Molecular & Cellular Proteomics, Journal Year: 2025, Volume and Issue: unknown, P. 100917 - 100917
Published: Jan. 1, 2025
Language: Английский
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: July 3, 2024
Summary Cis -regulatory elements (CREs) precisely control spatiotemporal gene expression in cells. Using a spatially resolved single-cell atlas of with chromatin accessibility across ten soybean tissues, we identified 103 distinct cell types and 303,199 accessible regions (ACRs). Nearly 40% the ACRs showed cell-type-specific patterns were enriched for transcription factor (TF) motifs defining diverse identities. We de novo TF explored conservation regulatory networks underpinning legume symbiotic nitrogen fixation. With comprehensive developmental trajectories endosperm embryo, uncovered functional transition three sub-cell endosperm, 13 sucrose transporters sharing DOF11 motif that co-up-regulated late peripheral key embryo cell-type specification regulators during embryogenesis, including homeobox promotes cotyledon parenchyma identity. This resource provides valuable foundation analyzing programs tissues life stages.
Language: Английский
Citations
6
Animals, Journal Year: 2024, Volume and Issue: 14(14), P. 2069 - 2069
Published: July 15, 2024
Online Mendelian Inheritance in Animals (OMIA is a freely available information resource, which includes for
Language: Английский
Citations
6
Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(10), P. 2506 - 2521
Published: Aug. 12, 2024
Abstract Staphylococcus aureus is a pulmonary pathogen associated with substantial human morbidity and mortality. As vaccines targeting virulence determinants have failed to be protective in humans, other factors are likely involved pathogenesis. Here we analysed transcriptomic responses of clinical isolates S. from initial chronic infections. We observed upregulated collagenase proline transporter gene expression infection isolates. Metabolomics bronchiolar lavage fluid fibroblast infection, growth assays analysis bacterial mutant strains showed that airway fibroblasts produce collagen during infection. Host-adapted bacteria upregulate collagenase, which degrades releases proline. then imports proline, fuels oxidative metabolism via the tricarboxylic acid cycle. Proline provides host-adapted metabolic benefit enabling out-competition non-adapted strains. These data suggest settings characterized by repair processes fibrosis provide milieu promotes adaptation supports
Language: Английский
Citations
6
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: April 22, 2024
Abstract The details surrounding the evolution of complex cells remain some most enduring mysteries in biology. Recent evidence has demonstrated that Asgard archaea are closest cellular relatives eukaryotes, but several eukaryotic enzymes involved key processes lack phylogenetic affinity with archaea. In particular, phylogenies DNA and RNA polymerases often support a 3-domain topology is not consistent an archaeal origin. Here we present comprehensive analysis family B multimeric show these core subunits derived from ancestors modern giant viruses (phylum Nucleocytoviricota ). Specifically, delta polymerase (Polδ), processive required for genome replication all clusters within ancient viral clade, strongly supporting By contrast, other (Polε), clade. Together, observations provide strong direct link between early archaea, viruses. Lastly, to confirm II, which responsible mRNA transcription also total, our results model eukaryogenesis emerged genomic chimera lineage.
Language: Английский
Citations
5
Bioinformatics, Journal Year: 2024, Volume and Issue: 40(Supplement_1), P. i287 - i296
Published: April 11, 2024
Abstract Summary Improvements in nanopore sequencing necessitate efficient classification methods, including pre-filtering and adaptive sampling algorithms that enrich for reads of interest. Signal-based approaches circumvent the computational bottleneck basecalling. But past methods signal-based do not scale efficiently to large, repetitive references like pangenomes, limiting their utility partial or individual genomes. We introduce Sigmoni: a rapid, multiclass method based on r-index scales hundreds Gbps. Sigmoni quantizes signal into discrete alphabet picoamp ranges. It performs approximate matching using statistics, classifying distributions statistics co-linearity all linear query time without need seed-chain-extend. is 10–100× faster than previous host depletion experiments with improved accuracy, can against large microbial human pangenomes. first tool complete genome pangenome while remaining fast enough applications. Availability implementation implemented Python, available open-source at https://github.com/vshiv18/sigmoni.
Language: Английский
Citations
5
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: July 31, 2024
Abstract The NCBI Sequence Read Archive (SRA) is the largest public repository of DNA sequencing data, containing most comprehensive snapshot Earth’s genetic diversity to date. As its size exceeds 50.0 petabases across >27 million datasets, entirety these data cannot be searched for sequences interest in a reasonable time. To drastically increase accessibility this we perform genome assembly over each SRA dataset using massively parallel cloud computing. resulting Logan assemblage assembled date, and believe will enable new-era accessible petabase-scale computational biology inquiry. We provide free unrestricted access disseminate datasets foster early adoption. illustrate usefulness align diverse set sequence queries all SRA, completing as little 11 hours.
Language: Английский
Citations
5
The Enzymes, Journal Year: 2024, Volume and Issue: unknown, P. 343 - 381
Published: Jan. 1, 2024
Language: Английский
Citations
5
Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 52(W1), P. W313 - W317
Published: May 23, 2024
Abstract Among the myriad of protein–protein interactions occurring in living organisms, a substantial amount involves small linear motifs (SLiMs) recognized by structured domains. However, predictions SLiM-based networks are tedious, due to abundance such and high portion false positive hits. For this reason, webserver SLiMAn (Short Linear Motif Analysis) was developed focus search on most relevant SLiMs. Using SLiMAn, one can navigate into given (meta-)interactome tune variety parameters associated each type SLiMs attempt identify functional ELM their recognition The IntAct BioGRID databases bring experimental information, while IUPred AlphaFold provide boundaries folded disordered regions. Post-translational modifications listed PhosphoSite+ highlighted. Links PubMed accelerate scrutiny literature, support (or not) putative pairings. Dedicated visualization features also incorporated, as Cytoscape for macromolecular BINANA intermolecular contacts within structural models generated SCWRL 3.0. use 2.0 is illustrated simple example. It freely available at https://sliman2.cbs.cnrs.fr.
Language: Английский
Citations
4
Mammalian Genome, Journal Year: 2024, Volume and Issue: 35(4), P. 556 - 564
Published: Aug. 14, 2024
Abstract Online Mendelian Inheritance in Animals (OMIA) is a freely available curated knowledgebase that contains information and facilitates research on inherited traits diseases animals. For the past 29 years, OMIA has been used by animal geneticists, breeders, veterinarians worldwide as definitive source of information. Recent increases curation capacity funding for software engineering support have resulted upgrades commencement several initiatives, which include enhancement variant links to human data resources, introduction ontology-based breed categories. We provide an overview current recent enhancements discuss how we are expanding integration into other resources databases via use ontologies adaptation tools genetics.
Language: Английский
Citations
4
Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 53(D1), P. D748 - D756
Published: Oct. 29, 2024
Abstract In 2025, the bacterial diversity database BacDive is leading for strain-level and archaeal information. It has been selected as an ELIXIR Core Data Resource well a Global Biodata Resource. Since its initial release more than ten years ago, (https://bacdive.dsmz.de) grown tremendously in content functionalities, comprehensive resource covering phenotypic of prokaryotes with data on taxonomy, morphology, physiology, cultivation, more. The current (2023.2) contains 2.6 million points 97 334 strains, reflecting increase by 52% since previous publication 2021. This remarkable growth can largely be attributed to integration world-wide largest collection Analytical Profile Index (API) test results, which are now fully integrated into searchable. A novel knowledge graph provides powerful search options through SPARQL endpoint, including possibility federated searches across multiple sources. high-quality provided increasingly being used training artificial intelligence models resulting genome-based predictions high confidence fill gaps database.
Language: Английский
Citations
4