Botanical rejuvenation of field margins and benefits for invertebrate fauna on a drystock farm in County Longford

peer-reviewedThis study investigates methods to rejuvenate the fl ora of previously degraded fi eld margins on a pastoral farm in County Longford. We also assess the effects of individual treatments on the abundance of various orders of invertebrates recorded within the experimental plots. Field margin treatments were 1.5m-wide unfenced control margins, 1.5m-wide fenced margins or 3.5m-wide fenced margins. Nutrient inputs were excluded from all of the experimental plots. The botanical composition of the plots was examined on four occasions between 2002 and 2004 using permanent, nested quadrats. Emergence traps were used to measure invertebrate abundance within treatment plots and the main sward. Results indicated that 1) exclusion of nutrient inputs had a positive effect on plant species richness within the fi eld margins; 2) plant species richness decreased with increased distance from the hedgerow; 3) herb species richness was greatest in the 1.5m closest to the hedgerow; 4) greater abundance of invertebrates occurred within the 3.5m-wide margins; 5) successful control of Pteridium aquilinum was achieved through spot treatment with the selective herbicide ‘Asulox’; and 6) a combination of management techniques such as cutting and grazing is likely to enhance plant species richness and facilitate the structural diversity of vegetation that is necessary for many invertebrate taxa.Teagasc Walsh Fellowship Programm

Active Inspiration Playmakers final report

Final Report the the 'Playmakers' project; a programme within the Virgin Active 'Active Inspiration' initiative.

Evaluation of the Efficacy and Safety of a Marine-Derived Bacillus Strain for Use as an In-Feed Probiotic for Newly Weaned Pigs

peer-reviewedForty eight individual pigs (8.7±0.26 kg) weaned at 28±1 d of age were used in a 22-d study to evaluate the effect of oral administration of a Bacillus pumilus spore suspension on growth performance and health indicators. Treatments (n = 16) were: (1) non-medicated diet; (2) medicated diet with apramycin (200 mg/kg) and pharmacological levels of zinc oxide (2,500 mg zinc/kg) and (3) B. pumilus diet (non-medicated diet + 1010 spores/day B. pumilus). Final body weight and average daily gain tended to be lower (P = 0.07) and feed conversion ratio was worsened (P<0.05) for the medicated treatment compared to the B. pumilus treatment. Ileal E. coli counts were lower for the B. pumilus and medicated treatments compared to the non-medicated treatment (P<0.05), perhaps as a result of increased ileal propionic acid concentrations (P<0.001). However, the medicated treatment reduced fecal (P<0.001) and cecal (P<0.05) Lactobacillus counts and tended to reduce the total cecal short chain fatty acid (SCFA) concentration (P = 0.10). Liver weights were lighter and concentrations of liver enzymes higher (P<0.05) in pigs on the medicated treatment compared to those on the non-medicated or B. pumilus treatments. Pigs on the B. pumilus treatment had lower overall lymphocyte and higher granulocyte percentages (P<0.001) and higher numbers of jejunal goblet cells (P<0.01) than pigs on either of the other two treatments or the non-medicated treatment, respectively. However, histopathological examination of the small intestine, kidneys and liver revealed no abnormalities. Overall, the B. pumilus treatment decreased ileal E. coli counts in a manner similar to the medicated treatment but without the adverse effects on growth performance, Lactobacillus counts, cecal SCFA concentration and possible liver toxicity experienced with the medicated treatment.The study was funded by the Higher Education Authority/Institutes of Technology Ireland Technological Sector Research Strand III Programme

Methylomic trajectories across human fetal brain development

Open access articleEpigenetic processes play a key role in orchestrating transcriptional regulation during development. The importance of DNA methylation in fetal brain development is highlighted by the dynamic expression of de novo DNA methyltransferases during the perinatal period and neurodevelopmental deficits associated with mutations in the methyl-CpG binding protein 2 (MECP2) gene. However, our knowledge about the temporal changes to the epigenome during fetal brain development has, to date, been limited. We quantified genome-wide patterns of DNA methylation at ∼ 400,000 sites in 179 human fetal brain samples (100 male, 79 female) spanning 23 to 184 d post-conception. We identified highly significant changes in DNA methylation across fetal brain development at >7% of sites, with an enrichment of loci becoming hypomethylated with fetal age. Sites associated with developmental changes in DNA methylation during fetal brain development were significantly underrepresented in promoter regulatory regions but significantly overrepresented in regions flanking CpG islands (shores and shelves) and gene bodies. Highly significant differences in DNA methylation were observed between males and females at a number of autosomal sites, with a small number of regions showing sex-specific DNA methylation trajectories across brain development. Weighted gene comethylation network analysis (WGCNA) revealed discrete modules of comethylated loci associated with fetal age that are significantly enriched for genes involved in neurodevelopmental processes. This is, to our knowledge, the most extensive study of DNA methylation across human fetal brain development to date, confirming the prenatal period as a time of considerable epigenomic plasticity.MRCUniversity of Exeter Medical SchoolWellcome Trus

Changes to the Oligosaccharide Profile of Bovine Milk at the Onset of Lactation

peer-reviewedNumerous bioactive components exist in human milk including free oligosaccharides, which represent some of the most important, and provide numerous health benefits to the neonate. Considering the demonstrated value of these compounds, much interest lies in characterising structurally similar oligosaccharides in the dairy industry. In this study, the impacts of days post-parturition and parity of the cows on the oligosaccharide and lactose profiles of their milk were evaluated. Colostrum and milk samples were obtained from 18 cows 1–5 days after parturition. Three distinct phases were identified using multivariate analysis: colostrum (day 0), transitional milk (days 1–2) and mature milk (days 3–5). LS-tetrasaccharide c, lacto-N-neotetraose, disialyllacto-N-tetraose, 3’-sial-N-acetyllactosamine, 3’-sialyllactose, lacto-N-neohexaose and disialyllactose were found to be highly affiliated with colostrum. Notably, levels of lactose were at their lowest concentration in the colostrum and substantially increased 1-day post-parturition. The cow’s parity was also shown to have a significant effect on the oligosaccharide profile, with first lactation cows containing more disialyllacto-N-tetraose, 6’-sialyllactose and LS-tetrasaccharide compared to cows in their second or third parity. Overall, this study identifies key changes in oligosaccharide and lactose content that clearly distinguish colostrum from transitional and mature milk and may facilitate the collection of specific streams with divergent biological functions

Representing kidney development using the gene ontology.

Gene Ontology (GO) provides dynamic controlled vocabularies to aid in the description of the functional biological attributes and subcellular locations of gene products from all taxonomic groups (www.geneontology.org). Here we describe collaboration between the renal biomedical research community and the GO Consortium to improve the quality and quantity of GO terms describing renal development. In the associated annotation activity, the new and revised terms were associated with gene products involved in renal development and function. This project resulted in a total of 522 GO terms being added to the ontology and the creation of approximately 9,600 kidney-related GO term associations to 940 UniProt Knowledgebase (UniProtKB) entries, covering 66 taxonomic groups. We demonstrate the impact of these improvements on the interpretation of GO term analyses performed on genes differentially expressed in kidney glomeruli affected by diabetic nephropathy. In summary, we have produced a resource that can be utilized in the interpretation of data from small- and large-scale experiments investigating molecular mechanisms of kidney function and development and thereby help towards alleviating renal disease

Whole-genome sequencing provides new insights into the clonal architecture of Barrett's esophagus and esophageal adenocarcinoma.

The molecular genetic relationship between esophageal adenocarcinoma (EAC) and its precursor lesion, Barrett's esophagus, is poorly understood. Using whole-genome sequencing on 23 paired Barrett's esophagus and EAC samples, together with one in-depth Barrett's esophagus case study sampled over time and space, we have provided the following new insights: (i) Barrett's esophagus is polyclonal and highly mutated even in the absence of dysplasia; (ii) when cancer develops, copy number increases and heterogeneity persists such that the spectrum of mutations often shows surprisingly little overlap between EAC and adjacent Barrett's esophagus; and (iii) despite differences in specific coding mutations, the mutational context suggests a common causative insult underlying these two conditions. From a clinical perspective, the histopathological assessment of dysplasia appears to be a poor reflection of the molecular disarray within the Barrett's epithelium, and a molecular Cytosponge technique overcomes sampling bias and has the capacity to reflect the entire clonal architecture

Choosing Short: An Explanation of the Similarities and Dissimilarities in the Distribution Patterns of Binding and Covaluation

Covaluation is the generalization of coreference introduced by Tanya Reinhart. Covaluation distributes in patterns that are very similar yet not entirely identical to those of binding. On a widespread view, covaluation and binding distribute similarly because binding is defined in terms of covaluation. Yet on Reinhart's view, binding and covaluation are not related that way: binding pertains to syntax, covaluation does not. Naturally, the widespread view can easily explain the similarities between binding and covaluation, whereas Reinhart can easily explain the dissimilarities. Reciprocally, the widespread view finds it harder to explain the dissimilarities, whereas Reinhart finds it harder to explain the similarities. Reinhart and others have proposed more than one explanation of the similarities, but as I argue, these explanations do not work. Hence although I adopt Reinhart's view, I propose a new explanation of the similarities and dissimilarities between binding and covaluation: While Reinhart has invoked semantic structure only to explain dissimilarities, I do so to explain both similarities and dissimilarities at once. Finally, I examine in light of this approach the topics of language acquisition, only-constructions, the identity predicate, the Partee/Bach/Higginbotham problem, the Dahl puzzle and its recent versions by Roelofsen

Community research report

University College Cork introduced its first Community-based Participatory Research (CBPR) module in 2016. The module was funded and supported by Horizon2020 funding, specifically the EnRRICH project (Enhancing Responsible Research and Innovation through Curricula in Higher Education). The module is a 5-credit module for PhD students from all disciplines in the early stages of their PhD at University College Cork. Following two fruitful partnerships in the areas of social justice / equality, community family support services and older persons, there was a keen interested to explore partnerships in markedly different areas such as environmental sustainability. A dialogue ensued with CEF where the opportunity and feasibility to collaborate on the CBPR module was explored