Crystal Geyser Travertine
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ABSTRACT:
PROVIDER: PRJNA961082 | ENA |
REPOSITORIES: ENA
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Project description:Microbially induced carbonate precipitation (MICP) refers to the biogeochemical process in which calcium carbonate is precipitated by altering the local geochemical environment (Mortensen et al. 2011). These alterations occur as a by-product of common microbial metabolic activities by increasing the local carbonate content as well as pH thereby saturating the solution in respect to carbonate. To better understand the microbial ecology of MICP on a community level in natural environments, we chose to evaluate microbial communities derived from travertine adjacent to Crystal Geyser (CG), Utah. CG is a cold-driven, CO2 rich geyser which is surrounded by colorful travertine that has been suggested to be generated through microbial processes. We used a cultivation-independent, multi-omics approach combined with geochemical measurements to investigate metabolic pathways and physiologies potentially involved in MICP at CG. We collected samples from the top 20 cm of travertine adjacent to Crystal Geyser, Utah in November 2019 and June 2021 (38.9384° N, 110.1354° W) wearing gloves at all times. We sampled 1 m away from the borehole (CG-1) and 10 m away from the borehole (CG-10). We preserved all collected samples in RNAlater-like solution (Menke et al., 2017, Front. Microbiol. 8) in a 1:10 sediment: RNAlater-like solution ratio as previously validated (Jensen et al. (2021, Micro. Spec. 2021, 9:2)
2024-11-18 | PXD041379 | Pride
Project description:Crystal cells are one of the 3 Drosophila blood cell lineages and represent less than 5% of the total hemocytes in wild type larvae. There development is notably controlled by mlf (myeloid leukemia factor), which regulate their number by stabilising the lineage-specific transcription factor Lozenge. To gain insight into the biology of this blood cell lineage and its regulation by mlf, we established the gene expression profile of the circulating crystal cells in wildtype and mlf mutant third instar larvae. This study provides a rich source of information to further characterise crystal cell function and regulation. In addition our data show that mlf is a major regulator of crystal cell gene expression programm and that mlf mutation leads to the accumulation of misdifferentiated crystal cells.
2017-07-20 | GSE93823 | GEO
Project description:Objective. To identify novel monosodium urate (MSU) crystal-induced mRNAs by transcript profiling of isolated murine air pouch membranes. Methods. Nine hours after injecting crystals into air pouches, membranes were meticulously dissected away from the adjacent soft tissues. mRNA expression differences between inflamed and control membranes were determined by oligonucleotide microarray analysis. Induction of selected mRNAs was validated by real-time relative quantitative reverse transcriptase PCR (qPCR) in pouch membranes and murine peritoneal macrophages. Results. Eleven of the 12 most highly upregulated mRNAs related to innate immunity and inflammation. They included mRNAs encoding histidine decarboxylase (the enzyme that synthesizes histamine), interleukin (IL)-6, the cell surface receptors PUMA-g and TREM-1, and the polypeptides Irg1 and PROK-2. MSU crystals induced dramatic rises in these mRNAs in the pouch membrane within 3-8 hours after the surge in pro-inflammatory cytokine (IL-6, IL-1beta and TNFalpha) and immediate early gene (Egr-1) transcription, which occurred 1h after crystal injection. MSU crystals induced these mRNAs in cultured macrophages with similar kinetics but lower fold changes. In keeping with their downregulation by MSU crystals according to the microarrays, qPCR confirmed that TREM-2 and granzyme D mRNAs decreased 79% and 94%, respectively, in MSU crystal inflamed membranes. Conclusions. This analysis disclosed several genes previously not implicated in MSU crystal inflammation. Their rise after the early surge in cytokine mRNAs suggests that they may, for instance, amplify or perpetuate inflammation. Transcript profiling of the isolated air pouch membrane promises to be a powerful tool to identify genes acting at different stages of inflammation.
2008-05-23 | GSE11498 | GEO
Project description:Cholesterol crystal (CC) embolism is a severe complication of atherosclerosis, associated with high morbidity and mortality due to its ability to cause acute kidney injury (AKI) and ischemic cortical necrosis. We have established a CC embolism mouse model induced by CC injection. Using this model, we observed significant transcriptomic changes across 17 cell types in the kidneys, with specific upregulation of genes like Cda in the proximal tubular cells, suggesting its potential as an AKI biomarker. Single-cell sequencing revealed the central role of CCL and MIF pathways in CC embolism and identified CCR5 and CD74 as potential therapeutic targets.
2026-01-01 | GSE298484 | GEO
Project description:The pathophysiology of Randall's plaque formation has been studied from various perspectives; however, few studies have investigated renal tissue and microenvironmental changes, such as tubular dilation occurring prior to plaque formation. Although previous reports have identified tubular dilation in the renal tissues of patients with kidney stones, the causal relationship between these changes and stone formation remains unclear. A histological approach is needed to determine which sites in the renal tissue are involved in stone formation. We aimed to identify the site of crystal formation and the early histological changes associated with crystal formation, as well as to identify new factors involved in crystal formation by identifying the genes that are specifically upregulated in the tissue and that participate in stone formation. To investigate the molecular changes occurring in the proximal tubules and the novel gene target, we divided the kidneys of each group of rats into the cortex and medulla, extracted the total RNA, and performed DNA microarray analysis.
2025-06-10 | GSE269407 | GEO
Project description:The present study aims to assess the potential changes in LncRNAs of proximal renal cells in response to the adhesion of calcium oxalate monohydrate (COM) crystals. lncRNA microarray were applied to evaluate the expression of HK-2 cells exposed to COM crystal for 0 and 24 hours.
2014-04-26 | E-GEOD-57111 | biostudies-arrayexpress
Project description:Potential Targets of Cholesterol Crystal Embolism
| PRJNA1269532 | ENA
Project description:Long-term nephrocalcinosis leads to kidney injury, fibrosis, and even chronic kidney disease (CKD). Reports have proved macrophages can transition into myofibroblasts(MMT), leading to collagen deposition and fibrosis in CKD. However, the effect of MMT in calcium oxalate (CaOx) crystal-induced kidney fibrosis remains unclear. This study demonstrated that histone methyltransferase EZH2-mediated MMT contributes to CaOx crystal-induced fibrosis. We identified abundant MMT cells by immunofluorescence and flow cytometry in kidney tissues of patients with CaOx-related CKD, CaOx nephrocalcinosis mouse model, and CaOx-treated RAW264.7 macrophage cells. A high level of MMT cell infiltration was associated with a decline in the glomerular filtration rate in CaOx nephrocalcinosis patients. Clodronate Liposomes-mediated macrophage depletion attenuates calcium oxalate crystal-induced fibrosis in mice. Subsequently, transcriptomic and single-cell sequencing revealed that EZH2 was highly expressed in kidneys with CaOx deposition, especially in macrophages. Further study demonstrated that EZH2 inducible knock-out or pharmacological inhibition by GSK-126 attenuated MMT and renal fibrosis in vivo and in vitro. Mechanistically, ChIP and transcriptomic sequencing showed that EZH2 inhibition reduced the enrichment of H3K27me3 on the DUSP23 gene promoter and elevated DUSP23 expression. The Co-IP and molecular docking analysis showed that DUSP23 mediated the dephosphorylation of pSMAD3 (S423/425), the key regulator of MMT. In addition, DUSP23 over-expression could alleviate SMAD3-mediated MMT. Thus, our study found that EZH2 promotes kidney fibrosis by meditating MMT via the DUSP23/SMAD3 pathway in nephrocalcinosis.
2024-10-26 | GSE280007 | GEO