DataManager, un système novateur de gestion et d’échange de données botaniques distribuées

National audienceDataManager, un système novateur de gestion et d'échange de données botaniques distribuées STRUCTURATION DES DONNÉES Cette application web est dédiée à des scientifiques souhaitant gérer des jeux de données spécifiques, avec le souhait de partager une partie de leur travail. Pl@ntNet-DataManager est développé avec un moteur de base de données NoSQL, offrant des fonctionnalités innovantes, notamment pour une structuration flexible des données, ainsi que des fonctions avancées de synchronisation. Ce système offre des fonctionnalités classiques de gestion de données, telles que la recherche libre, l'édition de requêtes structurées, l'import / export à différents formas, la gestion d'images ou de données géo-localisées. Ce travail a permis d'initier une nouvelle forme de gestion de gros volumes de données. Il se poursuit actuellement à travers son exploitation dans le cadre de la chaîne logicielle Pl@ntNet, notamment pour la gestion d'observations botaniques et des données visuelles associée

Building Shared Experience to Advance Practical Application of Pathway-Based Toxicology: Liver Toxicity Mode-of-Action

A workshop sponsored by the Human Toxicology Project Consortium (HTPC), “Building Shared Experience to Advance Practical Application of Pathway-Based Toxicology: Liver Toxicity Mode-of-Action” brought together experts from a wide range of perspectives to inform the process of pathway development and to advance two prototype pathways initially developed by the European Commission Joint Research Center (JRC): liver-specific fibrosis and steatosis. The first half of the workshop focused on the theory and practice of pathway development; the second on liver disease and the two prototype pathways. Participants agreed pathway development is extremely useful for organizing information and found that focusing the theoretical discussion on a specific AOP is helpful. It is important to include several perspectives during pathway development, including information specialists, pathologists, human health and environmental risk assessors, and chemical and product manufacturers, to ensure the biology is well captured and end use is considered

Identification of genetic variants associated with Huntington's disease progression: a genome-wide association study

Background Huntington's disease is caused by a CAG repeat expansion in the huntingtin gene, HTT. Age at onset has been used as a quantitative phenotype in genetic analysis looking for Huntington's disease modifiers, but is hard to define and not always available. Therefore, we aimed to generate a novel measure of disease progression and to identify genetic markers associated with this progression measure. Methods We generated a progression score on the basis of principal component analysis of prospectively acquired longitudinal changes in motor, cognitive, and imaging measures in the 218 indivduals in the TRACK-HD cohort of Huntington's disease gene mutation carriers (data collected 2008–11). We generated a parallel progression score using data from 1773 previously genotyped participants from the European Huntington's Disease Network REGISTRY study of Huntington's disease mutation carriers (data collected 2003–13). We did a genome-wide association analyses in terms of progression for 216 TRACK-HD participants and 1773 REGISTRY participants, then a meta-analysis of these results was undertaken. Findings Longitudinal motor, cognitive, and imaging scores were correlated with each other in TRACK-HD participants, justifying use of a single, cross-domain measure of disease progression in both studies. The TRACK-HD and REGISTRY progression measures were correlated with each other (r=0·674), and with age at onset (TRACK-HD, r=0·315; REGISTRY, r=0·234). The meta-analysis of progression in TRACK-HD and REGISTRY gave a genome-wide significant signal (p=1·12 × 10−10) on chromosome 5 spanning three genes: MSH3, DHFR, and MTRNR2L2. The genes in this locus were associated with progression in TRACK-HD (MSH3 p=2·94 × 10−8 DHFR p=8·37 × 10−7 MTRNR2L2 p=2·15 × 10−9) and to a lesser extent in REGISTRY (MSH3 p=9·36 × 10−4 DHFR p=8·45 × 10−4 MTRNR2L2 p=1·20 × 10−3). The lead single nucleotide polymorphism (SNP) in TRACK-HD (rs557874766) was genome-wide significant in the meta-analysis (p=1·58 × 10−8), and encodes an aminoacid change (Pro67Ala) in MSH3. In TRACK-HD, each copy of the minor allele at this SNP was associated with a 0·4 units per year (95% CI 0·16–0·66) reduction in the rate of change of the Unified Huntington's Disease Rating Scale (UHDRS) Total Motor Score, and a reduction of 0·12 units per year (95% CI 0·06–0·18) in the rate of change of UHDRS Total Functional Capacity score. These associations remained significant after adjusting for age of onset. Interpretation The multidomain progression measure in TRACK-HD was associated with a functional variant that was genome-wide significant in our meta-analysis. The association in only 216 participants implies that the progression measure is a sensitive reflection of disease burden, that the effect size at this locus is large, or both. Knockout of Msh3 reduces somatic expansion in Huntington's disease mouse models, suggesting this mechanism as an area for future therapeutic investigation

Determinants of the Proton Selectivity of the Colicin A Channel

International audienceThe channel formed by colicin A in planar lipid bilayers has an outsized selectivity for protons compared to any other ion, even though it allows large ions, such as tetraethylammonium, to permeate readily. A mechanism to account for this discrepancy remains obscure. We considered that protons may traverse a separate pathway but were unable to find any evidence for one. Manipulations that interfere with ionic conduction, such as replacing some of the water in the pore with a nonelectrolyte, reduce the proton current along with the ionic current. Lipids have been proposed to play a structural role in the channel, but we found that the proton selectivity was unaffected by various gross changes in the lipid composition of the bilayer, effectively ruling out any specific effect of lipids in the selectivity and offering no support for their role in structure. The 10-helix channel-forming domains of colicins Ia and E1 are structurally homologous to that of colicin A but do not select so remarkably for protons; thus we were able to use them to probe for the regions responsible for the high selectivity. Using hybrids made by helix swapping among these proteins, we found that the anomalous selectivity could be localized to the five C-terminal helices of colicin A

Intracellular Immunization of Prokaryotic Cells against a Bacteriotoxin

Intracellularly expressed antibodies have been designed to bind and inactivate target molecules inside eukaryotic cells. Here we report that an antibody fragment can be used to probe the periplasmic localization of the colicin A N-terminal domain. Colicins form voltage-gated ion channels in the inner membrane of Escherichia coli. To reach their target, they bind to a receptor located on the outer membrane and then are translocated through the envelope. The N-terminal domain of colicins is involved in the translocation step and therefore is thought to interact with proteins of the translocation system. To compete with this system, a single-chain variable fragment (scFv) directed against the N-terminal domain of the colicin A was synthesized and exported into the periplasmic space of E. coli. The periplasmic scFv inhibited the lethal activity of colicin A and had no effect on the lethal activity of other colicins. Moreover, the scFv was able to specifically inactivate hybrid colicins possessing the colicin A N-terminal domain without affecting their receptor binding. Hence, the periplasmic scFv prevents the translocation of colicin A and probably its interaction with import machinery. This indicates that the N-terminal domain of the toxin is accessible in the periplasm. Moreover, we show that production of antibody fragments to interfere with a biological function can be applied to prokaryotic systems

Integration of the colicin A pore-forming domain into the cytoplasmic membrane of Escherichia coli 1 1Edited by I. B. Holland

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The C-terminal half of the colicin A pore-forming domain is active in vivo and in vitro11Edited by I. B. Holland

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A single amino acid substitution can restore the solubility of aggregated colicin A mutants in Escherichia coli.

International audienceMutants of colicin A have been prepared in which the three tryptophan residues (Trp86, Trp130 and Trp140), localized in the C-terminal domain of the soluble wild-type protein, have been substituted by phenylalanine. The Trp140Phe single mutation had the effect of decreasing the percentage of protein that is expressed as insoluble aggregates. The created hydrophobic cavity decreased the stability of the protein during its folding, resulting in partial aggregation in the cytoplasm of the Escherichia coli-producing cells. Aggregation was increased when Trp140 was substituted by Lys, Leu or Cys, or if the Trp140 mutation was combined with the Trp86Phe and/or Trp130Phe mutations. A single mutation, Lys113Phe, however, was able to restore the solubility of the aggregated mutants in vivo. Detailed analysis of the 3-D structure of the C-terminal domain of colicin A suggests that filling of the hydrophobic cavity is responsible for this effect

The role of electrostatic charge in the membrane insertion of colicin A. Calculation and mutation

International audienceThe bacterial toxin colicin A binds spontaneously to the surfaces of negatively charged membranes. The surface-bound toxin must subsequently, however, become an acidic 'molten globule' before it can fully insert into the lipid bilayer. Clearly, electrostatic interactions must play a significant role in both events. The electrostatic field around the toxin in solution was calculated using the finite-difference Poisson-Boltzmann method of the Delphi programme and the known X-ray structure. A large positively charged surface was identified which could be involved in the binding of colicin to negatively charged membranes. The applicability of the result was tested by also calculating the fields around modelled structures of the closely related colicins B and N. Surprisingly, colicin N showed a similar charge distribution in spite of its isoelectric point of pI 10.20 (colicin A has pI 5.44). One reason for this is the strong conservation of certain negative charges in all colicins. There is a single highly conserved aspartate residue (Asp78) on the positively charged face which provides a small but discrete region of negative charge. This residue, Asp78, was replaced by asparagine in the mutant D78N. D78N binds faster to negatively charged vesicles but inserts only half as fast as the wild-type protein into the membrane core. This indicates that, first, the initial membrane binding has a significant electrostatic component and, second, that the isolated charge on Asp78 plays a role in the formation of the insertion intermediate

Lower-limb and whole-body tissue composition assessment in healthy active older women

International audienceZIEL: Die Studie untersuchte bei aktiven älteren Frauen die Genauigkeit und den Messfehler anthropometrischer und bioelektrischer Impedanzanalysen (BIA) von Messungen der Unterschenkel- und Ganzkörperzusammensetzung, wobei die Dual-energy Röntgenabsorptionsspektrometrie (dual-energy X-ray absorptiometry, DEXA) als Referenzmethode herangezogen wurde. METHODEN: 19 Personen (66,1 ± 4,2 Jahre) nahmen an der Untersuchung teil. Ganzkörperfettmasse (FM) und fettfreie Masse (FFM) wurden mittels Anthropometrie, BIA und DEXA bestimmt. Unterschenkelvolumen (lower-limb volume, LLV) und Unterschenkel FFM (LLFFM) wurden mittels Anthropometrie und DEXA bestimmt. ERGEBNISSE: LLV und LLFFM wurden bei Verwendung der Anthropometrie im Vergleich zu DEXA signifikant überschätzt (p0,25, p 0.25, p 0,25, p0,25 p<0,05]. On n'observe pas de différence significative entre MGA (A = anthropométrie) par rapport à la MGADX et entre MMA par rapport à MMADX et on observe des corrélations significatives [respectivement R2 = 0,93 p<0,001 coefficient de variation CV = 7,3% et R2 = 0,85 p<0,001, CV = 4,4%]. On n'observe pas de différence significative entre MGAIB et MGADX et une corrélation significative existe entre les deux mesures [R2 = 0,80, p<0,001, CV = 11, 6%]. La MM est significativement sous estimée par l'AIB par rapport à l'ADX. CONCLUSION: Chez les femmes âgées actives, (i) l'anthropométrie surestime le VMI et la MMMI par rapport à l'ADX ; (ii) l'anthropométrie peut être une méthode précise de la mesure de la composition corporelle et (iii) en dépit d'un écart non significatif pour les mesures de la MG, l'AIB tend à surestimer la MG et sous estimer la MM