• Identification of the key compounds responsible for Cheddar cheese flavour

      Beresford, Tom; Wallace, J.; Aherne, S.; Drinan, F.; Eason, D.; Corcoran, M.; Mulholland, E.; Hannon, J. (Teagasc, 2000-09-01)
      There is a poor understanding of the relationship between organoleptic assessment of cheese and quantitative analysis of flavour compounds. Further, the contribution of particular cheese-making parameters such as ripening temperature and starter culture has not been fully elucidated. During the ripening of most cheese varieties complex chemical conversions occur within the cheese matrix. In most cheese varieties breakdown of protein is the most important flavour development pathway. The primary cheese protein, casein, is degraded enzymatically to short peptides and free amino acids. The agents primarily responsible for these conversions are the residual rennet that is retained in the cheese curd at the end of the manufacturing phase and the proteinases and peptidases that are associated with the starter bacteria. While the rate and degree of proteolysis are of vital significance for desired flavour development, the direct products of proteolysis do not fully define cheese flavour. Much research is now demonstrating that the further biochemical and chemical conversions of the products of proteolysis, in particular the amino acids, are necessary for full flavour development. The products produced by these pathways are volatile at low boiling points and are thus released during mastication of the cheese in the mouth. Many of these volatile compounds contribute to the flavour sensation experienced by the consumer. A very wide spectrum of such compounds have been isolated from cheese, in excess of two hundred in some cheese varieties. It is now generally accepted that there is no individual compound which defines cheese flavour completely and that the flavour sensation is the result of numerous compounds present in the correct proportions. This has become known as the Component Balance Theory . The application of modern analytical techniques as proposed in this project would provide a greater understanding of the significant flavour compounds in Cheddar cheese and help to identify the impact of specific cheese-making parameters such as starter flora and ripening temperature on the production of volatile flavour compounds. This data would assist the general programme on flavour improvement of cheese which should ultimately benefit the cheese manufacturer. Hence this project set out to develop methods to identify the key flavour compounds in Cheddar cheese. These techniques would then be applied to experimental and commercial cheeses during ripening in an effort to identify key compounds and the influence of starter cultures and ripening temperature on their production.
    • Identification Of Environmental Variables For Use In Monitoring For The Evaluation Of The Rural Environment Protection Scheme

      Finn, John A.; Kavanagh, B.; Flynn, M. (Teagasc, 2005-04-01)
      The aim of this study was to identify and select quantitative environmental attributes for a monitoring programme that may be integrated into an environmental evaluation of Ireland’s agri-environmental scheme. This was achieved primarily by reviewing a range of agri-environmental indicators and suggesting indicators that would be appropriate for monitoring the REPS. The study conducted a desk review to collate information on current best practice in monitoring for environmental quality. A Project Group (comprising representatives from the Environmental Protection Agency [EPA], Department of Agriculture and Food [DAF], Teagasc, and the project supervisors) advised on the ongoing development of the project. There was a consultation process with national experts, and with a selection of stakeholder organisations with an interest in monitoring the environmental impact of the REPS.
    • Identification of existing and emerging chemical residue contamination concerns in milk

      Danaher, Martin; Jordan, Kieran (Teagasc (Agriculture and Food Development Authority), Ireland, 2013)
      In order to maintain the quality of Irish milk and meet increasingly demanding specifications, it is necessary to focus on chemical residues in milk, in addition to other quality issues. The objective of the work was to assess the current status of chemical contaminant analysis and to identify technological and knowledge needs. This was achieved through a review of literature with respect to chemical contaminants. Quaternary ammonium compounds (QACs) have been identified as an area of concern for the dairy industry because of the recent reports of QAC residues in dairy products internationally. Analytical support to analyse QAC residues in milk and dairy products on an ongoing basis is required. Furthermore, the source of QAC residues along the milk production chain needs to be identified. Similarly, analytical support and research is needed in the area of phthalates, to support the development of intervention strategies to reduce contamination, if present. Cephalosporin antibiotics have been a concern for the dairy industry because of the lack of suitable chemical tests to measure these substances.
    • Identification of short peptide sequences in the nanofiltration permeate of a bioactive whey protein hydrolysate

      Le Maux, Solene; Nongoniermaa, Alice B.; Murray, Brian; Kelly, Philip M.; Fitzgerald, Richard J. (Elsevier, 2015-09-16)
      Short peptides in food protein hydrolysates are of significant interest as they may be highly bioactive whilst also being bioavailable. A dipeptidyl peptidase IV (DPP-IV) inhibitory whey protein hydrolysate (WPH) was fractionated using nanofiltration (NF) with a 200 Da MWCO membrane. The DPP-IV half maximal inhibitory concentration of the NF permeate (IC50 = 0.66 ± 0.08 mg protein equivalent mL− 1) was significantly more potent (P > 0.05) than that of the starting WPH (IC50 = 0.94 ± 0.24 mg protein equivalent mL− 1) and associated retentate (IC50 = 0.82 ± 0.13 mg protein equivalent mL− 1). This confirmed the contribution of short peptides within the NF permeate to the overall DPP-IV inhibitory activity. An hydrophilic interaction liquid chromatography (HILIC-) and reverse-phase (RP-) liquid chromatography tandem mass spectrometry (LC–MS/MS) strategy, based on two retention time models, allowed detection of eight free amino acids and eight di- to tetrapeptides in the NF permeate. The potential sequences of the peptides within the NF permeate were then ranked on the basis of their highest probability of occurrence. A confirmatory study with synthetic peptides showed that valine–alanine (VA), valine–leucine (VL), tryptophan–leucine (WL) and tryptophan–isoleucine (WI) displayed DPP-IV IC50 values < 170 μM. The NF and LC–MS strategies employed herein represent a new approach for the targeted identification of short peptides within bioactive food protein hydrolysates.
    • The Identification of Sites and Farming Systems Prone to Pollution by Surface Runoff.

      Ryan, T.D. (Teagasc, 2000-09-01)
      There is mounting evidence that overland flow from land contributes to pollution of surface water. No convenient method exists to identify fields that generate overland flow. Therefore the WT model has been developed to predict overland flow from any small parcel of land. Water table tubes and flow meters were installed in three sites in Wexford and Carlow. The water table data, along with rainfall and evaporation data, were entered into the WT model to calculate overland flow and other parameters over a 7-month period. Additional measurements of water table level were taken using maximum level indicators with a view to reducing field costs. All three sites had layers of sand in the sub-soil. It is likely that the sand allowed water to flow under the soil and contributed to overland flow. Values from the WT model matched the field measurements of water table closely and predicted overland flow with reasonable accuracy. One pipe in each field was identified which could indicate when the field was sufficiently dry for spreading slurry. The maximum level indicators recorded water table accurately. However, the lack of synchronisation of this data, with weather data, reduced slightly the precision of the model. The WT model can identify fields prone to overland flow and show when a field is sufficiently dry to accept slurry. Proposed economies promise to reduce the cost of investigation.
    • Identifying Single Copy Orthologs in Metazoa

      Creevey, Christopher J.; Muller, Jean; Doerks, Tobias; Thompson, Julie D.; Arendt, Detlev; Bork, Peer (PLOS, 2011-12-01)
      The identification of single copy (1-to-1) orthologs in any group of organisms is important for functional classification and phylogenetic studies. The Metazoa are no exception, but only recently has there been a wide-enough distribution of taxa with sufficiently high quality sequenced genomes to gain confidence in the wide-spread single copy status of a gene. Here, we present a phylogenetic approach for identifying overlooked single copy orthologs from multigene families and apply it to the Metazoa. Using 18 sequenced metazoan genomes of high quality we identified a robust set of 1,126 orthologous groups that have been retained in single copy since the last common ancestor of Metazoa. We found that the use of the phylogenetic procedure increased the number of single copy orthologs found by over a third more than standard taxon-count approaches. The orthologs represented a wide range of functional categories, expression profiles and levels of divergence. To demonstrate the value of our set of single copy orthologs, we used them to assess the completeness of 24 currently published metazoan genomes and 62 EST datasets. We found that the annotated genes in published genomes vary in coverage from 79% (Ciona intestinalis) to 99.8% (human) with an average of 92%, suggesting a value for the underlying error rate in genome annotation, and a strategy for identifying single copy orthologs in larger datasets. In contrast, the vast majority of EST datasets with no corresponding genome sequence available are largely under-sampled and probably do not accurately represent the actual genomic complement of the organisms from which they are derived.
    • Illumina MiSeq 16S amplicon sequence analysis of bovine respiratory disease associated bacteria in lung and mediastinal lymph node tissue

      Johnston, Dayle; Earley, Bernadette; Cormican, Paul; Murray, Gerard; Kenny, David A; Waters, Sinead M; McGee, Mark; Kelly, Alan K; McCabe, Matthew S (Biomed Central, 2017-05-02)
      Background Bovine respiratory disease (BRD) is caused by growth of single or multiple species of pathogenic bacteria in lung tissue following stress and/or viral infection. Next generation sequencing of 16S ribosomal RNA gene PCR amplicons (NGS 16S amplicon analysis) is a powerful culture-independent open reference method that has recently been used to increase understanding of BRD-associated bacteria in the upper respiratory tract of BRD cattle. However, it has not yet been used to examine the microbiome of the bovine lower respiratory tract. The objective of this study was to use NGS 16S amplicon analysis to identify bacteria in post-mortem lung and lymph node tissue samples harvested from fatal BRD cases and clinically healthy animals. Cranial lobe and corresponding mediastinal lymph node post-mortem tissue samples were collected from calves diagnosed as BRD cases by veterinary laboratory pathologists and from clinically healthy calves. NGS 16S amplicon libraries, targeting the V3-V4 region of the bacterial 16S rRNA gene were prepared and sequenced on an Illumina MiSeq. Quantitative insights into microbial ecology (QIIME) was used to determine operational taxonomic units (OTUs) which corresponded to the 16S rRNA gene sequences. Results Leptotrichiaceae, Mycoplasma, Pasteurellaceae, and Fusobacterium were the most abundant OTUs identified in the lungs and lymph nodes of the calves which died from BRD. Leptotrichiaceae, Fusobacterium, Mycoplasma, Trueperella and Bacteroides had greater relative abundances in post-mortem lung samples collected from fatal cases of BRD in dairy calves, compared with clinically healthy calves without lung lesions. Leptotrichiaceae, Mycoplasma and Pasteurellaceae showed higher relative abundances in post-mortem lymph node samples collected from fatal cases of BRD in dairy calves, compared with clinically healthy calves without lung lesions. Two Leptotrichiaceae sequence contigs were subsequently assembled from bacterial DNA-enriched shotgun sequences. Conclusions The microbiomes of the cranial lung lobe and mediastinal lymph node from calves which died from BRD and from clinically healthy H-F calves have been characterised. Contigs corresponding to the abundant Leptotrichiaceae OTU were sequenced and found not to be identical to any known bacterial genus. This suggests that we have identified a novel bacterial species associated with BRD.
    • Illumina MiSeq Phylogenetic Amplicon Sequencing Shows a Large Reduction of an Uncharacterised Succinivibrionaceae and an Increase of the Methanobrevibacter gottschalkii Clade in Feed Restricted Cattle

      McCabe, Matthew Sean; Cormican, Paul; Keogh, Kate; O'Connor, Aaron; O'Hara, Eoin; Palladino, Rafael Alejandro; Kenny, David A.; Waters, Sinead M. (PLOS, 2015-07-30)
      Periodic feed restriction is used in cattle production to reduce feed costs. When normal feed levels are resumed, cattle catch up to a normal weight by an acceleration of normal growth rate, known as compensatory growth, which is not yet fully understood. Illumina Miseq Phylogenetic marker amplicon sequencing of DNA extracted from rumen contents of 55 bulls showed that restriction of feed (70% concentrate, 30% grass silage) for 125 days, to levels that caused a 60% reduction of growth rate, resulted in a large increase of relative abundance of Methanobrevibacter gottschalkii clade (designated as OTU-M7), and a large reduction of an uncharacterised Succinivibrionaceae species (designated as OTU-S3004). There was a strong negative Spearman correlation (ρ = -0.72, P = <1x10-20) between relative abundances of OTU-3004 and OTU-M7 in the liquid rumen fraction. There was also a significant increase in acetate:propionate ratio (A:P) in feed restricted animals that showed a negative Spearman correlation (ρ = -0.69, P = <1x10-20) with the relative abundance of OTU-S3004 in the rumen liquid fraction but not the solid fraction, and a strong positive Spearman correlation with OTU-M7 in the rumen liquid (ρ = 0.74, P = <1x10-20) and solid (ρ = 0.69, P = <1x10-20) fractions. Reduced A:P ratios in the rumen are associated with increased feed efficiency and reduced production of methane which has a global warming potential (GWP 100 years) of 28. Succinivibrionaceae growth in the rumen was previously suggested to reduce methane emissions as some members of this family utilise hydrogen, which is also utilised by methanogens for methanogenesis, to generate succinate which is converted to propionate. Relative abundance of OTU-S3004 showed a positive Spearman correlation with propionate (ρ = 0.41, P = <0.01) but not acetate in the liquid rumen fraction.
    • Image Processing of Outer-Product matrices - a new way to classify samples: Examples using visible/NIR/MIR spectral data.

      Jaillais, B.; Morrin, V.; Downey, Gerard (Elsevier, 2007)
      A chemometric analysis has been developed to emphasise the discrimination power of spectroscopic techniques such as near infrared, mid-infrared and visible spectroscopy. The combination of two spectral domains using outer product analysis (OPA) leads to the calculation of an outer product (OP) matrix. The representation of this matrix is called the "analytical fingerprint" of the samples and their classification is performed in the following steps. First, two different techniques are tested by subtracting the images one-by-one and the sum of all the elements of the resulting difference matrix gives a scalar, characteristic of the distance between the two images. Combining chemical analysis with image processing techniques provides an original approach to study butters and margarines in relation to their fat content. Best results were obtained with the OP matrix built from NIR and visible signals following the use of city block distance and average linkage. Samples were arranged in four groups: 100 %, 82-75 %, 70-59 % and 38-25 % w/w fat. The cophenetic correlation coefficient (validity of the cluster information generated by the linkage function) associated with these spectral data has a value of 0.973. Similar results were obtained using Ward's algorithm which generated four groups and a cophenetic correlation coefficient equal to 0.959.
    • Imaginal and ovicidal effect of some insecticides against Bruchus pisorum L. (Coleoptera: Chrisomelidae)

      Nikolova, I. M. (Teagasc (Agriculture and Food Development Authority), Ireland, 2016-01-13)
      Trials were conducted in 2011 and 2012 at the Institute of Forage Crops, Pleven, Bulgaria, in order to study the imaginal and possible ovicidal effect of some insecticides against Bruchus pisorum under field conditions. Treatments with insecticides were started after the appearance of the first pea weevils eggs on pods located on the bottom two nodes. It was found that treatment with acetamiprid; thiacloprid; thiacloprid+deltamethrin; 50 g cypermethrin+480 g chlorpyrifosethyl, 50 g cypermethrin+500 g chlorpyrifosethyl and zeta-cypermethrin resulted in the cessation of additional oviposition on the lower nodes by Bruchus pisorum, due to the toxic effect of the insecticides on the pea weevil. It was found that spraying with acetamiprid and zeta-cypermethrin was the most effective. These insecticides significantly reduced the proportion of infected pods in comparison with the proportion of pods with eggs before the treatment by 30.2 and 27.4% and by 15.8 and 24.0% in 2011 and 2012, respectively. The use of acetamiprid and zeta-cypermethrin was also associated with the lowest percentage of infected seeds (21.7 and 23.6%, respectively), with the lowest percentage of infected seed in infected pods (40.5 and 42.5%, respectively) and the highest weight of 1000 infected seeds (161.94 and 182.04 g, respectively). It was concluded that the management of pea weevils in the crop with acetamiprid and zetacypermethrin can lead to satisfactory results when spray timing is chosen when the first eggs are visible.
    • Impact analysis of the CAP reform on main agricultural commodities

      Donnellan, Trevor; Hanrahan, Kevin (Teagasc, 2007-03-15)
      This study has been carried out for the European Commission's Joint Research Centre to analyze agricultural policies at Member State, EU15 and EU25 levels as well as for Bulgaria and Romania. The modelling tool allows for projections and policy analysis (up to a 10 year horizon) for the enlarged EU.
    • Impact of agronomic practices of an intensive dairy farm on nitrogen concentrations in a karst aquifer in Ireland

      Huebsch, Manuela; Horan, Brendan; Blum, P; Richards, Karl G.; Grant, Jim; Fenton, Owen (Elsevier, 2013-09-24)
      Exploring the relationship between agricultural nitrogen loading on a dairy farm and groundwater reactive nitrogen concentration such as nitrate is particularly challenging in areas underlain by thin soils and karstified limestone aquifers. The objective of this study is to relate changes in detailed agronomic N-loading, local weather conditions, hydrogeological and geological site characteristics with groundwater N occurrence over an 11-year period on an intensive dairy farm with free draining soils and a vulnerable limestone aquifer. In addition, the concept of vertical time lag from source to receptor is considered. Statistical analysis used regression with automatic variable selection. Four scenarios were proposed to describe the relationships between paddock and groundwater wells using topographic and hydrogeological assumptions. Monitored nitrate concentrations in the studied limestone aquifer showed a general decrease in the observed time period (2002–2011). Statistical results showed that a combination of improved agronomic practices and site specific characteristics such as thicknesses of the soil and unsaturated zone together with hydrogeological connections of wells and local weather conditions such as rainfall, sunshine and soil moisture deficit were important explanatory variables for nitrate concentrations. Statistical results suggested that the following agronomic changes improved groundwater quality over the 11-year period: reductions in inorganic fertiliser usage, improvements in timing of slurry application, the movement of a dairy soiled water irrigator to less karstified areas of the farm and the usage of minimum cultivation reseeding on the farm. In many cases the explanatory variables of farm management practices tended to become more important after a 1- or 2-year time lag. Results indicated that the present approach can be used to elucidate the effect of farm management changes to groundwater quality and therefore the assessment of present and future legislation implementations.
    • Impact of chemical amendment of dairy cattle slurry on phosphorus, suspended sediment and metal loss to runoff from a grassland soil

      Brennan, R. B.; Fenton, Owen; Grant, Jim; Healy, Mark G. (Elsevier, 2011-11-01)
      Emerging remediation technologies such as chemical amendment of dairy cattle slurry have the potential to reduce phosphorus (P) solubility and consequently reduce P losses arising from land application of dairy cattle slurry. The aim of this study was to determine the effectiveness of chemical amendment of slurry to reduce incidental losses of P and suspended sediment (SS) from grassland following application of dairy cattle slurry and to examine the effect of amendments on metal concentrations in runoff water. Intact grassed-soil samples were placed in two laboratory runoff boxes, each 200-cm-long by 22.5-cm-wide by 5-cm-deep, before being amended with dairy cattle slurry (the study control) and slurry amended with either: (i) alum, comprising 8% aluminium oxide (Al2O3) (1.11:1 aluminium (Al):total phosphorus (TP) of slurry) (ii) poly-aluminium chloride hydroxide (PAC) comprising 10% Al2O3 (0.93:1 Al:TP) (iii) analytical grade ferric chloride (FeCl2) (2:1 Fe:TP), (iv) and lime (Ca(OH)2) (10:1 Ca:TP). When compared with the study control, PAC was the most effective amendment, reducing dissolved reactive phosphorus (DRP) by up to 86% while alum was most effective in reducing SS (88%), TP (94%), particulate phosphorus (PP) (95%), total dissolved phosphorus (TDP) (81%), and dissolved unreactive phosphorus (DUP) (86%). Chemical amendment of slurry did not appear to significantly increase losses of Al and Fe compared to the study control, while all amendments increased Ca loss compared to control and grass-only treatment. While chemical amendments were effective, the reductions in incidental P losses observed in this study were similar to those observed in other studies where the time from slurry application to the first rainfall event was increased. Timing of slurry application may therefore be a much more feasible way to reduce incidental P losses. Future work must examine the long-term effects of amendments on P loss to runoff and not only incidental losses.
    • Impact of chemically amended pig slurry on greenhouse gas emissions, soil properties and leachate

      O'Flynn, Cornelius J.; Healy, Mark G.; Lanigan, Gary; Troy, Shane M.; Somers, Cathal; Fenton, Owen (Elsevier, 2013-07-10)
      The effectiveness of chemical amendment of pig slurry to ameliorate phosphorus (P) losses in runoff is well studied, but research mainly has concentrated only on the runoff pathway. The aims of this study were to investigate changes to leachate nutrient losses, soil properties and greenhouse gas (GHG) emissions due to the chemical amendment of pig slurry spread at 19 kg total phosphorus (TP), 90 kg total nitrogen (TN), and 180 kg total carbon (TC) ha-1. The amendments examined were: (1) commercial grade liquid alum (8% Al2O3) applied at a rate of 0.88:1 [Al:TP] (2) commercial-grade liquid ferric chloride (38% FeCl3) applied at a rate of 0.89:1 [Fe:TP] and (3) commercial-grade liquid poly-aluminium chloride (PAC) (10% Al2O3) applied at a rate of 0.72:1 [Al:TP]. Columns filled with sieved soil were incubated for 8 mo at 10oC and were leached with 160 ml (19 mm) distilled water wk-1. All amendments reduced the Morgan’s phosphorus and water extractable P content of the soil to that of the soil-only treatment, indicating that they have the ability to reduce P loss in leachate following slurry application. There were no significant differences between treatments for nitrogen (N) or carbon (C) in leachate or soil, indicating no deleterious impact on reactive N emissions or soil C cycling. Chemical amendment posed no significant change to GHG emissions from pig slurry, and in the cases of alum and PAC, reduced cumulative N2O and CO2 losses. Chemical amendment of land applied pig slurry can reduce P in runoff without any negative impact on nutrient leaching and GHG emissions. Future work must be conducted to ascertain if more significant reductions in GHG emissions are possible with chemical amendments.
    • The Impact of Chemically Amended Pig Slurry on Surface Runoff, Leachate and Greenhouse Gasses

      O'Flynn, Cornelius J. (2013-05)
      In Ireland, the pig industry is concentrated in a small number of counties. Pig farms typically have a high stocking rate. Therefore, the disposal of slurry in a cost-effective and environmentally-responsible way is a serious issue for farmers. Slurry is commonly applied to land, but this may not be possible if the land is at, or approaching, phosphorus (P) saturation. As pig farmers dispose of slurry in the vicinity of their properties, most of the nearby land is at P saturation, so alternative treatment methods need to be utilised (e.g. constructed wetlands, anaerobic digestion, filtration) or the slurry needs to be transported to another location. These alternatives are not currently financially viable in Ireland. Existing legislation (S.I. 610 of 2010) and recent changes in the implementation of legislation governing the timing and quantities of slurry that may be applied to land, means that pig farmers will no longer be able to exceed the maximum legal application rate to land (from January 2017). European policy aiming to intensify pig production will only accentuate this problem. If pig farmers are forced, in exceptional circumstances, to land apply slurry to unsuitable land, surface and subsurface losses of nutrients and suspended solids (SS) may occur. This could be potentially problematic if the land is located in a critical source area (CSA), an area that is highly likely to pollute receiving waters. In these circumstances, a possible novel solution is to chemically amend the pig slurry prior to landspreading. This would mean that pig farmers may, in exceptional circumstances, utilise the land in the vicinity of their farms for landspreading, without releasing excessive nutrients and SS into receiving waters. However, knowledge gaps exist concerning the type of amendments to be used, the characteristics of the soil on which they can be most effectively used, and their impact on incidental (short-term) and chronic (long-term) losses of nutrients, SS and greenhouse gas (GHG) to surface and subsurface water and the atmosphere. Therefore, the aims of this project were to: (1) identify the most appropriate chemical amendments, and their addition rates, to reduce P losses in runoff from pig slurry based on effectiveness, cost and feasibility; (2) investigate the impacts of these chemical amendments on nutrient losses in leachate, soil properties and GHG emissions; and (3) identify suitable soil types on which to landspread chemically-amended pig slurry. Laboratory bench-scale experiments were designed to identify the amendments which had the potential to reduce P in overland runoff and to quantify the stoichiometric rates at which to add them to the slurry. Based on effectiveness, cost and feasibility, the amendments identified were alum, which reduced dissolved reactive phosphorus (DRP) in overlying water by 86%, poly-aluminium chloride (PAC) (73%) and ferric chloride (FeCl3) (71%). Following these bench-scale experiments, rainfall simulation experiments were conducted to quantify the impact of chemical amendments to slurry on surface runoff losses at various time intervals from the time of application. Poly-aluminium chloride performed best in these experiments. For the first time, the effect of these amendments on GHG emissions, soil properties and leachate was also examined. Chemical amendment did not adversely affect GHG emissions, soil properties or leachate from pig slurry, but FeCl3 increased nitrous oxide (N2O) and carbon dioxide (CO2) losses. Finally, a 3-mo incubation experiment was conducted using a range of soil types to examine the effect of amendments on the long-term plant availability of P in soil and P solubility. Alum reduced more water extractable P than PAC, but also resulted in less plant available P. Considering cost, surface runoff and subsurface leachate losses, GHG emissions and impacts on soil chemistry, PAC was found to be the most suitable amendment with which to chemically amend pig slurry. There is the potential, in combination with existing programmes of measures, to employ chemical amendment as a measure to mitigate the environmental impact arising from the landspreading of pig slurry. This should be conducted in targeted areas of the CSA and should take into account soil type and its chemical properties. Before implementation, these tests must first be validated in long-term testing at field-scale over a wide variety of soil types, and include repeated application and incorporation. At present, there is no provision in legislation for chemical amendments to be used as a mitigation measure in the land application of pig slurry, but if they are to be utilised, a regulatory framework will need to be introduced by the relevant bodies.
    • The Impact of Direct Payments on Farm Income Distribution.

      Frawley, J.P.; Keeney, M. (Teagasc, 2000-11-01)
      The switch in emphasis from market support systems in the 1992 CAP reform toward direct payments resulted in a dramatic increase in financial support terms, from £336.7 million in 1991 to £915.3 million in 1999 (current prices). The impact of this change in Irish agricultural policy was to increase substantially the dependency of farmers, with the exception of dairy farmers, on the ‘cheque in the post’ for a farm income. It is the impact of these changes on the distribution of farm income which is of concern in this study. In line with these policy changes the proportion of average family farm income derived from the market (as opposed to direct payments) decreased from 73.3 per cent in 1993 to 37.1 per cent in 1997. At the same time the corresponding proportions for direct payments increased from 26.7 per cent to 62.9 per cent. Analysis of the distribution of family farm income by deciles (based on FFI) and for all farms indicates a more equitable distribution of income between 1993 and 1997. This improvement in equity is attributed to the effects of direct payments on farm incomes. Analysis decomposing the individual effects of selected measures show that (i) the suckler cow premia, and (ii) the headage payments (Livestock headage payments in the Disadvantaged Areas) were the most effective measures in favouring income distribution equity. Cross compliance schemes (REPS and extensification) and the special beef premia had a more moderate effect in terms of equity while the arable aid payments contributed least to farm income equity. The market-derived income component had a high negative effect on equity of farm income distribution. The inclusion of a high proportion of dairy farmers among those with high farm incomes is a likely factor in this respect.
    • Impact of Environmental Factors on Bacteriocin Promoter Activity in Gut-Derived Lactobacillus salivarius

      Guinane, Caitriona M.; Piper, Clare; Draper, Lorraine A.; O'Connor, Paula M.; Hill, Colin; Ross, R. Paul; Cotter, Paul D. (American Society for Microbiology, 2015-09-04)
      Bacteriocin production is regarded as a desirable probiotic trait that aids in colonization and persistence in the gastrointestinal tract (GIT). Strains of Lactobacillus salivarius, a species associated with the GIT, are regarded as promising probiotic candidates and have a number of associated bacteriocins documented to date. These include multiple class IIb bacteriocins (salivaricin T, salivaricin P, and ABP-118) and the class IId bacteriocin bactofencin A, which show activity against medically important pathogens. However, the production of a bacteriocin in laboratory media does not ensure production under stressful environmental conditions, such as those encountered within the GIT. To allow this issue to be addressed, the promoter regions located upstream of the structural genes encoding the L. salivarius bacteriocins mentioned above were fused to a number of reporter proteins (green fluorescent protein [GFP], red fluorescent protein [RFP], and luciferase [Lux]). Of these, only transcriptional fusions to GFP generated signals of sufficient strength to enable the study of promoter activity in L. salivarius. While analysis of the class IIb bacteriocin promoter regions indicated relatively weak GFP expression, assessment of the promoter of the antistaphylococcal bacteriocin bactofencin A revealed a strong promoter that is most active in the absence of the antimicrobial peptide and is positively induced in the presence of mild environmental stresses, including simulated gastric fluid. Taken together, these data provide information on factors that influence bacteriocin production, which will assist in the development of strategies to optimize in vivo and in vitro production of these antimicrobials.
    • The impact of feed resource costs on the relative competitiveness of beef with other meats

      Dunne, William; Shanahan, Ultan; O’Connell, J.J. (Teagasc, 2008-11-01)
      These reforms represented a major turning point in fundamental structure of EU agricultural policy. This, at the time of implementation, created much uncertainty at both institutional and farm level in relation to future feed resource costs, cattle and beef prices and related market outlooks. However, as this report shows, the reality for Irish cattle farmers was rather different. As a result much of the research effort during the lifespan of the project was diverted to explaining the causes of the unforeseen outcomes together with the implications of policy decisions and related market developments.
    • The impact of grazing cattle on soil physical properties and nutrient concentrations in overland flow from pasture, Part B

      Kurz, Isabelle; O’Reilly, Conor; Tunney, Hubert; Bourke, David (Teagasc, 2007-06-01)
      The loss of nutrients from agricultural land to water bodies is a serious concern in many countries. To gain information on the contribution of grazing animals to diffuse nutrient losses from pasture areas to water, this study looked at the impact of cattle on nutrient concentrations in overland flow and on soil hydrology (bulk density, macroporosity and resistance to penetration). Rainfall simulations to produce overland flow were conducted and soil physical measurements were taken on experimental plots assigned to one of two treatments: 1) cattle had unrestricted access to the plot; 2) cattle could graze the plot but they could neither walk on the plot area nor deposit excrements on it. Areas to which the cattle had free access were characterised by 57%-83% lower macroporosity, by 8%-17% higher bulk density and by 27%-50% higher resistance to penetration than areas from which the cattle were excluded. The nutrients in overland flow from grassland that were affected by the presence of grazing animals were mainly the particulate nitrogen, the organic phosphorus and the potassium concentrations. Overall, the presence of cattle had a longer lasting effect on the soil hydrological parameters measured than on the nutrient concentrations in overland flow.
    • Impact of Livestock on Hill Environment

      Walsh, M. (Teagasc, 2002-01-01)
      The hill and mountain landscape of western Ireland is an area of high scenic value as well as contributing to the livelihood of local farmers mainly through extensive grazing. Measures that were intended to support lamb prices led to increased ewe numbers. Public concern attributed this increase to an apparent deterioration in the status of the semi-natural vegetation and to an increase in the rate of soil erosion. In the absence of an existing databank, Teagasc undertook a research programme to quantify the impact of hill sheep on the semi-natural vegetation, the progress of soil erosion and changes in certain weather elements e.g. ‘driving rain’. A detailed database of the physical background (physiography and soils) of the Teagasc hill sheep farm, Leenaun, was compiled on the basis of a grid, 100 m x 100 m. Changes in the frequency of vegetation on the unimproved hill were monitored, 1995-2002, by point quadrat. Ten permanent exclosures representing the main vegetation types and a controlled grazing experiment on the upper steep slope were established. Sequential aerial photography (1973/7-1996/8) for selected sites in western counties and wind and rain data (1957-2000) for five western synoptic stations were obtained. The classification of the peatland and heathland habitats was considered. Analysis of data highlighted a range of issues among which were the physical complexity and fragility of the landscape, the sustainability of the hill sheep system on the Teagasc hill sheep farm, the beneficial effects of controlled grazing, the progressive erosion of hill soils and an increase in high intensity levels of ‘driving rain’. The classification of the habitats, peatland and heathland, should encompass other forms of biodiversity as well as flora. The sustainable use of this landscape requires a deep knowledge of the of the grazing management system, which increasingly involves part-time farming, and its impact on the soils and semi-natural vegetation.