Using citizen science data for predicting the timing of ecological phenomena across regions.

The scarcity of long-term observational data has limited the use of statistical or machine-learning techniques for predicting intraannual ecological variation. However, time-stamped citizen-science observation records, supported by media data such as photographs, are increasingly available. In the present article, we present a novel framework based on the concept of relative phenological niche, using machine-learning algorithms to model observation records as a temporal sample of environmental conditions in which the represented ecological phenomenon occurs. Our approach accurately predicts the temporal dynamics of ecological events across large geographical scales and is robust to temporal bias in recording effort. These results highlight the vast potential of citizen-science observation data to predict ecological phenomena across space, including in near real time. The framework is also easily applicable for ecologists and practitioners already using machine-learning and statistics-based predictive approaches.

Spatial ecology of conflicts: unravelling patterns of wildlife damage at multiple scales.

Human encroachment into natural habitats is typically followed by conflicts derived from wildlife damage to agriculture and livestock. Spatial risk modelling is a useful tool to gain the understanding of wildlife damage and mitigate conflicts. Although resource selection is a hierarchical process operating at multiple scales, risk models usually fail to address more than one scale, which can result in the misidentification of the underlying processes. Here, we addressed the multi-scale nature of wildlife damage occurrence by considering ecological and management correlates interacting from household to landscape scales. We studied brown bear (Ursus arctos) damage to apiaries in the North-eastern Carpathians as our model system. Using generalized additive models, we found that brown bear tendency to avoid humans and the habitat preferences of bears and beekeepers determine the risk of bear damage at multiple scales. Damage risk at fine scales increased when the broad landscape context also favoured damage. Furthermore, integrated-scale risk maps resulted in more accurate predictions than single-scale models. Our results suggest that principles of resource selection by animals can be used to understand the occurrence of damage and help mitigate conflicts in a proactive and preventive manner.

Depletion of the membrane-fusion regulator Munc18c attenuates caerulein hyperstimulation-induced pancreatitis.

Epithelial pancreatic acinar cells perform crucial functions in food digestion, and acinar cell homeostasis required for secretion of digestive enzymes relies on SNARE-mediated exocytosis. The ubiquitously expressed Sec1/Munc18 protein mammalian uncoordinated-18c (Munc18c) regulates membrane fusion by activating syntaxin-4 (STX-4) to bind cognate SNARE proteins to form a SNARE complex that mediates exocytosis in many cell types. However, in the acinar cell, Munc18c's functions in exocytosis and homeostasis remain inconclusive. Here, we found that pancreatic acini from Munc18c-depleted mice (Munc18c+/-) and human pancreas (lenti-Munc18c-shRNA-treated) exhibit normal apical exocytosis of zymogen granules (ZGs) in response to physiologic stimulation with the intestinal hormone cholecystokinin (CCK-8). However, when stimulated with supraphysiologic CCK-8 levels to mimic pancreatitis, Munc18c-depleted (Munc18c+/-) mouse acini exhibited a reduction in pathological basolateral exocytosis of ZGs resulting from a decrease in fusogenic STX-4 SNARE complexes. This reduced basolateral exocytosis in part explained the less severe pancreatitis observed in Munc18c+/- mice after hyperstimulation with the CCK-8 analog caerulein. Likely as a result of this secretory blockade, Munc18c-depleted acini unexpectedly activated a component of the endoplasmic reticulum (ER) stress response that contributed to autophagy induction, resulting in downstream accumulation of autophagic vacuoles and autolysosomes. We conclude that Munc18c's role in mediating ectopic basolateral membrane fusion of ZGs contributes to the initiation of CCK-induced pancreatic injury, and that blockade of this secretory process could increase autophagy induction.

Variability in primary productivity determines metapopulation dynamics.

Temporal variability in primary productivity can change habitat quality for consumer species by affecting the energy levels available as food resources. However, it remains unclear how habitat-quality fluctuations may determine the dynamics of spatially structured populations, where the effects of habitat size, quality and isolation have been customarily assessed assuming static habitats. We present the first empirical evaluation on the effects of stochastic fluctuations in primary productivity--a major outcome of ecosystem functions--on the metapopulation dynamics of a primary consumer. A unique 13-year dataset from an herbivore rodent was used to test the hypothesis that inter-annual variations in primary productivity determine spatiotemporal habitat occupancy patterns and colonization and extinction processes. Inter-annual variability in productivity and in the growing season phenology significantly influenced habitat colonization patterns and occupancy dynamics. These effects lead to changes in connectivity to other potentially occupied habitat patches, which then feed back into occupancy dynamics. According to the results, the dynamics of primary productivity accounted for more than 50% of the variation in occupancy probability, depending on patch size and landscape configuration. Evidence connecting primary productivity dynamics and spatiotemporal population processes has broad implications for metapopulation persistence in fluctuating and changing environments.

Generation of functionally distinct hemogenic endothelial cell populations from pluripotent stem cells.

A diverse array of protocols have been established for the directed differentiation of human pluripotent stem cells (hPSCs) into a variety of cell types, including blood cells, for modeling development and disease, and for the development of cell-based therapeutics. These protocols recapitulate various signaling requirements essential for the establishment of the hematopoietic systems during embryonic development. However, in many instances the functional properties of those progenitors, and their relevance to human development, remains unclear. The human embryo, much like other vertebrate model organisms, generates hematopoietic cells via successive anatomical location- and time-specific waves, each yielding cells with distinct functional and molecular characteristics. Each of these progenitor "waves" is characterized at the time of emergence of the direct hematopoietic progenitor in the vasculature, the hemogenic endothelial cell (HEC). Critically, despite decades of study in model organisms, the origin(s) of each of these HEC populations remains unclear. Fortunately, through the directed differentiation of hPSCs, recent insights have been made into the earliest origins of each HEC population, revealing that each arises from transcriptionally and phenotypically distinct subsets of nascent mesoderm. Here, we outline the protocols to generate each mesodermal and HEC population, via the formation of embryoid bodies (EBs) and subsequent stage-specific signal manipulation. Through implementation of these discrete signal manipulations, it is possible to obtain human HEC populations that are exclusively extra-embryonic-like or exclusively intra-embryonic-like, enabling comparative developmental biology studies or specific translational applications.

Effects of ethanol metabolites on exocytosis of pancreatic acinar cells in rats.

BACKGROUND & AIMS: During development of alcoholic pancreatitis, oxidative (acetaldehyde) and nonoxidative metabolites (ethyl palmitate, ethyl oleate), rather than ethanol itself, mediate toxic injury. Exposure of pancreatic acini to ethanol blocks cholecystokinin (CCK)-8-stimulated apical exocytosis and redirects exocytosis to the basolateral plasma membrane, causing interstitial pancreatitis. We examined how each ethanol metabolite contributes to these changes in exocytosis. METHODS: Rat pancreatic acini were incubated with concentrations of ethanol associated with alcoholic pancreatitis (20-50 mmol/L) or ethanol metabolites (1-3 mmol/L) and then stimulated with CCK-8. We performed single zymogen granule (ZG) exocytosis assays, Ca(2+) imaging studies, ultrastructural analyses (with electron microscopy), and confocal microscopy to assess the actin cytoskeleton and track the movement of vesicle-associated membrane protein (VAMP)-8-containing ZGs. Coimmunoprecipitation assays were used to identify complexes that contain the distinct combinations of Munc18 and the soluble N-ethylmaleimide sensitive factor attachment protein receptor proteins, which mediate apical (ZG-apical plasma membrane) and basolateral exocytosis and fusion between ZGs (ZG-ZG). RESULTS: The ethanol metabolites acetaldehyde, ethyl palmitate, and ethyl oleate reduced CCK-8-stimulated apical exocytosis and formation of apical exocytotic complexes (between Munc18b and Syntaxin-2, synaptosomal-associated protein of 23 kilodaltons [SNAP23], and VAMP2) in rat pancreatic acini. Acetaldehyde and ethyl oleate redirected CCK-8-stimulated exocytosis to the basal and lateral plasma membranes and translocation of VAMP8-containing ZGs toward the basolateral plasma membrane. This process was mediated primarily via formation of basolateral exocytotic complexes (between Munc18c and Syntaxin-4, SNAP23, and VAMP8). Exposure of the acini to acetaldehyde and ethyl oleate followed by CCK-8 stimulation mildly perturbed the actin cytoskeleton and Ca(2+) signaling; exposure to ethyl palmitate severely affected Ca(2+) signaling. Acetaldehyde, like ethanol, promoted fusion between ZGs by the formation of ZG-ZG exocytotic complexes (between Munc18b and Syntaxin-3, SNAP23, and VAMP8), whereas ethyl palmitate and ethyl oleate reduced ZG-ZG fusion and formation of these complexes. CONCLUSIONS: The ethanol metabolites acetaldehyde, ethyl palmitate, and ethyl oleate perturb exocytosis processes in cultured rat pancreatic acini (apical blockade, basolateral exocytosis, and fusion between ZGs). Acetaldehyde and, to a lesser degree, ethyl oleate produce many of the same pathologic effects of ethanol on CCK-8-stimulated exocytosis in pancreatic acini.

Individual and spatio-temporal variations in the home range behaviour of a long-lived, territorial species.

Despite the fact that investigations of home range behaviour have exponentially evolved on theoretical, analytical and technological grounds, the factors that shape animal home range behaviour still represent an unsolved question and a challenging field of research. However, home range studies have recently begun to be approached under a new integrated conceptual framework, considering home range behaviour as the result of the simultaneous influences of temporal, spatial and individual-level processes, with potential consequences at the population level. Following an integrated approach, we studied the influence of both external and internal factors on variations in the home range behaviour of 34 radiotagged eagle owl (Bubo bubo) breeders. Home range behaviour was characterised through complementary analysis of space use, movement patterns and rhythms of activity at multiple spatio-temporal scales. The effects of the different phases of the biological cycle became considerably evident at the level of movement patterns, with males travelling longer distances than females during incubation and nestling periods. Both external (i.e. habitat structure and composition) and internal (i.e. sex and health state) factors explained a substantial amount of the variation in home range behaviour. At the broader temporal scale, home range and core area size were negatively correlated with landscape heterogeneity. Males showed (1) smaller home range and core area sizes, (2) more complex home range internal structure and (3) higher rates of movement. The better the physiological condition of the individuals, the simpler the internal home range structure. Finally, inter- and intra-individual effects contributed to shaping space use and movement patterns during the biological cycle. Because of the plurality of behavioural and ecological processes simultaneously involved in home range behaviour, we claim that an integrative approach is required for adequate investigation of its temporal and spatial variation.

Local colonisations and extinctions of European birds are poorly explained by changes in climate suitability.

Climate change has been associated with both latitudinal and elevational shifts in species' ranges. The extent, however, to which climate change has driven recent range shifts alongside other putative drivers remains uncertain. Here, we use the changing distributions of 378 European breeding bird species over 30 years to explore the putative drivers of recent range dynamics, considering the effects of climate, land cover, other environmental variables, and species' traits on the probability of local colonisation and extinction. On average, species shifted their ranges by 2.4 km/year. These shifts, however, were significantly different from expectations due to changing climate and land cover. We found that local colonisation and extinction events were influenced primarily by initial climate conditions and by species' range traits. By contrast, changes in climate suitability over the period were less important. This highlights the limitations of using only climate and land cover when projecting future changes in species' ranges and emphasises the need for integrative, multi-predictor approaches for more robust forecasting.

Mg/Ca partitioning between aqueous solution and aragonite mineral: a molecular dynamics study.

We have calculated the concentrations of Mg in the bulk and surfaces of aragonite CaCO(3) in equilibrium with aqueous solution, based on molecular dynamics simulations and grand-canonical statistical mechanics. Mg is incorporated in the surfaces, in particular in the (001) terraces, rather than in the bulk of aragonite particles. However, the total Mg content in the bulk and surface of aragonite particles was found to be too small to account for the measured Mg/Ca ratios in corals. We therefore argue that most Mg in corals is either highly metastable in the aragonite lattice, or is located outside the aragonite phase of the coral skeleton, and we discuss the implications of this finding for Mg/Ca paleothermometry.

Divergent roles of herbivory in eutrophying forests.

Ungulate populations are increasing across Europe with important implications for forest plant communities. Concurrently, atmospheric nitrogen (N) deposition continues to eutrophicate forests, threatening many rare, often more nutrient-efficient, plant species. These pressures may critically interact to shape biodiversity as in grassland and tundra systems, yet any potential interactions in forests remain poorly understood. Here, we combined vegetation resurveys from 52 sites across 13 European countries to test how changes in ungulate herbivory and eutrophication drive long-term changes in forest understorey communities. Increases in herbivory were associated with elevated temporal species turnover, however, identities of winner and loser species depended on N levels. Under low levels of N-deposition, herbivory favored threatened and small-ranged species while reducing the proportion of non-native and nutrient-demanding species. Yet all these trends were reversed under high levels of N-deposition. Herbivores also reduced shrub cover, likely exacerbating N effects by increasing light levels in the understorey. Eutrophication levels may therefore determine whether herbivory acts as a catalyst for the "N time bomb" or as a conservation tool in temperate forests.

Live pancreatic acinar imaging of exocytosis using syncollin-pHluorin.

In this report, a novel live acinar exocytosis imaging technique is described. An adenovirus was engineered, encoding for an endogenous zymogen granule (ZG) protein (syncollin) fused to pHluorin, a pH-dependent green fluorescent protein (GFP). Short-term culture of mouse acini infected with this virus permits exogenous adenoviral protein expression while retaining acinar secretory competence and cell polarity. The syncollin-pHluorin fusion protein was shown to be correctly localized to ZGs, and the pH-dependent fluorescence of pHluorin was retained. Coupled with the use of a spinning disk confocal microscope, the syncollin-pHluorin fusion protein exploits the ZG luminal pH changes that occur during exocytosis to visualize exocytic events of live acinar cells in real-time with high spatial resolution in three dimensions. Apical and basolateral exocytic events were observed on stimulation of acinar cells with maximal and supramaximal cholecystokinin concentrations, respectively. Sequential exocytic events were also observed. Coupled with the use of transgenic mice and/or adenovirus-mediated protein expression, this syncollin-pHluorin imaging method offers a superior approach to studying pancreatic acinar exocytosis. This assay can also be applied to acinar disease models to elucidate the mechanisms implicated in pancreatitis.

Priority list of biodiversity metrics to observe from space.

Monitoring global biodiversity from space through remotely sensing geospatial patterns has high potential to add to our knowledge acquired by field observation. Although a framework of essential biodiversity variables (EBVs) is emerging for monitoring biodiversity, its poor alignment with remote sensing products hinders interpolation between field observations. This study compiles a comprehensive, prioritized list of remote sensing biodiversity products that can further improve the monitoring of geospatial biodiversity patterns, enhancing the EBV framework and its applicability. The ecosystem structure and ecosystem function EBV classes, which capture the biological effects of disturbance as well as habitat structure, are shown by an expert review process to be the most relevant, feasible, accurate and mature for direct monitoring of biodiversity from satellites. Biodiversity products that require satellite remote sensing of a finer resolution that is still under development are given lower priority (for example, for the EBV class species traits). Some EBVs are not directly measurable by remote sensing from space, specifically the EBV class genetic composition. Linking remote sensing products to EBVs will accelerate product generation, improving reporting on the state of biodiversity from local to global scales.

The relative effects of habitat loss and fragmentation on population genetic variation in the red-cockaded woodpecker (Picoides borealis).

The relative influence of habitat loss, fragmentation and matrix heterogeneity on the viability of populations is a critical area of conservation research that remains unresolved. Using simulation modelling, we provide an analysis of the influence both patch size and patch isolation have on abundance, effective population size (N(e)) and F(ST). An individual-based, spatially explicit population model based on 15 years of field work on the red-cockaded woodpecker (Picoides borealis) was applied to different landscape configurations. The variation in landscape patterns was summarized using spatial statistics based on O-ring statistics. By regressing demographic and genetics attributes that emerged across the landscape treatments against proportion of total habitat and O-ring statistics, we show that O-ring statistics provide an explicit link between population processes, habitat area, and critical thresholds of fragmentation that affect those processes. Spatial distances among land cover classes that affect biological processes translated into critical scales at which the measures of landscape structure correlated best with genetic indices. Therefore our study infers pattern from process, which contrasts with past studies of landscape genetics. We found that population genetic structure was more strongly affected by fragmentation than population size, which suggests that examining only population size may limit recognition of fragmentation effects that erode genetic variation. If effective population size is used to set recovery goals for endangered species, then habitat fragmentation effects may be sufficiently strong to prevent evaluation of recovery based on the ratio of census:effective population size alone.

Revision of the family Carabodidae (Acari: Oribatida) XVII. Redescription of Diplobodes africanus Mahunka, 1987 from Kenia. Description of Diplobodes thailande sp. nov. from Thailand and Rwandabodes kayoveae gen. nov., sp. nov. from Rwanda.

Diplobodes africanus Mahunka, 1987, is redescribed by using Scanning Electron Microscopy (SEM) in order to complement optical microscopy. Diplobodes thailande sp. nov. from Thailand is described. For both species we include inclined views, to permit detailed analysis of ventral regions and to aid understanding of the complex relationships between elevated and depressed zones. Diplobodes thailande sp. nov. presents previously undescribed structures on legs III, which are involved in the leg folding process. Rwandabodes kayoveae gen. nov., sp. nov. presents a series of particular characteristics, such as: elevated interlamellar process on prodorsum, composed of a triangular structure, externally delimited by a low lamellar furrow; in setae inserted on elevated interlamellar process; large free lamellar tip; notogaster lacking ridges; anterior genital furrow extends into an oblique lateral depression; depressed area anterior to anal zone; both zones clearly delimited. These characteristics permit easy differentiation from related genera.

Rewilding complex ecosystems.

The practice of rewilding has been both promoted and criticized in recent years. Benefits include flexibility to react to environmental change and the promotion of opportunities for society to reconnect with nature. Criticisms include the lack of a clear conceptualization of rewilding, insufficient knowledge about possible outcomes, and the perception that rewilding excludes people from landscapes. Here, we present a framework for rewilding that addresses these concerns. We suggest that rewilding efforts should target trophic complexity, natural disturbances, and dispersal as interacting processes that can improve ecosystem resilience and maintain biodiversity. We propose a structured approach to rewilding projects that includes assessment of the contributions of nature to people and the social-ecological constraints on restoration.

Two new species of the family Nippobodidae (Acari, Oribatida), including a description of the leg-folding process.

Nippobodespanemorfis sp. n. and Leobodestrypasis sp. n. are described by means of optical and Scanning Electron Microscopy (SEM) and compared to other congeners. The leg-folding process is described and illustrated. Nippobodespanemorfis sp. n. is characterised by interlocking, double hook-shaped, posterior prodorsal condyle and anterior zone humeral apophysis; posterior prodorsal depression present. Tutorium a large lamina defining a pocket-shaped structure; bothridial opening ovoid, situated at the bottom of a U-shaped structure; deep, rounded-ovoid anterior notogastral depression present; ten pairs of notogastral setae; c setae looped, dentate, sharply tipped. Marginal setae h3 , p3 on large promontories, followed by deep V-shaped incision; notogaster completely surrounded by circumgastric depression; lateral genital zone with locking structure constituted by longitudinal cuticular elevation, with promontories and a parallel furrow involved in the leg-folding process; genital plate smaller than anal plate. Leobodestrypasis sp. n. is characterised by: the presence of posterior prodorsal depression and anterior notogastral depression; bridge-shaped anterior prodorsal condyles; heart-shaped frontal prodorsal orifice; ten pairs of notogastral setae; posterior prodorsal condyle and humeral condyle interlocked, forming double hook-like structure; circumgastric furrow surrounding entire notogaster; setae lp, h2, h1 situated on shallow medial furrow; notogastral setae lm, lp, h1 , h2 medially aligned; p1, p2, p3, h3 marginally situated. Legs I-IV, tutorium, pedotectum I, and pedotectum II involved in leg folding which is inferred to be a protection mechanism.

The family Lohmanniidae (Acari, Oribatida) II: two new Oribatid mites, Meristacarus perikopesis sp. n. from Costa Rica and Torpacarus eidikoterai sp. n. from Kenya.

Two very particular new species of the family Lohmanniidae were studied and described using optical and Scanning Electron Microscopy (SEM). Meristacarus perikopesissp. n. displays complex cuticular microsculpture with cross-shaped grooves and pusticulate porose areas; ten transversal bands, with reticulate-foveate microsculpture; S4, S5, S7, S10 not crossing medial notogastral plane, amongst other characters. Torpacarus eidikoteraisp. n. with: prodorsum - rostrum weakly bilobate with small central structure and CSO present. Six transversal depressions present, transversal bands absent; but six transversal depressions present, none of the depressions crossing medial notogastral plane.

Revision of the family Carabodidae (Acari: Oribatida) XVI. Synkrotima tsalakpmenoi sp. nov. from Zimbabwe and Kenya, and Congocepheus thailandae sp. nov. from Thailand, including a complementary study of Cavaecarabodes hauseri (Mahunka 1989).

Synkrotima tsalakpmenoi sp. nov. is described from material collected in Zimbabwe and Kenya. This species presents the following characteristics: notogastral integument formed by longitudinally aligned cuticular cords; thick, lanceolate notogastral setae; and genital neotrichy. Synkrotima tsalakpmenoi sp. nov. is compared to S. zimbabwae. Congocepheus thailandae sp. nov. is the first species of this genus described from Thailand, with the following present: large finger-like notogastral projection; notogastral setae c1, c2, da, dm, dp, la, lm, lp, h1, h2 situated on promontories; setae c1, c2 located adjacent and parallel.        A complementary study of Cavaecarabodes hauseri, making use of Scanning Electron Microscopy (SEM), allows for clarification of particularities regarding complex setae as well as some aspects of the integument, and provides a more detailed diagnosis.