RegulonDB is a database that contains the most comprehensive corpus of knowledge of the regulation of transcription initiation of Escherichia coli K-12, including data from both classical molecular biology and high-throughput methodologies. Here, we describe biological advances since our last NAR paper of 2019. We explain the changes to satisfy FAIR requirements. We also present a full reconstruction of the RegulonDB computational infrastructure, which has significantly improved data storage, retrieval and accessibility and thus supports a more intuitive and user-friendly experience. The integration of graphical tools provides clear visual representations of genetic regulation data, facilitating data interpretation and knowledge integration. RegulonDB version 12.0 can be accessed at https://regulondb.ccg.unam.mx.
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http://dx.doi.org/10.1093/nar/gkad1072 | DOI Listing |
ACS Infect Dis
January 2025
Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States.
Carbapenemase producing (CPEs) represent a group of multidrug resistant pathogens for which few, if any, therapeutics options remain available. CPEs generally harbor plasmids that encode resistance to last resort carbapenems and many other antibiotics. We previously performed a high throughput screen to identify compounds that can disrupt the maintenance and replication of resistance conferring plasmids through use of a synthetic screening plasmid introduced into K-12 cells.
View Article and Find Full Text PDFMicrobiol Resour Announc
December 2024
Research Department for Limnology, Mondsee, Universität Innsbruck, Mondsee, Austria.
mSystems
December 2024
Department of Bioengineering, University of California, San Diego, California, USA.
Unlabelled: The composition of bacterial transcriptomes is determined by the transcriptional regulatory network (TRN). The TRN regulates the transition from one physiological state to another. Here, we use independent component analysis to monitor the composition of the transcriptome during the transition from the exponential growth phase to the stationary phase.
View Article and Find Full Text PDFACS Omega
December 2024
School of Psychology, University of Wollongong, Wollongong, New South Wales 2522, Australia.
The biological effects of electromagnetic field (EMF) irradiation in the terahertz (THz) range remain ambiguous, despite numerous studies that have been conducted. In this paper, the metabolic response of K 12 to EMF irradiation was examined using a 1.0 W m incident synchrotron source (SS) in the range of 0.
View Article and Find Full Text PDFIndian J Microbiol
December 2024
Laboratory of BAS Purification and Certification, SPC "Armbiotechnology" Scientific and Production Center, National Academy of Science, Yerevan, Republic of Armenia.
Melanins have immense application potential in the fields of agriculture, cosmetics and pharmaceutical industries. To determine the antimicrobial properties of melanin, conditionally pathogenic bacteria, belonging to different taxonomic groups were used. The results have shown that melanin solution exhibited bacteriostatic or bactericide activity depending on test culture and melanin concentration.
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