nests. These experiments showed that darker biological fathers produce longer-tailed offspring. This sex-specific pattern is consistent with the hypothesis of non-physical linkage disequilibrium. In line with this hypothesis, darker coloured males were mated with longer-tailed females, whereas female coloration was not associated with tail length of their mate. The finding that dark nestlings had a longer tail than their pale siblings also supports the physical linkage and pleiotropy hypotheses. Therefore, non-random pairing can generate or strengthen a genetic covariation between a secondary sexual character and a morphological trait.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 475–488.