Glucose oxidase-mediated polymerization as a platform for dual-mode signal amplification and biodetection

We report the first use of a polymerization-based ELISA substrate solution employing enzymatically mediated radical polymerization as a dual-mode amplification strategy. Enzymes are selectively coupled to surfaces to generate radicals that subsequently lead to polymerization-based amplification (PBA) and biodetection. Sensitivity and amplification of the polymerization-based detection system were optimized in a microwell strip format using a biotinylated microwell surface with a glucose oxidase (GOx)-avidin conjugate. The immobilized GOx is used to initiate polymerization, enabling the detection of the biorecognition event visually or through the use of a plate reader. Assay response is compared to that of an enzymatic substrate utilizing nitroblue tetrazolium in a simplified assay using biotinylated wells. The polymerization substrate exhibits equivalent sensitivity (2 μg/mL of GOx-avidin) and over three times greater signal amplification than this traditional enzymatic substrate since each radical that is enzymatically generated leads to a large number of polymerization events. Enzyme-mediated polymerization proceeds in an ambient atmosphere without the need for external energy sources, which is an improvement upon previous PBA platforms. Substrate formulations are highly sensitive to both glucose and iron concentrations at the lowest enzyme concentrations. Increases in amplification time correspond to higher assay sensitivities with no increase in non-specific signal. Finally, the polymerization substrate generated a signal to noise ratio of 14 at the detection limit (156 ng/mL) in an assay of transforming growth factor-beta.     

A species‐centered approach for uncovering generalities in organism responses to habitat loss and fragmentation

Theoretical models predict strong influences of habitat loss and fragmentation on species distributions and demography, but empirical studies have shown relatively inconsistent support across species and systems. We argue that species’ responses to landscape‐scale habitat loss and fragmentation are likely to appear less idiosyncratic if it is recognized that species perceive the same landscapes in different ways. We present a new quantitative approach that uses species distribution models (SDMs) to measure landscapes (e.g. patch size, isolation, matrix amount) from the perspective of individual species. First, we briefly summarize the few efforts to date demonstrating that once differences in habitat distributions are controlled, consistencies in species’ responses to landscape structure emerge. Second, we present a detailed example providing step‐by‐step methods for application of a species‐centered approach using freely available land‐cover data and recent statistical modeling approaches. Third, we discuss pitfalls in current applications of the approach and recommend avenues for future developments. We conclude that the species‐centered approach offers considerable promise as a means to test whether sensitivity to habitat loss and fragmentation is mediated by phylogenetic, ecological, and life‐history traits. Cross‐species generalities in responses to habitat loss and fragmentation will be challenging to uncover unless landscape mosaics are defined using models that reflect differing species‐specific distributions, functional connectivity, and domains of scale. The emergence of such generalities would not only enhance scientific understanding of biotic processes driving fragmentation effects, but would allow managers to estimate species sensitivities in new regions.     

A test of non‐kin social foraging in the southern flying squirrel (Glaucomys volans)

It can be challenging to understand the evolution of sociality, particularly the occurrence of co‐operation by non‐kin. Southern flying squirrels (Glaucomys volans) are an interesting example of non‐kin co‐operation because of the mutual benefits obtained by social thermoregulation during winter. Because group survival confers benefits to the entire group, flying squirrels may also follow an aggregation economy, whereby co‐operative foraging during winter is advantageous. However, the extent of such social foraging in flying squirrels is unknown. We tested for social foraging of southern flying squirrels, and also for relatedness among foraging groups. To determine the structure of foraging groups, we set up and remotely monitored feeding stations and nest cavities. All squirrels at the study site were tagged with passive integrated transponder (PIT) tags and nests and feeding stations were monitored with automated PIT‐tag recorders for a 24‐month period. Squirrels were found most often foraging alone. Squirrels that were recorded foraging together comprised unrelated individuals that were also found to share nest cavities. Squirrels were also recorded travelling farther distances between nest cavity and feeding station in the winter season than in the summer season, suggesting that, during winter, squirrels trade‐off proximity to food caches for membership in a nest group. Our data suggest that squirrels forage and cache alone in their summer home range and make solitary returns to this summer range to collect their cache during the winter months, despite exhibiting social winter nesting. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 1126–1135.     

Using a rainforest-flame forest mosaic to test the hypothesis that leaf and litter fuel flammability is under natural selection

We used a mosaic of infrequently burnt temperate rainforest and adjacent, frequently burnt eucalypt forests in temperate eastern Australia to test whether: (1) there were differences in flammability of fresh and dried foliage amongst congeners from contrasting habitats, (2) habitat flammability was related to regeneration strategy, (3) litter fuels were more flammable in frequently burnt forests, (4) the severity of a recent fire influenced the flammability of litter (as this would suggest fire feedbacks), and (5) microclimate contributed to differences in fire hazard amongst habitats. Leaf-level comparisons were made among 11 congeneric pairs from rainforest and eucalypt forests. Leaf-level ignitability, combustibility and sustainability were not consistently higher for taxa from frequently burnt eucalypt forests, nor were they higher for species with fire-driven recruitment. The bulk density of litter-bed fuels strongly influenced flammability, but eucalypt forest litter was not less dense than rainforest litter. Ignitability, combustibility and flame sustainability of community surface fuels (litter) were compared using fuel arrays with standardized fuel mass and moisture content. Forests previously burned at high fire severity did not have consistently higher litter flammability than those burned at lower severity or long unburned. Thus, contrary to the Mutch hypothesis, there was no evidence of higher flammability of litter fuels or leaves from frequently burnt eucalypt forests compared with infrequently burnt rainforests. We suggest the manifest pyrogenicity of eucalypt forests is not due to natural selection for more flammable foliage, but better explained by differences in crown openness and associated microclimatic differences.     

Gut expansion and contraction in the predatory soil mite Pergamasus longicornis (Mesostigmata: Parasitidae): a stiff system

Mite digestive processes are inferred from gut expansion and contraction time in the free-living predatory soil mite Pergamasus longicornis (Berlese), estimated using a temporal series of histological sections. Gut regions (bar the rectal vesicle) behave broadly in unison for rapid initial filling (ingestion half-life about 2–3 min; max 8 min), but behave heterogeneously when slowly emptying (digestion/egestion half-life from about 2–3 h; max 8.5 h). Anterior gut regions fill and empty the earliest. Posterior gut regions take the longest to fill and to empty. Switching first from filling-predominating to emptying-predominating in the gut occurs around 2 h from the start of feeding. Median time for the initial completion of gut filling and for the commencement of gut emptying is 10 min and 12.5 h, respectively, from the start of feeding. Three phases of gut changes are critically discussed: rapid filling, concentration by fluid loss (via coxal glands), and slow emptying. Independent corroboration of coxal droplet formation is included. Predictions to confirm or refute postulated mechanisms of salivary, coxal or rectal water balance are given. Overall total gut filling (ingestion) plus gut emptying (digestion/egestion) time in this poikilotherm is approximately 29–52.5 h ( \(1^{+}-2^{+}\) days) at room temperature from the start of feeding on large dipteran prey ( \(\equiv 0.46-0.83\) gut emptyings per day). Pergamasus longicornis exhibits the stiff digestive system of an intermittent ‘bolus’ feeder.     

Terrestrial gross primary production inferred from satellite fluorescence and vegetation models

Determining the spatial and temporal distribution of terrestrial gross primary production (GPP) is a critical step in closing the Earth's carbon budget. Dynamical global vegetation models (DGVMs) provide mechanistic insight into GPP variability but diverge in predicting the response to climate in poorly investigated regions. Recent advances in the remote sensing of solar‐induced chlorophyll fluorescence (SIF) opens up a new possibility to provide direct global observational constraints for GPP. Here, we apply an optimal estimation approach to infer the global distribution of GPP from an ensemble of eight DGVMs constrained by global measurements of SIF from the Greenhouse Gases Observing SATellite (GOSAT). These estimates are compared to flux tower data in N. America, Europe, and tropical S. America, with careful consideration of scale differences between models, GOSAT, and flux towers. Assimilation of GOSAT SIF with DGVMs causes a redistribution of global productivity from northern latitudes to the tropics of 7–8 Pg C yr^?1 from 2010 to 2012, with reduced GPP in northern forests (~3.6 Pg C yr^?1) and enhanced GPP in tropical forests (~3.7 Pg C yr^?1). This leads to improvements in the structure of the seasonal cycle, including earlier dry season GPP loss and enhanced peak‐to‐trough GPP in tropical forests within the Amazon Basin and reduced growing season length in northern croplands and deciduous forests. Uncertainty in predicted GPP (estimated from the spread of DGVMs) is reduced by 40–70% during peak productivity suggesting the assimilation of GOSAT SIF with models is well‐suited for benchmarking. We conclude that satellite fluorescence augurs a new opportunity to quantify the GPP response to climate drivers and the potential to constrain predictions of carbon cycle evolution.     

Non-contiguous finished genome sequence of Staphylococcus capitis CR01 (pulsetype NRCS-A)

Staphylococcus capitis is a coagulase-negative staphylococcus (CoNS) commonly found in the human microflora. Recently, a clonal population of Staphylococcus capitis (denominated NRCS-A) was found to be a major cause of late-onset sepsis (LOS) in several neonatal intensive care units in France. Here, we report the complete genome sequence and annotation of the prototype Staphylococcus capitis NCRS-A strain CR01. The 2,504,472 bp long genome (1 chromosome and no plasmids) exhibits a G+C content of 32.81%, and contains 2,468 protein-coding and 59 tRNA genes and 4 rRNA genes.