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MetabolomicsMitochondrial NAD+ Deficiency in Vascular Smooth Muscle Impairs Collagen III Turnover to Trigger Aortic Disease

Aortic disease poses a significant mortality risk in adults, yet many of its underlying factors remain undiscovered. In this study, we identify mitochondrial NAD⁺ deficiency as a causal factor. Metabolomics analysis of 73 surgical aortic specimens revealed impaired NAD⁺ salvage and mitochondrial ...

2024-12-04 | MTBLS8062 | MetaboLights
GenomicsGenome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3
We developed a system to study the DNA replication-independent turnover nucleosomes containing the histone variant H3.3 in mammalian cells. By measuring the genome-wide incorporation of H3.3 at different time points following epitope-tagged H3.3 expression, we find three categories of H3.3-nucleosom...
ORGANISM(S): Mus musculus 
2013-10-23 | E-GEOD-51505 | biostudies-arrayexpress
ModelsXu2003 - Phosphoinositide turnover
Xu2003 - Phosphoinositide turnover The model reproduces the percentage change of PIP_PM, PIP2_PM and IP3_Cyt as depicted in Figure 1 of the paper. The model also contains the equations for the analysis of PH-GFP experiments, however the initial value of PH_GFP has been set to zer...
2024-09-02 | BIOMD0000000075 | BioModels
ProteomicsProtein turnover rate along the gastrointestinal tract is coordinated by the spatial location and the microbiota
The gastrointestinal tract is covered by a single layer of epithelial cells that, together with the mucus layers, protect the underlying tissue from bacterial invasion. The epithelium has one of the highest turnover rates in the body, renewing every 4-5 days. Using stable isotope labelling, high-res...
ORGANISM(S): Mus musculus (Mouse) 
2020-01-24 | PXD011457 | Pride
Germ-free Colon Mass spectrometry Protein turnover Commensals Lipid metabolism Proteomics Colonization Small intestine Bacteria 
TranscriptomicsGrowth-rate dependency of de novo resveratrol production in chemostat cultures of an engineered Saccharomyces cerevisiae strain
Saccharomyces cerevisiae has become a popular host for production of non-native compounds. The metabolic pathways involved generally require a net input of energy. To maximize the ATP yield on sugar in S. cerevisiae, industrial cultivation is typically performed in aerobic, sugar-limited fed-batch r...
ORGANISM(S): Saccharomyces cerevisiae 
2015-12-22 | E-GEOD-65942 | biostudies-arrayexpress
ProteomicsBank Vole Protein Turnover Study C4PR_LIV
We have used dietary administration of stable isotope labelled lysine to assess protein turnover rates for proteins from four tissues in the bank vole, Myodes glareolus. The annotated genome for this species is not available, so protein identification was attained through cross-species matching to t...
ORGANISM(S): Mus musculus (Mouse) Myodes glareolus (Bank vole) (Clethrionomys glareolus) 
2016-02-09 | PXD002054 | Pride
Vole protein turnover 
ProteomicsModeling SILAC Data to Assess Protein Turnover in a Cellular Model of Diabetic Nephropathy
Protein turnover rate is finely regulated through intracellular mechanisms and signals that are still incompletely understood but that are essential for the correct function of cellular processes. Indeed, a dysfunctional proteostasis often impacts on the ability of the cell to remove unfolded, misfo...
ORGANISM(S): Homo sapiens (Human) 
2023-02-13 | PXD038541 | Pride
Lc-ms/ms  protein turnover rate  protein half-life  silac  diabetes  nephropathy  fibroblasts 
ProteomicsProtein turnover analysis in Salmonella Typhimurium during infection by dynamic SILAC, Topograph and quantitative proteomics
Protein turnover affects protein abundance and phenotypes. Comprehensive investigation of protein turnover dynamics has the potential to provide substantial information about gene expression. Here we report a large-scale protein turnover study in Salmonella Typhimurium during infection by quantitati...
ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium 
2022-05-17 | PXD033623 | Pride
Proteomics Salmonella typhimurium Dynamic silac Protein turnover 
ProteomicsThylakoid protein turnover rate measurement in Col-0, stn7-1 and tap38-1 by 15N labelling
State transitions involve the phosphorylation and dephosphorylation of light-harvesting complex II, catalyzed by the thylakoid kinase STN7 and the phosphatase TAP38/PPH1 in algae and higher plants. These transitions enable algae and plants to coordinate the activation of photosystem I and II. Howeve...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2025-12-13 | PXD064731 | Pride
Tap38 State transition Stn7 Thylakoid Protein turnover 
ProteomicsMammalian Fibroblast Turnover Rates, Protein Abundance, and Protein Damage Response
Within a cell, proteins are in a dynamic state of turnover and are continuously synthesized and degraded. As an energetically expensive cellular process, protein turnover can have two opposing effects on maintaining a healthy proteome during the lifespan of an organism. Rapid protein turnover can re...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) 
2020-05-07 | PXD018325 | Pride
Mammalian Silac Lfq Primary Ibaq Fibroblast 
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