GNPS - WLECC_Metabologenomics_mzXML_April2024_LH_submission
Ontology highlight
ABSTRACT:
INSTRUMENT(S): 6545 Q-TOF LC/MS
ORGANISM(S): Microcystis Sp. (ncbitaxon:1127)
SUBMITTER: 
Greg Dick
PROVIDER: MSV000094628 | GNPS | Mon Apr 29 05:09:00 BST 2024
REPOSITORIES: GNPS
Similar Datasets
Project description:Title: Metabologenomics reveals strain-level genetic and chemical diversity of Microcystis secondary metabolism
Author list: Colleen E. Yancey, Lauren Hart, Sierra Hefferan, Osama G. Mohamed, Sean A. Newmister, Ashootosh Tripathi, David H. Sherman, Gregory J. Dick
Short description of submission: 20 mzXML files collected for the crude extracts of 20 isolates of Microcystis from the Western Lake Erie Culture Collection (WLECC, https://doi.org/10.1016/j.hal.2023.102440).
2024-04-29 | MSV000094628 | MassIVE
Project description:Whole genome trancription study of Citrobacter rodentium grown in rich media. Publication Title: Citrobacter rodentium is an Unstable Pathogen Showing Evidence of Significant Genomic Flux Publication Author List: Nicola K. Petty, Theresa Feltwell, Derek Pickard, Simon Clare, Ana L. Toribio, Maria Fookes, Kevin Roberts, Rita Monson, Satheesh Nair, Robert A. Kingsley, Richard Bulgin, Siouxsie Wiles, David Goulding, Craig Corton, Nicola Lennard, David Harris, David Willey, Richard Rance, Lu Yu, Jyoti S. Choudhary, Carol Churcher, Michael A. Quail, Julian Parkhill, Gad Frankel, Gordon Dougan, George P.C. Salmond, Nicholas R. Thomson ArrayExpress Release Date: 2011-02-12 Person Roles: investigator Person Last Name: Thomson Person First Name: Nicholas Person Mid Initials: Person Email: nrt@sanger.ac.uk Person Phone: Person Address: Wellcome Trust Genome Campus, Hinxton, Cambridge, UK Person Affiliation: Wellcome Trust Sanger Institute Person Roles: submitter Person Last Name: Service Person First Name: Submission Person Mid Initials: Person Email: datahose@sanger.ac.uk Person Phone: Person Address: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom Person Affiliation: Wellcome Trust Sanger Institute
2011-07-14 | GSE30610 | GEO
Project description:<p>Cyanobacterial blooms result from continued short-term succession of planktonic microbiomes, but these short-term variations are little known. Here we address this question with a field diel study in Lake Tai. By integrating untargeted metabolomics—verified by targeted metabolomics—and metagenomics, we reveal the diel cycle of planktonic microbiome in Lake Tai are highly dynamic and complex. First, metabolite abundance and their molecular mass display clear diel changes along with shift in the taxon abundance and biological functions, following the same environmental factors. Some taxa and biological functions (reactions) are highly correlated with the metabolite abundance, and large compounds appear to be more taxon specific. Second, phytoplanktonic and overall planktonic microbiome showed different temporal variation of abundance, opposite levels of abundance and different molecular sizes, and different inter- and intra-specific diversity dynamics. Last, planktonic microbiomes are highly dynamic and complex in inter- and intraspecific diversity in merely one diel cycle, which point to different temperature preference between species, Microcystis aeruginosa and Anabaena sp. This difference was experimentally confirmed in laboratory. Using a multi-omics approach, our study underscores the importance of diel interaction triad between population abundance, biological functions, and environmental factors in leading to microbiome structural change and blooms.</p>
2022-03-02 | MTBLS3038 | MetaboLights
Project description:This data is a case study done in the context of developing methods for assessing the taxonomic composition of microbial communities using metaproteomics. For this study with analyzed phototrophic biomats from two Soda Lakes in the Canadian Rocky Mountains using metaproteomics. For protein identification we generated a metagenome from which we predicted and annotated the protein sequences used to analyze the metaproteomes. The database is available in this PRIDE submission. Lake1 refers to Goodenough Lake (GEM, 51°19'47.64"N 121°38'28.90"W) and Lake2 referes to Last Chance Lake (LCM, 51°19'39.3" N 121°37'59.3"W).
2017-05-12 | PXD006343 | Pride
Project description:Microcystis aeruginosa cells were treated with phosphorus repletion, depletion and starvation. Isobaric tags for relative and absolute quantitation (iTRAQ) proteomic method was employed to explore to the effects of phosphorus limitation on Microcystis aeruginosa cells at the protein level. This investigation would contribute to the understanding of global cellular responses of Microcystis to phosphorus limitation and provide theoretical basis for deciding whether it is an effective way to control Microcystis blooms by phosphorus reduction.
2021-06-29 | PXD025188 | Pride
Project description:Five-vertebrate ChIP-seq reveals the evolutionary dynamics of trancription factor binding. The SRF files for this experiment can be found in the European Read Archive with study accession number ERP000054. ArrayExpress Submission Date: Apr 07 2010 ArrayExpress Release Date: Apr 08 2010 Publication Author List: Dominic Schmidt; Michael D Wilson; Benoit Ballester; Petra C Schwalie; Gordon D Brown; Aileen Marshall; Claudia Kutter; Stephen Watt; Celia P Martinez-Jimenz; Sarah MacKay; Iannis Talianidis; Paul Flicek; Duncan T Odom Publication Title: Transcription factor binding evolution in five vertebrates Person Roles: submitter Person Last Name: Flicek Person First Name: Paul Person Email: flicek@ebi.ac.uk Person Address: Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK Person Affiliation: EBI
2010-06-02 | GSE22078 | GEO
Project description:The molecular chaperone TRAP1, the mitochondrial isoform of cytosolic HSP90, remains poorly understood with respect to its pivotal role in the regulation of mitochondrial metabolism. To characterize the impact of TRAP1 in maintaining the cellular proteome under different energy sources we carried out a label free quantitation (LFQ) MS analysis of the total cellular proteome with WT and KO HEK293T and HCT116 cells cultured with the three different cocktails of carbon sources (Glc + Pyr + Gln, Gal + Pyr only, Gln only). Linked manuscript : Abhinav Joshi, Li Dai, Yanxin Liu, Jungsoon Lee, Nastaran Mohammadi Ghahhari, Gregory Segala, Kristin Beebe, Francis T.F. Tsai, David A. Agard, Len Neckers, and Didier Picard* (*corresponding author).
2020-01-16 | PXD015828 | Pride
Project description:Although cyanobacteria produce a wide range of natural toxins that impact aquatic organisms, food webs and water quality, the mechanisms of toxicity are still insufficiently understood. Here, we implemented a whole-genome expression microarray to identify pathways, gene networks and paralogous gene families responsive to Microcystis stress in Daphnia pulex. Therefore, neonates of a sensitive isolate were given a diet contaminated with Microcystis to contrast with those given a control diet for sixteen days. The microarray revealed 2247 differentially expressed (DE) genes (7.6% of the array) in response to Microcystis, of which 17% are lineage specific and 49% are gene duplicates (paralogs). We identified four pathways/gene networks and eight paralogous gene families affected by Microcystis. Differential regulation of the ribosome including 3 paralogous gene families encoding 40S, 60S and mitochondrial ribosomal proteins, suggests an impact of Microcystis on protein synthesis of Daphnia. In addition, differential regulation of the oxidative phosphorylation pathway, including the NADH ubquinone oxidoreductase gene family, and trypsin paralogous gene family, major component of the digestive system in Daphnia, could explain why fitness is reduced based on energy budget considerations. For others (.e.g Neurexin IV), a link with fitness remains to be established.
2012-07-27 | GSE36635 | GEO
Project description:Although cyanobacteria produce a wide range of natural toxins that impact aquatic organisms, food webs and water quality, the mechanisms of toxicity are still insufficiently understood. Here, we implemented a whole-genome expression microarray to identify pathways, gene networks and paralogous gene families responsive to Microcystis stress in Daphnia pulex. Therefore, neonates of a sensitive isolate were given a diet contaminated with Microcystis to contrast with those given a control diet for sixteen days. The microarray revealed 2247 differentially expressed (DE) genes (7.6% of the array) in response to Microcystis, of which 17% are lineage specific and 49% are gene duplicates (paralogs). We identified four pathways/gene networks and eight paralogous gene families affected by Microcystis. Differential regulation of the ribosome including 3 paralogous gene families encoding 40S, 60S and mitochondrial ribosomal proteins, suggests an impact of Microcystis on protein synthesis of Daphnia. In addition, differential regulation of the oxidative phosphorylation pathway, including the NADH ubquinone oxidoreductase gene family, and trypsin paralogous gene family, major component of the digestive system in Daphnia, could explain why fitness is reduced based on energy budget considerations. For others (.e.g Neurexin IV), a link with fitness remains to be established. RNA was isolated from three independent and concurrently replicated exposures of Daphnia to control and Microcystis conditions. RNA was hybridized to 4 microarrays using a standard, control vs. treated design that included dye swaps.
2012-07-26 | E-GEOD-36635 | biostudies-arrayexpress
Project description:Elevated levels of adsorbable organic bromine compounds (AOBr) have been detected in German lakes, and cyanobacteria like Microcystis, which are known for the synthesis of microcystins, are one of the main producers of natural organobromines. However, very little is known about how environmental realistic concentrations of organobromines impact invertebrates. Here, the nematode C. elegans was exposed to AOBr-containing surface water samples and to a Microcystis aeruginosa enriched batch culture (MC-BA) and compared to single organobromines and microcystin-LR exposures. Stimulatory effects were observed in certain life trait variables, which were particularly pronounced in nematodes exposed to MC-BA. A whole genome DNA-microarray revealed that MC-BA led to the differential expression of more than 2000 genes, many of which are known to be involved in metabolic, neurologic, and morphologic processes. Moreover, the up-regulation of cyp- and the down-regulation of abu-genes suggested the presence of chronic stress. However, the nematodes were not marked by negative phenotypic responses. The observed difference in MC-BA and microcystin-LR (which impacted lifespan, growth and reproduction) exposed nematodes was hypothesized to be likely due to other compounds within the batch culture. Most likely the exposure to low concentrations of organobromines appears to buffer the effects of toxic substances, like microcystin-LR. Nematodes were exposed to filtrated samples of Lake Stößensee Berlin (August and October) and compared to the control-group (exposure to water). Furthermore, nematodes were exposed to filtrated M. aeruinosa batch culture samples and compared to another control-group (exposure to Z-Medium). Three samples (biological replicates) were prepared for each group.
2015-05-12 | E-GEOD-68709 | biostudies-arrayexpress