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High-Throughput Proteomics Detection of Novel Splice Isoforms in Human Platelets
Karen A. Power, James P. McRedmond, Andreas de Stefani, William M. Gallagher, Peadar ó Gaora
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0005001
Abstract: Alternative splicing (AS) is an intrinsic regulatory mechanism of all metazoans. Recent findings suggest that 100% of multiexonic human genes give rise to splice isoforms. AS can be specific to tissue type, environment or developmentally regulated. Splice variants have also been implicated in various diseases including cancer. Detection of these variants will enhance our understanding of the complexity of the human genome and provide disease-specific and prognostic biomarkers. We adopted a proteomics approach to identify exon skip events - the most common form of AS. We constructed a database harboring the peptide sequences derived from all hypothetical exon skip junctions in the human genome. Searching tandem mass spectrometry (MS/MS) data against the database allows the detection of exon skip events, directly at the protein level. Here we describe the application of this approach to human platelets, including the mRNA-based verification of novel splice isoforms of ITGA2, NPEPPS and FH. This methodology is applicable to all new or existing MS/MS datasets.
Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser
David A Fitzpatrick, Peadar O'Gaora, Kevin P Byrne, Geraldine Butler
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-290
Abstract: CGOB assignments of homology were manually curated based on sequence similarity and synteny. In total CGOB includes 65617 genes arranged into 13625 homology columns. We have also generated improved Candida gene sets by merging/removing partial genes in each genome. Interrogation of CGOB revealed that the majority of tandemly duplicated genes are under strong purifying selection in all Candida species. We identified clusters of adjacent genes involved in the same metabolic pathways (such as catabolism of biotin, galactose and N-acetyl glucosamine) and we showed that some clusters are species or lineage-specific. We also identified one example of intron gain in C. albicans.Our analysis provides an important resource that is now available for the Candida community. CGOB is available at http://cgob.ucd.ie webcite.Fungal infections are the fourth most common nosocomial bloodstream infection in the United States. Candida species account for approximately 10% of all bloodstream infections [1] and worldwide are the most common cause of opportunistic fungal infection [2]. Due to their increasing clinical importance, recent sequencing projects have determined the complete sequence of ten Candida genomes, including common pathogenic species and species rarely, if ever, associated with disease [3-7].The term Candida was originally assigned to imperfect yeast species, with no known sexual cycle. This term now covers a variety of species of diverse origins (both sexual and asexual), and provides little information regarding evolutionary relationships. For example, Candida glabrata is more closely related to Saccharomyces cerevisiae than it is to Candida albicans. Debaryomyces hansenii and Pichia stipitis are close relatives of Candida species [8]. Some species, such as C. lusitaniae, were assigned two names, one (Candida lusitaniae) referring to the asexual (anamorph) form, and one (Clavispora lusitaniae) to the sexual (teleomorph) form. Similarly, Candida guilliermondii is also
Bi-directional gene set enrichment and canonical correlation analysis identify key diet-sensitive pathways and biomarkers of metabolic syndrome
Melissa J Morine, Jolene McMonagle, Sinead Toomey, Clare M Reynolds, Aidan P Moloney, Isobel C Gormley, Peadar ó Gaora, Helen M Roche
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-499
Abstract: Here, we apply an approach to gene set enrichment analysis that allows for detection of bi-directional enrichment within a gene set. Furthermore, we apply canonical correlation analysis and Fisher's exact test, using plasma marker data with known clinical relevance to aid identification of the most important gene and pathway changes in our transcriptomic dataset. After a 28-day dietary intervention with high-CLA beef, a range of plasma markers indicated a marked improvement in the metabolic health of genetically obese mice. Tissue transcriptomic profiles indicated that the effects were most dramatic in liver (1270 genes significantly changed; p < 0.05), followed by muscle (601 genes) and adipose (16 genes). Results from modified GSEA showed that the high-CLA beef diet affected diverse biological processes across the three tissues, and that the majority of pathway changes reached significance only with the bi-directional test. Combining the liver tissue microarray results with plasma marker data revealed 110 CLA-sensitive genes showing strong canonical correlation with one or more plasma markers of metabolic health, and 9 significantly overrepresented pathways among this set; each of these pathways was also significantly changed by the high-CLA diet. Closer inspection of two of these pathways - selenoamino acid metabolism and steroid biosynthesis - illustrated clear diet-sensitive changes in constituent genes, as well as strong correlations between gene expression and plasma markers of metabolic syndrome independent of the dietary effect.Bi-directional gene set enrichment analysis more accurately reflects dynamic regulatory behaviour in biochemical pathways, and as such highlighted biologically relevant changes that were not detected using a traditional approach. In such cases where transcriptomic response to treatment is exceptionally large, canonical correlation analysis in conjunction with Fisher's exact test highlights the subset of pathways showing strongest cor
Political Participation of Civil Society in Latin America
Peadar Kirby
European Review of Latin American and Caribbean Studies , 2013,
Abstract: Review Essay of: – Social Movements and Leftist Governments in Latin America: Confrontation or co-optation?, edited by Gary Prevost, Carlos Oliva Campos and Harry E. Vanden, Zed Books, 2012. – Culturas políticas en la región andina, edited by Christian Buschges, Olaf Kaltmeier and Sebastian Thies, Iberoamericana, 2011. – La plasmación política de la diversidad: Autonomía y participación política indígena en América Latina, edited by Felipe Gómez Isa and Susana Ardanaz Iriarte, Universidad de Deusto, 2011. – Venezuela's Bolivarian Democracy: Participation, Politics, and Culture under Chávez, edited by David Smilde and Daniel Hellinger, Duke University Press, 2011.
Primary ciliary dyskinesia: a report from ATS 2001, May 18–23, San Francisco
Peadar G Noone
Respiratory Research , 2001, DOI: 10.1186/rr75
Abstract: The American Thoracic Society Meeting was held this year in San Francisco, California. This meeting is the largest scientific meeting in the world targeted to diseases of the lung, with several thousand delegates in attendance in 2001. Clinicians, scientists, and clinician-scientists attended the meeting, together with a range of personnel from allied fields. Though the main emphasis of the meeting is on the common lung diseases, generally, each year relatively rare diseases get some special attention. This year, on consecutive days there were two sessions on primary ciliary dyskinesia (PCD), a genetic disease of ciliary structure and function. The sessions were well attended by delegates from a range of disciplines, and the speakers were selected from across the research spectrum. The aims of the presentations were to provide updates on the nature of the disease and its use as a human disease model, and also to report exciting new findings in relation to clinical aspects, cell biology and genetics.The aspects of the clinical features of PCD were reviewed by two featured speakers, Peter Cole (Host Defence Unit, Brompton Hospital London, UK) and Peadar Noone (University of North Carolina at Chapel Hill, USA). Aruna Sannuti (University of North Carolina at Chapel Hill, USA) also presented clinical and phenotypic data from a prospective study of a large cohort of patients with PCD. The high proportion of patients with a history of neonatal respiratory distress, recurrent otitis media, and a requirement for ear drainage tubes was again emphasized. The importance of a careful diagnostic work-up and accurate phenotyping for subsequent genetic studies was stressed. Of particular note was the report of isolation of mucoid Pseudomonas aeruginosa in older patients (9 out of 54) with PCD. This is usually regarded as a strong marker of cystic fibrosis (CF), a similar but distinct airway host defence disease. Normal ion transport in nasal epithelia in a subset of patients, the p
A review of factors influencing litter size in Irish sows
Peadar G Lawlor, P Brendan Lynch
Irish Veterinary Journal , 2007, DOI: 10.1186/2046-0481-60-6-359
Abstract: In the past 20 years, litter size in Irish sows has increased by almost one pig. However, most of this increase had occurred by 1996. Since then, litter size has increased by only 0.40 of a pig (Table 1). When broken down into quartiles, the 2005 PIGSYS data show that there is a difference of 1.1 pigs in number born alive and in total born between the top 25% and bottom 25% performing herds (Table 2). However, even the top quartile is falling behind our European competitors (Table 3). Denmark, for example, had an average born alive figure of 12.7 in 2004 compared to the 11.6 figure for the top 25% of Irish herds in 2005.This paper will attempt to address some of the factors that are limiting litter size in Ireland. Genetics is obviously an important factor in this regard (but will be discussed only briefly here). However, genetic improvements are worthless unless we possess the management and nutritional information to exploit these advances. Therefore, this paper will concentrate on some of the management and nutrition factors that can make the most improvements in litter size.As a result of heterosis, litter size of crossbred sows is on average 0.25 to 0.5 pigs greater than that of purebred sows [1]. Literature estimates of heritability of litter size range between 0 and 0.76 with an average of 0.10 [33]. A policy of selecting gilts from prolific sows, and serving them with boars from a prolific dam line, will gradually increase litter size over time because litter size and its component traits (ovulation rate, embryonic survival and uterine capacity) respond to selection [18]. However, it has been suggested that genetic improvement programmes should emphasise live born pigs and weight of live born pigs because of undesirable genetic relationships between ovulation rate and number of foetuses with numbers of stillborn and mummified pigs and because birth weight has decreased as litter size has increased [18].One of the most important determinants of litter size is
'CFTR-opathies': disease phenotypes associated with cystic fibrosis transmembrane regulator gene mutations
Peadar G Noone, Michael R Knowles
Respiratory Research , 2001, DOI: 10.1186/rr82
Abstract: Cystic fibrosis (CF) is a recessive genetic disease that is caused by mutations on both CFTR alleles, resulting in abnormal sweat electrolytes, sino-pulmonary disease, male infertility, and pancreatic exocrine insufficiency in 95% of patients [1,2]. In its classic form, the disease is easily diagnosed early in life, through a combination of clinical evaluation and laboratory testing (including sweat testing, and CFTR mutation analysis) [3]. Depending on the ethnic background of the populations tested, common genetic mutations are identified in the majority of cases of CF. In the USA, two-thirds of patients carry at least one copy of the ΔF508 mutation, with approximately 50% of CF patients being homozygous for this mutation [4].A wide spectrum of molecular abnormalities may occur in the CFTR gene, and uncommon mutations that result in partial (residual) CFTR function may be associated with nonclassic presentations of disease. Overall, 7% of CF patients are not diagnosed until age 10 years, with a proportion not diagnosed until after age 15 years; some of these patients present a considerable challenge in establishing a diagnosis of CF. Moreover, the phenotype in these patients may vary widely [5,6]. The focus of the present review is on nonclassic phenotypes associated with mutations in the CFTR gene, which may manifest as male infertility (congenital bilateral absence of the vas deferens [CBAVD]), mild pulmonary disease and idiopathic chronic pancreatitis (ICP). These phenotypes are included within the definition of 'atypical CF'.CFTR is a transmembrane spanning protein with multiple activities that are related to normal epithelial cell function [2]. Mutations in CFTR result in abnormalities in epithelial ion and water transport, which are associated with derangements in airway mucociliary clearance and other cellular functions related to normal cell biology [7]. Depending on the molecular abnormality, the defect in CFTR may be the equivalent of that associated wit
Prebiotics from Marine Macroalgae for Human and Animal Health Applications
Laurie O’Sullivan,Brian Murphy,Peter McLoughlin,Patrick Duggan,Peadar G. Lawlor,Helen Hughes,Gillian E. Gardiner
Marine Drugs , 2010, DOI: 10.3390/md8072038
Abstract: The marine environment is an untapped source of bioactive compounds. Specifically, marine macroalgae (seaweeds) are rich in polysaccharides that could potentially be exploited as prebiotic functional ingredients for both human and animal health applications. Prebiotics are non-digestible, selectively fermented compounds that stimulate the growth and/or activity of beneficial gut microbiota which, in turn, confer health benefits on the host. This review will introduce the concept and potential applications of prebiotics, followed by an outline of the chemistry of seaweed polysaccharides. Their potential for use as prebiotics for both humans and animals will be highlighted by reviewing data from both in vitro and in vivo studies conducted to date.
Measurements of the acid-binding capacity of ingredients used in pig diets
Peadar G Lawlor, P Brendan Lynch, Patrick J Caffrey, James J O'Reilly, M Karen O'Connell
Irish Veterinary Journal , 2005, DOI: 10.1186/2046-0481-58-8-447
Abstract: In the pig, protein digestion begins in the stomach with the action of pepsins, secreted as the enzyme precursors - pepsinogens - by stomach mucosa. Conversion of pepsinogen to pepsin occurs rapidly at pH 2.0 but only slowly at pH 5.0 to 6.0. In turn, pepsins work best in an acidic environment, pH 2.0 to 3.5, and activity declines rapidly above this pH. Carbohydrate hydrolysis in the stomach occurs by the action of salivary amylase, which, in contrast to pepsin, is inactivated once pH falls to 3.5 [14,18,22].In the suckling pig, acid secretion is low and the principal source of acidity is bacterial fermentation of lactose from sows milk to lactic acid [9,10,14]. A high level of lactate in the stomach tends to inhibit HCl secretion [10,22]. Ingestion of solid feed reduces the level of lactic acid in the stomach [22] and stimulates HCl production [10,7] but, in practice, creep feed consumption is low and variable at least up to four weeks of age [15].At weaning, a combination of low acid secretion, lack of lactose substrate, and consumption of large meals at infrequent intervals can result in elevated pH, often to over 5.0 and it may remain high for several days [14]. The high acid-binding/buffering capacity of the feed (its ability to neutralise feed acid) helps to further raise the stomach pH [20,13,6]. Inclusion of whey or lactose in the starter diet ensures continuation of bacterial fermentation and some, though reduced, lactic acid production [14,11]. Development of HCl secretory capacity occurs more rapidly in the weaned pig than in the suckling pig [8].Lowering the acid-binding capacity of diets for newly-weaned pigs can help ease the transition from milk to solid food at weaning.Raised stomach pH after weaning results in reduced digestion of feed which will then be fermented in the hind gut and may provoke diarrhoea. A high gastric pH will also allow pathogens to survive and allow them greater opportunity to colonise the digestive tract [6,22].The concept of m
The Effect of Feeding Bt MON810 Maize to Pigs for 110 Days on Intestinal Microbiota
Stefan G. Buzoianu, Maria C. Walsh, Mary C. Rea, Orla O’Sullivan, Fiona Crispie, Paul D. Cotter, R. Paul Ross, Gillian E. Gardiner, Peadar G. Lawlor
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0033668
Abstract: Objective To assess the effects of feeding Bt MON810 maize to pigs for 110 days on the intestinal microbiota. Methodology/Principal Findings Forty male pigs (~40 days old) were blocked by weight and litter ancestry and assigned to one of four treatments; 1) Isogenic maize-based diet for 110 days (Isogenic); 2) Bt maize-based diet (MON810) for 110 days (Bt); 3) Isogenic maize-based diet for 30 days followed by a Bt maize-based diet for 80 days (Isogenic/Bt); 4) Bt maize-based diet for 30 days followed by an isogenic maize-based diet for 80 days (Bt/Isogenic). Enterobacteriaceae, Lactobacillus and total anaerobes were enumerated in the feces using culture-based methods on days 0, 30, 60 and 100 of the study and in ileal and cecal digesta on day 110. No differences were found between treatments for any of these counts at any time point. The relative abundance of cecal bacteria was also determined using high-throughput 16 S rRNA gene sequencing. No differences were observed in any bacterial taxa between treatments, with the exception of the genus Holdemania which was more abundant in the cecum of pigs fed the isogenic/Bt treatment compared to pigs fed the Bt treatment (0.012 vs 0.003%; P≤0.05). Conclusions/Significance Feeding pigs a Bt maize-based diet for 110 days did not affect counts of any of the culturable bacteria enumerated in the feces, ileum or cecum. Neither did it influence the composition of the cecal microbiota, with the exception of a minor increase in the genus Holdemania. As the role of Holdemania in the intestine is still under investigation and no health abnormalities were observed, this change is not likely to be of clinical significance. These results indicate that feeding Bt maize to pigs in the context of its influence on the porcine intestinal microbiota is safe.
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