Contribution for new genetic markers of rheumatoid arthritis activity and severity : sequencing of the tumor necrosis factor-alpha gene promoter

© 2007 Fonseca et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly citedThe objective of this study was to assess whether clinical measures of rheumatoid arthritis activity and severity were influenced by tumor necrosis factor-alpha (TNF-alpha) promoter genotype/haplotype markers. Each patient's disease activity was assessed by the disease activity score using 28 joint counts (DAS28) and functional capacity by the Health Assessment Questionnaire (HAQ) score. Systemic manifestations, radiological damage evaluated by the Sharp/van der Heijde (SvdH) score, disease-modifying anti-rheumatic drug use, joint surgeries, and work disability were also assessed. The promoter region of the TNF-alpha gene, between nucleotides -1,318 and +49, was sequenced using an automated platform. Five hundred fifty-four patients were evaluated and genotyped for 10 single-nucleotide polymorphism (SNP) markers, but 5 of these markers were excluded due to failure to fall within Hardy-Weinberg equilibrium or to monomorphism. Patients with more than 10 years of disease duration (DD) presented significant associations between the -857 SNP and systemic manifestations, as well as joint surgeries. Associations were also found between the -308 SNP and work disability in patients with more than 2 years of DD and radiological damage in patients with less than 10 years of DD. A borderline effect was found between the -238 SNP and HAQ score and radiological damage in patients with 2 to 10 years of DD. An association was also found between haplotypes and the SvdH score for those with more than 10 years of DD. An association was found between some TNF-alpha promoter SNPs and systemic manifestations, radiological progression, HAQ score, work disability, and joint surgeries, particularly in some classes of DD and between haplotypes and radiological progression for those with more than 10 years of DD.This work was supported by grant POCTI/SAU-ESP/59111/2004 from Fundação Ciência e Tecnologia.info:eu-repo/semantics/publishedVersio

Vibrio parahaemolyticus ScrC Modulates Cyclic Dimeric GMP Regulation of Gene Expression Relevant to Growth on Surfaces▿

In Vibrio parahaemolyticus, scrC participates in controlling the decision to be a highly mobile swarmer cell or a more adhesive, biofilm-proficient cell type. scrC mutants display decreased swarming motility over surfaces and enhanced capsular polysaccharide production. ScrC is a cytoplasmic membrane protein that contains both GGDEF and EAL conserved protein domains. These domains have been shown in many organisms to respectively control the formation and degradation of the small signaling nucleotide cyclic dimeric GMP (c-di-GMP). The scrC gene is part of the three-gene scrABC operon. Here we report that this operon influences the cellular nucleotide pool and that c-di-GMP levels inversely modulate lateral flagellar and capsular polysaccharide gene expression. High concentrations of this nucleotide prevent swarming and promote adhesiveness. Further, we demonstrate that ScrC has intrinsic diguanylate cyclase and phosphodiesterase activities, and these activities are controlled by ScrAB. Specifically, ScrC acts to form c-di-GMP in the absence of ScrA and ScrB; whereas ScrC acts to degrade c-di-GMP in the presence of ScrA and ScrB. The scrABC operon is specifically induced by growth on a surface, and the analysis of mutant phenotypes supports a model in which the phosphodiesterase activity of ScrC plays a dominant role during surface translocation and in biofilms

A Mutational Analysis Defines Vibrio fischeri LuxR Binding Sites▿

Vibrio fischeri quorum sensing involves the LuxI and LuxR proteins. The LuxI protein generates the quorum-sensing signal N-3-oxohexanoyl-l-homoserine lactone (3OC6-HSL), and LuxR is a signal-responsive transcriptional regulator which activates the luminescence (lux) genes and 17 other V. fischeri genes. For activation of the lux genes, LuxR binds to a 20-base-pair inverted repeat, the lux box, which is centered 42.5 base pairs upstream of the transcriptional start of the lux operon. Similar lux box-like elements have been identified in only a few of the LuxR-activated V. fischeri promoters. To better understand the DNA sequence elements required for LuxR binding and to identify binding sites in LuxR-regulated promoters other than the lux operon promoter, we have systematically mutagenized the lux box and evaluated the activity of many mutants. By doing so, we have identified nucleotides that are critical for promoter activity. Interestingly, certain lux box mutations allow a 3OC6-HSL-independent LuxR activation of the lux operon promoter. We have used the results of the mutational analysis to create a consensus lux box, and we have used this consensus sequence to identify LuxR binding sites in 3OC6-HSL-activated genes for which lux boxes could not be identified previously

Transcriptome Analysis of the Vibrio fischeri LuxR-LuxI Regulon▿

The Vibrio fischeri quorum-sensing signal N-3-oxohexanoyl-l-homoserine lactone (3OC6-HSL) activates expression of the seven-gene luminescence operon. We used microarrays to unveil 18 additional 3OC6-HSL-controlled genes, 3 of which had been identified by other means previously. We show most of these genes are regulated by the 3OC6-HSL-responsive transcriptional regulator LuxR directly. This demonstrates that V. fischeri quorum sensing regulates a substantial number of genes other than those involved in light production

Metabolic Signatures of Triatomine Vectors of <i>Trypanosoma cruzi</i> Unveiled by Metabolomics

<div><p>Chagas disease is a trypanosomiasis whose causative agent is the protozoan parasite <i>Trypanosoma cruzi</i>, which is transmitted to humans by hematophagous insects known as triatomines and affects a large proportion of South America. The digestive tract of the insect vectors in which <i>T. cruzi</i> develops constitutes a dynamic environment that affects the development of the parasite. Thus, we set out to investigate the chemical composition of the triatomine intestinal tract through a metabolomics approach. We performed Direct Infusion Fourier Transform Ion Cyclotron Resonance Mass Spectrometry on fecal samples of three triatomine species (<i>Rhodnius prolixus</i>, <i>Triatoma infestans</i>, <i>Panstrongylus megistus</i>) fed with rabbit blood. We then identified groups of metabolites whose frequencies were either uniform in all species or enriched in each of them. By querying the Human Metabolome Database, we obtained putative identities of the metabolites of interest. We found that a core group of metabolites with uniform frequencies in all species represented approximately 80% of the molecules detected, whereas the other 20% varied among triatomine species. The uniform core was composed of metabolites of various categories, including fatty acids, steroids, glycerolipids, nucleotides, sugars, and others. Nevertheless, the metabolic fingerprint of triatomine feces differs depending on the species considered. The variable core was mainly composed of prenol lipids, amino acids, glycerolipids, steroids, phenols, fatty acids and derivatives, benzoic acid and derivatives, flavonoids, glycerophospholipids, benzopyrans, and quinolines. Triatomine feces constitute a rich and varied chemical medium whose constituents are likely to affect <i>T. cruzi</i> development and infectivity. The complexity of the fecal metabolome of triatomines suggests that it may affect triatomine vector competence for specific <i>T. cruzi</i> strains. Knowledge of the chemical environment of <i>T. cruzi</i> in its invertebrate host is likely to generate new ways to understand the factors influencing parasite proliferation as well as methods to control Chagas disease.</p></div

Metabolic classes in the variable core.

<p>Frequency is given in number of hits per metabolic category in the following comparisons: <i>P. megistus</i> vs. <i>T. infestans</i> and <i>R. prolixus</i> (white bars), <i>R. prolixus</i> vs. <i>T. infestans</i> and <i>P. megistus</i> (gray bars), and <i>T. infestans</i> vs. <i>R. prolixus</i> and <i>P. megistus</i> (black bars). Only metabolic classes with 5 or more hits are displayed.</p

Representation of relative metabolite distribution.

<p>Most metabolites were found at very low rates (below 0.025%). The distribution extends above 0.05, up to 14%, but was not shown for clarity.</p

Differences in ion frequencies among triatomine replicates.

<p>Plots are given for all replicate combinations considering the following triatomine pairs: <i>T. infestans</i> vs. <i>R. prolixus</i> (A), <i>T. infestans</i> vs. <i>P. megistus</i> (B) and <i>R. prolixus</i> vs. <i>P. megistus</i> (C). Dots between dashed lines are for the metabolites with small differences among pairs of triatomine species. Dots outside the dashed lines are for the metabolites displaying large differences among pairs of triatomine species (at <i>p</i>≤0.05). For plotting convenience, the scale of the <i>y</i> axis has been limited to the interval −1 to +1. Some pairs exist outside this range (data not shown).</p

Boolean operations on metabolite rate differences.

<p>Venn diagrams are given for all replicate combinations considering the following triatomine comparisons: <i>R. prolixus</i> vs. <i>T. infestans</i> AND <i>P. megistus</i> (A), <i>T. infestans</i> vs. <i>R. prolixus</i> AND <i>P. megistus</i> (B), <i>P. megistus</i> vs. <i>T. infestans</i> AND <i>R. prolixus</i> (C), and all comparisons above (D).</p

Metabolic classes in the uniform core.

<p>Frequency is given in number of hits per metabolic category in the uniform core. Only metabolic classes with 10 or more hits are displayed.</p