Using pentaploids as tools for studying genomic composition and allele transmission patterns in octoploid Fragaria

A unique pentaploid population of Fragaria (strawberry) was developed to gain insight into octoploid genome composition and allele transmission patterns. This population was produced by crossing representatives of two divergent subspecies of octoploid F. virginiana and then by crossing an octoploid hybrid plant with diploid F. vesca. To enable examination of allele transmission patterns, the intergenic region of the gRGA1-Subtilase gene pair locus was amplified, and PCR products were cloned, sequenced, and compared to define the allele composition of the hybrid octoploid. The sequencing data revealed three distinct major haplotypes and additional subtypes. The pentaploids were genotyped utilizing the FEL-CAPS method. From these results, it was possible to detect disomic inheritance of an allele pair within one major haplotype. This result establishes the potential value of the pentaploid population as a resource for analysis of octoploid allele transmission patterns in strawberry

Contributing to an autism biobank: Diverse perspectives from autistic participants, family members and researchers

A lot of autism research has focused on finding genes that might cause autism. To conduct these genetic studies, researchers have created 'biobanks' - collections of biological samples (such as blood, saliva, urine, stool and hair) and other health information (such as cognitive assessments and medical histories). Our study focused on the Australian Autism Biobank, which collected biological and health information from almost 1000 Australian autistic children and their families. We wanted to know what people thought about giving their information to the Biobank and why they chose to do so. We spoke to 71 people who gave to the Biobank, including 18 autistic adolescents and young adults, 46 of their parents and seven of their siblings. We also spoke to six researchers who worked on the Biobank project. We found that people were interested in giving their information to the Biobank so they could understand why some people were autistic. Some people felt knowing why could help them make choices about having children in the future. People also wanted to be involved in the Biobank because they believed it could be a resource that could help others in the future. They also trusted that scientists would keep their information safe and were keen to know how that information might be used in the future. Our findings show that people have lots of different views about autism biobanks. We suggest researchers should listen to these different views as they develop their work

Elimination of Porcine Epidemic Diarrhea Virus in an Animal Feed Manufacturing Facility

Citation: Huss AR, Schumacher LL, Cochrane RA, Poulsen E, Bai J, Woodworth JC, et al. (2017) Elimination of Porcine Epidemic Diarrhea Virus in an Animal Feed Manufacturing Facility. PLoS ONE 12(1): e0169612. doi:10.1371/journal.pone.0169612Porcine Epidemic Diarrhea Virus (PEDV) was the first virus of wide scale concern to be linked to possible transmission by livestock feed or ingredients. Measures to exclude pathogens, prevent cross-contamination, and actively reduce the pathogenic load of feed and ingredients are being developed. However, research thus far has focused on the role of chemicals or thermal treatment to reduce the RNA in the actual feedstuffs, and has not addressed potential residual contamination within the manufacturing facility that may lead to continuous contamination of finished feeds. The purpose of this experiment was to evaluate the use of a standardized protocol to sanitize an animal feed manufacturing facility contaminated with PEDV. Environmental swabs were collected throughout the facility during the manufacturing of a swine diet inoculated with PEDV. To monitor facility contamination of the virus, swabs were collected at: 1) baseline prior to inoculation, 2) after production of the inoculated feed, 3) after application of a quaternary ammonium-glutaraldehyde blend cleaner, 4) after application of a sodium hypochlorite sanitizing solution, and 5) after facility heat-up to 60°C for 48 hours. Decontamination step, surface, type, zone and their interactions were all found to impact the quantity of detectable PEDV RNA (P < 0.05). As expected, all samples collected from equipment surfaces contained PEDV RNA after production of the contaminated feed. Additionally, the majority of samples collected from non-direct feed contact surfaces were also positive for PEDV RNA after the production of the contaminated feed, emphasizing the potential role dust plays in cross-contamination of pathogen throughout a manufacturing facility. Application of the cleaner, sanitizer, and heat were effective at reducing PEDV genomic material (P < 0.05), but did not completely eliminate it

Characterizing the rapid spread of porcine epidemic diarrhea virus (PEDV) through an animal food manufacturing facility

New regulatory and consumer demands highlight the importance of animal feed as a part of our national food safety system. Porcine epidemic diarrhea virus (PEDV) is the first viral pathogen confirmed to be widely transmissible in animal food. Because the potential for viral contamination in animal food is not well characterized, the objectives of this study were to 1) observe the magnitude of virus contamination in an animal food manufacturing facility, and 2) investigate a proposed method, feed sequencing, to decrease virus decontamination on animal food-contact surfaces. A U.S. virulent PEDV isolate was used to inoculate 50 kg swine feed, which was mixed, conveyed, and discharged into bags using pilot-scale feed manufacturing equipment. Surfaces were swabbed and analyzed for the presence of PEDV RNA by quantitative real-time polymerase chain reaction (qPCR). Environmental swabs indicated complete contamination of animal food-contact surfaces (0/40 vs. 48/48, positive baseline samples/total baseline samples, positive subsequent samples/total subsequent samples, respectively; P \u3c 0.05) and near complete contamination of non-animal food-contact surfaces (0/24 vs. 16/18, positive baseline samples/total baseline samples, positive subsequent samples/total subsequent samples, respectively; P \u3c 0.05). Flushing animal food-contact surfaces with low-risk feed is commonly used to reduce cross-contamination in animal feed manufacturing. Thus, four subsequent 50 kg batches of virus-free swine feed were manufactured using the same system to test its impact on decontaminating animal food-contact surfaces. Even after 4 subsequent sequences, animal food-contact surfaces retained viral RNA (28/33 positive samples/total samples), with conveying system being more contaminated than the mixer. A bioassay to test infectivity of dust from animal food-contact surfaces failed to produce infectivity. This study demonstrates the potential widespread viral contamination of surfaces in an animal food manufacturing facility and the difficulty of removing contamination using conventional feed sequencing, which underscores the importance for preventing viruses from entering and contaminating such facilities

Soil and Plant Responses to Phosphorus Inputs from Different Phytase-Associated Animal Diets

Publication history: Accepted - 4 January 2022; Published - 5 January 2022.The over-supplementation of animal feeds with phosphorus (P) within livestock-production systems leads to high rates of P excretion and thus to high P loads and losses, which negatively impact the natural environment. The addition of phytase to pig and poultry diets can contribute to reducing P excretion; however, cascading effects of phytase on plant–soil systems remain poorly understood. Here, we addressed how three different diets containing various levels of exogenous phytase, i.e., (1) no-phytase, (2) phytase (250 FTU), and (3) superdose phytase (500 FTU) for pigs (Sus scrofa domesticus) and broilers (Gallus gallus domesticus) might affect P dynamics in two different plant–soil systems including comfrey (Symphytum uplandicum) and ryegrass (Lolium perenne). We found that differences in phytase supplementation significantly influenced total P content (%) of broiler litter and also pig slurry (although not significantly) as a result of dietary P content. P Use Efficiency (PUE) of comfrey and ryegrass plants was significantly higher under the intermediate ‘phytase’ dose (i.e., commercial dose of 250 FTU) when compared to ‘no-phytase’ and ‘superdose phytase’ associated with pig slurry additions. Soil P availability (i.e., water soluble P, WSP) in both comfrey and ryegrass mesocosms significantly decreased under the intermediate ‘phytase’ treatment following pig slurry additions. Dietary P content effects on P losses from soils (i.e., P leaching) were variable and driven by the type of organic amendment. Our study shows how commercial phytase levels together with higher dietary P contents in pig diets contributed to increase PUE and decrease WSP thus making the plant–soil system more P conservative (i.e., lower risks of P losses). Our evidence is that dietary effects on plant–soil P dynamics are driven by the availability of P forms (for plant uptake) in animal excretes and the type of organic amendment (pig vs. broiler) rather than plant species identity (comfrey vs. ryegrass).This work has received funding from the European Research Area Network (ERA-NET) co-funds on Sustainable Animal Production (SusAn) as part of the PEGaSus project (2817ERA02D) and the Department for Environment, Food and Rural Affairs (DEFRA) in the UK

Experimental infection of conventional nursing pigs and their dams with \u3ci\u3ePorcine deltacoronavirus\u3c/i\u3e

Porcine deltacoronavirus (PDCoV) is a newly identified virus that has been detected in swine herds of North America associated with enteric disease. The aim of this study was to demonstrate the pathogenicity, course of infection, virus kinetics, and aerosol transmission of PDCoV using 87 conventional piglets and their 9 dams, including aerosol and contact controls to emulate field conditions. Piglets 2–4 days of age and their dams were administered an oronasal PDCoV inoculum with a quantitative real-time reverse transcription (qRT)-PCR quantification cycle (Cq) value of 22 that was generated from a field sample having 100% nucleotide identity to USA/Illinois121/2014 determined by metagenomic sequencing and testing negative for other enteric disease agents using standard assays. Serial samples of blood, serum, oral fluids, nasal and fecal swabs, and tissues from sequential autopsy, conducted daily on days 1–8 and regular intervals thereafter, were collected throughout the 42-day study for qRT-PCR, histopathology, and immunohistochemistry. Diarrhea developed in all inoculated and contact control pigs, including dams, by 2 days post-inoculation (dpi) and in aerosol control pigs and dams by 3–4 dpi, with resolution occurring by 12 dpi. Mild to severe atrophic enteritis with PDCoV antigen staining was observed in the small intestine of affected piglets from 2 to 8 dpi. Mesenteric lymph node and small intestine were the primary sites of antigen detection by immunohistochemistry, and virus RNA was detected in these tissues to the end of the study. Virus RNA was detectable in piglet fecal swabs to 21 dpi, and dams to 14–35 dpi

Effect of Benzoic Acid and Essential Oil Blends on Viral Load in Swine Feed and Vitamin Premix

Feed has been shown to harbor viable virus of interest to swine producers over an extended period of time. The use of mitigants and kill steps have been investigated with variable results. This study investigated the use of benzoic acid (BA) and an essential oil blend (EO) to mitigate the presence of porcine epidemic diarrhea virus (PEDV), porcine reproductive and respiratory syndrome virus (PRRSV), and Senecavirus A (SVA) in a complete diet (Exp. 1) and a vitamin premix (Exp. 2). Four treatments consisting of 0.5% BA; 0.5% BA and 200 ppm EO; 0.3% BA and 120 ppm EO; and 0.25% BA and 100 ppm EO were used in the complete feed, in addition to a control with no feed additive to test the mitigant’s effect on PEDV, PRRSV, and SVA detection. For Exp. 2, a vitamin premix without chemical treatment acted as the control and the other treatment was the vitamin premix treated with 2.68% EO, with both used to determine PEDV detection. The inoculated feed or premix was stored for up to 15 d with sampling points at 2, 5, and 15 d post-inoculation. Samples were analyzed using a triplex qRT-PCR to detect changes in RNA quantities for all three viruses. A significant treatment × day interaction was observed in the feed for both PEDV (P = 0.008) and SVA (P \u3c 0.001). Per the decreased cycle threshold (Ct) value, the 0.5% BA treatment had higher (P \u3c 0.05) measurements of detectible PEDV on d 2 and 5, and lower amounts of detectible PEDV on d 15, as compared to the control. The 0.5% BA treated feed had lower (P \u3c 0.05) detectable SVA on d 2 but higher detectible SVA on d 15 compared to the control. There was no evidence of difference in detectable PRRSV between treatments. During this experiment, PEDV and SVA showed a degradation over time with rates of degradation varying between treatments. Increasing time from d 2 to 15 decreased (quadratic, P = 0.038) detectable PRRSV. The use of the EO in the vitamin premix had no evidence of a treatment × day interaction, treatment effect, or degradation over time. In conclusion, the use of 0.5% BA had an increased PEDV Ct on d 15 compared to the control (33.8 vs. 32.7 Ct, respectively). However, the use of BA and EO mitigant in this model did not provide consistent evidence for increased viral degradation, but viral load was reduced in the feed matrix over time

Effect of Benzoic Acid and Essential Oil Blends on Viral Load in Swine Feed and Vitamin Premix

Feed has been shown to harbor viable virus of interest to swine producers over an extended period of time. The use of mitigants and kill steps have been investigated with variable results. This study investigated the use of benzoic acid (BA) and an essential oil blend (EO) to mitigate the presence of porcine epidemic diarrhea virus (PEDV), porcine reproductive and respiratory syndrome virus (PRRSV), and Senecavirus A (SVA) in a complete diet (Exp. 1) and a vitamin premix (Exp. 2). Four treatments consisting of 0.5% BA; 0.5% BA and 200 ppm EO; 0.3% BA and 120 ppm EO; and 0.25% BA and 100 ppm EO were used in the complete feed, in addition to a control with no feed additive to test the mitigant’s effect on PEDV, PRRSV, and SVA detection. For Exp. 2, a vitamin premix without chemical treatment acted as the control and the other treatment was the vitamin premix treated with 2.68% EO, with both used to determine PEDV detection. The inoculated feed or premix was stored for up to 15 d with sampling points at 2, 5, and 15 d post-inoculation. Samples were analyzed using a triplex qRT-PCR to detect changes in RNA quantities for all three viruses. A significant treatment × day interaction was observed in the feed for both PEDV (P = 0.008) and SVA (P \u3c 0.001). Per the decreased cycle threshold (Ct) value, the 0.5% BA treatment had higher (P \u3c 0.05) measurements of detectible PEDV on d 2 and 5, and lower amounts of detectible PEDV on d 15, as compared to the control. The 0.5% BA treated feed had lower (P \u3c 0.05) detectable SVA on d 2 but higher detectible SVA on d 15 compared to the control. There was no evidence of difference in detectable PRRSV between treatments. During this experiment, PEDV and SVA showed a degradation over time with rates of degradation varying between treatments. Increasing time from d 2 to 15 decreased (quadratic, P = 0.038) detectable PRRSV. The use of the EO in the vitamin premix had no evidence of a treatment × day interaction, treatment effect, or degradation over time. In conclusion, the use of 0.5% BA had an increased PEDV Ct on d 15 compared to the control (33.8 vs. 32.7 Ct, respectively). However, the use of BA and EO mitigant in this model did not provide consistent evidence for increased viral degradation, but viral load was reduced in the feed matrix over time

The key glycolytic enzyme phosphofructokinase is involved in resistance to antiplasmodial glycosides

ABSTRACT Plasmodium parasites rely heavily on glycolysis for ATP production and for precursors for essential anabolic pathways, such as the methylerythritol phosphate (MEP) pathway. Here, we show that mutations in the Plasmodium falciparum glycolytic enzyme, phosphofructokinase (PfPFK9), are associated with in vitro resistance to a primary sulfonamide glycoside (PS-3). Flux through the upper glycolysis pathway was significantly reduced in PS-3-resistant parasites, which was associated with reduced ATP levels but increased flux into the pentose phosphate pathway. PS-3 may directly or indirectly target enzymes in these pathways, as PS-3-treated parasites had elevated levels of glycolytic and tricarboxylic acid (TCA) cycle intermediates. PS-3 resistance also led to reduced MEP pathway intermediates, and PS-3-resistant parasites were hypersensitive to the MEP pathway inhibitor, fosmidomycin. Overall, this study suggests that PS-3 disrupts core pathways in central carbon metabolism, which is compensated for by mutations in PfPFK9, highlighting a novel metabolic drug resistance mechanism in P. falciparum. IMPORTANCE Malaria, caused by Plasmodium parasites, continues to be a devastating global health issue, causing 405,000 deaths and 228 million cases in 2018. Understanding key metabolic processes in malaria parasites is critical to the development of new drugs to combat this major infectious disease. The Plasmodium glycolytic pathway is essential to the malaria parasite, providing energy for growth and replication and supplying important biomolecules for other essential Plasmodium anabolic pathways. Despite this overreliance on glycolysis, no current drugs target glycolysis, and there is a paucity of information on critical glycolysis targets. Our work addresses this unmet need, providing new mechanistic insights into this key pathway

Bridging Gaps in the Agricultural Phosphorus Cycle from an Animal Husbandry Perspective—The Case of Pigs and Poultry

Publication history: Accepted - 29 May 2018; Published online - 1 June 2018Since phosphorus (P) is an essential element for life, its usage and application across agricultural production systems requires great attention. Monogastric species such as pigs and poultry can significantly contribute to global food security but these animals remain highly dependent on the supply of mineral inorganic P in their feeds. Pig and poultry, which represent 70% of the global meat production, are also major P excretors and thus represent important sources of environmental P inputs. Balancing the P cycle within farming systems is crucial to achieve P sustainable and resilient livestock production. Therefore, the interconnection of animal feed, livestock farming, manure, and soil/aquatic ecosystems requires multidisciplinary approaches to improve P management. With regard to a sustainable agricultural P cycle, this study addresses aspects of feeding strategies and animal physiology (e.g., phase feeding, P conditioning, liquid feeding, phytase supplementation, genetics), soil agroecosystems (e.g., P cycling, P losses, P gains), reuse and recycling (e.g., manure, slaughter waste), measures of farmers’ economic performance (e.g., bio-economic models), and P governance/policy instruments (e.g., P quota, P tax). To reconcile the economic and ecological sustainability of animal husbandry, the strategic objective of future research will be to provide solutions for a sufficient supply of high-quality animal products from resource-efficient and economically competitive agro-systems which are valued by society and preserve soil and aquatic ecosystems.: This work was partly funded by the Leibniz Science Campus Phosphorus Research Rostock and has received funding from the European Research Association Networks (ERA-NETs) Cofunds Sustainable Animal Production (SusAn) as part of the PEGaSus project (2817ERA02D). The Leibniz Institute for Farm Animal Biology (FBN) provided own matched funding. Department of Animal Science, Aarhus University covered some of the expenditures for running the pig experiments. The publication of this article was funded by the Open Access Fund of the Leibniz Association and the Open Access Fund of the Leibniz Institute for Farm Animal Biology (FBN)