Ama_Flag7Bulk_FBMN-IIN_Input_2024_0805
Ontology highlight
ABSTRACT:
INSTRUMENT(S): 6545 Q-TOF LC/MS
ORGANISM(S): Stromatolite, Marine
SUBMITTER: 
Kerry McPhail
PROVIDER: MSV000095592 | MassIVE | Tue Aug 13 19:37:00 BST 2024
REPOSITORIES: MassIVE
Similar Datasets
Project description:Sewage samples were collected and concentrated for Human and animal viruses. Viruses were cultured on Buffalo Green Monkey Cells (BGMK) and their genomic DNA/RNA were extracted and labeled with Cy3 and Cy5 respectively. Labeled DNA/RNA were hybridized unto the array and signals generated were analyzed to indicate the presence of target viruses. Keywords: Detection of pathogens within environmental sample (Viruses) Environmental viruses were concentrated using organic flocculation with Beef Extract supplemented with glycine. Viruses were concentrated using 2 successive rounds of centrifugation and resuspended in Sodium Phosphate buffer. Viral nucleic acid was extracted, labeled and hybridized unto the microarray to determine the presence of target viruses within the sample.
2008-04-18 | E-GEOD-11195 | biostudies-arrayexpress
Project description:We investigated the toxicity of soil samples derived from a former municipal landfill site in the South of the Netherlands, where a bioremediation project is running aiming at reusing the site for recreation. Both an organic soil extract and the original soil sample was investigated using the ISO standardised Folsomia soil ecotoxicological testing and gene expression analysis. The 28 day survival/reproduction test revealed that the ecologically more relevant original soil sample was more toxic than the organic soil extract. Microarray analysis showed that the more toxic soil samples induced gene regulatory changes in twice as less genes compared to the soil extract. Consequently gene regulatory changes were highly dependent on sample type, and were to a lesser extent caused by exposure level. An important biological process shared among the two sample types was the detoxification pathway for xenobiotics (biotransformation I, II and III) suggesting a link between compound type and observed adverse effects. Finally, we were able to retrieve a selected group of genes that show highly significant dose-dependent gene expression and thus were tightly linked with adverse effects on reproduction. Expression of four cytochrome P450 genes showed highest correlation values with reproduction, and maybe promising genetic markers for soil quality. However, a more elaborate set of environmental soil samples is needed to validate the correlation between gene expression induction and adverse phenotypic effects.
2012-04-16 | GSE37154 | GEO
Project description:We investigated the toxicity of soil samples derived from a former municipal landfill site in the South of the Netherlands, where a bioremediation project is running aiming at reusing the site for recreation. Both an organic soil extract and the original soil sample was investigated using the ISO standardised Folsomia soil ecotoxicological testing and gene expression analysis. The 28 day survival/reproduction test revealed that the ecologically more relevant original soil sample was more toxic than the organic soil extract. Microarray analysis showed that the more toxic soil samples induced gene regulatory changes in twice as less genes compared to the soil extract. Consequently gene regulatory changes were highly dependent on sample type, and were to a lesser extent caused by exposure level. An important biological process shared among the two sample types was the detoxification pathway for xenobiotics (biotransformation I, II and III) suggesting a link between compound type and observed adverse effects. Finally, we were able to retrieve a selected group of genes that show highly significant dose-dependent gene expression and thus were tightly linked with adverse effects on reproduction. Expression of four cytochrome P450 genes showed highest correlation values with reproduction, and maybe promising genetic markers for soil quality. However, a more elaborate set of environmental soil samples is needed to validate the correlation between gene expression induction and adverse phenotypic effects. paired reference design was used testing animals exposed to two concentrations of an environemntal soil sample and two concentrations of the subsequent soil extract. 4 biological replicates per condition containing 25 grams of soil and 10 23day-old animals per replicate.
2012-04-15 | E-GEOD-37154 | biostudies-arrayexpress
Project description:Microbial communities for soil organic matter fractions
| PRJNA1135446 | ENA
Project description:We reported the gene expression profile of T47D cells treated with the organic extract of Particulate matter 2.5 (PM2.5) sampled next to the municipal solid waste incineration plant of Bologna city. Based on a air pollution distribution model that takes the incinaration plant as point source of emission, two sites were chosen to sample particulate matter near incineration plant: "FrulloEst" representing the maximum effect of the incineration plant, "Calamosco" representing the negative control of "FrulloEst" (minimun effect of incineration plant, same effect of other air pollution fonts). Another site, "Giardini Margherita", is chosen to sample the urban background air pollution. for each site sample collection was performed in winter and in summer season.
2018-01-31 | E-MEXP-3686 | biostudies-arrayexpress
Project description:The aim of this study was to perform comparative analysis of global gene expression changes in lung BEAS-2B cells in response to treatment with extracts of particulate matter produced by conventional gasoline (E0) or biogasoline (E15) differing in the content of organic compounds, particularly PAHs. To examine the toxicity, we monitored genome-wide gene expression changes in human lung BEAS-2B cells, exposed for 4h and 24h to a subtoxic dose of each PM extract. After 4h exposure, numerous dysregulated genes and processes such as oxidative stress, lipid and steroid metabolism, PPARα signaling and immune response, were found to be common for both extract treatments. Twenty four hour exposure resulted in more distinctive gene expression patterns. Although several common modulated processes indicating the metabolism of PAHs and activation of aryl hydrocarbon receptor (AhR) were identified, E15 specifically dysregulated a variety of other genes and pathways related to cancer promotion and progression, possibly due to the increased PAH content in PM organic extract.
2021-07-28 | GSE180932 | GEO
Project description:Peripheral blood samples from children enrolled in the URECA cohort were collected at age 2. In short, at each URECA research center, within 16 hours of blood collection, mononuclear cells were separated and incubated (48 hours, 37C, 5% CO2) in the presence of German cockroach extract (10mg/mL; CR), dust mite extract (Dermatophagoides pteronyssinus, 10mg/mL; DM), tetanus toxoid (5mg/mL; TT), or medium alone (NS).
2018-03-27 | GSE96783 | GEO
Project description:Microarray analysis was performed on a well-defined set of potato tuber samples grown under different, well-recorded environmental conditions. The data were analysed to assess the potential of transcriptomics to detect differences in gene expression as a result of these environmental conditions. Differences were found for both factors, both in PCA and in ANOVA analysis. Factorial design; 1 potato cultivar (Sante); 2 fertilizers (organic, conventional); 2 crop protection treatments (organic, conventional), 4 biological replicates, 16 samples. Raw data files: columns 1 - 11 is Cy3, 12 - 21 is Cy5
2012-01-31 | E-GEOD-27662 | biostudies-arrayexpress
Project description:Background: Environmental lipopolysaccharide (LPS) and microbial component-enriched organic dusts cause significant lung diseases. These environmental exposures induce the recruitment and activation of distinct lung monocyte/macrophage subpopulations involved in disease pathogenesis. Given monocyte/macrophage activation is tightly linked to metabolism, the objective of these studies was to determine the role of the immunometabolic regulator, aconitate decarboxylase 1 (ACOD1), in environmental exposure-induced lung inflammation. Methods: Wild-type (WT) mice were intratracheally instilled (I.T.) with 10 ug LPS or saline. Whole lungs were profiled using bulk RNA sequencing or sorted to isolate monocyte/macrophage subpopulations. Sorted subpopulations were then characterized transcriptomically using a NanoString innate immunity multiplex array 48 hours post-exposure. Next, WT and Acod1-/- mice were instilled with LPS, 25% organic dust extract (ODE), or saline with serum, bronchoalveolar lavage fluid (BALF), and lung tissues collected. BALF metabolites of the tricarboxylic acid (TCA) cycle were quantified by mass-spectrometry. Cytokines/chemokines and tissue remodeling mediators were quantitated by ELISA. Lung immune cells were characterized by flow cytometry. Whole body plethysmography was performed 3 hours post-LPS with WT and Acod1-/- mice. Results: By bulk sequencing, Acod1 was one of the most significantly upregulated genes following LPS (vs. saline) exposure of murine whole lungs. Transcriptomic profiling of sorted lung monocyte/macrophage subpopulations corroborated Acod1 significance. Acod1-/- mice treated with LPS (vs. WT) demonstrated decreased BALF levels of itaconate, TCA cycle reprogramming, decreased BALF neutrophils, increased lung CD4+ T cells, decreased BALF and lung levels of TNF-a, and decreased BALF CXCL1. In comparison, Acod1-/- mice treated with ODE (vs. WT) demonstrated decreased serum pentraxin-2, BALF levels of itaconate, lung total cell, neutrophil, monocyte, and B cell infiltrates with decreased BALF levels of TNF-a, IL-6, and decreased lung CXCL1. Mediators of tissue remodeling (TIMP1, MMP8, MMP9) were also decreased in the LPS-exposed Acod1-/- mice, with MMP-9 also decreased in the ODE-exposed Acod1-/- mice. Lung function assessments demonstrated a blunted response to LPS-induced airway hyper-responsiveness in Acod1-/- mice. Conclusion: Acod1 is robustly upregulated in the lungs following LPS-exposure and encodes a key immunometabolic regulator. ACOD1 mediates the pro-inflammatory response to acute inhaled, environmental LPS and organic dust exposure-induced lung inflammation.
2024-10-15 | GSE267022 | GEO
Project description:Welan gum is mainly produced by Sphingomonas sp. ATCC 31555 and has broad applications in industry such as that in cement production. Both carbon and nitrogen sources are essential for welan production. However, how nitrogen sources affect the metabolism and gene transcription of welan remains elusive. Here, we used next-generation sequencing RNA-seq to analyze the transcriptome of Sphingomonas sp. ATCC 31555 in the presence of inorganic or organic nitrogen sources. Enriched gene expression and pathway analysis suggest that organic nitrogen sources significantly enhanced the expression of genes in central metabolic pathways of Sphingomonas sp. ATCC 31555 and those critical for welan synthesis compared to that observed using inorganic nitrogen sources. The present study improves our understanding of the molecular mechanism underlying the use of nitrogen in welan synthesis in Sphingomonas sp., as well as provides an important transcriptome resource for Sphingomonas sp. in relation to nitrogen sources. Sphingomonas sp. ATCC 31555 strain (stored in our laboratory) was first seeded in an inoculum medium (20 g/L glucose, 3 g/L yeast extract, 3 g/L malt extract, and 5 g/L fish meal protein peptone, pH 7.0), and then cultured in a fermentation medium containing 40 g/L sucrose, 4.0 g/L nitrogen source, 0.6 g/L KH2PO4, and 0.2 g/L MgSO4.7H2O at 37°C. The nitrogen sources used in the present study were as follows: NaNO3 (4.0 g/L) as inorganic nitrogen (IN), beef extract (4.0 g/L) as organic nitrogen (ON), and NaNO3 (1.5 g/L) + beef extract (2.5 g/L) as complex nitrogen (CN). All cultivations were conducted in flasks with constant rotary shaking at 400â??1,000 rpm and 37°C.
2016-03-25 | E-GEOD-79497 | biostudies-arrayexpress