Neutron structure of type-III antifreeze protein allows the reconstruction of AFP-ice interface.

Antifreeze proteins (AFPs) inhibit ice growth at sub-zero temperatures. The prototypical type-III AFPs have been extensively studied, notably by X-ray crystallography, solid-state and solution NMR, and mutagenesis, leading to the identification of a compound ice-binding surface (IBS) composed of two adjacent ice-binding sections, each which binds to particular lattice planes of ice crystals, poisoning their growth. This surface, including many hydrophobic and some hydrophilic residues, has been extensively used to model the interaction of AFP with ice. Experimentally observed water molecules facing the IBS have been used in an attempt to validate these models. However, these trials have been hindered by the limited capability of X-ray crystallography to reliably identify all water molecules of the hydration layer. Due to the strong diffraction signal from both the oxygen and deuterium atoms, neutron diffraction provides a more effective way to determine the water molecule positions (as D(2) O). Here we report the successful structure determination at 293 K of fully perdeuterated type-III AFP by joint X-ray and neutron diffraction providing a very detailed description of the protein and its solvent structure. X-ray data were collected to a resolution of 1.05 Å, and neutron Laue data to a resolution of 1.85 Å with a "radically small" crystal volume of 0.13 mm(3). The identification of a tetrahedral water cluster in nuclear scattering density maps has allowed the reconstruction of the IBS-bound ice crystal primary prismatic face. Analysis of the interactions between the IBS and the bound ice crystal primary prismatic face indicates the role of the hydrophobic residues, which are found to bind inside the holes of the ice surface, thus explaining the specificity of AFPs for ice versus water.

Evaluation des résultats du traitement chirurgical des luxations acromio-claviculaires de type III selon un score cinématique

Introduction : Le traitement des entorses acromio-claviculaires (AC) est aujourd'hui encore controversé. Les luxations AC avec lésion du fascia delto-trapézoidale (grade IV, V et VI) sont généralement traitées par une chirurgie de stabilisation. A l'inverse les entorses sans luxation de la clavicule (grade I et II) sont traitées conservativement avec de bons résultats. Il reste une interrogation concernant le traitement des luxations AC sans lésion du fascia delto-trapézoidale (grade III). Le but de notre étude est d'évaluer les résultats du traitement chirurgical des entorses AC de grade III selon un score cinématique. Matériel et Méthode : 30 patients avec une entorse AC de grade III ont été opérés d'une stabilisation de la clavicule entre 2003 et 2011 par le service d'Orthopédie et traumatologie du CHUV. Tous ont été cliniquement évalués selon le score de Constant. L'évaluation cinématique a été effectuée à l'aide d'un iPod touch, fixé sur l'humérus. Cet outil de mesure, décrit et validé par l'EPFL, prend en considération l'accélération et la vitesse angulaire du membre supérieur pour 7 différents mouvements des deux bras. L'évaluation cinématique a été effectuée en comparant le côté opéré par rapport au côté sain selon 2 scores (RAV et P) provenant de ces variables. Les scores RAV et P sont calculés par l'application installée sur l'iPod touch, ils sont donnés en pourcentage par rapport à l'épaule saine. Nous avons défini un score de Constant relatif de plus de 60 et un score cinématique de plus de 75% comme satisfaisant. Résultats : Nous avons revus dix patients avec un recul moyen de 36 mois (6 à 72 mois) d'un âge moyen de 42 ans (27 à 62 ans). Le score de Constant moyen est de 75.9 ± 21.7. Le score P moyen est de 89.3% ± 23.4 et le score RAV moyen est de 91.8% ± 15.8 (tab.1). Quatre sujets obtiennent un excellent score de Constant pour le bras opéré, 2 sujets obtiennent un bon score et un sujet obtient un score moyen, tandis que 3 sujets obtiennent un mauvais score. Huit patients obtiennent un score cinématique satisfaisant alors que nous observons 2 résultats non satisfaisants. Les mauvais résultats tant cliniques que cinématiques ont été observés chez des patients travailleurs de force, nécessitant d'effectuer des mouvements de l'épaule au-dessus du niveau du buste. Discussion et Conclusion : Sur la base d'une évaluation clinique et cinématique, le traitement chirugical des entorses AC de grade III donne des résultats satisfaisants. Notre étude ne comportant pas de groupe contrôle et notre série étant non homogène, avec un nombre limité de sujet, nous ne pouvons conclure que le traitement chirurgical est le traitement le mieux adapté aux patients avec une entorse acromio-claviculaires de type III. Nous recommandons toutefois un traitement chirugical chez les patients actifs, et les patients exerçant un métier avec nécessité de mobilisation de l'épaule au dessus du buste. Un travail manuel lourd représente un facteur de mauvais pronostic.

The development of decision limits for the GH-2000 detection methodology using additional insulin-like growth factor-I and amino-terminal pro-peptide of type III collagen assays.

The GH-2000 and GH-2004 projects have developed a method for detecting GH misuse based on measuring insulin-like growth factor-I (IGF-I) and the amino-terminal pro-peptide of type III collagen (P-III-NP). The objectives were to analyze more samples from elite athletes to improve the reliability of the decision limit estimates, to evaluate whether the existing decision limits needed revision, and to validate further non-radioisotopic assays for these markers. The study included 998 male and 931 female elite athletes. Blood samples were collected according to World Anti-Doping Agency (WADA) guidelines at various sporting events including the 2011 International Association of Athletics Federations (IAAF) World Athletics Championships in Daegu, South Korea. IGF-I was measured by the Immunotech A15729 IGF-I IRMA, the Immunodiagnostic Systems iSYS IGF-I assay and a recently developed mass spectrometry (LC-MS/MS) method. P-III-NP was measured by the Cisbio RIA-gnost P-III-P, Orion UniQ? PIIINP RIA and Siemens ADVIA Centaur P-III-NP assays. The GH-2000 score decision limits were developed using existing statistical techniques. Decision limits were determined using a specificity of 99.99% and an allowance for uncertainty because of the finite sample size. The revised Immunotech IGF-I - Orion P-III-NP assay combination decision limit did not change significantly following the addition of the new samples. The new decision limits are applied to currently available non-radioisotopic assays to measure IGF-I and P-III-NP in elite athletes, which should allow wider flexibility to implement the GH-2000 marker test for GH misuse while providing some resilience against manufacturer withdrawal or change of assays. Copyright © 2015 John Wiley & Sons, Ltd.

A descriptive study on the surgery and the microbiology of Gustilo type III fractures in an university hospital in Switzerland.

OBJECTIVE: To describe the epidemiology, the surgical treatment, the microbiology, the antibiotic prophylaxis and the outcome of patients with the most severe type of open fractures. METHODS: Retrospective chart reviews of patients with Gustilo type III open fracture admitted to an university hospital in Switzerland between January 2007 and December 2011. The patient's and fracture's characteristics, surgery, antibiotic prophylaxis, and microbiology findings at the initial and at the revision surgery were described. RESULTS: Thirty patients were included (83% male, mean age 41 years). More than half of the patients had polytrauma. In all patients, debridement and stabilization surgery (70% using external fixation) were performed at admission. Soft tissue reconstruction was performed in 87% and in 23% immediate bone graft was performed. Antibiotic prophylaxis were given in all patients for a median duration of 9 days (60% received amoxicillin/clavulanic acid). Positive bacterial culture was found in 53% of the patients at initial surgery and in 88% at revision surgery. At initial and revision surgery, 47% and 88% of the pathogens were amoxicillin/clavulanic acid-resistant. Treatment outcome was favorable in 24 of 30 patients (80%) and in six cases (20%) an amputation had to be performed. None of the patients had chronic bone infection. CONCLUSIONS: Positive cultures were found often in open fractures. Amoxicillin/clavulanic acid which is often mentioned in many guidelines as prophylaxis in open fractures does not cover the most common isolated organisms. The combination of surgery and antibiotic prophylaxis leads to good outcome in Gustilo type III fracture.

The awr gene family encodes a novel class of Ralstonia solanacearum type III effectors displaying virulence and avirulence activities

We present here the characterization of a new gene family, awr, found in all sequenced Ralstonia solanacearum strains and in other bacterial pathogens. We demonstrate that the five paralogues in strain GMI1000 encode type III-secreted effectors and that deletion of all awr genes severely impairs its capacity to multiply in natural host plants. Complementation studies show that the AWR (alanine-tryptophanarginine tryad) effectors display some functional redundancy, although AWR2 is the major contributor to virulence. In contrast, the strain devoid of all awr genes (¿awr1-5) exhibits enhanced pathogenicity on Arabidopsis plants. A gain-of-function approach expressing AWR in Pseudomonas syringae pv. tomato DC3000 proves that this is likely due to effector recognition, because AWR5 and AWR4 restrict growth of this bacterium in Arabidopsis. Transient overexpression of AWR in nonhost tobacco species caused macroscopic cell death to varying extents, which, in the case of AWR5, shows characteristics of a typical hypersensitive response. Our work demonstrates that AWR, which show no similarity to any protein with known function, can specify either virulence or avirulence in the interaction of R. solanacearum with its plant hosts.

The calcium-modulated proteins, S100A1 and S100B, as potential regulators of the dynamics of type III intermediate filaments

The Ca2+-modulated, dimeric proteins of the EF-hand (helix-loop-helix) type, S100A1 and S100B, that have been shown to inhibit microtubule (MT) protein assembly and to promote MT disassembly, interact with the type III intermediate filament (IF) subunits, desmin and glial fibrillary acidic protein (GFAP), with a stoichiometry of 2 mol of IF subunit/mol of S100A1 or S100B dimer and an affinity of 0.5-1.0 µM in the presence of a few micromolar concentrations of Ca2+. Binding of S100A1 and S100B results in inhibition of desmin and GFAP assemblies into IFs and stimulation of the disassembly of preformed desmin and GFAP IFs. S100A1 and S100B interact with a stretch of residues in the N-terminal (head) domain of desmin and GFAP, thereby blocking the head-to-tail process of IF elongation. The C-terminal extension of S100A1 (and, likely, S100B) represents a critical part of the site that recognizes desmin and GFAP. S100B is localized to IFs within cells, suggesting that it might have a role in remodeling IFs upon elevation of cytosolic Ca2+ concentration by avoiding excess IF assembly and/or promoting IF disassembly in vivo. S100A1, that is not localized to IFs, might also play a role in the regulation of IF dynamics by binding to and sequestering unassembled IF subunits. Together, these observations suggest that S100A1 and S100B may be regarded as Ca2+-dependent regulators of the state of assembly of two important elements of the cytoskeleton, IFs and MTs, and, potentially, of MT- and IF-based activities.

Collagen content, but not the ratios of collagen type III/I mRNAs, differs among hypertensive, alcoholic, and idiopathic dilated cardiomyopathy

Cardiac interstitial fibrosis may contribute to ventricular dysfunction and the prognosis of patients with dilated cardiomyopathy. The objective of the present study was to determine if total myocardial collagen content and collagen type III/I (III/I ratio) mRNAs differ in hypertensive, alcoholic, and idiopathic dilated cardiomyopathy subjects. Echocardiography and exercise cardiopulmonary testing were performed in patients with idiopathic (N = 22), hypertensive (N = 12), and alcoholic (N = 11) dilated cardiomyopathy. Morphometric analysis of collagen was performed in fragments obtained by endomyocardial biopsy with picrosirius red staining. The collagen III/I ratio was determined by reverse transcription polymerase chain reaction. Samples of controls (N = 10) were obtained from autopsy. Echocardiographic variables and maximal oxygen uptake were not different among dilated cardiomyopathy groups. Collagen was higher in all dilated cardiomyopathy groups (idiopathic, hypertensive and alcoholic, 7.36 ± 1.09%) versus controls (1.12 ± 0.18%), P < 0.05. Collagen was lower in idiopathic dilated cardiomyopathy (4.97 ± 0.83%) than hypertensive (8.50 ± 1.11%) and alcoholic (10.77 ± 2.09%) samples (P < 0.005 for both). The collagen III/I ratio in all samples from dilated cardiomyopathy patients was higher compared to that in controls (0.29 ± 0.04, P < 0.05) but was the same in the samples from idiopathic (0.77 ± 0.07), hypertensive (0.75 ± 0.07), and alcoholic (0.81 ± 0.16) dilated cardiomyopathy groups. Because of the different physical properties of the types of collagen, the higher III/I ratio may contribute to progressive ventricular dilation and dysfunction in dilated cardiomyopathy patients.

A Type-Preserving Compiler from System F to Typed Assembly Language

L'utilisation des méthodes formelles est de plus en plus courante dans le développement logiciel, et les systèmes de types sont la méthode formelle qui a le plus de succès. L'avancement des méthodes formelles présente de nouveaux défis, ainsi que de nouvelles opportunités. L'un des défis est d'assurer qu'un compilateur préserve la sémantique des programmes, de sorte que les propriétés que l'on garantit à propos de son code source s'appliquent également au code exécutable. Cette thèse présente un compilateur qui traduit un langage fonctionnel d'ordre supérieur avec polymorphisme vers un langage assembleur typé, dont la propriété principale est que la préservation des types est vérifiée de manière automatisée, à l'aide d'annotations de types sur le code du compilateur. Notre compilateur implante les transformations de code essentielles pour un langage fonctionnel d'ordre supérieur, nommément une conversion CPS, une conversion des fermetures et une génération de code. Nous présentons les détails des représentation fortement typées des langages intermédiaires, et les contraintes qu'elles imposent sur l'implantation des transformations de code. Notre objectif est de garantir la préservation des types avec un minimum d'annotations, et sans compromettre les qualités générales de modularité et de lisibilité du code du compilateur. Cet objectif est atteint en grande partie dans le traitement des fonctionnalités de base du langage (les «types simples»), contrairement au traitement du polymorphisme qui demande encore un travail substantiel pour satisfaire la vérification de type.

Étude d'un modèle de Gause généralisé avec récolte de proies et fonction de Holling type III généralisée

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal

Effects of resistant starch type III polymorphs on human colon microbiota and short chain fatty acids in human gut models

This study probed the possible effects of type III resistant starch (RS) crystalline polymorphism on RS fermentability by human gut microbiota and the short chain fatty acids production in vitro. Human fecal pH-controlled batch cultures showed RS induces an ecological shift in the colonic microbiota with polymorph B inducing Bifidobacterium spp. and polymorph A inducing Atopobium spp. Interestingly, polymorph B also induced higher butyrate production to levels of 0.79 mM. In addition, human gut simulation demonstrated that polymorph B promotes the growth of bifidobacteria in the proximal part of the colon and double their relative proportion in the microbiota in the distal colon. These findings suggest that RS polymorph B may promote large bowel health. While the findings are limited by study constraints, they do raise the possibility of using different thermal processing to delineate differences in the prebiotic capabilities of RS, especially its butryrogenicity in the human colon.

A novel radix-3/9 algorithm for type-III generalized discrete Hartley transform

A novel radix-3/9 algorithm for type-III generalized discrete Hartley transform (GDHT) is proposed, which applies to length-3(P) sequences. This algorithm is especially efficient in the case that multiplication is much more time-consuming than addition. A comparison analysis shows that the proposed algorithm outperforms a known algorithm when one multiplication is more time-consuming than five additions. When combined with any known radix-2 type-III GDHT algorithm, the new algorithm also applies to length-2(q)3(P) sequences.

A ‘Boscastle-type’ quasi-stationary convective system over the UK Southwest Peninsula

An investigation is presented of a quasi-stationary convective system (QSCS) which occurred over the UK Southwest Peninsula on 21 July 2010. This system was remarkably similar in its location and structure to one which caused devastating flash flooding in the coastal village of Boscastle, Cornwall on 16 August 2004. However, in the 2010 case rainfall accumulations were around four times smaller and no flooding was recorded. The more extreme nature of the Boscastle case is shown to be related to three factors: (1) higher rain rates, associated with a warmer and moister tropospheric column and deeper convective clouds; (2) a more stationary system, due to slower evolution of the large-scale flow; and (3) distribution of the heaviest precipitation over fewer river catchments. Overall, however, the synoptic setting of the two events was broadly similar, suggesting that such conditions favour the development of QSCSs over the Southwest Peninsula. A numerical simulation of the July 2010 event was performed using a 1.5-km grid length configuration of the Met Office Unified Model. This reveals that convection was repeatedly initiated through lifting of low-level air parcels along a quasi-stationary coastal convergence line. Sensitivity tests are used to show that this convergence line was a sea breeze front which temporarily stalled along the coastline due to the retarding influence of an offshore-directed background wind component. Several deficiencies are noted in the 1.5-km model’s representation of the storm system, including delayed convective initiation; however, significant improvements are observed when the grid length is reduced to 500 m. These result in part from an improved representation of the convergence line, which enhances the associated low-level ascent allowing air parcels to more readily reach their level of free convection. The implications of this finding for forecasting convective precipitation are discussed.

Genetic Diversity of a Brazilian Strain Collection of Xanthomonas citri subsp citri Based on the Type III Effector Protein Genes

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)