Gap analysis revealed a low efficiency of Natura 2000 network for the conservation of endemic species in Mediterranean temporary freshwater habitats

Listed and rare species are abundant in temporary freshwater habitats. Among them, the endemic contingent represents a crucial conservation target particularly in the areas characterized by abundant endemic flora for which the local administrations have a high level of responsibility. The aim of this research was to test how the endemic plants found in Mediterranean temporary ponds were represented in Natura 2000 network in a biodiversity hotspot of the Mediterranean region. The results of our research at regional scale pointed out that the existing Nature 2000 sites provide a limited degree of protection and that the gap analysis should be taken into account when conservation priorities are set.     

Integrating GIS and expert judgment in a multi-criteria analysis to map and develop a habitat suitability index: A case study of large mammals on the Malayan Peninsula

Many habitat patches in tropical landscapes have become less suitable for wildlife due to an increase in anthropogenic disturbances. An index of habitat suitability based on the ecological factors that collectively determine the suitability of an organism's habitat is important for conservation planning. However, a widely accepted and comprehensive multi-criteria habitat suitability index for umbrella species is still lacking, particularly in areas where information related to the biology and ecology of the species of interest is not available. Therefore we develop preliminary habitat maps and measure the degree of habitat suitability for large mammals, focusing on four umbrella species in the State of Selangor, Peninsular Malaysia: Panthera tigris jacksoni (Malayan tiger), Tapirus indicus (Malayan tapir), Helarctos malayanus malayanus (Malayan sun bear), and Rusa unicolor cambojensis (sambar deer). The former two are endangered and the latter two are vulnerable according to the IUCN Red List. The suitability of habitat patches for each species was measured across the entire study area as well as in nine wildlife protected areas by integrating GIS data and expert opinion. Expert opinions were used as the source of information regarding the stresses faced by the species because there was insufficient information available from ground surveys.We developed an index and maps of habitat suitability for each species, which were then integrated to represent a combined index (ranging from 0 to 27) and spatially explicit maps of the area's habitat suitability for large mammals. The average large mammal habitat suitability index value of the State of Selangor (9) indicates that many habitat patches have become unsuitable for such species. Of the nine wildlife protected areas, Fraser's Hill (22), Sungai Dusun (22), and Bukit Kutu (21) are very suitable; Klang Gate (20) and Templers Park (17) are suitable; and the remaining four are unsuitable for large mammals. We assume that this preliminary habitat suitability index and mapping are useful for conservation planning of wildlife habitats at both landscape and regional scales, as well as providing an initial foundation for revision by future research with significant new information.     

Do species population parameters and landscape characteristics affect the relationship between local population abundance and surrounding habitat amount?

In landscape ecology, correlational approaches are typically used to analyse links between local population abundance, and the surrounding habitat amount to estimate biologically-relevant landscape size (extent) for managing endangered or pest populations. The direction, strength, and spatial extent of the correlations are then sometimes interpreted in terms of species population parameters. Here we simulated the population dynamics of generalized species across spatially explicit landscapes that included two distinct habitat types. We investigated how characteristics of a landscape (structure), including the variation in habitat quality and spatial aggregation of the habitat, and the precise population-dynamic properties of the simulated species (dispersal and growth rates) affect the correlation between population abundance and amount of surrounding favourable habitat in the landscape. To evaluate these spatial extents of correlation, proportions of favourable habitat were calculated within several circles of increasing diameter centred on sampling patches of favourable habitat where population abundance was recorded.We found that the value of the correlation coefficients between population abundance and amount of surrounding favourable habitat depended on both population dynamic parameters and landscape characteristics. Coefficients of correlation increased with the variation in habitat quality and the aggregation of favourable habitat in the landscape, but decreased with the dispersal distance. The distance at which the correlation was maximized was sensitive to an interaction between the level of aggregation of the habitat and the dispersal distance; whereas the greatest distance at which a significant correlation occurred was more sensitive to the variation in habitat quality. Our results corroborate the view that correlational analyses do provide information on the local population dynamics of a species in a given habitat type and on its dispersal rate parameters. However, even in simplified, model frameworks, direct relationships are often difficult to disentangle and global landscape characteristics should be reported in any studies intended to derive population-dynamic parameters from correlations. Where possible, replicated landscapes should be examined in order to control for the interaction between population dynamics and landscape structure. Finally, we recommend using species-specific, population-dynamic modelling in order to interpret correctly the observed patterns of correlation in the landscape.     

Understanding extracellular vesicle diversity – current status

ABSTRACT

Introduction: Extracellular vesicles (EVs) represent an important mode of intercellular communication. There is now a growing awareness that predominant EV subtypes; exosomes from endosomal origin, and shed microvesicles from plasma membrane budding, can be further stratified into distinct subtypes, however specific approaches in their isolation and markers that allow them to be discriminated are lacking.

Areas covered: Knowledge about these distinct EV subpopulations is important including the regulation of composition, release, targeting/localization, uptake, and function. This review discusses the mechanisms of distinct EV biogenesis and release, defining select EV classes (and subpopulations), which will be crucial for development of EV-based functions and clinical applications. We review the dynamics of cargo sorting leading to the mechanisms of EV heterogeneity, their mechanisms of formation, intracellular trafficking pathways, and provide an uptake about biochemical/functional differences. With advances in purification strategies and proteomic-based quantitation, allows significant benefit in accurately describing differences in EV protein cargo composition and modification.

Expert commentary: The advent of quantitative mass spectrometry-based proteomics, in conjunction with advances in molecular cell biology, and EV purification strategies, has contributed significantly to our improved characterization and understanding of the molecular composition and functionality of these distinct EV subpopulations.     

Drove roads: Keystone structures that promote ant diversity in Mediterranean forest landscapes

Drove roads are the traditional corridors used by pastoralists for seasonal movements of livestock (transhumance). They cover a considerable land area in Mediterranean countries and, although they are an obvious source of landscape diversity, their influence on the diversity and composition of animal assemblages has not been documented. Ant communities were studied on four active drove roads, two in forests (submediterranean and conifer) and two in open environments (croplands and rangelands). They were compared with the respective matrix communities and their contribution to local species richness was evaluated. The effects were heavily dependent on the open or closed nature of the matrix. In forest environments, drove roads increased ant species richness at the local scale, acting as clear keystone structures. Their species richness and functional diversity were highest on the fine scale, species composition was different, and a slight edge effect in the matrix was detected. In contrast, drove roads had little or even a negative effect in open environment locations. We conclude that drove roads have a high conservation value for ants in Mediterranean forest environments, in addition to their importance as reservoirs of plant biodiversity and generators of ecological goods and services.     

Local temperatures inferred from plant communities suggest strong spatial buffering of climate warming across Northern Europe

Recent studies from mountainous areas of small spatial extent (<2500 km²) suggest that fine‐grained thermal variability over tens or hundreds of metres exceeds much of the climate warming expected for the coming decades. Such variability in temperature provides buffering to mitigate climate‐change impacts. Is this local spatial buffering restricted to topographically complex terrains? To answer this, we here study fine‐grained thermal variability across a 2500‐km wide latitudinal gradient in Northern Europe encompassing a large array of topographic complexities. We first combined plant community data, Ellenberg temperature indicator values, locally measured temperatures (LmT) and globally interpolated temperatures (GiT) in a modelling framework to infer biologically relevant temperature conditions from plant assemblages within <1000‐m² units (community‐inferred temperatures: CiT). We then assessed: (1) CiT range (thermal variability) within 1‐km² units; (2) the relationship between CiT range and topographically and geographically derived predictors at 1‐km resolution; and (3) whether spatial turnover in CiT is greater than spatial turnover in GiT within 100‐km² units. Ellenberg temperature indicator values in combination with plant assemblages explained 46–72% of variation in LmT and 92–96% of variation in GiT during the growing season (June, July, August). Growing‐season CiT range within 1‐km² units peaked at 60–65°N and increased with terrain roughness, averaging 1.97 °C (SD = 0.84 °C) and 2.68 °C (SD = 1.26 °C) within the flattest and roughest units respectively. Complex interactions between topography‐related variables and latitude explained 35% of variation in growing‐season CiT range when accounting for sampling effort and residual spatial autocorrelation. Spatial turnover in growing‐season CiT within 100‐km² units was, on average, 1.8 times greater (0.32 °C km^?1) than spatial turnover in growing‐season GiT (0.18 °C km^?1). We conclude that thermal variability within 1‐km² units strongly increases local spatial buffering of future climate warming across Northern Europe, even in the flattest terrains.     

Novel Systems for Dynamically Assessing Insulin Action in Live Cells Reveals Heterogeneity in the Insulin Response

Regulated GLUT4 trafficking is a key action of insulin. Quantitative stepwise analysis of this process provides a powerful tool for pinpointing regulatory nodes that contribute to insulin regulation and insulin resistance. We describe a novel GLUT4 construct and workflow for the streamlined dissection of GLUT4 trafficking; from simple high throughput screens to high resolution analyses of individual vesicles. We reveal single cell heterogeneity in insulin action highlighting the utility of this approach – each cell displayed a unique and highly reproducible insulin response, implying that each cell is hard‐wired to produce a specific output in response to a given stimulus. These data highlight that the response of a cell population to insulin is underpinned by extensive heterogeneity at the single cell level. This heterogeneity is pre‐programmed within each cell and is not the result of intracellular stochastic events.     

Plant functional traits and community assembly along interacting gradients of productivity and fragmentation

Quantifying the association of plant functional traits to environmental gradients is a promising approach for understanding and projecting community responses to land use and climatic changes. Although habitat fragmentation and climate are expected to affect plant communities interactively, there is a lack of empirical studies addressing trait associations to fragmentation in different climatic regimes.In this study, we analyse data on the key functional traits: specific leaf area (SLA), plant height, seed mass and seed number. First, we assess the evidence for the community assembly mechanisms habitat filtering and competition at different spatial scales, using several null-models and a comprehensive set of community-level trait convergence and divergence indices. Second, we analyse the association of community-mean traits with patch area and connectivity along a south–north productivity gradient.We found clear evidence for trait convergence due to habitat filtering. In contrast, the evidence for trait divergence due to competition fundamentally depended on the null-model used. When the null-model controlled for habitat filtering, there was only evidence for trait divergence at the smallest sampling scale (0.25 m × 0.25 m). All traits varied significantly along the S–N productivity gradient. While plant height and SLA were consistently associated with fragmentation, the association of seed mass and seed number with fragmentation changed along the S–N gradient.Our findings indicate trait convergence due to drought stress in the arid sites and due to higher productivity in the mesic sites. The association of plant traits to fragmentation is likely driven by increased colonization ability in small and/or isolated patches (plant height, seed number) or increased persistence ability in isolated patches (seed mass).Our study provides the first empirical test of trait associations with fragmentation along a productivity gradient. We conclude that it is crucial to study the interactive effects of different ecological drivers on plant functional traits.     

Intratumoral heterogeneity: Clonal cooperation in epithelial-to-mesenchymal transition and metastasis

Although phenotypic intratumoral heterogeneity was first described many decades ago, the advent of next-generation sequencing has provided conclusive evidence that in addition to phenotypic diversity, significant genotypic diversity exists within tumors. Tumor heterogeneity likely arises both from clonal expansions, as well as from differentiation hierarchies existent in the tumor, such as that established by cancer stem cells (CSCs) and non-CSCs. These differentiation hierarchies may arise due to genetic mutations, epigenetic alterations, or microenvironmental influences. An additional differentiation hierarchy within epithelial tumors may arise when only a few tumor cells trans-differentiate into mesenchymal-like cells, a process known as epithelial-to-mesenchymal transition (EMT). Again, this process can be influenced by both genetic and non-genetic factors. In this review we discuss the evidence for clonal interaction and cooperation for tumor maintenance and progression, particularly with respect to EMT, and further address the far-reaching effects that tumor heterogeneity may have on cancer therapy.     

Specific and high-resolution identification of monoclonal antibody fragments detected by capillary electrophoresis–sodium dodecyl sulfate using reversed-phase HPLC with top-down mass spectrometry analysis

ABSTRACT

In recent years, capillary electrophoresis–sodium dodecyl sulfate (cSDS) has been widely used for high resolution separation and quantification of the fragments and aggregates of monoclonal antibodies (mAbs) to ensure the quality of mAb therapeutics. However, identification of the low-molecular-weight (LMW) and high-molecular-weight (HMW) species detected in cSDS electropherograms has been based primarily on the approximate MWs calculated from standard curves using known MW standards and correlations with fragments and aggregates identified by other methods. It is not easy to collect sufficient amounts of H/LMW species from cSDS for analysis by orthogonal methods and the direct coupling of cSDS with mass spectrometry (MS) is very difficult due to interference from SDS. In this study, we describe the precise identification of H/LMW species detected by cSDS using reversed-phase high performance liquid chromatography (RP-HPLC) coupled with top-down tandem MS analysis. The H/LMW species were first identified by on-line RP-HPLC MS analysis and the RP-HPLC fractions were then analyzed by cSDS to connect the identified H/LMW species with the peaks in the cSDS electropherogram. With this method, 58 unique H/LMW species were identified from an immunoglobulin G1 (IgG1) mAb. The identified fragments ranged from 10 kDa single chain fragments to 130 kDa triple chain fragments, including some with post-translational modifications. This is the first study to clearly identify the antibody fragments, including the exact clipping sites, observed in cSDS electropherograms. The methodology and results presented here should be applicable to most other IgG1 mAbs.