Advanced REACH Tool (ART): calibration of the mechanistic model

The mechanistic model of the Advanced Reach Tool (ART) provides a relative ranking of exposure levels from different scenarios. The objectives of the calibration described in this paper are threefold: to study whether the mechanistic model scores are accurately ranked in relation to exposure measurements; to enable the mechanistic model to estimate actual exposure levels rather than relative scores; and to provide a method of quantifying model uncertainty. Stringent data quality guidelines were applied to the collated data. Linear mixed effects models were used to evaluate the association between relative ART model scores and measurements. A random scenario and company component of variance were introduced to reflect the model uncertainty. Stratified analyses were conducted for different forms of exposure (abrasive dust, dust, vapours and mists). In total more than 2000 good quality measurements were available for the calibration of the mechanistic model. The calibration showed that after calibration the mechanistic model of ART was able to estimate geometric mean (GM) exposure levels with 90% confidence for a given scenario to lie within a factor between two and six of the measured GM depending upon the form of exposure.     

Characterization of bacterial contaminants in the air of a duck hatchery by cultivation based and molecular methods

Today's large-scale poultry production is often accompanied by high concentrations of airborne microorganisms at working places. However, the microbial communities in those bioaerosols are rarely characterised. In this study, we investigated the bacterial population in bioaerosols from a duck hatchery by both cultivation based and molecular methods and compared the results. Depending on used media, concentrations of airborne culturable bacteria varied between 6 × 10(1) and 7 × 10(6) CFU per m(3) air. The corresponding total cell count of DAPI stained cells was 2 × 10(7) cells per m(3) air. 16S rRNA gene analyses of bacterial isolates and clone libraries revealed a low species richness in hatcheries air, respectively. More than 50% of bacterial isolates were phylogenetically most closely related to bacterial species of the risk group 2 (German TRBA). The sequence composition in clone libraries supported the result of cultivation based approaches, whereby sequences assigned to Staphylococcus, Acinetobacter and Enterococcus are the most common. The high concentration of airborne bacteria which are most closely related to species of potential health risk requires further detailed investigations for these bacterial species.     

Prenatal diagnosis of bilateral anophthalmia: Identifying de novo SOX2 variant

A 26 year old nulligravida presented at 24 weeks gestation for the second opinion of abnormal fetal profile and mid-face views on ultrasound at another institution. A detailed fetal anatomic ultrasound at our facility revealed the absence of fetal lens and globes bilaterally consistent with bilateral anophthalmia (HP: 0000528) without other anomalies. Karyotype and chromosomal microarray analysis were completed from amniocentesis sample. After these results, duo exome testing with paternal sequencing was completed from proband amniotic fluid sample and parental blood samples. A pathogenic variant in SOX2 (NM_003106.3: c.513C>G p.(Tyr171*Ter)) with heterozygous autosomal dominant inheritance resulted. On duo exome testing with paternal segregation analysis, the variant was found to be consistent with likely sporadic de novo inheritance. The SOX2 variant reported is consistent with the fetal phenotype in this case. While germline mosaicism could exist, this identified variant provided the family with a likely explanation for this proband's finding. This ultrasound and genetic testing allowed the family to make decisions related to planning in current and future pregnancies.     

Turner syndrome-omphalocele association: Incidence,karyotype, phenotype and fetal outcome

Objective

Omphalocele is known to be associated with genetic anomalies like trisomy 13, 18 and Beckwith–Wiedemann syndrome, but not with Turner syndrome (TS). Our aim was to assess the incidence of omphalocele in fetuses with TS, the phenotype of this association with other anomalies, their karyotype, and the fetal outcomes.

Method

Retrospective multicenter study of fetuses with confirmed diagnosis of TS. Data were extracted from a detailed questionnaire sent to specialists in prenatal ultrasound.

Results

680 fetuses with TS were included in this analysis. Incidence of small omphalocele in fetuses diagnosed ≥12 weeks was 3.1%. Including fetuses diagnosed before 12 weeks, it was 5.1%. 97.1% (34/35) of the affected fetuses had one or more associated anomalies including increased nuchal translucency (≥3 mm) and/or cystic hygroma (94.3%), hydrops/skin edema (71.1%), and cardiac anomalies (40%). The karyotype was 45,X in all fetuses. Fetal outcomes were poor with only 1 fetus born alive.

Conclusion

TS with 45,X karyotype but not with X chromosome variants is associated with small omphalocele. Most of these fetuses have associated anomalies and a poor prognosis. Our data suggest an association of TS with omphalocele, which is evident from the first trimester.     

Substratum preferences in planula larvae of two species of scleractinian corals, Goniastrea retiformis and Stylaraea punctata

To test whether coral planulae recruit randomly to different coral reef habitats or have specific substratum preferences, the settling behavior of planulae from two shallow water coral species from Pago Bay, Guam (13°25.02N, 144°47.30E) were examined in the laboratory in June and July of 1995. Goniastrea retiformis is generally restricted to the shallow reef front (<10 m depth) in areas dominated by crustose coralline algae (CCA), while Stylaraea punctata is abundant on inner reef flats were CCA coverage is low and sand and carbonate rubble covered by biofilms is common. When presented with four substrata (1) carbonate rock scrubbed free of biofilm and dried as a control, (2) the CCA Hydrolithon reinboldii, (3) the CCA Peyssonelia sp., and (4) naturally conditioned carbonate rubble covered by a biofilm, G. retiformis larvae showed a significant preference for H. reinboldii, and S. punctata larvae for the carbonate biofilm treatment. The preference shown by S. punctata larvae for biofilmed surfaces did not diminish with increasing larval age up to 11 days. These results suggest that the larvae of both species are capable of habitat selection, and that the preferred substrata among those tested bears a relationship to the habitats in which adult colonies were found. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Electrokinetic ion transport through unsaturated soil: 1. Theory, model development, and testing

An electromigration transport model for non-reactive ion transport in unsaturated soil was developed and tested against laboratory experiments. This model assumed the electric potential field was constant with respect to time, an assumption valid for highly buffered soil, or when the electrode electrolysis reactions are neutralized. The model also assumed constant moisture contents and temperature with respect to time, and that electroosmotic and hydraulic transport of water through the soil was negligible. A functional relationship between ionic mobility and the electrolyte concentration was estimated using the chemical activity coefficient. Tortuosity was calculated from a mathematical relationship fitted to the electrical conductivity of the bulk pore water and soil moisture data. The functional relationship between ionic mobility, pore-water concentration, and tortuosity as a function of moisture content allowed the model to predict ion transport in heterogeneous unsaturated soils. The model was tested against laboratory measurements assessing anionic electromigration as a function of moisture content. In the test cell, a strip of soil was spiked with red dye No 40 and monitored for a 24-h period while a 10-mA current was maintained between the electrodes. Electromigration velocities predicted by the electromigration transport model were in agreement with laboratory experimental results. Both laboratory-measured and model-predicted dye migration results indicated a maximum transport velocity at moisture contents less than saturation due to competing effects between current density and tortuosity as moisture content decreases.     

A stochastic model for estimating sustainable limits to wildlife mortality in a changing world

Human-caused mortality of wildlife is a pervasive threat to biodiversity. Assessing the population-level impact of fisheries bycatch and other human-caused mortality of wildlife has typically relied upon deterministic methods. However, population declines are often accelerated by stochastic factors that are not accounted for in such conventional methods. Building on the widely applied potential biological removal (PBR) equation, we devised a new population modeling approach for estimating sustainable limits to human-caused mortality and applied it in a case study of bottlenose dolphins affected by capture in an Australian demersal otter trawl fishery. Our approach, termed sustainable anthropogenic mortality in stochastic environments (SAMSE), incorporates environmental and demographic stochasticity, including the dependency of offspring on their mothers. The SAMSE limit is the maximum number of individuals that can be removed without causing negative stochastic population growth. We calculated a PBR of 16.2 dolphins per year based on the best abundance estimate available. In contrast, the SAMSE model indicated that only 2.3–8.0 dolphins could be removed annually without causing a population decline in a stochastic environment. These results suggest that reported bycatch rates are unsustainable in the long term, unless reproductive rates are consistently higher than average. The difference between the deterministic PBR calculation and the SAMSE limits showed that deterministic approaches may underestimate the true impact of human-caused mortality of wildlife. This highlights the importance of integrating stochasticity when evaluating the impact of bycatch or other human-caused mortality on wildlife, such as hunting, lethal control measures, and wind turbine collisions. Although population viability analysis (PVA) has been used to evaluate the impact of human-caused mortality, SAMSE represents a novel PVA framework that incorporates stochasticity for estimating acceptable levels of human-caused mortality. It offers a broadly applicable, stochastic addition to the demographic toolbox to evaluate the impact of human-caused mortality on wildlife.     

Using land-use history and multiple baselines to determine bird responses to cocoa agroforestry

Agroforests can play an important role in biodiversity conservation in complex landscapes. A key factor distinguishing among agroforests is land-use history – whether agroforests are established inside forests or on historically forested but currently open lands. The disparity between land-use histories means the appropriate biodiversity baselines may differ, which should be accounted for when assessing the conservation value of agroforests. Specifically, comparisons between multiple baselines in forest and open land could enrich understanding of species’ responses by contextualizing them. We made such comparisons based on data from a recently published meta-analysis of the effects of cocoa (Theobroma cacao) agroforestry on bird diversity. We regrouped rustic, mixed shade cocoa, and low shade cocoa agroforests, based on land-use history, into forest-derived and open-land-derived agroforests and compared bird species diversity (species richness, abundance, and Shannon's index values) between forest and open land, which represented the 2 alternative baselines. Bird diversity was similar in forest-derived agroforests and forests (Hedges’ g* estimate [SE] = -0.3144 [0.3416], p = 0.36). Open-land-derived agroforests were significantly less diverse than forests (g* = 1.4312 [0.6308], p = 0.023) and comparable to open lands (g* = -0.1529 [0.5035], p = 0.76). Our results highlight how land-use history determined the conservation value of cocoa agroforests. Forest-derived cocoa agroforests were comparable to the available – usually already degraded – forest baselines, but entail future degradation risks. In contrast, open-land-derived cocoa agroforestry may offer restoration opportunities. Our results showed that comparisons among multiple baselines may inform relative contributions of agroforestry systems to bird conservation on a landscape scale.     

Mercury content in fish from drinking-water reservoirs in the Morava River Basin (Czech Republic)

Environmental Science and Pollution Research - This study focused on the total mercury content in fish from seven drinking-water reservoirs located in the Morava River Basin: Bojkovice, Boskovice,...     

Constitutive and induced defenses to herbivory in above- and belowground plant tissues

A recent surge in attention devoted to the ecology of soil biota has prompted interest in quantifying similarities and differences between interactions occurring in above- and belowground communities. Furthermore, linkages that interconnect the dynamics of these two spatially distinct ecosystems are increasingly documented. We use a similar approach in the context of understanding plant defenses to herbivory, including how they are allocated between leaves and roots (constitutive defenses), and potential cross-system linkages (induced defenses). To explore these issues we utilized three different empirical approaches. First, we manipulated foliar and root herbivory on tobacco (Nicotiana tabacum) and measured changes in the secondary chemistry of above- and belowground tissues. Second, we reviewed published studies that compared levels of secondary chemistry between leaves and roots to determine how plants distribute putative defense chemicals across the above- and belowground systems. Last, we used meta-analysis to quantify the impact of induced responses across plant tissue types. In the tobacco system, leaf-chewing insects strongly induced higher levels of secondary metabolites in leaves but had no impact on root chemistry. Nematode root herbivores, however, elicited changes in both leaves and roots. Virtually all secondary chemicals measured were elevated in nematode-induced galls, whereas the impact of root herbivory on foliar chemistry was highly variable and depended on where chemicals were produced within the plant. Importantly, nematodes interfered with aboveground metabolites that have biosynthetic sites located in roots (e.g., nicotine) but had the opposite effect (i.e., nematodes elevated foliar expression) on chemicals produced in shoots (e.g., phenolics and terpenoids). Results from our literature review suggest that, overall, constitutive defense levels are extremely similar when comparing leaves with roots, although certain chemical classes (e.g., alkaloids, glucosinolates) are differentially allocated between above- and belowground parts. Based on a meta-analysis of induced defense studies we conclude that: (1) foliar induction generates strong responses in leaves, but much weaker responses in roots, and (2) root induction elicits responses of equal magnitude in both leaves and roots. We discuss the importance of this asymmetry and the paradox of cross-system induction in relation to optimal defense theory and interactions between above- and belowground herbivory.