Life Scienceshttps://research.thea.ie/handle/20.500.12065/22882024-03-28T21:53:59Z2024-03-28T21:53:59ZCharacterisation of the complete mitochondrial genome of the insect-parasitic nematode heterorhabditis bacteriophora: an idiosyncratic gene order and the presence of multiple long non-coding regionsRegeai, Sassia OmarFitzpatrick, David A.Burnell, Ann M.Kakouli-Duarte, Thomaishttps://research.thea.ie/handle/20.500.12065/44172023-03-07T03:00:51Z2021-06-01T00:00:00ZCharacterisation of the complete mitochondrial genome of the insect-parasitic nematode heterorhabditis bacteriophora: an idiosyncratic gene order and the presence of multiple long non-coding regions
Regeai, Sassia Omar; Fitzpatrick, David A.; Burnell, Ann M.; Kakouli-Duarte, Thomais
We present here the complete mtDNA genome (mitogenome) of Heterorhabditis bacteriophora, an important biological control agent of soil-dwelling insect pests in agriculture and horticulture. This is the first description of a mitogenome for a member of the family Heterorhabditidae. The genome contains the typical chromadorean complement of 12 protein-coding genes, 22 tRNA genes and two rRNA genes. All genes are transcribed in the same direction and have a nucleotide composition high in A and T. For the entire genome, the nucleotide contents are 47.02% (T), 28.81% (A), 16.10% (G), 8.08% (C) and 75.83% (AT). Heterorhabditis bacteriophora has a unique, idiosyncratic gene arrangement. It differs from that of Caenorhabditis elegans in having a block of seven genes: trnQ-trnF-cytb-trnL1-cox3-trnT-nad4 translocated to a position between nad3 and nad5, as well as having a change in the position of the four tRNA block gene cluster, trnC-trnM-trnD-trnG, where trnC and trnM have switched places and trnD and trnG have translocated between nad4 and nad5 genes. The H. bacteriophora mitogenome is 18 128 bp long, and thus is ca 4 kb larger than the mitogenomes of most chromadoreans. This relatively large genome is due to the presence of five non-coding regions (NCR): NCR1 (114 bp), NCR2 (159 bp), NCR3 (498 bp), NCR4 (1917 bp) and NCR5 (2154 bp), which make up 26.7% of the genome. The NCR5 had the highest A + T content of 83.47% indicating that this region is the likely AT-rich control region. The complete 498 bp NCR3 sequence is duplicated in NCR4 and in NCR5 (the putative AT-rich control region). Such an organisation has not been reported previously in nematode mtDNA.
2021-06-01T00:00:00ZUsing the biocheck.ugent™ scoring tool in Irish farrow-to-finish pig farms: assessing biosecurity and its relation to productive performanceRodrigues da Costa, MariaGasa, JosepCalderón Díaz, Julia AdrianaPostma, MerelDewulf, JeroenMcCutcheon, GerardManzanilla, Edgar Garciahttps://research.thea.ie/handle/20.500.12065/44002023-03-06T03:00:51Z2019-03-01T00:00:00ZUsing the biocheck.ugent™ scoring tool in Irish farrow-to-finish pig farms: assessing biosecurity and its relation to productive performance
Rodrigues da Costa, Maria; Gasa, Josep; Calderón Díaz, Julia Adriana; Postma, Merel; Dewulf, Jeroen; McCutcheon, Gerard; Manzanilla, Edgar Garcia
Background
Biosecurity is one of the main factors affecting disease occurrence and antimicrobial use, and it is associated with performance in pig production. However, the importance of specific measures could vary depending on the (national) context. The aim of this study was to describe the biosecurity status in a cohort of Irish pig farms, to investigate which of those biosecurity aspects are more relevant by using the Biocheck.UGent™ scoring system, and to study the impact of such aspects on farm performance.
Results
External biosecurity score was high compared to most countries due to the characteristics of the Irish pig sector (i.e. purchasing only semen and breeding gilts on farm). The internal biosecurity score was lower and had greater variability among farms than other EU countries. Using multivariable linear regression, the biosecurity practices explained 8, 23, and 16% of variability in piglet mortality, finisher mortality, and average daily gain, respectively. Three clusters of farms were defined based on their biosecurity scores (0 to 100) using principal components and hierarchical clustering analysis. Scores for clusters 1, 2 and 3 were (mean ± SD) 38 ± 7.6, 61 ± 7.0 and 66 ± 9.8 for internal and 73 ± 5.1, 74 ± 5.3 and 86 ± 4.5 for external biosecurity. Cluster 3 had lower piglet mortality (P = 0.022) and higher average daily gain (P = 0.037) when compared to cluster 2.
Conclusions
Irish farms follow European tendencies with internal biosecurity posing as the biggest liability. Our results suggest that practices related to the environment and region, feed, water and equipment supply, and the management of the different stages, need to be addressed in lower performing farms to improve productive performance. Further studies on the economic impact of these biosecurity practices including complementary data on herd health, gilt rearing, piglet management, vaccination and feeding strategies are needed.
2019-03-01T00:00:00ZInsights into the mechanisms of Cronobacter sakazakii virulencePhair, KatieGonçalves Pereira, SóniaKealey, CarmelFanning, SéamusBrady, Damien B.https://research.thea.ie/handle/20.500.12065/40352022-09-10T02:02:09Z2022-06-01T00:00:00ZInsights into the mechanisms of Cronobacter sakazakii virulence
Phair, Katie; Gonçalves Pereira, Sónia; Kealey, Carmel; Fanning, Séamus; Brady, Damien B.
Cronobacter species have adapted to survive harsh conditions, particularly in the food manufacture environment, and can cause life-threatening infections in susceptible hosts. These opportunistic pathogens employ a multitude of mechanisms to aid their virulence throughout three key stages: environmental persistence, infection strategy, and systemic persistence in the human host. Environmental persistence is aided by the formation of biofilms, development of subpopulations, and high tolerance to environmental stressors. Successful infection in the human host involves several mechanisms such as protein secretion, motility, quorum sensing, colonisation, and translocation. Survival inside the host is achieved via competitive acquisition and utilization of minerals and metabolites respectively, coupled with host immune system evasion and antimicrobial resistance (AMR) mechanisms. Across the globe, Cronobacter sakazakii is associated with often fatal systemic infections in populations including neonates, infants, the elderly and the immunocompromised. By providing insight into the mechanisms of virulence utilised by this pathogen across these three stages, this review identifies current gaps in the literature. Further research into these virulence mechanisms is required to inform novel mitigation measures to improve global food safety with regards to this food-borne pathogen.
2022-06-01T00:00:00ZNematode-based indices in soil ecology: Application, utility, and future directionsDu Preez, GerhardDaneel, MiekeDe Goede, RonDu Toit, Marié JoeyFerris, HowardFourie, HendrikaGeisen, StefanKakouli-Duarte, ThomaisKorthals, GerardSánchez-Moreno, SaraSchmidt, Jan Henrikhttps://research.thea.ie/handle/20.500.12065/39492022-05-20T16:51:15Z2022-04-09T00:00:00ZNematode-based indices in soil ecology: Application, utility, and future directions
Du Preez, Gerhard; Daneel, Mieke; De Goede, Ron; Du Toit, Marié Joey; Ferris, Howard; Fourie, Hendrika; Geisen, Stefan; Kakouli-Duarte, Thomais; Korthals, Gerard; Sánchez-Moreno, Sara; Schmidt, Jan Henrik
The health and functioning of soil ecosystems are the foundation of sustainable food production and land management. Of key importance in achieving sustainability, is the frequent measurement of soil health, and indices based on the community structure of nematodes are amongst the most widely used toolsets by soil ecologists. Thirty years after the development of the Maturity Index, we aimed to evaluate the application, utility, and future directions of nematode-based indices (NBIs). This review focused on NBIs that are calculated using the coloniser-persister classification of nematodes. Data from 672 empirical studies in terrestrial environments revealed that the NBIs presented a dissimilar usage trend. The Channel Index and Metabolic Footprints showed the strongest increase in application rates over time, thus indicating a greater interest in studying decomposition pathways and ecosystem functioning, respectively. Furthermore, nematode-based indices were mostly applied in agricultural systems associated with herbaceous crops and in studies investigating, for example, soil nutrient enrichment following manure and/or inorganic fertilizer application. We further provide a framework for selecting a focus-orientated subset of NBIs for testing hypotheses based on the underlying ecological mechanisms. Also, we highlight important considerations, including the unexpected behaviour of some nematode taxa, in the interpretation of NBIs. The improvement of NBIs relies on advancing our understanding of the autecology of nematodes. Finally, we deliver insight into the further development of NBIs considering recent methodological advancements. We highlight that NBIs have been and might become increasingly important in providing valuable information on soil ecosystem health and functioning, especially considering the urgent need for more sustainable land use.
2022-04-09T00:00:00Z