Biomarqueurs associés à la dyspnée et douleurs thoraciques: quelle utilité clinique [Biomarkers associated with dyspnea and chest pain: which cinical utility?].

Dyspnea and chest pain are typical reasons for consultations. biomarkers (CRP, procalcitonin, NT-proBNP, troponins, D-dimers) can have an interest for the diagnosis, the prognosis and the follow-up of several pathologies. There are however numerous pitfalls and limitations between the discovery of a biomarker and the utility in clinical practice. It is essential to always estimate a pre-test probability based on an attentive history and a careful physical examination, to know the intrinsic and extrinsic qualities of a test, and to determine a threshold of care. A biomarker should be used only if it modifies the patient's care and if it brings him a benefit compared to the patient who has no biomarker.

Calprotectine fécale: outil diagnostique dans les maladies inflammatoires chroniques de l'intestin [Fecal calprotectin: a diagnostic tool for inflammatory bowel disease].

Fecal calprotectin (FC) is a valid biomarker to discriminate with a good sensitivity and specificity the presence of mucosal lesions of the gastrointestinal tube (e.g. ulcers in the context of inflammatory bowel disease (IBD)) from functional disorders (e.g. irritable bowel syndrome). FC is not specific for IBD and can be elevated also in gastrointestinal infections, ischemic colitis or neoplasia. An elevated FC should stimulate further investigations, notably an endoscopic workup. The level of FC correlates with the endoscopic score in Crohn's disease and ulcerative colitis. The correlation of FC and the endoscopic severity is better than the one of CRP or blood leukocytes. Thus, FC can also be used in the follow-up of IBD patients.

Usefulness of postmortem biochemistry in forensic pathology: illustrative case reports.

The aim of this work is to present some practical, postmortem biochemistry applications to illustrate the usefulness of this discipline and reassert the importance of carrying out biochemical investigations as an integral part of the autopsy process. Five case reports are presented pertaining to diabetic ketoacidosis in an adult who was not known to suffer from diabetes and in presence of multiple psychotropic substances; fatal flecainide intoxication in a poor metabolizer also presenting an impaired renal function; diabetic ketoacidosis showing severe postmortem changes; primary aldosteronism presented with intracranial hemorrhage and hypothermia showing severe postmortem changes. The cases herein presented can be considered representative examples of the importance of postmortem biochemistry investigations, which may provide significant information useful in determining the cause of death in routine forensic casework or contribute to understanding the pathophysiological mechanisms involved in the death process.

Indexing strategies for rapid searches of short words in genome sequences.

Searching for matches between large collections of short (14-30 nucleotides) words and sequence databases comprising full genomes or transcriptomes is a common task in biological sequence analysis. We investigated the performance of simple indexing strategies for handling such tasks and developed two programs, fetchGWI and tagger, that index either the database or the query set. Either strategy outperforms megablast for searches with more than 10,000 probes. FetchGWI is shown to be a versatile tool for rapidly searching multiple genomes, whose performance is limited in most cases by the speed of access to the filesystem. We have made publicly available a Web interface for searching the human, mouse, and several other genomes and transcriptomes with oligonucleotide queries.

Toxicokinetic modeling of folpet fungicide and its ring-biomarkers of exposure in humans.

A human in vivo toxicokinetic model was built to allow a better understanding of the toxicokinetics of folpet fungicide and its key ring biomarkers of exposure: phthalimide (PI), phthalamic acid (PAA) and phthalic acid (PA). Both PI and the sum of ring metabolites, expressed as PA equivalents (PAeq), may be used as biomarkers of exposure. The conceptual representation of the model was based on the analysis of the time course of these biomarkers in volunteers orally and dermally exposed to folpet. In the model, compartments were also used to represent the body burden of folpet and experimentally relevant PI, PAA and PA ring metabolites in blood and in key tissues as well as in excreta, hence urinary and feces. The time evolution of these biomarkers in each compartment of the model was then mathematically described by a system of coupled differential equations. The mathematical parameters of the model were then determined from best fits to the time courses of PI and PAeq in blood and urine of five volunteers administered orally 1 mg kg(-1) and dermally 10 mg kg(-1) of folpet. In the case of oral administration, the mean elimination half-life of PI from blood (through feces, urine or metabolism) was found to be 39.9 h as compared with 28.0 h for PAeq. In the case of a dermal application, mean elimination half-life of PI and PAeq was estimated to be 34.3 and 29.3 h, respectively. The average final fractions of administered dose recovered in urine as PI over the 0-96 h period were 0.030 and 0.002%, for oral and dermal exposure, respectively. Corresponding values for PAeq were 24.5 and 1.83%, respectively. Finally, the average clearance rate of PI from blood calculated from the oral and dermal data was 0.09 ± 0.03 and 0.13 ± 0.05 ml h(-1) while the volume of distribution was 4.30 ± 1.12 and 6.05 ± 2.22 l, respectively. It was not possible to obtain the corresponding values from PAeq data owing to the lack of blood time course data.

Prediction of plant species distributions across six millennia.

The usefulness of species distribution models (SDMs) in predicting impacts of climate change on biodiversity is difficult to assess because changes in species ranges may take decades or centuries to occur. One alternative way to evaluate the predictive ability of SDMs across time is to compare their predictions with data on past species distributions. We use data on plant distributions, fossil pollen and current and mid-Holocene climate to test the ability of SDMs to predict past climate-change impacts. We find that species showing little change in the estimated position of their realized niche, with resulting good model performance, tend to be dominant competitors for light. Different mechanisms appear to be responsible for among-species differences in model performance. Confidence in predictions of the impacts of climate change could be improved by selecting species with characteristics that suggest little change is expected in the relationships between species occurrence and climate patterns.

Novel use of a whole cell E. coli bioreporter as a urinary exposure biomarker.

Bacterial bioreporters have substantial potential for contaminant assessment but their real world application is currently impaired by a lack of sensitivity. Here, we exploit the bioconcentration of chemicals in the urine of animals to facilitate pollutant detection. The shore crab Carcinus maenas was exposed to the organic contaminant 2-hydroxybiphenyl, and urine was screened using an Escherichia coli-based luciferase gene (luxAB) reporter assay specific to this compound. Bioassay measurements differentiated between the original contaminant and its metabolites, quantifying bioconcentration factors of up to one hundred-fold in crab urine. Our results reveal the substantial potential of using bacterial bioreporter assays in real-time monitoring of biological matricesto determine exposure histories, with wide ranging potential for the in situ measurement of xenobiotics in risk assessments and epidemiology.

Autoanticorps en neurologie: implications cliniques [Autoantibodies in neurological diseases: clinical implications]

Autoantibodies are defined as antibodies directed against self antigens, i.e., against a normal antigenic endogenous tissue constituent. They can be the immediate cause of the neurological syndrome or be detected as an epiphenomenon of the pathogenic process. Autoantibodies are often considered useful biomarkers for the improvement of diagnostic accuracy, for the staging of disease progression or for the follow up of a biological response to a therapeutic intervention. The purpose of this article is to review the autoantibodies that are available to investigate immune-mediated neurological conditions. The detection of some of these autoantibodies may help the clinician to establish a definite diagnosis which may further facilitate the therapeutic decision.

Comparative genomics of yeast species: new insights into their biology

The genomes of two hemiascomycetous yeasts (Saccharomyces cerevisiae and Candida albicans) and one archiascomycete (Schizosaccharomyces pombe) have been completely sequenced and the genes have been annotated. In addition, the genomes of 13 more Hemiascomycetes have been partially sequenced. The amount of data thus obtained provides information on the evolutionary relationships between yeast species. In addition, the differential genetic characteristics of the microorganisms explain a number of distinctive biological traits. Gene order conservation is observed between phylogenetically close species and is lost in distantly related species, probably due to rearrangements of short regions of DNA. However, gene function is much more conserved along evolution. Compared to S. cerevisiae and S. pombe, C. albicans has a larger number of specific genes, i.e., genes not found in other organisms, a fact that can account for the biological characteristics of this pathogenic dimorphic yeast which is able to colonize a large variety of environments.

Do mediterranean genera not included in Tachet et al. (2002) have mediterranean trait characteristics?

Do mediterranean genera not included in Tachet et al. 2002 have mediterranean trait characteristics? Multiple-trait databases are increasingly used in community ecology in different regions of the world. In Europe, Tachet et al.(2002) compiled an aquatic macroinvertebrate database for 473 taxa using information on 11 biological traits described by 63 categories. However, less studied regions, at the time of the compilation of the database, such as the mediterranean Basin, can harbour exclusive genera, which were not included in Tachet"s database. In a large-scale study across the mediterranean Basin, we found 44 genera that were not included in Tachet"s database (NEW genera). Our main aim was to compile trait information for these NEW genera and assess whether these genera had specific traits that could explain their exclusivity to the Mediterranean region. We compared the trait characteristics of NEW genera to those of genera only found in Mediterranean or temperate regions that were included in the Tachet"s database (MED and TEM genera, respectively). We found that NEW genera had more mediterranean characteristics than TEM genera and that some trait categories of NEW genera were even more mediterranean-like than the traits of MED genera (e.g., diapause). Therefore, our results suggest that the specific biological traits of these NEW genera allow them to cope successfully and exclusively with the harsh environmental conditions of the mediterranean climate rivers, which could partially explain their absence in Tachet"s database. Other explanations, such as the limited dispersal ability of these NEW genera to reach and colonize temperate Europe or the rarity of these NEW genera, should also be considered. We provide biological traits of the NEW genera to be used in future studies on the mediterranean river ecology.

Effects of artisanal fisheries on the scorpaenids (Scorpaena spp.) reproduction in the marine protected area of Cap de Creus (NW Mediterranean)

Rockfish species are considered important to the ecology of rocky-reef communities which constitute a key habitat in many coastal marine protected areas (MPAs). These species, which are commercially valuable for artisanal fisheries in the Mediterranean, display particular biological traits that could render them vulnerable to fishing. In this study we monitored the artisanal fisheries of scorpaenids (Scorpaena spp.) in the MPA of Cap de Creus (northwestern Mediterranean) in order to estimate the status of their populations, to link captures with the reproduction of these species, and to evaluate the potential impact that artisanal fishing may have on them. Data from onboard sampling with artisanal fishermen and from fisheries statistics (total landings) were used. Total landings and catch per unit of effort (CPUE) follow a clearly seasonal cycle, with a prominent peak during the summer months coinciding with their spawning season, which may be due to mating behavior prior to fertilization. Although maximum sizes are bigger inside the MPA than in non-protected areas situated close by, a significant percentage of individuals caught inside the MPA are below their size at sexual maturity. Although rockfish seem to be favored by the partial protection of the MPA, the allowed artisanal fisheries are probably impacting the reproduction of these species

A Comparative Study of Desktop, Fishtank, and Cave Systems for the Exploration of Volume Rendered Confocal Data Sets

We present a participant study that compares biological data exploration tasks using volume renderings of laser confocal microscopy data across three environments that vary in level of immersion: a desktop, fishtank, and cave system. For the tasks, data, and visualization approach used in our study, we found that subjects qualitatively preferred and quantitatively performed better in the cave compared with the fishtank and desktop. Subjects performed real-world biological data analysis tasks that emphasized understanding spatial relationships including characterizing the general features in a volume, identifying colocated features, and reporting geometric relationships such as whether clusters of cells were coplanar. After analyzing data in each environment, subjects were asked to choose which environment they wanted to analyze additional data sets in - subjects uniformly selected the cave environment.