Genome-wide association study to identify genetic loci associated with gastrointestinal nematode resistance in Katahdin sheep

Resistance to gastrointestinal nematodes has previously been shown to be a moderately heritable trait in some breeds of sheep, but the mechanisms of resistance are not well understood. Selection for resistance currently relies upon faecal egg counts (FEC), blood packed cell volumes and FAMACHA visual indicator scores of anaemia. Identifying genomic markers associated with disease resistance would potentially improve the selection process and provide a more reliable means of classifying and understanding the biology behind resistant and susceptible sheep. A GWAS was conducted to identify possible genetic loci associated with resistance to Haemonchus contortus in Katahdin sheep. Forty animals were selected from the top and bottom 10% of estimated breeding values for FEC from a total pool of 641 sires and ram lambs. Samples were genotyped using Applied BiosystemsTM AxiomTM Ovine Genotyping Array (50K) consisting of 51 572 SNPs. Following quality control, 46 268 SNPs were included in subsequent analyses. Analyses were conducted using a linear regression model in PLINK v1.90 and a single-locus mixed model in SNP AND VARIATION SUITE. Genome-wide significance was determined by a Bonferroni correction for multiple testing. Using linear regression, loci on chromosomes 2, 3, 16, 23 and 24 were significantly associated at the genome level with FEC estimated breeding values, and we identified a region on chromosome 2 that was significant using both statistical analyses. We suggest a potential role for the gene DIS3L2 for gastrointestinal nematode resistance in Katahdin sheep, although further research is needed to validate these findings

Sequential Broadening of CTL Responses in Early HIV-1 Infection Is Associated with Viral Escape

BACKGROUND: Antigen-specific CTL responses are thought to play a central role in containment of HIV-1 infection, but no consistent correlation has been found between the magnitude and/or breadth of response and viral load changes during disease progression. METHODS AND FINDINGS: We undertook a detailed investigation of longitudinal CTL responses and HIV-1 evolution beginning with primary infection in 11 untreated HLA-A2 positive individuals. A subset of patients developed broad responses, which selected for consensus B epitope variants in Gag, Pol, and Nef, suggesting CTL-induced adaptation of HIV-1 at the population level. The patients who developed viral escape mutations and broad autologous CTL responses over time had a significantly higher increase in viral load during the first year of infection compared to those who did not develop viral escape mutations. CONCLUSIONS: A continuous dynamic development of CTL responses was associated with viral escape from temporarily effective immune responses. Our results suggest that broad CTL responses often represent footprints left by viral CTL escape rather than effective immune control, and help explain earlier findings that fail to show an association between breadth of CTL responses and viral load. Our results also demonstrate that CTL pressures help to maintain certain elements of consensus viral sequence, which likely represent viral escape from common HLA-restricted CTL responses. The ability of HIV to evolve to escape CTL responses restricted by a common HLA type highlights the challenges posed to development of an effective CTL-based vaccine

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

Tilth Producers Quarterly, Spring 2010

"Internal nitrogen supplies for perennial crops" is an article on the first two years of a large-scale on-farm trial of direct seeding legumes into orchard alleys for internal nitrogen production

Characterizing inland Pacific Northwest American Viticultural Areas with geospatial data.

American Viticultural Areas are officially recognized appellations for wine grapes (Vitis vinifera L.). They represent not only geographic identification for growers, but also economic significance through price premiums for grapes from desirable appellations and wines sourcing grapes from such appellations. Petitions for establishment and official descriptions of American Viticultural Areas in the inland Pacific Northwest have traditionally relied on general descriptions of physical attributes and data from point measurements, namely weather stations. Examination of spatial datasets in a geographic information system provides a more holistic means of assessing viticultural areas and a spatially continuous representation of an area. Comparison of spatial datasets to official appellation descriptions largely corroborate petitioners' claims, often with greater detail, but also highlight some shortcomings of official appellation descriptions. By focusing on spatial data representing environmental factors most important to wine grape production, viticultural areas can be described more thoroughly and accurately and appellations may be more appropriately delineated. We examined inland Pacific Northwest American Viticultural Areas with a geographic information system approach, illustrating the utility of spatial datasets in characterization and delineation of American Viticultural Areas

Leaf Tissue Macronutrient Standards for Northern Highbush Blueberry Grown in Contrasting Environments

Leaf tissue testing is a useful tool for monitoring nutrient requirements in northern highbush blueberry (Vaccinium corymbosum L.; abbreviated as “blueberry”) but may require adaptation to specific growing environments. The objective of this study was to evaluate macronutrient concentrations in early-, mid-, and late-season blueberry cultivars grown in two contrasting environments, specifically eastern and western Washington. Climate and soil conditions between these two regions differ tremendously with eastern Washington being more arid with naturally calcareous soils lower in soil organic matter. Sampling was conducted over a 3-year period in commercial fields. Leaf tissue nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg) and sulfur (S) concentrations were affected by year (Y), growing region (R), cultivar (C), and Day of Year (DOY) that the samples were collected with many interactions. Leaf nutrient concentrations were higher, on average, in western than eastern Washington except for Ca and Mg, indicating sufficiency levels should differ between these regions. Leaf macronutrients generally stabilized between DOY 212–243 (1–31 August), suggesting this period is optimal for tissue sampling. Findings from this study demonstrate the importance of considering regional effects and may be applicable for blueberry cultivated in similar pedo-climactic conditions around the world

Monitoring Uptake of Legume N by Apple Tree Using Nitrogen Isotope Discrimination

Intercropped legumes can supply nitrogen to fruit trees and reduce the need for purchased nitrogen fertilizer, potentially reducing costs and environmental footprint. The project evaluated nitrogen isotope techniques (comparing the 15 N and 14 N signal from the legume N versus other sources) to monitor the degree of uptake by apple trees of legume N grown in the orchard. The project involved two components: 1) a greenhouse study using 15 N-labeled clover residue added to potted apple trees to quantify legume-N uptake and a comparison to values using nitrogen isotope natural abundance; 2) a field study in an existing orchard legume cover crop trial using natural abundance for a qualitative evaluation of legume N and the ability to detect this signal in an ambient field environment. The 15 N enrichment technique is known to be more sensitive than the natural isotope abundance technique, but is not suitable for routine field use by growers or consultants. The objective of the project was to determine the uptake of legume-derived N in a quantitative manner and compare it with a more qualitative method to assess its utility on farms. Lower tree leaf 15 N atom% with legume alleys versus grass was detected in several instances in both trials, indicating that the natural isotope abundance method does have potential use for monitoring the timing of legume uptake by trees. PROJECT DESCRIPTION Objectives. Trial 1. Compare legume-N uptake by potted apple trees using the 15 N enrichment technique versus the natural isotope abundance technique. Trial 2. Monitor natural isotope abundance of legumes, soil, and apple trees in an existing legume cover crop trial to determine the magnitude of the signal difference in the different orchard components. Methods. Trial 1 was repeated using potted trees under shade cloth outdoors, after the initial trial (2014) was compromised by saline water in the greenhouse. Trees ('Golden Delicious'/B.9) were planted on 9 April 2015 in 20 " diameter pots filled with virgin Warden silt loam soil (no history of cropping). Forty-five trees were planted; 20 for each phase of the trial, with 5 extras. The trees were grown through the 2015 season without treatment due to the lack of enough 15 N labeled clover, and then they were placed in cold storage for the winter. There was not enough labeled 'Alice' white clover biomass to do spring 2016 treatments either, so trees and clover were grown through the summer. Fall treatments were applied on 9/13/16 to 20 trees. Prior to this, soil samples (0-10 ") and tree leaves (10 per tree) were collected for a pre-treatment baseline. All trees had received a Hoagland's nutrient solution during 2015 and 2016 in order for them to grow, and there appears to be a small amount of 15 N enrichment in this material tha