Olive DSI
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ABSTRACT:
PROVIDER: PRJEB53314 | ENA |
REPOSITORIES: ENA
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Project description:Analysis of gene-expression profiles by microarrays can be very useful to characterize new potential candidate genes, key regulatory networks, and to define phenotypes or molecular signatures to improve the diagnosis or classification of the disease. We have used this approach in the study of one of the major causes of allergic diseases in Mediterranean countries, the olive pollen response, in order to find differential molecular markers among five clinical groups, Non-allergic, Asymptomatic, Allergic but not to olive pollen, Non-treated, olive pollen allergic patients and Olive pollen allergic patients (under specific-immunotherapy). The results of gene-expression by principal components analysis (PCA) clearly showed five clusters of samples that correlated with the five clinical groups. Analysis of differential gene-expression by multiple testing, and functional analysis by KEGG and Gene-Ontology revealed differential genes and pathways among the 5 clinical groups. The study population comprised 28 subjects, selected from a previous immunological study (Aguerri et al. Eur. J. Inflammation 2012, in press), from Andalusia, who were recruited in 2 olive pollen exposure situations: during (April-June) and outside the pollen season (October-December). We established 5 groups, and 6 subjects from each group were selected for gene-expression analysis: Group 1, non-allergic subjects; Group 2, asymptomatic subjects (diagnosed with olive pollen allergy by skin testing, with no seasonal respiratory symptoms [rhinitis and/or asthma], and who consulted for adverse reaction to drugs); Group 3, patients who were allergic, but not to olive pollen; Group 4, non-treated olive pollenM-bM-^@M-^Sallergic; and Group 5, olive pollenM-bM-^@M-^Sallergic patients (receiving olive pollenM-bM-^@M-^Sspecific immunotherapy).The subjects were unrelated and recruited at the Allergy Service of 4 hospitals in Andalusia (Granada, JaM-CM-)n, Sevilla, and MM-CM-!laga). Olive pollenM-bM-^@M-^Sallergic patients fulfilled the following criteria: seasonal rhinitis and/or asthma from April to June, a positive skin prick test result for O. europaea pollen extract (ALK AbellM-CM-3, Madrid, Spain), and no previous immunotherapy. Informed consent was obtained from each subject. Ethical approval for the study was obtained from the Ethical and Research Committee of the participating hospitals. PBMCs were isolated from heparin-containing peripheral blood samples taken during and outside pollen season, by gradient centrifugation on Lymphoprep (Comercial Rafer, Zaragoza, Spain) following the manufacturerM-bM-^@M-^Ys instructions.
2013-02-28 | E-GEOD-37157 | biostudies-arrayexpress
Project description:Olive oil is protective against risk factors for cardiovascular and cancer diseases. A nutrigenomic approach was performed to assess whether olive oil, the main fat of the Mediterranean diet modifies the gene expression in human peripheral blood mononuclear cells. Six healthy male volunteers ingested, at fasting state, 50 ml of olive oil, and continued with the same olive oil as a source of raw fat (25ml/day) during 3 weeks. Prior to intervention a 1-week washout period with sunflower oil as the only source of fat was followed. During the 3 days before, and on the intervention day, a very low phenolic compound diet was followed. At baseline (0h), at post ingestion (6h), and at fasting state after 3 weeks of sustained consumption of olive oil total RNA was isolated from PBMC. Gene expression was evaluated by microarray and verified by qRT-PCR. Keywords: Olive oil, gene expression, single dose, sustained consumption
2008-02-21 | GSE10590 | GEO
Project description:Supplementing diets with olive by-products offers promising benefits for alleviating animal feeding stress without compromising growth. The aim of this study was to explore the transcriptome of backfat in Iberian pigs fed with two diets based in olive by-products. The pigs were divided in three diet groups: a Control (C) group, a dry olive pulp (DOP) group, which was fed a compound feed elaborated with olive pulp, and a wet crude olive cake (WCOC) group, which was fed a compound feed and olive cake silage supplied ad libitum. Subcutaneous fat biopsies were taken, and transcriptome analysis performed. Compared to a C group, we identified 411 and 924 genes as differentially expressed (DEG; q<0.05, Fold Change>1.5) between the DOP and WCOC diets, respectively. In DOP diet, functions related to polysaccharides metabolism were significantly activated, while WCOC exhibited activated biological processes associated with apoptosis and cellular death. Both diets showed inhibition of functions involved in inflammatory and immune responses, as well as reactive oxygen species production, although enriched by different DEGs. Furthermore, in the WCOC diet, functions related to cholesterol and lipid metabolism were suppressed. In both comparisons, the ADIPOQ gene was overexpressed, playing a key role in the majority of affected functions. In conclusion, our findings suggest that olive by-products may significantly influence the health status of animals, offering potential benefits in enhancing their overall well-being.
2024-07-01 | GSE264195 | GEO
Project description:The delineation of the olive pollen proteome and its allergogram can improve the clinical management of patients with this pollinosis. We here integrated the recently described wild olive genomic data in a comprehensive proteomic approach to get the annotated olive (Olea europaea) pollen proteome and complete its complex allergogram. Olive pollen proteins were identified by LC-MS/MS using predicted protein sequences from its genome. GO annotation, KEGG Pathway analysis and identification of allergen families were performed by bioinformatics. Recombinant DNA, protein expression and purification, and immunological analyses were used to characterize putative allergens. A total of 1,907 proteins were identified. 60% of the proteins were predicted to possess catalytic activity and be involved in metabolic processes. 203 proteins belonging to 47 allergen families were found, with 37 non-previously described in olive pollen. Of four potential allergens produced in Escherichia coli, a peptidyl-prolyl cis-trans isomerase -cyclophilin-, masked in the protein extract by the major allergen Ole e 1, was found as a new olive pollen allergen (Ole e 15). 63% of the Ole e 15-sensitized patients were children and showed strong IgE recognition of the allergen. Ole e 15 shared high sequence identity with other plant, animal and fungal cyclophilins and a high IgE cross-reactivity with pollen, plant food and animal extracts. Taken together, the combination of available genomic data with proteomics permitted the profiling of the olive pollen proteome, revealing the spectrum of allergen families and cyclophilin as a new relevant allergen implicated in cross-reactivity.
2019-06-17 | PXD012279 | Pride
Project description:Olive oil is protective against risk factors for cardiovascular and cancer diseases. A nutrigenomic approach was performed to assess whether olive oil, the main fat of the Mediterranean diet modifies the gene expression in human peripheral blood mononuclear cells. Six healthy male volunteers ingested, at fasting state, 50 ml of olive oil, and continued with the same olive oil as a source of raw fat (25ml/day) during 3 weeks. Prior to intervention a 1-week washout period with sunflower oil as the only source of fat was followed. During the 3 days before, and on the intervention day, a very low phenolic compound diet was followed. At baseline (0h), at post ingestion (6h), and at fasting state after 3 weeks of sustained consumption of olive oil total RNA was isolated from PBMC. Gene expression was evaluated by microarray and verified by qRT-PCR. Keywords: Olive oil, gene expression, single dose, sustained consumption Three pools of total RNA were prepared in triplicates (9 samples in total). Each pool refers to different time point of the study (0h-wash out, 6h postprandial and 3 weeks intervention). Pool at 0h serves as reference sample.
2010-05-26 | E-GEOD-10590 | biostudies-arrayexpress
Project description:HLA-B27 transgenic rats, experimental model of chronic colitis, fed with a diet in which the lipid component was provided by corn oil (CO group), extra-virgin olive oil rich in phenols, 718.8 mg of total phenols/kg of olive oil (EVOO group) or the same extra-virgin olive oil, deprived of phenolic compounds but retaining other minor components such as a-tocopherol (ROO group).
2018-11-26 | E-MTAB-6218 | biostudies-arrayexpress
Project description:The delineation of the olive pollen proteome and its allergogram can improve the clinical management of patients with this pollinosis. We here integrated the recently described wild olive genomic data in a comprehensive proteomic approach to get the annotated olive (Olea europaea) pollen proteome and complete its complex allergogram. Olive pollen proteins were identified by LC-MS/MS using predicted protein sequences from its genome. GO annotation, KEGG Pathway analysis and identification of allergen families were performed by bioinformatics. Recombinant DNA, protein expression and purification, and immunological analyses were used to characterize putative allergens. A total of 1,907 proteins were identified. 60% of the proteins were predicted to possess catalytic activity and be involved in metabolic processes. 203 proteins belonging to 47 allergen families were found, with 37 non-previously described in olive pollen. Of four potential allergens produced in Escherichia coli, a peptidyl-prolyl cis-trans isomerase -cyclophilin-, masked in the protein extract by the major allergen Ole e 1, was found as a new olive pollen allergen (Ole e 15). 63% of the Ole e 15-sensitized patients were children and showed strong IgE recognition of the allergen. Ole e 15 shared high sequence identity with other plant, animal and fungal cyclophilins and a high IgE cross-reactivity with pollen, plant food and animal extracts. Taken together, the combination of available genomic data with proteomics permitted the profiling of the olive pollen proteome, revealing the spectrum of allergen families and cyclophilin as a new relevant allergen implicated in cross-reactivity.
2019-06-17 | PXD012280 | Pride
Project description:The delineation of the olive pollen proteome and its allergogram can improve the clinical management of patients with this pollinosis. We here integrated the recently described wild olive genomic data in a comprehensive proteomic approach to get the annotated olive (Olea europaea) pollen proteome and complete its complex allergogram. Olive pollen proteins were identified by LC-MS/MS using predicted protein sequences from its genome. GO annotation, KEGG Pathway analysis and identification of allergen families were performed by bioinformatics. Recombinant DNA, protein expression and purification, and immunological analyses were used to characterize putative allergens. A total of 1,907 proteins were identified. 60% of the proteins were predicted to possess catalytic activity and be involved in metabolic processes. 203 proteins belonging to 47 allergen families were found, with 37 non-previously described in olive pollen. Of four potential allergens produced in Escherichia coli, a peptidyl-prolyl cis-trans isomerase -cyclophilin-, masked in the protein extract by the major allergen Ole e 1, was found as a new olive pollen allergen (Ole e 15). 63% of the Ole e 15-sensitized patients were children and showed strong IgE recognition of the allergen. Ole e 15 shared high sequence identity with other plant, animal and fungal cyclophilins and a high IgE cross-reactivity with pollen, plant food and animal extracts. Taken together, the combination of available genomic data with proteomics permitted the profiling of the olive pollen proteome, revealing the spectrum of allergen families and cyclophilin as a new relevant allergen implicated in cross-reactivity.
2019-06-17 | PXD012334 | Pride
Project description:Plant architecture is a critical trait in fruit crops that can significantly influence yield, pruning, planting density and harvesting. Most of the existing varieties of olive are traditional and their architecture is poorly suited for modern growing and harvesting systems. This study focuses on the identification of candidate genes involved in determining plant architecture in olive that could help in selecting phenotypes adapted to modern cultivation practices. We previously developed the first microarray for olive, as a means to discover candidate genes involved in relevant agronomical traits. The microarray has already been applied to identify candidates genes involved in regulating juvenile to adult transition in the shoot apex of seedlings. In the present study, made in the framework of an olive breeding program, varieties displaying differences in architecture and pooled seedlings grouped by their architecture-related phenotypes, were analysed using microarray analysis of meristematic tissue. We identify 2,258 differentially expressed genes potentially involved in determining plant architecture. Varieties with opposite architecture phenotypes and individuals from segregating progenies displaying extreme architecture features, constitute our key to linking phenotype to expression. We analyze some of the genes with potentially interesting functional annotation using quantitative RT-PCR assays, in the reference varieties and individual seedlings. Arabidopsis mutants in putative orthologs of some of the candidate genes show altered architecture, indicating functional conservation between the two species and supporting both, the biological relevance of the results, and the potential of the identified genes as markers for assisted breeding for olive varieties suited for high density orchards.
2016-02-15 | GSE60284 | GEO
Project description:Proteins and peptides are minor components of vegetal oils. The presence of these compounds in virgin olive oil was first reported in 2001, but the nature of the olive oil proteome is still a puzzling question for food science researchers. In this project, we have compiled for a first time a comprehensive proteomic dataset of olive fruit and fungal proteins that are present at low but measurable concentrations in a vegetable oil from a crop of great agronomical relevance as olive (Olea europaea L.). Accurate mass nLC-MS data were collected in high definition direct data analysis (HD-DDA) mode using the ion mobility separation step. Protein identification was performed using the Mascot Server v2.2.07 software (Matrix Science) against an ad hoc database made of olive protein entries. Starting from this proteomic record, the impact of these proteins on olive oil stability and quality could be tested. Moreover, the effect of olive oil proteins on human health and their potential use as functional food components could be also evaluated. In addition, this dataset provides a resource for use in further functional comparisons across other vegetable oils, and also expands the proteomic resources to non-model species, thus also allowing further comparative inter-species studies.
2020-09-29 | PXD019894 | Pride