THEA: ontology-driven analysis of microarray data

MOTIVATION: Microarray technology makes it possible to measure thousands of variables and to compare their values under hundreds of conditions. Once microarray data are quantified, normalized and classified, the analysis phase is essentially a manual and subjective task based on visual inspection of classes in the light of the vast amount of information available. Currently, data interpretation clearly constitutes the bottleneck of such analyses and there is an obvious need for tools able to fill the gap between data processed with mathematical methods and existing biological knowledge. RESULTS: THEA (Tools for High-throughput Experiments Analysis) is an integrated information processing system allowing convenient handling of data. It allows to automatically annotate data issued from classification systems with selected biological information coming from a knowledge base and to either manually search and browse through these annotations or automatically generate meaningful generalizations according to statistical criteria (data mining). AVAILABILITY: The software is available on the website http://thea.unice.fr/     

Processing of vitamin A and E in the human gastrointestinal tract

We aimed to provide basic data on the processing of vitamin A and E in the human gastrointestinal tract and to assess whether the size of emulsion fat globules affects the bioavailability of these vitamins. Eight healthy men received intragastrically two lipid formulas differing in their fat-globule median diameter (0.7 vs. 10. 1 microm. Formulas provided 28 mg vitamin A as retinyl palmitate and 440 mg vitamin E as all-rac alpha-tocopherol. Vitamins were measured in gastric and duodenal aspirates, as well as in chylomicrons, during the postprandial period. The gastric emptying rate of lipids and vitamin A and E was similar. The free retinol/total vitamin A ratio was not significantly modified in the stomach, whereas it was dramatically increased in the duodenum. The proportion of ingested lipid and vitamins was very similar in the duodenal content. The chylomicron response of lipids and vitamins was not significantly different between the two emulsions. Our main conclusions are as follows: 1) there is no significant metabolism of vitamin A and E in the human stomach, 2) the enzyme(s) present in the duodenal lumen is significantly involved in the hydrolysis of retinyl esters, and 3) the size of emulsion fat globules has no major effect on the overall absorption of vitamin A and E.     

Règles applicables aux essais cliniques portant sur les dispositifs médicaux

It is sometimes not easy to navigate in the meanders of the national regulation dealing with medical devices. This article intends to present the ethical framework as well as the practical methods of application of the French regulation for clinical trials in this field. In particular, we review the major steps and the key sensitive elements concerning the protection of the people and the protection of collected data.     

In vivo and in vitro modulation of HLA-DM and HLA-DO is induced by B lymphocyte activation.

Ag presentation via HLA class II molecules in B lymphocytes depends on the coordinated action of HLA-DM, the catalyst of class II-peptide loading, and HLA-DO, a pH-dependent modulator of DM, the expression of which is almost completely restricted to B lymphocytes. The relative expression levels of both class II modulators are critical for the composition of the HLA class II peptide repertoire. The data in this work demonstrate that DO and DM expression are both dependent on the cellular activation status in primary human B lymphocytes. In vivo low-density activated primary human B lymphocytes show a prominent reduction in DO and DM expression when compared with high-density resting primary B lymphocytes. In vitro, reduction of DO and DM expression can be induced by B lymphocyte activation via the B cell receptor or by use of the phorbol ester, PMA. Specific inhibition of protein kinase C resulted in a significant reduction of HLA-DO and is potentially due to protein degradation in lysosomal compartments as the phenomenon is reversed by chloroquine. Thus, the expression of the dedicated HLA class II chaperone DM and its pH-dependent modulator DO is regulated and tightly controlled by the activation status of the B lymphocyte.     

An automatic MRI quality control procedure: Multisite reports for slice thickness and geometric accuracy

In this work, we report multi-scanner quality control monitoring using a standard and automated protocol. This magnetic resonance imaging quality control protocol, based on the American College of Radiology procedures, includes weekly scans of a dedicated phantom followed by specific measurements. The processing step commonly involves manually-performed operations which can be tedious and time-consuming hence motivating their automation. QC data were collected in four sites; data from one of them served for the validation of the automatic analysis tool. Designed as a package of MATLAB^® functions, this tool was successfully validated using Student's t-test and the correlation between automatic measurements and the manual ones. Besides, the multisite QC study enabled to compare the performances of these four MR facilities. In order to avoid misinterpretation or errors in multicenter clinical studies, such approach can be recommended as a preliminary step for including a site in the studies.     

Cloning of the unculturable parasite Pasteuria ramosa and its Daphnia host reveals extreme genotype-genotype interactions

The degree of specificity in host-parasite interactions has important implications for ecology and evolution. Unfortunately, specificity can be difficult to determine when parasites cannot be cultured. In such cases, studies often use isolates of unknown genetic composition, which may lead to an underestimation of specificity. We obtained the first clones of the unculturable bacterium Pasteuria ramosa, a parasite of Daphnia magna. Clonal genotypes of the parasite exhibited much more specific interactions with host genotypes than previous studies using isolates. Clones of P. ramosa infected fewer D. magna genotypes than isolates and host clones were either fully susceptible or fully resistant to the parasite. Our finding enhances our understanding of the evolution of virulence and coevolutionary dynamics in this system. We recommend caution when using P. ramosa isolates as the presence of multiple genotypes may influence the outcome and interpretation of some experiments.     

Improving Microstructured TiO2 Photoanodes for Dye Sensitized Solar Cells by Simple Surface Treatment

TiCl₄ surface treatment studies of porous electrode structure of TiO₂ aggregates synthesized using an acidic precursor and CTAB as a templating agent are carried out in order to understand and improve upon recombination kinetics in the photonanode film matrix, together with enhancing the intrinsic light scattering. The key beneficial features of the photoanode included high surface roughness, necessary for superior dye adsorption, nanocrystallite aggregates leading to diffuse light scattering within the film matrix, and a hierarchical macro‐ and mesopore structure allowing good access of electrolyte to the dye, thereby assisting in dye regeneration (enhanced charge transfer). Pre‐treatment of the TiO₂ electrodes reduced recombination at the fluorine‐doped tin oxide (FTO)/electrolyte interface. The post‐treatment study showed enhanced surface roughness through the deposition of a thin overlayer of amorphous TiO₂ on the film structure. This led to a notable improvement in both dye adsorption and inherent light scattering effects by the TiO₂ aggregates, resulting in enhanced energy harvesting. The thin TiO₂ overlayer also acted as a barrier in a core‐shell configuration within the porous TiO₂ matrix, and thereby reduced recombination. This allowed the hierarchical macro‐ and mesoporosity of the film matrix to be utilized more effectively for enhanced charge transfer during dye regeneration. Post‐treatment of the aggregated TiO₂ matrix resulted in a 36% enhancement in power conversion efficiency from 4.41% of untreated cells to 6.01%.     

Population genetics of duplicated alternatively spliced exons of the Dscam gene in Daphnia and Drosophila

In insects and crustaceans, the Down syndrome cell adhesion molecule (Dscam) occurs in many different isoforms. These are produced by mutually exclusive alternative splicing of dozens of tandem duplicated exons coding for parts or whole immunoglobulin (Ig) domains of the Dscam protein. This diversity plays a role in the development of the nervous system and also in the immune system. Structural analysis of the protein suggested candidate epitopes where binding to pathogens could occur. These epitopes are coded by regions of the duplicated exons and are therefore diverse within individuals. Here we apply molecular population genetics and molecular evolution analyses using Daphnia magna and several Drosophila species to investigate the potential role of natural selection in the divergence between orthologs of these duplicated exons among species, as well as between paralogous exons within species. We found no evidence for a role of positive selection in the divergence of these paralogous exons. However, the power of this test was low, and the fact that no signs of gene conversion between paralogous exons were found suggests that paralog diversity may nonetheless be maintained by selection. The analysis of orthologous exons in Drosophila and in Daphnia revealed an excess of non-synonymous polymorphisms in the epitopes putatively involved in pathogen binding. This may be a sign of balancing selection. Indeed, in Dr. melanogaster the same derived non-synonymous alleles segregate in several populations around the world. Yet other hallmarks of balancing selection were not found. Hence, we cannot rule out that the excess of non-synonymous polymorphisms is caused by segregating slightly deleterious alleles, thus potentially indicating reduced selective constraints in the putative pathogen binding epitopes of Dscam.     

γ-Actin regulates cell migration and modulates the ROCK signaling pathway

Cell migration plays a crucial role in numerous cellular functions, and alterations in the regulation of cell migration are required for invasive transformation of a tumor cell. While the mechanistic process of actin-based migration has been well documented, little is known as to the specific function of the nonmuscle actin isoforms in mammalian cells. Here, we present a comprehensive examination of γ-actin's role in cell migration using an RNAi approach. The partial suppression of γ-actin expression in SH-EP neuroblastoma cells resulted in a significant decrease in wound healing and transwell migration. Similarly, the knockdown of γ-actin significantly reduced speed of motility and severely affected the cell's ability to explore, which was, in part, due to a loss of cell polarity. Moreover, there was a significant increase in the size and number of paxillin-containing focal adhesions, coupled with a significant decrease in phosphorylated paxillin in γ-actin-knockdown cells. In addition, there was a significant increase in the phosphorylation of cofilin and myosin regulatory light chain, suggesting an overactivated Rho-associated kinase (ROCK) signaling pathway in γ-actin-knockdown cells. The alterations in the phosphorylation of paxillin and myosin regulatory light chain were unique to γ-actin and not β-actin knockdown. Inhibition of the ROCK pathway with the inhibitor Y-27632 restored the ability of γ-actin-knockdown cells to migrate. This study demonstrates γ-actin as a potential upstream regulator of ROCK mediated cell migration.