Evidence for an association of prenatal exposure to particulate matter with clinical severity of Autism Spectrum Disorder.

Early-life exposure to air pollutants, including ozone (O3), particulate matter (PM2.5 or PM10, depending on diameter of particles), nitrogen dioxide (NO2) and sulfur dioxide (SO2) has been suggested to contribute to the etiology of Autism Spectrum Disorder (ASD). In this study, we used air quality monitoring data to examine whether mothers of children with ASD were exposed to high levels of air pollutants during critical periods of pregnancy, and if higher exposure levels may lead to a higher clinical severity in their offspring. We used public data from the Portuguese Environment Agency to estimate exposure to these pollutants during the first, second and third trimesters of pregnancy, full pregnancy and first year of life of the child, for 217 subjects with ASD born between 2003 and 2016. These subjects were stratified in two subgroups according to clinical severity, as defined by the Autism Diagnostic Observational Schedule (ADOS). For all time periods, the average levels of PM2.5, PM10 and NO2 to which the subjects were exposed were within the admissible levels defined by the European Union. However, a fraction of these subjects showed exposure to levels of PM2.5 and PM10 above the admissible threshold. A higher clinical severity was associated with higher exposure to PM2.5 (p = 0.001), NO2 (p = 0.011) and PM10 (p = 0.041) during the first trimester of pregnancy, when compared with milder clinical severity. After logistic regression, associations with higher clinical severity were identified for PM2.5 exposure during the first trimester (p = 0.002; OR = 1.14, 95%CI: 1.05-1.23) and full pregnancy (p = 0.04; OR = 1.07, 95%CI: 1.00-1.15) and for PM10 (p = 0.02; OR = 1.07, 95%CI: 1.01-1.14) exposure during the third trimester. Exposure to PM is known to elicit neuropathological mechanisms associated with ASD, including neuroinflammation, mitochondrial disruptions, oxidative stress and epigenetic changes. These results offer new insights on the impact of early-life exposure to PM in ASD clinical severity.

Deep into the Apoplast: Grapevine and Plasmopara viticola Proteomes Reveal the Secret Beneath Host and Pathogen Communication at 6 h After Contact.

The apoplast is the first hub of plant-pathogen communication where pathogen effectors are recognized by plant defensive proteins and cell receptors, thus activating signal transduction pathways. As a result of this first contact, the host triggers a defense response that involves the modulation of extra- and intracellular proteins. In grapevine-pathogen interactions, little is known about the trafficking between extra- and intracellular spaces. Grapevine is an economically important crop that relies on heavy fungicide use to control several diseases, and a deeper knowledge on the activation of its immune response is crucial to define new control strategies. In this study, we focused on the first 6 h postinoculation with Plasmopara viticola to evaluate grapevine proteome modulation in the apoplast. The in planta P. viticola proteome was also assessed to enable a deeper understanding of plant-pathogen communication. Our results showed that several plant mechanisms are triggered in the tolerant grapevine cultivar Regent after inoculation, such as oomycete recognition, plant cell wall modifications, reactive oxygen species signaling, and secretion of proteins to disrupt oomycete structures. On the other hand, P. viticola proteins related to development and virulence were the most predominant. This pioneer study highlights the early dynamics of cellular communication in grapevine defense that leads to the successful establishment of an incompatible interaction.

Transcriptomic and methylation analysis of susceptible and tolerant grapevine genotypes following Plasmopara viticola infection.

Downy mildew, caused by the biotrophic oomycete Plasmopara viticola, is one of the most economically significant grapevine diseases worldwide. Current strategies to cope with this threat rely on the massive use of chemical compounds during each cultivation season. The economic costs and negative environmental impact associated with these applications increased the urge to search for sustainable strategies of disease control. Improved knowledge of plant mechanisms to counteract pathogen infection may allow the development of alternative strategies for plant protection. Epigenetic regulation, in particular DNA methylation, is emerging as a key factor in the context of plant-pathogen interactions associated with the expression modulation of defence genes. To improve our understanding of the genetic and epigenetic mechanisms underpinning grapevine response to P. viticola, we studied the modulation of both 5-mC methylation and gene expression at 6 and 24 h post-infection (hpi). Leaves of two table grape genotypes (Vitis vinifera), selected by breeding activities for their contrasting level of susceptibility to the pathogen, were analysed. Following pathogen infection, we found variations in the 5-mC methylation level and the gene expression profile. The results indicate a genotype-specific response to pathogen infection. The tolerant genotype (N23/018) at 6 hpi exhibits a lower methylation level compared to the susceptible one (N20/020), and it shows an early modulation (at 6 hpi) of defence and epigenetic-related genes during P. viticola infection. These data suggest that the timing of response is an important mechanism to efficiently counteract the pathogen attack.

A Role for Gene-Environment Interactions in Autism Spectrum Disorder Is Supported by Variants in Genes Regulating the Effects of Exposure to Xenobiotics.

Heritability estimates support the contribution of genetics and the environment to the etiology of Autism Spectrum Disorder (ASD), but a role for gene-environment interactions is insufficiently explored. Genes involved in detoxification pathways and physiological permeability barriers (e.g., blood-brain barrier, placenta and respiratory airways), which regulate the effects of exposure to xenobiotics during early stages of neurodevelopment when the immature brain is extremely vulnerable, may be particularly relevant in this context. Our objective was to identify genes involved in the regulation of xenobiotic detoxification or the function of physiological barriers (the XenoReg genes) presenting predicted damaging variants in subjects with ASD, and to understand their interaction patterns with ubiquitous xenobiotics previously implicated in this disorder. We defined a panel of 519 XenoReg genes through literature review and database queries. Large ASD datasets were inspected for in silico predicted damaging Single Nucleotide Variants (SNVs) (N = 2,674 subjects) or Copy Number Variants (CNVs) (N = 3,570 subjects) in XenoReg genes. We queried the Comparative Toxicogenomics Database (CTD) to identify interaction pairs between XenoReg genes and xenobiotics. The interrogation of ASD datasets for variants in the XenoReg gene panel identified 77 genes with high evidence for a role in ASD, according to pre-specified prioritization criteria. These include 47 genes encoding detoxification enzymes and 30 genes encoding proteins involved in physiological barrier function, among which 15 are previous reported candidates for ASD. The CTD query revealed 397 gene-environment interaction pairs between these XenoReg genes and 80% (48/60) of the analyzed xenobiotics. The top interacting genes and xenobiotics were, respectively, CYP1A2, ABCB1, ABCG2, GSTM1, and CYP2D6 and benzo-(a)-pyrene, valproic acid, bisphenol A, particulate matter, methylmercury, and perfluorinated compounds. Individuals carrying predicted damaging variants in high evidence XenoReg genes are likely to have less efficient detoxification systems or impaired physiological barriers. They can therefore be particularly susceptible to early life exposure to ubiquitous xenobiotics, which elicit neuropathological mechanisms in the immature brain, such as epigenetic changes, oxidative stress, neuroinflammation, hypoxic damage, and endocrine disruption. As exposure to environmental factors may be mitigated for individuals with risk variants, this work provides new perspectives to personalized prevention and health management policies for ASD.

COVID-19: Nothing is Normal in this Pandemic.

This manuscript brings attention to inaccurate epidemiological concepts that emerged during the COVID-19 pandemic. In social media and scientific journals, some wrong references were given to a "normal epidemic curve" and also to a "log-normal curve/distribution". For many years, textbooks and courses of reputable institutions and scientific journals have disseminated misleading concepts. For example, calling histogram to plots of epidemic curves or using epidemic data to introduce the concept of a Gaussian distribution, ignoring its temporal indexing. Although an epidemic curve may look like a Gaussian curve and be eventually modelled by a Gauss function, it is not a normal distribution or a log-normal, as some authors claim. A pandemic produces highly-complex data and to tackle it effectively statistical and mathematical modelling need to go beyond the "one-size-fits-all solution". Classical textbooks need to be updated since pandemics happen and epidemiology needs to provide reliable information to policy recommendations and actions.

Validation of the international 7-item falls efficacy scale in portuguese community-dwelling older adults / Validación de la escala falls efficacy scale internacional de 7 ítems en ancianos portugueses residentes en la comunidad / Validação da falls efficacy scale internacional 7 itens em idosos portugueses residentes na comunidade

ABSTRACT Objective to determine the psychometric properties of the international 7-item Falls Efficacy Scale. Method a psychometric study. Convenience sample consisting of 170 older adults living in the Madeira Autonomous Region, Portugal. A two-part instrument was used (sociodemographic characterization and the Falls Efficacy Scale-International-Portugal). The starting point was the translation and transcultural adaptation already carried out for the Falls Efficacy Scale - International (16 items). Construct validity (factorial analysis and discriminant validity) and the reliability (Cronbach's α) of the 7-item scale were evaluated. Previous authorization was obtained from the Ethics Commission and from the people involved. Results in the exploratory factorial analysis, the International 7-item Falls Efficacy Scale presents an explained variance of 65.8%. The Spearman's correlation between the score obtained based on the 7 items and the score obtained based on the 16 items is significant and very strong (r=0.987, p<0.0001). Internal consistency was 0.958. Conclusion the validity and reliability study of the International 7-item Falls Efficacy Scale revealed that it is an adequate scale for the evaluation of the fear of falling in the community-dwelling older adults.

RESUMEN Objetivo determinar las propiedades psicométricas de la escala Falls Efficacy Scale Internacional de 7 ítems. Método estudio psicométrico. Muestra por conveniencia de 170 ancianos que viven en la Región Autónoma da Madeira, Portugal. Se empleó un instrumento constituido por dos partes (caracterización sociodemográfica y la escala Falls Efficacy Scale Internacional - Portugal). Se partió de la traducción y adaptación transcultural ya realizada de la escala Falls Efficacy Scale Internacional (16 ítems). Se evaluó la validez de constructo (análisis factorial y validez discriminante) y la confiabilidad (α de Cronbach) de la escala de 7 ítems. Previamente se obtuvo la autorización de la Comisión de Ética y de las personas involucradas. Resultados en el análisis factorial exploratorio, la escala Falls Efficacy Scale Internacional de 7 ítems presenta una varianza explicada del 65,8%. La correlación de Spearman entre la puntuación obtenida sobre la base de los 7 ítems y la obtenida sobre la base de los 16 ítems es significativa y muy fuerte (r=0,987, p<0,0001). La consistencia interna fue de 0,958. Conclusión el estudio de la validez y la confiabilidad de la escala Falls Efficacy Scale Internacional de 7 ítems reveló que es una escala adecuada para evaluar el miedo a caer en el anciano que vive en la comunidad.

RESUMO Objetivo determinar as propriedades psicométricas da Falls Efficacy Scale Internacional 7 itens. Método estudo psicométrico. Amostra de conveniência, de 170 idosos residentes em Região Autónoma da Madeira, Portugal. Recorreu-se a instrumento constituído por duas partes (caracterização sociodemográfica e a Falls Efficacy Scale Internacional Portugal). Partiu-se da tradução e adaptação transcultural já realizada para a Falls Efficacy Scale Internacional (16 itens). Avaliou-se a validade de constructo (análise fatorial e validade discriminante) e a confiabilidade (α de Cronbach) da escala de 7 itens. Obteve-se previamente autorização da Comissão de Ética e das pessoas envolvidas. Resultados na análise fatorial exploratória a Falls Efficacy Scale Internacional 7 itens apresenta uma variância explicada de 65,8%. A correlação de Spearman entre a pontuação obtida com base nos 7 itens e a pontuação obtida com base nos 16 itens é significativa e muito forte (r=0.987, p<0.0001). A consistência interna foi de 0,958. Conclusão o estudo da validade e a confiabilidade da Falls Efficacy Scale Internacional 7 itens revelou ser uma escala adequada para a avaliação do medo de cair na pessoa idosa residente na comunidade.

Validation of the Falls Efficacy Scale - International in a sample of Portuguese elderly.

OBJECTIVE: to translate and adapt Falls Efficacy Scale - International (FES-I). To analyze the psychometric properties of the FES-I Portugal version. METHOD: psychometric study. Sample consisting of 170 elderly people residing in the Autonomous Region of Madeira. A two- part form was used (sociodemographic characterization and FES-I Portugal). The cross-cultural adaptation was performed and the following psychometric properties were evaluated: validity (construct, predictive, and discriminant), reliability (Cronbach's alpha), and inter-rater reliability. RESULTS: the results allow us to verify a dimension of less demanding physical activities and another of more demanding physical activities. The inter-rater reliability study was 0.62, with an interclass correlation coefficient of 0.859, for a 95% confidence interval. The internal consistency of the Portuguese version was 0.962. CONCLUSION: the validity and reliability of the FES-I Portugal are consistent with the original version and proved to be appropriate instruments for evaluating the "impaired walking" and "risk of falls" nursing diagnoses in the older people.

Validation of the Falls Efficacy Scale - International in a sample of Portuguese elderly / Validación da Falls Efficacy Scale International en una muestra de ancianos portugueses / Validação da Falls Efficacy Scale International numa amostra de idosos portugueses

ABSTRACT Objective: to translate and adapt Falls Efficacy Scale - International (FES-I). To analyze the psychometric properties of the FES-I Portugal version. Method: psychometric study. Sample consisting of 170 elderly people residing in the Autonomous Region of Madeira. A two- part form was used (sociodemographic characterization and FES-I Portugal). The cross-cultural adaptation was performed and the following psychometric properties were evaluated: validity (construct, predictive, and discriminant), reliability (Cronbach's alpha), and inter-rater reliability. Results: the results allow us to verify a dimension of less demanding physical activities and another of more demanding physical activities. The inter-rater reliability study was 0.62, with an interclass correlation coefficient of 0.859, for a 95% confidence interval. The internal consistency of the Portuguese version was 0.962. Conclusion: the validity and reliability of the FES-I Portugal are consistent with the original version and proved to be appropriate instruments for evaluating the "impaired walking" and "risk of falls" nursing diagnoses in the older people.

RESUMEN Objetivo: Traducir y adaptar Falls Efficacy Scale Internacional (FES-I). Analizar las propiedades psicométricas de la versión FES-I Portugal. Método: Estudio psicométrico. Muestra constituida por 170 ancianos residentes en la Región Autónoma de Madeira. Se utilizó un formulario compuesto por dos partes (caracterización sociodemográfica y FES-I Portugal). Se realizó la adaptación transcultural y se evaluaron las propiedades psicométricas: validez (constructo, predictiva y discriminante), confiabilidad (α de Cronbach) y fiabilidad interobservador. Resultados: Los resultados permitieron verificar una dimensión de actividades físicas menos exigentes y otra de actividades físicas más exigentes. El estudio de fiabilidad interobservadores fue de 0,62, con un coeficiente de correlación intraclase de 0,859, para un intervalo de confianza de un 95 %. La consistencia interna de la versión portuguesa fue de 0,962. Conclusión: La validez y la confiabilidad de la FES-I Portugal son consistentes con la versión original y se revelan como instrumentos adecuados para la evaluación de los diagnósticos de enfermería «deterioro de la deambulación¼ y «riesgo de caídas¼ en ancianos.

RESUMO Objetivo: traduzir e adaptar Falls Efficacy Scale Internacional (FES-I). Analisar as propriedades psicométricas da versão FES-I Portugal. Método: estudo psicométrico. Amostra constituída por 170 idosos a residir na Região Autónoma da Madeira. Utilizou-se um formulário com duas partes (caracterização sociodemográfica e FES-I Portugal). Fez-se a adaptação transcultural e avaliaram-se as propriedades psicométricas: validade (constructo, preditiva e discriminante), confiabilidade (α de Cronbach) e fiabilidade interobservador. Resultados: os resultados permitiram verificar uma dimensão de atividades físicas menos exigentes e outra de atividades físicas mais exigentes. O estudo de fiabilidade interobservadores foi de 0,62, com um coeficiente de correlação interclasse de 0,859, para um intervalo de confiança de 95%. A consistência interna da versão portuguesa foi de 0,962. Conclusão: a validade e a confiabilidade da FES-I Portugal são consistentes com a versão original e revelam ser instrumentos adequados à avaliação dos diagnósticos de enfermagem "andar comprometido" e "risco de quedas" em idosos.

Functional coherence metrics in protein families.

BACKGROUND: Biological sequences, such as proteins, have been provided with annotations that assign functional information. These functional annotations are associations of proteins (or other biological sequences) with descriptors characterizing their biological roles. However, not all proteins are fully (or even at all) annotated. This annotation incompleteness limits our ability to make sound assertions about the functional coherence within sets of proteins. Annotation incompleteness is a problematic issue when measuring semantic functional similarity of biological sequences since they can only capture a limited amount of all the semantic aspects the sequences may encompass. METHODS: Instead of relying uniquely on single (reductive) metrics, this work proposes a comprehensive approach for assessing functional coherence within protein sets. The approach entails using visualization and term enrichment techniques anchored in specific domain knowledge, such as a protein family. For that purpose we evaluate two novel functional coherence metrics, mUI and mGIC that combine aspects of semantic similarity measures and term enrichment. RESULTS: These metrics were used to effectively capture and measure the local similarity cores within protein sets. Hence, these metrics coupled with visualization tools allow an improved grasp on three important functional annotation aspects: completeness, agreement and coherence. CONCLUSIONS: Measuring the functional similarity between proteins based on their annotations is a non trivial task. Several metrics exist but due both to characteristics intrinsic to the nature of graphs and extrinsic natures related to the process of annotation each measure can only capture certain functional annotation aspects of proteins. Hence, when trying to measure the functional coherence of a set of proteins a single metric is too reductive. Therefore, it is valuable to be aware of how each employed similarity metric works and what similarity aspects it can best capture. Here we test the behaviour and resilience of some similarity metrics.

Clinical indicators of sexual dysfunction in pregnant women: integrative literature review.

OBJECTIVE: to identify the nursing diagnosis clinical indicators of sexual dysfunction in pregnant women. METHOD: it is an integrative literature review, with research in databases using the keywords "sexual*", "pregnan*" and "function*". Studies included had an abstract available for analysis, referring to pregnant women over 18 years old, written in Portuguese, French, Spanish and English, with publication date between 2010 and 2014. Studies that reporting pregnant women with an associated pathology were excluded. RESULTS: sexual dysfunction in pregnant women is consistent in the literature. Nine defining characteristics were identified and 16 related factors, some not classified in NANDA International. CONCLUSION: clinical indicators can be added to the nursing diagnosis to favor an accurate diagnosis and effective interventions in the surveillance of pregnancy as a period of healthy sexual experience.

Indicadores clínicos de disfunção sexual em mulheres grávidas: revisão integrativa de literatura / Indicadores clínicos de disfunción sexual en mujeres embarazadas: revisión integradora de literatura / Clinical indicators of sexual dysfunction in pregnant women: integrative literature review

RESUMO Objetivo: identificar os indicadores clínicos do diagnóstico de enfermagem disfunção sexual em mulheres grávidas. Método: revisão integrativa da literatura, com pesquisa em bases de dados, utilizando os descritores "sexual*", "pregnan*" e"function*". Foram incluídos estudos com resumo disponível para análise, referentes a grávidas com idade igual ou superior a 18 anos, escritos em português, francês, espanhol e inglês, com data de publicação entre 2010 e 2014. Foram excluídos estudos que reportassem grávidas com patologia associada. Resultados: a disfunção sexual na grávida é consistente na literatura. Foram identificadas nove características definidoras e 16 fatores relacionados, alguns não classificados na NANDA Internacional. Conclusão: indicadores clínicos podem ser adicionados ao diagnóstico de enfermagem de modo a favorecer um diagnóstico acurado e intervenções efetivas na vigilância da gravidez como um período de vivência sexual saudável.

RESUMEN Objetivo: identificar los indicadores clínicos del diagnóstico de enfermería disfunción sexual en mujeres embarazadas. Método: revisión integradora de la literatura, con investigación en bases de datos, utilizando las palabras clave "sexual*", "pregnan*" y "function*". Fueron incluidos estudios con resumen disponible para análisis, referentes a embarazadas con edad igual o superior a 18 anos, escritos en português, francés, espanol e inglés, con fecha de publicación entre 2010 y 2014. Fueron excluidos estudios que reportasen embarazadas con patología asociada. Resultados: la disfunción sexual en la embarazada es consistente en la literatura. Fueron identificadas nueve características definidoras y 16 factores relacionados, algunos no clasificados en la NANDA Internacional. Conclusión: indicadores clínicos pueden ser agregados al diagnóstico de enfermería de modo a favorecer un diagnóstico preciso e intervenciones efectivas en la vigilancia del embarazo como un período de vivencia sexual sana.

ABSTRACT Objective: to identify the nursing diagnosis clinical indicators of sexual dysfunction in pregnant women. Method: it is an integrative literature review, with research in databases using the keywords "sexual*", "pregnan*" and "function*". Studies included had an abstract available for analysis, referring to pregnant women over 18 years old, written in Portuguese, French, Spanish and English, with publication date between 2010 and 2014. Studies that reporting pregnant women with an associated pathology were excluded. Results: sexual dysfunction in pregnant women is consistent in the literature. Nine defining characteristics were identified and 16 related factors, some not classified in NANDA International. Conclusion: clinical indicators can be added to the nursing diagnosis to favor an accurate diagnosis and effective interventions in the surveillance of pregnancy as a period of healthy sexual experience.

The Nursing diagnosis 'impaired walking' in elderly: systematic literature review / O diagnóstico de Enfermería 'deterioro de la deambulación' en ancianos: revisión sistemática de la literatura / O diagnóstico de Enfermagem 'andar comprometido' nos idosos: revisão sistemática da literatura

ABSTRACT Walk is an activity that requires different skills and can be highly complex particularly for the elderly. The aim was to identify the defined characteristics and related factors of the nursing diagnosis impaired walking in elderly. A Systematic literature review, based on a search done between January and March 2014, in the electronic platforms EBSCO Host (r) , SCOPUS and ISI, and using the search strategy walk* OR gait AND Nurs*. A sample of 36 studies was obtained. A total of 17 defined characteristics and 34 related factors were identified. Among all, nine defined characteristics and 20 related factors are not listed in the diagnosis of NANDA International. This research identified new defined characteristics and related factors not listed in NANDA International. This study is a contribution to the development of the taxonomy of NANDA International, which should represent nursing knowledge, and this highlights some implications for clinical practice, education and further research.

RESUMEN Caminar es una función que requiere diferentes habilidades y puede ser muy complejo sobre todo para las personas mayores. Lo objetivo fue identificar las características definitorias y factores relacionados de diagnósticos de enfermería marcha comprometida en los ancianos. Revisión sistemática de la literatura, con búsqueda entre enero y marzo de 2014, en las plataformas electrónicas EBSCO Host (r) , SCOPUS e ISI, a través de la estrategia de búsqueda walk* OR gait AND Nurs*. Se obtuvo una muestra de 36 estudios. Se identificó 17 y 34 características que definen los factores relacionados. Se encontró que los factores 9 y 20 características definitorias relacionados no se enumeran en el diagnóstico de la NANDA Internacional. Mediante esta Revisión fueron identificados nuevos indicadores clínicos y factores relacionados, en relación a los clasificados hasta la fecha por la NANDA Internacional. Este estudio constituye una contribución para el desarrollo de la taxonomía NANDA Internacional, que representa el conocimiento en Enfermería, con implicaciones para la práctica clínica, la educación y las investigaciones futuras.

RESUMO Andar é uma função que pressupõe competências diversas e pode ser altamente complexa particularmente para os idosos. O objetivo foi identificar as características definidoras e os fatores relacionados do diagnóstico de enfermagem andar comprometido no idoso. Foi feita revisão sistemática da literatura, com pesquisa entre janeiro e março de 2014, nas plataformas eletrónicas EBSCOhost(r), SCOPUS e ISI, através da estratégia de pesquisa walk* OR gait AND Nurs*. Obteve-se uma amostra de 36 estudos. Identificou-se 17 características definidoras e 34 fatores relacionados. Constatou-se que nove caraterísticas definidoras e 20 fatores relacionados não estão listados no diagnóstico da NANDA Internacional. Esta pesquisa permitiu identificar indicadores clínicos e factores relacionados para além dos que estão classificados na NANDA Internacional. Este estudo constitui um contributo ao desenvolvimento da taxonomia da NANDA Internacional, que deve representar o conhecimento da disciplina de Enfermagem, e que tem implicações na prática clínica, na educação e em novas pesquisas.

Transcriptome meta-analysis reveals common differential and global gene expression profiles in cystic fibrosis and other respiratory disorders and identifies CFTR regulators.

A meta-analysis of 13 independent microarray data sets was performed and gene expression profiles from cystic fibrosis (CF), similar disorders (COPD: chronic obstructive pulmonary disease, IPF: idiopathic pulmonary fibrosis, asthma), environmental conditions (smoking, epithelial injury), related cellular processes (epithelial differentiation/regeneration), and non-respiratory "control" conditions (schizophrenia, dieting), were compared. Similarity among differentially expressed (DE) gene lists was assessed using a permutation test, and a clustergram was constructed, identifying common gene markers. Global gene expression values were standardized using a novel approach, revealing that similarities between independent data sets run deeper than shared DE genes. Correlation of gene expression values identified putative gene regulators of the CF transmembrane conductance regulator (CFTR) gene, of potential therapeutic significance. Our study provides a novel perspective on CF epithelial gene expression in the context of other lung disorders and conditions, and highlights the contribution of differentiation/EMT and injury to gene signatures of respiratory disease.

GRYFUN: a web application for GO term annotation visualization and analysis in protein sets.

Functional context for biological sequence is provided in the form of annotations. However, within a group of similar sequences there can be annotation heterogeneity in terms of coverage and specificity. This in turn can introduce issues regarding the interpretation of actual functional similarity and overall functional coherence of such a group. One way to mitigate such issues is through the use of visualization and statistical techniques. Therefore, in order to help interpret this annotation heterogeneity we created a web application that generates Gene Ontology annotation graphs for protein sets and their associated statistics from simple frequencies to enrichment values and Information Content based metrics. The publicly accessible website http://xldb.di.fc.ul.pt/gryfun/ currently accepts lists of UniProt accession numbers in order to create user-defined protein sets for subsequent annotation visualization and statistical assessment. GRYFUN is a freely available web application that allows GO annotation visualization of protein sets and which can be used for annotation coherence and cohesiveness analysis and annotation extension assessments within under-annotated protein sets.

Transcriptome and metabolome reprogramming in Vitis vinifera cv. Trincadeira berries upon infection with Botrytis cinerea.

Vitis vinifera berries are sensitive towards infection by the necrotrophic pathogen Botrytis cinerea, leading to important economic losses worldwide. The combined analysis of the transcriptome and metabolome associated with fungal infection has not been performed previously in grapes or in another fleshy fruit. In an attempt to identify the molecular and metabolic mechanisms associated with the infection, peppercorn-sized fruits were infected in the field. Green and veraison berries were collected following infection for microarray analysis complemented with metabolic profiling of primary and other soluble metabolites and of volatile emissions. The results provided evidence of a reprogramming of carbohydrate and lipid metabolisms towards increased synthesis of secondary metabolites involved in plant defence, such as trans-resveratrol and gallic acid. This response was already activated in infected green berries with the putative involvement of jasmonic acid, ethylene, polyamines, and auxins, whereas salicylic acid did not seem to be involved. Genes encoding WRKY transcription factors, pathogenesis-related proteins, glutathione S-transferase, stilbene synthase, and phenylalanine ammonia-lyase were upregulated in infected berries. However, salicylic acid signalling was activated in healthy ripening berries along with the expression of proteins of the NBS-LRR superfamily and protein kinases, suggesting that the pathogen is able to shut down defences existing in healthy ripening berries. Furthermore, this study provided metabolic biomarkers of infection such as azelaic acid, a substance known to prime plant defence responses, arabitol, ribitol, 4-amino butanoic acid, 1-O-methyl- glucopyranoside, and several fatty acids that alone or in combination can be used to monitor Botrytis infection early in the vineyard.

Oak root response to ectomycorrhizal symbiosis establishment: RNA-Seq derived transcript identification and expression profiling.

Ectomycorrhizal symbiosis is essential for the life and health of trees in temperate and boreal forests where it plays a major role in nutrient cycling and in functioning of the forest ecosystem. Trees with ectomycorrhizal root tips are more tolerant to environmental stresses, such as drought, and biotic stresses such as root pathogens. Detailed information on these molecular processes is essential for the understanding of symbiotic tissue development in order to optimize the benefits of this natural phenomenon. Next generation sequencing tools allow the analysis of non model ectomycorrhizal plant-fungal interactions that can contribute to find the "symbiosis toolkits" and better define the role of each partner in the mutualistic interaction. By using 454 pyrosequencing we compared ectomycorrhizal cork oak roots with non-symbiotic roots. From the two cDNA libraries sequenced, over 2 million reads were obtained that generated 19,552 cork oak root unique transcripts. A total of 2238 transcripts were found to be differentially expressed when ECM roots were compared with non-symbiotic roots. Identification of up- and down-regulated gens in ectomycorrhizal roots lead to a number of insights into the molecular mechanisms governing this important symbiosis. In cork oak roots, ectomycorrhizal colonization resulted in extensive cell wall remodelling, activation of the secretory pathway, alterations in flavonoid biosynthesis, and expression of genes involved in the recognition of fungal effectors. In addition, we identified genes with putative roles in symbiotic processes such as nutrient exchange with the fungal partner, lateral root formation or root hair decay. These findings provide a global overview of the transcriptome of an ectomycorrhizal host root, and constitute a foundation for future studies on the molecular events controlling this important symbiosis.

Perturbation of polyamine catabolism affects grape ripening of Vitis vinifera cv. Trincadeira.

Grapes are economically the most important fruit worldwide. However, the complexity of biological events that lead to ripening of nonclimacteric fruits is not fully understood, particularly the role of polyamines' catabolism. The transcriptional and metabolic profilings complemented with biochemical data were studied during ripening of Trincadeira grapes submitted to guazatine treatment, a potent inhibitor of polyamine oxidase activity. The mRNA expression profiles of one time point (EL 38) corresponding to harvest stage was compared between mock and guazatine treatments using Affymetrix GrapeGen(®) genome array. A total of 2113 probesets (1880 unigenes) were differentially expressed between these samples. Quantitative RT-PCR validated microarrays results being carried out for EL 35 (véraison berries), EL 36 (ripe berries) and EL 38 (harvest stage berries). Metabolic profiling using HPLC and (1)H NMR spectroscopy showed increase of putrescine, proline, threonine and 1-O-ethyl-ß-glucoside in guazatine treated samples. Genes involved in amino acid, carbohydrate and water transport were down-regulated in guazatine treated samples suggesting that the strong dehydrated phenotype obtained in guazatine treated samples may be due to impaired transport mechanisms. Genes involved in terpenes' metabolism were differentially expressed between guazatine and mock treated samples. Altogether, results support an important role of polyamine catabolism in grape ripening namely in cell expansion and aroma development.

Search for transcriptional and metabolic markers of grape pre-ripening and ripening and insights into specific aroma development in three Portuguese cultivars.

BACKGROUND: Grapes (Vitis species) are economically the most important fruit crop worldwide. However, the complexity of molecular and biochemical events that lead to ripening of berries as well as how aroma is developed are not fully understood. METHODOLOGY/PRINCIPAL FINDINGS: In an attempt to identify the common mechanisms associated with the onset of ripening independently of the cultivar, grapes of Portuguese elite cultivars, Trincadeira, Aragonês, and Touriga Nacional, were studied. The mRNA expression profiles corresponding to veraison (EL35) and mature berries (EL36) were compared. Across the three varieties, 9,8% (2255) probesets corresponding to 1915 unigenes were robustly differentially expressed at EL 36 compared to EL 35. Eleven functional categories were represented in this differential gene set. Information on gene expression related to primary and secondary metabolism was verified by RT-qPCR analysis of selected candidate genes at four developmental stages (EL32, EL35, EL36 and EL 38). Gene expression data were integrated with metabolic profiling data from GC-EI-TOF/MS and headspace GC-EI-MS platforms. CONCLUSIONS/SIGNIFICANCE: Putative molecular and metabolic markers of grape pre-ripening and ripening related to primary and secondary metabolism were established and revealed a substantial developmental reprogramming of cellular metabolism. Altogether the results provide valuable new information on the main metabolic events leading to grape ripening. Furthermore, we provide first hints about how the development of a cultivar specific aroma is controlled at transcriptional level.

Changes in transcriptome of native nasal epithelium expressing F508del-CFTR and intersecting data from comparable studies.

BACKGROUND: Microarray studies related to cystic fibrosis (CF) airway gene expression have gone some way in clarifying the complex molecular background of CF lung diseases, but have made little progress in defining a robust "molecular signature" associated with mutant CFTR expression. Disparate methodological and statistical analyses complicate comparisons between independent studies of the CF transcriptome, and although each study may be valid in isolation, the conclusions reached differ widely. METHODS: We carried out a small-scale whole genome microarray study of gene expression in human native nasal epithelial cells from F508del-CFTR homozygotes in comparison to non-CF controls. We performed superficial comparisons with other microarray datasets in an attempt to identify a subset of regulated genes that could act as a signature of F508del-CFTR expression in native airway tissue samples. RESULTS: Among the alterations detected in CF, up-regulation of genes involved in cell proliferation, and down-regulation of cilia genes were the most notable. Other changes involved gene expression changes in calcium and membrane pathways, inflammation, defence response, wound healing and the involvement of estrogen signalling. Comparison of our data set with previously published studies allowed us to assess the consistency of independent microarray data sets, and shed light on the limitations of such snapshot studies in measuring a system as subtle and dynamic as the transcriptome. Comparison of in-vivo studies nevertheless yielded a small molecular CF signature worthy of future investigation. CONCLUSIONS: Despite the variability among the independent studies, the current CF transcriptome meta-analysis identified subsets of differentially expressed genes in native airway tissues which provide both interesting clues to CF pathogenesis and a possible CF biomarker.