RNA sequencing to study the molecular relationships between temperature, aging, and NPR-8
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ABSTRACT:
PROVIDER: PRJNA772952 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To gain molecular insights into NPR-8-dependent longevity response to temperature, we employed RNA-seq to compare gene expression in young and old wild-type and npr-8(ok1439) animals propagated at different temperatures.
2023-05-24 | GSE186202 | GEO
Project description:To gain molecular insights on how NPR-8 regulates C. elegans defense against pathogen infection, we used RNA sequencing to profile gene expression in npr-8(ok1439) animals relative to wild-type animals with or without P. aeruginosa infection. We found that NPR-8 suppresses the expression of genes related to cuticle structure activity including collagen genes, and lack of NPR-8-mediated suppression in npr-8(ok1439) animals contributes to their improved survival against P. aeruginosa infection.
2019-10-15 | GSE122544 | GEO
Project description:Purpose: To uncover immune genes and pathways that are modulated by the GPCR/NPR-15 Methods: RNA was extracted from synchronized L4 stage npr-15(tm12539) and WT animals grown at 20 C using Qiagen extraction kits and following standard methods Results: RNA seq analyses shows enriched and signficant upregulated immune, neuropeptide, synaptic signaling and metabolism genes and pathways that are dependent on NPR-15 Conclusions: Our study uncovered NPR-15 to be modulator of the innate immunity in C. elegans
2024-03-04 | GSE173367 | GEO
Project description:The nematode Caenorhabditis elegans feeds on microbes in its natural environment. Some of these microbes are pathogenic and thus harmful to C. elegans. To minimize resulting fitness reductions, C. elegans has evolved various defence mechanisms including behavioural responses (e.g. avoidance behaviour) that reduce contact with the infectious microbes. In this study, we characterized the genetic architecture of natural variation in C. elegans avoidance behaviour against the infectious stages of the Gram-positive bacterium Bacillus thuringiensis. We performed an analysis of quantitative trait loci (QTLs) using recombinant inbred lines (RILs) and introgression lines (ILs) generated from a cross of two genetically as well as phenotypically distinct natural isolates N2 and CB4856. The analysis identified several QTLs that underlie variation in the behavioural response to pathogenic and/or non-pathogenic bacteria. One of the candidates is the npr-1 gene. This gene encodes a homolog of the mammalian neuropeptide receptor. Npr-1 was previously indicated to fully contribute to behavioural defence against the Gram-negative bacterium Pseudomonas aeruginosa and food patch-leaving behaviour on Escherichia coli. Interestingly, in our study, npr-1 is not the only gene mediating avoidance behaviour toward Bacillus thuringiensis. Moreover, our functional analyses show that npr-1 alleles appear to influence survival and avoidance behaviour toward Bacillus thuringiensis in exactly the opposite way than toward Pseudomonas aeruginosa. Our findings highlight the role of npr-1 in fine-tuning nematode behaviour in an ecological context depending on the microbe to which C. elegans is exposed. These opposite phenotypes reflect the diversity in innate immunity to pathogens. To understand the mechanism involved in these opposite phenotypes, we carried out a whole-genome transcriptomics study by RNA-Sequencing. This study includes two pathogens: Pseudomonas aeruginosa PA14 and Bacillus thuringiensis B-18247 (BT247), two strains: N2 and npr-1 (ur89), two time points (12 and 24h) and standard lab food E. coli OP50 as control. mRNA profiles of wild type (WT) and npr-1 (ur89) C.elegans exposed to either Bacillus thuringiensis B-18247, Pseudomonas aeruginosa PA14 or standard lab food E. coli OP50 at 12h or 24h were generated by deep sequencing, in double or triplicate, using Illumina HiSeq2000.
2016-03-31 | E-GEOD-60063 | biostudies-arrayexpress
Project description:The mechanistic basis for how genetic variants cause differences in phenotypic traits is often elusive. We identified a quantitative trait locus in C. elegans that affects three seemingly unrelated phenotypic traits: lifetime fecundity, adult body size, and susceptibility to the human pathogen Staphyloccus aureus. We found a QTL for all three traits arises from variation in the neuropeptide receptor gene npr-1. Moreover, we found that variation in npr-1 is also responsive for differences in 247 gene expression traits. Variation in npr-1 is known to determine whether animals disperse throughout a bacterial lawn or aggregate at the edges of the lawn. We found that the allele that leads to aggregation is associated with reduced growth and reproductive output. The altered gene expression pattern caused by this allele suggests that the aggregation behavior might cause a weak starvation state, which is known to reduce growth rate and fecundity. Importantly, we show that variation in npr-1 causes each of these phenotypic differences through behavioral avoidance of ambient oxygen concentrations. These results suggest that variation in npr-1 has broad pleiotropic effects mediated by altered exposure to bacterial food. Two-channel experiment comparing mixed stage sample to mixed stage mixed 50:50 N2,CB4856 common reference
2013-07-30 | E-GEOD-49307 | biostudies-arrayexpress
Project description:Purpose: To uncover immune genes and pathways that are modulated by the GPCR/NPR-15 during S. aureus infection Methods: RNA was extracted from synchronized L4 stage npr-15(tm12539) and WT animals grown at 20 C and infected with S. aureus for 8 hours, followed by Qiagen extraction kits and following standard methods Results: RNA seq analyses shows enriched and signficant upregulated immune, neuropeptide, synaptic signaling and metabolism genes and pathways that are dependent on NPR-15 Conclusions: Our study uncovered NPR-15 to be modulator of the innate immunity in C. elegans under infection
2024-03-04 | GSE174176 | GEO
Project description:The mechanistic basis for how genetic variants cause differences in phenotypic traits is often elusive. We identified a quantitative trait locus in C. elegans that affects three seemingly unrelated phenotypic traits: lifetime fecundity, adult body size, and susceptibility to the human pathogen Staphyloccus aureus. We found a QTL for all three traits arises from variation in the neuropeptide receptor gene npr-1. Moreover, we found that variation in npr-1 is also responsive for differences in 247 gene expression traits. Variation in npr-1 is known to determine whether animals disperse throughout a bacterial lawn or aggregate at the edges of the lawn. We found that the allele that leads to aggregation is associated with reduced growth and reproductive output. The altered gene expression pattern caused by this allele suggests that the aggregation behavior might cause a weak starvation state, which is known to reduce growth rate and fecundity. Importantly, we show that variation in npr-1 causes each of these phenotypic differences through behavioral avoidance of ambient oxygen concentrations. These results suggest that variation in npr-1 has broad pleiotropic effects mediated by altered exposure to bacterial food.
2013-07-30 | GSE49307 | GEO
Project description:Natriuretic peptide receptor-A (NPR-A) is the principal receptor for the natriuretic peptides ANP and BNP. Targeted deletion of NPR-A in mouse glomerular podocytes significantly enhances renal injury in vivo in the DOCA-salt experimental model. It was therefore hypothesized that natriuretic peptides exert a direct protective effect on glomerular barrier integrity through activation of NPR-A and modulation of gene expression patterns in podocytes. RNA-seq analysis revealed a total of 158 DEGs with 81 downregulated DEGs and 77 upregulated DEGs in Npr1 deficient podocytes. Among the downregulated genes were protein S and semaphorin 3G, which are known to have a protective effect in podocytes. Protein S was also expressed in and secreted from isolated human glomeruli. GO enrichment analysis revealed that the upregulated DEGs in NPR-A deficient podocytes were associated with cell migration and motility. In line, BNP significantly decreased podocyte outgrowth from cultured glomeruli.
2024-10-02 | GSE249221 | GEO
Project description:The nematode Caenorhabditis elegans feeds on microbes in its natural environment. Some of these microbes are pathogenic and thus harmful to C. elegans. To minimize resulting fitness reductions, C. elegans has evolved various defence mechanisms including behavioural responses (e.g. avoidance behaviour) that reduce contact with the infectious microbes. In this study, we characterized the genetic architecture of natural variation in C. elegans avoidance behaviour against the infectious stages of the Gram-positive bacterium Bacillus thuringiensis. We performed an analysis of quantitative trait loci (QTLs) using recombinant inbred lines (RILs) and introgression lines (ILs) generated from a cross of two genetically as well as phenotypically distinct natural isolates N2 and CB4856. The analysis identified several QTLs that underlie variation in the behavioural response to pathogenic and/or non-pathogenic bacteria. One of the candidates is the npr-1 gene. This gene encodes a homolog of the mammalian neuropeptide receptor. Npr-1 was previously indicated to fully contribute to behavioural defence against the Gram-negative bacterium Pseudomonas aeruginosa and food patch-leaving behaviour on Escherichia coli. Interestingly, in our study, npr-1 is not the only gene mediating avoidance behaviour toward Bacillus thuringiensis. Moreover, our functional analyses show that npr-1 alleles appear to influence survival and avoidance behaviour toward Bacillus thuringiensis in exactly the opposite way than toward Pseudomonas aeruginosa. Our findings highlight the role of npr-1 in fine-tuning nematode behaviour in an ecological context depending on the microbe to which C. elegans is exposed. These opposite phenotypes reflect the diversity in innate immunity to pathogens. To understand the mechanism involved in these opposite phenotypes, we carried out a whole-genome transcriptomics study by RNA-Sequencing. This study includes two pathogens: Pseudomonas aeruginosa PA14 and Bacillus thuringiensis B-18247 (BT247), two strains: N2 and npr-1 (ur89), two time points (12 and 24h) and standard lab food E. coli OP50 as control.
2016-03-31 | GSE60063 | GEO
Project description:RNA-seq profiling of BAG neurons in C. elegans npr-1 and npr-1 arcp-1 animals
| PRJNA559676 | ENA