A novel hepatitis C virus (HCV) subtype from Somalia and its classification into HCV clade 3.

Hepatitis C virus (HCV) sequences from throughout the world have been grouped into six clades, based on recently proposed criteria. Here, the partial sequences and clade assignment are reported for three HCV isolates from chronic hepatitis C patients from Somalia, for whom conventional assays failed to identify the genotype. Phylogenetic analysis of the sequences of the core, envelope 1 and part of the non- structural 5b regions suggests that all three isolates belong to a distinct HCV genetic group, tentatively classified as subtype 3h. This novel HCV subtype shows the highest sequence similarity with HCV isolates from Indonesia. Despite the fact that these patients were infected with HCV clade 3, none of them responded to standard interferon treatment

Novel resistance to imipenem associated with an altered PBP-4 in a Pseudomonas aeruginosa clinical isolate

A Pseudomonas aeruginosa (isolate 416) from a patient with pneumonia, was initially susceptible to imipenem (MIC: 2 mg/l) but became resistant to this antibiotic (isolate 470, MIC: 32 mg/l) during imipenem therapy. Treatment failed. No parallel increases in MIC were observed for other antimicrobials tested. Isolates 416 and 470 shared the same pyocin type and serotype, produced small amounts of an inducible β-lactamase, and had similar lipopolysaccharide compositions. On electrophoresis of outer membrane proteins, the porin F, identified by the monoclonal antibody MA4-4, was expressed similarly by the two isolates but the production of one band (apparent molecular weight 47,000) was diminished in isolate 470. [14C]-Imipenem labelling of intact cells proceeded more slowly in 470 than in 416, especially when bacterial cells were treated by antibody MA4-4 to block the porin F channel. [14C]-Imipenem labelling of penicillin binding proteins (PBP) showed that the band identified as PBP-4 bound markedly less radioactivity in isolate 470 than in 416. After isolate 470 was passaged several times in antibiotic-free broth, the imipenem MIC was decreased from 32 to 8 mg/l, and the [14C]-imipenem PBP pattern recovered the initial profile as exhibited by isolate 416. Two resistance mechanisms, affecting imipenem electively, could have combined their effect in the post-therapy isolate, altered target protein and reduced permeabilit

Desarrollo de un medio de cultivo para potenciar la producción de componentes bioactivos en la microalga autóctona Scenedesmus obliquus

Se estudió el efecto de fuentes de nitrógeno (nitrato de sodio y urea) y de carbono (acetato de sodio y glucosa), así como el estrés salino (cloruro de sodio) sobre cultivo de la microalga Scenedesmus obliquus que potencien la producción de carotenoides totales, proteínas totales y fenoles totales. Se empleó como medio de cultivo base Allen & Arnon y la microalga Scenedesmus obliquus autóctona del Embalse de Salto Grande. Las condiciones experimentales que favorecieron la obtención de biomasa de microalga Scenedesmus obliquus rica en componentes bioactivos fueron: para carotenoides totales 0,24g urea/L; 3,68g glucosa/L y 54,71µmol/(m2s); proteínas totales 0,24g urea/L; 5,02g acetato de sodio/L y 54,71µmol/(m2s) y fenoles totales 31,00g urea/L; 3,68g glucosa/L y 45,04µmol/(m2 s). La concentración de carotenoides totales obtenida fue 473,85±11,00mg β-caroteno/g ms; de proteínas totales 7,09±0,23mg ASB/g ms y de fenoles totales, 16,78±0,84mg EAG/g ms. El estrés salino se desestimó ya que provocó una disminución de la concentración de los componentes de interés. De lo expuesto se concluye que el cultivo de Scenedesmus obliquus, bajo las condiciones de estrés señaladas, representa un proceso biotecnológico atractivo para la obtención de biomasa rica en componentes bioactivos con potencialidad para ser utilizada como aditivo natural en la formulación de alimentos ARK: http://id.caicyt.gov.ar/ark:/s22504559/t9bmfmnb

Text mining for the biocuration workflow

Molecular biology has become heavily dependent on biological knowledge encoded in expert curated biological databases. As the volume of biological literature increases, biocurators need help in keeping up with the literature; (semi-) automated aids for biocuration would seem to be an ideal application for natural language processing and text mining. However, to date, there have been few documented successes for improving biocuration throughput using text mining. Our initial investigations took place for the workshop on ‘Text Mining for the BioCuration Workflow’ at the third International Biocuration Conference (Berlin, 2009). We interviewed biocurators to obtain workflows from eight biological databases. This initial study revealed high-level commonalities, including (i) selection of documents for curation; (ii) indexing of documents with biologically relevant entities (e.g. genes); and (iii) detailed curation of specific relations (e.g. interactions); however, the detailed workflows also showed many variabilities. Following the workshop, we conducted a survey of biocurators. The survey identified biocurator priorities, including the handling of full text indexed with biological entities and support for the identification and prioritization of documents for curation. It also indicated that two-thirds of the biocuration teams had experimented with text mining and almost half were using text mining at that time. Analysis of our interviews and survey provide a set of requirements for the integration of text mining into the biocuration workflow. These can guide the identification of common needs across curated databases and encourage joint experimentation involving biocurators, text mining developers and the larger biomedical research community

BioCreative III interactive task: an overview

The BioCreative challenge evaluation is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain. The biocurator community, as an active user of biomedical literature, provides a diverse and engaged end user group for text mining tools. Earlier BioCreative challenges involved many text mining teams in developing basic capabilities relevant to biological curation, but they did not address the issues of system usage, insertion into the workflow and adoption by curators. Thus in BioCreative III (BC-III), the InterActive Task (IAT) was introduced to address the utility and usability of text mining tools for real-life biocuration tasks. To support the aims of the IAT in BC-III, involvement of both developers and end users was solicited, and the development of a user interface to address the tasks interactively was requested

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

Social capital and natural hazards : trust and cohesion in the eastern visayas of the Philippines

Cette thèse porte sur le capital social et les mesures prises afin de se préparer aux aléas naturels aux Philippines. L’archipel est régulièrement soumis à de nombreux risques de catastrophe, générant parfois des conséquences désastreuses pour la population et le patrimoine économique du pays. Par ailleurs, ces îles portent un lourd héritage colonial rendant omniprésents les inégalités socioéconomiques, le manque de solidarité et la pauvreté. Le concept du capital social demeure encore très polémique, cependant nous croyons qu'il peut s'avérer utile afin de mieux réfléchir à la façon dont les sociétés humaines interagissent avec les aléas naturels. Nos recherches mettent en avant l’importance des inégalités socioéconomiques, du contexte et de l'échelle géographique dans l’analyse du capital social et de la préparation aux aléas. Elles soulignent d'autre part que la compréhension des dynamiques sociales, telles que la confiance et la participation communautaire, ne peut être atteinte sans une considération des contextes politiques. Nous avons porté une attention particulière à l'examen des contextes et des différentes formes de capital social, et ce, à plusieurs niveaux géographiques (village, municipalité, région, pays). Un nombre croissant d'études montre que l'inégalité économique entraîne des conséquences néfastes sur le capital social. Des recherches récentes ont également commencé à interroger les rapports entre le capital social et les catastrophes dites « naturelles ». Notre thèse établit un lien entre ces deux approches en couplant une analyse générale de la situation des Philippines à une étude approfondie d'une municipalité rurale isolée de la région des Visayas orientales. L'argument central de cette thèse est que l'inégalité économique produit des effets néfastes sur le capital social, entraînant des répercussions négatives sur la prévention des catastrophes « naturelles ». Par le biais de l'analyse de plusieurs échelles géographiques, cette thèse entend montrer comment les inégalités, de par leur impact sur le capital social, contribuent à augmenter les chances de voir les aléas naturels se constituer en désastres. Nous avançons qu'un usage circonspect du concept de capital social, prenant en compte les complexités politiques, historiques, et géographiques du contexte auquel il s'applique, a la capacité d'améliorer la manière dont les gens se préparent collectivement afin d'éviter que les aléas ne se transforment en catastrophes.This thesis analyzes social capital and preparations for natural hazards in the Philippines. The research emphasizes the importance of inequalities, contextualization, and scale. It underlines the significance of historical and political contexts to better understand social dynamics. There is a growing body of scholarly literature that shows the detrimental repercussions of inequality on social capital. Social capital is still a debated concept but it can be useful for thinking about how human societies interact with natural hazards. The thesis thus contributes to the growing scientific inquiries which have begun to address the connections between social capital and “natural” disasters. This dissertation contributes to the links between these two fields of knowledge by analyzing the Filipino situation in general, as well as making a specific case study of a rural municipality in the Eastern Visayas region. The thesis’ central argument is that economic inequality is detrimental to social capital which then has negative repercussions on preparing for natural hazards. In an analysis at several geographical scales, this thesis shows how inequality, via social capital, makes societies more at risk of having natural hazards turn into disasters. The thesis argues that a cautious use of the concept of social capital, which is cognizant of the complexities of the context it is applied to, has the potential to improve the way people collectively prevent hazards from turning into disasters

Focused microwave-assisted extraction of cocaine and benzoylecgonine from coca leaves

Extraction of cocaine and benzoylecgonine from coca leaves was performed by focused microwave-assisted extraction (FMAE). Cocaine extraction was optimised with respect to the nature of the extracting solvent, the particle size distribution, the moisture of the sample, the applied microwave power and the radiation time. A central composite design was used to optimise the two latter parameters and to assess the robustness of the extraction method around the best conditions. FMAE generated extracts similar to those obtained by conventional solid-liquid extraction but in a more efficient manner, i.e. 30 s were sufficient to extract cocaine quantitatively from leaves. Analyses of cocaine and benzoylecgonine in coca leaves was carried out by capillary GC-FID and GC-MS for peak identification, as well as by capillary electrophoresis with UV detection

Optimization of derivatization parameters with 9-fluorenylmethyl chloroformate for amphetamine and catecholamine separation by supercritical fluid chromatography

The separation of amino compounds by supercritical fluid chromatography (SFC) is a difficult problem to solve, owing to the apolar nature of CO2. The derivatization of amino functions with the 9-fluorenylmethyl chloroformate (FMOC-Cl) allows to obtain apolar UV-absorbing compounds easily eluted with a supercritical mobile phase. Optimization of derivatization parameters allows us to analyze quantitatively amphetamines and catecholamines. These compounds can be separated in less than 5 min with a small addition of methanol as polar modifier. The total procedure takes no more than 15 min and can be automatized to gain time. As presented in this study, this method can be employed to physiological fluids as urine