A Genome-Wide Association Study of Respiratory Syncytial Virus Infection Severity in Infants.

BACKGROUND: Respiratory syncytial virus (RSV) is a significant cause of infant morbidity and mortality worldwide. Most children experience at least one 1 RSV infection by the age of two 2 years, but not all develop severe disease. However, the understanding of genetic risk factors for severe RSV is incomplete. Consequently, we conducted a genome-wide association study of RSV severity. METHODS: Disease severity was assessed by the ReSVinet scale, in a cohort of 251 infants aged 1 week to 1 year. Genotyping data were collected from multiple European study sites as part of the RESCEU Consortium. Linear regression models were used to assess the impact of genotype on RSV severity and gene expression as measured by microarray. RESULTS: While no SNPs reached the genome-wide statistical significance threshold (P < 5 × 10-8), we identified 816 candidate SNPs with a P-value of <1 × 10-4. Functional annotation of candidate SNPs highlighted genes relevant to neutrophil trafficking and cytoskeletal functions, including LSP1 and RAB27A. Moreover, SNPs within the RAB27A locus significantly altered gene expression (false discovery rate, FDR P < .05). CONCLUSIONS: These findings may provide insights into genetic mechanisms driving severe RSV infection, offering biologically relevant information for future investigations.

Vi-specific serological correlates of protection for typhoid fever.

Typhoid Vi vaccines have been shown to be efficacious in children living in endemic regions; however, a widely accepted correlate of protection remains to be established. We applied a systems serology approach to identify Vi-specific serological correlates of protection using samples obtained from participants enrolled in an experimental controlled human infection study. Participants were vaccinated with Vi-tetanus toxoid conjugate (Vi-TT) or unconjugated Vi-polysaccharide (Vi-PS) vaccines and were subsequently challenged with Salmonella Typhi bacteria. Multivariate analyses identified distinct protective signatures for Vi-TT and Vi-PS vaccines in addition to shared features that predicted protection across both groups. Vi IgA quantity and avidity correlated with protection from S. Typhi infection, whereas higher fold increases in Vi IgG responses were associated with reduced disease severity. Targeted antibody-mediated functional responses, particularly neutrophil phagocytosis, were also identified as important components of the protective signature. These humoral markers could be used to evaluate and develop efficacious Vi-conjugate vaccines and assist with accelerating vaccine availability to typhoid-endemic regions.

Projecting the effects of agricultural conservation practices on stream fish communities in a changing climate.

How anticipated climate change might affect long-term outcomes of present-day agricultural conservation practices remains a key uncertainty that could benefit water quality and biodiversity conservation planning. To explore this issue, we forecasted how the stream fish communities in the Western Lake Erie Basin (WLEB) would respond to increasing amounts of agricultural conservation practice (ACP) implementation under two IPCC future greenhouse gas emission scenarios (RCP4.5: moderate reductions; RCP8.5: business-as-usual conditions) during 2020-2065. We used output from 19 General Circulation Models to drive linked agricultural land use (APEX), watershed hydrology (SWAT), and stream fish distribution (boosted regression tree) models, subsequently analyzing how projected changes in habitat would influence fish community composition and functional trait diversity. Our models predicted both positive and negative effects of climate change and ACP implementation on WLEB stream fishes. For most species, climate and ACPs influenced species in the same direction, with climate effects outweighing those of ACP implementation. Functional trait analysis helped clarify the varied responses among species, indicating that more extreme climate change would reduce available habitat for large-bodied, cool-water species with equilibrium life-histories, many of which also are of importance to recreational fishing (e.g., northern pike, smallmouth bass). By contrast, available habitat for warm-water, benthic species with more periodic or opportunistic life-histories (e.g., northern hogsucker, greater redhorse, greenside darter) was predicted to increase. Further, ACP implementation was projected to hasten these shifts, suggesting that efforts to improve water quality could come with costs to other ecosystem services (e.g., recreational fishing opportunities). Collectively, our findings demonstrate the need to consider biological outcomes when developing strategies to mitigate water quality impairment and highlight the value of physical-biological modeling approaches to agricultural and biological conservation planning in a changing climate.

Western Lake Erie Basin: Soft-data-constrained, NHDPlus resolution watershed modeling and exploration of applicable conservation scenarios.

Complex watershed simulation models are powerful tools that can help scientists and policy-makers address challenging topics, such as land use management and water security. In the Western Lake Erie Basin (WLEB), complex hydrological models have been applied at various scales to help describe relationships between land use and water, nutrient, and sediment dynamics. This manuscript evaluated the capacity of the current Soil and Water Assessment Tool (SWAT) to predict hydrological and water quality processes within WLEB at the finest resolution watershed boundary unit (NHDPlus) along with the current conditions and conservation scenarios. The process based SWAT model was capable of the fine-scale computation and complex routing used in this project, as indicated by measured data at five gaging stations. The level of detail required for fine-scale spatial simulation made the use of both hard and soft data necessary in model calibration, alongside other model adaptations. Limitations to the model's predictive capacity were due to a paucity of data in the region at the NHDPlus scale rather than due to SWAT functionality. Results of treatment scenarios demonstrate variable effects of structural practices and nutrient management on sediment and nutrient loss dynamics. Targeting treatment to acres with critical outstanding conservation needs provides the largest return on investment in terms of nutrient loss reduction per dollar spent, relative to treating acres with lower inherent nutrient loss vulnerabilities. Importantly, this research raises considerations about use of models to guide land management decisions at very fine spatial scales. Decision makers using these results should be aware of data limitations that hinder fine-scale model interpretation.

Are harmful algal blooms becoming the greatest inland water quality threat to public health and aquatic ecosystems?

In this Focus article, the authors ask a seemingly simple question: Are harmful algal blooms (HABs) becoming the greatest inland water quality threat to public health and aquatic ecosystems? When HAB events require restrictions on fisheries, recreation, and drinking water uses of inland water bodies significant economic consequences result. Unfortunately, the magnitude, frequency, and duration of HABs in inland waters are poorly understood across spatiotemporal scales and differentially engaged among states, tribes, and territories. Harmful algal bloom impacts are not as predictable as those from conventional chemical contaminants, for which water quality assessment and management programs were primarily developed, because interactions among multiple natural and anthropogenic factors determine the likelihood and severity to which a HAB will occur in a specific water body. These forcing factors can also affect toxin production. Beyond site-specific water quality degradation caused directly by HABs, the presence of HAB toxins can negatively influence routine surface water quality monitoring, assessment, and management practices. Harmful algal blooms present significant challenges for achieving water quality protection and restoration goals when these toxins confound interpretation of monitoring results and environmental quality standards implementation efforts for other chemicals and stressors. Whether HABs presently represent the greatest threat to inland water quality is debatable, though in inland waters of developed countries they typically cause more severe acute impacts to environmental quality than conventional chemical contamination events. The authors identify several timely research needs. Environmental toxicology, environmental chemistry, and risk-assessment expertise must interface with ecologists, engineers, and public health practitioners to engage the complexities of HAB assessment and management, to address the forcing factors for HAB formation, and to reduce the threats posed to inland surface water quality.

Metal and nanoparticle occurrence in biosolid-amended soils.

Metals can accumulate in soils amended with biosolids in which metals have been concentrated during wastewater treatment. The goal of this study is to inspect agricultural sites with long-term biosolid application for a suite of regulated and unregulated metals, including some potentially present as commonly used engineered nanomaterials (ENMs). Sampling occurred in fields at a municipal and a privately operated biosolid recycling facilities in Texas. Depth profiles of various metals were developed for control soils without biosolid amendment and soils with different rates of biosolid application (6.6 to 74 dry tons per hectare per year) over 5 to 25 years. Regulated metals of known toxicity, including chromium, copper, cadmium, lead, and zinc, had higher concentrations in the upper layer of biosolid-amended soils (top 0-30 cm or 0-15 cm) than in control soils. The depth profiles of unregulated metals (antimony, hafnium, molybdenum, niobium, gold, silver, tantalum, tin, tungsten, and zirconium) indicate higher concentrations in the 0-30 cm soil increment than in the 70-100 cm soil increment, indicating low vertical mobility after entering the soils. Titanium-containing particles between 50 nm and 250 nm in diameter were identified in soil by transmission electron microscopy (TEM) coupled with energy dispersive x-ray spectroscopy (EDX) analysis. In conjunction with other studies, this research shows the potential for nanomaterials used in society that enter the sewer system to be removed at municipal biological wastewater treatment plants and accumulate in agricultural fields. The metal concentrations observed herein could be used as representative exposure levels for eco-toxicological studies in these soils.

Genotypic variation in traits linked to climate and aboveground productivity in a widespread C4 grass: evidence for a functional trait syndrome.

Examining intraspecific variation in growth and function in relation to climate may provide insight into physiological evolution and adaptation, and is important for predicting species responses to climate change. Under common garden conditions, we grew nine genotypes of the C4 species Panicum virgatum originating from different temperature and precipitation environments. We hypothesized that genotype productivity, morphology and physiological traits would be correlated with climate of origin, and a suite of adaptive traits would show high broad-sense heritability (H(2)). Genotype productivity and flowering time increased and decreased, respectively, with home-climate temperature, and home-climate temperature was correlated with genotypic differences in a syndrome of morphological and physiological traits. Genotype leaf and tiller size, leaf lamina thickness, leaf mass per area (LMA) and C : N ratios increased with home-climate temperature, whereas leaf nitrogen per unit mass (Nm ) and chlorophyll (Chl) decreased with home-climate temperature. Trait variation was largely explained by genotypic differences (H(2) = 0.33-0.85). Our results provide new insight into the role of climate in driving functional trait coordination, local adaptation and genetic divergence within species. These results emphasize the importance of considering intraspecific variation in future climate change scenarios.

Determination of percentage of RoundUp Ready soya in soya flour using real-time polymerase chain reaction: interlaboratory study.

An interlaboratory study was conducted to evaluate a method for determination of the percentage of RoundUp Ready (RR) soya in soya flour using Taqman technology. The method included DNA extraction from the test portion with cetyltrimethylammonium bromide buffer followed by chloroform extraction and Wizard resin cleanup steps. The DNA was then assayed with primer and probe sets specific for lectin as the endogenous control and the RR insert as the target. The percentage of RR soya in the soya fraction of the sample was calculated by using a matrix-matched standard curve. Ten samples of split-level blind duplicates were sent to 22 laboratories in 12 countries worldwide. Test portions contained 0, 0.5, 0.7,1.6, 2, and 3.9% (w/w) RR soya prepared gravimetrically from commercially available RR standard reference materials. Based on the results for test materials, the relative standard deviation for repeatability (RSDr) for the method ranged from 9.3 to 19.3% and, for reproducibility (RSDR), ranged from 20.3 to 33.7%.