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MetabolomicsBioaccumulation of therapeutic drugs by human gut bacteria: cross-feeding metabolite analysis (FIA-MS) (E.rectale;S.salivarius assays)

Bacteria in the gut can modulate the availability and efficacy of therapeutic drugs. Interactions at this level have only recently started to being systematically mapped and the main underlying mechanism proposed is chemical transformation of drugs by microbes (biotransformation). Here, we invest...

2021-07-20 | MTBLS1792 | MetaboLights
ProteomicsEpitope and paratope mapping of a SUMO-remnant antibody using cross-linking mass spectrometry and molecular docking
The small ubiquitin-like modifier (SUMO) is an important post-translational modification that regulates the function of various proteins essential for DNA damage repair, genome integrity and cell homeostasis. To identify protein SUMOylation effectively, an enrichment step is necessary, often require...
ORGANISM(S): Oryctolagus cuniculus (Rabbit) 
2025-02-19 | PXD055077 | Pride
Antibody Cross-linking Mass spectrometry Molecular docking Paratope mapping Sumo 
ProteomicsEpitope and paratope mapping of a SUMO-remnant antibody using cross-linking mass spectrometry and molecular docking
The small ubiquitin-like modifier (SUMO) is an important post-translational modification that regulates the function of various proteins essential for DNA damage repair, genome integrity and cell homeostasis. To identify protein SUMOylation effectively, an enrichment step is necessary, often require...
ORGANISM(S): Oryctolagus sp. 'Rabbit_OD' 
2025-02-19 | PXD055085 | Pride
Antibody Cross-linking Mass spectrometry Molecular docking Paratope mapping Sumo 
ProteomicsEpitope and paratope mapping of a SUMO-remnant antibody using cross-linking mass spectrometry and molecular docking
The small ubiquitin-like modifier (SUMO) is an important post-translational modification that regulates the function of various proteins essential for DNA damage repair, genome integrity and cell homeostasis. To identify protein SUMOylation effectively, an enrichment step is necessary, often require...
ORGANISM(S): Oryctolagus cuniculus (Rabbit) 
2025-02-19 | PXD060724 | Pride
Antibody Cross-linking Mass spectrometry Molecular docking Paratope mapping Sumo 
MetabolomicsMetabolomic and Metataxonomic Fingerprinting of Human Milk Suggests Compositional Stability over a Natural Term of Breastfeeding to 24 Months
Sparse data exist regarding the normal range of composition of maternal milk beyond the first postnatal weeks. This single timepoint, observational study in collaboration with the 'Parenting Science Gang' citizen science group evaluated the metabolite and bacterial composition of human milk from 62 ...
2022-02-11 | MTBLS1370 | MetaboLights
ProteomicsEndo-Lysosomal Proteins and Ubiquitin CSF Concentrations in Alzheimer’s and Parkinson’s Disease
Alzheimer’s (AD) and Parkinson’s disease (PD) are neurodegenerative disorders characterized by an accumulation of protein aggregates in the brain. AD is the most common cause of dementia and presents with impairment of memory and cognition. PD results from the loss of dopaminergic neurons which resu...
ORGANISM(S): Homo Sapiens 
PXD013451 | panorama
TranscriptomicsThe DNMT1 associated lncRNA Dali is an epigenetic regulator of neural differentiation [4]
Many intergenic long noncoding RNA (lncRNA) loci regulate the expression of adjacent protein coding genes. Less clear is whether intergenic lncRNAs commonly regulate transcription by modulating chromatin at genomically distant loci. Here, we report both genomically local and distal RNA-dependent rol...
ORGANISM(S): Mus musculus 
2014-12-03 | E-GEOD-62034 | biostudies-arrayexpress
TranscriptomicsThe long non-coding RNA Paupar regulates the expression of both local and distal genes [CHART-seq]
Although some long noncoding RNAs (lncRNAs) have been shown to regulate gene expression in cis, it remains unclear whether lncRNAs can directly regulate transcription in trans by interacting with chromatin genome-wide independently of their sites of synthesis. Here, we describe the genomically local...
ORGANISM(S): Mus musculus 
2013-11-21 | E-GEOD-52570 | biostudies-arrayexpress
GenomicsPlants regenerated from tissue culture contain stable epigenome changes in rice
Most transgenic crops are produced through tissue culture. The impact of utilizing such methods on the plant epigenome is poorly understood. Here we generated whole-genome, single-nucleotide resolution maps of DNA methylation in several transgenic rice lines. We found that all tested transgenic plan...
ORGANISM(S): Oryza sativa Japonica Group 
2013-03-26 | E-GEOD-42410 | biostudies-arrayexpress
MetabolomicsMetabolic Phenotyping and Strain Characterisation of Pseudomonas aeruginosa Isolates from Cystic Fibrosis Patients Using Rapid Evaporative Ionisation Mass Spectrometry
Rapid evaporative ionisation mass spectrometry (REIMS) is a novel technique for the real-time analysis of biological material. It works by conducting an electrical current through a sample, causing it to rapidly heat and evaporate, with the analyte containing vapour channelled to a mass spectrometer...
2022-01-26 | MTBLS644 | MetaboLights
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