It has been hypothesized that in the era just before the last universal common ancestor emerged, life on earth was fundamentally collective. Ancient life forms shared their genetic material freely through massive horizontal gene transfer (HGT). At a certain point, however, life made a transition to the modern era of individuality and vertical descent. Here we present a minimal model for stochas...

Orthologs are widely used for phylogenetic analysis of species; however, identifying genuine orthologs among distantly related species is challenging, because genes obtained through horizontal gene transfer (HGT) and out-paralogs derived from gene duplication before speciation are often present among the predicted orthologs. We developed a program, "Ortholog-Finder," to obtain ortholog data set...

Horizontal acquisition of DNA by bacteria dramatically increases genetic diversity and hence successful bacterial colonization of several niches, including the human host. A relevant issue is how this newly acquired DNA interacts and integrates in the regulatory networks of the bacterial cell. The global modulator H-NS targets both core genome and HGT genes and silences gene expression in respo...

Abstract Background Low- and high-affinity glucose transport system is a conserved strategy of microorganism to cope with environmental fluctuation for their growth competitiveness. In Neurospora crassa , the dual-affinity consists low-affinity transporter GLT-1 two transporters HGT-1/HGT-2, which play diverse roles in transport, carbon metabolism, cellulase expression regulation. However, regu...

Abstract Horizontal gene transfer (HGT) plays an important role in the dissemination of antibiotic resistance genes. In sewer systems, human-associated and environmental bacteria are mixed together exposed to many substances known increase HGT, including various antibacterial compounds. wastewaters, those most often detected below concentrations induce HGT individually. Still, it is possible th...

The development and application of metagenomic approaches have provided an opportunity to study and define horizontal gene transfer (HGT) on the level of microbial communities. However, no current metagenomic data simulation tools offers the option to introduce defined HGT within a microbial community. Here, we present HgtSIM, a pipeline to simulate HGT event among microbial community members w...

With the rapid accumulation of genomic information from various eukaryotes in the last decade, genes proposed to have been derived from recent horizontal gene transfer (HGT) events have been reported even in non-phagotrophic unicellular and multicellular organisms, but the molecular pathways underlying HGT remain to be explained. The development of in vitro HGT detection systems, which permit t...

BACKGROUND Horizontal gene transfer (HGT) is one of the major mechanisms contributing to microbial genome diversification. A number of computational methods for finding horizontally transferred genes have been proposed in the past decades; however none of them has provided a reliable detector yet. In existing parametric approaches, only one single compositional property can participate in the d...

Twenty-one sediment samples in 11 sites along the Haihe River and Dagu Drainage River, Tianjin, China, were analyzed to investigate the pollution status and bioavailability of mercury (Hg). The results showed that the Haihe River was slightly polluted with Hg when flowing through Tianjin city. On the contrary, the sediments collected from Dagu Drainage River, an important drainage river in Tian...