Quantification of singlet oxygen generation from photodynamic hydrogels

Recently, we described a series of novel porphyrin-impregnated hydrogels capable of producing microbicidal singlet oxygen (1O2) on photoactivation. Indirect assessment of the efficacy of 1O2 production from such hydrogels has been previously described using microbiological techniques, but here we report a novel, direct method of quantification. Anthracene-9,10-dipropionic acid (ADPA) is known to irreversibly form an endoperoxide on reaction with 1O2, causing photobleaching of its absorbance band at approximately 378 nm. Here, the reaction of this probe is exploited in a novel way to provide a simple, inexpensive, and convenient measurement of 1O2 generation from the surface of porphyrin-incorporated photosensitising hydrogels, with the ability to account for effects due to hydrogel porosity. Ingress of the probe into the materials was observed, with rates of up to 3.83 x 103 s-1. This varied by up to 200-fold with material composition and surface modification. Rates of 1O2 generation in these porphyrin-incorporated hydrogels, after compensating for ADPA ingress, ranged from 1.86x103 – 5.86x103 s-1. This work demonstrates a simple and straightforward method for direct 1O2 quantification from porous materials, with general utility.

Rapid quantification of microRNAs in plasma using a fast real time PCR system

The ability to rapidly detect circulating small RNAs, in particular microRNAs (miRNAs), would further increase their already established potential as biomarkers in a range of conditions. One rate-limiting factor is the time taken to perform quantitative real time PCR amplification. We therefore evaluated the ability of a novel thermal cycler to perform this step in less than 10 minutes. Quantitative PCR was performed on an xxpress® thermal cycler (BJS Biotechnologies, Perivale, UK), which employs a resistive heating system and forced air cooling to achieve thermal ramp rates of 10 °C/s, and a conventional peltier-controlled LightCycler 480 system (Roche, Basel, Switzerland) ramping at 4.8 °C/s. The threshold cycle (Ct) for detection of 18S rDNA from a standard genomic DNA sample was significantly more variable across the block (F-test, p=2.4x10-25) for the xxpress (20.01±0.47SD) than the LightCycler (19.87±0.04SD). RNA was extracted from human plasma, reverse transcribed and a panel of miRNAs amplified and detected using SYBR green (Kapa Biosystems, Wilmington, Ma, USA). The sensitivity of both systems was broadly comparable and both detected a panel of miRNAs reliably and indicated similar relative abundances. The xxpress thermal cycler facilitates rapid qPCR detection of small RNAs and brings point-of care diagnostics based upon circulating miRNAs a step closer to reality.

A new statistical framework for the quantification of covariate associations with species distributions

Identifying processes that shape species geographical ranges is a prerequisite for understanding environmental change. Currently, species distribution modelling methods do not offer credible statistical tests of the relative influence of climate factors and typically ignore other processes (e.g. biotic interactions and dispersal limitation). We use a hierarchical model fitted with Markov Chain Monte Carlo to combine ecologically plausible niche structures using regression splines to describe unimodal but potentially skewed response terms. We apply spatially explicit error terms that account for (and may help identify) missing variables. Using three example distributions of European bird species, we map model results to show sensitivity to change in each covariate. We show that the overall strength of climatic association differs between species and that each species has considerable spatial variation in both the strength of the climatic association and the sensitivity to climate change. Our methods are widely applicable to many species distribution modelling problems and enable accurate assessment of the statistical importance of biotic and abiotic influences on distributions.

Strategies for detection and quantification of cysteine cathepsins-evolution from bench to bedside

The cysteine cathepsins are a family of closely related thiol proteases, normally found in the endosomal and lysosomal compartments of cells. A growing body of evidence has clearly linked the dysregulated activity of these proteases with many diseases and pathological conditions, offering therapeutic, prognostic and diagnostic potential. However, these proteases are synthesised as inactive precursors and once activated, are controlled by factors such as pH and presence of endogenous inhibitors, meaning that overall protein and activity levels do not necessarily correlate. In order to fully appreciate the role and potential of these proteases, tools are required that can detect and quantify overall cathepsin activity. Two main strategies have evolved; synthetic substrates and protease-labelling with affinity-binding probes (or activity-based probes). This review examines recent innovations in these approaches as the field moves towards developing tools that could ultimately be used in patients for diagnostic or prognostic applications.

Quantification of Type VI secretion system activity in macrophages infected with Burkholderia cenocepacia

The Gram-negative bacterial type VI Secretion System (T6SS) delivers toxins to kill orinhibit the growth of susceptible bacteria, while others target eukaryotic cells. Deletionof atsR, a negative regulator of virulence factors in B. cenocepacia K56-2, increasesT6SS activity. Macrophages infected with a K56-2 ΔatsR mutant display dramaticalterations in their actin cytoskeleton architecture that rely on the T6SS, which isresponsible for the inactivation of multiple Rho-family GTPases by an unknownmechanism. We employed a strategy to standardize the bacterial infection ofmacrophages and densitometrically quantify the T6SS-associated cellular phenotype,which allowed us to characterize the phenotype of systematic deletions of each genewithin the T6SS cluster and ten vgrG encoding genes in K56-2 ΔatsR. None of thegenes from the T6SS core cluster and the individual vgrGs were directly responsiblefor the cytoskeletal changes in infected cells. However, a mutant strain with all vgrGgenes deleted was unable to cause macrophage alterations. Despite not being able toidentify a specific effector protein responsible for the cytoskeletal defects inmacrophages, our strategy resulted in the identification of the critical core componentsand accessory proteins of the T6SS assembly machinery and provides a screeningmethod to detect T6SS effectors targeting the actin cytoskeleton in macrophages byrandom mutagenesis.

A novel fluorescence-based assay for the rapid detection and quantification of cellular deoxyribonucleoside triphosphates

Current methods for measuring deoxyribonucleoside triphosphates (dNTPs) employ reagent and labor-intensive assays utilizing radioisotopes in DNA polymerase-based assays and/or chromatography-based approaches. We have developed a rapid and sensitive 96-well fluorescence-based assay to quantify cellular dNTPs utilizing a standard real-time PCR thermocycler. This assay relies on the principle that incorporation of a limiting dNTP is required for primer-extension and Taq polymerase-mediated 5-3' exonuclease hydrolysis of a dual-quenched fluorophore-labeled probe resulting in fluorescence. The concentration of limiting dNTP is directly proportional to the fluorescence generated. The assay demonstrated excellent linearity (R(2) > 0.99) and can be modified to detect between ∼0.5 and 100 pmol of dNTP. The limits of detection (LOD) and quantification (LOQ) for all dNTPs were defined as <0.77 and <1.3 pmol, respectively. The intra-assay and inter-assay variation coefficients were determined to be <4.6% and <10%, respectively with an accuracy of 100 ± 15% for all dNTPs. The assay quantified intracellular dNTPs with similar results obtained from a validated LC-MS/MS approach and successfully measured quantitative differences in dNTP pools in human cancer cells treated with inhibitors of thymidylate metabolism. This assay has important application in research that investigates the influence of pathological conditions or pharmacological agents on dNTP biosynthesis and regulation.

LL-37 quantification in gingival crevicular fluid (GCF) from periodontitis patients

Background: LL-37, an anti-microbial peptide belonging to the cathelicidin family, derives its name from two N-terminal leucine residues and the 37 amino acids comprising the peptide. LL-37 is the only known cathelicidin to exist in humans. It exhibits both anti-bacterial and immunomodulatory properties. Objectives: In the current study, LL-37 was quantified in GCF from periodontitis patients. Previous studies have relied on qualitative results from Western blotting to detect LL-37 in GCF. This study aims to quantitatively determine LL-37 levels in GCF. Methods: GCF and bacterial plaque samples, pre- and post non-surgical periodontal treatment, were collected from 4 sites in 12 patients presenting with advanced periodontitis. Plaque samples were analysed by QPCR for the presence or absence of the periodontopathic bacterium Porphyromonas gingivalis (P. gingivalis). The concentrations of LL-37 in patient samples pre- and post-treatment were deduced by indirect enzyme linked immunosorbent assay (ELISA). Results: Concentrations of LL-37 in samples varied between a minimum and maximum of 1 and 40 ng/ml. LL-37 levels were shown, pre-treatment, to be higher in deep pockets (6-9 mm) compared with shallower pockets (3-5 mm) and highest in those sites which were positive for P. gingivalis. Non-surgical therapy resulted in a significant improvement in clinical indices while expression levels of P. gingivalis were reduced. Following treatment, LL-37 levels in GCF decreased from an average of 6.5 ± 1 - 5.8 ± 1.2 ng/ml. The most interesting observation however was the reduction in LL-37 levels, from an average of 7 ± 1.3 – 2.5 ± 1.1 ng/ml in those sites where P. gingivalis infection was eradicated post-treatment. Conclusions: LL-37 levels are increased at sites showing advanced periodontal disease, reduce following treatment and appear to be linked to the presence of P. gingivalis. This study will further our knowledge of host defence in chronic diseases such as periodontitis.

Quantification of HER2 heterogeneity in breast cancer-implications for identification of sub-dominant clones for personalised treatment

Breast cancer is a heterogeneous disease, at both an inter- and intra-tumoural level. Appreciating heterogeneity through the application of biomarkers and molecular signatures adds complexity to tumour taxonomy but is key to personalising diagnosis, treatment and prognosis. The extent to which heterogeneity exists, and its interpretation remains a challenge to pathologists. Using HER2 as an exemplar, we have developed a simple reproducible heterogeneity index. Cell-to-cell HER2 heterogeneity was extensive in a proportion of both reported 'amplified' and 'non-amplified' cases. The highest levels of heterogeneity objectively identified occurred in borderline categories and higher ratio non-amplified cases. A case with particularly striking heterogeneity was analysed further with an array of biomarkers in order to assign a molecular diagnosis. Broad biological complexity was evident. In essence, interpretation, depending on the area of tumour sampled, could have been one of three distinct phenotypes, each of which would infer different therapeutic interventions. Therefore, we recommend that heterogeneity is assessed and taken into account when determining treatment options.

Quantification of the smoking-associated cancer risk with rate advancement periods: meta-analysis of individual participant data from cohorts of the CHANCES consortium

BACKGROUND: Smoking is the most important individual risk factor for many cancer sites but its association with breast and prostate cancer is not entirely clear. Rate advancement periods (RAPs) may enhance communication of smoking related risk to the general population. Thus, we estimated RAPs for the association of smoking exposure (smoking status, time since smoking cessation, smoking intensity, and duration) with total and site-specific (lung, breast, colorectal, prostate, gastric, head and neck, and pancreatic) cancer incidence and mortality.

METHODS: This is a meta-analysis of 19 population-based prospective cohort studies with individual participant data for 897,021 European and American adults. For each cohort we calculated hazard ratios (HRs) for the association of smoking exposure with cancer outcomes using Cox regression adjusted for a common set of the most important potential confounding variables. RAPs (in years) were calculated as the ratio of the logarithms of the HRs for a given smoking exposure variable and age. Meta-analyses were employed to summarize cohort-specific HRs and RAPs.

RESULTS: Overall, 140,205 subjects had a first incident cancer, and 53,164 died from cancer, during an average follow-up of 12 years. Current smoking advanced the overall risk of developing and dying from cancer by eight and ten years, respectively, compared with never smokers. The greatest advancements in cancer risk and mortality were seen for lung cancer and the least for breast cancer. Smoking cessation was statistically significantly associated with delays in the risk of cancer development and mortality compared with continued smoking.

CONCLUSIONS: This investigation shows that smoking, even among older adults, considerably advances, and cessation delays, the risk of developing and dying from cancer. These findings may be helpful in more effectively communicating the harmful effects of smoking and the beneficial effect of smoking cessation.

Colaboração em didática: utopia, desencanto e possibilidade

O presente estudo ocupa-se de uma problemática em Didática – as relações entre a investigação científica e o desenvolvimento do campo – e assenta no pressuposto de que essas relações se constroem conjugando o pensamento e a atuação de investigadores, académicos, professores, e formadores de professores, numa ação conjunta conduzida com a participação comprometida das suas instituições profissionais e orientada para o desenvolvimento de todos os intervenientes, da sua área de atividade e, assim, do ensino/aprendizagem e dos alunos. Nesse sentido, o estudo foi concebido no intuito de criar condições propícias ao estreitamento das relações em foco, tendo em vista, simultaneamente, o aprofundamento do conhecimento sobre a problemática. Assumiu, pois, uma finalidade de intervenção no terreno e uma finalidade científica de avaliação da experiência proporcionada por essa intervenção, na expectativa do alargamento da compreensão do objeto de estudo. Na confluência dessas finalidades, a investigação desenvolveu-se como um estudo de caso norteado por duas proposições teóricas: - A colaboração entre académicos e professores, no âmbito de projetos de investigação em Didática, e o comprometimento das instituições profissionais de ambos com essas iniciativas colaborativas poderão favorecer o desenvolvimento do campo, dos atores que nele intervêm e das instituições implicadas. - A formação contínua de professores centrada na investigação em Didática poderá constituir espaço privilegiado para o desenvolvimento dessas dinâmicas de colaboração. No alinhamento destas proposições com a finalidade interventiva do estudo, diferentes atores em Didática foram desafiados a envolver-se numa iniciativa de investigação/formação colaborativa e daí resultou o caso analisado nesta investigação, o projeto ICA/DL (Investiga, Colabora e Atua em Didática de Línguas). Tal projeto, realizado no âmbito de uma parceria formalizada num Protocolo de Colaboração, envolveu uma equipa composta por cinco docentes do Departamento de Didática e Tecnologia Educativa (atual Departamento de Educação) da Universidade de Aveiro e por 4 professores da Escola Secundária Dr. João Carlos Celestino Gomes – Ílhavo e implicou ainda, institucionalmente, a universidade, a escola e o Centro de Formação das Escolas do Concelho de Ílhavo (atualmente, Centro de Formação de Associação de Escolas dos Concelhos de Ílhavo, Vagos e Oliveira do Bairro). As atividades do projeto iniciaram-se no final de 2003, com os primeiros encontros de negociação da parceria, e prolongaram-se até meados de 2007, altura em que a equipa reuniu pela última vez. O programa operacional central desenvolveu-se entre janeiro de 2004 e novembro de 2005 e concretizou-se num percurso de investigação e de formação em colaboração entre académicos e professores, concebido e implementado pela equipa e acreditado pelo Conselho Científico-Pedagógico da Formação Contínua. Tal programa centrou-se no estudo de um tópico em Didática de Línguas (a competência de aprendizagem plurilingue), na realização de intervenções de ensino/aprendizagem, no âmbito do mesmo tópico, junto dos alunos na escola e na avaliação da experiência com base em dados empíricos. A investigação que sobre o caso se conduziu, ao orientar-se, na prossecução da segunda finalidade estabelecida, para a compreensão da influência das dinâmicas colaborativas de investigação/formação sobre o desenvolvimento dos intervenientes (equipa, parceiros institucionais e alunos na escola), é também um estudo de impacte. A condução do processo empírico deu prioridade à produção de uma leitura integrada e complexa, capaz de evidenciar os impactes do projeto, interpretando-os com base na análise dos processos que terão condicionado a sua ocorrência. Nessa medida, a metodologia revestiu-se, intencionalmente, de uma natureza eminentemente interpretativa e qualitativa, socorrendo-se da triangulação de fontes, dados e procedimentos de análise. Contudo, o método integrou também procedimentos quantitativos, em particular, um exercício estatístico que, correlacionando totais de evidências verificadas e totais de evidências possíveis, procurou tornar mais precisa a avaliação da dimensão do impacte alcançado pelo projeto. Ensaiou-se, assim, uma abordagem metodológica em estudos de impacte em Educação, que propõe potenciar a compreensão de casos complexos, conjugando interpretação e objetivação/quantificação. A análise desvendou constrangimentos e obstáculos na vivência dos princípios conceptuais fundadores da noção de investigação/formação colaborativa que sustentou as proposições de partida e que fez emergir o ICA/DL. Tais dificuldades limitaram a assunção de responsabilidades partilhadas na condução processual da experiência, condicionaram dinâmicas supervisivas nem sempre colaborativas e facilitadoras e manifestaram-se em atitudes de compromisso por vezes frágil com o projeto. E terão afetado a concretização das expectativas iniciais de desenvolvimento de todos os participantes, determinando impactes de dimensão globalmente algo dececionante, assimetrias substantivas de influência da experiência levada a cabo no desenvolvimento profissional dos elementos da equipa e no desenvolvimento institucional e repercutindo-se em efeitos pouco expressivos no desenvolvimento dos alunos, no que toca a capacidades ativas de comunicação e de aprendizagem, enquadradas pelo tópico didático trabalhado no âmbito do projeto. Mas revelaram-se também sinais claros de que se avançou no sentido da concretização dos pressupostos colaborativos que sustentaram a iniciativa. Foi possível reunir académicos, professores e instituições educativas em torno da ideia de investigação/formação em colaboração e mobilizá-los como parceiros que se comprometeram na construção de um projeto assente nessa ideia. E percebeu-se que, apesar de pouco expressivo, houve impacte, pois há indicadores de que o projeto contribuiu positivamente para o desenvolvimento dos intervenientes. Na equipa, sinalizaram-se efeitos sobretudo nas práticas de ensino/aprendizagem das professoras e, no caso particular de uma delas, que teve uma participação mais envolvida em atividades de investigação, manifestaram-se impactes substancialmente mais notórios do que nos restantes elementos do grupo e que abrangeram diferentes dimensões da profissionalidade. As académicas, embora menos do que as professoras, também evidenciaram desenvolvimento, dominantemente, nos planos da investigação em Didática de Línguas e da formação de professores. E o ICA/DL parece ter proporcionado também impactes positivos junto das instituições implicadas, especialmente junto da universidade, designadamente, no que toca ao aprofundamento do pensamento sobre a problemática que sustentou a experiência e ao desenvolvimento de projetos de investigação. Por seu turno, os alunos, tendo revelado sinais modestos de reforço das suas capacidades de ação como interlocutores em situações de comunicação plurilingue e como aprendentes de línguas, deram mostras claras de terem tomado consciência de atitudes e de recursos que favorecem o desenvolvimento desses dois papéis. Para além disso, os responsáveis pela parceria, apesar dos obstáculos que limitaram o alcance dos seus propósitos, reafirmaram, na conclusão do projeto, a sua confiança nos princípios colaborativos que os uniram, antecipando a continuidade de uma experiência que entenderam como primeiro passo na concretização desses princípios. No balanço das fragilidades vividas e dos ganhos conquistados pelo ICA/DL, o estudo permite renovar a convicção inicial no poder transformador das práticas de investigação/formação colaborativa em Didática, e assim, na emergência de uma comunidade una de professores e de académicos, movida por um projeto comum de desenvolvimento da Educação. Nessa perspetiva, avançam-se sugestões que abrangem a investigação, o processo de ensino/aprendizagem nas escolas, a formação de professores, as políticas em Didática e a Supervisão.

Le rôle de l'éducation spécialisée brésilienne en temps d'inclusion application d'une méthode d'analyse de contenu aux politiques éducatives de 1990-2008

Ce mémoire est le résultat d'une étude descriptive et exploratoire sur le rôle de l'éducation spécialisée dans le contexte éducatif brésilien, qui favorise l'inclusion scolaire. Cette recherche présente les résultats d'une analyse des politiques éducatives depuis les années 90 concernant l'éducation spécialisée et l'inclusion scolaire au Brésil. La démarche ainsi entreprise procède à une analyse de contenu thématique réalisée sur un échantillon de six documents officiels. Au Brésil, on compte sur l'éducation spécialisée pour promouvoir l'inclusion scolaire. Mais, étant donné que le paradigme de l'éducation spécialisée est substantiellement différent de celui de l'inclusion scolaire, l'objectif premier de notre recherche a été de décrire et d'analyser les politiques éducatives concernant l'éducation spécialisée et l'inclusion scolaire au Brésil. Les résultats de notre analyse nous ont montré que l'inclusion a peu de chances de faire des progrès si des changements au plan des politiques éducatives ne sont pas effectués.

Les mécanismes de l'interprétation dans la chanson populaire (d'expression francophone) proposition d'une méthode d'analyse

Pour montrer comment s'articulent les mécanismes de l'interprétation dans la chanson populaire, nous nous sommes inspirée [inspirés] de travaux de sociologues qui se sont penchés sur la chanson depuis une vingtaine d'années (Authelain, Buxton, Calvet, Giroux, Hennion, Frith, Middleton) ou sur le marché des biens symboliques (Bourdieu), ainsi que de la sémiologie musicale de Jean-Jacques Nattiez. Comme lui, nous avons identifié un processus poïétique, un niveau neutre et un processus esthésique dans la pratique de la chanson, processus qui se dédoublent dans la chanson populaire selon le point d'ancrage de l'analyse: la partition (la trace, constituant un premier"niveau neutre") puis la chanson interprétée (ou résultat musical, qui constitue un second"niveau neutre"). Nous avons par la suite identifié les différents lieux où entre en jeu l'interprétation: chez les exécutants (musiciens et interprètes) qui actualisent la partition, produisant ainsi la chanson interprétée; dans le processus de production/promotion, où s'élaborent l'image de marque de l'artiste et les discours promotionnels; chez le public où l'interprétation apparaît aussi sous ses deux facettes, c'est-à-dire l'exécution possible par les auditeurs/spectateurs, mais surtout la lecture que propose le discours critique. Un exemple précis, l'album D'instinct (1995) de l'auteur/compositeur/interprète Richard Séguin, nous a permis de mettre à l'épreuve ce modèle ainsi qu'une méthode d'analyse qui permet à la fois de se pencher sur une chanson et sur la chanson. Dans un premier temps, nous avons analysé une chanson à partir de la partition puis de la chanson interprétée (sous forme de chanson, d'album, de vidéoclip et de spectacle), sans tenir compte des discours que l'on tient sur cette chanson. Dans un deuxième temps, notre attention s'est portée sur la chanson, analysant l'objet"chanson" transformé par les discours, puis les discours eux-mêmes. Ces analyses nous ont permis de nous pencher sur l'interprétation, d'abord comme exécution (de la partition), et surtout comme lecture, puis de schématiser le réseau des discours, promotionnels et critiques, qui circulent entre l'artiste (et sa musique) et l'auditeur/spectateur. Notre recherche s'intéresse ainsi de façon nouvelle à la chanson populaire et la méthode d'analyse que nous proposons permet de tenir compte de la spécificité de son objet: une approche multidisciplinaire s'imposait pour étudier un phénomène pluridimensionnel comme la chanson. Aussi, les résultats de nos analyses confirment que le modèle et la méthode sont opératoires, mais surtout, ils laissent entrevoir de nombreuses possibilités d'analyses nouvelles d'une/de la chanson, analyses qui permettraient d'en saisir le caractère stylistique, les qualités esthétiques, etc. et même, il nous semble qu'ils pourraient s'avérer tout aussi opératoires appliqués à d'autres corpus."--Résumé abrégé par UMI

Caractérisation du pergélisol : application d’une nouvelle méthode afin d’estimer la conductivité thermique à l’aide de la tomodensitométrie

La construction dans l’Arctique nécessite une connaissance précise des propriétés thermiques et géotechniques du pergélisol. La connaissance de ces propriétés est également nécessaire pour le paramétrage des modèles de transfert de chaleur. Des études antérieures ont démontré le grand potentiel de l’utilisation de la tomodensitométrie pour les mesures du volume des composantes du pergélisol et la visualisation de la cryostructure. Une nouvelle approche est proposée pour mesurer la conductivité thermique du pergélisol. Les objectifs généraux de ce projet sont (1) d’élaborer une nouvelle méthode de caractérisation du pergélisol à l’aide de la tomodensitométrie et de modèle éprouvés et (2) de comparer et mettre au point une méthode novatrice pour mesurer la conductivité thermique et des paramètres géotechniques. Les résultats démontrent que les tests effectués à l’aide de la tomodensitométrie donnent des résultats d’une valeur scientifique comparable aux autres méthodes existantes de mesure de déjà existantes de conductivité thermique du pergélisol.