GNPS - UV_Pinus radiata_Metabolomics
Ontology highlight
ABSTRACT:
INSTRUMENT(S): TSQ Quantum
ORGANISM(S): Pinus Radiata (ncbitaxon:3347)
SUBMITTER: Luis Valledor
PROVIDER: MSV000080217 | GNPS | Mon Oct 03 23:27:00 BST 2016
REPOSITORIES: GNPS
Similar Datasets
Project description:Proteomics dataset of a UV stress and recovery assay in Pinus radiata using an LTQ Orbitrap and UV doses mimicking the expected near future environmental scenario regarding UV radiation. The mass spectrometry Raw Spectrum files and SEQUEST searching msf files are provided.
2016-10-06 | MSV000080230 | MassIVE
Project description:Background: The International Space Station is an orbiting laboratory for microbial research in space, where microorganisms can be exposed to multiple extremes. Dehydrated cell clusters of extremophilic bacterium Deinococcus radiodurans have survived 3-year exposure outside the International Space Station in frames of the Tanpopo mission. We investigated the robust molecular machinery of Deinococcus radiodurans involved in its recovery after long-term space travel. Methods: The space-exposed and ground control cells of Deinococcus radiodurans were recovered in a complex medium for 5 and 15 h and investigated using integrative –omics techniques combined with electron microscopy tools. Consolidative transcriptomic, proteomic, and metabolomic analyses were performed to investigate molecular kinetics of cell recovery after 3-year exposure to low Earth orbit. Results: Ultrastructure analysis showed that Deinococcus radiodurans cells remained intact after low Earth orbit exposure for 3 years. Multiscale molecular analysis revealed significant alterations in response to long-term space travel. Key adaptations included upregulated DNA repair genes,stress response regulators, and oxidative stress scavenging enzymes. Proteins associated with transmembrane processes, cell division, and stress defence were also upregulated. Metabolomic analysis showed that only a few amino acids, sugars, and specific metabolites were more abundant after low Earth orbit exposure, suggesting energy conservation for molecular repair and regulation.Primordial stress molecule spermidine is also involved in cells recovery, helping combat the stress factors after space travel. Conclusion: Comparative –omics profile of extracted mRNA, proteins and metabolites allowed us to propose a multiscale dynamic molecular response of Deinococcus radiodurans after 3 years of space exposure. The kinetic profile with 2 timepoints during post-exposure analysis enabled the identification of foreground molecular targets employed by this microorganism in recovery after a space journey. Altogether, a multi-omics approach towards space-exposed cells revealed a strong focus on repair mechanisms, stress defence, and the utilization of external resources during the initial recovery phase. These findings expand our understanding of the molecular mechanisms employed by extremophiles to survive in space, providing implications for astrobiology and future space exploration.
2025-02-27 | E-MTAB-13969 | biostudies-arrayexpress
Project description:This dataset includes 60 BAM files from HF2354, HF3016 glioblastoma cell lines subjected to continuous stress (hypoxia, 3-day and 9-day), stress followed by recovery (irradiation, 4-day stress exposure and 5-day recovery), and no stress/normoxia controls and profiled using reduced-representation bisulfite sequencing.
| EGAD00001007770 | EGA
Project description:Abstract Background The extraordinarily resistant bacterium Deinococcus radiodurans withstands harsh environmental conditions present in outer space. Deinococcus radiodurans was exposed for one year outside the International Space Station within Tanpopo orbital mission to investigate microbial survival and space travel. In addition, a ground-based simulation experiment with conditions, mirroring those from Low Earth orbit, was performed. Methods We monitored Deinococcus radiodurans cells during early stage of recovery after Low Earth orbit exposure using electron microscopy tools. Furthermore, proteomic, transcriptomic and metabolomic analyses were performed to identify molecular mechanisms responsible for the survival of Deinococcus radiodurans in Low Earth orbit. Results D. radiodurans cells exposed to low Earth orbit conditions do not exhibit any morphological damage. However, an accumulation of numerous outer-membrane associated vesicles was observed. On levels of proteins and transcripts, a multifaceted response was detected to alleviate cell stress. The UvrABC endonuclease excision repair mechanism was triggered to cope with DNA damage. Defense against reactive oxygen species is mirrored by the increased abundance of catalases and is accompanied by the increased abundance of putrescine which works as scavenging molecule. In addition, several proteins and mRNAs, responsible for regulatory and transporting functions showed increased abundances. The decrease in primary metabolites indicate alternations in the energy status, which is needed to repair damaged molecules. Conclusion Low Earth orbit induced molecular rearrangements trigger multiple components of metabolic stress response and regulatory networks in exposed microbial cells. Presented results show that the non-sporulating bacterium Deinococcus radiodurans survived long-term Low Earth orbit exposure if wavelength below 200 nm are not present, which mirrors the UV spectrum of Mars, where CO2 effectively provides a shield below 190 nm. These results should be considered in the context of planetary protection concerns and the development of new sterilization techniques for future space missions.
2021-09-09 | PXD020047 | Pride
Project description:Horse urine is easily collected and contains molecules readily measurable using mass spectrometry that can be used as biomarkers representative of health, disease or drug tampering. This study aimed at analyzing microliter levels of horse urine to purify, identify and quantify proteins, polar metabolites and non-polar lipids. Urine from a healthy 12 year old quarter horse mare on a diet of grass hay and vitamin/mineral supplements with limited pasture access was collected for serial-omics characterization. The urine was treated with methyl tert-butyl ether (MTBE) and methanol to partition into three distinct layers for protein, non-polar lipid and polar metabolite content from a single liquid-liquid extraction and was repeated two times. Each layer was analyzed by high performance liquid chromatography – high resolution tandem mass spectrometry (LC-MS/MS) to obtain protein sequence and relative protein levels as well as identify and quantify small polar metabolites and lipids. The results show 46 urine proteins, many related to normal kidney function, structural and circulatory proteins as well as 474 small polar metabolites but only 10 lipid molecules. Metabolites were mostly related to urea cycle and ammonia recycling as well as amino acid related pathways, plant diet specific molecules, etc. The few lipids represented triglycerides and phospholipids. These data show a complete mass spectrometry based –omics characterization of equine urine from a single 333 uL mid-stream urine aliquot. The data can be used as a baseline for healthy urine composition and analyses can be used to monitor disease progression, health status, monitor drug use, etc.
2018-07-23 | PXD007646 | Pride
Project description:Climate change increases both the frequency and duration of heat events. Direct negative effects of such heat stress may be exacerbated through heat-induced stress propagation (via stress metabolites) between aquatic animals. Whilst early life stages are vulnerable to stress-induced damage, they also deploy cellular mechanisms to protect cells against their naturally mutagenic environment. Little is known about the fate and performance of fish embryos which have experienced direct or indirect heat stress in a mutagenic environment. Natural environmental mutation rates are typically low which poses an observational challenge. To circumvent this, the present study exposed zebrafish embryos to three treatments consisting of direct heat stress, indirect heat-induced stress metabolites, and combined heat + heat-induced metabolites before undergoing a UVB/UVA damage/repair assay to mimic a mutagenic environment. Indirect heat stress led to expression of keratin and cell structuring-related genes in receivers, associated with longer embryos displaying over-developed pericardial widths and behavioural hypoactivity. Heat stress had a hormetic effect by stimulating the cellular stress response, and presumably facilitating DNA repair, which protected and/or rescued embryos from subsequent UV damage and improved their fitness. However, heat stress combined with stress metabolites emitted by heat-stressed conspecifics overwhelmed embryos, which annihilated the hormetic effect, introduced RNA mutations, and lowered overall fitness indicators. Whilst generated in the laboratory, these findings provide an important baseline for understanding the consequences of thermal stress history in natural environments, where direct and indirect heat stress co-occur.
2025-04-23 | GSE223685 | GEO
Project description:Molecular Elasticity and Adjustment of Drought Recovery Dynamics of 14N- and 15N-fertilized Legume Medicago truncatula. Climate change in conjunction with population growth necessitates a systems biology approach to characterize plant drought response and a more thorough understanding of the underlying molecular mechanisms. During drought stress and recovery, the metabolome and proteome regulate and are regulated through diverse mechanisms including synthesis and degradation. In order to study this complex regulation network, a front-end multilevel analysis is presented for the first time, investigating protein turnover, regulatory classes of proteins and metabolites as well as post translational ubiquitination of a target set of proteins during a severe stress and recovery scenario in the model legume Medicago truncatula. Evidence for enhanced translational proteome regulation was observed during drought recovery and functional clusters of differentially dynamic phases during the course of recovery were defined. The data give novel insights into molecular elasticity that enable recovery of drought stressed plants. Additionally, these results offer putative targets and metabolic pathways for future plant-bioengineering towards enhanced drought stress tolerance.
2016-03-29 | PXD001728 | Pride
Project description:Global Genomic Repair (GGR) and Transcription-Coupled Repair (TCR) have been viewed, respectively, as major and minor sub-pathways of the nucleotide excision repair (NER) process that removes bulky lesions from the genome. Here we applied a next generation sequencing assay, CPD-seq, in E. coli to measure the levels of cyclobutane pyrimidine dimer (CPD) lesions before, during, and after UV-induced genotoxic stress, and, therefore, to determine the rate of genomic recovery by NER at a single nucleotide resolution. We find that active transcription is necessary for the repair of not only the template strand (TS), but also the non-template strand (NTS), and that the bulk of TCR is independent of Mfd – a DNA translocase that is thought to be necessary and sufficient for TCR in bacteria. We further show that repair of both TS and NTS is enhanced by increased readthrough past Rho-dependent terminators. We demonstrate that UV-induced genotoxic stress promotes global antitermination so that TCR is more accessible to the antisense, intergenic, and other low transcribed regions. Overall, our data suggests that GGR and TCR are essentially the same process required for complete repair of the bacterial genome.
2022-02-05 | GSE171971 | GEO
Project description:Global Genomic Repair (GGR) and Transcription-Coupled Repair (TCR) have been viewed, respectively, as major and minor sub-pathways of the nucleotide excision repair (NER) process that removes bulky lesions from the genome. Here we applied a next generation sequencing assay, CPD-seq, in E. coli to measure the levels of cyclobutane pyrimidine dimer (CPD) lesions before, during, and after UV-induced genotoxic stress, and, therefore, to determine the rate of genomic recovery by NER at a single nucleotide resolution. We find that active transcription is necessary for the repair of not only the template strand (TS), but also the non-template strand (NTS), and that the bulk of TCR is independent of Mfd – a DNA translocase that is thought to be necessary and sufficient for TCR in bacteria. We further show that repair of both TS and NTS is enhanced by increased readthrough past Rho-dependent terminators. We demonstrate that UV-induced genotoxic stress promotes global antitermination so that TCR is more accessible to the antisense, intergenic, and other low transcribed regions. Overall, our data suggests that GGR and TCR are essentially the same process required for complete repair of the bacterial genome.
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Project description:Global Genomic Repair (GGR) and Transcription-Coupled Repair (TCR) have been viewed, respectively, as major and minor sub-pathways of the nucleotide excision repair (NER) process that removes bulky lesions from the genome. Here we applied a next generation sequencing assay, CPD-seq, in E. coli to measure the levels of cyclobutane pyrimidine dimer (CPD) lesions before, during, and after UV-induced genotoxic stress, and, therefore, to determine the rate of genomic recovery by NER at a single nucleotide resolution. We find that active transcription is necessary for the repair of not only the template strand (TS), but also the non-template strand (NTS), and that the bulk of TCR is independent of Mfd – a DNA translocase that is thought to be necessary and sufficient for TCR in bacteria. We further show that repair of both TS and NTS is enhanced by increased readthrough past Rho-dependent terminators. We demonstrate that UV-induced genotoxic stress promotes global antitermination so that TCR is more accessible to the antisense, intergenic, and other low transcribed regions. Overall, our data suggests that GGR and TCR are essentially the same process required for complete repair of the bacterial genome.
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