ORCID Profile
0000-0001-7183-1555
Current Organisation
Queen's University Belfast
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Publisher: Elsevier BV
Date: 09-2023
Publisher: Springer Science and Business Media LLC
Date: 03-2010
DOI: 10.1038/NMETH.1434
Abstract: Software for visualizing sequence alignments and trees are essential tools for life scientists. In this review, we describe the major features and capabilities of a selection of stand-alone and web-based applications useful when investigating the function and evolution of a gene family. These range from simple viewers, to systems that provide sophisticated editing and analysis functions. We conclude with a discussion of the challenges that these tools now face due to the flood of next generation sequence data and the increasingly complex network of bioinformatics information sources.
Publisher: Public Library of Science (PLoS)
Date: 27-01-2022
DOI: 10.1371/JOURNAL.PONE.0263188
Abstract: Schistosomiasis is a neglected tropical parasitic and chronic disease affecting hundreds of millions of people. Adult schistosomes reside in the blood stream of the definitive mammalian host. These helminth parasites possess two epithelial surfaces, the tegument and the gastrodermis, both of which interact with the host during immune evasion and in nutrient uptake. Female ARC Swiss mice (4–6 weeks old) were infected percutaneously with Schistosoma japonicum cercariae freshly shed from Oncomelania hupensis quadrasi snails (Philippines strain). Fluorescent in situ hybridisation (FISH) was performed by using fresh adult S . japonicum perfused from those infected mice. Adult S . japonicum worms were processed to isolate the tegument from the carcass containing the gastrodermis blood and bile were collected in idually from infected and uninfected mice. Total DNA extracted from all those s les were used for microbiome profiling. FISH and microbiome profiling showed the presence of bacterial populations on two epithelial surfaces of adult worms, suggesting they were distinct not only from the host blood but also from each other. Whereas microbial ersity was reduced overall in the parasite epithelial tissues when compared with that of host blood, specific bacterial taxa, including Anoxybacillus and Escherichia , were elevated on the tegument. Minimal differences were evident in the microbiome of host blood during an active infection, compared with that of control uninfected blood. However, s ling of bile from infected animals identified some differences compared with controls, including elevated levels of Limnohabitans , Clostridium and Curvibacter . Using FISH and microbial profiling, we were able to demonstrate, for the first time, that bacteria are presented on the epithelial surfaces of adult schistosomes. These schistosome surface-associated bacteria, which are distinct from the host blood microenvironment, should be considered as a new and important component of the host-schistosome interaction. The importance of in idual bacterial species in relation to schistosome parasitism needs further elucidation.
Publisher: Springer Science and Business Media LLC
Date: 12-05-2014
Publisher: Frontiers Media SA
Date: 25-09-2018
Publisher: Springer Science and Business Media LLC
Date: 19-03-2018
DOI: 10.1038/NBT.4110
Publisher: Frontiers Media SA
Date: 25-05-2018
Publisher: Springer Science and Business Media LLC
Date: 20-05-2012
Abstract: The liver is central to most economically important metabolic processes in cattle. However, the changes in expression of genes that drive these processes remain incompletely characterised. RNA-seq is the new gold standard for whole transcriptome analysis but so far there are no reports of its application to analysis of differential gene expression in cattle liver. We used RNA-seq to study differences in expression profiles of hepatic genes and their associated pathways in in idual cattle in either mild negative energy balance (MNEB) or severe negative energy balance (SNEB). NEB is an imbalance between energy intake and energy requirements for lactation and body maintenance. This aberrant metabolic state affects high-yielding dairy cows after calving and is of considerable economic importance because of its negative impact on fertility and health in dairy herds. Analysis of changes in hepatic gene expression in SNEB animals will increase our understanding of NEB and contribute to the development of strategies to circumvent it. RNA-seq analysis was carried out on total RNA from liver from early post partum Holstein Friesian cows in MNEB (n = 5) and SNEB (n = 6). 12,833 genes were deemed to be expressed ( reads per gene per animal), 413 of which were shown to be statistically significantly differentially expressed (SDE) at a false discovery rate (FDR) of 0.1% and 200 of which were SDE (FDR of 0.1%) with a ≥2-fold change between MNEB and SNEB animals. GOseq/KEGG pathway analysis showed that SDE genes with ≥2- fold change were associated ( P .05) with 9 KEGG pathways. Seven of these pathways were related to fatty acid metabolism and unexpectedly included ‘Steroid hormone biosynthesis’, a process which mainly occurs in the reproductive organs rather than the liver. RNA-seq analysis showed that the major changes at the level of transcription in the liver of SNEB cows were related to fat metabolism. 'Steroid hormone biosynthesis', a process that normally occurs in reproductive tissue, was significantly associated with changes in gene expression in the liver of SNEB cows. Changes in gene expression were found in this pathway that have not been previously been identified in SNEB cows.
Publisher: Cold Spring Harbor Laboratory
Date: 06-10-2023
Publisher: Springer Science and Business Media LLC
Date: 13-01-2017
Abstract: Many microbes in complex competitive environments share genes for acquiring and utilising nutrients, questioning whether niche specialisation exists and if so, how it is maintained. We investigated the genomic signatures of niche specialisation in the rumen microbiome, a highly competitive, anaerobic environment, with limited nutrient availability determined by the biomass consumed by the host. We generated in idual metagenomic libraries from 14 cows fed an ad libitum diet of grass silage and calculated functional isoform ersity for each microbial gene identified. The animal replicates were used to calculate confidence intervals to test for differences in ersity of functional isoforms between microbes that may drive niche specialisation. We identified 153 genes with significant differences in functional isoform ersity between the two most abundant bacterial genera in the rumen ( Prevotella and Clostridium). We found Prevotella possesses a more erse range of isoforms capable of degrading hemicellulose, whereas Clostridium for cellulose. Furthermore, significant differences were observed in key metabolic processes indicating that isoform ersity plays an important role in maintaining their niche specialisation. The methods presented represent a novel approach for untangling complex interactions between microorganisms in natural environments and have resulted in an expanded catalogue of gene targets central to rumen cellulosic biomass degradation.
Publisher: Frontiers Media SA
Date: 09-10-2018
Publisher: Frontiers Media SA
Date: 26-03-2020
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Chris Creevey.