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GNPS Comparative metabolomics with Metaboseek reveals functions of peroxisomal alpha-oxidation in C. elegans

ABSTRACT: Helf MJ, Fox BW, Artyukhin AB, Zhang YK, Schroeder FC (2021) Comparative metabolomics with Metaboseek reveals functions of peroxisomal alpha-oxidation in C. elegans

INSTRUMENT(S): Q Exactive HF, Q Exactive

ORGANISM(S): Caenorhabditis Elegans (ncbitaxon:6239)

SUBMITTER: Frank Schroeder

PROVIDER: MSV000087885 | GNPS | Mon Jul 26 13:36:00 BST 2021

REPOSITORIES: GNPS

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Publications

Comparative metabolomics with Metaboseek reveals functions of a conserved fat metabolism pathway in C. elegans.

Helf Maximilian J MJ Fox Bennett W BW Artyukhin Alexander B AB Zhang Ying K YK Schroeder Frank C FC

Nature communications 20220210 1

Untargeted metabolomics via high-resolution mass spectrometry can reveal more than 100,000 molecular features in a single sample, many of which may represent unidentified metabolites, posing significant challenges to data analysis. We here introduce Metaboseek, an open-source analysis platform designed for untargeted comparative metabolomics and demonstrate its utility by uncovering biosynthetic functions of a conserved fat metabolism pathway, α-oxidation, using C. elegans as a model. Metaboseek ...[more]

PMID: 35145075

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Comparative metabolomics with Metaboseek reveals functions of peroxisomal alpha-oxidation in C. elegans

Project description:Helf MJ, Fox BW, Artyukhin AB, Zhang YK, Schroeder FC (2021) Comparative metabolomics with Metaboseek reveals functions of peroxisomal alpha-oxidation in C. elegans

2021-07-26 | MSV000087885 | MassIVE

Microarray of five Caenorhabiditis elegans genotypes with or without a human alpha-synuclein transgene in the genetic background

Project description:Previous studies in Caenorhabditis elegans expressing the human alpha-synuclein protein, have shown that protein aggregation and some aetiologies of Parkinsons disease can be recapitulated in this model nematode. However, it is known that the genetic background is important in how the disease progresses in humans. This study sought to address this topic in the model nematode C. elegans. In this study we measured gene expression in C. elegans nematodes with different genetic backgrounds (JU511, JU1926, JU1931, and JU1941) with an introgression of and N2 region with the alpha-synuclein protein in chromosome IV. We measured expression in the wild-type strains and strains with the transgene. Each strain was measured in three biological replica's at an age of 48 hours post synchronization by bleaching.

2019-02-11 | E-MTAB-6960 | biostudies-arrayexpress

DNA sequencing of Caenorhabditis elegans recombinant inbred lines containing a human alpha-synuclein trans-gene

Project description:Recombinant inbred lines were created by crossing the alpha-synuclein containing Caenorhabditis elegans strains NL5901 and SCH4856. These strains contain the human alpha-synuclein gene fused to YFP and under the control of an unc-54 promotor (unc-54p::alpha-synnuclein::YFP) in an N2 and CB4856 genetic background, respectively. These two strains were used to generate a total of 212 recombinant inbred lines, of which 88 were genotyped by whole-genome sequencing using a MiSeq. These recombinant inbred lines can be used for mapping genetic modifiers affecting protein accumulation.

2023-06-30 | E-MTAB-12575 | biostudies-arrayexpress

Metabolic regulation of cytoskeleton functions by HDAC6-catalyzed α-tubulin lactylation

Project description:Metabolic regulation of cytoskeleton functions by HDAC6-catalyzed α-tubulin lactylation

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Metabolic rescue of α-synuclein-induced neurodegeneration through propionate supplementation and intestine-neuron signaling in C. elegans

Project description:Vitamin B12 depletion or propionate supplementation can reverse the transcriptomic aberration in the C. elegans model of PD with neuronal overexpression of alpha-synuclein A53T

2023-04-28 | GSE230786 | GEO

Blastomere-specific transcriptome sequencing reveals a determinant of anterior specification in C. elegans

Project description:We sequenced amplified mRNA from 20 pooled AB and 20 pooled P1 blastomeres hand isolated from 2-cell stage C. elegans embryos three replicates each.

2015-03-05 | GSE59943 | GEO

Gene expression by microarray of Caenorhabditis elegans introgression lines carrying human alpha-synuclein

Project description:We conducted an experiment on introgression lines of Caenorhabditis elegans derived from a NL5901 cross with three previously constructed CB4856>N2 ILs (WN268, WN269, and WN270). The tested ILs carry a combination of chromosome V introgressions and the alpha-synuclein trans-gene: CB4856>N2 / aS, CB4856>N2 / -, - / aS, and - / -. We grew synchronized populations of the nematodes (12 ILs, N2, CB4856, NL5901, and SCH4856) under normal conditions (20 degrees Celcius, feeding on Escherichia coli OP50) for 120 hours. This experiment was repeated three times. The goal of the experiment was to identify loci affecting gene expression in the presence of human alpha-synuclein

2023-07-30 | E-MTAB-11661 | biostudies-arrayexpress

Gene expression by microarray of a Caenorhabditis elegans recombinant inbred line panel carrying human alpha-synuclein

Project description:We conducted a timeseries experiment on a recombinant inbred line (RIL) panel of Caenorhabditis elegans derived from a NL5901 x SCH4856 cross. These RILs carry a human alpha-synuclein gene in an N2 and a CB4856 genetic background respectively. We grew synchronized populations of the nematodes (70 RILs, N2, CB4856, NL5901, and SCH4856) under normal conditions (20 degrees Celcius, feeding on Escherichia coli OP50) for 120 hours. The goal of the experiment was to identify loci affecting gene expression in the presence of human alpha-synuclein

2023-07-30 | E-MTAB-11658 | biostudies-arrayexpress

The C. elegans PTPN22 ortholog functions in diverse developmental processes

Project description:Non-receptor type protein tyrosine phosphatases (PTPNs) have been studied extensively in the context of the adaptive immune system, however, their roles beyond immunoregulation are less unexplored. Here we identify novel functions for the conserved C. elegans phosphatase, PTPN-22, establishing new links to worm molting, cell adhesion, and cytoskeletal regulation. Through a non-biased genetic screen, we found that loss of PTPN-22 phosphatase activity suppresses molting defects caused by loss-of-function mutations in the conserved NIMA-related kinases, NEKL-2 (human NEK8/9) and NEKL-3 (human NEK6/7), which act at the interface of membrane trafficking and actin regulation. To better understand the functions of PTPN-22 we carried out proximity labeling studies to identify candidate interactors of PTPN-22 during development. Through this approach we identified the CDC42 guanine-nucleotide exchange factor DNBP-1 (human DNMBP) as an in vivo partner of PTPN-22 and showed that loss of DNBP-1 also suppresses nekl-associated molting defects and partially co-localizes with PTPN-22 in the epidermis. Genetics analysis, co-localization studies, and proximity labeling also revealed roles for PTPN-22 in several epidermal adhesion complexes including C. elegans hemidesmosomes, suggesting that PTPN-22 plays a broad role in maintaining the structural integrity of tissues. Localization and proximity labeling also implicated PTPN-22 in functions connected to nucleocytoplasmic transport and mRNA regulation, particularly within the germline, as nearly one third of proteins identified by PTPN-22 proximity labeling are known P granule components. Collectively, our studies highlight the utility of combined genetic and proteomic approaches for identifying novel gene functions.

2024-07-31 | MSV000095492 | MassIVE

Blastomere-specific transcriptome sequencing reveals a determinant of anterior specification in C. elegans

Project description:We sequenced amplified mRNA from 20 pooled AB and 20 pooled P1 blastomeres hand isolated from 2-cell stage C. elegans embryos three replicates each. Transcriptome profiles of each blastomere at the 2-cell stage of the C. elegans early embryo.

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