The OpenAI maths dump and what AI news is worth paying attention to I’ve been reflecting on the recent OpenAI maths dump [1] and Google DeepMind’s AlphaProof [2] from the perspective of a research mic...

Abstract. Broad-host-range IncA and IncC (A/C) conjugative plasmids propagate multidrug resistance in bacteria and mobilize chromosomal resistance islands,

Abstract. One of the biggest misconceptions about clonal bacterial populations is that all members act identically. In fact, microbiologists have known for

Author summary Klebsiella pneumoniae (Kp) is a major human pathogen responsible for severe infections, including pneumonia and bloodstream infections. To establish infection, Kp must withstand multipl...

Background: Optimising sampling frames for genomic surveillance of E. coli and Klebsiella may support interventions to mitigate bloodstream infections (BSIs), but approaches to estimating sample size ...

Donate to the Wikimedia Foundation, the nonprofit that hosts Wikipedia and other crucial free knowledge projects. Each year, the generosity of the 2% of readers who donate allows us to expand the reac...

De novo protein design has advanced rapidly, yet designing binders to polar, solvent-exposed epitopes and small, flexible ligands remains challenging. Such hydrated surfaces and flexible molecules, in...

High-dimensional data are visualized through representation on tree structures.

Rising incidence and severity of climate-induced wildfires test traditional top-down fire governance regimes worldwide. This systematic review assesses Australian Community-Based Bushfire Management (...

Author summary Owing to its ability to acquire multidrug resistance via horizontal gene transfer, Enterococcus faecium is a major opportunistic pathogen responsible for severe healthcare-associated in...

Klebsiella pneumoniae is a WHO critical-priority pathogen for which strain-specific bacteriophages are being explored as precision antimicrobials, yet rapid phage-host matching remains a major barrier...

Large language models (LLMs) are increasingly being used in the systematic review process. Our objective was to explore data extraction performance of six LLMs from a published systematic review of in...

Precise regulation of gene expression ensures gene products are produced at the right time and in the right amounts. Recent works uncovered a new mechanism of bacterial gene regulation based on a clamp sliding and locking in a multi-drug resistance plasmid, RK2. KorB functions as a CTP-dependent DNA-sliding clamp capable of traveling over a long genomic distance. Sliding KorB is captured and locked in place by a partner protein, KorA, forming a stable complex at target promoters to repress transcription. Here, we show that another RK2 regulator, TrbA, also uses this clamp sliding-locking mechanism, and identify an aromatic interface enabling TrbA-KorB-mediated transcriptional repression. Our findings show how a single sliding clamp integrates multiple partners to build a complex transcriptional regulatory network.

GOOSE enables the design and testing of thousands of disordered protein region sequences to reveal distinct sequence-to-function relationships.

a blog for miscellaneous bioinformatics stuff

Plasmids are frequently AT-rich relative to their bacterial hosts. Despite this tendency towards lower GC content, plasmid and host chromosome GC content are positively correlated across diverse collections of plasmid-host pairs. However, the evolutionary processes underlying this pattern remain unclear. The classic model of amelioration predicts that horizontally acquired DNA gradually converges on host nucleotide composition. However, because plasmids can repeatedly transfer between bacterial hosts, the opportunity for such host-associated evolution may depend on their transmission dynamics. Using 50,936 plasmid-host pairs from a public sequence database, we found that the apparent global correlation between plasmid and host chromosome GC content was largely driven by differences between bacterial species rather than within species. We therefore accounted for plasmid and host population structure when testing how plasmid mobility shaped host-associated compositional evolution. We compared two contrasting regimes: a population of 3,682 Enterobacterales plasmids distributed across diverse host backgrounds, and six long-term host-associated plasmids from a Rhizobium leguminosarum lineage with INSeq-determined gene essentiality data. In the Enterobacterales population, GC content variation was overwhelmingly explained by plasmid lineage rather than host phylogeny, and conjugative plasmids showed greater similarity to their host chromosomes than mobilisable or non-mobilisable plasmids. In the Rhizobium leguminosarum plasmids, synonymous-site composition was more similar to the host chromosome among genes required across multiple host life stages. Together, these results support a model in which plasmid mobility influences the opportunity for host-associated evolutionary processes to alter nucleotide composition. ### Competing Interest Statement The authors have declared no competing interest. Wellcome Trust, 319534/Z/24/Z St. John's College, University of Oxford, UK

Nature Ecology & Evolution - Genomic characterization and toxicity assays identify Karenia cristata as a brevetoxin-producing species that is the dominant component of the prolonged microalgal...