Mechanism of hcnA mRNA recognition in the Gac/Rsm signal transduction pathway of Pseudomonas fluorescens.

In the plant-beneficial bacterium Pseudomonas fluorescens CHA0, the expression of antifungal exoproducts is controlled by the GacS/GacA two-component system. Two RNA binding proteins (RsmA, RsmE) ensure effective translational repression of exoproduct mRNAs. At high cell population densities, GacA induces three small RNAs (RsmX, RsmY, RsmZ) which sequester both RsmA and RsmE, thereby relieving translational repression. Here we systematically analyse the features that allow the RNA binding proteins to interact strongly with the 5' untranslated leader mRNA of the P. fluorescens hcnA gene (encoding hydrogen cyanide synthase subunit A). We obtained evidence for three major RsmA/RsmE recognition elements in the hcnA leader, based on directed mutagenesis, RsmE footprints and toeprints, and in vivo expression data. Two recognition elements were found in two stem-loop structures whose existence in the 5' leader region was confirmed by lead(II) cleavage analysis. The third recognition element, which overlapped the hcnA Shine-Dalgarno sequence, was postulated to adopt either an open conformation, which would favour ribosome binding, or a stem-loop structure, which may form upon interaction with RsmA/RsmE and would inhibit access of ribosomes. Effective control of hcnA expression by the Gac/Rsm system appears to result from the combination of the three appropriately spaced recognition elements.

Iowa Department of Transportation Major Items - Preliminary Quantity Report, January 20, 2016; With Addendums

Weekly letting report

Heavy metal ions are potent inhibitors of protein folding.

Environmental and occupational exposure to heavy metals such as cadmium, mercury and lead results in severe health hazards including prenatal and developmental defects. The deleterious effects of heavy metal ions have hitherto been attributed to their interactions with specific, particularly susceptible native proteins. Here, we report an as yet undescribed mode of heavy metal toxicity. Cd2+, Hg2+ and Pb2+ proved to inhibit very efficiently the spontaneous refolding of chemically denatured proteins by forming high-affinity multidentate complexes with thiol and other functional groups (IC(50) in the nanomolar range). With similar efficacy, the heavy metal ions inhibited the chaperone-assisted refolding of chemically denatured and heat-denatured proteins. Thus, the toxic effects of heavy metal ions may result as well from their interaction with the more readily accessible functional groups of proteins in nascent and other non-native form. The toxic scope of heavy metals seems to be substantially larger than assumed so far.

Lung Function and Risk for Heart Failure Among Older Adults: The Health ABC Study.

BACKGROUND: The impact of abnormal spirometric findings on risk for incident heart failure among older adults without clinically apparent lung disease is not well elucidated.METHODS: We evaluated the association of baseline lung function with incident heart failure, defined as first hospitalization for heart failure, in 2125 participants of the community-based Health, Aging, and Body Composition (Health ABC) Study (age, 73.6 +/- 2.9 years; 50.5% men; 62.3% white; 37.7% black) without prevalent lung disease or heart failure. Abnormal lung function was defined either as forced vital capacity (FVC) or forced expiratory volume in 1(st) second (FEV1) to FVC ratio below lower limit of normal. Percent predicted FVC and FEV1 also were assessed as continuous variables.RESULTS: During follow-up (median, 9.4 years), heart failure developed in 68 of 350 (19.4%) participants with abnormal baseline lung function, as compared with 172 of 1775 (9.7%) participants with normal lung function (hazard ratio [HR] 2.31; 95% confidence interval [CI], 1.74-3.07; P <.001). This increased risk persisted after adjusting for previously identified heart failure risk factors in the Health ABC Study, body mass index, incident coronary heart disease, and inflammatory markers (HR 1.83; 95% CI, 1.33-2.50; P <.001). Percent predicted (%) FVC and FEV 1 had a linear association with heart failure risk (HR 1.21; 95% CI, 1.11-1.32 and 1.18; 95% CI, 1.10-1.26, per 10% lower % FVC and % FEV1, respectively; both P <.001 in fully adjusted models). Findings were consistent in sex and race subgroups and for heart failure with preserved or reduced ejection fraction.CONCLUSIONS: Abnormal spirometric findings in older adults without clinical lung disease are associated with increased heart failure risk. (C) 2011 Elsevier Inc. All rights reserved. The American Journal of Medicine (2011) 124, 334-341

Influence of biocontrol strain Pseudomonas fluorescens CHA0 and its antibiotic overproducing derivative on the diversity of root colonizing pseudomonads

Non-target effects of biocontrol strains of Pseudomonas on the population of resident pseudomonads should be assessed prior to their large scale application in the environment. The rifampicin resistant bacterium P. fluorescens CHA0-Rif and its antibiotic overproducing derivative CHA0-Rif/pME3424 were introduced into soil microcosms and the population of resident pseudomonads colonizing cucumber roots was investigated after 10 and 52 days. Both CHA0-Rif and CHA0-Rif/pME3424 displaced a part of the resident pseudomonad population after 10 days. To investigate the population structure, utilization of 10 carbon sources and production of two exoenzymes was assessed for 5600 individual pseudomonad isolates and 1700 isolates were subjected to amplified ribosomal DNA restriction analysis of the spacer region (spacer-ARDRA). After 10 days, only the proportion of pseudomonads able to degrade -tryptophan was reduced in treatments inoculated with either biocontrol strain. In parallel the phenotypic diversity was reduced. These effects were only observed 10 days after inoculation, and they were similar for inoculation with CHA0-Rif and CHA0-Rif/pME3424. Changes in the population structure of resident pseudomonads on cucumber roots during plant growth were more pronounced than changes due to the inoculants. The inoculants did not affect the genotypic diversity detected with spacer-ARDRA, but the genotypic fingerprints corresponded only partially to the phenotypic profiles. Overall CHA0-Rif had a small and transient impact on the population of resident pseudomonads and the effect was essentially the same for the genetically engineered derivative CHA0-

[Pérouse. Rocca Paolina, Porta Marzia]

Référence bibliographique : Weigert, 341

Quantification of Myocardial Perfusion Using 13N-ammonia PET: a Cross-Comparison Study on Analysis Software Packages - Carimas, PMOD and FlowQuant

Aim. Several software packages (SWP) and models have been released for quantification of myocardial perfusion (MP). Although they all are validated against something, the question remains how well their values agree. The present analysis focused on cross-comparison of three SWP for MP quantification of 13N-ammonia PET studies. Materials & Methods. 48 rest and stress MP 13N-ammonia PET studies of hypertrophic cardiomyopathy (HCM) patients (Sciagrà et al., 2009) were analysed with three SW packages - Carimas, PMOD, and FlowQuant - by three observers blinded to the results of each other. All SWP implement the one-tissue-compartment model (1TCM, DeGrado et al. 1996), and first two - the two-tissue-compartment model (2TCM, Hutchins et al. 1990) as well. Linear mixed model for the repeated measures was fitted to the data. Where appropriate we used Bland-Altman plots as well. The reproducibility was assessed on global, regional and segmental levels. Intraclass correlation coefficients (ICC), differences between the SWPs and between models were obtained. ICC≥0.75 indicated excellent reproducibility, 0.4≤ICC<0.75 indicated fair to good reproducibility, ICC<0.4 - poor reproducibility (Rosner, 2010). Results. When 1TCM MP values were compared, the SW agreement on global and regional levels was excellent, except for Carimas vs. PMOD at RCA: ICC=0.715 and for PMOD vs. FlowQuant at LCX:ICC=0.745 which were good. In segmental analysis in five segments: 7,12,13, 16, and 17 the agreement between all SWP was excellent; in the remaining 12 segments the agreement varied between the compared SWP. Carimas showed excellent agreement with FlowQuant in 13 segments and good in four - 1, 5, 6, 11: 0.687≤ICCs≤0.73; Carimas had excellent agreement with PMOD in 11 segments, good in five_4, 9, 10, 14, 15: 0.682≤ICCs≤0.737, and poor in segment 3: ICC=0.341. PMOD had excellent agreement with FlowQuant in eight segments and substantial-to-good in nine_1, 2, 3, 5, 6,8-11: 0.585≤ICCs≤0.738. Agreement between Carimas and PMOD for 2TCM was good at a global level: ICC=0.745, excellent at LCX (0.780) and RCA (0.774), good at LAD (0.662); agreement was excellent for ten segments, fair-to-substantial for segments 2, 3, 8, 14, 15 (0.431≤ICCs≤0.681), poor for segments 4 (0.384) and 17 (0.278). Conclusions. The three SWP used by different operators to analyse 13N-ammonia PET MP studies provide results that agree well at a global level, regional levels, and mostly well even at a segmental level. Agreement is better for 1TCM. Poor agreement at segments 4 and 17 for 2TCM needs further clarification.

Endocardite infectieuse: mise au point [Infective endocarditis: update]

The pathogenesis of infective endocarditis (IE) is being dissected at the molecular level, which should help redefine new preventive and therapeutic strategies against IE. In spite of improving health care, the incidence of IE has not decreased over the last decades. While classical predisposing conditions such as rheumatic heart disease were being eradicated, new features of IE have emerged. These include IE in intravenous drug users, IE in elderly patients with sclerotic valve disease, prosthetic valve IE and nosocomial IE. The epidemiology, pathogenesis, diagnosis, prevention and treatment of IE are being reviewed in this article.

Le Roman de Renart

F. 1-48. Le Roman de Renart. Le manuscrit, qui a été doté du sigle O dans les différentes éditions, est incomplet de la fin et mixte, proposant une structure relativement inédite. Il a récemment fait l’objet d’une édition critique par Aurélie Barre : Édition critique et littéraire du manuscrit O du « Roman de Renart » ( f. fr. 12583), doctorat, Université Lyon III, 2005. F. 1a-14b. Branche I.F. 1a-7e. [Branche Ia : « Le jugement de Renart »]. « Pierres qui son enging et s’art / Mist es vers faire de Renart…-… Tant qu’il [re]fu en sa santé / Com il avoit devant esté ». – F. 7e-10b. [Branche Ib : « Le Siège de Maupertuis »]. « Messires Nobles l’empereres / Vint au chastel ou Renart ere …-… Et Renart ainsi s’en eschape, / Des or gart bien chascun sa chape ! ». – F. 10b-14b. [Branche Ic : « Renart teinturier, Renart jongleur »]. « Li rois a fait son ban crier, / Par tout plevir et afier …-… Puis fu Renart lonc tens en mue ; / Ne va, ne vient, ne se remue » (éd. Barre, p.117-233, v. 1-3217). . F. 14b-20bBranche II. F. 14b-20b. [Branche II : « Le duel judiciaire »]. « Messires Nobles li lions / O lui avoit toz ses barons …-… Et autre redirai aprés, / A itant de cestui vos lés » (éd. Barre, p. 235-289, v. 1-1522). F. 20b-25c. Branche III.F. 20b-22a. [Branche IIIa : « Renart et Chantecler »]. « Seignors, oï avez maint conte, / Que maint contierres vos aconte …-… Dou coc qui li est eschapez, / Quant il ne s’en est saoulez ». – F. 22a-22f. [Branche IIIb : « Renart et la mésange »]. « Que que cil se plaint et demente, / Atant es vos une mesenge …-… Assez a grant travail eü / de ce dont li est mescheü ». – F. 22f-23c. [Branche IIIc. « Renart et Tibert »]. « Que qu’il se plaint de s’aventure, / Qui li avient et pesme et dure …-… Tornez s’en est a mout grant paine …-… Si com aventure le maine ». – F. 23c-24e. [Branche IIId : « Renart et l’andouille »]. «Renart qui mout sot de treslüe, / Et qui mout ot grant fain eüe …-… Esfondree ert entr’eus la guerre, / Mes ne velt trive ne pes querre ». – F. 24e-25c. [Branche IIIe : « Tibert et les deux prêtres »]. « Thibert li chaz, dont je a dit, / Doute Renart assez petit …-… Qui touz nos a enfantosmez : / A paine en sui vis eschapez ! » (éd. Barre, p. 291-340, v. 1-1265). F. 25c-27d. Branche IV. F. 25c-26a. [Branche IVa : « Renart et Tiercelin »]. « Entre .II. mons, en une plangne / Tout droit au pié d’une montaigne …-… Fuiant s’en va les sauz menuz : / Ses anemis a confonduz ». – F. 26a-27d. [Branche IVb : « Le viol d’Hersent »]. « Cis plaiz fu ainsi deffinez / Et Renars s’est acheminez …-… Et est venuz a sa mesnie / Qui soz la roche est entasnie » (éd. Barre, p. 341-359, v. 1-524). F. 27d-29d. Branche V. [« Renart et les anguilles »]. « Seignors, ce fu en cest termine / Que li douz tens d’esté decline …-…Que de Renart se vengera / Ne jamés jor ne l’amera » (éd. Barre, p. 361-378, v. 1-514). F. 29d-31e. Branche VI. [« Le puits »]. « Prime covient tel chose dire / Dont je vos puisse faire rire …-… Et il le puet prandre en sa marge, / Sachiez qu’i li fera domage ! » (éd. Barre, p. 379-396, v. 1-537).. 31e-39c. Branche VII. F. 31e-32e. [Branche VIIa : « Le jambon enlevé »]. « [U]n jour issit hors de la lande / Isengrins por querre viande …-… .XV. jours va a grant baudour, / Onques Renars n’i fist sejour ». – F. 32c-32e. [Branche VIIb : « Renart et le grillon »]. « Renart s’en va tout son chemin. / Or veut (en) engignier Isengrin …-… Tornez s’en est grant aleüre / Et vet aillors querre droiture ». – F. 32e-36e. [Branche VIIc : « L’Escondit »]. « Atant s’apense d’une chose / Dont il sa fame sovent chose …-…Tant defoulé et tant batu / Qu’a Malpertuis l’ont enbatu ». – F. 36e-39c. [Branche VIId : « La confession de Renart »]. « Foux est qui croit sa male pense : / Mout remaint de ce que fox panse …-…L’escofle lor donne a mengier, / Qu’il en avoient grant mestier (éd. Barre, p. 397-470, v. 1-1960). F. 36c-48e. Branche VIII. [« Renart et Liétart »]. « Uns prestres de la Croiz en Brie, / Que Damediex doint bone vie …-… Ou au chiés ou a la parclose, / Qui n’est aüsés de la chose » (éd. Barre, p. 471-554, v. 1-2470). F. 48e. Branche IX (v. 1-86). [« Les Vêpres de Tibert »]. « Oiez une novele estoire / Qui bien doit estre en mémoire …-… Jel conterai a Hameline, / La foi et la reconnoissance… » (éd. Barre, p. 555-557, v. 1-85).

Detection and chemical profiling of medicine counterfeits by Raman spectroscopy and chemometrics

Raman spectroscopy combined with chemometrics has recently become a widespread technique for the analysis of pharmaceutical solid forms. The application presented in this paper is the investigation of counterfeit medicines. This increasingly serious issue involves networks that are an integral part of industrialized organized crime. Efficient analytical tools are consequently required to fight against it. Quick and reliable authentication means are needed to allow the deployment of measures from the company and the authorities. For this purpose a method in two steps has been implemented here. The first step enables the identification of pharmaceutical tablets and capsules and the detection of their counterfeits. A nonlinear classification method, the Support Vector Machines (SVM), is computed together with a correlation with the database and the detection of Active Pharmaceutical Ingredient (API) peaks in the suspect product. If a counterfeit is detected, the second step allows its chemical profiling among former counterfeits in a forensic intelligence perspective. For this second step a classification based on Principal Component Analysis (PCA) and correlation distance measurements is applied to the Raman spectra of the counterfeits.

Novel method to estimate the phenotypic variation explained by genome-wide association studies reveals large fraction of the missing heritability.

Genome-wide association studies (GWAS) are conducted with the promise to discover novel genetic variants associated with diverse traits. For most traits, associated markers individually explain just a modest fraction of the phenotypic variation, but their number can well be in the hundreds. We developed a maximum likelihood method that allows us to infer the distribution of associated variants even when many of them were missed by chance. Compared to previous approaches, the novelty of our method is that it (a) does not require having an independent (unbiased) estimate of the effect sizes; (b) makes use of the complete distribution of P-values while allowing for the false discovery rate; (c) takes into account allelic heterogeneity and the SNP pruning strategy. We applied our method to the latest GWAS meta-analysis results of the GIANT consortium. It revealed that while the explained variance of genome-wide (GW) significant SNPs is around 1% for waist-hip ratio (WHR), the observed P-values provide evidence for the existence of variants explaining 10% (CI=[8.5-11.5%]) of the phenotypic variance in total. Similarly, the total explained variance likely to exist for height is estimated to be 29% (CI=[28-30%]), three times higher than what the observed GW significant SNPs give rise to. This methodology also enables us to predict the benefit of future GWA studies that aim to reveal more associated genetic markers via increased sample size.