Conserved synteny at the protein family level reveals genes underlying Shewanella species’ cold tolerance and predicts their novel phenotypes

© The Authors 2009. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License. The definitive version was published in Functional & Integrative Genomics 10 (2010): 97-110, doi:10.1007/s10142-009-0142-y.Bacteria of the genus Shewanella can thrive in different environments and demonstrate significant variability in their metabolic and ecophysiological capabilities including cold and salt tolerance. Genomic characteristics underlying this variability across species are largely unknown. In this study, we address the problem by a comparison of the physiological, metabolic, and genomic characteristics of 19 sequenced Shewanella species. We have employed two novel approaches based on association of a phenotypic trait with the number of the trait-specific protein families (Pfam domains) and on the conservation of synteny (order in the genome) of the trait-related genes. Our first approach is top-down and involves experimental evaluation and quantification of the species’ cold tolerance followed by identification of the correlated Pfam domains and genes with a conserved synteny. The second, a bottom-up approach, predicts novel phenotypes of the species by calculating profiles of each Pfam domain among their genomes and following pair-wise correlation of the profiles and their network clustering. Using the first approach, we find a link between cold and salt tolerance of the species and the presence in the genome of a Na+/H+ antiporter gene cluster. Other cold-tolerance-related genes include peptidases, chemotaxis sensory transducer proteins, a cysteine exporter, and helicases. Using the bottom-up approach, we found several novel phenotypes in the newly sequenced Shewanella species, including degradation of aromatic compounds by an aerobic hybrid pathway in Shewanella woodyi, degradation of ethanolamine by Shewanella benthica, and propanediol degradation by Shewanella putrefaciens CN32 and Shewanella sp. W3-18-1.This research was supported by the U.S. Department of Energy (DOE) Office of Biological and Environmental Research under the Genomics: GTL Program via the Shewanella Federation consortium

Tumour antigen expression in hepatocellular carcinoma in a low-endemic western area

Background: Identification of tumour antigens is crucial for the development of vaccination strategies against hepatocellular carcinoma (HCC). Most studies come from eastern-Asia, where hepatitis-B is the main cause of HCC. However, tumour antigen expression is poorly studied in low-endemic, western areas where the aetiology of HCC differs. Methods: We constructed tissue microarrays from resected HCC tissue of 133 patients. Expression of a comprehensive panel of cancer-testis (MAGE-A1, MAGE-A3/4, MAGE-A10, MAGE-C1, MAGE-C2, NY-ESO-1, SSX-2, sperm protein 17), onco-fetal (AFP, Glypican-3) and overexpressed tumour antigens (Annexin-A2, Wilms tumor-1, Survivin, Midkine, MUC-1) was determined by immunohistochemistry. Results: A higher prevalence of MAGE antigens was observed in patients with hepatitis-B. Patients with expression of more tumour antigens in general had better HCC-specific survival (P=0.022). The four tumour antigens with high expression in HCC and no, or weak, expression in surrounding tumour-free-liver tissue, were Annexin-A2, GPC-3, MAGE-C1 and MAGE-C2, expressed in 90, 39, 17 and 20% of HCCs, respectively. Ninety-five percent of HCCs expressed at least one of these four tumour antigens. Interestingly, GPC-3 was associated with SALL-4 expression (P=0.001), an oncofetal transcription factor highly expressed in embryonal stem cells. SALL-4 and GPC-3 expression levels were correlated with vascular invasion, poor differentiation and higher AFP levels before surgery. Moreover, patients who co-expressed higher levels of both GPC-3 and SALL-4 had worse HCC-specific survival (P=0.018). Conclusions: We describe a panel of four tumour antigens with excellent coverage and good tumour specificity in a western area, low-endemic for hepatitis-B. The association between GPC-3 and SALL-4 is a novel finding and suggests that GPC-3 targeting may specifically attack the tumour stem-cell compartment

Physiologie, biomécanique et blessures au tennis de table : une revue systématique

International audienceObjectives: Table tennis is a widely practiced sport, often described as a reaction sport. Therefore, players need to practice extensively that may expose them to overuse injuries. For optimizing training with limitation of the injury risk, the knowledges of table tennis physiology, biomechanics and epidemiology are of primary interest.Methods: For that purpose, a literature review has been made through a systematic search on three scientific databases. Overall, table tennis physiology is complex due to intense and intermittent efforts. It results that some technological challenges still need to be addressed to accurately quantify this physiology. Besides, current rules changes may modify the table tennis physiological requirements.Results: Findings in neurophysiology tend to define table tennis as an anticipation sport rather than a reaction sport and higher occulo-motor skills were found in table tennis population with respect to average population. Regarding biomechanics, some rare studies have been done but none had investigated the energy flow between the upper- and the lower-body, which would be interesting to understand how the energy generated by the footwork contributes to racket velocity.Conclusion: Finally, epidemiological studies lack of details on injury locations and diagnosis. These data could be of high interest to improve medical and training care.Objectifs: Le tennis de table est un sport très pratiqué, souvent décrit comme un sport de réaction. De ce fait, les joueurs ont besoin de beaucoup pratiquer, ce qui peut les exposer à des blessures. Pour l’optimisation de l’entraînement, tout en réduisant le risque de blessure, les connaissances de la physiologie, de la biomécanique et de l’épidémiologie du tennis de table sont primordiales.Méthode: Dans ce but, une revue systématique de la littérature a été effectuée au travers de trois bases de données. Globalement, la physiologie du tennis de table est complexe à cause d’efforts intenses et intermittents. Il reste alors des challenges techniques à relever pour quantifier précisément cette physiologie. De plus, certains changements dans le règlement tendent à faire évoluer les exigences physiologiques du tennis de table.Résultats: Les résultats en neurophysiologie tendent à définir le tennis de table comme un sport d’anticipation plutôt qu’un sport de réaction et des compétences oculomotrices plus élevées ont été trouvées en comparaison à la population moyenne. En ce qui concerne la biomécanique, quelques rares études ont été réalisées mais aucune n’a étudié les contributions d’énergie mécanique dans l’ensemble du corps, ce qui permettrait notamment de mieux comprendre l’effet de la puissance des membres inférieurs sur la vitesse de la raquette et de la balle.Conclusion: Finalement, les études épidémiologiques manquent de détails sur le diagnostic et la localisation des blessures. Ces données pourraient être de grand intérêt pour améliorer les soins médicaux et la surveillance de l’entraînement

Retinal sensitivity is reduced in patients with obstructive sleep apnea.

PURPOSE: To evaluate the outcomes of standard automated perimetry (SAP) in patients with obstructive sleep apnea (OSA). METHODS: Eighty OSA patients and 111 age-matched controls were consecutively and prospectively enrolled. One eye per subject was randomly selected. All participants underwent at least one reliable SAP (24-2 SITA Standard algorithm). The peripapillary retinal nerve fiber layer thickness (RNFL) was measured with spectral-domain optical coherence tomography (OCT). Patients with OSA were classified into three groups according to the apnea/hypopnea index: mild, moderate, or severe OSA. Parameters of SAP and OCT were compared between healthy controls and OSA patients. Correlation of apnea/hypopnea index with OCT and SAP measurements were calculated. RESULTS: Mean age, best-corrected visual acuity, and central corneal thickness were similar between groups. Intraocular pressure, however, was lower in the OSA group. Mean deviation of SAP was -0.23 \ub1 0.8 dB in the control group and -1.74 \ub1 2.8 dB in the OSA group (P < 0.001). Thickness of RNFL measured with OCT did not differ significantly between groups. Patients with OSA showed reduced sensitivity at most points tested by white-on-white perimetry compared with healthy individuals. The threshold values were more depressed in the peripheral visual field. The apnea/hypopnea index was related to the SAP indices: Pearson correlations were -0.432 with mean deviation, 0.467 with pattern standard deviation, and -0.416 with the visual field index (P < 0.001). CONCLUSIONS: Patients with OSA exhibited reduced retinal sensitivity measured with SAP compared with healthy controls

Spinal cystic echinococcosis - a systematic analysis and review of the literature : part 1. Epidemiology and anatomy

Bone involvement in human cystic echinococcosis (CE) is rare, but affects the spine in approximately 50% of cases. Despite significant advances in diagnostic imaging techniques as well as surgical and medical treatment of spinal CE, our basic understanding of the parasite's predilection for the spine remains incomplete. To fill this gap, we systematically reviewed the published literature of the last five decades to summarize and analyze the currently existing data on epidemiological and anatomical aspects of spinal CE

Phenylacetyl Coenzyme A Is an Effector Molecule of the TetR Family Transcriptional Repressor PaaR from Thermus thermophilusHB8 ▿ †

Phenylacetic acid (PAA) is a common intermediate in the catabolic pathways of several structurally related aromatic compounds. It is converted into phenylacetyl coenzyme A (PA-CoA), which is degraded to general metabolites by a set of enzymes. Within the genome of the extremely thermophilic bacterium Thermus thermophilusHB8, a cluster of genes, including a TetR family transcriptional regulator, may be involved in PAA degradation. The gene product, which we named T. thermophilusPaaR, negatively regulated the expression of the two operons composing the gene cluster in vitro. T. thermophilusPaaR repressed the target gene expression by binding pseudopalindromic sequences, with a consensus sequence of 5′-CNAACGNNCGTTNG-3′, surrounding the promoters. PA-CoA is a ligand of PaaR, with a proposed binding stoichiometry of 1:1 protein monomer, and was effective for transcriptional derepression. Thus, PaaR is a functional homolog of PaaX, a GntR transcriptional repressor found in Escherichia coliand Pseudomonasstrains. A three-dimensional structure of T. thermophilusPaaR was predicted by homology modeling. In the putative structure, PaaR adopts the typical three-dimensional structure of the TetR family proteins, with 10 α-helices. A positively charged surface at the center of the molecule is similar to the acyl-CoA-binding site of another TetR family transcriptional regulator, T. thermophilusFadR, which is involved in fatty acid degradation. The CoA moiety of PA-CoA may bind to the center of the PaaR molecule, in a manner similar to the binding of the CoA moiety of acyl-CoA to FadR