• Evaluation of the n-alkane technique for estimating herbage dry matter intake of dairy cows offered herbage harvested at two different stages of growth in summer and autumn

      Wright, Marliene; Lewis, Eva; Garry, B.; Galvin, Norann; Dunshea, Frank; Hannah, M.C.; Auldist, Martin J.; Wales, W.J.; Dillon, Pat; Kennedy, Emer; et al. (Elsevier, 2018-11-10)
      The n-alkane technique for estimating herbage dry matter intake (DMI) of dairy cows was investigated in this experiment. Eight Holstein-Friesian dairy cows were offered perennial ryegrass ad libitum that had been harvested at two different herbage masses and during two different seasons, in order to assess the effect of herbage mass and season on the accuracy of the n-alkane technique. Two pre-harvested herbage mass treatments (low, target 1500 kg DM/ha versus high, target 4000 kg DM/ha, measured above 4 cm), were investigated in a crossover factorial arrangement within each of two seasons (summer versus autumn), in Ireland. Each season consisted of two periods, each 12 days in length. Cows were housed in individual metabolism stalls to allow for accurate determination of measured DMI. Herbage DMI was estimated, with the n-alkane technique, by dosing cows twice daily with a C32 n-alkane. Pre-harvest herbage mass and season did not affect the n-alkane estimated DMI, although lack of season and herbage mass effects may have been masked by variation that occurred between swards within the same herbage mass and season. However, there were a number of differences between summer and autumn in the fecal recovery rates of a number of n-alkanes suggesting that the effect of season requires further investigation prior to the application of recovery rates from literature values when investigating diet selection and botanical composition. Overall, the n-alkane technique provided good estimates of DMI; the discrepancy had a standard deviation due to sward of 1.2 and 1.0 kg DM/cow per day, and hence potential bias of up to twice this, and a measurement error standard deviation of 1.3 and 1.0 kg DM/cow per day, for the C33/C32 and C31/C32 n-alkane pair methods respectively. Two n-alkane pairs were tested, and C33/C32 n-alkane provided the most precise estimates of DMI, compared with the C31/C32 n-alkane pair. This research provides some strong evidence for future use of the n-alkane technique including that the accuracy of the technique has not been influenced by contemporary changes to herbage management, is not affected by seasonal changes, and overall is an accurate and precise technique for estimating DMI.
    • Exploring genome wide bisulfite sequencing for DNA methylation analysis in livestock: a technical assessment

      Doherty, Rachael; Couldrey, Christine; AgResearch AR&C; Teagasc (Frontiers Media SA, 2014-05-13)
      Recent advances made in “omics” technologies are contributing to a revolution in livestock selection and breeding practices. Epigenetic mechanisms, including DNA methylation are important determinants for the control of gene expression in mammals. DNA methylation research will help our understanding of how environmental factors contribute to phenotypic variation of complex production and health traits. High-throughput sequencing is a vital tool for the comprehensive analysis of DNA methylation, and bisulfite-based strategies coupled with DNA sequencing allows for quantitative, site-specific methylation analysis at the genome level or genome wide. Reduced representation bisulfite sequencing (RRBS) and more recently whole genome bisulfite sequencing (WGBS) have proven to be effective techniques for studying DNA methylation in both humans and mice. Here we report the development of RRBS and WGBS for use in sheep, the first application of this technology in livestock species. Important technical issues associated with these methodologies including fragment size selection and sequence depth are examined and discussed.
    • Extending the Grazing Period for Bulls, Prior to Finishing on a Concentrate Ration: Composition, Collagen Structure and Organoleptic Characteristics of Beef.

      Mezgebo, Gebrehawerya B; Monahan, Frank J; McGee, Mark; O'Riordan, Edward G; Marren, Declan; Listrat, Anne; Picard, Brigitte; Richardson, R Ian; Moloney, Aidan P; Teagasc (2019-07-23)
      The biochemical and organoleptic characteristics of the longissimus thoracis muscle from suckler bulls (n = 56) finished on a concentrate-based system (C) or raised in a pasture-based system (P) incorporating 99 (P99), 162 (P162) or 231 days (P231) of grazing prior to indoor finishing on the concentrate-based diet were investigated. Age at slaughter increased with increasing period at pasture. Intramuscular fat concentration was lower (p < 0.001) for P99 than for C, P162 and P231 bulls, which did not differ. Soluble collagen proportion was lower (p < 0.01) for P162 and P231 than for P99 and C bulls. Collagen cross-link content was higher (p < 0.05) for P231 than for P99 and C bulls and for P162 than for C bulls. The proportion of type I muscle fibres was higher (p < 0.01) for P231 and P162 than for P99 and C bulls. Sensory tenderness was higher (p < 0.001) for C and P162 than for P99 and P231 bulls and overall liking was higher (p < 0.01) for C than for P99 and P231 bulls but similar to P162 bulls. Extending the grazing period to 162 days did not negatively influence the sensory qualities of beef compared to the intensive concentrate-based system.
    • Fertility of fresh and frozen sex-sorted semen in dairy cows and heifers in seasonal-calving pasture-based herds

      Maicas, C.; Hutchinson, Ian A.; Kenneally, Jonathon; Grant, Jim; Cromie, A. R.; Lonergan, P.; Butler, Stephen T.; Teagasc Walsh Fellowship programme; Teagasc postdoctoral fellowship; Dovea Genetics; et al. (Elsevier, 2019-08-22)
      Our objective in this study was to evaluate the reproductive performance of dairy heifers and cows inseminated with fresh or frozen sex-sorted semen (SS) in seasonal-calving pasture-based dairy herds. Ejaculates of 10 Holstein-Friesian bulls were split and processed to provide (1) fresh conventional semen at 3 × 106 sperm per straw (CONV); (2) fresh SS at 1 × 106 sperm per straw (SS-1M); (3) fresh SS semen at 2 × 106 sperm per straw (SS-2M); and (4) frozen SS at 2 × 106 sperm per straw (SS-FRZ). Generalized linear mixed models were used to evaluate the effect of semen treatment and other explanatory variables on pregnancy per artificial insemination (P/AI) in heifers (n = 3,214) and lactating cows (n = 5,457). In heifers, P/AI was greater for inseminations with CONV (60.9%) than with SS-FRZ (52.8%) but did not differ from SS-1M (54.2%) or SS-2M (53.5%). Cows inseminated with CONV had greater P/AI (48.0%) than cows inseminated with SS, irrespective of treatment (SS-1M, SS-2M, and S-FROZEN; 37.6, 38.9, and 40.6%, respectively). None of the SS treatments differed from each other with regard to P/AI in either heifers or cows. The relative performance of SS compared with CONV was also examined [i.e., relative P/AI = (SS P/AI)/(CONV P/AI) × 100]. Frozen SS achieved relative P/AI >84%. Bull affected P/AI in both heifers and cows, but no bull by semen treatment interaction was observed. In heifers, P/AI increased with increasing Predicted Transmitting Ability for milk protein percentage. In cows, P/AI increased with increasing Economic Breeding Index (EBI) and with days in milk (DIM) at AI but decreased with increasing EBI milk subindex, parity and with DIM2. Cows in parity ≥5 had the lowest P/AI and differed from cows in parities 1, 2, or 3. Dispatch-to-AI interval of fresh semen did not affect P/AI in lactating cows, but a dispatch-to-AI interval by bull interaction was detected whereby P/AI was constant for most bulls but increased with greater dispatch-to-AI intervals for 2 bulls. In conclusion, frozen SS achieved greater P/AI relative to conventional semen than was previously reported in lactating cows. Fresh SS did not achieve greater P/AI than frozen SS, regardless of whether the sperm dose per straw was 1 × 106 or 2 × 106. A bull effect for all semen treatments, as well as a dispatch-to-AI interval by bull interaction for fresh semen, highlights the importance of using a large team of bulls for breeding management.
    • Forage type influences milk yield and ruminal responses to wheat adaptation in late-lactation dairy cows

      Russo, Victoria M.; Leury, B.J.; Kennedy, Emer; Hannah, M.C.; Auldist, M.J.; Wales, W.J.; Agriculture Victoria Research; Dairy Australia; Teagasc; The University of Melbourne (Elsevier, 2018-08-23)
      The effects of different wheat adaptation strategies on ruminal fluid pH, dry matter intake (DMI) and energy-corrected milk (ECM) were measured in 28 late-lactation dairy cows. Cows were fed either perennial ryegrass (PRG) hay or alfalfa hay and had no previous wheat adaptation. Wheat was gradually substituted for forage in 3 even increments, over 6 or 11 d, until wheat made up 40% of DMI (∼8 kg of dry matter/cow per day). We found no differences in DMI between adaptation strategies (6 or 11 d) within forage type; however, cows fed alfalfa hay consumed more overall and produced more ECM. The rate of ruminal pH decline after feeding, as well as the decrease in mean, minimum, and maximum ruminal pH with every additional kilogram of wheat was greater for cows fed alfalfa hay. Cows fed alfalfa hay and on the 6-d adaptation strategy had the lowest mean and minimum ruminal fluid pH on 3 consecutive days and were the only treatment group to record pH values below 6.0. Despite ruminal pH declining to levels typically considered low, no other measured parameters indicated compromised fermentation or acidosis. Rather, cows fed alfalfa hay and adapted to wheat over 6 d had greater ECM yields than cows on the 11-d strategy. This was due to the 6-d adaptation strategy increasing the metabolizable energy intake in a shorter period than the 11-d strategy, as substituting wheat for alfalfa hay caused a substantial increase in the metabolizable energy concentration of the diet. We found no difference in ECM between adaptation strategies when PRG hay was fed, as there was no difference in metabolizable energy intake. The higher metabolizable energy concentration and lower intake of the PRG hay meant the increase in metabolizable energy intake with the substitution of wheat was less pronounced for cows consuming PRG hay compared with alfalfa hay. Neither forage type nor adaptation strategy affected time spent ruminating. The higher intakes likely contributed to the lower ruminal pH values from the alfalfa hay treatments. However, both forages allowed the rumen contents to resist the large declines in ruminal pH typically seen during rapid grain adaptation. Depending on the choice of base forage, rapid grain introduction may not result in poor adaptation. In situations where high-energy grains are substituted for a low-energy, high-fiber basal forage, rapid introduction could prove beneficial over gradual strategies.
    • Gut microbiota as a source of novel antimicrobials

      Garcia-Gutierrez, Enriqueta; Mayer, Melinda J.; Cotter, Paul D.; Narbad, Arjan; Teagasc; Science Foundation Ireland; Biotechnology and Biological Sciences Research Council; 2015066; SFI/12/RC/2273; SFI/11/PI/1137; et al. (Taylor & Francis, 2019-05-22)
      Bacteria, Archaea, Eukarya and viruses coexist in the human gut, and this coexistence is functionally balanced by symbiotic or antagonistic relationships. Antagonism is often characterized by the production of antimicrobials against other organisms occupying the same environmental niche. Indeed, close co-evolution in the gut has led to the development of specialized antimicrobials, which is attracting increased attention as these may serve as novel alternatives to antibiotics and thereby help to address the global problem of antimicrobial resistance. The gastrointestinal (GI) tract is especially suitable for finding novel antimicrobials due to the vast array of microbes that inhabit it, and a considerable number of antimicrobial producers of both wide and narrow spectrum have been described. In this review, we summarize some of the antimicrobial compounds that are produced by bacteria isolated from the gut environment, with a special focus on bacteriocins. We also evaluate the potential therapeutic application of these compounds to maintain homeostasis in the gut and the biocontrol of pathogenic bacteria.
    • Identification of the blue light intensity administered to one eye required to suppress bovine plasma melatonin and investigation into effects on milk production in grazing dairy cows

      Murphy, Barbara A.; Herlihy, Mary M.; Nolan, Margaret B.; O'Brien, Christiane; Furlong, John G.; Butler, Stephen T.; Equiliume Ltd.; Teagasc (American Dairy Science Association, 2021-08)
      Long-day photoperiod is known to positively affect milk production in confinement dairy systems, and it has been hypothesized that pineal melatonin (MT) secretion plays a substantial role in this process. Specialized mammalian photoreceptors that regulate MT secretion are optimally stimulated by short wavelength blue light. We investigated the blue light intensity administered to one eye required to suppress MT secretion in nonlactating dairy cows, and subsequently examined effects on milk production in grazing dairy cows. Following a 14-d light-dark 8:16 h environmental conditioning period, 5 nonlactating Holstein-Friesian cows were exposed to treatments of <1, 70, 125, 175, and 225 lx for 8 additional hours using a 5 × 5 Latin square design. Light was administered via headpieces fitted with light-emitting diodes emitting blue light (465 nm) to the right eye. All cows were then exposed to a light-dark 16:8 h cycle for one night via the indoor lighting system (>200 lx white light). Plasma samples collected at regular intervals were assayed for MT. A dose-dependent effect of light treatment on mean circulating MT concentrations (and 95% CI) was observed [9.4 (7.2, 12.3), 5.0 (3.8, 6.6), 4.4 (3.3, 5.7), 3.3 (2.5, 4.3) and 1.7 (1.3, 2.3) ng/mL for treatments of 0, 70, 125, 175, and 225 lx, respectively. Only the 225 lx treatment acutely suppressed plasma melatonin concentration to levels similar to the light-dark 16:8 h treatment [1.9 (1.4, 2.5) ng/mL]. Forty spring-calving cows were blocked on parity, calving date and Economic Breeding Index for milk production and assigned to the control treatment or blue light to a single eye (LT) treatment from calving through 32 wk of lactation. The cows assigned to LT treatment were fitted with headpieces providing 225 lx of blue light to the right eye from 1700 until 0000 h. Mean milk production (and 95% CI) during 32 wk of lactation was not affected by treatment [20.3 (19.3, 21.3) vs. 20.9 (19.8, 22.0) kg/d, control and LT, respectively]. Within multiparous cows, a treatment by week interaction was detected, whereby LT treatment increased milk production during the first 12 wk of lactation [25.8 (24.3, 27.3) vs. 28.0 (26.5, 29.5) kg/d; +8.5%], but had no effect thereafter. Treatment did not affect plasma insulin-like growth factor 1. We identified the blue light intensity to one eye required to acutely suppress MT concentrations. Transient favorable effects on milk production were observed in multiparous cows. It remains unclear how single-eye blue light treatment affects galactopoiesis in grazing dairy cows, and further research is needed to explore whether this modality of light delivery represents a useful means to aid productivity in pasture-based dairy systems. Key words: melatonin, photoperiod, blue light, milk production, insulin-like growth factor
    • InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

      Breuer, Karin; Foroushani, Amir K.; Laird, Matthew R; Chen, Carol; Sribnaia, Anastasia; Lo, Raymond; Winsor, Geoffrey L; Hancock, Robert E.W.; Brinkman, Fiona S. L.; Lynn, David J; et al. (Oxford University Press, 2012-11-24)
      InnateDB (http://www.innatedb.com) is an integrated analysis platform that has been specifically designed to facilitate systems-level analyses of mammalian innate immunity networks, pathways and genes. In this article, we provide details of recent updates and improvements to the database. InnateDB now contains >196 000 human, mouse and bovine experimentally validated molecular interactions and 3000 pathway annotations of relevance to all mammalian cellular systems (i.e. not just immune relevant pathways and interactions). In addition, the InnateDB team has, to date, manually curated in excess of 18 000 molecular interactions of relevance to innate immunity, providing unprecedented insight into innate immunity networks, pathways and their component molecules. More recently, InnateDB has also initiated the curation of allergy- and asthma-related interactions. Furthermore, we report a range of improvements to our integrated bioinformatics solutions including web service access to InnateDB interaction data using Proteomics Standards Initiative Common Query Interface, enhanced Gene Ontology analysis for innate immunity, and the availability of new network visualizations tools. Finally, the recent integration of bovine data makes InnateDB the first integrated network analysis platform for this agriculturally important model organism.
    • Manipulation of the pre-partum diet of dairy cows to promote early adaptation to perennial ryegrass herbage

      Russo, V.M.; Wales, W.J.; Leury, B.J.; Hannah, M.C.; Kennedy, Emer; Teagasc; Agriculture Victoria Research; Dairy Australia; University of Melbourne (Teagasc, 2021-11-18)
      The diet of dairy cows in Ireland traditionally changes abruptly from predominantly pasture silage before calving to grazed perennial ryegrass immediately after calving. This potentially leads to problems with adaptation of microbes in the rumen with consequences of reduced intake and ultimately lower milk production. This experiment aimed to determine if introducing first-lactation dairy cows to perennial ryegrass herbage in the final weeks of pregnancy, thus eliminating a major dietary change at calving, could improve the adaptation process, potentially increasing dry matter intake (DMI) and milk production in early lactation. Three weeks prior to their expected calving date, 14 spring calving dairy cows were assigned to one of two treatments (n = 7): pasture silage pre-partum and perennial ryegrass herbage post-partum, or perennial ryegrass herbage both pre- and post-partum. Treatment diets were fed for 11 (±7) d pre-partum and for 14 (±0) d post-partum. For both treatments, DMI increased post-partum, but there was no difference between treatments, pre- or post-partum (5.9 and 8.8 kg DM/cow per day, respectively). There were no differences in milk yield or composition between the treatments. Body condition score declined following parturition but there were no differences between treatments. Plasma non-esterified fatty acids, glucose and β-hydroxybutyrate were also unaffected by treatment but did indicate a state of negative energy balance in early lactation. The results of this experiment suggest that pre-partum adaptation to perennial ryegrass herbage would not benefit milk production in first-lactation dairy cows in early lactation in Irish dairy farms employing this system.
    • MicroRNA profiling of the bovine alveolar macrophage response to Mycobacterium bovis infection suggests pathogen survival is enhanced by microRNA regulation of endocytosis and lysosome trafficking

      Vegh, Peter; Magee, David A.; Nalpas, Nicolas C.; Bryan, Kenneth; McCabe, Matthew S.; Browne, John A.; Conlon, Kevin M.; Gordon, Stephen V.; Bradley, Daniel G.; MacHugh, David E.; et al. (Elsevier, 2014-11-05)
      Mycobacterium bovis, the causative agent of bovine tuberculosis, a major problem for global agriculture, spreads via an airborne route and is taken up by alveolar macrophages (AM) in the lung. Here, we describe the first next-generation sequencing (RNA-seq) approach to temporally profile miRNA expression in primary bovine AMs post-infection with M. bovis. One, six, and forty miRNAs were identified as significantly differentially expressed at 2, 24 and 48 h post-infection, respectively. The differential expression of three miRNAs (bta-miR-142-5p, bta-miR-146a, and bta-miR-423-3p) was confirmed by RT-qPCR. Pathway analysis of the predicted mRNA targets of differentially expressed miRNAs suggests that these miRNAs preferentially target several pathways that are functionally relevant for mycobacterial pathogenesis, including endocytosis and lysosome trafficking, IL-1 signalling and the TGF-β pathway. Over-expression studies using a bovine macrophage cell-line (Bomac) reveal the targeting of two key genes in the innate immune response to M. bovis, IL-1 receptor-associated kinase 1 (IRAK1) and TGF-β receptor 2 (TGFBR2), by miR-146. Taken together, our study suggests that miRNAs play a key role in tuning the complex interplay between M. bovis survival strategies and the host immune response.
    • MicroRNA regulation of bovine monocyte inflammatory and metabolic networks in an in vivo infection model.

      Lawless, Nathan; Reinhardt, Timothy A.; Bryan, Kenneth; Baker, Mike; Pesch, Bruce; Zimmerman, Duane; Zuelke, Kurt; Sonstegard, Tad; O'Farrelly, Cliona; Lippolis, John D.; et al. (Genetics Society of America, 2014-01-27)
      Bovine mastitis is an inflammation-driven disease of the bovine mammary gland that costs the global dairy industry several billion dollars per annum. Because disease susceptibility is a multi-factorial complex phenotype, an integrative biology approach is required to dissect the molecular networks involved. Here, we report such an approach, using next generation sequencing combined with advanced network and pathway biology methods to simultaneously profile mRNA and miRNA expression at multiple time-points (0, 12, 24, 36 and 48h) in both milk and blood FACS-isolated CD14+ monocytes from animals infected in vivo with Streptococcus uberis. More than 3,700 differentially expressed (DE) genes were identified in milk-isolated monocytes (MIMs), a key immune cell recruited to the site of infection during mastitis. Up-regulated genes were significantly enriched for inflammatory pathways, while down-regulated genes were enriched for non-glycolytic metabolic pathways. Monocyte transcriptional changes in the blood, however, were more subtle but highlighted the impact of this infection systemically. Genes up-regulated in blood-isolated-monocytes (BIMs) showed a significant association with interferon and chemokine signalling. Furthermore, twenty-six miRNAs were differentially expressed in MIMs and three in BIMs. Pathway analysis revealed that predicted targets of down-regulated miRNAs were highly enriched for roles in innate immunity (FDR < 3.4E-8) in particular TLR signalling, while up-regulated miRNAs preferentially targeted genes involved in metabolism. We conclude that during S. uberis infection miRNAs are key amplifiers of monocyte inflammatory response networks and repressors of several metabolic pathways.
    • Plant traits of grass and legume species for flood resilience and N2O mitigation

      Oram, Natalie J.; Sun, Yan; Abalos, Diego; Groenigen, Jan Willem; Hartley, Sue; De Deyn, Gerlinde B.; European Union; Teagasc; 754380 (Wiley, 2021-07-11)
      1. Flooding threatens the functioning of managed grasslands by decreasing primary productivity and increasing nitrogen losses, notably as the potent greenhouse gas nitrous oxide (N2O). Sowing species with traits that promote flood resilience and mitigate flood-induced N2O emissions within these grasslands could safeguard their productivity while mitigating nitrogen losses. We tested how plant traits and resource acquisition strategies could predict flood resilience and N2O emissions of 12 common grassland species (eight grasses and four legumes) grown in field soil in monocultures in a 14-week greenhouse experiment. We found that grasses were more resistant to flooding while legumes recovered better. Resource-conservative grass species had higher resistance while resource-acquisitive grasses species recovered better. Resilient grass and legume species lowered cumulative N2O emissions. Grasses with lower inherent leaf and root δ13C (and legumes with lower root δ13C) lowered cumulative N2O emissions during and after the flood. Our results highlight the differing responses of grasses with contrasting resource acquisition strategies, and of legumes to flooding. Combining grasses and legumes based on their traits and resource acquisition strategies could increase the flood resilience of managed grasslands, and their capability to mitigate flood-induced N2O emissions. A free Plain Language Summary can be found within the Supporting Information of this article.
    • Systematic review and meta-analysis of the effect of feed enzymes on growth and nutrient digestibility in grow-finisher pigs: Effect of enzyme type and cereal source

      Torres-Pitarch, Alberto; Manzanilla, Edgar G; Gardiner, Gillian E.; O'Doherty, John V.; Lawlor, Peadar G; Teagasc; European Union’s Seventh Framework Programme; Teagasc Walsh Fellowship Programme; PDPG6671; 311794 (Elsevier, 2019-12-28)
      Dietary supplementation of pig diets with exogenous enzymes has been suggested as a strategy to increase nutrient digestibility and improve feed efficiency in grow-finisher pigs. However, inconsistent results are found in the literature. Ingredient composition of the diets is one of the most important sources of variation that may affect enzyme efficacy and consistency of results. A systematic review and a meta-analysis was therefore conducted to determine which exogenous enzymes with which diet type most consistently improve pig growth, nutrient digestibility and feed efficiency. Enzyme type and dietary cereal source were the main explanatory variables included in the models. The mean difference effects of enzyme supplementation on average daily gain (ADG), average daily feed intake (ADFI), gain to feed (G:F), apparent ileal digestibility (AiD) and apparent total tract digestibility (ATTD) of dry matter (DM), crude protein (CP), and gross energy (GE) were calculated for each study and these were used as the effect size estimates in the meta-analysis. A dataset with 139 comparisons from 67 peer-reviewed publications was used in the meta-analysis. In response to enzyme supplementation, G:F was improved in 38 of the 120 comparisons reporting pig growth data, remained un-changed in 78 and deteriorated in 4. Overall, DM and GE AiD, and ATTD were improved by xylanase, xylanase + β-glucanase, mannanase and protease dietary supplementation (P < 0.05). Crude protein AiD was only improved by protease dietary supplementation (P < 0.001). Dietary supplementation with xylanase alone improved ADG of maize- (P < 0.05) and co-product- (P < 0.05) based diets but had no effect on the G:F of grow-finisher pigs. Dietary supplementation with xylanase + β-glucanase had no effect on ADG, ADFI and G:F. Protease supplementation tended to improve the ADG of grow-finisher pigs fed co-product-based diets (P = 0.08) but had no effect on G:F. Dietary supplementation with multi-enzyme complexes improved the ADG (P < 0.05) and G:F (P < 0.01) of maize-, wheat-, barley- and co-product-based diets. In conclusion, dietary supplementation with all enzyme types improved nutrient digestibility depending on ingredient content, while mannanase and multi-enzyme complex supplementation most consistently improved growth and feed efficiency.
    • Whole blood gene expression profiling of neonates with confirmed bacterial sepsis

      Dickinson, Paul; Smith, Claire L.; Forster, Thorsten; Craigon, Marie; Ross, Alan J.; Khondoker, Mizan R; Ivens, Alasdair; Lynn, David J.; Orme, Judith; Jackson, Allan; et al. (ElsevierDickinson, P., Smith, C., Forster, T., Craigon, M., Ross, A., Khondoker, M., Ivens, A., Lynn, D., Orme, J., Jackson, A., Lacaze, P., Flanagan, K., Stenson, B. and Ghazal, P. Whole blood gene expression profiling of neonates with confirmed bacterial sepsis. Genomics Data, [online] 3, pp.41-48. Available at: https://dx.doi.org/10.1016/j.gdata.2014.11.003 [Accessed 1 Aug. 2019]., 2014-11-15)
      Neonatal infection remains a primary cause of infant morbidity and mortality worldwide and yet our understanding of how human neonates respond to infection remains incomplete. Changes in host gene expression in response to infection may occur in any part of the body, with the continuous interaction between blood and tissues allowing blood cells to act as biosensors for the changes. In this study we have used whole blood transcriptome profiling to systematically identify signatures and the pathway biology underlying the pathogenesis of neonatal infection. Blood samples were collected from neonates at the first clinical signs of suspected sepsis alongside age matched healthy control subjects. Here we report a detailed description of the study design, including clinical data collected, experimental methods used and data analysis workflows and which correspond with data in Gene Expression Omnibus (GEO) data sets (GSE25504). Our data set has allowed identification of a patient invariant 52-gene classifier that predicts bacterial infection with high accuracy and lays the foundation for advancing diagnostic, prognostic and therapeutic strategies for neonatal sepsis.