Bacterial biofilms and quorum sensing

The paper develops a computational model and software tool to study spatial organization in microbial consortia through quorum sensing and synthetic communication strategies.

The paper introduces an open-source tool to measure morphological changes and growth kinetics of Bacillus subtilis biofilms exposed to chlorhexidine.

This study uses transcriptomic data to construct a regulatory network of Pseudomonas aeruginosa, revealing roles of efflux pumps and media composition in antibiotic responses.

The paper analyzes transcriptional patterns of core and accessory genes in P. aeruginosa strains using a transcriptome compendium, revealing stable core gene expression patterns across strains.

The paper develops a mathematical framework to predict community-level properties from local cell-cell interactions in two-cell-type systems, showing how molecular parameters influence community dynamics.

The paper analyzes the agr operon across S. aureus genomes to identify frameshift mutations and their evolutionary patterns, finding over 5% of strains have non-functional agr systems.

The paper identifies temporally essential genes for biofilm formation in E. coli using transposon mutagenesis and validates their roles at different stages of biofilm development.

The paper develops an in vitro cell-free system to evaluate quorum sensing inhibitors by reconstituting Pseudomonas aeruginosa pathways in Escherichia coli.

RRNPP_detector identifies RRNPP quorum sensing systems in gram-positive bacteria genomes, revealing expanded diversity and novel regulatory mechanisms.

This study uses genome-wide association methods to identify genetic factors associated with biofilm production in Pseudomonas aeruginosa isolates.

The paper models how additional regulatory modules in bacterial quorum sensing improve response speed and control.

This paper introduces an optogenetic system to control bacterial pathogenicity in specific host tissues by engineering the Gac/Rsm signaling cascade in Pseudomonas aeruginosa.

This study investigates the FleS/FleR two-component system in Pseudomonas aeruginosa, showing it regulates virulence traits and biofilm formation through transcriptional control of multiple genes.

This study inhibits the accA gene in E. coli using antisense RNA, suppressing luxS expression and increasing antibiotic susceptibility.

The paper validates a model system to identify genes involved in biofilm formation and antibiotic resistance in Pseudomonas aeruginosa MPAO1 using genomics and experimental approaches.

The paper demonstrates that the quorum sensing peptide EntF* from gut microbiota promotes colorectal cancer metastasis in mice, identifying it as a novel mediator of microbiome-host interaction.

This paper uses machine learning to predict the virulence of Pseudomonas aeruginosa isolates based on genomic data, achieving 75% accuracy using random forest models.

This study characterizes the quorum sensing system in Hafnia alvei FB1, showing its role in cell division, nutrient uptake, and antibiotic resistance through genomic and transcriptomic analyses.

The paper models the protein-protein interaction between TasA(28-261) and TapA(33-253) in Bacillus subtilis using computational methods to identify critical residues for biofilm formation.

This study investigates the association between biofilm formation and carbapenem resistance in Klebsiella pneumoniae isolates, finding a positive correlation and significant impact on patient outcomes.

This study uses Boolean modelling to analyze the dynamic mechanisms of Pseudomonas aeruginosa quorum sensing and virulence networks, revealing the roles of stochasticity and node connectivity in network dynamics and robustness.

The paper develops a minimal differential equation model to describe metabolic oscillations in Bacillus subtilis biofilms, using a known chemical oscillator and validating it against biological observations.

The paper develops a mathematical framework to analyze paradoxical signaling in synthetic circuits for population control in E. coli, showing non-monotonic growth rate relationships and stability benefits.

The paper shows that Pseudomonas aeruginosa uses integrated diffusive cues to stabilize cooperative swarming behavior against cheating.

This paper identifies flavone derivatives, specifically benzamides, as potential inhibitors of LasR in Pseudomonas aeruginosa through virtual screening and docking analysis.

The paper develops a cellular automata model to simulate Pseudomonas aeruginosa biofilm formation and shows that azithromycin delays but does not prevent biofilm formation by affecting single-cell motility.

The paper shows quorum sensing in bacteria can detect environmental changes and uses a new signaling mechanism involving protein synthesis and dilution rates to process dynamic inputs.

This study shows that metabolic activity variation in structured microbial populations affects single-cell responses to nutrient switches, with cross-feeding cells having higher growth resumption probability.

The paper identifies orthogonal HSL-synthase-regulator pairs that minimize crosstalk in synthetic gene regulation systems in E. coli.

The paper presents a cell-free method for sensing and quantifying the quorum sensing molecule 3OC12HSL in Pseudomonas infections using droplet microfluidics.