Genome sequencing of the plant pathogen Taphrina deformans, the causal agent of peach leaf curl.

Taphrina deformans is a fungus responsible for peach leaf curl, an important plant disease. It is phylogenetically assigned to the Taphrinomycotina subphylum, which includes the fission yeast and the mammalian pathogens of the genus Pneumocystis. We describe here the genome of T. deformans in the light of its dual plant-saprophytic/plant-parasitic lifestyle. The 13.3-Mb genome contains few identifiable repeated elements (ca. 1.5%) and a relatively high GC content (49.5%). A total of 5,735 protein-coding genes were identified, among which 83% share similarities with other fungi. Adaptation to the plant host seems reflected in the genome, since the genome carries genes involved in plant cell wall degradation (e.g., cellulases and cutinases), secondary metabolism, the hallmark glyoxylate cycle, detoxification, and sterol biosynthesis, as well as genes involved in the biosynthesis of plant hormones. Genes involved in lipid metabolism may play a role in its virulence. Several locus candidates for putative MAT cassettes and sex-related genes akin to those of Schizosaccharomyces pombe were identified. A mating-type-switching mechanism similar to that found in ascomycetous yeasts could be in effect. Taken together, the findings are consistent with the alternate saprophytic and parasitic-pathogenic lifestyles of T. deformans. IMPORTANCE: Peach leaf curl is an important plant disease which causes significant losses of fruit production. We report here the genome sequence of the causative agent of the disease, the fungus Taphrina deformans. The genome carries characteristic genes that are important for the plant infection process. These include (i) proteases that allow degradation of the plant tissues; (ii) secondary metabolites which are products favoring interaction of the fungus with the environment, including the host; (iii) hormones that are responsible for the symptom of severely distorted leaves on the host; and (iv) drug detoxification enzymes that confer resistance to fungicides. The availability of the genome allows the design of new drug targets as well as the elaboration of specific management strategies to fight the disease.

Defining and searching for structural motifs using DeepView/Swiss-PdbViewer.

BACKGROUND: Today, recognition and classification of sequence motifs and protein folds is a mature field, thanks to the availability of numerous comprehensive and easy to use software packages and web-based services. Recognition of structural motifs, by comparison, is less well developed and much less frequently used, possibly due to a lack of easily accessible and easy to use software. RESULTS: In this paper, we describe an extension of DeepView/Swiss-PdbViewer through which structural motifs may be defined and searched for in large protein structure databases, and we show that common structural motifs involved in stabilizing protein folds are present in evolutionarily and structurally unrelated proteins, also in deeply buried locations which are not obviously related to protein function. CONCLUSIONS: The possibility to define custom motifs and search for their occurrence in other proteins permits the identification of recurrent arrangements of residues that could have structural implications. The possibility to do so without having to maintain a complex software/hardware installation on site brings this technology to experts and non-experts alike.

Performance of a new gadolinium-based intravascular contrast agent in free-breathing inversion-recovery 3D coronary MRA.

In three-dimensional (3D) coronary magnetic resonance angiography (MRA), the in-flow contrast between the coronary blood and the surrounding myocardium is attenuated as compared to thin-slab two-dimensional (2D) techniques. The application of a gadolinium (Gd)-based intravascular contrast agent may provide an additional source of signal and contrast by reducing T(1blood) and supporting the visualization of more distal or branching segments of the coronary arterial tree. In six healthy adults, the left coronary artery (LCA) system was imaged pre- and postcontrast with a 0.075-mmol/kg bodyweight dose of the intravascular contrast agent B-22956. For imaging, an optimized free-breathing, navigator-gated and -corrected 3D inversion recovery (IR) sequence was used. For comparison, state-of-the-art baseline 3D coronary MRA with T(2) preparation for non-exogenous contrast enhancement was acquired. The combination of IR 3D coronary MRA, sophisticated navigator technology, and B-22956 allowed for an extensive visualization of the LCA system. Postcontrast, a significant increase in both the signal-to-noise ratio (SNR; 46%, P < 0.05) and contrast-to-noise ratio (CNR; 160%, P < 0.01) was observed, while vessel sharpness of the left anterior descending (LAD) artery and the left coronary circumflex (LCX) were improved by 20% (P < 0.05) and 18% (P < 0.05), respectively.

A bio-inspired agent-based programming environment for pervasive platforms

Abstract in English : Ubiquitous Computing is the emerging trend in computing systems. Based on this observation this thesis proposes an analysis of the hardware and environmental constraints that rule pervasive platforms. These constraints have a strong impact on the programming of such platforms. Therefore solutions are proposed to facilitate this programming both at the platform and node levels. The first contribution presented in this document proposes a combination of agentoriented programming with the principles of bio-inspiration (Phylogenesys, Ontogenesys and Epigenesys) to program pervasive platforms such as the PERvasive computing framework for modeling comPLEX virtually Unbounded Systems platform. The second contribution proposes a method to program efficiently parallelizable applications on each computing node of this platform. Résumé en Français : Basée sur le constat que les calculs ubiquitaires vont devenir le paradigme de programmation dans les années à venir, cette thèse propose une analyse des contraintes matérielles et environnementale auxquelles sont soumises les plateformes pervasives. Ces contraintes ayant un impact fort sur la programmation des plateformes. Des solutions sont donc proposées pour faciliter cette programmation tant au niveau de l'ensemble des noeuds qu'au niveau de chacun des noeuds de la plateforme. La première contribution présentée dans ce document propose d'utiliser une alliance de programmation orientée agent avec les grands principes de la bio-inspiration (Phylogénèse, Ontogénèse et Épigénèse). Ceci pour répondres aux contraintes de programmation de plateformes pervasives comme la plateforme PERvasive computing framework for modeling comPLEX virtually Unbounded Systems . La seconde contribution propose quant à elle une méthode permettant de programmer efficacement des applications parallélisable sur chaque noeud de calcul de la plateforme

The ability model of emotional intelligence: Searching for valid measures

Current measures of ability emotional intelligence (EI)--including the well-known Mayer-Salovey-Caruso Emotional Intelligence Test (MSCEIT)--suffer from several limitations, including low discriminant validity and questionable construct and incremental validity. We show that the MSCEIT is largely predicted by personality dimensions, general intelligence, and demographics having multiple R's with the MSCEIT branches up to .66; for the general EI factor this relation was even stronger (Multiple R = .76). As concerns the factor structure of the MSCEIT, we found support for four first-order factors, which had differential relations with personality, but no support for a higher-order global EI factor. We discuss implications for employing the MSCEIT, including (a) using the single branches scores rather than the total score, (b) always controlling for personality and general intelligence to ensure unbiased parameter estimates in the EI factors, and (c) correcting for measurement error. Failure to account for these methodological aspects may severely compromise predictive validity testing. We also discuss avenues for the improvement of ability-based tests.

Characterization of PhlG, a hydrolase that specifically degrades the antifungal compound 2,4-diacetylphloroglucinol in the biocontrol agent Pseudomonas fluorescens CHA0.

The potent antimicrobial compound 2,4-diacetylphloroglucinol (DAPG) is a major determinant of biocontrol activity of plant-beneficial Pseudomonas fluorescens CHA0 against root diseases caused by fungal pathogens. The DAPG biosynthetic locus harbors the phlG gene, the function of which has not been elucidated thus far. The phlG gene is located upstream of the phlACBD biosynthetic operon, between the phlF and phlH genes which encode pathway-specific regulators. In this study, we assigned a function to PhlG as a hydrolase specifically degrades DAPG to equimolar amounts of mildly toxic monoacetylphloroglucinol (MAPG) and acetate. DAPG added to cultures of a DAPG-negative DeltaphlA mutant of strain CHA0 was completely degraded, and MAPG was temporarily accumulated. In contrast, DAPG was not degraded in cultures of a DeltaphlA DeltaphlG double mutant. To confirm the enzymatic nature of PhlG in vitro, the protein was histidine tagged, overexpressed in Escherichia coli, and purified by affinity chromatography. Purified PhlG had a molecular mass of about 40 kDa and catalyzed the degradation of DAPG to MAPG. The enzyme had a kcat of 33 s(-1) and a Km of 140 microM at 30 degrees C and pH 7. The PhlG enzyme did not degrade other compounds with structures similar to DAPG, such as MAPG and triacetylphloroglucinol, suggesting strict substrate specificity. Interestingly, PhlG activity was strongly reduced by pyoluteorin, a further antifungal compound produced by the bacterium. Expression of phlG was not influenced by the substrate DAPG or the degradation product MAPG but was subject to positive control by the GacS/GacA two-component system and to negative control by the pathway-specific regulators PhlF and PhlH.

Thrombin-sensitive dual fluorescence imaging and therapeutic agent for detection and treatment of synovial inflammation in murine rheumatoid arthritis.

We have developed a thrombin-sensitive polymeric photosensitizer prodrug (T-PS) to selectively image and eradicate inflammatory lesions in rheumatoid arthritis (RA). Thrombin is a serine protease up-regulated in synovial tissues of rheumatoid arthritis (RA) patients. T-PS consists of a polymeric backbone, to which multiple photosensitizer (PS) units are tethered via short thrombin-cleavable peptide linkers. Fluorescence emission and phototoxicity of the prodrug are efficiently quenched due to the interaction of neighboring photosensitizer units. The prodrug is passively delivered to the inflammation site via the enhanced permeability and retention (EPR) effect. Subsequent site-selective proteolytic cleavage of the peptide linkers restores its photoactivity by increasing the mutual distance between PS. Whole animal imaging in murine collagen-induced arthritis, an experimental model of RA revealed a dose-dependent fluorescence increase in arthritic paws after systemic prodrug injection. In addition, administration of T-PS resulted in much higher fluorescence selectivity for arthritic joints as compared to the free PS. Irradiation of the arthritic joints induced light dose dependent phototoxic effects such as apoptosis, vascular damage and local hemorrhage. Long-term observations showed complete regression of the latter. Irradiated non-arthritic tissues or non-irradiated arthritic tissues showed no histological effects after photodynamic therapy with T-PS. This illustrates that T-PS can localize inflammatory lesions with excellent selectivity and induce apoptosis and vascular shut down after irradiation.

Postmortem angiography after vascular perfusion with diesel oil and a lipophilic contrast agent.

OBJECTIVE: The objective of our study was to establish optimal perfusion conditions for high-resolution postmortem angiography that would permit dynamic visualization of the arterial and venous systems. MATERIALS AND METHODS: Cadavers of two dogs and one cat were perfused with diesel oil through a peristaltic pump. The lipophilic contrast agent Lipiodol Ultra Fluide was then injected, and angiography was performed. The efficiency of perfusion was evaluated in the chick chorioallantoic membrane. RESULTS: Vessels could be seen up to the level of the smaller supplying and draining vessels. Hence, both the arterial and the venous sides of the vascular system could be distinguished. The chorioallantoic membrane assay revealed that diesel oil enters microvessels up to 50 microm in diameter and that it does not penetrate the capillary network. CONCLUSION: After establishing a postmortem circulation by diesel oil perfusion, angiography can be performed by injection of Lipiodol Ultra Fluide. The resolution of the images obtained up to 3 days after death is comparable to that achieved in clinical angiography.

A pilot study on ocular safety and efficacy of infliximab as an antifibrotic agent after experimental filtration surgery

Purpose To evaluate the safety and efficacy of infliximab as an antifibrotic agent after experimental glaucoma filtration surgery in rabbits. Methods In a randomized, prospective, masked-observer study, 30 New Zealand Albino rabbits underwent glaucoma filtration surgery. The animals were allocated to receive either intraoperative application of infliximab (group A) or mitomycin C (MMC) at a concentration of 0.2mg/ml (group B) or balanced salt solution (BSS, control)(group C). Different infliximab doses, namely 1.0mg, 2.0mg, 3.0mg, 4.0mg, 5.0mg in 0.1ml were applied. Bleb survival and characteristics were evaluated over a 30day period. The animals were killed on postoperative day 15 and 30. Histology of the operated eyes was performed to evaluate and grade the amount of scarring in each group.Cellular density was evaluated in each case. Results Infliximab did not appear to improve the outcome of filtration surgery in this model of glaucoma filtration surgery.There was a significant decrease in cellular density in the MMC group compared to the control group (p=0.0352). There was neither a significant decrease in cellular density between the infliximab group and the control group nor between the infliximab group and the MMC group. Overall there was no difference in terms of fibrosis between the three different groups. There was slightly less inflammation in the infliximab group, but not significant. Conclusions In this study intraoperative application of infliximab does not appear to be superior to the application of MMC or a control with regard to bleb survival and fibrosis. This study however demonstrates that intraoperative application of MMC significantly reduces the cellular density of the filtration bleb.

Systematic assessment of factors influencing preferences of crohn's disease patients in selecting an anti-tumor necrosis factor agent (CHOOSE TNF TRIAL).

BACKGROUND: Infliximab (IFX), adalimumab (ADA), and certolizumab pegol (CZP) have similar efficacy in induction and maintenance of clinical remission in Crohn's disease (CD). Given the comparable nature of these drugs, patient preferences may influence the choice of the product. We aimed to identify factors that may contribute to CD patients' decision in selecting one anti-tumor necrosis factor (TNF) agent over the others. METHODS: A prospective survey was performed among anti-TNF-naïve CD patients. Prior to completion of a questionnaire, patients were provided with a written description of the three anti-TNF agents, focusing on indications, mode of administration, side effects, and scientific evidence of efficacy and safety for each drug. RESULTS: One hundred patients (47 females, mean age 45 ± 16 years, range 19-81) with an ileal, colonic, or ileocolonic (33%, 40%, and 27%, respectively) disease location completed the questionnaire. Based on the information provided, 36% of patients preferred ADA, 28% CZP, and 25% IFX, whereas 11% were undecided. The patients' decision in selecting a specific anti-TNF drug was influenced by the following factors: ease of use (69%), time required for therapy (34%), time interval between application of the drug (31%), scientific evidence for efficacy (19%), and fear of syringes (10%). CONCLUSIONS: The majority of patients preferred anti-TNF medications that were administered by subcutaneous injection rather than by intravenous infusion. Ease of use and time required for therapy were two major factors influencing the patients' selection of a specific anti-TNF drug. Patients' individual preferences should be taken into account when prescribing anti-TNF drugs. (Inflamm Bowel Dis 2012).

Regulation of mucoidy in the biological control agent Pseudomonas fluorescens CHA0 and construction of an exopolysaccharide-overproducing variant

Pseudomonas fluorescens CHA0, an effective biological control agent of soilborne plant diseases, is naturally non-mucoid. We have isolated a highly mucoid Tn5 insertion mutant of strain CHA0. The mucoid phenotype was found to be due to the overproduction of exopolysaccharide (EPS), as a result of a mutation in the mucA gene. The wild-type mucA gene was cloned by a two-step, Tn5-dependent cloning procedure previously described and the deduced amino acid sequence showed 71% identity with MucA of P. aeruginosa, a negative regulator of the alternative sigma factor AlgU (=s22, sE). As in P. aeruginosa, mucA is preceded by the algU gene encoding s22 (91% identity at the amino acid sequence level). A mucA in-frame deletion mutant of CHA0 overproduced EPS and formed mucoid colonies, whereas an algU in-frame deletion mutant showed a non-mucoid phenotype. Pyoluteorin, an antibiotic produced by P. fluorescens, was found to be entrapped in EPS of a mucoid mutant. In natural soil, mucoidy negatively affected survival of the bacteria, suggesting that under these conditions the potential to produce abundant EPS does not confer a selective advantage on the bacteria.

Volume-targeted and whole-heart coronary magnetic resonance angiography using an intravascular contrast agent.

PURPOSE: To compare volume-targeted and whole-heart coronary magnetic resonance angiography (MRA) after the administration of an intravascular contrast agent. MATERIALS AND METHODS: Six healthy adult subjects underwent a navigator-gated and -corrected (NAV) free breathing volume-targeted cardiac-triggered inversion recovery (IR) 3D steady-state free precession (SSFP) coronary MRA sequence (t-CMRA) (spatial resolution = 1 x 1 x 3 mm(3)) and high spatial resolution IR 3D SSFP whole-heart coronary MRA (WH-CMRA) (spatial resolution = 1 x 1 x 2 mm(3)) after the administration of an intravascular contrast agent B-22956. Subjective and objective image quality parameters including maximal visible vessel length, vessel sharpness, and visibility of coronary side branches were evaluated for both t-CMRA and WH-CMRA. RESULTS: No significant differences (P = NS) in image quality were observed between contrast-enhanced t-CMRA and WH-CMRA. However, using an intravascular contrast agent, significantly longer vessel segments were measured on WH-CMRA vs. t-CMRA (right coronary artery [RCA] 13.5 +/- 0.7 cm vs. 12.5 +/- 0.2 cm; P < 0.05; and left circumflex coronary artery [LCX] 11.9 +/- 2.2 cm vs. 6.9 +/- 2.4 cm; P < 0.05). Significantly more side branches (13.3 +/- 1.2 vs. 8.7 +/- 1.2; P < 0.05) were visible for the left anterior descending coronary artery (LAD) on WH-CMRA vs. t-CMRA. Scanning time and navigator efficiency were similar for both techniques (t-CMRA: 6.05 min; 49% vs. WH-CMRA: 5.51 min; 54%, both P = NS). CONCLUSION: Both WH-CMRA and t-CMRA using SSFP are useful techniques for coronary MRA after the injection of an intravascular blood-pool agent. However, the vessel conspicuity for high spatial resolution WH-CMRA is not inferior to t-CMRA, while visible vessel length and the number of visible smaller-diameter vessels and side-branches are improved.