EADock: docking of small molecules into protein active sites with a multiobjective evolutionary optimization.

In recent years, protein-ligand docking has become a powerful tool for drug development. Although several approaches suitable for high throughput screening are available, there is a need for methods able to identify binding modes with high accuracy. This accuracy is essential to reliably compute the binding free energy of the ligand. Such methods are needed when the binding mode of lead compounds is not determined experimentally but is needed for structure-based lead optimization. We present here a new docking software, called EADock, that aims at this goal. It uses an hybrid evolutionary algorithm with two fitness functions, in combination with a sophisticated management of the diversity. EADock is interfaced with the CHARMM package for energy calculations and coordinate handling. A validation was carried out on 37 crystallized protein-ligand complexes featuring 11 different proteins. The search space was defined as a sphere of 15 A around the center of mass of the ligand position in the crystal structure, and on the contrary to other benchmarks, our algorithm was fed with optimized ligand positions up to 10 A root mean square deviation (RMSD) from the crystal structure, excluding the latter. This validation illustrates the efficiency of our sampling strategy, as correct binding modes, defined by a RMSD to the crystal structure lower than 2 A, were identified and ranked first for 68% of the complexes. The success rate increases to 78% when considering the five best ranked clusters, and 92% when all clusters present in the last generation are taken into account. Most failures could be explained by the presence of crystal contacts in the experimental structure. Finally, the ability of EADock to accurately predict binding modes on a real application was illustrated by the successful docking of the RGD cyclic pentapeptide on the alphaVbeta3 integrin, starting far away from the binding pocket.

trome, trEST and trGEN: databases of predicted protein sequences.

We previously introduced two new protein databases (trEST and trGEN) of hypothetical protein sequences predicted from EST and HTG sequences, respectively. Here, we present the updates made on these two databases plus a new database (trome), which uses alignments of EST data to HTG or full genomes to generate virtual transcripts and coding sequences. This new database is of higher quality and since it contains the information in a much denser format it is of much smaller size. These new databases are in a Swiss-Prot-like format and are updated on a weekly basis (trEST and trGEN) or every 3 months (trome). They can be downloaded by anonymous ftp from ftp://ftp.isrec.isb-sib.ch/pub/databases.

Application of text-mining for updating protein post-translational modification annotation in UniProtKB.

BACKGROUND: The annotation of protein post-translational modifications (PTMs) is an important task of UniProtKB curators and, with continuing improvements in experimental methodology, an ever greater number of articles are being published on this topic. To help curators cope with this growing body of information we have developed a system which extracts information from the scientific literature for the most frequently annotated PTMs in UniProtKB. RESULTS: The procedure uses a pattern-matching and rule-based approach to extract sentences with information on the type and site of modification. A ranked list of protein candidates for the modification is also provided. For PTM extraction, precision varies from 57% to 94%, and recall from 75% to 95%, according to the type of modification. The procedure was used to track new publications on PTMs and to recover potential supporting evidence for phosphorylation sites annotated based on the results of large scale proteomics experiments. CONCLUSIONS: The information retrieval and extraction method we have developed in this study forms the basis of a simple tool for the manual curation of protein post-translational modifications in UniProtKB/Swiss-Prot. Our work demonstrates that even simple text-mining tools can be effectively adapted for database curation tasks, providing that a thorough understanding of the working process and requirements are first obtained. This system can be accessed at http://eagl.unige.ch/PTM/.

Pediatric drug-related problems: a multicenter study in four French-speaking countries.

BACKGROUND: Pediatric intensive care patients represent a population at high risk for drug-related problems. There are few studies that compare the activity of clinical pharmacists between countries. OBJECTIVE: To describe the drug-related problems identified and interventions by four pharmacists in a pediatric cardiac and intensive care unit. SETTING: Four pediatric centers in France, Quebec, Switzerland and Belgium. METHOD: This was a six-month multicenter, descriptive and prospective study conducted from August 1, 2009 to January 31, 2010. Drug-related problems and clinical interventions were compiled from four pediatric centers in France, Quebec, Switzerland and Belgium. Data on patients, drugs, intervention, documentation, approval and estimated impact were compiled. MAIN OUTCOME MEASURE: Number and type of drug-related problems encountered in a large pediatric inpatient population. RESULTS: A total of 996 interventions were recorded: 238 (24 %) in France, 278 (28 %) in Quebec, 351 (35 %) in Switzerland and 129 (13 %) in Belgium. These interventions targeted 270 patients (median 21 months old, 53 % male): 88 (33 %) in France, 56 (21 %) in Quebec, 57 (21 %) in Switzerland and 69 (26 %) in Belgium. The main drug-related problems were inappropriate administration technique (29 %), untreated indication (25 %) and supra-therapeutic dose (11 %). The pharmacists' interventions were mostly optimizing the mode of administration (22 %), dose adjustment (20 %) and therapeutic monitoring (16 %). The two major drug classes that led to interventions were anti-infectives for systemic use (23 %) and digestive system and metabolism drugs (22 %). Interventions mainly involved residents and all clinical staff (21 %). Among the 878 (88 %) proposed interventions requiring physician approval, 860 (98 %) were accepted. CONCLUSION: This descriptive study illustrates drug-related problems and the ability of clinical pharmacists to identify and resolve them in pediatric intensive care units in four French-speaking countries.

Molecular evidence of interhuman transmission of Pneumocystis pneumonia among renal transplant recipients hospitalized with HIV-infected patients.

Ten Pneumocystis jirovecii pneumonia (PCP) cases were diagnosed in renal transplant recipients (RTRs) during a 3-year period. Nosocomial transmission from HIV-positive patients with PCP was suspected because these patients shared the same hospital building, were not isolated, and were receiving suboptimal anti-PCP prophylaxis or none. P. jirovecii organisms were typed with the multitarget polymerase chain reaction-single-strand conformation polymorphism method. Among the 45 patients with PCP hospitalized during the 3-year period, 8 RTRs and 6 HIV-infected patients may have encountered at least 1 patient with active PCP within the 3 months before the diagnosis of their own PCP episode. In six instances (five RTRs, one HIV-infected patient), the patients harbored the same P. jirovecii molecular type as that found in the encountered PCP patients. The data suggest that part of the PCP cases observed in this building, particularly those observed in RTRs, were related to nosocomial interhuman transmission.

Whole-mount confocal immunofluorescence of mammalian CNS.

Bright-field wholemount labeling techniques applied to the mammalian central nervous system (CNS) offer advantages over conventional methods based on sections since an immediate and three-dimensional view of the stained components is provided. It thereby becomes possible to survey and count large number of cells and fibers in their natural relationships. The ability of confocal laser scanning microscopy to visualize in one focal plane the fluorescence associated with multiple markers could be most valuable by the availability of reliable wholemount fluorescent techniques. Accordingly, based in our previously published bright-field wholemount protocols [Brain Res. Prot. 2 (1998) 165-173], we have devised an effective immmunofluorescence wholemount procedure. We show that reliable wholemount fluorescent staining can be obtained using isolated complete CNS aged up to rat embryonic day 17, with antibodies penetration in the millimeter range. Examples are shown of preparations in which colocalization can be observed in nerve cells of cytoskeletal and calcium-binding proteins.

Risk factors, aetiology and outcome of ischaemic stroke in young adults: the Swiss Young Stroke Study (SYSS).

Ischaemic stroke (IS) in young adults has been increasingly recognized as a serious health condition. Stroke aetiology is different in young adults than in the older population. This study aimed to investigate aetiology and risk factors, and to search for predictors of outcome and recurrence in young IS patients. We conducted a prospective multicentre study of consecutive IS patients aged 16-55 years. Baseline demographic data, risk factors, stroke aetiology including systematic genetic screening for Fabry disease and severity were assessed and related to functional neurological outcome (modified Rankin Scale, mRS), case fatality, employment status, place of residence, and recurrent cerebrovascular events at 3 months. In 624 IS patients (60 % men), median age was 46 (IQR 39-51) years and median NIHSS on admission 3 (IQR 1-8). Modifiable vascular risk factors were found in 73 %. Stroke aetiology was mostly cardioembolism (32 %) and of other defined origin (24 %), including cervicocerebral artery dissection (17 %). Fabry disease was diagnosed in 2 patients (0.3 %). Aetiology remained unknown in 20 %. Outcome at 3 months was favourable (mRS 0-1) in 61 % and fatal in 2.9 %. Stroke severity (p < 0.001) and diabetes mellitus (p = 0.023) predicted unfavourable outcome. Stroke recurrence rate at 3 months was 2.7 %. Previous stroke or TIA predicted recurrent cerebrovascular events (p = 0.012). In conclusion, most young adults with IS had modifiable vascular risk factors, emphasizing the importance of prevention strategies. Outcome was unfavourable in more than a third of patients and was associated with initial stroke severity and diabetes mellitus. Previous cerebrovascular events predicted recurrent ones.

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article.

Neurophysiologic diagnosis, clinical symptoms and neuropathologic findings in polyneuropathies

Tausta: Polyneuropatia (PNP) on ääreishermoston sairaus, joka aiheuttaa laaja-alaisia, yleensä symmetrisiä vaurioita ääreishermostossa. PNP:aan johtavia syitä on satoja. Tavoitteet: Löytää parhaat neurofysiologiset menetelmät uremian, myelooman hoidossa käytettävän talidomidin sekä Fabryn taudin aiheuttaman PNP:n diagnosoimiseksi. Fabryn taudissa tutkin lisäksi ohutsäieneuropatian aiheuttamia neuropatologisia löydöksiä iholta otetusta koepalasta. Tutkimuksissa kartoitettiin lisäksi PNP:n aiheuttamien subjektiivisten oireiden korrelaatio neurofysiologisten ja neuropatologisten löydösten kanssa. Munuaisten vajaatoimintaa sairastavilla potilailla tavoitteena oli tutkia dialyysihoidon tehon vaikutusta autonomisen hermoston toimintaan sekä yhden dialyysikerran vaikutusta neurofysiologisiin löydöksiin. Aineisto ja menetelmät: I: Tutkittiin 21 uremiapotilaan sensoristen ja motoristen hermojen vasteet, värinä- sekä lämpötuntokynnykset ennen ja jälkeen hemodialyysin. Subjektiiviset PNP oireet kartoitettiin PNP oireita kysyvillä kaavakkeella. II:12 talidomidi hoitoa saavaa myeloomapotilasta, tutkimuksen menetelmät olivat samat kuin tutkimuksessa I. III: 12 Fabryn tautia sairastavaa potilasta, edellä mainittujen neurofysiologisten tutkimusten lisäksi potilailta otettiin ihobiopsia säären alueelta. Ihobiopsiasta laskettiin ohuiden hermosyiden määrä koepalan värjäyksen jälkeen. Subjektiiviset PNP oireet kartoitettiin kyselykaavakkeella. Sydämen sykevaihtelu tutkittiin levossa taajuustason analyysillä. IV: 32 uremiapotilaan autonomisen hermoston toimintaa tutkittiin sydämen sykevaihtelun aikatason analysillä, paksujen myelinoituneiden säikeiden toimintaa tutkittiin perifeeristen sensoristen hermojen mittauksilla toistetusti noin 2.9 vuoden aikana. Tulokset: Ureemisen PNP:n diagnostiikassa herkimmät tutkimukset ovat F-aaltojen parametrit alaraajojen motorisista hermoista, värinätuntokynnys alaraajoista sekä suralishermon amplitudi. Positiiviset PNP oireet uremiassa korreloivat värinätunto-kynnyksen sekä sensoristen hermojen neurografialöydösten kanssa. Neurofysiologisten tutkimusten ajankohdalla dialyysiajankohtaan nähden ei ole merkitystä. Talidomidi-PNP on pääasiassa sensorinen, mutta motoriset syyt ovat lievästi vaurioituneet. Talidomidi PNP:ssa subjektiiviset oireet korreloivat huonosti neurofysiologisten löydösten kanssa. Fabryn taudissa naisilla on oletettua enemmän ohutsäieneuropatian aiheuttamia oireita ja löydöksiä. Paksujen säikeiden löydöksiä ei tullut esiin. Ohutsäieneuropatian diagnostiikassa ihobiopsia ja kvantitatiiviset tuntokynnysmittaustestit täydentävät toisiaan. Tehokas dialyysi parantaa autonomisen hermoston toimintaa uremiapotilailla. Päätelmät: Erityyppisten polyneuropatioiden diagnostiikassa pitää etukäteen valita PNP tyypille oikeat tutkimusmenetelmät raskaiden tutkimuspatterien vähentämiseksi sekä diagnostiikan parantamiseksi. PNP:n aiheuttamat oireet ja kliiniset löydökset pitää aina tutkia, mutta yksin ne eivät ole herkkiä PNP:n diagnostiikassa.

Obtenção de bactérias para a o biocontrole de Meloidogyne javanica por meio de aquecimento de solo e tratamento com filtrado de raízes de plantas antagonistas a fitonematóides

Cinco amostras de solo com alto teor de matéria orgânica (10,14 dag/kg) de 1 kg cada foram autoclavadas (120 °C/1h), cinco foram aquecidas em forno de microondas a 660 watts e 2450 Hz por 4 min e cinco não foram aquecidas. Raízes de Mucuna aterrima, Crotalaria juncea, Tagetes erecta e Lycopersicon esculentum foram maceradas separadamente em liquidificador à baixa velocidade durante 30 s em 1000 mL de água e peneiradas. As suspensões resultantes foram adicionadas às amostras de solos as quais foram acondicionadas em saco plástico e submetidas aos três tratamentos térmicos e posteriormente mantidas a 28 ºC por 24 h. Setenta e oito isolados bacterianos foram obtidos das amostras de solo por diluição em série e submetidos à seleção para o biocontrole de M. javanica. Sementes de tomate foram microbiolizadas por imersão em suspensão de propágulos de cada uma das culturas e semeadas em substrato dentro de tubetes em casa de vegetação. As mudas resultantes foram inoculadas com 400 ovos do nematóide, cada. O isolado UFV-6 de Escherichia coli reduziu o número de galhas em maior magnitude (80%) ao passo que o isolado UFV-8 de Citrobacter freundii foi o mais eficiente na redução do número de ovos (83%). A identificação dos isolados foi feita por análise de ácidos graxos esteres de metil e testes bioquímicos.

Ação nematicida de extratos de alho, mostarda, pimenta malagueta, de óleo de mostarda e de dois produtos à base de capsainóides e alil isotiocianato sobre juvenis de Meloidogyne javanica, (treub) Chitwood, 1949, em casa de vegetação

Neves, W.S; Freitas, L.G.; Coutinho, M.M.; Giaretta-Dallemole, R.; Fabry, C.F.S.; Dhingra, O.D. & Ferraz, S. Atividade nematicida de extratos botânicos de pimenta malagueta (Capsicum frutescens), mostarda (Brassica campestris) e alho (Allium sativum) sobre o nematóide das galhas, Meloidogyne javanica, em casa de vegetação. Summa Phytopathologica, v.35, n.4, p.255-261, 2009 O experimento teve como objetivo avaliar a atividade nematicida de extratos botânicos dos frutos de pimenta malagueta (Capsicum frutescens), plantas de mostarda (Brassica campestris), de bulbos de alho (Allium sativum) e óleo de mostarda sobre o nematóide das galhas, Meloidogyne javanica, em tomateiro em casa de vegetação e posteriormente comparar os extratos que apresentassem maior redução de número de galhas e de ovos com dois produtos à base de capsaicina, capsainóides e alil isotiocianato. Uma mistura peneirada de solo e areia na proporção 1:1 (v:v) foi colocada em vasos de plástico e infestada com 4000 ovos de M. javanica. Quatro dias após 20 mL de cada extrato, na concentração de 1000 ppm, foram espalhados sobre o solo. Apenas água foi derramada sobre o solo infestado no tratamento testemunha. Mudas de tomate com 20 dias de idade foram transplantadas quatro dias após a colocação dos extratos ao solo. Após quarenta e cinco dias avaliou-se o número de ovos e o número de galhas do sistema radicular de cada planta. Os extratos clorofórmico e cetônico de pimenta malagueta e o óleo de mostarda apresentaram melhor controle do nematóide, diferindo estatisticamente da testemunha quanto ao número de galhas. Porém, somente o óleo de mostarda reduziu significativamente o número de ovos quando comparado com a testemunha. Os extratos cetônico e clorofórmico de pimenta e o óleo de mostarda reduziram em 34,5%, 40,4% e 99,9% o número de galhas, respectivamente e o óleo de mostarda reduziu em 99,9% o número de ovos. No experimento seguinte foram avaliados o extrato clorofórmico de pimenta, o óleo de mostarda, o produto comercial Champon® e um produto em desenvolvimento na UFV, chamado DS, a base de capsaicina, capsainóides e alil isotiocianato em diferentes concentrações. Os produtos Champon® e DS e o óleo de mostarda reduziram o número de ovos e galhas quando comparados à testemunha em todas as concentrações testadas. O extrato de pimenta apresentou o melhor resultado na concentração de 400 ppm, reduzindo o número de ovos e galhas em relação à testemunha, porém esse foi bem maior quando comparado com os demais produtos testados.

Magnetic Resocance Imaging Methods in the Follow-up of Multiple Sclerosis and in Farby Disease

Multiple sclerosis (MS) is a chronic immune-mediated inflammatory disorder of the central nervous system. MS is the most common disabling central nervous system (CNS) disease of young adults in the Western world. In Finland, the prevalence of MS ranges between 1/1000 and 2/1000 in different areas. Fabry disease (FD) is a rare hereditary metabolic disease due to mutation in a single gene coding α-galactosidase A (alpha-gal A) enzyme. It leads to multi-organ pathology, including cerebrovascular disease. Currently there are 44 patients with diagnosed FD in Finland. Magnetic resonance imaging (MRI) is commonly used in the diagnostics and follow-up of these diseases. The disease activity can be demonstrated by occurrence of new or Gadolinium (Gd)-enhancing lesions in routine studies. Diffusion-weighted imaging (DWI) and diffusion tensor imaging (DTI) are advanced MR sequences which can reveal pathologies in brain regions which appear normal on conventional MR images in several CNS diseases. The main focus in this study was to reveal whether whole brain apparent diffusion coefficient (ADC) analysis can be used to demonstrate MS disease activity. MS patients were investigated before and after delivery and before and after initiation of diseasemodifying treatment (DMT). In FD, DTI was used to reveal possible microstructural alterations at early timepoints when excessive signs of cerebrovascular disease are not yet visible in conventional MR sequences. Our clinical and MRI findings at 1.5T indicated that post-partum activation of the disease is an early and common phenomenon amongst mothers with MS. MRI seems to be a more sensitive method for assessing MS disease activity than the recording of relapses. However, whole brain ADC histogram analysis is of limited value in the follow-up of inflammatory conditions in a pregnancy-related setting because the pregnancy-related physiological effects on ADC overwhelm the alterations in ADC associated with MS pathology in brain tissue areas which appear normal on conventional MRI sequences. DTI reveals signs of microstructural damage in brain white matter of FD patients before excessive white matter lesion load can be observed on conventional MR scans. DTI could offer a valuable tool for monitoring the possible effects of enzyme replacement therapy in FD.

Cultivar, harvest year, and storage conditions affecting nutritional quality of common beans (Phaseolus vulgaris L.

Sixteen common bean cultivars were compared concerning the physicochemical characteristics of their raw seeds in the course of two consecutive harvests, as well as the effect of storage conditions on starch and dietary fiber content of cooked beans. Using cluster analysis it was possible to identify groups of cultivars with different nutritional features. Bean cultivars were categorized into four different groups according either to their macronutrient content (crude protein-PROT, total dietary fiber-TDF, insoluble dietary fiber-IDF, soluble dietary fiber-SDF, digestible starch-DS, and resistant starch-RS) or to their micronutrient levels (Fe, Zn, Mn, Cu, Ca, Mg, and P). Guateian 6662 and Rio Tibagi appeared to be the most suitable cultivars to prevent nutritional deficiencies, because they had high PROT, DS, Fe, and Zn content. The high total dietary fiber and RS content of Iraí, Minuano, and TPS Bonito cultivars, and specially the high soluble fiber content of Guateian 6662 and Rio Tibagi cultivars suggests that they could have a beneficial role in controlling blood lipid and glucose levels. Cooked beans had a decrease in DS and an increase in RS content after storage (4 °C or -20 °C), but these changes were more prominent in beans that had low RS content before cooking than in those of high RS content. TDF, IDF, and SDF did not change after storage.