Recombination of short DNA fragments via horizontal gene transfer (HGT) can introduce beneficial alleles, create genomic disharmony through negative epistasis, and create adaptive gene combinations through positive epistasis. For non-core (accessory) genes, the negative epistatic cost is likely to be minimal because the incoming genes have not co-evolved with the recipient genome and are frequently observed as tightly linked cassettes with major effects. By contrast, interspecific recombination in the core genome is expected to be rare because disruptive allelic replacement is likely to introduce negative epistasis. Why then is homologous recombination common in the core of bacterial genomes? To understand this enigma, we take advantage of an exceptional model system, the common enteric pathogens Campylobacter jejuni and C. coli that are known for very high magnitude interspecies gene flow in the core genome. As expected, HGT does indeed disrupt co-adapted allele pairings, indirect evidence of negative epistasis. However, multiple HGT events enable recovery of the genome's co-adaption between introgressing alleles, even in core metabolism genes (e.g., formate dehydrogenase). These findings demonstrate that, even for complex traits, genetic coalitions can be decoupled, transferred, and independently reinstated in a new genetic background—facilitating transition between fitness peaks. In this example, the two-step recombinational process is associated with C. coli that are adapted to the agricultural niche.

The COVID-19 pandemic, a period of great turmoil, was coupled with the emergence of an "infodemic", a state when the public was bombarded with vast amounts of unverified information from dubious sources that led to a chaotic information landscape. The excessive flow of messages to citizens, combined with the justified fear and uncertainty imposed by the unknown virus, cast a shadow on the credibility of even well-intentioned sources and affected the emotional state of the public. Several studies highlighted the mental toll this environment took on citizens by analyzing their discourse on online social networks (OSNs). In this study, we focus on the activity of prominent pharmaceutical companies on Twitter, currently known as X, as well as the public's response during the COVID-19 pandemic. Communication between companies and users is examined and compared in two discrete channels, the COVID-19 and the non-COVID-19 channel, based on the content of the posts circulated in them in the period between March 2020 and September 2022, while the emotional profile of the content is outlined through a state-of-the-art emotion analysis model. Our findings indicate significantly increased activity in the COVID-19 channel compared to the non-COVID-19 channel while the predominant emotion in both channels is joy. However, the COVID-19 channel exhibited an upward trend in the circulation of fear by the public. The quotes and replies produced by the users, with a stark presence of negative charge and diffusion indicators, reveal the public's preference for promoting tweets conveying an emotional charge, such as fear, surprise, and joy. The findings of this research study can inform the development of communication strategies based on emotion-aware messages in future crises.

Motivation
Bacterial genomes present more variability than human genomes, which requires important adjustments in computational tools that are developed for human data. In particular, bacteria exhibit a mosaic structure due to homologous recombinations, but this fact is not sufficiently captured by standard read mappers that align against linear reference genomes. The recent introduction of pangenomics provides some insights in that context, as a pangenome graph can represent the variability within a species. However, the concept of sequence-to-graph alignment that captures the presence of recombinations has not been previously investigated.

Results
In this paper, we present the extension of the notion of sequence-to-graph alignment to a variation graph that incorporates a recombination, so that the latter are explicitly represented and evaluated in an alignment. Moreover, we present a dynamic programming approach for the special case where there is at most a recombination–we implement this case as RecGraph. From a modeling point of view, a recombination corresponds to identifying a new path of the variation graph, where the new arc is composed of two halves, each extracted from an original path, possibly joined by a new arc. Our experiments show that RecGraph accurately aligns simulated recombinant bacterial sequences that have at most a recombination, providing evidence for the presence of recombination events.