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Subject = gene expression;
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Displaying Results 1 - 25 of 139 on page 1 of 6
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A cDNA microarray assessment of gene expression in the liver of rainbow trout (Oncorhynchus mykiss) in response to a handling and confinement stressor
(2016)
Cairns, Michael T.; Johnson, M. C.; Talbot, A. T.; Pernmasani, J. K.; McNeill, R. E.; H...
A cDNA microarray assessment of gene expression in the liver of rainbow trout (Oncorhynchus mykiss) in response to a handling and confinement stressor
(2016)
Cairns, Michael T.; Johnson, M. C.; Talbot, A. T.; Pernmasani, J. K.; McNeill, R. E.; Houeix, Benoit; Sangrador-Vegas, A.; Pottinger, T. G.
Abstract:
A purpose-designed microarray platform (Stressgenes, Phase 1) was utilised to investigate the changes in gene expression within the liver of rainbow trout during exposure to a prolonged period of confinement. Tissue and blood samples were collected from trout at intervals up to 648 h after transfer to a standardised confinement stressor, together with matched samples from undisturbed control fish. Plasma ACTH, cortisol, glucose and lactate were analysed to confirm that the neuroendocrine response to confinement was consistent with previous findings and to provide a phenotypic context to assist interpretation of gene expression data. Liver samples for suppression subtractive hybridisation (SSH) library construction were selected from within the experimental groups comprising “early” stress (2–48 h) and “late” stress (96–504 h). In order to reduce redundancy within the four SSH libraries and yield a higher number of unique clones an additional subtraction was carried out. After printi...
http://hdl.handle.net/10379/5667
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A cdna microarray assessment of gene expression in the liver of rainbow trout (oncorhynchus mykiss) in response to a handling and confinement stressor
(2018)
Cairns, M.T.; Johnson, M.C.; Talbot, A.T.; Pemmasani, J.K.; McNeill, R.E.; Houeix, B.; ...
A cdna microarray assessment of gene expression in the liver of rainbow trout (oncorhynchus mykiss) in response to a handling and confinement stressor
(2018)
Cairns, M.T.; Johnson, M.C.; Talbot, A.T.; Pemmasani, J.K.; McNeill, R.E.; Houeix, B.; Sangrador-Vegas, A.; Pottinger, T.G.
http://hdl.handle.net/10379/10648
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A differential interplay between the expression of Th1/Th2/Treg related cytokine genes in Teladorsagia circumcincta infected DRB1*1101 carrier lambs
(2012)
Hassan, Musa; Hanrahan, James P; Good, Barbara; Mulcahy, Grace; Sweeney, Torres
A differential interplay between the expression of Th1/Th2/Treg related cytokine genes in Teladorsagia circumcincta infected DRB1*1101 carrier lambs
(2012)
Hassan, Musa; Hanrahan, James P; Good, Barbara; Mulcahy, Grace; Sweeney, Torres
Abstract:
Substantial debate exists on whether the immune response between sheep resistant and susceptible to gastrointestinal nematodes can be differentiated into a Th1 and Th2 phenotype. The present study addresses the hypothesis that variation in resistance to Teladorsagia circumcincta between DRB1*1101 (associated with reduced faecal egg count and worm burden) carriers and non-carriers is due to a differential interplay in the expression of Th1/Th2 and regulatory T (Treg) related cytokine genes. Lambs from each genotype were either slaughtered at day 0 (un-infected control) or infected with 3 × 104 Teladorsagia circumcincta L3 and slaughtered at 3, 7, 21, and 35 days later. Lambs carrying the DRB1*1101 allele had a significantly lower worm burden (P < 0.05) compared to the non-carriers. Abomasal mucosal cytokine gene expression was evaluated by quantitative real-time PCR and comparison made for time and genotype effects. The response generated varied through the course of infection and...
http://hdl.handle.net/11019/227
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A fundamental regulatory mechanism operating through OmpR and DNA topology controls expression of Salmonella pathogenicity islands SPI-1 and SPI-2
(2012)
DORMAN, CHARLES
A fundamental regulatory mechanism operating through OmpR and DNA topology controls expression of Salmonella pathogenicity islands SPI-1 and SPI-2
(2012)
DORMAN, CHARLES
Abstract:
DNA topology has fundamental control over the ability of transcription factors to access their target DNA sites at gene promoters. However, the influence of DNA topology on protein?DNA and protein?protein interactions is poorly understood. For example, relaxation of DNA supercoiling strongly induces the well-studied pathogenicity gene ssrA (also called spiR) in Salmonella enterica, but neither the mechanism nor the proteins involved are known. We have found that relaxation of DNA supercoiling induces expression of the Salmonella pathogenicity island (SPI)-2 regulator ssrA as well as the SPI-1 regulator hilC through a mechanism that requires the two-component regulator OmpR-EnvZ. Additionally, the ompR promoter is autoregulated in the same fashion. Conversely, the SPI-1 regulator hilD is induced by DNA relaxation but is repressed by OmpR. Relaxation of DNA supercoiling caused an increase in OmpR binding to DNA and a concomitant decrease in binding by the nucleoid-associated protein F...
http://hdl.handle.net/2262/71400
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A non-classical LysR-type transcriptional regulator PA2206 is required for an effective oxidative stress response in Pseudomonas aeruginosa
(2013)
Reen, F. Jerry; Haynes, Jill M.; Mooij, Marlies J.; O'Gara, Fergal
A non-classical LysR-type transcriptional regulator PA2206 is required for an effective oxidative stress response in Pseudomonas aeruginosa
(2013)
Reen, F. Jerry; Haynes, Jill M.; Mooij, Marlies J.; O'Gara, Fergal
Abstract:
LysR-type transcriptional regulators (LTTRs) are emerging as key circuit components in regulating microbial stress responses and are implicated in modulating oxidative stress in the human opportunistic pathogen Pseudomonas aeruginosa. The oxidative stress response encapsulates several strategies to overcome the deleterious effects of reactive oxygen species. However, many of the regulatory components and associated molecular mechanisms underpinning this key adaptive response remain to be characterised. Comparative analysis of publically available transcriptomic datasets led to the identification of a novel LTTR, PA2206, whose expression was altered in response to a range of host signals in addition to oxidative stress. PA2206 was found to be required for tolerance to H2O2 in vitro and lethality in vivo in the Zebrafish embryo model of infection. Transcriptomic analysis in the presence of H2O2 showed that PA2206 altered the expression of 58 genes, including a large repertoire of oxid...
http://hdl.handle.net/10468/2395
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A wheat cytochrome P450 enhances both resistance to deoxynivalenol and grain yield
(2019)
Gunupuru, Lokanadha R.; Arunachalam, Chanemougasoundharam; Malla, Keshav B.; Kahla, Ama...
A wheat cytochrome P450 enhances both resistance to deoxynivalenol and grain yield
(2019)
Gunupuru, Lokanadha R.; Arunachalam, Chanemougasoundharam; Malla, Keshav B.; Kahla, Amal; Perochon, Alexandre; Jia, Jianguang; Thapa, Ganesh; Doohan, Fiona M.
Abstract:
The mycotoxin deoxynivalenol (DON) serves as a plant disease virulence factor for the fungi Fusarium graminearum and F. culmorum during the development of Fusarium head blight (FHB) disease on wheat. A wheat cytochrome P450 gene from the subfamily CYP72A, TaCYP72A, was cloned from wheat cultivar CM82036. TaCYP72A was located on chromosome 3A with homeologs present on 3B and 3D of the wheat genome. Using gene expression studies, we showed that TaCYP72A variants were activated in wheat spikelets as an early response to F. graminearum, and this activation was in response to the mycotoxic Fusarium virulence factor deoxynivalenol (DON). Virus induced gene silencing (VIGS) studies in wheat heads revealed that this gene family contributes to DON resistance. VIGS resulted in more DON-induced discoloration of spikelets, as compared to mock VIGS treatment. In addition to positively affecting DON resistance, TaCYP72A also had a positive effect on grain number. VIGS of TaCYP72A genes reduced gr...
http://hdl.handle.net/10197/10593
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Acute phase gene expression in rainbow trout (Oncorhynchus mykiss) after exposure to a confinement stressor: A comparison of pooled and individual data
(2014)
Talbot, Anita T.; Smith, Terry; Cairns, Michael T.
Acute phase gene expression in rainbow trout (Oncorhynchus mykiss) after exposure to a confinement stressor: A comparison of pooled and individual data
(2014)
Talbot, Anita T.; Smith, Terry; Cairns, Michael T.
Abstract:
Journal article
This study set out to investigate whether differential expression of genes for acute phase proteins in rainbow trout (Oncorhynchus mykiss) could be induced by confinement stress, a non-invasive method of activating the neuroendocrine stress response. In addition, a second objective was to assess the variation in gene expression between individual fish within the population of stressed fish in an attempt to identify APP genes having uniform and consistent changes in expression during stress. The liver was chosen for this investigation as it is the primary site of acute phase protein synthesis. Relative expression of the eight genes including transferrin, fibrinogen-like protein 2 (flp2), alpha-1-anti-proteinase-like protein (alpha 1-antiprot), leukocyte cell-derived chemotaxin 2 (LECT2), pentraxin, serum amyloid A (SAA), haptoglobin (Hp), and differentially regulated trout protein 1 (DRTP1) was analysed by quantitative real-time PCR (qPCR) over 5 experimental time...
http://hdl.handle.net/10379/4671
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Allelic differences between Europeans and Chinese for CREB1 SNPs and their implications in gene expression regulation, hippocampal structure and function, and bipolar disorder susceptibility
(2014)
DONOHOE, GARY; MORRIS, DEREK; GILL, MICHAEL
Allelic differences between Europeans and Chinese for CREB1 SNPs and their implications in gene expression regulation, hippocampal structure and function, and bipolar disorder susceptibility
(2014)
DONOHOE, GARY; MORRIS, DEREK; GILL, MICHAEL
http://hdl.handle.net/2262/69355
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An examination of the molecular mechanisms controlling the tissue accumulation of conjugated linoleic acid (CLA) in cattle
(2015)
Waters, Sinead M.; Hynes, A.C.; Killeen, Aideen P.; Moloney, Aidan P; Kenny, David A.
An examination of the molecular mechanisms controlling the tissue accumulation of conjugated linoleic acid (CLA) in cattle
(2015)
Waters, Sinead M.; Hynes, A.C.; Killeen, Aideen P.; Moloney, Aidan P; Kenny, David A.
Abstract:
End of project report
Long chain n-3 polyunsaturated fatty acids (n-3 PUFA) and conjugated linoleic acid (CLA) have demonstrable and potential human health benefits in terms of preventing cancer, diabetes, chronic inflammation, obesity and coronary heart disease. Supplementation of cattle diets with a blend of oils rich in n-3 PUFA and linoleic acid have a synergistic effect on the accumulation of ruminal and tissue concentrations of trans vaccenic acid (TVA), the main substrate for ?-9 desaturase which is responsible for de novo tissue synthesis of the cis 9, trans 11 isomer of CLA. This dietary strategy translates into increases in milk concentrations of CLA in dairy cows; however, concentrations in the muscle of beef animals have not always been increased. There is an apparent paradox in that n-3 PUFA supplementation enhances ruminal synthesis of trans-vaccenic acid (TVA), but then inhibits its conversion to CLA possibly through altering the activity of ?-9 desaturase. Recent...
http://hdl.handle.net/11019/859
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An in vitro bone tissue regeneration strategy combining chondrogenic and vascular priming enhances the mineralization potential of mesenchymal stem cells In vitro while also allowing for vessel formation
(2016)
Freeman, Fiona E.; Haugh, Matthew G.; McNamara, Laoise M.
An in vitro bone tissue regeneration strategy combining chondrogenic and vascular priming enhances the mineralization potential of mesenchymal stem cells In vitro while also allowing for vessel formation
(2016)
Freeman, Fiona E.; Haugh, Matthew G.; McNamara, Laoise M.
Abstract:
Chondrogenic priming (CP) of mesenchymal stem cells (MSCs) and coculture of MSCs with human umbilical vein endothelial stem cells (HUVECs) both have been shown to significantly increase the potential for MSCs to undergo osteogenic differentiation and mineralization in vitro and in vivo. Such strategies mimic cartilage template formation or vascularization that occur during endochondral ossification during early fetal development. However, although both chondrogenesis and vascularization are crucial precursors for bone formation by endochondral ossification, no in vitro bone tissue regeneration strategy has sought to incorporate both events simultaneously. The objective of this study is to develop an in vitro bone regeneration strategy that mimics critical aspects of the endochondral ossification process, specifically (1) the formation of a cartilage template and (2) subsequent vascularization of this template. We initially prime the MSCs with chondrogenic growth factors, to ensure t...
http://hdl.handle.net/10379/6223
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Analysis of short-term metabolic alterations in arabidopsis following changes in the prevailing environmental conditions
(2018)
Florian, Alexandra; Nikoloski, Zoran; Sulpice, Ronan; Timm, Stefan; Araújo, Wagner L.; ...
Analysis of short-term metabolic alterations in arabidopsis following changes in the prevailing environmental conditions
(2018)
Florian, Alexandra; Nikoloski, Zoran; Sulpice, Ronan; Timm, Stefan; Araújo, Wagner L.; Tohge, Takayuki; Bauwe, Hermann; Fernie, Alisdair R.
Abstract:
Although a considerable increase in our knowledge concerning the importance of metabolic adjustments to unfavorable growth conditions has been recently provided, relatively little is known about the adjustments which occur in response to fluctuation in environmental factors. Evaluating the metabolic adjustments occurring under changing environmental conditions thus offers a good opportunity to increase our current understanding of the crosstalk between the major pathways which are affected by such conditions. To this end, plants growing under normal conditions were transferred to different light and temperature conditions which were anticipated to affect (amongst other processes) the rates of photosynthesis and photorespiration and characterized at the physiological, molecular, and metabolic levels following this transition. Our results revealed similar behavior in response to both treatments and imply a tight connectivity of photorespiration with the major pathways of plant metabol...
http://hdl.handle.net/10379/11523
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Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli
(2014)
Sharma, Virag; Prère, Marie-Francoise; Canal, Isabelle; Firth, Andrew E.; Atkins, John ...
Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli
(2014)
Sharma, Virag; Prère, Marie-Francoise; Canal, Isabelle; Firth, Andrew E.; Atkins, John F.; Baranov, Pavel V.; Fayet, Olivier
Abstract:
Programmed ribosomal -1 frameshifting is a non-standard decoding process occurring when ribosomes encounter a signal embedded in the mRNA of certain eukaryotic and prokaryotic genes. This signal has a mandatory component, the frameshift motif: it is either a Z_ZZN tetramer or a X_XXZ_ZZN heptamer (where ZZZ and XXX are three identical nucleotides) allowing cognate or near-cognate repairing to the -1 frame of the A site or A and P sites tRNAs. Depending on the signal, the frameshifting frequency can vary over a wide range, from less than 1% to more than 50%. The present study combines experimental and bioinformatics approaches to carry out (i) a systematic analysis of the frameshift propensity of all possible motifs (16 Z_ZZN tetramers and 64 X_XXZ_ZZN heptamers) in Escherichia coli and (ii) the identification of genes potentially using this mode of expression amongst 36 Enterobacteriaceae genomes. While motif efficiency varies widely, a major distinctive rule of bacterial -1 framesh...
http://hdl.handle.net/10468/5017
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Analyzing time-course microarray data using functional data analysis - a review
(2011)
Coffey, Norma; Hinde, John
Analyzing time-course microarray data using functional data analysis - a review
(2011)
Coffey, Norma; Hinde, John
Abstract:
Gene expression over time can be viewed as a continuous process and therefore represented as a continuous curve or function. Functional data analysis (FDA) is a statistical methodology used to analyze functional data that has become increasingly popular in the analysis of time-course gene expression data. Several FDA techniques have been applied to gene expression profiles including functional regression analysis (to describe the relationship between expression profiles and other covariate(s)), functional discriminant analysis (to discriminate and classify groups of genes) and functional principal components analysis (for dimension reduction and clustering). This paper reviews the use of FDA and it¿s associated methods to analyze time-course microarray gene expression data.
http://hdl.handle.net/10379/1903
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Apoptosis is Signalled Early by Low Doses of Ionizing Radiation in a Radiation-Induced Bystander Effect
(2013)
Furlong, Hayley; Mothersill, Carmel; Lyng, Fiona; Howe, Orla
Apoptosis is Signalled Early by Low Doses of Ionizing Radiation in a Radiation-Induced Bystander Effect
(2013)
Furlong, Hayley; Mothersill, Carmel; Lyng, Fiona; Howe, Orla
Abstract:
It is known that ionising radiation (IR) induces a complex signalling apoptotic cascade post-exposure to low doses ultimately to remove damaged cells from a population, specifically via the intrinsic pathway. Therefore, it was hypothesised that bystander reporter cells may initiate a similar apoptotic response if exposed to low doses of IR (0.05 Gy and 0.5 Gy) and compared to directly irradiated cells. Key apoptotic genes were selected according to their role in the apoptotic cascade; tumour suppressor gene TP53, pro-apoptotic Bax and anti-apoptotic Bcl2, pro-apoptotic JNK and anti-apoptotic ERK, initiator caspase 2 and 9 and effector caspase 3, 6 and 7. The data generated consolidated the role of apoptosis following direct IR exposure for all doses and time points as pro-apoptotic genes such as Bax and JNK as well as initiator caspase 7 and effector caspase 3 and 9 were up-regulated. However, the gene expression profile for the bystander response was quite different and more comple...
https://arrow.dit.ie/scschbioart/85
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Application of simulated annealing to the biclustering of gene expression data
(2006)
BOLSHAKOVA, NADIA; CUNNINGHAM, PADRAIG
Application of simulated annealing to the biclustering of gene expression data
(2006)
BOLSHAKOVA, NADIA; CUNNINGHAM, PADRAIG
Abstract:
In a gene expression data matrix, a bicluster is a submatrix of genes and conditions that exhibits a high correlation of expression activity across both rows and columns. The problem of locating the most significant bicluster has been shown to be NP-complete. Heuristic approaches such as Cheng and Church?s greedy node deletion algorithm have been previously employed. It is to be expected that stochastic search techniques such as evolutionary algorithms or simulated annealing might improve upon such greedy techniques. In this paper we show that an approach based on simulated annealing is well suited to this problem, and we present a comparative evaluation of simulated annealing and node deletion on a variety of datasets.We show that simulated annealing discovers more significant biclusters in many cases. Furthermore, we also test the ability of our technique to locate biologically verifiable biclusters within an annotated set of genes.
http://hdl.handle.net/2262/27024
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Aspirin and P2Y12 inhibition attenuate platelet-induced ovarian cancer cell invasion.
(2015)
Cooke, Niamh M; Spillane, Cathy D; Sheils, Orla; O'Leary, John; Kenny, Dermot
Aspirin and P2Y12 inhibition attenuate platelet-induced ovarian cancer cell invasion.
(2015)
Cooke, Niamh M; Spillane, Cathy D; Sheils, Orla; O'Leary, John; Kenny, Dermot
Abstract:
<p>The original article is available at www.biomedcentral.com</p>
<p>BACKGROUND: Platelet-cancer cell interactions play a key role in successful haematogenous metastasis. Disseminated malignancy is the leading cause of death among ovarian cancer patients. It is unknown why different ovarian cancers have different metastatic phenotypes. To investigate if platelet-cancer cell interactions play a role, we characterized the response of ovarian cancer cell lines to platelets both functionally and at a molecular level.</p> <p>METHODS: Cell lines 59 M and SK-OV-3 were used as in vitro model systems of metastatic ovarian cancer. Platelet cloaking of each cell line was quantified by flow cytometry. Matrigel invasion chamber assays were used to assess the invasive capacity of the cell lines. The induction of an EMT was assessed by morphology analysis and by gene expression analysis of a panel of 11 EMT markers using TaqMan RT-PCR.</p> <p>RESULTS: ...
https://epubs.rcsi.ie/mctart/76
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Autoinducer-2 plays a crucial role in gut colonization and probiotic functionality of Bifidobacterium breve UCC2003
(2014)
Christiaen, Steven E. A.; O'Connell Motherway, Mary; Bottacini, Francesca; Lanigan...
Autoinducer-2 plays a crucial role in gut colonization and probiotic functionality of Bifidobacterium breve UCC2003
(2014)
Christiaen, Steven E. A.; O'Connell Motherway, Mary; Bottacini, Francesca; Lanigan, Noreen; Casey, Pat G.; Huys, Geert; Nelis, Hans J.; van Sinderen, Douwe; Coenye, Tom
Abstract:
In the present study we show that luxS of Bifidobacterium breve UCC2003 is involved in the production of the interspecies signaling molecule autoinducer-2 (AI-2), and that this gene is essential for gastrointestinal colonization of a murine host, while it is also involved in providing protection against Salmonella infection in Caenorhabditis elegans. We demonstrate that a B. breve luxS-insertion mutant is significantly more susceptible to iron chelators than the WT strain and that this sensitivity can be partially reverted in the presence of the AI-2 precursor DPD. Furthermore, we show that several genes of an iron starvation-induced gene cluster, which are downregulated in the luxS-insertion mutant and which encodes a presumed iron-uptake system, are transcriptionally upregulated under in vivo conditions. Mutation of two genes of this cluster in B. breve UCC2003 renders the derived mutant strains sensitive to iron chelators while deficient in their ability to confer gut pathogen pr...
http://hdl.handle.net/10468/2338
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Avian Resistance to Campylobacter jejuni Colonization Is Associated with an Intestinal Immunogene Expression Signature Identified by mRNA Sequencing
(2014)
Connell, Sarah; Meade, Kieran G; Allan, Brenda; Lloyd, Andrew T; Kenny, Elaine; Cormica...
Avian Resistance to Campylobacter jejuni Colonization Is Associated with an Intestinal Immunogene Expression Signature Identified by mRNA Sequencing
(2014)
Connell, Sarah; Meade, Kieran G; Allan, Brenda; Lloyd, Andrew T; Kenny, Elaine; Cormican, Paul; Morris, Derek W.; Bradley, Daniel G; O'Farrelly, Cliona
Abstract:
This research was funded by the The Irish Department of Agriculture and Food’s Food Institutional Research Measure (http://www.agriculture.gov.ie/ research/foodinstitutionalresearchmeasurefirm) – Grant No: 06_RDD_486.
Campylobacter jejuni is the most common cause of human bacterial gastroenteritis and is associated with several post-infectious manifestations, including onset of the autoimmune neuropathy Guillain-Barré syndrome, causing significant morbidity and mortality. Poorly-cooked chicken meat is the most frequent source of infection as C. jejuni colonizes the avian intestine in a commensal relationship. However, not all chickens are equally colonized and resistance seems to be genetically determined. We hypothesize that differences in immune response may contribute to variation in colonization levels between susceptible and resistant birds. Using high-throughput sequencing in an avian infection model, we investigate gene expression associated with resistance or susceptibil...
http://hdl.handle.net/11019/709
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Bifidobacterium breve UCC2003 metabolises the human milk oligosaccharides lacto-N-tetraose and lacto-N-neo-tetraose through overlapping, yet distinct pathways
(2016)
James, Kieran; O'Connell Motherway, Mary; Bottacini, Francesca; van Sinderen, Douwe
Bifidobacterium breve UCC2003 metabolises the human milk oligosaccharides lacto-N-tetraose and lacto-N-neo-tetraose through overlapping, yet distinct pathways
(2016)
James, Kieran; O'Connell Motherway, Mary; Bottacini, Francesca; van Sinderen, Douwe
Abstract:
In this study, we demonstrate that the prototype B. breve strain UCC2003 possesses specific metabolic pathways for the utilisation of lacto-N-tetraose (LNT) and lacto-N-neotetraose (LNnT), which represent the central moieties of Type I and Type II human milk oligosaccharides (HMOs), respectively. Using a combination of experimental approaches, the enzymatic machinery involved in the metabolism of LNT and LNnT was identified and characterised. Homologs of the key genetic loci involved in the utilisation of these HMO substrates were identified in B. breve, B. bifidum, B. longum subsp. infantis and B. longum subsp. longum using bioinformatic analyses, and were shown to be variably present among other members of the Bifidobacterium genus, with a distinct pattern of conservation among human-associated bifidobacterial species.
http://hdl.handle.net/10468/3448
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CD44 enhances invasion of basal-like breast cancer cells by upregulating serine protease and collagen-degrading enzymatic expression and activity.
(2012)
Montgomery, Nicola; Hill, Ashleigh; McFarlane, Suzanne; Neisen, Jessica; O'Grady, ...
CD44 enhances invasion of basal-like breast cancer cells by upregulating serine protease and collagen-degrading enzymatic expression and activity.
(2012)
Montgomery, Nicola; Hill, Ashleigh; McFarlane, Suzanne; Neisen, Jessica; O'Grady, Anthony; Conlon, Susie; Jirstrom, Karin; Kay, Elaine W; Waugh, David JJ
Abstract:
<p>This article is also available from www. biomedcentral.com</p>
<p>ABSTRACT: INTRODUCTION: Basal-like breast cancers (BL-BCa) have the worst prognosis of all subgroups of this disease. Hyaluronan (HA) and the HA receptor CD44 have a long-standing association with cell invasion and metastasis of breast cancer. The purpose of this study was to establish the relation of CD44 to BL-BCa and to characterize how HA/CD44 signaling promotes a protease-dependent invasion of breast cancer (BrCa) cells. METHODS: CD44 expression was determined with immunohistochemistry (IHC) analysis of a breast cancer tissue microarray (TMA). In vitro experiments were performed on a panel of invasive BL-BCa cell lines, by using quantitative polymerase chain reaction (PCR), immunoblotting, protease activity assays, and invasion assays to characterize the basis of HA-induced, CD44-mediated invasion. RESULTS: Expression of the hyaluronan (HA) receptor CD44 associated with the basal-like sub...
https://epubs.rcsi.ie/pathart/6
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Ceratopteris richardii (C-Fern): a model for investigating adaptive modification of vascular plant cell walls
(2017)
Leroux, Olivier; Eeckhout, Sharon; Viane, Ronald L. L.; Popper, Zoë A.
Ceratopteris richardii (C-Fern): a model for investigating adaptive modification of vascular plant cell walls
(2017)
Leroux, Olivier; Eeckhout, Sharon; Viane, Ronald L. L.; Popper, Zoë A.
Abstract:
Plant cell walls are essential for most aspects of plant growth, development, and survival, including cell division, expansive cell growth, cell-cell communication, biomechanical properties, and stress responses. Therefore, characterizing cell wall diversity contributes to our overall understanding of plant evolution and development. Recent biochemical analyses, concomitantly with whole genome sequencing of plants located at pivotal points in plant phylogeny, have helped distinguish between homologous characters and those which might be more derived. Most plant lineages now have at least one fully sequenced representative and although genome sequences for fern species are in progress they are not yet available for this group. Ferns offer key advantages for the study of developmental processes leading to vascularisation and complex organs as well as the specific differences between diploid sporophyte tissues and haploid gametophyte tissues and the interplay between them. Ceratopteris...
http://hdl.handle.net/10379/6469
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Changes in the endometrial transcriptome during the bovine estrous cycle: effect of low circulating progesterone and consequences for conceptus elongation
(2014)
Forde, Niamh; Beltman, Marijke Eileen; Duffy, G. B.; Duffy, P.; Mehta, J. P.; Ó'Ga...
Changes in the endometrial transcriptome during the bovine estrous cycle: effect of low circulating progesterone and consequences for conceptus elongation
(2014)
Forde, Niamh; Beltman, Marijke Eileen; Duffy, G. B.; Duffy, P.; Mehta, J. P.; Ó'Gaora, P.; Roche, J. F.; Lonergan, Patrick; Crowe, Mark
Abstract:
In cattle, elevated concentrations of circulating progesterone (P4) in the immediate post-conception period have been associated with an advancement of conceptus elongation, an associated increase in interferon-tau production and higher pregnancy rates. Low P4 has been implicated as a causative factor in the low pregnancy rates observed in dairy cows. The aims of this study were (1) to describe the changes that occur in the bovine endometrial transcriptome during the estrous cycle, (2) to determine how elevated P4 affects the temporal pattern of gene expression in the endometrium of cyclic heifers, (3) to determine if the expression of these genes is altered in heifers with low P4 and (4) to determine the consequences of low P4 for conceptus development following embryo transfer. The main findings were that 1) relatively few differences occurred in endometrial gene expression during the early luteal phase of the estrous cycle under normal concentrations of P4 (Day 5 versus Day 7) bu...
http://hdl.handle.net/10197/5265
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Characterisation of the Whole Blood mRNA Transcriptome in Holstein-Friesian and Jersey Calves in Response to Gradual Weaning
(2016)
Johnston, Dayle; Earley, Bernadette; Cormican, Paul; Kenny, David A.; McCabe, Matthew; ...
Characterisation of the Whole Blood mRNA Transcriptome in Holstein-Friesian and Jersey Calves in Response to Gradual Weaning
(2016)
Johnston, Dayle; Earley, Bernadette; Cormican, Paul; Kenny, David A.; McCabe, Matthew; Kelly, Alan K; McGee, Mark; Waters, Sinead M.
Abstract:
Weaning of dairy calves is an early life husbandry management practice which involves the changeover from a liquid to a solid feed based diet. The objectives of the study were to use RNA-seq technology to examine the effect of (i) breed and (ii) gradual weaning, on the whole blood mRNA transcriptome of artificially reared Holstein-Friesian and Jersey calves. The calves were gradually weaned over 14 days (day (d) -13 to d 0) and mRNA transcription was examined one day before gradual weaning was initiated (d -14), one day after weaning (d 1), and 8 days after weaning (d 8). On d -14, 550 genes were differentially expressed between Holstein-Friesian and Jersey calves, while there were 490 differentially expressed genes (DEG) identified on d 1, and 411 DEG detected eight days after weaning (P < 0.05; FDR < 0.1). No genes were differentially expressed within breed, in response to gradual weaning (P > 0.05). The pathways, gene ontology terms, and biological functions consistently...
http://hdl.handle.net/11019/1082
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Clinical Applications of Molecular Profiling in Colorectal Cancer
(2012)
Kheirelseid, Elrasheid Ahmed Hassan
Clinical Applications of Molecular Profiling in Colorectal Cancer
(2012)
Kheirelseid, Elrasheid Ahmed Hassan
Abstract:
Despite developments in diagnosis and treatment, 20% of colorectal cancer (CRC) patients present with metastatic disease and 30% of cases recur after curative surgery. Furthermore, the molecular factors involved in prognosis and response to therapy in CRC are poorly understood. The objectives of this study were to examine the expression patterns of candidate miRNAs and mRNAs and proteins in CRC in order to identify molecular biomarkers for disease classification and prognostication. Expression patterns of miRNA and mRNA species were determined in FFPE and fresh colorectal tissues by microarray analysis and real-time quantitative PCR. Protein expression was determined by immunohistochemistry. Statistical analysis and correlation with clinicopathological data was performed using SPSS software. MiRNA signatures predictive of response of rectal cancer to neoadjuvant therapy were determined. Expression levels of CXCL12 (p=0.000), CDH17 (P=0.026), MUC2 (p=0.000), L-FABP (p=0.000) and PDCD...
http://hdl.handle.net/10379/2961
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Co-acting gene networks predict trail responsiveness of tumour cells with high accuracy
(2018)
O’Reilly, Paul; Ortutay, Csaba; Gernon, Grainne; O’Connell, Enda; Seoighe, Cathal; Boyc...
Co-acting gene networks predict trail responsiveness of tumour cells with high accuracy
(2018)
O’Reilly, Paul; Ortutay, Csaba; Gernon, Grainne; O’Connell, Enda; Seoighe, Cathal; Boyce, Susan; Serrano, Luis; Szegezdi, Eva
Abstract:
Background: Identification of differentially expressed genes from transcriptomic studies is one of the most common mechanisms to identify tumor biomarkers. This approach however is not well suited to identify interaction between genes whose protein products potentially influence each other, which limits its power to identify molecular wiring of tumour cells dictating response to a drug. Due to the fact that signal transduction pathways are not linear and highly interlinked, the biological response they drive may be better described by the relative amount of their components and their functional relationships than by their individual, absolute expression. Results: Gene expression microarray data for 109 tumor cell lines with known sensitivity to the death ligand cytokine tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) was used to identify genes with potential functional relationships determining responsiveness to TRAIL-induced apoptosis. The machine learning technique...
http://hdl.handle.net/10379/13313
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