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First report of the Phytophthora infestans EU_43_A1 clonal lineage and associated PiCesA3 mutation G1105S in Ireland
No full textDatafile: Effects of experimental drought and plant diversity on ecosystem multifunctionality
No full textDatasetContains a dataset, ReadMe file and statistical code for a multivariate analysis of six agronomic responses from a field experiment that manipulated diversity from one to six plant species within multi-species mixtures. The experiment also imposed an experimental drought to investigate the effect of plant diversity and drought on the selected responses
Effect of breed and dietary composition on the miRNA profile of beef steers divergent for feed efficiency
No full textIdentifying and breeding cattle that are more feed efficient is of great benefit to beef production. Additionally, it is crucial that genes contributing to feed efficiency are robust across varying management settings including dietary source as well as being relevant across contrasting breeds of cattle. The aim of this study was to determine miRNAs that are contributing to the expression of residual feed intake (RFI) across two breeds and dietary sources. miRNA profiling was undertaken in Longissimus dorsi tissue of Charolais and Holstein–Friesian steers divergent for RFI phenotype following two contrasting consecutive diets (high-forage and high-concentrate). Ten miRNA were identified as differentially expressed (adj. P < 0.1) across the breed and diet contrasts examined. Of particular interest was the differential expression of miR-2419-5p and miR-2415-3p, both of which were up-regulated in the Low-RFI Charolais steers across each dietary phase. Pathway analysis of target mRNA genes of differentially expressed miRNA revealed enrichment (P < 0.05) for pathways including metabolic related pathways, insulin receptor signalling, adipogenesis as well as pathways related to skeletal muscle growth. These results provide insight into the skeletal muscle miRNAome of beef cattle and their potential molecular regulatory mechanisms relating to feed efficiency in beef cattle
Using biological systems to develop high value products and processes
No full textHigh value biorenewables are bio-based products, typically valued at greater than £10/kg
and produced at low volumes using industrial biotechnology methods (i.e., produced using
biological systems). They range from small bio-derived molecules to complex molecules
(e.g., polymers, proteins, and enzymes) and cells.
• High value biorenewables have a wide variety of applications across industrial sectors that
underpin the UK economy. For example, they can be used as ingredients in
pharmaceuticals, cosmetics, agrochemicals, home and personal care products, and
foods.
• There are opportunities for new and improved products using high value biorenewables,
and they can also provide sustainability benefits such as decreased greenhouse gas
emissions or reduced reliance on fossil feedstocks or unsustainable natural resources.
Deploying high value biorenewables at scale could also offer broader environmental,
economic, and social benefits.
• The UK is well placed to reap the potential benefits of high value biorenewables due to its
wealth of research and industrial expertise. However, there are barriers to developing and
deploying these products at commercial scales, and action across industry, academia,
and government will be required to overcome them.
• Government intervention will be required to create an enabling environment for this sector
to continue to grow. This includes appropriate funding at all stages of research and
innovation, a supportive regulatory environment, investment in skills, and policies that
encourage the use of sustainable products
Semi-dynamic in vitro digestion of sourdough bread enriched with flaxseed oil coacervates
No full textFood structure and addition of encapsulated compounds can impact the gastro-intestinal digestion of food. Flaxseed oil was encapsulated by complex coacervation using soluble pea protein and gum arabic as shell materials, dried by either spray or electrostatic spray drying and incorporated into sourdough dough before baking. Three bread formulations were prepared using spray-dried (B-SD), electrospray-dried coacervates (B-ES) and free ingredients used in the encapsulation (B). The standardised semi-dynamic INFOGEST in vitro digestion method was used. Cumulated protein/free NH2 release and cumulated free fatty acids (FFA) release were used to assess protein and lipid digestion. Coacervates were resistant to bread preparation since they were visible in B-SD and B-ES. The total release of protein, free NH2 and FFA by the end of intestinal digestions ranged between 41.58–45.23%, 1.08–1.22 µmol/g protein and 22.26–63.54%, respectively. There were no significant differences between formulations. There was a statistically significant increase (p < 0.5) of about three times in FFA release between the oral and gastric phases. Our findings help to understand the behaviour of coacervates when incorporated into solid food. In this study, the delivery structures did not affect in vitro digestion and may be used to increase the polyunsaturated fatty acid content by 50%
Relationship between the rumen microbiome and liver transcriptome in beef cattle divergent for feed efficiency
Full text linkAbstract
Background
Feed costs account for a high proportion of the variable cost of beef production, ultimately impacting overall profitability. Thus, improving feed efficiency of beef cattle, by way of determining the underlying genomic control and selecting for feed efficient cattle provides a method through which feed input costs may be reduced whilst also contributing to the environmental sustainability of beef production. The rumen microbiome dictates the feed degradation capacity and consequent nutrient supply in ruminants, thus potentially impacted by feed efficiency phenotype. Equally, liver tissue has been shown to be responsive to feed efficiency phenotype as well as dietary intake. However, although both the rumen microbiome and liver transcriptome have been shown to be impacted by host feed efficiency phenotype, knowledge of the interaction between the rumen microbiome and other peripheral tissues within the body, including the liver is lacking. Thus, the objective of this study was to compare two contrasting breed types (Charolais and Holstein-Friesian) divergent for residual feed intake (RFI) over contrasting dietary phases (zero-grazed grass and high-concentrate), based on gene co-expression network analysis of liver transcriptome data and microbe co-abundance network of rumen microbiome data. Traits including RFI, dry matter intake (DMI) and growth rate (ADG), as well as rumen concentrations of volatile fatty acids were also included within the network analysis.
Results
Overall, DMI had the greatest number of connections followed by RFI, with ADG displaying the fewest number of significant connections. Hepatic genes related to lipid metabolism were correlated to both RFI and DMI phenotypes, whilst genes related to immune response were correlated to DMI. Despite the known relationship between RFI and DMI, the same microbes were not directly connected to these phenotypes, the Succiniclasticum genus was however, negatively connected to both RFI and ADG. Additionally, a stepwise regression analysis revealed significant roles for both Succiniclasticum genus and Roseburia.faecis sp. in predicting RFI, DMI and ADG.
Conclusions
Results from this study highlight the interactive relationships between rumen microbiome and hepatic transcriptome data of cattle divergent for RFI, whilst also increasing our understanding of the underlying biology of both DMI and ADG in beef cattle
Continuous Cover Forestry in Ireland - Informing through research and accessible Massive Open Online Courses
Full text linkThis article describes some of the work conducted by Teagasc related to continuous cover forestry management. This includes: long-term research; collaborating with European partners in developing the first Massive Open Online Course on Continuous Cover Forest management; in-forest interactive training in marteloscopes
Learning from Agricultural Land Market Regulation Policies in EU Member States
Full text linkThis article draws from economic theory and the recent European Commission report on agricultural land market regulation to assess the suitability of selected regulatory policies for agricultural land markets in Ireland. Insights from policy in other EU Member States indicates that some flexibility is always required to permit the existence of temporary land leasing contracts. Farmland rental prices in Ireland have mainly followed the underlying returns to agriculture and been much less influenced by
speculative bubbles relative to farmland sales markets. The land rental data for 2019 do not point to the need for maximum price regulation. The availability of reliable statistics is not a sufficient condition to prevent bubbles from emerging, but farmland markets need to be closely monitored with up-to-date official statistics informing potential market participants and public policy
The first survey using high-throughput sequencing of cereal and barley yellow dwarf viruses in Irish spring and winter barley crops
Full text linkPeer-reviewedYellow dwarf viruses (YDVs) are the most economically important plant viruses impacting cereal production worldwide and include viruses from the genus Luteovirus (e.g., barely yellow dwarf virus (BYDV)-PAV, BYDV-PAS, BYDV-MAV, BYDV-kerII, BYDV-kerIII) and Polerovirus (e.g., cereal yellow dwarf virus (CYDV)-RPV, CYDV-RPS). Until now, much of our knowledge on YDVs infecting Irish barley crops (Hordeum vulgare L.) has come from serological assays; however, due to cross-reactivity it can be difficult to discriminate between viruses of different species. In this study, we have carried out a high-throughput sequencing survey of symptomatic crops, positive with serological assays, to identify YDVs infecting Irish spring and winter barley crops and establish reference genomes to support further development of molecular surveillance tools. In total, RNA was extracted from 45 symptomatic crop samples that were collected across Ireland over 2 yr and sequenced following rRNA depletion. Three samples of barley plants from BYDV-infected aphid colonies were also included. BYDV-MAV was identified in all field samples sequenced. This confirms previous evidence based on serological assays that BYDV-MAV is the dominant YDV in Irish barley crops. We have also identified BYDV-PAS in 29% of symptomatic field samples, the first report of this species in Ireland. In addition, BYDV-PAV was also found, and crop samples with mixed infections were common; although in mixed infections the greatest proportion of YDV reads originated from BYDV-MAV. Finally, CYDV-RPS, the more severe variant of CYDV-RPV belonging to the genus Polerovirus, was identified in a single sample. The complete genomes, assembled from this first sequence-based survey, will enable the development of molecular surveillance tools with greater virus specificity, to further support the Irish aphid and YDV monitoring network
EUKARYOME: the rRNA gene reference database for identification of all eukaryotes
Full text linkPeer-reviewedMolecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database EUKARYOME for nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS) and 28S rRNA markers for all eukaryotes, including metazoans (animals), protists, fungi and plants. It is particularly useful for the identification of arbuscular mycorrhizal fungi as it bridges the four commonly used molecular markers—ITS1, ITS2, 18S V4–V5 and 28S D1–D2 subregions. The key benefits of this database over other annotated reference sequence databases are that it is not restricted to certain taxonomic groups and it includes all rRNA markers. EUKARYOME also offers a number of reference long-read sequences that are derived from (meta)genomic and (meta)barcoding—a unique feature that can be used for taxonomic identification and chimera control of third-generation, long-read, high-throughput sequencing data. Taxonomic assignments of rRNA genes in the database are verified based on phylogenetic approaches. The reference datasets are available in multiple formats from the project homepage, http://www.eukaryome.org.King Saud Universit