Human gut metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB10599 | ENA |
REPOSITORIES: ENA
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Project description:Fifty-six children and adolescents with type 1 diabetes at least one year after diagnosis, aged 6-17 years old and fifty-six healthy age- and sex-matched subjects were enrolled in this cross-sectional study. Tear samples were collected using Schirmer strips placed on the lower eyelid. The proteomic analysis was based on a detergent-assisted protein extraction and their digestion from the tears, analysis of the tryptic peptides with LC-MS/ enabling the identification, and quantification of the Shirmer strip protein content via DIA-NN, and subsequently the statistical and bioinformatic analysis using the R and Metascape enrichment analysis tool.
2024-10-17 | PXD052994 | Pride
Project description:The ‘Genetic Epidemiology of Asthma in Costa Rica’ is a family-based cross-sectional cohort ascertained between February 2001 and August 2008 on a Hispanic population isolate from the Central Valley of Costa Rica. The study recruited children between 6 to 14 years of age with moderate persistent asthma.
2022-05-21 | GSE203482 | GEO
Project description:Low-grade, chronic inflammation during ageing (“inflammageing”) is suggested to be involved in the development of frailty in older age. However, studies on the association between frailty, using the frailty index definition, and inflammatory markers are limited. The aim of this study was to investigate the relationship between inflammatory markers and frailty index (FI) in older, home-dwelling adults. Home-dwelling men and women aged ≥ 70 years old, living in South-East Norway were recruited and included in a cross-sectional study. The FI used in the current study was developed according to Rockwood’s frailty index and included 38 variables, resulting in an FI score between 0 and 1 for each participant. Circulating inflammatory markers (IL-6, CRP, IGF-1, cystatin C, cathepsin S, and glycoprotein Acetyls) were analyzed from non-fasting blood samples using ELISA. Whole-genome PBMC transcriptomics was used to study the association between FI score and inflammation. The present study was a cross-sectional study that included home-dwelling men and women aged ≥ 70 years old, living in the Skedsmo area, South-East Norway. The study was conducted in 2014/2015 and has been described previously [Ottestad I, Ulven SM, Øyri LKL, Sandvei KS, Gjevestad GO, Bye A, et al. Reduced plasma concentration of branched-chain amino acids in sarcopenic older subjects: a cross-sectional study. Br J Nutr. 2018;120(4):445-53]. The participants were recruited by the National Register and received an invitation letter by mail. Briefly, a total of 2820 subjects were invited, and 437 subjects participated in the study. The participants met for a single study visit, and data was collected on dietary intake, body weight and composition, physical performance, medical history, cognitive function, risk of malnutrition, anthropometric measurements, blood pressure, heart rate, and quality of life. Non-fasting blood samples were also collected.
2023-09-01 | GSE236927 | GEO
Project description:Overall, the widely disparate transcriptomes identified prior to RT among the three clusters support the notion that at least some of the inter-individual heterogeneity in propensity for RT-induced myofiber hypertrophy is likely pre-determined. Baseline comparisons of skeletal muscle transcript profiles from 44 subjects previously clustered (K-means cluster analysis) as non-, modest-, and extreme-responders (Non, n=15; Mod, n=14; Xtr, n=15) based on the magnitudes of change in vastus lateralis myofiber cross-sectional area (CSA) following 16-wk, 3-d/wk, high-intensity RT.
2013-05-24 | E-GEOD-42507 | biostudies-arrayexpress
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2016-06-28 | E-MTAB-4187 | biostudies-arrayexpress
Project description:To further unravel the potential molecular mechanisms involved in the loss of muscle function during an acute exacerbation, a cross-sectional microarray study was designed to compare the gene expression profile of the vastus lateralis muscle in patients with an acute COPD exacerbation and in stable COPD patients. Keywords: cross-sectional patient study
2009-03-14 | GSE10828 | GEO
Project description:In June 2009, the World Health Organization declared the first influenza pandemic of the 21st century, due to the emergence and rapid spread of new swine origin H1N1 influenza A virus. In contrast to seasonal influenza infections, which typically cause morbidity and mortality in the elderly, this virus caused severe infection in young adults and not the elderly. This phenomenon was attributed to the presence of cross-neutralizing antibodies acquired by older individuals from previous exposure to swine origin influenza. However, this hypothesis could not be empirically tested using clinical data. To address this question, we investigated viral replication and the development of the immune response in naï12 years old) and aged (20 to 24 years old) female rhesus macaques infected with A/California/04/2009 (H1N1), one of the circulating pandemic strains in 2009. We compared viral loads as well as the kinetics and magnitude of the adaptive immune response in peripheral blood and bronchoalveolar lavage samples (BAL) collected longitudinally for 99 days post-infection. Although, adult animals exhibited earlier T cell responses in peripheral blood, aged animals generated a robust T cell response with comparable kinetics and magnitude as those observed in young animals in BAL. Moreover, aged animals generated a higher hemagglutination inhibition titer compared to young animals. We also measured the concentration of several cytokines in BAL supernatant. With the exception of IL-8, which was higher in aged animals, we found no differences in IFNa, IFNb, TNFa, IL-1r, IL-6, IL-15, IL-17, or MCP1 levels. Finally, we compared gene expression infection using microarray analysis of BAL samples taken on days 0, 4, 7, 10, and 14 pi. Our analyses revealed that the largest difference in host response between aged and young animals was detected day 4 post-infection, with significant enrichment for genes associated with inflammation, the innate immune response, and T cell activation in aged animals. The ability of aged animals to generate a robust immune response, especially antibody response, following infection with 2009 H1N1 virus could explain the lack of morbidity normally observed with seasonal influenza viruses in this vulnerable population. 16 female rhesus macaques (Macaca Mulatta) 10-12 (Adult) and 20-24 years (Old/Aged) of age were used in these studies. Animals were infected with A/California/04/ 2009 H1N1 using a combinatory of intra-tracheal (4ml), intranasal (0.5 ml/nostril), and conjunctival (0.5 ml/eyelid) routes for a total dose of 7x106 TCID50 dose. Microarray analysis was performed on Bronchoalveolar lavage (BAL) samples collected on days 0, 4, 7, 10 and 14. Note: One of the Day 0 array did not pass QC metrics so for this animal the average of the other Day 0 samples from that group was utilized. At the end of the study animals were released back to the colony.
2012-06-05 | E-GEOD-38502 | biostudies-arrayexpress
Project description:We used a nonhuman primate (NHP) model of ligature-induced periodontitis to identify gingival transcriptome changes associated with aging during the phases of periodontitis lesions (initiation, progression, and resolution). Four age groups of nonhuman primate were studied: Young (<3 years of age); Adolescent (3 to 7 years), Adult (12 to 15 years), and Aged (17-23 years)
2021-07-22 | GSE180588 | GEO
Project description:To further unravel the potential molecular mechanisms involved in the loss of muscle function during an acute exacerbation, a cross-sectional microarray study was designed to compare the gene expression profile of the vastus lateralis muscle in patients with an acute COPD exacerbation and in stable COPD patients. Keywords: cross-sectional patient study A cross-sectional microarray study was designed. The microarray screening was performed on a vastus lateralis biopsy obtained from 4 patients with an acute COPD exacerbation and 5 stable COPD patients. No replicates or dye-swaps were included.
2009-03-13 | E-GEOD-10828 | biostudies-arrayexpress
Project description:Study question: Are the molecular signatures of cumulus cells (CCs) and follicular fluid (FF) of adolescents undergoing fertility preservation differ from that of reproductively adult oocyte donors? Summary answer: The microenvironment immediately surrounding the oocyte, including the CCs and FF, is altered in adolescents undergoing fertility preservation compared to oocyte donors. What is known already: Adolescents experience a period of subfecundity following menarche. Recent evidence suggests that this may be at least partially due to increased oocyte aneuploidy. Reproductive juvenescence in mammals is associated with suboptimal oocyte quality. Study design, size, duration: This was a prospective cohort study. Adolescents (10-19 years old, N=23) and oocyte donors (22-30 years old, N=31) undergoing ovarian stimulation and oocyte retrieval at the Northwestern Fertility and Reproductive Medicine Center between November 1, 2020 and May 1, 2023 were enrolled in this study. Participants/materials, setting, method: Patient demographics, ovarian stimulation, and oocyte retrieval outcomes were collected for all participants. The transcriptome of CCs associated with mature oocytes was compared between adolescents (10-19 years old, n=19), and oocyte donors (22-30 years old, n=19) using bulk RNA-sequencing. FF cytokine profiles (10-19 years old, n=18 vs. 25-30 years old, n=16) were compared using cytokine arrays. Main results and the role of chance: RNA-seq analysis revealed 581 differentially expressed genes (DEGs) in cumulus cells of adolescents relative to oocyte donors, with 361 genes downregulated and 220 upregulated. Genes enriched in pathways involved in cell cycle and cell division (e.g., GO:1903047, p= 3.5 x 10-43; GO:0051983, p= 4.1 x 10- 30; GO:0000281, p= 7.7 x 10-15; GO:0044839, p= 5.3 x 10-13) were significantly downregulated, while genes enriched in several pathways involved in cellular and vesicle organization (e.g., GO:0010256, p= 1.2 x 10-8; GO:0051129, p= 6.8 x 10-7; GO:0016050, p= 7.4 x 10-7; GO:0051640, p= 8.1 x 10-7) were upregulated in CCs of adolescents compared to oocyte donors. The levels of 9 cytokines were significantly increased in FF of adolescents compared to oocyte donors: IL-1 alpha (2-fold), IL-1 beta (1.7-fold), I-309 (2-fold), IL-15 (1.6-fold), TARC (1.9-fold), TPO (2.1-fold), IGFBP-4 (2-fold), IL-12-p40 (1.7-fold) and ENA-78 (1.4-fold). Interestingly, 7 of these cytokines have known pro-inflammatory roles. Importantly, neither the CC transcriptomes or FF cytokine profiles were different in adolescents with or without cancer. Large scale data: Original high-throughput sequencing data will be deposited in Gene Expression Omnibus (GEO) before publication, and the GEO accession number will be provided here. Limitations, reasons for caution: This study aims to gain insights into the associated gamete quality by studying the immediate oocyte microenvironment. The direct study of oocytes is more challenging due to sample scarcity, as they are cryopreserved for future use, but will provide a more accurate assessment of oocyte reproductive potential. Wider implications of the findings: Understanding the underpinnings of altered immediate oocyte microenvironment of adolescent patients may provide insights into the reproductive potential of the associated gametes in the younger end of the age spectrum. This has implications for the fertility preservation cycles for very young patients.
2024-05-15 | GSE265995 | GEO