Genome-Wide and Transcriptome-Wide Association Studies on Northern New England and Ohio Amyotrophic Lateral Sclerosis Cohorts.

Background and Objectives: Amyotrophic lateral sclerosis (ALS) is an age-associated, fatal neurodegenerative disorder causing progressive paralysis and respiratory failure. The genetic architecture of ALS is still largely unknown. Methods: We performed a genome-wide association study (GWAS) and transcriptome-wide association study (TWAS) to understand genetic risk factors for ALS using a population-based case-control study of 435 ALS cases and 279 controls from Northern New England and Ohio. Single nucleotide polymorphism (SNP) genotyping was conducted using the Illumina NeuroChip array. Odds ratios were estimated using covariate-adjusted logistic regression. We also performed a genome-wide SNP-smoking interaction screening. TWAS analyses used PrediXcan to estimate associations between predicted gene expression levels across 15 tissues (13 brain tissues, skeletal muscle, and whole blood) and ALS risk. Results: GWAS analyses identified the p.A382T missense variant (rs367543041, p = 3.95E-6) in the TARDBP gene, which has previously been reported in association with increased ALS risk and was found to share a close affinity with the Sardinian haplotype. Both GWAS and TWAS analyses suggested that ZNF235 is associated with decreased ALS risk. Discussion: Our results support the need for future evaluation to clarify the role of these potential genetic risk factors for ALS and to understand genetic susceptibility to environmental risk factors.

Wind Speed and Landscape Context Mediate Campylobacter Risk among Poultry Reared in Open Environments.

Foodborne pathogens cause over 9 million illnesses in the United States each year, and Campylobacter from chickens is the largest contributor. Rearing poultry outdoors without the use of antibiotics is becoming an increasingly popular style of farming; however, little is understood about how environmental factors and farm management alter pathogen prevalence. Our survey of 27 farms in California, Oregon, Washington, and Idaho, USA, revealed a diversity of management practices used to rear poultry in the open environment. Here, we assess environmental and management factors that impact Campylobacter spp. prevalence in 962 individual chicken fecal samples from 62 flocks over a three-year period. We detected Campylobacter spp. in 250/962 (26.0%) of fecal samples screened, in 69.4% (43/62) of flocks, and on 85.2% (23/27) of farms. We found that Campylobacter spp. prevalence was predicted to increase in poultry on farms with higher average wind speeds in the seven days preceding sampling; on farms embedded in more agricultural landscapes; and in flocks typified by younger birds, more rotations, higher flock densities, and the production of broilers. Collectively, our results suggest that farms in areas with higher wind speeds and more surrounding agriculture face greater risk of Campylobacter spp. introduction into their flocks.

Diversity and Prevalence of Ectoparasites on Poultry from Open Environment Farms in the Western-United States of Washington, Idaho, Oregon, and California.

Open-environment poultry farms that allow chickens to forage outdoors are becoming increasingly common throughout the United States and Europe; however, there is little information regarding the diversity and prevalence of ectoparasites in these farming systems. Eight to 25 birds were captured and surveyed for ectoparasites on each of 17 farms across the states of Washington, Idaho, Oregon, and California. Among the farms sampled, six louse species (Phthiraptera: Ischnocera & Amblycera) and two parasitic mite species (Acari: Mesostigmata) were collected and identified: Goniodes gigas (Taschenberg, 1879; Phthiraptera: Menoponidae) on one farm, Menacathus cornutus (Schömmer, 1913; Phthiraptera: Menoponidae) on one farm, Menopon gallinae (Linnaeus, 1758; Phthiraptera: Menoponidae) on six farms, Lipeurus caponis (Linnaeus, 1758; Phthiraptera: Philopteridae) on five farms, Menacanthus stramineus (Nitzsch, 1818; Phthiraptera: Menoponidae) on nine farms, Goniocotes gallinae De Geer (Phthiraptera: Philopteridae) on 11 farms, Dermanyssus gallinae (De Geer, 1778; Mesostigmata: Dermanyssidae) on two farms, and Ornithonyssus sylviarum (Canestrini & Fanzago, 1877; Mesostigmata: Macronyssidae) on one farm. The diversity of ectoparasites on these open environment poultry farms highlights a need for additional research on ectoparasite prevalence and intensity in these poultry farming systems.

Prevalence Patterns for Enteric Parasites of Chickens Managed in Open Environments of the Western United States.

Growing demand for poultry meat and eggs labeled as organic, cage free, or pasture raised has increased the number of producers that manage chickens outdoors. In these open environments, there are likely diverse enteric parasites sustained by fecal-oral transmission or passage through intermediate invertebrate hosts (e.g., worms and insects) that chickens consume. Enteric parasites can reduce chicken health and productivity, but there are few published data describing the identities or prevalence of these parasites on farms that use open environments in the United States. We surveyed 27 poultry farms with open environments that were situated across a wide geographic range, including California, Oregon, Idaho, and Washington. These farms did not use anticoccidial drugs, coccidia vaccines, or parasiticides. Flock size, enclosure area, flock density, flock rotation frequency, and average flock age were highly correlated for all the farms in this study. We analyzed how enclosure size and flock rotations per year (which represented two axes of variation in management) correlated with prevalence of five observed parasite taxa at the farm level. Across all flocks, we detected by fecal flotation Eimeria spp. (95% flocks), Ascaridia galli (69%), Heterakis gallinarum (52%), Capillaria spp. (39%), Strongyloides avium (13%), tapeworm species (29%), Cryptosporidium spp. (3%), and Dispharynx nasuta (1%). Eighty-five percent of samples were coinfected with two or more parasite taxa. Sixty-seven percent of farms raised only layer chicken breeds, 4% raised only broiler breeds, and 30% raised both layer and broiler breeds. The average age of the broiler flocks was 11.0 wk (±1.1 SE), and flocks were moved 54.7 (±17.9) times annually to new locations in pastures (hereafter, "rotation"). Layer flocks averaged 84.9 (±7.67) wk of age and were moved less often on farms being rotated 20.0 (±6.05) times per year. Generalized linear mixed models indicated that for every 1 m2 increase in enclosure size, the odds of detecting Eimeria spp. increased by 0.03%. Furthermore, for every additional rotation per year, the odds of detecting A. galli decreased by 1.3%. For every additional rotation per year, the odds of detecting tapeworm species increased by 2.2%. We found no evidence that flock spatial management affected prevalence of the other parasites observed on the farms. Farming practices and parasite responses in these systems are highly varied, which makes it difficult to identify potential management interventions for reducing these infections.

Patrones de prevalencia de parásitos entéricos de pollos manejados en ambientes abiertos en el oeste de los Estados Unidos. La creciente demanda de carne de pollo y huevos etiquetados como orgánicos, sin jaula o criados en pastoreo ha aumentado el número de productores que manejan pollos al aire libre. En estos entornos abiertos, es probable que existan diversos parásitos entéricos que permanecen debido a la transmisión fecal-oral o por su paso a través de huéspedes invertebrados intermedios (por ejemplo, gusanos e insectos) que son consumidos por los pollos. Los parásitos entéricos pueden reducir la salud y la productividad de los pollos, pero existe poca información publicada que describa las identidades o la prevalencia de estos parásitos en granjas que utilizan entornos abiertos en los Estados Unidos. Se realizó una encuesta incluyendo 27 granjas avícolas con entornos abiertos que estaban situadas en un amplio rango geográfico, incluyendo California, Oregón, Idaho y Washington. Estas granjas no usaban medicamentos anticoccidiales, vacunas contra coccidias ni parasiticidas. El tamaño de la parvada, el área de pastoreo, la densidad de la parvada, la frecuencia de rotación de la parvada y la edad promedio de la parvada estuvieron altamente correlacionados para todas las granjas en este estudio. Se analizó cómo el tamaño del recinto y las rotaciones de parvadas por año (que representaban dos ejes de variación en el manejo) se correlacionaban con la prevalencia de cinco taxones de parásitos observados a nivel de granja. En todas las parvadas, se detectó por flotación fecal Eimeria spp. (95% de las parvadas), Ascaridia galli (69%), Heterakis gallinarum (52%), Capillaria spp. (39%), Strongyloides avium (13%), especies de nemátodos planos (29%), Cryptosporidium spp. (3%) y Dispharynx nasuta (1%). El ochenta y cinco por ciento de las muestras estaban coinfectadas con dos o más taxones de parásitos. El sesenta y siete por ciento de las granjas criaban solo razas de gallinas de postura, el 4% solo criaban razas de pollos de engorde y el 30% criaban razas de gallinas de postura y de pollos de engorde. La edad promedio de las parvadas de pollos de engorde fue de 11.0 semanas (±1.1 SE) y las parvadas se trasladaron 54.7 (±17.9) veces al año a nuevas ubicaciones en los pastos (en adelante, "rotación"). Las parvadas ponedoras promediaron 84.9 (± 7.67) semanas de edad y se trasladaron con menos frecuencia en granjas que se rotaron 20.0 (± 6.05) veces al año. Los modelos lineales mixtos generalizados indicaron que por cada aumento de un metro cuadrado en el tamaño del área de pastoreo, las probabilidades de detectar Eimeria spp. se incrementaron en un 0.03%. Además, por cada rotación adicional por año, las probabilidades de detectar A. galli disminuyeron en un 1.3%. Por cada rotación adicional por año, las probabilidades de detectar especies de tenia aumentaron en un 2.2%. No encontramos evidencia de que el manejo del espacio de la parvada afectara la prevalencia de los otros parásitos observados en las granjas. Las prácticas agrícolas y las respuestas de los parásitos en estos sistemas son muy variadas, lo que dificulta la identificación de posibles intervenciones de manejo para reducir estas infecciones.

A trait-based framework for predicting foodborne pathogen risk from wild birds.

Recent foodborne illness outbreaks have heightened pressures on growers to deter wildlife from farms, jeopardizing conservation efforts. However, it remains unclear which species, particularly birds, pose the greatest risk to food safety. Using >11,000 pathogen tests and 1565 bird surveys covering 139 bird species from across the western United States, we examined the importance of 11 traits in mediating wild bird risk to food safety. We tested whether traits associated with pathogen exposure (e.g., habitat associations, movement, and foraging strategy) and pace-of-life (clutch size and generation length) mediated foodborne pathogen prevalence and proclivities to enter farm fields and defecate on crops. Campylobacter spp. were the most prevalent enteric pathogen (8.0%), while Salmonella and Shiga-toxin producing Escherichia coli (STEC) were rare (0.46% and 0.22% prevalence, respectively). We found that several traits related to pathogen exposure predicted pathogen prevalence. Specifically, Campylobacter and STEC-associated virulence genes were more often detected in species associated with cattle feedlots and bird feeders, respectively. Campylobacter was also more prevalent in species that consumed plants and had longer generation lengths. We found that species associated with feedlots were more likely to enter fields and defecate on crops. Our results indicated that canopy-foraging insectivores were less likely to deposit foodborne pathogens on crops, suggesting growers may be able to promote pest-eating birds and birds of conservation concern (e.g., via nest boxes) without necessarily compromising food safety. As such, promoting insectivorous birds may represent a win-win-win for bird conservation, crop production, and food safety. Collectively, our results suggest that separating crop production from livestock farming may be the best way to lower food safety risks from birds. More broadly, our trait-based framework suggests a path forward for co-managing wildlife conservation and food safety risks in farmlands by providing a strategy for holistically evaluating the food safety risks of wild animals, including under-studied species.

Landscape context affects the sustainability of organic farming systems.

Organic agriculture promotes sustainability compared to conventional agriculture. However, the multifunctional sustainability benefits of organic farms might be mediated by landscape context. Assessing how landscape context affects sustainability may aid in targeting organic production to landscapes that promote high biodiversity, crop yields, and profitability. We addressed this using a meta-analysis spanning 60 crop types on six continents that assessed whether landscape context affected biodiversity, yield, and profitability of organic vs. conventional agroecosystems. We considered landscape metrics reflecting landscape composition (percent cropland), compositional heterogeneity (number and diversity of cover types), and configurational heterogeneity (spatial arrangement of cover types) across our study systems. Organic sites had greater biodiversity (34%) and profits (50%) than conventional sites, despite lower yields (18%). Biodiversity gains increased as average crop field size in the landscape increased, suggesting organic farms provide a "refuge" in intensive landscapes. In contrast, as crop field size increased, yield gaps between organic and conventional farms increased and profitability benefits of organic farming decreased. Profitability of organic systems, which we were only able to measure for studies conducted in the United States, varied across landscapes in conjunction with production costs and price premiums, suggesting socioeconomic factors mediated profitability. Our results show biodiversity benefits of organic farming respond differently to landscape context compared to yield and profitability benefits, suggesting these sustainability metrics are decoupled. More broadly, our results show that the ecological, but not the economic, sustainability benefits of organic agriculture are most pronounced in more intensive agricultural landscapes.

Steric stabilization of nanoparticles with grafted low molecular weight ligands in highly concentrated brines including divalent ions.

Whereas numerous studies of stabilization of nanoparticles (NPs) in electrolytes have examined biological fluids, the interest has grown recently in media with much higher ionic strengths including seawater and brines relevant to environmental science and subsurface oil and gas reservoirs. Given that electrostatic repulsion is limited at extremely high ionic strengths due to charge screening, we have identified ligands that are well solvated in concentrated brine containing divalent cations and thus provide steric stabilization of silica nanoparticles. Specifically, the hydrodynamic diameter of silica nanoparticles with grafted low molecular weight ligands, a diol ether, [3-(2,3-dihydroxypropoxy)propyl]-trimethoxysilane, and a zwitterionic sulfobetaine, 3-([dimethyl(3-trimethoxysilyl)propyl]ammonio)propane-1-sulfonate, is shown with dynamic light scattering to remain essentially constant, indicating lack of aggregation, at room temperature and up to 80 °C for over 30 days. An extended DLVO model signifies that steric stabilization is strongly dominant against van der Waals attraction for ∼10 nm particles given that these ligands are well solvated even in highly concentrated brine. In contrast, polyethylene glycol oligomers do not provide steric stabilization at elevated temperatures, even at conditions where the ligands are soluble, indicating complicating factors including bridging of the ether oxygens by divalent cations.

Modified montmorillonite clay microparticles for stable oil-in-seawater emulsions.

Environmentally benign clay particles are of great interest for the stabilization of Pickering emulsions. Dodecane-in-synthetic seawater (SSW) emulsions formed with montmorillonite (MMT) clay microparticles modified with bis(2-hydroxyethyl)oleylamine were stable against coalescence, even at clay concentrations down to 0.1% w/v. Remarkably, as little as 0.001% w/v surfactant lowered the hydrophilicity of the clay to a sufficient level for stabilization of oil-in-SSW emulsions. The favorable effect of SSW on droplet size reduction and emulsion stability enhancement is hypothesized to be due to reduced electrostatic repulsion between adsorbed clay particles and a consequent increase in the continuous phase (an aqueous clay suspension) viscosity. Water/oil (W/O) emulsions were inverted to O/W either by decreasing the mass ratio of surfactant-to-clay (transitional inversion) or by increasing the water volume fraction (catastrophic inversion). For both types of emulsions, coalescence was minimal and the sedimentation or creaming was highly correlated with the droplet size. For catastrophic inversions, the droplet size of the emulsions was smaller in the case of the preferred curvature. Suspensions of concentrated clay in oil dispersions in the presence of surfactant were stable against settling. The mass transfer pathways during emulsification of oil containing the clay particles were analyzed on the droplet size/stability phase diagrams to provide insight for the design of dispersant systems for remediating surface and subsurface oceanic oil spills.