• Saturation Mutagenesis of Lysine 12 Leads to the Identification of Derivatives of Nisin A with Enhanced Antimicrobial Activity

      Molloy, Evelyn M.; Field, Des; O'Connor, Paula M.; Cotter, Paul D.; Hill, Colin; Ross, R Paul (PLOS, 2013-03-11)
      It is becoming increasingly apparent that innovations from the “golden age” of antibiotics are becoming ineffective, resulting in a pressing need for novel therapeutics. The bacteriocin family of antimicrobial peptides has attracted much attention in recent years as a source of potential alternatives. The most intensively studied bacteriocin is nisin, a broad spectrum lantibiotic that inhibits Gram-positive bacteria including important food pathogens and clinically relevant antibiotic resistant bacteria. Nisin is gene-encoded and, as such, is amenable to peptide bioengineering, facilitating the generation of novel derivatives that can be screened for desirable properties. It was to this end that we used a site-saturation mutagenesis approach to create a bank of producers of nisin A derivatives that differ with respect to the identity of residue 12 (normally lysine; K12). A number of these producers exhibited enhanced bioactivity and the nisin A K12A producer was deemed of greatest interest. Subsequent investigations with the purified antimicrobial highlighted the enhanced specific activity of this modified nisin against representative target strains from the genera Streptococcus, Bacillus, Lactococcus, Enterococcus and Staphylococcus.
    • Screening of Irish Fruit and Vegetable Germplasm for Novel Anti-tumour and Pesticidal Compounds

      Alqudah, J.M. I.; Reilly, Kim; Gaffney, Micheal T.; Martin-Diana, A. B.; Barry-Ryan, C. (Teagasc, 2012)
      Phytochemicals are a rich source of novel therapeutic and insecticidal agents (McLaughlin and Chang, 1999). Considerable research effort has been directed at screening exotic and medicinal plants in the search for novel products. However, plants which have traditional food uses have been little explored. In addition the range, type and level of individual bioactive compounds can vary significantly between different species, different cultivars of the same species and different tissue types of the plant (Reilly, in press) Therefore, the objective of this study was to screen a range of fruits and vegetables which can be grown in Ireland for novel bioactive compounds for use in food production and as bio-pesticides.
    • Seasonality and Costs of Production on Irish dairy farms from 1994-2008

      Smyth, Paul; Harte, Laurence; Henessy, Thia (Teagasc, Oak Park, Carlow, Ireland, 2010)
      Previous research has highlighted the economic advantages of spring calving in countries such as Ireland that have a long spring/summer grazing season. However, the widespread adoption of such a production system leads to a highly seasonal milk supply and a range of problems that are associated with seasonality. The objective of this paper is to use historical data to quantify the economic benefits of a spring calving system. Data from over 400 dairy farms in Ireland over a period of 15 years is examined. Fixed, random and between effects panel models are estimated to test the significance of calving season on production costs. The results show the effect of calving season is significant at lowering production costs. These models returned results suggesting that high compact early Spring herds have significantly lower costs than over seasons. However the fixed effect model demonstrates little difference between production costs in different seasons suggesting individual effects such as the ability of the farmer may play a role in reduction of costs. Herds that are calved over a shorter period tend to have lower production costs.
    • Seasonality of nitrogen uptake, apparent recovery of fertilizer nitrogen and background nitrogen supply in two Irish grassland soils

      Murphy, P. N. C.; O'Connell, K.; Watson, S.; Watson, C. J.; Humphreys, James (Teagasc (Agriculture and Food Development Authority), Ireland, 2013)
      Improving fertilizer nitrogen (N) use efficiency is central to sustainable and profitable grassland agriculture. A plot experiment with a control and fertilizer N (calcium ammonium nitrate, 25–50 kg/ha N) applied on nine occasions from February to September 2002 was conducted at two sites in southwest Ireland to assess N uptake and apparent recovery of fertilizer N (ARFN). Apparent recovery of fertilizer N after eight weeks varied from low in February (21%) and March (46%) to high from April to August (69–98%), indicating that high N use efficiency can be achieved in Irish grasslands at these times. Low recovery in spring suggested that N was applied in excess of immediate crop requirements. Note that N uptake and ARFN values from this study are likely to be somewhat conservative, particularly for spring applications. Over the 8 weeks during which growth was monitored, most (70%) of the grass yield and N uptake response to fertilizer N were in weeks 1 to 4 after application; however, a significant (30%) response occurred in weeks 5–8. This suggested that residual N availability following grazing at 4 weeks can be significant and that there may be scope to decrease N application rates in a grazing rotation. This can potentially improve N use efficiency and decrease N surpluses, with associated economic and environmental benefits. Apparent recovery of fertilizer N was closely related to soil temperature, with a 5.8% increase in ARFN with a 1 °C increase in temperature. Background (non-fertilizer) N supply contributed an average of 164 kg/ha per year (49%) taken up by the fertilized sward, highlighting the potential importance of soil N mineralisation to grassland productivity. Note that these results are for one year at two sites and that conditions may vary between years and at other sites and also that the experiment did not reproduce the cumulative effect of repeated fertilizer application over the grazing year.
    • Second generation GM foods: perspectives on likely future acceptance by Irish consumers

      O'Connor, Elaine; Cowan, Cathal; Williams, Gwilym; O'Connell, John; Boland, Maurice; Downey, Gerard (Teagasc, 2005-07)
      Two hypothetical second-generation genetically-modified (GM) products, a yogurt and a dairy spread, were evaluated by consumers. Second-generation GM food products offer specific consumer benefits - in the case of this study, health benefits.
    • Second Generation GM Foods: Perspectives on Likely Future Acceptance by Irish Consumers

      O'Connor, Elaine; Cowan, Cathal; Williams, Gwilym; O'Connell, John; Boland, Maurice; Downey, Gerard (Teagasc, 2005-07-01)
      Two hypothetical second-generation genetically-modified (GM) products, a yogurt and a dairy spread, were evaluated by consumers. Second-generation GM food products offer specific consumer benefits - in the case of this study, health benefits.
    • Selection of calibration sub-sets to predict ryegrass quality using principle component analysis for near infrared spectroscopy

      Burns, G. A.; O'Kiely, Padraig; Gilliland, T. J. (British Grassland Society, 2015-09)
      Near infrared reflectance spectroscopy (NIRS) has become the routine method of assessing forage quality on grass evaluation and breeding programmes. NIRS requires predictive calibration models that relate spectral data to reference values developed using a calibration set (Burns et al. 2013). The samples that form the calibration set influence the accuracy and reliability of these models and need to be representative of samples that will likely be analysed (Shenk and Westerhaus, 1991; Burns et al. 2014). Analysing samples from the calibration set using reference techniques has a significant cost and time associated and needs to be considered in the context of the desired accuracy and robustness of calibration models. Calibration selection techniques can therefore maximise the accuracy and robustness of calibration models whilst reducing the number of samples requiring reference analysis. One such method is principal component analysis (PCA; Shenk and Westerhaus, 1991) whereby Shetty et al. (2012) reported that the number of samples could be reduced by up to 80% with a minimal loss in accuracy of calibration model. PCA selects representative calibration sub-sets through plotting all the samples in hyper-dimensional space, based on spectral data, and a sample is selected to represent a local neighbourhood cluster of samples for reference analysis. The aim of this research was to assess the accuracy of NIRS calibration models for buffering capacity, in vitro dry matter digestibility (DMD) and water soluble carbohydrate (WSC) content developed using calibration sub-sets selected by PCA.
    • Selective enrichment of dairy phospholipids in a buttermilk substrate through investigation of enzymatic hydrolysis of milk proteins in conjunction with ultrafiltration

      Barry, Kate M.; Dinan, Timothy G.; Kelly, Philip M. (Elsevier, 2017-02-04)
      Extensive enzymatic hydrolysis of milk proteins in reconstituted buttermilk powder was combined with ultrafiltration to generate a phospholipid (PL) enriched fraction with maximum permeation of hydrolysed peptides. Buttermilk, naturally high in PLs, is the ideal substrate for enrichment of these bio- and techno-functionally active compounds. A 7.8 fold increase in PL was achieved in the 50 kDa retentate; 6.16 ± 0.02% total PL compared with 0.79 ± 0.01% in the starting substrate, an increase considerably greater than previously reported. Total lipid content (% dry matter) increased 6.3 fold in the retentate, 43.43 ± 0.61%, from the starting substrate, 6.84 ± 0.17%. This combined strategic approach enabled maximum enrichment of PLs with no transmission of lipid material into the permeate, 0.09 ± 0.02% total lipid, and non-detectable levels of PLs recovered in the permeate, 0.00 ± 0.01% total PL.
    • Semi-supervised linear discriminant analysis

      Toher, Deirdre; Downey, Gerard; Murphy, Thomas Brendan (Wiley, 2012-07-02)
      Fisher's linear discriminant analysis is one of the most commonly used and studied classification methods in chemometrics. The method finds a projection of multivariate data into a lower dimensional space so that the groups in the data are well separated. The resulting projected values are subsequently used to classify unlabeled observations into the groups. A semi-supervised version of Fisher's linear discriminant analysis is developed, so that the unlabeled observations are also used in the model fitting procedure. This approach is advantageous when few labeled and many unlabeled observations are available. The semi-supervised linear discriminant analysis method is demonstrated on a number of data sets where it is shown to yield better separation of the groups and improved classification over Fisher's linear discriminant analysis.
    • Sequencing-Based Analysis of the Bacterial and Fungal Composition of Kefir Grains and Milks from Multiple Sources

      Marsh, Alan J.; O'Sullivan, Orla; Hill, Colin; Ross, R Paul; Cotter, Paul D. (PLOS, 2013-07-19)
      Kefir is a fermented milk-based beverage to which a number of health-promoting properties have been attributed. The microbes responsible for the fermentation of milk to produce kefir consist of a complex association of bacteria and yeasts, bound within a polysaccharide matrix, known as the kefir grain. The consistency of this microbial population, and that present in the resultant beverage, has been the subject of a number of previous, almost exclusively culture-based, studies which have indicated differences depending on geographical location and culture conditions. However, culture-based identification studies are limited by virtue of only detecting species with the ability to grow on the specific medium used and thus culture-independent, molecular-based techniques offer the potential for a more comprehensive analysis of such communities. Here we describe a detailed investigation of the microbial population, both bacterial and fungal, of kefir, using high-throughput sequencing to analyse 25 kefir milks and associated grains sourced from 8 geographically distinct regions. This is the first occasion that this technology has been employed to investigate the fungal component of these populations or to reveal the microbial composition of such an extensive number of kefir grains or milks. As a result several genera and species not previously identified in kefir were revealed. Our analysis shows that the bacterial populations in kefir are dominated by 2 phyla, the Firmicutes and the Proteobacteria. It was also established that the fungal populations of kefir were dominated by the genera Kazachstania, Kluyveromyces and Naumovozyma, but that a variable sub-dominant population also exists.
    • Short Communication: The effect of dry period duration and dietary energy density on the rennet gelation properties of milk in early lactation

      Butler, Stephen T.; de Feu, M.A.; O'Brien, Bernadette; Guinee, Timothy P.; Murphy, J.J. (American Dairy Science Association and Elsevier Inc., 2010-02)
      This study was carried out to examine the effects of decreasing dry period duration (DP) and altering the energy density of the diet during early lactation on the rheological characteristics of milk. Forty mature Holstein-Friesian cows were used in a completely randomized design with a 2 × 2 factorial arrangement of treatments. Cows were randomly assigned to one of two dry period treatments and one of two nutritional treatments. The dry period treatments were continuous milking (CM) or an 8-week standard dry period (SDP), and the nutritional treatments were a standard energy diet (SE) or a high energy diet (HE). Actual dry period lengths were 6.3 ± 1.7 days and 62.1 ± 1.9 days for cows for the CM and SDP treatments, respectively. Milk samples were collected at 2, 6 and 10 weeks postpartum. The concentration of fat, protein and lactose was determined in each sample. The rennet gelation properties were measured at 31 ° C using dynamic low-amplitude strain oscillatory rheometry. The following parameters were obtained from the resultant elastic shear modulus (G′): gelation time (GT), maximum curd firming rate (CFRmax) and gel strength (GS). Reducing dry period duration from 62 to 6 days resulted in increases in milk protein concentration (31.8 vs. 34.7 g/kg; P < 0.001), CFRmax (2.58 vs. 3.60 Pa/min; P < 0.001) and GS (69.4 vs. 90.5 Pa; P = 0.003). Raising the dietary energy density decreased percentage milk fat (43.1 vs. 37.7 g/kg; P < 0.001) but otherwise had no effect. GS was correlated with CFRmax (r = 0.98; P < 0.001), and both variables were correlated with milk protein concentration (r = 0.71; P < 0.001, and r = 0.73; P < 0.001, respectively). The results indicate that decreasing the duration of DP increased milk protein concentration and improved the rennet gelation properties of milk, but that dietary energy density had little effect.
    • The short-term effects of management changes on watertable position and nutrients in shallow groundwater in a harvested peatland forest

      Finnegan, Joanne; Regan, J. T.; Fenton, Owen; Lanigan, Gary; Brennan, R. B.; Healy, Mark G. (Elsevier, 2014-05-08)
      Management changes such as drainage, fertilisation, afforestation and harvesting (clearfelling) of forested peatlands influence watertable (WT) position and groundwater concentrations of nutrients. This study investigated the impact of clearfelling of a peatland forest on WT and nutrient concentrations. Three areas were examined: (1) a regenerated riparian peatland buffer (RB) clearfelled four years prior to the present study (2) a recently clearfelled coniferous forest (CF) and (3) a standing, mature coniferous forest (SF), on which no harvesting took place. The WT remained consistently below 0.3 m during the pre-clearfelling period. Results showed there was an almost immediate rise in the WT after clearfelling and a rise to 0.15 m below ground level (bgl) within 10 months of clearfelling. Clearfelling of the forest increased dissolved reactive phosphorus concentrations (from an average of 28–230 μg L−1) in the shallow groundwater, likely caused by leaching from degrading brash mats.
    • Shortening the interval to resumption of ovarian cycles in postpartum beef cows.

      Diskin, Michael G.; Mackey, D.R.; Stagg, K.; Roche, J.F.; Sreenan, J.M. (Teagasc, 2001-02-01)
      • In beef cows the interval from calving to first ovulation, or postpartum interval, is affected by nutrition and by the suckling effect of the calf. • The suckling effect is the biggest determinant of this interval, comprising: (i) physical contact and (ii) maternal bonding between cow and calf. Restricted suckling and calf isolation induce a rapid resumption of oestrous cycles. • Prepartum nutrition is the next most important determinant of the postpartum interval. Cows that calve in poor body condition have a longer interval than cows that calve in good body condition. • Increasing the level of nutrition in the postpartum period has only a limited effect in shortening the postpartum interval. • In most cows the first postpartum ovulation is silent and is succeeded by a short oestrous cycle of approximately 8-10 days. The first observed oestrus occurs prior to the second ovulation. • When used in combination with calf isolation and restricted suckling, progesterone pre-treatment for 6 days induces oestrus in the majority of cows and eliminates the short oestrous cycle. • The prolonged postpartum interval in beef cows is not due to failure of ovarian follicle development but to failure of successive dominant follicles to ovulate due to the inadequate frequency of LH pulses.
    • The Significance of Heavy Metal and Organic Micropollutants in Soils.

      McGrath, D.; McCormack, R.J. (Teagasc, 1999-11-01)
      The southeastern region of Ireland, representing 22% of the land area of the country, has been systematically sampled. Soils have been analysed for a range of heavy metals and persistent organics. These soils have now been archived and are available for future analyses as required. Analyses conducted to date, the results of which are discussed here, are for soil parameters pH and organic matter, for major components, aluminum, iron, and manganese, for trace elements (heavy metals) arsenic, cadmium, chromium, cobalt, copper, lead, mercury, nickel, selenium and zinc and for organics, hexachlorobenzene, hexachloro-cyclohexanes, and for DDT and its metabolites. Other organics, polychlorinated biphenyls and polycyclic aromatic hydrocarbons, were examined in a proportion of soils. Results have been statistically analysed and frequency distributions have been calculated. Geographic distributions have also been plotted and localized concentrations have been found for most elements. Geochemical factors are considered to be largely responsible for most of these localized concentrations. Aerial deposition of lead and selenium was also indicated. Historic usage of DDT and g - HCH was detected in soils with different land uses. Overall, little serious contamination of soils, especially that caused by man, by toxic elements was evident. However, as many as 21% of soils breached the provisions of the EU Sewage Sludge Directive for heavy metals in soil.
    • Significance of Lactobacilli in Cheddar Cheese

      Cogan, Tim; Beresford, Tom; Drinan, Finbarr; Palles, Tony; Fitzsimons, Nora (Teagasc, 1998-09-01)
      The objectives of this project were to isolate and identify the non-starter lactobacilli in mature Cheddar cheese, identify strains which impart mature flavours to cheese and determine their role in developing cheese flavour. The main conclusions were as follows: Based on an analysis of 18 mature Cheddar cheeses, selected from 7 commercial manufacturers, non-starter lactic acid bacteria typically numbered, as expected, 106-108 per gram and were dominated (97 percent) by Lactobacillus paracasei. Although a small number of strains (typically 1 to 4) was found in each cheese there was considerable strain diversity in cheeses within as well as between manufacturing plants. When selected strains were investigated for survival and flavour enhancement when added (as starter adjuncts) with the normal starter cultures in Cheddar cheese manufacture, it was found that they remained dominant for up to 3 months of ripening. Commercial grading of these cheeses at 3 and 6 months confirmed that the added strains did modify flavour development and one (DPC 4103), in particular, had a beneficial effect. It was confirmed that two selected strains of non-starter lactobacilli were capable of metabolising citrate under the conditions of Cheddar cheese ripening and, consequently, if present in sufficient numbers, would influence flavour development. The work was greatly facilitated by the successful and novel adaptation of a modern rapid molecular technique (RAPD) for species and strain classification. In summary these studies found that one species of lactobacilli (Lb. paracasei) was the dominant non-starter lactic acid bacteria in mature Cheddar cheese. Although a wide variety of strains were identified, only a few were found in any particular cheese, suggesting their likely role in cheese flavour diversity even within the same manufacturing plant. This suggests the potential for flavour control or enhancement through the selective and controlled use of non-starter lactic acid bacteria. Preliminary investigations of the metabolism of those organisms supports this view and a follow-up study now in progress should provide greater clarity on this matter.
    • The significance of livestock as a contributor to global greenhouse gas emissions today and in the near future

      O'Mara, Frank P. (Elsevier Inc., 2011-06-23)
      Animal agriculture is responsible for 8–10.8% of global greenhouse gas (GHG) emissions as assessed by IPCC accounting and, on the basis of lifecycle analysis, the contribution of livestock is up to 18% of global emissions. Asia is the source of the most enteric CH4 emissions with Latin America, Africa, Western Europe and North America being significant sources. These emissions are dominated by emissions from cattle. When GHG emissions are related to food production, the four most efficient regions are Eastern and Western Europe, North America, and the non-EU former Soviet Union which produced 46.3% of ruminant meat and milk energy and only 25.5% of enteric CH4 emissions in 2005. In comparison, the three least efficient producers (Asia, Africa, Latin America) produced an equivalent amount (47.1%) of ruminant meat and milk energy, and almost 69% of enteric CH4 emissions in 2005. Livestock related emissions will increase as world population and food demand increases; enteric CH4 emissions are projected to grow by over 30% from 2000 to 2020. There are mitigations available now, but it is imperative to develop new mitigations and ways to implement existing technologies more cost effectively.
    • Silvicultural Guidelines for the Tending and Thinning of Broadleaves

      Short, Ian; Radford, Toddy (Teagasc, Oak Park, Carlow, Ireland & Coford, Ireland, 2008-12)
      This publication provides guidelines for the tending and thinning of ash, alder, sycamore, Norway maple, oak and beech. Some silvicultural procedures to follow during these operations are also provided.
    • A Simple Method for the Purification of Nisin

      Gough, Ronan; Gomez-Sala, Beatriz; O'Connor, Paula M.; Rea, Mary C.; Miao, Song; Hill, Colin; Brodkorb, Andre (Springer, 2017-05-29)
      Nisin, an antimicrobial peptide showing activity against a broad range of Gram-positive bacteria, is widely used as a food preservative and has potential as a therapeutic for a range of infectious diseases. Here, we present a simple purification method, based on a salting-out approach, which can produce a powder containing ∼33% nisin, from a nisin-producing culture in a whey permeate-based medium. This process removes over 99% of the lactic acid, NaCl, lactose and non-nisin proteins from the cell-free culture supernatant. The approach can also enrich a commonly used commercial nisin preparation over 30-fold to a purity of ∼58%. These are higher purities than comparable published methods. The simplicity of this approach facilitates its use in research and also its scale-up.
    • Simulated gastrointestinal digestion of nisin and interaction between nisin and bile

      Gough, Ronan; O'Connor, Paula M.; Rea, Mary C.; Gomez-Sal, Beatriz; Miao, Song; Hill, Colin; Brodkorb, Andre (Elsevier, 2017-08-14)
      Nisin, an antimicrobial peptide showing activity against many Gram positive bacteria, is widely used as a food preservative. The simulated gastrointestinal digestion of nisin (variant A) was studied using the in vitro INFOGEST digestion method. Following oral, gastric and small intestinal digestion, there was no intact nisin in the system and the nisin was primarily digested by pancreatin. After digestion, six nisin fragments (1–11, 1–12, 1–20, 1–21, 1–29 and 1–32) were identified by reversed phase high performance liquid chromatography and mass spectroscopy and four of these nisin fragments (1–20, 1–21, 1–29 and 1–32) demonstrated low antibacterial activity against Lactococcus lactis HP in agar diffusion activity assays. Additionally, it was observed that bile salts form a complex with nisin. This was examined by atomic force microscopy, turbidity and dynamic light scattering, which showed that this interaction resulted in significantly larger bile salt micelles. The presence of bile salts at physiological levels significantly altered the relative amounts of the nisin fragments 1–12, 1–20 and 1–29 produced during an in vitro digestion. This study highlights the importance of including bile in simulated digestions of antimicrobial peptides in order to obtain a more accurate simulation of the in vivo digestion products and their activity.
    • Single nucleotide polymorphisms at the imprinted bovine insulin-like growth factor 2 (IGF2) locus are associated with dairy performance in Irish Holstein-Friesian cattle

      Berkowicz, Erik W; Magee, David A; Sikora, Klaudia M.; Berry, Donagh P.; Howard, Dawn J.; Mullen, Michael Paul; Evans, Ross D.; Spillane, Charles; MacHugh, David E (Cambridge University Press: Published for the Institute of Food Research and the Hannah Research Institute, 2010-09)
      The imprinted insulin-like growth factor 2 gene (IGF2) encodes a fetal mitogenic hormone protein (IGF-II) and has previously been shown to be associated with performance in dairy cattle. In this study we assessed genotype-phenotype associations between four single nucleotide polymorphisms (SNPs) located within the bovine IGF2 locus on chromosome 29 and a range of performance traits related to milk production, animal growth and body size, fertility and progeny survival in 848 progeny-tested Irish Holstein-Friesian sires. Two of the four SNPs (rs42196909 and IGF2.g-3815A>G), which were in strong linkage disequilibrium (r 2=0.995), were associated with milk yield (Pf0.01) and milk protein yield (Pf0.05); the rs42196901 SNP was also associated (Pf0.05) with milk fat yield. Associations (Pf0.05) with milk fat percentage and milk protein percentage were observed at the rs42196901 and IGF2.g-3815A>G SNPs, respectively. The rs42196909 and IGF2.g-3815A>G SNPs were also associated with progeny carcass conformation (Pf0.05), while an association (Pf0.01) with progeny carcass weight was observed at the rs42194733 SNP locus. None of the four SNPs were associated with body size, fertility and progeny survival. These findings support previous work which suggests that the IGF2 locus is an important biological regulator of milk production in dairy cattle and add to an accumulating body of research showing that imprinted genes influence many complex performance traits in cattle.