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MetabolomicsProtein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase

Metabolic networks are interconnected and influence diverse cellular processes. The protein-metabolite interactions that mediate these networks are frequently low affinity and challenging to systematically discover. We developed mass spectrometry integrated with equilibrium dialysis for the disco...

2023-08-07 | MTBLS7237 | MetaboLights
MetabolomicsAlcohol-Induced Bone Loss: Driven by Dysregulated Spatial Distribution of Gut Microbiota and PGD2-IL17 Pathway-Mediated Osteoclast Activation

Purpose: Alcohol-induced damage to bone microstructure leads to alcoholic osteopenia (AOP). While prior studies have demonstrated alcohol's negative impact on bone density, the mechanisms by which alcohol induces osteoporosis through immune pathways, gut microbiota dysbiosis, and metabolic altera...

2025-03-28 | MTBLS11887 | MetaboLights
MetabolomicsNew plasma preparation approach to enrich metabolome coverage in untargeted metabolomics: plasma protein bound hydrophobic metabolite release with proteinase K
Plasma untargeted metabolomics is a common method for evaluation of the mechanisms underlying human pathologies and identification of novel biomarkers. The plasma proteins provide the environment for transport of hydrophobic metabolites. The current sample preparation protocol relies on the immediat...
2022-03-18 | MTBLS670 | MetaboLights
ProteomicsMASP-II for Mapping the Whole-tissue Spatial Proteome and the Intra-brain Distribution of Monoclonal Antibodies
Spatial proteomics at whole-tissue level provides critical insights into region-specific biological regulations but remains challenging. Previously, we introduced the Micro-scaffold Assisted Spatial Proteomics (MASP) technique, permitting whole-tissue mapping. While promising, this prototype require...
ORGANISM(S): Mus musculus (Mouse) 
2026-08-24 | PXD068767 | Pride
Masp Whole tissue mapping Accurate protein distribution In-depth spatial proteomics Mab intra-brain distribution 
UnknownAccurate protein crystallography at ultra-high resolution: valence electron distribution in crambin.
Not available
S-EPMC16211 | biostudies-literature
MetabolomicsAspartate aminotransferase Rv3722c governs aspartate-dependent nitrogen metabolism in Mycobacterium tuberculosis

Gene rv3722c of Mycobacterium tuberculosis is essential for in vitro growth, and encodes a putative pyridoxal phosphate-binding protein of unknown function. Here we use metabolomic, genetic and structural approaches to show that Rv3722c is the primary aspartate aminotransferase of M. tuberculosis...

2020-05-01 | MTBLS1559 | MetaboLights
TranscriptomicsDetermination of prognosis in metastatic melanoma through integration of clinico-pathologic, mutation, mRNA, microRNA, and protein information
In patients with metastatic melanoma, the identification and validation of accurate prognostic biomarkers will assist rational treatment planning. Studies based on "-omics" technologies have focussed on a single high-throughput data type such as gene or microRNA transcripts. Occasionally, ...
ORGANISM(S): Homo sapiens 
2014-08-18 | E-GEOD-54467 | biostudies-arrayexpress
GenomicsCENTDIST: Discovery of Co-associated Factors by Motif Distribution
Transcription factors (TFs) do not function alone but work together with other TFs (called co-TFs) in a combinatorial fashion to precisely control the transcription of target genes. Mining co-TFs is thus important to understand the mechanism of transcriptional regulation. Although existing methods c...
ORGANISM(S): Homo sapiens 
2012-04-25 | E-GEOD-28857 | biostudies-arrayexpress
TranscriptomicsInvolvement of a chromatin remodeling complex in damage tolerance during DNA replication
ATP-dependent chromatin remodeling complexes have been shown to participate in DNA replication in addition to transcription and DNA repair. However, the mechanisms of their involvement in DNA replication remain unclear. Here, we reveal a specific function of the yeast INO80 chromatin remodeling comp...
ORGANISM(S): Saccharomyces cerevisiae 
2010-06-20 | E-GEOD-18570 | biostudies-arrayexpress
UnknownCARd: Carbon distribution analysis program for protein sequences.
Not available
S-EPMC3398768 | biostudies-literature
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