A framework for estimating the sensitivity of eDNA surveys

Imperfect sensitivity, or imperfect detection, is a feature of all survey methods that needs to be accounted for when interpreting survey results. Detection of environmental DNA (eDNA) is increasingly being used to infer species distributions, yet the sensitivity of the technique has not been fully evaluated. Sensitivity, or the probability of detecting target DNA given it is present at a site, will depend on both the survey method and the concentration and dispersion of target DNA molecules at a site. We present a model to estimate target DNA concentration and dispersion at survey sites and to estimate the sensitivity of an eDNA survey method. We fitted this model to data from a species‐specific eDNA survey for Oriental weatherloach, Misgurnus anguillicaudatus, at three sites sampled in both autumn and spring. The concentration of target DNA molecules was similar at all three sites in autumn but much higher at two sites in spring. Our analysis showed the survey method had ≥95% sensitivity at sites where target DNA concentrations were ≥11 molecules per litre. We show how these data can be used to compare sampling schemes that differ in the number of field samples collected per site and number of PCR replicates per sample to achieve ≥95% sensitivity at a given target DNA concentration. These models allow researchers to quantify the sensitivity of eDNA survey methods to optimize the probability of detecting target species, and to compare DNA concentrations spatially and temporarily.     

Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding

Freshwater fauna are particularly sensitive to environmental change and disturbance. Management agencies frequently use fish and amphibian biodiversity as indicators of ecosystem health and a way to prioritize and assess management strategies. Traditional aquatic bioassessment that relies on capture of organisms via nets, traps and electrofishing gear typically has low detection probabilities for rare species and can injure individuals of protected species. Our objective was to determine whether environmental DNA (eDNA) sampling and metabarcoding analysis can be used to accurately measure species diversity in aquatic assemblages with differing structures. We manipulated the density and relative abundance of eight fish and one amphibian species in replicated 206‐L mesocosms. Environmental DNA was filtered from water samples, and six mitochondrial gene fragments were Illumina‐sequenced to measure species diversity in each mesocosm. Metabarcoding detected all nine species in all treatment replicates. Additionally, we found a modest, but positive relationship between species abundance and sequencing read abundance. Our results illustrate the potential for eDNA sampling and metabarcoding approaches to improve quantification of aquatic species diversity in natural environments and point the way towards using eDNA metabarcoding as an index of macrofaunal species abundance.     

Simulated impact of the renewable fuels standard on US Conservation Reserve Program enrollment and conversion

A socioeconomic model is used to estimate the land‐use implications on the U.S. Conservation Reserve Program from potential increases in second‐generation biofuel production. A baseline scenario with no second‐generation biofuel production is compared to a scenario where the Renewable Fuels Standard (RFS2) volumes are met by 2022. We allow for the possibility of converting expiring CRP lands to alternative uses such as conventional crops, dedicated second‐generation biofuel crops, or harvesting existing CRP grasses for biomass. Results indicate that RFS2 volumes (RFS2‐v) can be met primarily with crop residues (78% of feedstock demand) and woody residues (19% of feedstock demand) compared with dedicated biomass (3% of feedstock demand), with only minimal conversion of cropland (0.27 million hectares, <1% of total cropland), pastureland (0.28 million hectares of pastureland, <1% of total pastureland), and CRP lands (0.29 million hectares of CRP lands, 3% of existing CRP lands) to biomass production. Meeting RFS2 volumes would reduce CRP re‐enrollment by 0.19 million hectares, or 4%, below the baseline scenario where RFS2 is not met. Yet under RFS2‐v scenario, expiring CRP lands are more likely to be converted to or maintain perennial cover, with 1.78 million hectares of CRP lands converting to hay production, and 0.29 million hectares being harvested for existing grasses. A small amount of CRP is harvested for existing biomass, but no conversion of CRP to dedicated biomass crops, such as switchgrass, are projected to occur. Although less land is enrolled in CRP under RFS2‐v scenario, total land in perennial cover increases by 0.15 million hectares, or 2%, under RFS2‐v. Sensitivity to yield, payment and residue retention assumptions are evaluated.     

Inducing Acute Traumatic Coagulopathy In Vitro: The Effects of Activated Protein C on Healthy Human Whole Blood

Introduction

Acute traumatic coagulopathy has been associated with shock and tissue injury, and may be mediated via activation of the protein C pathway. Patients with acute traumatic coagulopathy have prolonged PT and PTT, and decreased activity of factors V and VIII; they are also hypocoagulable by thromboelastometry (ROTEM) and other viscoelastic assays. To test the etiology of this phenomenon, we hypothesized that such coagulopathy could be induced in vitro in healthy human blood with the addition of activated protein C (aPC).

Methods

Whole blood was collected from 20 healthy human subjects, and was “spiked” with increasing concentrations of purified human aPC (control, 75, 300, 2000 ng/mL). PT/PTT, factor activity assays, and ROTEM were performed on each sample. Mixed effect regression modeling was performed to assess the association of aPC concentration with PT/PTT, factor activity, and ROTEM parameters.

Results

In all subjects, increasing concentrations of aPC produced ROTEM tracings consistent with traumatic coagulopathy. ROTEM EXTEM parameters differed significantly by aPC concentration, with stepwise prolongation of clotting time (CT) and clot formation time (CFT), decreased alpha angle (α), impaired early clot formation (a10 and a20), and reduced maximum clot firmness (MCF). PT and PTT were significantly prolonged at higher aPC concentrations, with corresponding significant decreases in factor V and VIII activity.

Conclusion

A phenotype of acute traumatic coagulopathy can be induced in healthy blood by the in vitro addition of aPC alone, as evidenced by viscoelastic measures and confirmed by conventional coagulation assays and factor activity. This may lend further mechanistic insight to the etiology of coagulation abnormalities in trauma, supporting the central role of the protein C pathway. Our findings also represent a model for future investigations in the diagnosis and treatment of acute traumatic coagulopathy.     

The Role of Physical Activity in Harm Reduction among Betel Quid Chewers from a Prospective Cohort of 419,378 Individuals

ObjectiveTo assess the benefits of regular exercise in reducing harms associated with betel quid (BQ) chewing.MethodsThe study cohort, 419,378 individuals, participated in a medical screening program between 1994 and 2008, with 38,324 male and 1,495 female chewers, who consumed 5–15 quids of BQ a day. Physical activity of each individual, based on “MET-hour/week”, was classified as “inactive” or “active”, where activity started from a daily 15 minutes/day or more of brisk walking (≥3.75 MET-hour/week). Hazard ratios for mortality and remaining years in life expectancy were calculated.ResultsNearly one fifth (18.7%) of men, but only 0.7% of women were chewers. Chewers had a 10-fold increase in oral cancer risk; and a 2-3-fold increase in mortality from lung, esophagus and liver cancer, cardiovascular disease, and diabetes, with doubling of all-cause mortality. More than half of chewers were physically inactive (59%). Physical activity was beneficial for chewers, with a reduction of all-cause mortality by 19%. Inactive chewers had their lifespan shortened by 6.3 years, compared to non-chewers, but being active, chewers improved their health by gaining 2.5 years. The improvement, however, fell short of offsetting the harms from chewing.ConclusionsChewers had serious health consequences, but being physically active, chewers could mitigate some of these adverse effects, and extend life expectancy by 2.5 years and reduce mortality by one fifth. Encouraging exercise, in addition to quitting chewing, remains the best advice for 1.5 million chewers in Taiwan.     

Comparison of the Morphology Development of Polymer–Fullerene and Polymer–Polymer Solar Cells during Solution‐Shearing Blade Coating

In this work, the detailed morphology studies of polymer poly(3‐hexylthiophene‐2,5‐diyl) (P3HT):fullerene(PCBM) and polymer(P3HT):polymer naphthalene diimide thiophene (PNDIT) solar cell are presented to understand the challenge for getting high performance all‐polymer solar cells. The in situ X‐ray scattering and optical interferometry and ex situ hard and soft X‐ray scattering and imaging techniques are used to characterize the bulk heterojunction (BHJ) ink during drying and in dried state. The crystallization of P3HT polymers in P3HT:PCBM bulk heterojunction shows very different behavior compared to that of P3HT:PNDIT BHJ due to different mobilities of P3HT in the donor:acceptor glass. Supplemented by the ex situ grazing incidence X‐ray diffraction and soft X‐ray scattering, PNDIT has a lower tendency to form a mixed phase with P3HT than PCBM, which may be the key to inhibit the donor polymer crystallization process, thus creating preferred small phase separation between the donor and acceptor polymer.     

New species and reports of <Emphasis Type="Italic">Hypoxylon</Emphasis> from Argentina recognized by a polyphasic approach

A preliminary account of Hypoxylon species (Xylariaceae) from the hitherto widely unexplored “Yungas” mountain forests of Northwest Argentina is presented. Two new species are described based on extensive morphological, molecular (ITS region of rDNA, partial β-tubulin gene) and chemotaxonomic data. Hypoxylon spegazzinianum is close to H. erythrostroma, but differs by larger ascospores and a virgariella-like asexual morph. Hypoxylon calileguense resembles H. subgilvum when growing on wood, but can be distinguished by larger ascospores and a fawn to brick stromatal surface colour. Stromata found on bark have affinities to H. pelliculosum, but differ in their stromatal surface colour and conspicuous amyloid apical apparatus. In addition, nine taxa of Hypoxylon are reported for Argentina for the first time, and some details on their asexual state and stromatal secondary metabolites are reported. An updated dichotomous key for Hypoxylon species from Argentina is provided.     

Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention

Pulmonary symptoms in cystic fibrosis (CF) begin in early life with chronic lung infections and concomitant airway inflammation leading to progressive loss of lung function. Gradual pulmonary function decline is interspersed with periods of acute worsening of respiratory symptoms known as CF pulmonary exacerbations (CFPEs). Cumulatively, CFPEs are associated with more rapid disease progression. In this study multiple sputum samples were collected from adult CF patients over the course of CFPEs to better understand how changes in microbiota are associated with CFPE onset and management. Data were divided into five clinical periods: pre-CFPE baseline, CFPE, antibiotic treatment, recovery, and post-CFPE baseline. Samples were treated with propidium monoazide prior to DNA extraction, to remove the impact of bacterial cell death artefacts following antibiotic treatment, and then characterised by 16S rRNA gene-targeted high-throughput sequencing. Partitioning CF microbiota into core and rare groups revealed compositional resistance to CFPE and resilience to antibiotics interventions. Mixed effects modelling of core microbiota members revealed no significant negative impact on the relative abundance of Pseudomonas aeruginosa across the exacerbation cycle. Our findings have implications for current CFPE management strategies, supporting reassessment of existing antimicrobial treatment regimens, as antimicrobial resistance by pathogens and other members of the microbiota may be significant contributing factors.