580 research outputs found
Computational Bacterial Genome-Wide Analysis of Phylogenetic Profiles Reveals Potential Virulence Genes of Streptococcus agalactiae
The phylogenetic profile of a gene is a reflection of its evolutionary history
and can be defined as the differential presence or absence of a gene in a set of
reference genomes. It has been employed to facilitate the prediction of gene
functions. However, the hypothesis that the application of this concept can also
facilitate the discovery of bacterial virulence factors has not been fully
examined. In this paper, we test this hypothesis and report a computational
pipeline designed to identify previously unknown bacterial virulence genes using
group B streptococcus (GBS) as an example. Phylogenetic profiles of all GBS
genes across 467 bacterial reference genomes were determined by
candidate-against-all BLAST searches,which were then used to identify candidate
virulence genes by machine learning models. Evaluation experiments with known
GBS virulence genes suggested good functional and model consistency in
cross-validation analyses (areas under ROC curve, 0.80 and 0.98 respectively).
Inspection of the top-10 genes in each of the 15 virulence functional groups
revealed at least 15 (of 119) homologous genes implicated in virulence in other
human pathogens but previously unrecognized as potential virulence genes in GBS.
Among these highly-ranked genes, many encode hypothetical proteins with possible
roles in GBS virulence. Thus, our approach has led to the identification of a
set of genes potentially affecting the virulence potential of GBS, which are
potential candidates for further in vitro and in
vivo investigations. This computational pipeline can also be
extended to in silico analysis of virulence determinants of
other bacterial pathogens
Validation of the Tetracycline Regulatable Gene Expression System for the Study of the Pathogenesis of Infectious Disease
Understanding the pathogenesis of infectious disease requires the examination and successful integration of parameters related to both microbial virulence and host responses. As a practical and powerful method to control microbial gene expression, including in vivo, the tetracycline-regulatable system has recently gained the favor of many investigative groups. However, some immunomodulatory effects of the tetracyclines, including doxycycline, could potentially limit its use to evaluate host responses during infection. Here we have used a well-established murine model of disseminated candidiasis, which is highly dependent on both the virulence displayed by the fungal cells and on the host immune status, to validate the use of this system. We demonstrate that the pathogenesis of the wild type C. albicans CAF2-1 strain, which does not contain any tet-regulatable element, is not affected by the presence of doxycycline. Moreover levels of key cytokines, chemokines and many other biomarkers, as determined by multi-analyte profiling, remain essentially unaltered by the presence of the antibiotic during infection. Our results indicate that the levels of doxycycline needed to control the tetracycline regulatable promoter gene expression system have no detectable effect on global host responses during candidiasis. Because tet-regulatable systems are now being increasingly used in a variety of pathogenic microorganisms, these observations have wide implications in the field of infectious diseases
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