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T-Stór is Teagasc’s Open Access Repository, maintained by the Teagasc Library Service. Stór is the Gaelic word for Repository or Store or Warehouse, and T-Stór is an online “store” of Teagasc Research outputs and related documents. T-Stór collects preserves and makes freely available scholarly communication, including peer-reviewed articles, working papers and conference papers created by Teagasc researchers. Where material has already been published it is made available subject to the open-access policies of the original publishers. About Teagasc
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Easy phylotyping of Escherichia coli via the EzClermont web app and command-line toolThe Clermont PCR method for phylotyping Escherichia coli remains a useful classification scheme even though genome sequencing is now routine, and higher-resolution sequence typing schemes are now available. Relating present-day whole-genome E. coli classifications to legacy phylotyping is essential for harmonizing the historical literature and understanding of this important organism. Therefore, we present EzClermont – a novel in silico Clermont PCR phylotyping tool to enable ready application of this phylotyping scheme to whole-genome assemblies. We evaluate this tool against phylogenomic classifications, and an alternative software implementation of Clermont typing. EzClermont is available as a web app at www.ezclermont.org, and as a command-line tool at https://nickp60.github.io/EzClermont/.
Fabrication of Ligusticum chuanxiong polylactic acid microspheres: A promising way to enhance the hepatoprotective effect on bioactive ingredientsLigusticum chuanxiong extract-polylactic acid sustained-release microspheres (LCE-PLA) are fabricated in this study for enhancing both duration and hepatoprotective efficacy of the main bioactive ingredients. LCE-PLA in vitro release, cytotoxicity and in vivo hepatoprotective effect were discussed to evaluate its efficiency and functionality. Results demonstrated that the optimal drug-loading rate and encapsulation efficiency of tetramethylpyrazine (TMP, the main active ingredient) were 8.19%, 83.72%, respectively. The LCE-PLA in vitro release of TMP showed prolong 5-fold and in vitro cytotoxicity declined 25.00% compared with naked LCE. After 6 weeks of in vivo intervention in high fat diet mice, both liver aspartate aminotransferase and alanine aminotransferase levels were higher in LCE-PLA group than LCE group. The above results indicated that TMP had a higher bioavailability of hepatoprotection when encapsulation of LCE-PLA was applied. The current study has provided a promising novel way to enhance the efficacy of short half-life ingredients.
Establishing nationally representative benchmarks of farm-gate nitrogen and phosphorus balances and use efficiencies on Irish farms to encourage improvementsAgriculture faces considerable challenges of achieving more sustainable production that minimises nitrogen (N) and phosphorus (P) losses and meets international obligations for water quality and greenhouse gas emissions. This must involve reducing nutrient balance (NB) surpluses and increasing nutrient use efficiencies (NUEs), which could also improve farm profitability (a win-win). To set targets and motivate improvements in Ireland, nationally representative benchmarks were established for different farm categories (sector, soil group and production intensity). Annual farm-gate NBs (kg ha−1) and NUEs (%) for N and P were calculated for 1446 nationally representative farms from 2008 to 2015 using import and export data collected by the Teagasc National Farm Survey (part of the EU Farm Accountancy Data Network). Benchmarks for each category were established using quantile regression analysis and percentile rankings to identify farms with the lowest NB surplus per production intensity and highest gross margins (€ ha−1). Within all categories, large ranges in NBs and NUEs between benchmark farms and poorer performers show considerable room for nutrient management improvements. Results show that as agriculture intensifies, nutrient surpluses, use efficiencies and gross margins increase, but benchmark farms minimise surpluses to relatively low levels (i.e. are more sustainable). This is due to, per ha, lower fertiliser and feed imports, greater exports of agricultural products, and for dairy, sheep and suckler cattle, relatively high stocking rates. For the ambitious scenario of all non-benchmark farms reaching the optimal benchmark zone, moderate reductions in farm nutrient surpluses were found with great improvements in profitability, leading to a 31% and 9% decrease in N and P surplus nationally, predominantly from dairy and non-suckler cattle. The study also identifies excessive surpluses for each level of production intensity, which could be used by policy in setting upper limits to improve sustainability.
Application of the TruCulture® whole blood stimulation system for immune response profiling in cattleCapturing the phenotypic variation in immune responses holds enormous promise for the development of targeted treatments for disease as well as tailored vaccination schedules. However, accurate detection of true biological variation can be obscured by the lack of standardised immune assays. The TruCulture® whole blood stimulation system has now been extensively used to detect basal and induced immune responses to a range of pathogen-associated molecular patterns (PAMPs) in human peripheral blood. This study demonstrates the optimisation of this commercially available assay for systemic immune phenotyping in cattle. The early immune response in Holstein-Friesian bull calves (n = 10) was assessed by haematology, flow cytometry and cytokine expression profiling after 24 h ex-vivo PAMP (LPS, poly (I:C) and zymosan) stimulation in TruCulture® tubes. A comparative analysis was also performed with a traditional whole blood stimulation assay and cell viability using both systems was also evaluated. Results: Supernatant collected from TruCulture® tubes showed a significant increase in IL-1β and IL-8 expression compared to null stimulated tubes in response to both LPS and zymosan. In contrast, a detectable immune response was not apparent at the standard concentration of poly (I:C). Conventional whole blood cultures yielded similar response profiles, although the magnitude of the response was higher to both LPS and zymosan, which may be attributed to prokaryotic strain-specificity or batch of the stimulant used. Despite being a closed system, HIF1A expression – used as a measure of hypoxia was not increased, suggesting the TruCulture® assay did not negatively affect cell viability. This represents the first reported use of this novel standardised assay in cattle, and indicates that the concentration of poly (I:C) immunogenic in humans is insufficient to induce cytokine responses in cattle. We conclude that the low blood volume and minimally invasive TruCulture® assay system offers a practical and informative technique to assess basal and induced systemic immune responses in cattle.
Influence of sodium hexametaphosphate addition on the functional properties of milk protein concentrate solutions containing transglutaminase cross-linked proteinsThe functional properties of milk protein concentrate (MPC) powders are often hindered by their poor solubility. Calcium chelating salts have been shown to improve powder solubility, but generally their action contributes to higher viscosity due to disintegration of casein micelles and higher levels of serum-phase calcium. To help mitigate increases in viscosity associated with calcium chelation, transglutaminase (TGase), an enzyme that covalently crosslinks protein, was employed in an effort to stabilise the casein micelle structure. Sodium hexametaphosphate (SHMP) was added to control (C-MPC) and TGase crosslinked MPC (TG-MPC) dispersions at concentrations of 5, 12.5 and 25 mm prior to analysis. TG-MPC dispersions had lower viscosity than C-MPC dispersions across all SHMP concentrations studied. Crosslinking limited micelle dissociation on SHMP addition and led to greater retention of the white colour of the protein dispersions, while the turbidity of C-MPC dispersions decreased with increasing SHMP addition.