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Comparative transcriptomic analysis of HUVECs cultured on hydroxyapatite doping with Mg2+ versus Trio-Active bone scaffold

ABSTRACT: Comparative transcriptomic analysis of HUVECs cultured on hydroxyapatite doping with Mg2+ (HA/Mg) versus Trio-Active bone scaffold (TABS)

ORGANISM(S): Homo sapiens

PROVIDER: GSE315261 | GEO | 2026/01/06

REPOSITORIES: GEO

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Comparative transcriptomic analysis of Raw264.7 cells cultured on hydroxyapatite doping with Mg2+ versus Trio-Active bone scaffold

Project description:Comparative transcriptomic analysis of Raw264.7 cells cultured on hydroxyapatite doping with Mg2+ (HA/Mg) versus Trio-Active bone scaffold (TABS)

2026-01-06 | GSE315260 | GEO

Comparative transcriptomic analysis of MC3T3-E1 cells cultured on hydroxyapatite doping with Mg2+ versus Trio-Active bone scaffold

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Proof of Gene Doping in a Mouse Model with a Human Erythropoietin Gene Transferred Using an Adenoviral Vector

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Recurrent TRIO fusion in non-translocation-related sarcomas

Project description:We used NGS on a cohort of complex genetics sarcomas to study their transcriptomes (RNA-seq technology), looking for recurrent and specific gene fusions. We identified multiple TRIO fusions with different partners in our cohort. No TRIO fusions were reported in negative-control cells (normal tissues) and in simple genetics sarcomas.

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Effect of nano-hydroxyapatite and phosphate on thorium toxicity – Arabidopsis transcriptomic study

Project description:Thorium (Th) is a ubiquitous element but elevated concentrations caused by anthropogenic or natural activities pose health and environmental risks. Nowadays, Th is obtained mainly as by-product during the mining and extraction rare earth element. However, due to its abundance in nature, which is higher than the abundance of uranium, Th is considered as a potential fuel for the reactors. Therefore, in this study, we focused on the effect of thorium on Arabidopsis plants at the transcriptomic level. Since Th and phosphorus form insoluble phosphates, we focused on the effect of Th in the presence/absence of phosphate. Furthermore, we investigated the effect of hydroxyapatite nanoparticles, which are considered as material for in situ remediation, on Th toxicity. Not surprisingly, the highest number of DEGs was recorded in the combination of P absence and Th presence followed by the presence of Th in the standard hydroponic medium, the absence of P in the medium, the presence of nano-hydroxyapatite, and the presence of Th together with hydroxyapatite. Besides a high number of genes involved in stress response, Th also induced the transcription of genes involved in response to P starvation, indicating that Th decreased the availability of P. P deficiency caused by Th contributed to the phytotoxic effect of Th. Nano-hydroxyapatite significantly reduced Th toxicity. Nano-hydroxyapatite also served as a source of inorganic P for the plants, but caused deficiency of essential metals indicated by up-regulation of genes involved in their acquisition.

2023-06-24 | GSE233480 | GEO

Integrating whole blood transcriptomic collection procedures into the current anti-doping testing system, including long-term storage and re-testing of anti-doping samples [Long-term]

Project description:Purpose: Recombinant human erythropoietin administration studies involving “omics” approaches have demonstrated a gene-expression signature that could aid detection of blood doping. However, current anti-doping testing does not involve blood collection into tubes with RNA preservative. This study investigated if whole blood in long-term storage could be used for transcriptomic analysis despite lacking RNA preservation. Methods: Whole blood samples were collected from thirteen male healthy individuals. Long-term storage: whole blood collected into Tempus™ tubes and K2EDTA tubes and subjected to long-term (i.e., −80°C) storage and RNA extracted. After storage, Tempus and K2EDTA tubes were thawed and extracted using Tempus™ Spin RNA Isolation Kit (Life Technologies, Carlsbad, CA, USA). Samples from seven subjects that presented higher RIN value (≥7) were selected for RNA_Seq analysis. Results: The experiment provided RNA quality and purity for gene expression analysis. Total of 19239 genes were mapped and the gene expression analysis showed that 658 genes were differentially expressed (which means 3.4% of mapped genes). With 269 being up-regulated and 389 down-regulated. None of the transcripts described in previous studies as biomarkers for blood doping (Durussel et al. 2016; Wang, Durussel, et al. 2017) were differently expressed. Conclusion: RNA quantity, purity and integrity was not significantly compromised from long-term storage in blood storage tubes lacking RNA stabilisation, indicating that transcriptomic/omics analysis could be conducted using anti-doping samples collected or biobanked without RNA preservation.

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Cellular Mg2+ decrease causes a distinctive NF-κB-dependent form of cell death

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2026-01-03 | GSE309910 | GEO

Mg2+-dependent mechanism of environmental versatility in a multidrug efflux pump

Project description:Tripartite resistance nodulation and cell division multidrug efflux pumps span the periplasm and are major drivers of multidrug resistance among Gram-negative bacteria. Cations, such as Mg2+, become concentrated within the periplasm and, in contrast to the cytoplasm, it’s pH is sensitive to conditions outside the cell. Here, we reveal an interplay between Mg2+ and pH in modulating the structural dynamics of the periplasmic adaptor protein, AcrA, and its function within the prototypical AcrAB-TolC multidrug pump from Escherichia coli. In the absence of Mg2+, AcrA becomes increasingly plastic within acidic conditions, but when Mg2+ is bound this is ameliorated, resulting instead in domain specific organisation. We establish a unique histidine residue directs these dynamics and is essential for sustaining pump activity across acidic, neutral, and basic regimes. Overall, we propose Mg2+ conserves AcrA structural mobility to ensure optimal AcrAB-TolC function within rapid changing environments commonly faced during bacterial infection and colonization.

2024-12-30 | PXD057200 | Pride

Integrating whole blood transcriptomic collection procedures into the current anti-doping testing system, including long-term storage and re-testing of anti-doping samples

Project description:Recombinant human erythropoietin administration studies involving transcriptomic approaches have demonstrated a gene-expression signature that could aid detection of blood doping. However, current anti-doping testing does not involve blood collection into tubes with RNA preservative. This study investigated if whole blood in long-term storage and whole blood leftover from standard haematological testing in short-term storage could be used for transcriptomic analysis despite lacking RNA preservative. Whole blood samples were collected from thirteen and fourteen healthy males, for long-term and short-term storage experiments. Long-term storage: whole blood collected into Tempus™ tubes and K2EDTA tubes and subjected to long-term (i.e., −80°C) storage and RNA extracted. After storage, K2EDTA tubes were thawed and extracted using GeneJET RNA Purification Kit (Thermo Fisher Scientific, Vilnius, Lithuania) or Tempus™ Spin RNA Isolation Kit (Life Technologies, Carlsbad, CA, USA). RNA quality and purity was sufficient for gene expression analysis. Principle Component Analysis of microarray and RNA-seq gene expression data for long-term storage: When comparing gene expression between blood tubes with and without RNA preservation, 6% (4058 transcripts) were differentially expressed. RNA quantity, purity and integrity was not significantly compromised from long-term storage in blood storage tubes lacking RNA preservative, indicating that transcriptomic analysis could be conducted using anti-doping samples collected or biobanked without RNA preservation.

2021-08-13 | GSE181970 | GEO

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