Genome sequences of new species isolated from the Nebraska Salt Marshes
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ABSTRACT:
PROVIDER: PRJNA1308161 | ENA |
REPOSITORIES: ENA
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Project description:We have developed the HRS-seq method (High-salt Recovered Sequences-sequencing), a straightforward genome-wide approach whereby we isolated and sequenced genomic regions associated with large high-salt insoluble RNP complexes. Using mouse embryonic stem cells (ESC), we showed that HRS are over-represented into the active A chromosomal compartment. The vast majority of HRS-associated genes are very highly expressed. They include both cell type-specific genes, like pluripotency genes, and housekeeping genes, like histone and snRNA genes that are central components of Histone Locus Bodies and Cajal bodies. We conclude that large, high-salt insoluble, RNP complexes including nuclear bodies are associated to the active A chromosomal compartment.
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Project description:Salt sensitivity of blood pressure (SSBP) is associated with persistent immune activation after sodium normalization, suggesting immune “salt memory.” Prior work identified that sodium entry into antigen-presenting cells (APCs) via epithelial sodium channels triggers NLRP3 inflammasome activation through the formation of isolevuglandins (IsoLGs), highly reactive lipid aldehydes. IsoLG scavenging with 2-hydroxybenzylamine (2-HOBA) reduces NLRP3 expression and attenuates salt-induced hypertension, implicating IsoLGs as upstream immune regulators. This study tested whether IsoLGs also act as epigenetic modifiers by covalently modifying histone H1, thereby altering chromatin accessibility at inflammatory loci such as NLRP3. PBMCs from 10 hypertensive adults classified as salt-sensitive (SS) or salt-resistant (SR) were collected at baseline, after salt loading, and after depletion. Integrated single-cell RNA-seq and ATAC-seq revealed that SS monocytes exhibited salt-induced enhancer activation and increased chromatin accessibility at the NLRP3 locus. IsoLG–protein adducts correlated with blood pressure changes and were most prominent in CD14⁺ monocytes. In murine APCs, high salt induced IsoLG adduction of histone H1, attenuated by 2-HOBA. Knockdown of H1F0 reduced high salt–induced NLRP3 expression, supporting a role for H1.0 in transcriptional regulation. These findings identify IsoLG modification of histone H1 as a potential mechanism linking extracellular sodium exposure to persistent chromatin remodeling and sustained inflammatory gene expression in SS individuals. IsoLG–histone adducts may represent novel therapeutic targets for immune-driven hypertension.
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Project description:Seven different Solanaceae species, Potato (Solanum tubersosum), Tomato (Solanum lycopersicum), Eggplant (Solanum melangena), Pepper (Capsicum annuum), Tobacco (Nicotiana tabaccum), Petunia and Nicotiana benthiamana were subjected to salt stress. The stress applied was 150mM NaCl and control plants were watered without the additional salt. Samples were collected at 0, 6, 12, 24, 48 and 96 hours after the first application of the salt. RNA was isolated using Qiagen RNeasy. Keywords: Direct comparison
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Project description:Five allotetraploid cotton species have adapted, through their transcriptional responses, to unique environments with distinct levels of inherent abiotic stresses. The transcriptional responses of leaf and root tissue in five allotetraploid cotton species (Gossypium hirsutum, G. barbadense, G. tomentosum, G. mustelinum, and G. darwinii) under salt stress have been investigated in this study using cotton long oligonucleotide microarrays. Physiological responses to salinity such as stomatal conductance, ion and osmoprotectant contents were also measured as indicators of imposed stress. Accessions from these five cotton species were hydroponically grown and gradually introduced to a NaCl treatment (15 dS m-1). The microarray results identified 2721 and 2460 differentially expressed genes under salt stress that were significant in leaf and root tissue, respectively. Many of these genes were classified under gene ontology (GO) categories that suggest abiotic stress. These allotetraploid cottons shared transcriptional responses to salinity, but also showed responses that were species-specific. No consistent differences in transcriptional response among the previously estimated phylogenetic branches were found. Stomatal conductance, ion accumulation, and betaine, trigonelline, and trehalose contents also indicated salt stress. This global assessment of transcriptional and physiological responses to salt stress of these cotton species may identify possible gene targets for crop improvement and evolutionary studies of cotton. Keywords: CEGC Cotton oligo salt stress
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Project description:The complete genome sequences of four Pseudomonas fluorescens bacteriophages, UNO-SLW1 to UNO-SLW4, isolated from freshwater samples, are 39,092 to 39,215 bp long. The genomes are highly similar (identity, >0.995) but dissimilar from that of Pseudomonas phage Pf-10 (the closest relative, 0.685 to 0.686 identity), with 48 to 49 protein-coding genes and 66 regulatory sites predicted.
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Project description:Samples from salt marshes in the south of England
| PRJEB19235 | ENA