The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

The SWISS-PROT protein knowledgebase (http://www.expasy.org/sprot/ and http://www.ebi.ac.uk/swissprot/) connects amino acid sequences with the current knowledge in the Life Sciences. Each protein entry provides an interdisciplinary overview of relevant information by bringing together experimental results, computed features and sometimes even contradictory conclusions. Detailed expertise that goes beyond the scope of SWISS-PROT is made available via direct links to specialised databases. SWISS-PROT provides annotated entries for all species, but concentrates on the annotation of entries from human (the HPI project) and other model organisms to ensure the presence of high quality annotation for representative members of all protein families. Part of the annotation can be transferred to other family members, as is already done for microbes by the High-quality Automated and Manual Annotation of microbial Proteomes (HAMAP) project. Protein families and groups of proteins are regularly reviewed to keep up with current scientific findings. Complementarily, TrEMBL strives to comprise all protein sequences that are not yet represented in SWISS-PROT, by incorporating a perpetually increasing level of mostly automated annotation. Researchers are welcome to contribute their knowledge to the scientific community by submitting relevant findings to SWISS-PROT at [email protected]

Rhizosheath-root system changes exopolysaccharide content but stabilizes bacterial community across contrasting seasons in a desert environment

Abstract Background In hot deserts daily/seasonal fluctuations pose great challenges to the resident organisms. However, these extreme ecosystems host unique microenvironments, such as the rhizosheath–root system of desert speargrasses in which biological activities and interactions are facilitated by milder conditions and reduced fluctuations. Here, we examined the bacterial microbiota associated with this structure and its surrounding sand in the desert speargrass Stipagrostis pungens under the contrasting environmental conditions of summer and winter in the Sahara Desert. Results The belowground rhizosheath–root system has higher nutrient and humidity contents, and cooler temperatures than the surrounding sand. The plant responds to the harsh environmental conditions of the summer by increasing the abundance and diversity of extracellular polymeric substances (EPS) compared to the winter. On the contrary, the bacterial community associated with the rhizosheath–root system and its interactome remain stable and, unlike the bulk sand, are unaffected by the seasonal environmental variations. The rhizosheath–root system bacterial communities are consistently dominated by Actinobacteria and Alphaproteobacteria and form distinct bacteria communities from those of bulk sand in the two seasons. The microbiome-stabilization mediated by the plant host acts to consistently retain beneficial bacteria with multiple plant growth promoting functions, including those capable to produce EPS, which increase the sand water holding capacity ameliorating the rhizosheath micro-environment. Conclusions Our results reveal the capability of plants in desert ecosystems to stabilize their below ground microbial community under seasonal contrasting environmental conditions, minimizing the heterogeneity of the surrounding bulk sand and contributing to the overall holobiont resilience under poly-extreme conditions

The pathophysiology of allergic bronchoconstriction in conscious guinea pigs

Pulmonary resistance was measured in conscious, spontaneously breathing guinea pigs sensitized to horseradish peroxidase before and during 2 aerosolized challenges with this antigen. The first challenge was administered to ensure that all animals were sensitized. A second challenge was administered 10-30 minute later, with the animal having received either atropine or indomethacin. The increase in resistance during the second challenge was similar to that of the first challenge in the indomethacin treated group, but decreased significantly in the atropine treated group. These results show that vagal reflexes are important in allergic bronchoconstriction and that indomethacin in doses large enough to block the synthesis of prostaglandins had no effect on this model of allergic airway disease

Modalités et résultats du traitement endovasculaire du syndrome cave supérieur d origine bénigne

Objectifs : Évaluer les modalités et les résultats du traitement endovasculaire des syndromes caves supérieurs (SCS) d origine bénigne. Matériel et méthodes : Étude rétrospective monocentrique de 90 patients entre 1995 et 2010 présentant un SCS d origine bénigne et traités par voie endovasculaire. Les principales étiologies sont une complication d un cathéter veineux central (CVC) (n=46) ou d une fistule artério-veineuse (FAV) (n=39). Une angioplastie (ATP) seule (n=20) ou complétée d une endoprothèse (ATP+EP) (n=61) a été pratiquée. Le critère de jugement principal est la survenue d une récidive clinique confirmée par un examen morphologique. Les critères de jugements secondaires sont les taux de perméabilité primaire, assistée et secondaire ainsi que le devenir des patients ayant une atteinte de la veine sous-clavière (VSC) dans le défilé thoraco-brachial. Résultats : Les taux de succès technique et clinique sont de 91.1% et de 87.6 %. Une récidive clinique survient chez 38% des patients, plus fréquente en cas de FAV (p=0.001) ou d atteinte de la VSC dans le défilé thoraco-brachial (p=0.007). Elle est plus fréquente en cas d ATP seule par rapport à une ATP+EP (p=0.06). Les taux de perméabilité primaire, primaire assistée et secondaire sont de 76%, 83% et 93% à un an. La perméabilité primaire est en moyenne de 20.3 mois (+/-2.8 DS). Les antiagrégants plaquettaires ne sont pas associés à une diminution significative du taux de récurrence (p=0.7). Conclusion : Le traitement endovasculaire des SCS d origine bénigne est efficace et peu invasif. Les récidives restent fréquentes, surtout chez les patients ayant une FAV, sans qu une modalité de traitement ne montre de supériorité.Purpose: Evaluate endovascular modalities and results to treat benign superior vena cava syndrome (SCS). Material and methods: From 1995 to 2010, 90 patients with SCS from non malignant cause and treated by endovascular approach at the CHU of Grenoble were retrospectively included. Central venous catheters (CVC) (n=46) or arterio-venous fistulae (AVF) for hemodialysis (n=39) are the most frequent etiologies. Endovascular procedure consists in angioplasty (PTA) (n=20) or angioplasty with stenting (PTS) (n=61). Primary end-point is clinical recurrence confirmed by a morphological exam. Secondary end-points are primary, assisted primary and secondary patency. We isolated patients becoming in case of subclavian vein lesion in thoracic outlet. Results: Technical and clinical success rates are 91.1% and 87.6 %. Recurrence occurs in 38% of patients and are more frequent (p=0.001) in patients with AVF or subclavian vein lesion in thoracic outlet (p=0.007). PTA is associated with higher recurrence rate than PTS, but without significative difference (p=0.06). Primary, assisted primary and secondary patency rates are 76%, 83% and 93% at one year. Mean primary patency is 20.3 months (+/- 2.8 SD). Antiplatelets after procedure are not associated with lower recurrences and could be responsible of hemorrhagic complications (p=0.7). Conclusion: Endovascular treatment of benign SCS is safe and efficient. No modality between angioplasty and stenting is better to prevent clinical recurrence. These are more frequent on AVF dialysed patients, who needed multiple re-interventions.GRENOBLE1-BU Médecine pharm. (385162101) / SudocSudocFranceF

Polaron formation and symmetry breaking

In a molecular semiconductor, a charged molecule experiences a lattice relaxation which reorganizes it into a cation or an anion-radical. This species is not, in general, a polaron. By using calculations of the geometry and the electronic structure both ab initio and at the semi-empirical levels, we have explored the conditions of polaron formation in a molecular model system: oligophenylene–vinylenes, PVs of increasing sizes. The symmetry breaking occurs at sizes larger than five monomers for the anion and six monomers for the cation. The driving force for this process is primarily the charge–lattice coupling through the stretching mode at 1600 cm−1