• A temporal assessment of nematode community structure and diversity in the rhizosphere of cisgenic Phytophthora infestans-resistant potatoes

      Ortiz, Vilma; Phelan, Sinead; Mullins, Ewen; European Union; KBBE.2011.3.5-01 (Biomed Central, 01/12/2016)
      Background Nematodes play a key role in soil processes with alterations in the nematode community structure having the potential to considerably influence ecosystem functioning. As a result fluctuations in nematode diversity and/or community structure can be gauged as a ‘barometer’ of a soil’s functional biodiversity. However, a deficit exists in regards to baseline knowledge and on the impact of specific GM crops on soil nematode populations and in particular in regard to the impact of GM potatoes on the diversity of nematode populations in the rhizosphere. The goal of this project was to begin to address this knowledge gap in regards to a GM potato line, cisgenically engineered for resistance to Phytophthora infestans (responsible organism of the Irish potato famine causing late blight disease). For this, a 3 year (2013, 2014, 2015) field experimental study was completed, containing two conventional genotypes (cvs. Desiree and Sarpo Mira) and a cisgenic genotype (cv. Desiree + Rpi-vnt1). Each potato genotype was treated with different disease management strategies (weekly chemical applications and corresponding no spray control). Hence affording the opportunity to investigate the temporal impact of potato genotype, disease management strategy (and their interaction) on the potato rhizosphere nematode community. Results Nematode structure and diversity were measured through established indices, accounts and taxonomy with factors recording a significant effect limited to the climatic conditions across the three seasons of the study and chemical applications associated with the selected disease management strategy. Based on the metrics studied, the cultivation of the cisgenic potato genotype exerted no significant effect (P > 0.05) on nematode community diversity or structure. The disease management treatments led to a reduction of specific trophic groups (e.g. Predacious c–p = 4), which of interest appeared to be counteracted by a potato genotype with vigorous growth phenotype e.g. cv. Sarpo Mira. The fluctuating climates led to disparate conditions, with enrichment conditions (bacterial feeding c–p = 1) dominating during the wet seasons of 2014 and 2015 versus the dry season of 2013 which induced an environmental stress (functional guild c–p = 2) on nematode communities. Conclusions Overall the functional guild indices in comparison to other indices or absolutes values, delivered the most accurate quantitative measurement with which to determine the occurrence of a specific disturbance relative to the cultivation of the studied cisgenic P. infestans-resistant potatoes.
    • Quantitative trait loci associated with different polar metabolites in perennial ryegrass - providing scope for breeding towards increasing certain polar metabolites

      Foito, Alexandre; Hackett, Christine A; Stewart, Derek; Velmurugan, Janaki; Milbourne, Dan; Byrne, Stephen L; Barth, Susanne; Department of Agriculture, Food and the Marine; RSF 06–346 (Biomed Central, 10/10/2017)
      Background Recent advances in the mapping of biochemical traits have been reported in Lolium perenne. Although the mapped traits, including individual sugars and fatty acids, contribute greatly towards ruminant productivity, organic acids and amino acids have been largely understudied despite their influence on the ruminal microbiome. Results In this study, we used a targeted gas-chromatography mass spectrometry (GC-MS) approach to profile the levels of 25 polar metabolites from different classes (sugars, amino acids, phenolic acids, organic acids and other nitrogen-containing compounds) present in a L. perenne F2 population consisting of 325 individuals. A quantitative trait (QTL) mapping approach was applied and successfully identified QTLs regulating seven of those polar metabolites (L-serine, L-leucine, glucose, fructose, myo-inositol, citric acid and 2, 3-hydroxypropanoic acid).Two QTL mapping approaches were carried out using SNP markers on about half of the population only and an imputation approach using SNP and DArT markers on the entire population. The imputation approach confirmed the four QTLs found in the SNP-only analysis and identified a further seven QTLs. Conclusions These results highlight the potential of utilising molecular assisted breeding in perennial ryegrass to modulate a range of biochemical quality traits with downstream effects in livestock productivity and ruminal digestion.
    • A hybrid next generation transcript sequencing-based approach to identify allelic and homeolog-specific single nucleotide polymorphisms in allotetraploid white clover

      Nagy, Istvan; Barth, Susanne; Mehenni-Ciz, Jeanne; Abberton, Michael T; Milbourne, Dan; Department of Agriculture, Food and the Marine; RSF 07–566 (Biomed Central, 13/02/2013)
      Background: White clover (Trifolium repens L.) is an allotetraploid species possessing two highly collinear ancestral sub-genomes. The apparent existence of highly similar homeolog copies for the majority of genes in white clover is problematic for the development of genome-based resources in the species. This is especially true for the development of genetic markers based on single nucleotide polymorphisms (SNPs), since it is difficult to distinguish between homeolog-specific and allelic variants. Robust methods for categorising single nucleotide variants as allelic or homeolog-specific in large transcript datasets are required. We illustrate one potential approach in this study. Results: We used 454-pyrosequencing sequencing to generate ~760,000 transcript sequences from an 8th generation white clover inbred line. These were assembled and partially annotated to yield a reference transcript set comprising 71,545 sequences. We subsequently performed Illumina sequencing on three further white clover samples, generating 14 million transcript reads from a mixed sample comprising 24 divergent white clover genotypes, and 50 million reads on two further eighth generation white clover inbred lines. Mapping these reads to the reference transcript set allowed us to develop a significant SNP resource for white clover, and to partition the SNPs from the inbred lines into categories reflecting allelic or homeolog-specific variation. The potential for using haplotype reconstruction and progenitor genome comparison to assign haplotypes to specific ancestral sub-genomes of white clover is demonstrated for sequences corresponding to genes encoding dehydration responsive element binding protein and acyl-coA oxidase. Conclusions: In total, 208,854 independent SNPs in 31,715 reference sequences were discovered, approximately three quarters of which were categorised as representing allelic or homeolog-specific variation using two inbred lines. This represents a significant resource for white clover genomics and genetics studies. We discuss the potential to extend the analysis to identify a “core set” of ancestrally derived homeolog specific variants in white clover.
    • Exploiting the inter-strain divergence of Fusarium oxysporum for microbial bioprocessing of lignocellulose to bioethanol

      Ali, Shahin S; Khan, Mojibur; Fagan, Brian; Mullins, Ewen; Doohan, Fiona M (Biomed Central, 15/03/2012)
      Microbial bioprocessing of lignocellulose to bioethanol still poses challenges in terms of substrate catabolism. A targeted evolution-based study was undertaken to determine if inter-strain microbial variability could be exploited for bioprocessing of lignocellulose to bioethanol. The microorganism studied was Fusarium oxysporum because of its capacity to both saccharify and ferment lignocellulose. Strains of F. oxysporum were isolated and assessed for their genetic variability. Using optimised solid-state straw culture conditions, experiments were conducted that compared fungal strains in terms of their growth, enzyme activities (cellulases, xylanase and alcohol dehydrogenase) and yield of bioethanol and the undesirable by-products acetic acid and xylitol. Significant inter-strain divergence was recorded in regards to the capacity of studied F. oxysporum strains to produce alcohol from untreated straw. No correlation was observed between bioethanol synthesis and either the biomass production or microbial enzyme activity. A strong correlation was observed between both acetic acid and xylitol production and bioethanol yield. The level of diversity recorded in the alcohol production capacity among closely-related microorganism means that a targeted screening of populations of selected microbial species could greatly improve bioprocessing yields, in terms of providing both new host strains and candidate genes for the bioethanol industry.
    • Markers associated with heading and aftermath heading in perennial ryegrass full-sib families

      Arojju, Sai K; Barth, Susanne; Milbourne, Dan; Conaghan, Patrick; Velmurugan, Janaki; Hodkinson, Trevor R; Byrne, Stephen L; Department of Agriculture, Food and the Marine; Teagasc Walsh Fellowship Programme; EU Marie-Sklodowska-Curie Fellowship; RSF 14/S/819; H2020-MSCA-IF: 658031 (Biomed Central, 16/07/2016)
      Background Heading and aftermath heading are important traits in perennial ryegrass because they impact forage quality. So far, genome-wide association analyses in this major forage species have only identified a small number of genetic variants associated with heading date that overall explained little of the variation. Some possible reasons include rare alleles with large phenotypic affects, allelic heterogeneity, or insufficient marker density. We established a genome-wide association panel with multiple genotypes from multiple full-sib families. This ensured alleles were present at the frequency needed to have sufficient statistical power to identify associations. We genotyped the panel via partial genome sequencing and performed genome-wide association analyses with multi-year phenotype data collected for heading date, and aftermath heading. Results Genome wide association using a mixed linear model failed to identify any variants significantly associated with heading date or aftermath heading. Our failure to identify associations for these traits is likely due to the extremely low linkage disequilibrium we observed in this population. However, using single marker analysis within each full-sib family we could identify markers and genomic regions associated with heading and aftermath heading. Using the ryegrass genome we identified putative orthologs of key heading genes, some of which were located in regions of marker-trait associations. Conclusion Given the very low levels of LD, genome wide association studies in perennial ryegrass populations are going to require very high SNP densities. Single marker analysis within full-sibs enabled us to identify significant marker-trait associations. One of these markers anchored proximal to a putative ortholog of TFL1, homologues of which have been shown to play a key role in continuous heading of some members of the rose family, Rosaceae.
    • EST-derived SSR markers used as anchor loci for the construction of a consensus linkage map in ryegrass (Lolium spp.)

      Studer, Bruno; Kolliker, Roland; Muylle, Hilde; Asp, Torben; Frei, Ursula; Roldan-Ruiz, Isabel; Barre, Philippe; Tomaszewski, Celine; Meally, Helena; Barth, Susanne; Skot, Leif; Armstead, Ian P; Dolstra, Oene; Lubberstedt, Thomas (Biomed Central, 16/08/2010)
      Background: Genetic markers and linkage mapping are basic prerequisites for marker-assisted selection and map-based cloning. In the case of the key grassland species Lolium spp., numerous mapping populations have been developed and characterised for various traits. Although some genetic linkage maps of these populations have been aligned with each other using publicly available DNA markers, the number of common markers among genetic maps is still low, limiting the ability to compare candidate gene and QTL locations across germplasm. Results: A set of 204 expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers has been assigned to map positions using eight different ryegrass mapping populations. Marker properties of a subset of 64 EST-SSRs were assessed in six to eight individuals of each mapping population and revealed 83% of the markers to be polymorphic in at least one population and an average number of alleles of 4.88. EST-SSR markers polymorphic in multiple populations served as anchor markers and allowed the construction of the first comprehensive consensus map for ryegrass. The integrated map was complemented with 97 SSRs from previously published linkage maps and finally contained 284 EST-derived and genomic SSR markers. The total map length was 742 centiMorgan (cM), ranging for individual chromosomes from 70 cM of linkage group (LG) 6 to 171 cM of LG 2. Conclusions: The consensus linkage map for ryegrass based on eight mapping populations and constructed using a large set of publicly available Lolium EST-SSRs mapped for the first time together with previously mapped SSR markers will allow for consolidating existing mapping and QTL information in ryegrass. Map and markers presented here will prove to be an asset in the development for both molecular breeding of ryegrass as well as comparative genetics and genomics within grass species.
    • Effects of Different Rearing Methods on Health Status, Immunity and Performance of Artificially Reared Calves

      Earley, Bernadette (Biomed Central, 2003-03-31)
      Morbidity and mortality of the young calf represent a major cause of economic concern for producers [1]. The objective of the study was to evaluate the performance and immune status of calves reared in the presence or absence of quartz linear heating lamps (CD 3000) and fed calf milk replacer either by bucket or by teat. Mart-purchased Holstein/Friesian calves were approximately 21 days of age at arrival at the research centre. The calves were allocated randomly to one of the following four treatments (n = 16 calves per treatment) using a 2 × 2 factorial design; 1). Teat fed + quartz linear lamp (QLL) (2). Bucket fed + QLL; 3). Teat fed + no QLL and 4). Bucket fed + no QLL. For the 42-day experimental period, 8 groups of 8 calves were penned (2.4 × 10.0 m) on straw in a naturally ventilated Monopitch calf house. A quartz linear heating lamp (3 k output) was positioned in the centre of the individual sheds, 10 feet above the floor of the straw bedded pens for these on QLL treatments, and remained switched on for the duration of the study. The calves received an individual allowance of 25 kg of milk replacer powder offered warm (38°C) by bucket and had ad libitum access to a concentrate ration. Individual disease episodes were determined by the requirement to treat with antibiotics for either enteric disease or respiratory disease. Serum immunoglobulins (IgG1) were measured quantitatively by single radial immunodiffusion standard and calculated via an internal Ig standard (100 mg/L) on days 1, 14 and 28 of the study. Haematological parameters were measured on days 1, 14 and 42 of the study and included red blood cell number, haemoglobin, packed cell volume, mean cell volume and total white cell counts. The data were analysed using a model appropriate to factorial design, with terms for QLL and teat in the main plot. The average temperature and relative humidity of the shed compartments with and without the QLL heating lamps were recorded continuously and were 11.3°C and 81% and 10.5°C and 86%, respectively. There was no significant difference (P > 0.05) between treatments with respect to liveweight gain from day of arrival (day 1) to day 42 of the study. There was no significant interaction between QLL, no QLL, teat fed and bucket fed treatments with respect to serum IgG1 concentrations and haematological parameters throughout the study period (P > 0.05). The incidence of respiratory disease and enteric disease was similar across the treatment groups (P > 0.05). It is concluded that the rearing of calves indoors, in the presence of quartz linear heating lamps, and either fed calf milk replacer by teat or bucket had no beneficial effect on calf health and performance when compared with calves reared in a natural ventilated environment.
    • Temporal trends in reproductive performance in Irish dairy herds and associated risk factors

      Mee, John F (Biomed Central, 2004-03-01)
      Irish dairy herd fertility has been declining since the 1980s. The extent, nature and causes of this decline in fertility and the current status of Irish dairy herd fertility were described. An increase in calving interval of approximately one day per year has been recorded. The principal components of this trend have been an increased incidence of postpartum endocrinopathies, reduced expression of oestrus and a fall in conception rate. Both submission rate and calving-to-service interval have increased slightly over time. Significant risk factors associated with these trends have been strain substitution within the Holstein-Friesian breed and single trait selection for milk production. Critically, these changes have been reflected in loss of body condition. Contributory factors included increased herd size and possibly increased use of DIYAI. The most recent Irish study showed that 48% of cows conceived to first service and 14% of cows were not pregnant at the end of the industry-average 15-week spring breeding season. However, the top quartile of herds achieved a first-service conception rate of 59%, illustrating the wide variation between herds. These phenotypic trends were attributed to both genetic and environmental factors and their interactions. Recent Irish dairy herd fertility performance falls short of the targets set for seasonal compact calving.
    • Prevalence of antibodies to Leptospira interrogans serovar hardjo in bulk tank milk from unvaccinated irish dairy herds

      Leonard, Nola; Mee, John F; Snijders, Sylvia; Mackie, Dermot (Biomed Central, 2004-04-01)
      Bulk tank milk samples, collected from 347 herds throughout the Republic of Ireland using a sampling frame based on seven milk-recording organisations, were tested by ELISA for antibodies to Leptospira interrogans serovar hardjo. These herds, which had not been vaccinated against leptospirosis within the previous five years, were categorised according to their province, milk-recording organisation and size. Two-hundred-and-seventy-three herds (79%) had a positive ELISA titre. Both the probability of a herd being seropositive and the antibody level in the herd milk sample were affected by the province (P < 0.05 and P < 0.01, respectively) and the herd size category (P < 0.05 and P < 0.01, respectively). Larger herds were significantly more likely to have positive reactions and higher mean concentrations of antibody. It was concluded that a high proportion of unvaccinated Irish dairy herds have been exposed to infection with Leptospira hardjo.
    • Effect of liner design, pulsator setting, and vacuum level on bovine teat tissue changes and milking characteristics as measured by ultrasonography

      Gleeson, David E; O'Callaghan, Edmond J; Rath, Myles V (Biomed Central, 2004-05-01)
      Friesian-type dairy cows were milked with different machine settings to determine the effect of these settings on teat tissue reaction and on milking characteristics. Three teat-cup liner designs were used with varying upper barrel dimensions (wide-bore WB = 31.6 mm; narrow-bore NB = 21.0 mm; narrow-bore NB1 = 25.0 mm). These liners were tested with alternate and simultaneous pulsation patterns, pulsator ratios (60:40 and 67:33) and three system vacuum levels (40, 44 and 50 kPa). Teat tissue was measured using ultrasonography, before milking and directly after milking. The measurements recorded were teat canal length (TCL), teat diameter (TD), cistern diameter (CD) and teat wall thickness (TWT). Teat tissue changes were similar with a system vacuum level of either 50 kPa (mid-level) or 40 kPa (low-level). Widening the liner upper barrel bore dimension from 21.0 mm (P < 0.01) or 25.0 mm (P < 0.001) to 31.6 mm increased the magnitude of changes in TD and TWT after machine milking. Milk yield per cow was significantly (P < 0.05) higher and cluster-on time was reduced (P < 0.01) with the WB cluster as compared to the NB1 cluster. Minimum changes in teat tissue parameters were achieved with system vacuum level of 40 kPa and 50 kPa using NB and WB clusters, respectively. Similar changes in teat tissue and milk yield per cow were observed with alternate and simultaneous pulsation patterns. Widening pulsator ratio from 60:40 to 67:33 did not have negative effects on changes in teat tissue and had a positive effect on milk yield and milking time. Milk liner design had a bigger effect on teat tissue changes and milking characteristics than pulsation settings.
    • Dry cow therapy with a non-antibiotic intramammary teat seal - a review

      Crispie, Fiona; Flynn, James; Ross, R Paul; Hill, Colin; Meaney, William J (Biomed Central, 2004-07-01)
      Dry cow antibiotic therapy is used to eliminate existing intramammary infections and to prevent new infections in the dry period. It is implemented as part of a total management system known as the 'Five-Point Plan' for mastitis control. Recent public concerns over the widespread prophylactic use of antibiotics, coupled with an increasing interest in organic farming, have lead to a re-evaluation of the treatment of cows at drying-off. As a result, attention has focussed on the use of novel alternatives to antibiotic therapy at the end of lactation. One such therapy involves the application of a non-antibiotic bismuth-based intramammary teat seal designed for use in cows with low cell counts at the end of lactation. Like the keratin plug that forms naturally in teats of cows that have been dried-off, teat seal forms a physical barrier to invading pathogens. To date, a number of independent studies have shown that teat seal is as effective as traditional dry cow antibiotic products in preventing the occurrence of new infection during the dry period in cows with somatic cell counts of ≤200,000 cells ml-1 at drying-off. This paper reviews the efficacy of teat seal in preventing dry period mastitis in both conventional and organic dairying systems.
    • Update on the development of a novel dry cow therapy using a bismuth-based intramammary teat seal in combination with the bacteriocin lacticin 3147

      Crispie, Fiona; Flynn, James; Ross, R Paul; Hill, Colin; Meaney, William J (Biomed Central, 2004-11-01)
      Public concerns over the widespread prophylactic use of antibiotics have led to a search for alternatives to dry cow therapy for the prevention of intramammary infections. A popular alternative is to infuse a teat seal at drying-off. The teat seal is a viscous non-antibiotic formulation and when it is infused into the teat canal and the teat sinus it forms an internal seal that provides a physical barrier to invasion by mastitis-causing pathogens. Enhancement of teat seal formulations may be achieved using non-antibiotic additives such as bacteriocins, potent proteins produced by some bacteria that have the ability to kill other microorganisms. This paper traces the history of investigations at Moorepark Research Centre into the efficacy of teat seal plus lacticin 3147, a bacteriocin produced by Lactococcus lactis DPC3147, in the prevention of intramammary infections in dry cows. Indications from on-going investigations are that a dry cow formulation combining the two products has considerable potential as a non-antibiotic prophylactic product.
    • Measurements of the acid-binding capacity of ingredients used in pig diets

      Lawlor, Peadar G; Lynch, P Brendan; Caffrey, Patrick J.; O'Reilly, James J; O'Connell, M Karen (Biomed Central, 2005-08-01)
      Some feed ingredients bind more acid in the stomach than others and for this reason may be best omitted from pig starter foods if gastric acidity is to be promoted. The objective of this study was to measure the acid-binding capacity (ABC) of ingredients commonly used in pig starter foods. Ingredients were categorised as follows: (i) milk products (n = 6), (ii) cereals (n = 10), (iii) root and pulp products (n = 5), (iv) vegetable proteins (n = 11), (v) meat and fish meal (n = 2), (vi) medication (n = 3), (vii) amino acids (n = 4), (viii) minerals (n = 16), (ix) acid salts (n = 4), (x) acids (n = 10). A 0.5 g sample of food was suspended in 50 ml distilled de-ionised water with continuous stirring. This suspension was titrated with 0.1 mol/L HCl or 0.1 mol/L NaOH so that approximately 10 additions of titrant was required to reach pH 3.0. The pH readings after each addition were recorded following equilibration for three minutes. ABC was calculated as the amount of acid in milliequivalents (meq) required to lower the pH of 1 kg food to (a) pH 4.0 (ABC-4) and (b) pH 3.0 (ABC-3). Categories of food had significantly different (P < 0.01) ABC values. Mean ABC-4 and ABC-3 values of the ten categories were: (i) 623 (s.d. 367.0) and 936 (s.d. 460.2), (ii) 142 (s.d. 79.2) and 324 (s.d. 146.4), (iii) 368 (s.d. 65.3) and 804 (s.d. 126.7), (iv) 381 (s.d. 186.1) and 746 (s.d. 227.0), (v) 749 (s.d. 211.6) and 1508 (s.d. 360.8), (vi) 120 (s.d. 95.6) and 261 (s.d. 163.2), (vii) 177 (s.d. 60.7) and 1078 (s.d. 359.0), (viii) 5064 (s.d. 5525.1) and 7051 (s.d. 5911.6), (ix) 5057 (s.d. 1336.6) and 8945 (s.d. 2654.1) and (x) -5883 (s.d. 4220.5) and -2591 (s.d. 2245.4) meq HCl per kg, respectively. Within category, ABC-3 and ABC- 4 values were highly correlated: R2 values of 0.80 and greater for food categories i, iv, v, vi, vii and viii. The correlation between predicted and observed ABC values of 34 mixed diets was 0.83 for ABC-4 and 0.71 for ABC-3. It was concluded that complete diets with low ABC values may be formulated through careful selection of ingredients. The final pH to which ABC is measured should matter little as ABC-3 and ABC-4 are highly correlated.
    • A general method for selection of riboflavin-overproducing food grade micro-organisms

      Burgess, Catherine M; Smid, Eddy J; Rutten, Ger; van Sinderen, Douwe (Biomed Central, 2006-07-18)
      Background: This study describes a strategy to select and isolate spontaneous riboflavin-overproducing strains of Lactobacillus (Lb.) plantarum, Leuconostoc (Lc.) mesenteroides and Propionibacterium (P.) freudenreichii. Results: The toxic riboflavin analogue roseoflavin was used to isolate natural riboflavin-overproducing variants of the food grade micro-organisms Lb. plantarum, Lc. mesenteroides and P. freudenreichii strains. The method was successfully employed for strains of all three species. The mutation(s) responsible for the observed overproduction of riboflavin were identified for isolates of two species. Conclusion: Selection for spontaneous roseoflavin-resistant mutants was found to be a reliable method to obtain natural riboflavin-overproducing strains of a number of species commonly used in the food industry. This study presents a convenient method for deriving riboflavin-overproducing strains of bacterial starter cultures, which are currently used in the food industry, by a non-recombinant methodology. Use of such starter strains can be exploited to increase the vitamin content in certain food products.
    • Relatedness between the two-component lantibiotics lacticin 3147 and staphylococcin C55 based on structure, genetics and biological activity

      O'Connor, Eileen B; Cotter, Paul D.; O'Connor, Paula M.; O'Sullivan, Orla; Tagg, John R; Ross, R Paul; Hill, Colin (Biomed Central, 2007-04-02)
      Background: Two component lantibiotics, such as the plasmid-encoded lacticin 3147 produced by Lactococcus lactis DPC3147 and staphylococcin C55 produced by Staphylococcus aureus C55, represent an emerging subgroup of bacteriocins. These two bacteriocins are particularly closely related, exhibiting 86% (LtnA1 and C55α) and 55% (LtnA2 and C55β) identity in their component peptides. The aim of this study was to investigate, for the first time for any two component bacteriocins, the significance of the relatedness between these two systems. Results: So close is this relatedness that the hybrid peptide pairs LtnA1:C55β and C55α:LtnA2 were found to have activities in the single nanomolar range, comparing well with the native pairings. To determine whether this flexibility extended to the associated post-translational modification/processing machinery, the staphylococcin C55 structural genes were directly substituted for their lacticin 3147 counterparts in the ltn operon on the large conjugative lactococcal plasmid pMRC01. It was established that the lacticin LtnA1 post-translational and processing machinery could produce functionally active C55α, but not C55β. In order to investigate in closer detail the significance of the differences between LtnA1 and C55α, three residues in LtnA1 were replaced with the equivalent residues in C55α. Surprisingly, one such mutant LtnA1-Leu21Ala was not produced. This may be significant given the positioning of this residue in a putative lipid II binding loop. Conclusion: It is apparent, despite sharing striking similarities in terms of structure and activity, that these two complex bacteriocins display some highly dedicated features particular to either system.
    • A review of factors influencing litter size in Irish sows

      Lawlor, Peadar G; Lynch, P Brendan (Biomed Central, 2007-06-01)
      Many factors influence litter size. These include genetics, gilt management, lactation length, parity distribution, disease, stress and boar fertility. In the past 20 years, litter size in Irish sows has increased by only one pig. Born alive figures now average at 11.2 pigs per litter. In this regard, Ireland is falling behind our European competitors who have made significant advances over this time. Denmark, for example, has an average figure of 12.7 pigs born alive per litter and France an average of 12.5. The single area that could be improved immediately is sow feeding. It is important that sows are fed correctly throughout pregnancy. If over-fed during pregnancy, sows will have depressed appetite during lactation. If underfed in pregnancy, sows will be too thin at farrowing. The correct way to feed a pregnant sow is to match her feed allocation to her requirement for maintenance, body growth and growth of her developing foetuses. During lactation, sows should be given as much feed as they can eat to prevent excessive loss of body condition. Liquid-feed curves should be such that lactating sows are provided with a minimum mean daily feed supply of 6.2 kg. A small proportion of sows will eat more and this could be given as supplementary dry feed. Where dry feeding is practised in the farrowing house, it is difficult to hand-feed sows to match their appetite. Ideally ad libitum wet/dry feeders should be used. From weaning to service, sows should once again be fed ad libitum. If liquid feeding, this means giving at least 60 MJ DE (digestible energy) per day during this period. If dry feeding, at least 4 kg of lactation diet should be fed daily. The effort spent perfecting sow feeding management on units should yield high dividends in the form of increased pigs born alive per litter.
    • Effect of restricting silage feeding prepartum on time of calving, dystocia and stillbirth in Holstein-Friesian cows

      Gleeson, David E; O'Brien, Bernadette; Mee, John F (Biomed Central, 2007-11-01)
      A study was carried out to investigate the effect of restricting silage feeding on time of calving and calving performance in Holstein-Friesian cows. In the treatment group (n = 1,248 cows, 12 herds) silage feeding commenced in the evening (17:00 to 20:00 h), after a period of restricted access (2 to 10 h) while in the control group ad-libitum access to silage was provided over the 24 h period (n = 1,193 cows, 12 herds). Daytime and nighttime calvings were defined as calvings occurring between the hours of 06:30 and 00:29 and between 00:30 and 06:29, respectively. Restricting access to silage resulted in less calvings at night compared to cows with ad-libitum access to silage (18 vs 22%, P < 0.05). Cows with restricted access to silage had a higher percentage of difficult calvings (11 vs 7%, P < 0.001) and stillbirths (7 vs 5%, P < 0.05) compared to cows in the control group. The percentage of calvings at night was lower (13%) when access to silage was restricted for 10 h compared to 2, 4 or 6 h (22, 18, 25%, respectively) (P < 0.001). Calf sire breed, calf gender or cow parity did not influence time of calving. In conclusion, offering silage to pregnant Holstein-Friesian cows in the evening, after a period of restricted access, reduced the incidence of nighttime calvings, but increased the incidence of dystocia and stillbirth.
    • Long-term stability of RNA in post-mortem bovine skeletal muscle, liver and subcutaneous adipose tissues

      Bahar, Bojlul; Monahan, Frank J; Moloney, Aidan P; Schmidt, Olaf; MacHugh, David E; Sweeney, Torres (Biomed Central, 2007-11-29)
      Background: Recovering high quality intact RNA from post-mortem tissue is of major concern for gene expression studies in animals and humans. Since the availability of post-mortem tissue is often associated with substantial delay, it is important that we understand the temporal variation in the stability of total RNA and of individual gene transcripts so as to be able to appropriately interpret the data generated from such studies. Hence, the objective of this experiment was to qualitatively and quantitatively assess the integrity of total and messenger RNA extracted from bovine skeletal muscle, subcutaneous adipose tissue and liver stored at 4°C at a range of time points up to 22 days post-mortem. These conditions were designed to mimic the environment prevailing during the transport of beef from the abattoir to retail outlets. Results: The 28S and 18S rRNA molecules of total RNA were intact for up to 24 h post-mortem in liver and adipose tissues and up to 8 days post-mortem in skeletal muscle. The mRNA of housekeeping genes (GAPDH and ACTB) and two diet-related genes (RBP5 and SCD) were detectable up to 22 days post-mortem in skeletal muscle. While the mRNA stability of the two housekeeping genes was different in skeletal muscle and liver, they were similar to each other in adipose tissue. After 22 days post-mortem, the relative abundance of RBP5 gene was increased in skeletal muscle and in adipose tissue and decreased in liver. During this period, the relative abundance of SCD gene also increased in skeletal muscle whereas it decreased in both adipose tissue and liver. Conclusion: Stability of RNA in three tissues (skeletal muscle, subcutaneous adipose tissue and liver) subjected to long-term post-mortem storage at refrigeration temperature indicated that skeletal muscle can be a suitable tissue for recovering biologically useful RNA for gene expression studies even if the tissue is subjected to post-mortem storage for weeks, whereas adipose tissue and liver should be processed within 24 hours post-mortem.
    • Development of a real-time multiplex PCR assay for the detection of multiple Salmonella serotypes in chicken samples.

      O'Regan, Edel; McCabe, Evonne; Burgess, Catherine M; McGuinness, Sheila; Barry, Thomas; Duffy, Geraldine; Whyte, Paul; Fanning, Seamus (Biomed Central, 2008-09-21)
      Background: A real-time multiplex PCR assay was developed for the detection of multiple Salmonella serotypes in chicken samples. Poultry-associated serotypes detected in the assay include Enteritidis, Gallinarum, Typhimurium, Kentucky and Dublin. The traditional cultural method according to EN ISO 6579:2002 for the detection of Salmonella in food was performed in parallel. The real-time PCR based method comprised a pre-enrichment step in Buffered Peptone Water (BPW) overnight, followed by a shortened selective enrichment in Rappaport Vasilliadis Soya Broth (RVS) for 6 hours and subsequent DNA extraction. Results: The real-time multiplex PCR assay and traditional cultural method showed 100% inclusivity and 100% exclusivity on all strains tested. The real-time multiplex PCR assay was as sensitive as the traditional cultural method in detecting Salmonella in artificially contaminated chicken samples and correctly identified the serotype. Artificially contaminated chicken samples resulted in a detection limit of between 1 and 10 CFU per 25 g sample for both methods. A total of sixty-three naturally contaminated chicken samples were investigated by both methods and relative accuracy, relative sensitivity and relative specificity of the real-time PCR method were determined to be 89, 94 and 87%, respectively. Thirty cultures blind tested were correctly identified by the real-time multiplex PCR method. Conclusion: Real-time PCR methodology can contribute to meet the need for rapid identification and detection methods in food testing laboratories.
    • Farm management factors associated with bulk tank total bacterial count in Irish dairy herds during 2006/07

      Kelly, PT; O'Sullivan, K; Berry, Donagh P.; More, Simon J; Meaney, William J; O'Callaghan, Edmond J; O'Brien, Bernadette (Biomed Central, 2009-01-01)
      Research has shown that total bacterial count (TBC), which is the bacterial growth per ml of milk over a fixed period of time, can be decreased by good hygiene and farm management practices. The objective of the current study was to quantify the associations between herd management factors and bulk tank TBC in Irish spring calving, grass-based dairy herds. The relationship between bulk tank TBC and farm management and infrastructure was examined using data from 400 randomly selected Irish dairy farms where the basal diet was grazed grass. Herd management factors associated with bulk tank TBC were identified using linear models with herd annual total bacterial score (i.e., arithmetic mean of the natural logarithm of bulk tank TBC) included as the dependent variable. All herd management factors were individually analysed in a separate regression model, that included an adjustment for geographical location of the farm. A multiple stepwise regression model was subsequently developed. Median bulk tank TBC for the sample herds was 18,483 cells/ml ranging from 10,441 to 130,458 cells/ml. Results from the multivariate analysis indicated that the following management practices were associated with low TBC; use of heated water in the milking parlour; participation in a milk recording scheme; and tail clipping of cows at a frequency greater than once per year. Increased level of hygiene of the parlour and cubicles were also associated with lower TBC. Herd management factors associated with bulk tank TBC in Irish grazing herds were generally in agreement with most previous studies from confinement systems of milk production.