Evaluation of VirB binding site contribution to the regulation of the icsP promoter in Shigella flexneri

Shigella species are gram-negative, rod-shaped bacteria that are closely related to Escherichia coli. Virulent Shigella spp. are intracellular pathogens that invade, replicate and spread through epithelial cells of the lower intestine and cause bacillary dysentery in humans. This disease is characterized by a robust inflammatory response that results in fever, abdominal pain, and bloody diarrhea (3). According to the CDC, approximately 14,000 cases are reported each year in the United States alone. This number however, does not reflect the actual incidence of this disease as many cases go unreported. The molecular pathogenesis of these bacteria lies in the large virulence plasmid (~230-kb) that is found in all virulent Shigella spp. Two key virulence determinants include the ability to invade colonic epithelia (mediated by the ipa-mxi-spa gene locus) and the ability to spread to adjacent cells, a process known as actin-based-motility (mediated and controlled by icsA and icsP respectively). These events are largely regulated by VirB, a transcription factor (2, 3). Canonically, transcription factors are known to bind sequences proximal to the transcriptional start site (within 200-bp). Recent work has focused on the regulation of icsP (encodes a protease of the outer membrane) by VirB and has shed light on a novel regulatory strategy, whereby VirB regulates the activation of icsP from sites located more than 1-kb upstream of the transcriptional start site (1). Nine putative VirB binding sites have been found upstream of the icsP gene. This work seeks to characterize the contribution made by these putative binding sites to the VirB-dependent regulation of icsP

Combination of VirB binding site mutations to evaluate collective impact on icsP promoter activity in Shigella flexneri

Shigella flexneri is a gram-negative, invasive bacterial pathogen that afflicts the human colonic epithelium, causing shigellosis, an illness triggering severe dysentery. The World Health Organization cites the disease burden of shigellosis near 90 million episodes and 108,000 deaths per year. The motility and spread of Shigella is modulated by icsP, a virulence gene. The transcription factor VirB positively regulates many virulence genes encoded by the Shigella virulence plasmid. Two distal binding sites of VirB have been shown to regulate the promoter activity of icsP, despite their location of more than 1 kb upstream of the transcription start site. Five VirB binding sites are located between these two sites and the transcription start site, and two are located in close proximity downstream of the transcription start site. Investigation into the impact of the VirB binding sites is part of a larger effort to understand the workings of VirB, which is the major switch that controls virulence gene expression in Shigella

A microarray study of MPP(+)-treated PC12 Cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools

BACKGROUND: This paper describes a microarray study including data quality control, data analysis and the analysis of the mechanism of toxicity (MOT) induced by 1-methyl-4-phenylpyridinium (MPP(+)) in a rat adrenal pheochromocytoma cell line (PC12 cells) using bioinformatics tools. MPP(+ )depletes dopamine content and elicits cell death in PC12 cells. However, the mechanism of MPP(+)-induced neurotoxicity is still unclear. RESULTS: In this study, Agilent rat oligo 22K microarrays were used to examine alterations in gene expression of PC12 cells after 500 μM MPP(+ )treatment. Relative gene expression of control and treated cells represented by spot intensities on the array chips was analyzed using bioinformatics tools. Raw data from each array were input into the NCTR ArrayTrack database, and normalized using a Lowess normalization method. Data quality was monitored in ArrayTrack. The means of the averaged log ratio of the paired samples were used to identify the fold changes of gene expression in PC12 cells after MPP(+ )treatment. Our data showed that 106 genes and ESTs (Expressed Sequence Tags) were changed 2-fold and above with MPP(+ )treatment; among these, 75 genes had gene symbols and 59 genes had known functions according to the Agilent gene Refguide and ArrayTrack-linked gene library. The mechanism of MPP(+)-induced toxicity in PC12 cells was analyzed based on their genes functions, biological process, pathways and previous published literatures. CONCLUSION: Multiple pathways were suggested to be involved in the mechanism of MPP(+)-induced toxicity, including oxidative stress, DNA and protein damage, cell cycling arrest, and apoptosis

A microarray study of MPP⁺-treated PC12 Cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools

Abstract Background This paper describes a microarray study including data quality control, data analysis and the analysis of the mechanism of toxicity (MOT) induced by 1-methyl-4-phenylpyridinium (MPP+) in a rat adrenal pheochromocytoma cell line (PC12 cells) using bioinformatics tools. MPP+ depletes dopamine content and elicits cell death in PC12 cells. However, the mechanism of MPP+-induced neurotoxicity is still unclear. Results In this study, Agilent rat oligo 22K microarrays were used to examine alterations in gene expression of PC12 cells after 500 μM MPP+ treatment. Relative gene expression of control and treated cells represented by spot intensities on the array chips was analyzed using bioinformatics tools. Raw data from each array were input into the NCTR ArrayTrack database, and normalized using a Lowess normalization method. Data quality was monitored in ArrayTrack. The means of the averaged log ratio of the paired samples were used to identify the fold changes of gene expression in PC12 cells after MPP+ treatment. Our data showed that 106 genes and ESTs (Expressed Sequence Tags) were changed 2-fold and above with MPP+ treatment; among these, 75 genes had gene symbols and 59 genes had known functions according to the Agilent gene Refguide and ArrayTrack-linked gene library. The mechanism of MPP+-induced toxicity in PC12 cells was analyzed based on their genes functions, biological process, pathways and previous published literatures. Conclusion Multiple pathways were suggested to be involved in the mechanism of MPP+-induced toxicity, including oxidative stress, DNA and protein damage, cell cycling arrest, and apoptosis.</p

Contribution de la biodiversité à l’alimentation

Ce numéro réunit une partie des communications présentées au 26th Symposium of the International Commission for the Anthropology of Food (ICAF) of the International Union of Anthropological & Ethnological Sciences (IUAES), à Paris en décembre 2009. Une deuxième partie paraîtra dans un dossier du numéro 3 de la Revue d'Ethnoécologie, et une troisième partie dans la collection Estudio del Hombre, éditée par l'Université de Guadalajara (Mexique). Ce numéro est offert à Igor de Garin