oalib

Publish in OALib Journal

ISSN: 2333-9721

APC: Only $99

Submit

Any time

2019 ( 12 )

2018 ( 12 )

2017 ( 16 )

2016 ( 16 )

Custom range...

Search Results: 1 - 10 of 1258 matches for " Cathal Grace "
All listed articles are free for downloading (OA Articles)
Page 1 /1258
Display every page Item
Evolution: a view from the 21st century
Cathal Seoighe
Trends in Evolutionary Biology , 2012, DOI: 10.4081/eb.2012.e6
Abstract:
Stromal Expression of Decorin, Semaphorin6D, SPARC, Sprouty1 and Tsukushi in Developing Prostate and Decreased Levels of Decorin in Prostate Cancer
Alexander Henke, O. Cathal Grace, George R. Ashley, Grant D. Stewart, Antony C. P. Riddick, Henry Yeun, Marie O’Donnell, Richard A. Anderson, Axel A. Thomson
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0042516
Abstract: Background and Aim During prostate development, mesenchymal-epithelial interactions regulate organ growth and differentiation. In adult prostate, stromal-epithelial interactions are important for tissue homeostasis and also play a significant role in prostate cancer. In this study we have identified molecules that show a mesenchymal expression pattern in the developing prostate, and one of these showed reduced expression in prostate cancer stroma. Methodology and Principal Findings Five candidate molecules identified by transcript profiling of developmental prostate mesenchyme were selected using a wholemount in situ hybridisation screen and studied Decorin (Dcn), Semaphorin6D (Sema6D), SPARC/Osteonectin (SPARC), Sprouty1 (Spry-1) and Tsukushi (Tsku). Expression in rat tissues was evaluated using wholemount in situ hybridisation (postnatal day (P) 0.5) and immunohistochemistry (embryonic day (E) E17.5, E19.5; P0.5; P6; 28 & adult). Four candidates (Decorin, SPARC, Spry-1, Tsukushi) were immunolocalised in human foetal prostate (weeks 14, 16, 19) and expression of Decorin was evaluated on a human prostate cancer tissue microarray. In embryonic and perinatal rats Decorin, Semaphorin6D, SPARC, Spry-1 and Tsukushi were expressed with varying distribution patterns throughout the mesenchyme at E17.5, E19.5, P0.5 and P6.5. In P28 and adult prostates there was either a decrease in the expression (Semaphorin6D) or a switch to epithelial expression of SPARC, and Spry-1, whereas Decorin and Tsukushi were specific to mesenchyme/stroma at all ages. Expression of Decorin, SPARC, Spry-1 and Tsukushi in human foetal prostates paralleled that in rat. Decorin showed mesenchymal and stromal-specific expression at all ages and was further examined in prostate cancer, where stromal expression was significantly reduced compared with non-malignant prostate. Conclusion and Significance We describe the spatio-temporal expression of Decorin, Semaphorin6D, SPARC, Spry-1 and Tsukushi in developing prostate and observed similar mesenchymal expression patterns in rat and human. Additionally, Decorin showed reduced expression in prostate cancer stroma compared to non-malignant prostate stroma.
Transcriptional profiling of inductive mesenchyme to identify molecules involved in prostate development and disease
Griet Vanpoucke, Brigid Orr, O Cathal Grace, Ray Chan, George R Ashley, Karin Williams, Omar E Franco, Simon W Hayward, Axel A Thomson
Genome Biology , 2007, DOI: 10.1186/gb-2007-8-10-r213
Abstract: SAGE libraries were constructed from prostatic inductive mesenchyme and from the complete prostatic rudiment (including inductive mesenchyme, epithelium, and smooth muscle). By comparing these two SAGE libraries, we generated a list of 219 transcripts that were enriched or specific to inductive mesenchyme and that may act as mesenchymal regulators of organogenesis and tumorigenesis. We identified Scube1 as enriched in inductive mesenchyme from the list of 219 transcripts; also, quantitative RT-PCR and whole-mount in situ hybridization revealed Scube1 to exhibit a highly restricted expression pattern. The expression of Scube1 in a subset of mesenchymal cells suggests a role in prostatic induction and branching morphogenesis. Additionally, Scube1 transcripts were expressed in prostate cancer stromal cells, and were less abundant in cancer associated fibroblasts relative to matched normal prostate fibroblasts.The use of a precisely defined subset of cells and a back-comparison approach allowed us to identify rare mRNAs that could be overlooked using other approaches. We propose that Scube1 encodes a novel stromal molecule that is involved in prostate development and tumorigenesis.The mesenchymal compartment is involved in the induction and organogenesis of various organs, including lung, limb, kidney, pancreas, prostate, and mammary gland. In general, the process of organ induction begins with the formation of a specialized area of mesenchyme that acts upon adjacent epithelia to specify organ identity and subsequently dictates epithelial morphogenesis into the required form and function within the organ. The role played by inductive mesenchyme has been established using classical embryologic methods such as tissue recombination and engraftment, which have assayed the ability of spatially defined areas of mesenchyme to control morphogenesis and organogenesis. During organogenesis reciprocal interactions and signaling occur between the mesenchymal and epithelial compartm
The Pancreas Is Altered by In Utero Androgen Exposure: Implications for Clinical Conditions Such as Polycystic Ovary Syndrome (PCOS)
Mick Rae, Cathal Grace, Kirsten Hogg, Lisa Marie Wilson, Sophie L. McHaffie, Seshadri Ramaswamy, Janis MacCallum, Fiona Connolly, Alan S. McNeilly, Colin Duncan
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0056263
Abstract: Using an ovine model of polycystic ovary syndrome (PCOS), (pregnant ewes injected with testosterone propionate (TP) (100 mg twice weekly) from day (d)62 to d102 of d147 gestation (maternal injection – MI-TP)), we previously reported female offspring with normal glucose tolerance but hyperinsulinemia. We therefore examined insulin signalling and pancreatic morphology in these offspring using quantitative (Q) RT-PCR and western blotting. In addition the fetal pancreatic responses to MI-TP, and androgenic and estrogenic contributions to such responses (direct fetal injection (FI) of TP (20 mg) or diethylstilbestrol (DES) (20 mg) at d62 and d82 gestation) were assessed at d90 gestation. Fetal plasma was assayed for insulin, testosterone and estradiol, pancreatic tissue was cultured, and expression of key β-cell developmental genes was assessed by QRT-PCR. In female d62MI-TP offspring insulin signalling was unaltered but there was a pancreatic phenotype with increased numbers of β-cells (P<0.05). The fetal pancreas expressed androgen receptors in islets and genes involved in β-cell development and function (PDX1, IGF1R, INSR and INS) were up-regulated in female fetuses after d62MI-TP treatment (P<0.05–0.01). In addition the d62MI-TP pancreas showed increased insulin secretion under euglycaemic conditions (P<0.05) in vitro. The same effects were not seen in the male fetal pancreas or when MI-TP was started at d30, before the male programming window. As d62MI-TP increased both fetal plasma testosterone (P<0.05) and estradiol concentrations (P<0.05) we assessed the relative contribution of androgens and estrogens. FI-TP (commencing d62) (not FI-DES treatment) caused elevated basal insulin secretion in vitro and the genes altered by d62MI-TP treatment were similarly altered by FI-TP but not FI-DES. In conclusion, androgen over-exposure alters fetal pancreatic development and β-cell numbers in offspring. These data suggest that that there may be a primary pancreatic phenotype in models of PCOS, and that there may be a distinct male and female pancreas.
Modelling Financially Optimal Afforestation and Forest Management Scenarios Using a Bio-Economic Model  [PDF]
Mary Ryan, Cathal O’Donoghue, Henry Phillips
Open Journal of Forestry (OJF) , 2016, DOI: 10.4236/ojf.2016.61003
Abstract: The expansion of non-industrial private forests (NIPF) in Ireland is unique in the European context in which the almost doubling of forest cover within the last thirty years has taken place largely on farmland. This is not surprising as Ireland has some of the highest growth rates for conifers in Europe and also has a large proportion of land which is marginal for agriculture but highly productive under forests. However, in recent years, afforestation in Ireland as in many European countries has fallen well short of policy targets. As the farm afforestation decision essentially involves an inter-temporal land use change, farmers need comprehensive information on forest market returns under different environmental conditions and forest management regimes. This paper describes the systematic development of a cohort forest bio-economic model which examines financially optimal afforestation and management choices. Simulating a range of productivity and harvesting scenarios for Sitka spruce, we find that different objectives result in different outcomes. We see substantial differences between the biologically optimal rotation, the reduced rotation in common usage and the financially optimal rotation which maximises net present value and find that the results are particularly sensitive to the choice of management and methodological assumptions. Specifically, we find that better site productivity and thin versus no-thin options result in shorter rotations across all optimisations, reinforcing the usefulness of this type of financial modelling approach. This information is critical for future policy design to further incentivise afforestation of agricultural land.
Heritability in the Efficiency of Nonsense-Mediated mRNA Decay in Humans
Cathal Seoighe,Chris Gehring
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0011657
Abstract: In eukaryotes mRNA transcripts of protein-coding genes in which an intron has been retained in the coding region normally result in premature stop codons and are therefore degraded through the nonsense-mediated mRNA decay (NMD) pathway. There is evidence in the form of selective pressure for in-frame stop codons in introns and a depletion of length three introns that this is an important and conserved quality-control mechanism. Yet recent reports have revealed that the efficiency of NMD varies across tissues and between individuals, with important clinical consequences.
A flexible R package for nonnegative matrix factorization
Renaud Gaujoux, Cathal Seoighe
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-367
Abstract: Our objective is to provide the bioinformatics community with an open-source, easy-to-use and unified interface to standard NMF algorithms, as well as with a simple framework to help implement and test new NMF methods. For that purpose, we have developed a package for the R/BioConductor platform. The package ports public code to R, and is structured to enable users to easily modify and/or add algorithms. It includes a number of published NMF algorithms and initialization methods and facilitates the combination of these to produce new NMF strategies. Commonly used benchmark data and visualization methods are provided to help in the comparison and interpretation of the results.The NMF package helps realize the potential of Nonnegative Matrix Factorization, especially in bioinformatics, providing easy access to methods that have already yielded new insights in many applications. Documentation, source code and sample data are available from CRAN.The factorization of matrices representing complex multidimensional datasets is the basis of several commonly applied techniques for pattern recognition and unsupervised clustering. Similarly to principal components analysis (PCA) or independent component analysis (ICA), the objective of non-negative matrix factorization (NMF) is to explain the observed data using a limited number of basis components, which when combined together approximate the original data as accurately as possible. The distinguishing features of NMF are that both the matrix representing the basis components as well as the matrix of mixture coefficients are constrained to have non-negative entries, and that no orthogonality or independence constraints are imposed on the basis components. This leads to a simple and intuitive interpretation of the factors in NMF, and allows the basis components to overlap.Since its formal definition in [1,2], the NMF approach has been applied successfully in several fields including image and pattern recognition, signal process
Application of statistical process control to qualitative molecular diagnostic assays
Cathal P. O'Brien
Frontiers in Molecular Biosciences , 2014, DOI: 10.3389/fmolb.2014.00018
Abstract: Modern pathology laboratories and in particular high throughput laboratories such as clinical chemistry have developed a reliable system for statistical process control (SPC). Such a system is absent from the majority of molecular laboratories and where present is confined to quantitative assays. As the inability to apply SPC to an assay is an obvious disadvantage this study aimed to solve this problem by using a frequency estimate coupled with a confidence interval calculation to detect deviations from an expected mutation frequency. The results of this study demonstrate the strengths and weaknesses of this approach and highlight minimum sample number requirements. Notably, assays with low mutation frequencies and detection of small deviations from an expected value require greater sample numbers to mitigate a protracted time to detection. Modeled laboratory data was also used to highlight how this approach might be applied in a routine molecular laboratory. This article is the first to describe the application of SPC to qualitative laboratory data.
Prioritizing Software Inspection Results using Static Profiling
Cathal Boogerd,Leon Moonen
Computer Science , 2006,
Abstract: Static software checking tools are useful as an additional automated software inspection step that can easily be integrated in the development cycle and assist in creating secure, reliable and high quality code. However, an often quoted disadvantage of these tools is that they generate an overly large number of warnings, including many false positives due to the approximate analysis techniques. This information overload effectively limits their usefulness. In this paper we present ELAN, a technique that helps the user prioritize the information generated by a software inspection tool, based on a demand-driven computation of the likelihood that execution reaches the locations for which warnings are reported. This analysis is orthogonal to other prioritization techniques known from literature, such as severity levels and statistical analysis to reduce false positives. We evaluate feasibility of our technique using a number of case studies and assess the quality of our predictions by comparing them to actual values obtained by dynamic profiling.
Evidence for intron length conservation in a set of mammalian genes associated with embryonic development
Seoighe Cathal,Korir Paul K
BMC Bioinformatics , 2011, DOI: 10.1186/1471-2105-12-s9-s16
Abstract: Background We carried out an analysis of intron length conservation across a diverse group of nineteen mammalian species. Motivated by recent research suggesting a role for time delays associated with intron transcription in gene expression oscillations required for early embryonic patterning, we searched for examples of genes that showed the most extreme conservation of total intron content in mammals. Results Gene sets annotated as being involved in pattern specification in the early embryo or containing the homeobox DNA-binding domain, were significantly enriched among genes with highly conserved intron content. We used ancestral sequences reconstructed with probabilistic models that account for insertion and deletion mutations to distinguish insertion and deletion events on lineages leading to human and mouse from their last common ancestor. Using a randomization procedure, we show that genes containing the homeobox domain show less change in intron content than expected, given the number of insertion and deletion events within their introns. Conclusions Our results suggest selection for gene expression precision or the existence of additional development-associated genes for which transcriptional delay is functionally significant.
Page 1 /1258
Display every page Item


Home
Copyright © 2008-2017 Open Access Library. All rights reserved.