The Xylella fastidosa RTX operons: evidence for the evolution of protein mosaics through novel genetic exchanges.

Background: Xylella fastidiosa (Xf) is a gram negative bacterium inhabiting the plant vascular system. In most species this bacterium lives as a benign symbiote, but in several agriculturally important plants (e.g.

Evolutionary implications of horizontal gene transfer.

The flow of genes between different species represents a form of genetic variation whose implications have not been fully appreciated. Here I examine some key findings on the extent of horizontal gene transfer (HGT) revealed by comparative genome analysis and their theoretical implications. In theoretical terms, HGT affects ideas pertaining to the tree of life, the notion of a last universal common ancestor, and the biological unities, as well as the rules of taxonomic nomenclature.

The gut mucosal viral reservoir in HIV-infected patients is not the major source of rebound plasma viremia following interruption of highly active antiretroviral therapy.

Interruption of suppressive highly active antiretroviral therapy (HAART) in HIV-infected patients leads to increased HIV replication and viral rebound in peripheral blood. Effects of therapy interruption on gut-associated lymphoid tissue (GALT) have not been well investigated. We evaluated longitudinal changes in viral replication and emergence of viral variants in the context of T cell homeostasis and gene expression in GALT of three HIV-positive patients who initiated HAART during primary HIV infection but opted to interrupt therapy thereafter.

Evolution of nef variants in gut associated lymphoid tissue of rhesus macaques during primary simian immunodeficiency virus infection.

We utilized the simian immunodeficiency virus model of AIDS to examine evolution of nef gene in gut-associated lymphoid tissue (GALT) during primary and early asymptomatic stages of infection. Macaques were infected with a cloned virus, SIVmac239/nef-stop harboring a premature stop codon in the nef gene. Restoration of the nef open reading frame occurred in GALT early at 3 days post-infection.

Transcription profile of Helicobacter pylori in the human stomach reflects its physiology in vivo.

Background: Little is known about levels of expression of Helicobacter pylori genes in the human host. We therefore developed a quantitative real-time reverse-transcriptase polymerase chain reaction (qRT-PCR) assay to measure transcript profiles of H. pylori in the human stomach.

Modification of Helicobacter pylori outer membrane protein expression during experimental infection of rhesus macaques.

Clinical isolates of Helicobacter pylori show marked diversity, which may derive from genomic changes that occur during the often lifelong association of the bacterium with its human host. We used the rhesus macaque model, together with DNA microarrays, to examine genomic changes in H. pylori that occur early during experimental infection.

Rates of ribosomal RNA evolution are uniquely accelerated in eukaryotes.

A novel procedure for testing the relative rates of evolution is described. The procedure, the distance-matrix rate test, consists of creating a graph that displays two complete distance matrices for two different genes derived from the same group of species, an approach made practical by numerous whole genomic sequences. The results in this paper show that the molecular clock of ribosomal RNA from Eukaryotes is uniquely accelerated and highly variable while those of Archaea and Bacteria are not.

Recent emergence of the modern genetic code: a proposal.

This article proposes that the genetic code was not fully formed before the divergence of life into three kingdoms. Rather, at least arginine and tryptophan evolved after the diversification of archaea, bacteria and eukaryotes, and were spread by horizontal gene transfer. Evidence for this hypothesis is based on data suggesting that enzymes for biosynthesis of arginine and tryptophan, and for arginine tRNA ligase, have shorter divergence times than the underlying lineages.

On the occurrence of horizontal gene transfer among an arbitrarily chosen group of 26 genes.

The deduced amino acid sequences from 1200 Haemophilus influenzae genes was compared to a data set that contained the orfs from yeast, two different Archaea and the Gram+ and Gramminus sign bacteria, Bacillus subtilis and Escherichia coli. The results of the comparison yielded a 26 orthologous gene set that had at least one representative from each of the four groups. A four taxa phylogenetic relationship for these 26 genes was determined.