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MetabolomicsUntargeted Metabolomics for Integrative Taxonomy: Metabolomics, DNA Marker-Based Sequencing, and Phenotype Bioimaging

Integrative taxonomy is a fundamental part of biodiversity and combines traditional morphology with additional methods such as DNA sequencing or biochemistry. Here, we aim to establish untargeted metabolomics for use in chemotaxonomy. We used three thallose liverwort species Riccia glauca

2026-01-30 | MTBLS4668 | MetaboLights
MetabolomicsDNA nanomachines reveal an adaptive energy mode in confinement-induced amoeboid migration powered by polarized mitochondrial distribution

Energy metabolism is highly interdependent with adaptive cell migration in vivo. Mechanical confinement is a critical physical cue that induces switchable migration modes of the mesenchymal-to-amoeboid transition (MAT). However, the energy states in distinct migration modes, especially a...

2024-03-25 | MTBLS9657 | MetaboLights
MetabolomicsChemocoding as an identification tool where morphological- and DNA-based methods fall short: Inga as a case study
The need for species identification and taxonomic discovery has led to the development of innovative technologies for large-scale plant identification. DNA barcoding has been useful, but fails to distinguish among many species in species-rich plant genera, particularly in tropical regions. Here, we ...
2018-01-22 | MTBLS574 | MetaboLights
MetabolomicsAn LC–MS-based lipidomics pre-processing framework underpins rapid hypothesis generation towards CHO systems biotechnology

INTRODUCTION: Given a raw LC–MS dataset, it is often required to rapidly generate initial hypotheses, in conjunction with other ‘omics’ datasets, without time-consuming lipid verifications. Furthermore, for meta-analysis of many datasets, it may be impractical to conduct exhausti...

2018-07-17 | MTBLS493 | MetaboLights
GenomicsHistone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells [ChIP-Seq]
Variation in chromatin composition and organization often reflects differences in genome function. Histone variants, for example, replace canonical histones to contribute to regulation of numerous nuclear processes including transcription, DNA repair and chromosome segregation. Here we focus on H2A....
ORGANISM(S): Homo sapiens 
2012-07-16 | E-GEOD-38284 | biostudies-arrayexpress
ProteomicsIntegrative Structural Model of DNA-PK Synapsis
In non-homologous end joining repair of DNA double strand breaks, DNA dependent protein kinase catalytic subunit (DNA-PKcs) and Ku70/80 binds the free DNA ends forming the holoenzyme DNA-PK. DNA-PK synapses across the break to tether the broken ends in the initial long range synaptic complex. We gen...
ORGANISM(S): Homo sapiens (Human) 
2021-01-20 | PXD017931 | Pride
Dna-pk Hydrogen deuterium exchange Crosslinking 
ProteomicsComparative proteomic analysis of Neisseria meningitidis wildtype and dprA null mutant strains links DNA processing to pilus biogenesis
DNA processing chain A (DprA) is a DNA binding protein which is ubiquitous in bacteria and required for DNA transformation. However, the interaction of DprA with competence proteins and recombination is poorly understood. Therefore, the proteomes of whole Neisseria meningitidis (Nm) wildtype and dp...
ORGANISM(S): Neisseria meningitidis serogroup B 
2017-04-26 | PXD006121 | Pride
Dna processing Proteomics Pilus biogenesis Mass spectrometry Neisseria meningitides Dpra Pilg 
TranscriptomicsA novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity
Here we identify a Dicer-independent miRNA biogenesis pathway that employs the slicer catalytic activity of Argonaute2 (Ago2). To uncover Dicer-independent miRNAs, we sequenced small RNAs in wild type, maternal-zygotic dicer (MZdicer) and MZago2 mutants, using zebrafish as a model system. We find t...
ORGANISM(S): Danio rerio 
2010-07-01 | E-GEOD-21503 | biostudies-arrayexpress
TranscriptomicsGenome-wide screen reveals rhythmic regulation of genes involved in odor processing in the olfactory epithelium
Odor discrimination behavior displays circadian fluctuations in mice indicating that mammalian olfactory function is under control of the circadian system. This is further supported by the facts that odor discrimination rhythms depend on the presence of clock genes and that olfactory tissues contain...
ORGANISM(S): Mus musculus 
2015-11-04 | E-GEOD-69853 | biostudies-arrayexpress
ProteomicsProteome-wide analysis of SUMO2 targets in response to pathological DNA replication stress in human cells
SUMOylation is a form of post-translational modification involving covalent attachment of SUMO (Small Ubiquitin-like Modifier) polypeptides to specific lysine residues in the target protein. In human cells, there are four SUMO proteins, SUMO1–4, with SUMO2 and SUMO3 forming a closely related subfami...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-28 | MSV000080699 | MassIVE
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