Indicator taxa of benthic diatom communities: a case study in Mediterranean streams

A key issue in the implementation of the Water Framework Directive is the classification of streams and rivers using biological quality parameters and type-specific reference conditions. Four groups of stream types were defined in NE Spain on the basis of 152 diatom samples by means of detrended correspondence analysis and classification techniques. Diatom analysis was restricted to epilithic taxa, and the sites included gradients ranging from near-natural streams to sites with poor ecological quality. The main gradient shows a clear separation of sites in relation to the degree of human influence: polluted streams (mainly located in the lowlands) differ from streams in mountainous areas and in the Pyrenees. A second gradient is related to physiographical features. Headwater streams can be distinguished by their catchment geology. The type-specific diatom taxa for the stream types studied were determined by using indicator species analysis (IndVal). The type-specific taxa from near-natural streams are coincident with the indicator taxa for high ecological status. Human impact reduced the typological heterogeneity of the diatom community composition. Overall, the diatom communities in NE Spain exhibit a regional distribution pattern that closely corresponds with that observed in river systems elsewhere. Physiographical differences are only evident in undisturbed sites, while nutrient enrichment and other human disturbances may mask the regional differences in the distribution of diatom communities

Adaptation au codage CIM-10 de 15 indicateurs de la sécurité des patients proposés par l'Agence étasunienne pour la recherche et la qualité des soins de santé (AHRQ) [ICD-10 adaptation of 15 Agency for Healthcare Research and Quality patient safety indicators].

BACKGROUND: In the United States, the Agency for Healthcare Research and Quality (AHRQ) has developed 20 Patient Safety Indicators (PSIs) to measure the occurrence of hospital adverse events from medico-administrative data coded according to the ninth revision of the international classification of disease (ICD-9-CM). The adaptation of these PSIs to the WHO version of ICD-10 was carried out by an international consortium. METHODS: Two independent teams transcoded ICD-9-CM diagnosis codes proposed by the AHRQ into ICD-10-WHO. Using a Delphi process, experts from six countries evaluated each code independently, stating whether it was "included", "excluded" or "uncertain". During a two-day meeting, the experts then discussed the codes that had not obtained a consensus, and the additional codes proposed. RESULTS: Fifteen PSIs were adapted. Among the 2569 proposed diagnosis codes, 1775 were unanimously adopted straightaway. The 794 remaining codes and 2541 additional codes were discussed. Three documents were prepared: (1) a list of ICD-10-WHO codes for the 15 adapted PSIs; (2) recommendations to the AHRQ for the improvement of the nosological frame and the coding of PSI with ICD-9-CM; (3) recommendations to the WHO to improve ICD-10. CONCLUSIONS: This work allows international comparisons of PSIs among the countries using ICD-10. Nevertheless, these PSIs must still be evaluated further before being broadly used.

Open minded and open access: introducing NeoBiota, a new peer-reviewed journal of biological invasions

The Editorial presents the focus, scope, policies, and the inaugural issue of NeoBiota, a new open access peer-reviewed journal of biological invasions. The new journal NeoBiota is a continuation of the former NEOBIOTA publication series. The journal will deal with all aspects of invasion biology and impose no restrictions on manuscript size neither on use of color. NeoBiota implies an XML-based editorial workflow and several cutting-edge innovations in publishing and dissemination, such as semantic markup of and enhancements to published texts, data publication, and extensive cross-linking within the journal and to external sources

Using environmental niche modeling to understand biological invasions in a changing world

L'activité humaine affecte particulièrement la biodiversité, qui décline à une vitesse préoccupante. Parmi les facteurs réduisant la biodiversité, on trouve les espèces envahissantes. Symptomatiques d'un monde globalisé où l'échange se fait à l'échelle de la planète, certaines espèces, animales ou végétales, sont introduites, volontairement ou accidentellement par l'activité humaine (par exemple lors des échanges commerciaux ou par les voyageurs). Ainsi, ces espèces atteignent des régions qu'elles n'auraient jamais pu coloniser naturellement. Une fois introduites, l'absence de compétiteur peut les rendre particulièrement nuisibles. Ces nuisances sont plus ou moins directes, allant de problèmes sanitaires (p. ex. les piqûres très aigües des fourmis de feu, originaires d'Amérique du Sud et colonisant à une vitesse fulgurante les USA, l'Australie ou la Chine) à des nuisances sur la biodiversité (p. ex. les ravages de la perche du Nil sur la diversité unique des poissons Cichlidés du Lac Victoria). Il est donc important de pouvoir prévenir de telles introductions. De plus, pour le biologiste, ces espèces représentent une rare occasion de pouvoir comprendre les mécanismes évolutifs et écologiques qui expliquent le succès des envahissantes dans un monde où les équilibres sont bouleversés. Les modèles de niche environnementale sont un outil particulièrement utile dans le cadre de cette problématique. En reliant des observations d'espèces aux conditions environnementales où elles se trouvent, ils peuvent prédire la distribution potentielle des envahissantes, permettant d'anticiper et de mieux limiter leur impact. Toutefois, ils reposent sur des hypothèses pas évidentes à démontrer. L'une d'entre elle étant que la niche d'une espèce reste constante dans le temps, et dans l'espace. Le premier objectif de mon travail est de comparer si la niche d'une espèce envahissante diffère entre sa distribution d'origine native et celle d'origine introduite. En étudiant 50 espèces de plantes et 168 espèces de Mammifères, je démontre que c'est le cas et que par corolaire, il est possible de prédire leurs distributions. La deuxième partie de mon travail consiste à comprendre quelles seront les interactions entre le changement climatiques et les envahissantes, afin d'estimer leur impact sous un climat réchauffé. En étudiant la distribution de 49 espèces de plantes envahissantes, je démontre que les montagnes, régions relativement préservée par ce problème, deviendront bien plus exposées aux risques d'invasions biologiques. J'expose aussi comment les interactions entre l'activité humaine, le réchauffement climatique et les espèces envahissantes menacent la vigne sauvage en Europe et propose des zones géographiques particulièrement adaptée pour sa conservation. Enfin, à une échelle beaucoup plus locale, je montre qu'il est possible d'utiliser ces modèles de niches le long d'une rivière à une échelle extrêmement fine (1 mètre), potentiellement utile pour rationnaliser des mesures de conservations sur le terrain. - Biodiversity is significantly negatively affected by human activity. Invasive species are one of the most important factors causing biodiversity's decline. Intimately linked to the era of global trade, some plant or animal species can be accidentally or casually introduced with human activity (e.g. trade or travel). In this way, these species reach areas they could never reach through natural dispersal. Once naturalized, the lack of competitors can make these species highly noxious. Their effect is more or less direct, from sanitary problems (e.g. the harmful sting of Fire Ants, originating from South America and now spreading throughout USA, China and Australia) or can affect biodiversity (e.g. the Nile perch, devastating the one of the richest hotspot of Cichlid fishes diversity in Lake Victoria). It is thus important to prevent such harmful introductions. Moreover, invasive species represent for biologists one of the rare occasions to understand the evolutionary and ecological mechanisms behind the success of invaders in a world where natural equilibrium is already disturbed. Environmental niche models are particularly useful to tackle this problematic. By relating species observation to the environmental conditions where they occur, they can predict the potential distribution of invasive species, allowing a better anticipation and thus limiting their impact. However, they rely on strong assumption, one of the most important being that the modeled niche remains constant through space and time. The first aim of my thesis is to quantify the difference between the native and the invaded niche. By investigating 50 plant and 168 mammal species, I show that the niche is at least partially conserved, supporting for reliable predictions of invasive' s potential distributions. The second aim of my thesis is to understand the possible interactions between climate change and invasive species, such as to assess their impact under a warmer climate. By studying 49 invasive plant species, I show that mountain areas, which were relatively preserved, will become more suitable for biological invasions. Additionally, I show how interactions between human activity, global warming and invasive species are threatening the wild grapevine in Europe and propose geographical areas particularly adapted for conservation measures. Finally, at a much finer scale where conservation plannings ultimately take place, I show that it is possible to model the niche at very high resolution (1 meter) in an alluvial area allowing better prioritizations for conservation.

Blood plasma lipidomic signature of epicardial fat in healthy obese women.

OBJECTIVES: A lipidomic approach was employed in a clinically well-defined cohort of healthy obese women to explore blood lipidome phenotype ascribed to body fat deposition, with emphasis on epicardial adipose tissue (EAT). METHODS: The present investigation delivered a lipidomics signature of epicardial adiposity under healthy clinical conditions using a cohort of 40 obese females (age: 25-45 years, BMI: 28-40 kg/m(2) ) not showing any metabolic disease traits. Lipidomics analysis of blood plasma was employed in combination with in vivo quantitation of mediastinal fat depots by computerized tomography. RESULTS: All cardiac fat depots correlated to indicators of hepatic dysfunctions (ALAT and ASAT), which describe physiological connections between hepatic and cardiac steatosis. Plasma lipidomics encompassed overall levels of lipid classes, fatty acid profiles, and individual lipid species. EAT and visceral fat associated with diacylglycerols (DAG), triglycerides, and distinct phospholipid and sphingolipid species. A pattern of DAG and phosphoglycerols was specific to EAT. CONCLUSIONS: Human blood plasma lipidomics appears to be a promising clinical and potentially diagnostic readout for patient stratification and monitoring. Association of blood lipidomics signature to regio-specific mediastinal and visceral adiposity under healthy clinical conditions may help provide more biological insights into obese patient stratification for cardiovascular disease risks.

gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution

One of the important questions in biological evolution is to know if certain changes along protein coding genes have contributed to the adaptation of species. This problem is known to be biologically complex and computationally very expensive. It, therefore, requires efficient Grid or cluster solutions to overcome the computational challenge. We have developed a Grid-enabled tool (gcodeml) that relies on the PAML (codeml) package to help analyse large phylogenetic datasets on both Grids and computational clusters. Although we report on results for gcodeml, our approach is applicable and customisable to related problems in biology or other scientific domains.

Reaction-diffusion wave fronts: Multigeneration biological species under climate change

A generalization of reaction-diffusion models to multigeneration biological species is presented. It is based on more complex random walks than those in previous approaches. The new model is developed analytically up to infinite order. Our predictions for the speed agree to experimental data for several butterfly species better than existing models. The predicted dependence for the speed on the number of generations per year allows us to explain the change in speed observed for a specific invasion

Multifunctional ligands for application in Alzheimer’s Disease: molecular modelling and biological evaluation

Projecte de recerca elaborat a partir d’una estada a la University of British Columbia, Canadà, entre 2010 i 2012 La malaltia d'Alzheimer (MA) representa avui la forma més comuna de demència en la població envellida. Malgrat fa 100 anys que va ser descoberta, encara avui no existeix cap tractament preventiu i/o curatiu ni cap agent de diagnòstic que permeti valorar quantitativament l'evolució d'aquesta malaltia. L'objectiu en el que s'emmarca aquest treball és contribuir a aportar solucions al problema de la manca d'agents terapèutics i de diagnosi, unívocs i rigorosos, per a la MA. Des del camp de la química bioinorgànica és fàcil fixar-se en l'excessiva concentració d'ions Zn(II) i Cu(II) en els cervells de malalts de MA, plantejar-se la seva utilització com a dianes terapèutica i, en conseqüència, cercar agents quelants que evitin la formació de plaques senils o contribueixin a la seva dissolució. Si bé aquest va ser el punt de partida d’aquest projecte, els múltiples factors implicats en la patogènesi de la MA fan que el clàssic paradigma d’ ¨una molècula, una diana¨ limiti la capacitat de la molècula de combatre aquesta malaltia tan complexa. Per tant, un esforç considerable s’ha dedicat al disseny d’agentsmultifuncionals que combatin els múltiples factors que caracteritzen el desenvolupament de la MA. En el present treball s’han dissenyat agents multifuncionals inspirats en dos esquelets moleculars ben establers i coneguts en el camp de la química medicinal: la tioflavina-T (ThT) i la deferiprona (DFP). La utilització de tècniques in silico que inclouen càlculs farmacocinètics i modelatge molecular ha estat un procés cabdal per a l’avaluació dels millors candidats en base als següents requeriments: (a) compliment de determinades propietats farmacocinètiques que estableixin el seu possible ús com a fàrmac (b) hidrofobicitat adequada per travessar la BBB i (c) interacció amb el pèptid Aen solució.

Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights.

With the widespread availability of high-throughput sequencing technologies, sequencing projects have become pervasive in the molecular life sciences. The huge bulk of data generated daily must be analyzed further by biologists with skills in bioinformatics and by "embedded bioinformaticians," i.e., bioinformaticians integrated in wet lab research groups. Thus, students interested in molecular life sciences must be trained in the main steps of genomics: sequencing, assembly, annotation and analysis. To reach that goal, a practical course has been set up for master students at the University of Lausanne: the "Sequence a genome" class. At the beginning of the academic year, a few bacterial species whose genome is unknown are provided to the students, who sequence and assemble the genome(s) and perform manual annotation. Here, we report the progress of the first class from September 2010 to June 2011 and the results obtained by seven master students who specifically assembled and annotated the genome of Estrella lausannensis, an obligate intracellular bacterium related to Chlamydia. The draft genome of Estrella is composed of 29 scaffolds encompassing 2,819,825 bp that encode for 2233 putative proteins. Estrella also possesses a 9136 bp plasmid that encodes for 14 genes, among which we found an integrase and a toxin/antitoxin module. Like all other members of the Chlamydiales order, Estrella possesses a highly conserved type III secretion system, considered as a key virulence factor. The annotation of the Estrella genome also allowed the characterization of the metabolic abilities of this strictly intracellular bacterium. Altogether, the students provided the scientific community with the Estrella genome sequence and a preliminary understanding of the biology of this recently-discovered bacterial genus, while learning to use cutting-edge technologies for sequencing and to perform bioinformatics analyses.

TACI, an enigmatic BAFF/APRIL receptor, with new unappreciated biochemical and biological properties.

BAFF is a B cell survival factor that binds to three receptors BAFF-R, TACI and BCMA. BAFF-R is the receptor triggering naïve B cell survival and maturation while BCMA supports the survival of plasma cells in the bone marrow. Excessive BAFF production leads to autoimmunity, presumably as the consequence of inappropriate survival of self-reactive B cells. The function of TACI has been more elusive with TACI(-/-) mice revealing two sides of this receptor, a positive one driving T cell-independent immune responses and a negative one down-regulating B cell activation and expansion. Recent work has revealed that the regulation of TACI expression is intimately linked to the activation of innate receptors on B cells and that TACI signalling in response to multimeric BAFF and APRIL provides positive signals to plasmablasts. How TACI negatively regulates B cells remains elusive but may involve an indirect control of BAFF levels. The discovery of TACI mutations associated with common variable immunodeficiency (CVID) in humans not only reinforces its important role for humoral responses but also suggests a more complex role than first anticipated from knockout animals. TACI is emerging as an unusual TNF receptor-like molecule with a sophisticated mode of action.

Biological Assessment of Iowa's Wadeable Streams, October 2004

The TMDL and Water Quality Assessment Section of the Iowa DNR Environmental Services Division have released the report entitled, “Biological Assessment of Iowa’s Wadeable Streams.” The report describes a framework for conducting stream bioassessments and how it is used to evaluate the biological condition of Iowa’s wadeable rivers and streams. The document also serves as a foundation for developing biological water quality standards for the protection of designated aquatic life uses and measuring progress toward the achievement of Federal Clean Water Act goals.

New Radicals and new applications of Dynamic Nuclear Polarization of biological systems

Dynamic Nuclear Polarization (DNP) is an emerging technique that could revolutionize the NMR study of small molecules at very low concentrations by the increase in sensitivity that results from transfer of polarization between electronic and nuclear spins. Although the underlying physics has been known for a long time, in the last few years there has been a lot of excitement on the chemistry and biology NMR community caused by the demonstration that the highly polarized nuclei that are prepared in solid state at very low temperatures (1-2 K) could be rapidly transferred to liquid samples at room temperature and studied in solution by conventional NMR techniques. In favorable cases several order of magnitude increases in sensitivity have been achieved. The technique is now mature enough that a commercial instrument is available. The efficiency of DNP depends on two crucial aspects: i) the efficiency of the nuclear polarization process and ii) the efficiency of the transfer from the initial solid state to the fluid state in which NMR is measured. The preferred areas of application (iii) will be dictated by situations in which the low concentration of the sample or its intrinsic low receptivity are the limiting factors .

Evaluating thermal treeline indicators based on air and soil temperature using an air-to-soil temperature transfer model

In recent research, both soil (root-zone) and air temperature have been used as predictors for the treeline position worldwide. In this study, we intended to (a) test the proposed temperature limitation at the treeline, and (b) investigate effects of season length for both heat sum and mean temperature variables in the Swiss Alps. As soil temperature data are available for a limited number of sites only, we developed an air-to-soil transfer model (ASTRAMO). The air-to-soil transfer model predicts daily mean root-zone temperatures (10cm below the surface) at the treeline exclusively from daily mean air temperatures. The model using calibrated air and root-zone temperature measurements at nine treeline sites in the Swiss Alps incorporates time lags to account for the damping effect between air and soil temperatures as well as the temporal autocorrelations typical for such chronological data sets. Based on the measured and modeled root-zone temperatures we analyzed. the suitability of the thermal treeline indicators seasonal mean and degree-days to describe the Alpine treeline position. The root-zone indicators were then compared to the respective indicators based on measured air temperatures, with all indicators calculated for two different indicator period lengths. For both temperature types (root-zone and air) and both indicator periods, seasonal mean temperature was the indicator with the lowest variation across all treeline sites. The resulting indicator values were 7.0 degrees C +/- 0.4 SD (short indicator period), respectively 7.1 degrees C +/- 0.5 SD (long indicator period) for root-zone temperature, and 8.0 degrees C +/- 0.6 SD (short indicator period), respectively 8.8 degrees C +/- 0.8 SD (long indicator period) for air temperature. Generally, a higher variation was found for all air based treeline indicators when compared to the root-zone temperature indicators. Despite this, we showed that treeline indicators calculated from both air and root-zone temperatures can be used to describe the Alpine treeline position.