The genomic diversification of grapevine clones.

BACKGROUND:Vegetatively propagated clones accumulate somatic mutations. The purpose of this study was to better appreciate clone diversity and involved defining the nature of somatic mutations throughout the genome. Fifteen Zinfandel winegrape clone genomes were sequenced and compared to one another using a highly contiguous genome reference produced from one of the clones, Zinfandel 03. RESULTS:Though most heterozygous variants were shared, somatic mutations accumulated in individual and subsets of clones. Overall, heterozygous mutations were most frequent in intergenic space and more frequent in introns than exons. A significantly larger percentage of CpG, CHG, and CHH sites in repetitive intergenic space experienced transition mutations than in genic and non-repetitive intergenic spaces, likely because of higher levels of methylation in the region and because methylated cytosines often spontaneously deaminate. Of the minority of mutations that occurred in exons, larger proportions of these were putatively deleterious when they occurred in relatively few clones. CONCLUSIONS:These data support three major conclusions. First, repetitive intergenic space is a major driver of clone genome diversification. Second, clones accumulate putatively deleterious mutations. Third, the data suggest selection against deleterious variants in coding regions or some mechanism by which mutations are less frequent in coding than noncoding regions of the genome

Social support and Quality of Life: a cross-sectional study on survivors eight months after the 2008 Wenchuan earthquake

<p>Abstract</p> <p>Background</p> <p>The 2008 Wenchuan earthquake resulted in extensive loss of life and physical and psychological injuries for survivors. This research examines the relationship between social support and health-related quality of life for the earthquake survivors.</p> <p>Methods</p> <p>A multistage cluster sampling strategy was employed to select participants from 11 shelters in nine counties exposed to different degrees of earthquake damage, for a questionnaire survey. The participants were asked to complete the Short Form 36 and the Social Support Rating Scale eight months after the earthquake struck. A total of 1617 participants returned the questionnaires. The quality of life of the survivors (in the four weeks preceding the survey) was compared with that of the general population in the region. Multivariate logistic regression analysis and canonical correlation analysis were performed to determine the association between social support and quality of life.</p> <p>Results</p> <p>The earthquake survivors reported poorer quality of life than the general population, with an average of 4.8% to 19.62% reduction in scores of the SF-36 (p < 0.001). The multivariate logistic regression analysis showed that those with stronger social support were more likely to have better quality of life. The canonical correlation analysis found that there was a discrepancy between actual social support received and perceived social support available, and the magnitude of this discrepancy was inversely related to perceived general health (rs = 0.467), and positively related to mental health (rs = 0.395).</p> <p>Conclusion</p> <p>Social support is associated with quality of life in the survivors of the earthquake. More attention needs to be paid to increasing social support for those with poorer mental health.</p

Epidemiology of intra-abdominal infection and sepsis in critically ill patients: “AbSeS”, a multinational observational cohort study and ESICM Trials Group Project

Purpose: To describe the epidemiology of intra-abdominal infection in an international cohort of ICU patients according to a new system that classifies cases according to setting of infection acquisition (community-acquired, early onset hospital-acquired, and late-onset hospital-acquired), anatomical disruption (absent or present with localized or diffuse peritonitis), and severity of disease expression (infection, sepsis, and septic shock). Methods: We performed a multicenter (n = 309), observational, epidemiological study including adult ICU patients diagnosed with intra-abdominal infection. Risk factors for mortality were assessed by logistic regression analysis. Results: The cohort included 2621 patients. Setting of infection acquisition was community-acquired in 31.6%, early onset hospital-acquired in 25%, and late-onset hospital-acquired in 43.4% of patients. Overall prevalence of antimicrobial resistance was 26.3% and difficult-to-treat resistant Gram-negative bacteria 4.3%, with great variation according to geographic region. No difference in prevalence of antimicrobial resistance was observed according to setting of infection acquisition. Overall mortality was 29.1%. Independent risk factors for mortality included late-onset hospital-acquired infection, diffuse peritonitis, sepsis, septic shock, older age, malnutrition, liver failure, congestive heart failure, antimicrobial resistance (either methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, extended-spectrum beta-lactamase-producing Gram-negative bacteria, or carbapenem-resistant Gram-negative bacteria) and source control failure evidenced by either the need for surgical revision or persistent inflammation. Conclusion: This multinational, heterogeneous cohort of ICU patients with intra-abdominal infection revealed that setting of infection acquisition, anatomical disruption, and severity of disease expression are disease-specific phenotypic characteristics associated with outcome, irrespective of the type of infection. Antimicrobial resistance is equally common in community-acquired as in hospital-acquired infection

Identification of metabolic markers of ripening near harvest in Pinot Noir

At the onset of berry ripening, four developmentally different berry classes exist simultaneously within the same cluster and represent the most and least developed berries. They were designated Green Hard (GH), Green Soft (GS), Pink Soft (PS) and Red Soft (RS). These classes are assumed indistinguishable from one another at harvest and that the four berry classes follow the ripening curve shown below. However, whether or not this synchronization occurs metabolically at commercial harvest has not been demonstrated. This study will describe the metabolome of Pinot noir near harvest. The objective of this study is to describe which metabolites exhibit minimal variability or persistent variability among the four classes of berries near harvest to clarify the contribution of ripeness heterogeneity to overall fruit quality

Rootstock influences the effect of grapevine leafroll‐associated viruses on berry development and metabolism via abscisic acid signalling

Grapevine leafroll-associated virus (GLRaV) infections are accompanied by symptoms influenced by host genotype, rootstock, environment, and which individual or combination of GLRaVs is present. Using a dedicated experimental vineyard, we studied the responses to GLRaVs in ripening berries from Cabernet Franc grapevines grafted to different rootstocks and with zero, one, or pairs of leafroll infection(s). RNA sequencing data were mapped to a high-quality Cabernet Franc genome reference assembled to carry out this study and integrated with hormone and metabolite abundance data. This study characterized conserved and condition-dependent responses to GLRaV infection(s). Common responses to GLRaVs were reproduced in two consecutive years and occurred in plants grafted to different rootstocks in more than one infection condition. Though different infections were inconsistently distinguishable from one another, the effects of infections in plants grafted to different rootstocks were distinct at each developmental stage. Conserved responses included the modulation of genes related to pathogen detection, abscisic acid (ABA) signalling, phenylpropanoid biosynthesis, and cytoskeleton remodelling. ABA, ABA glucose ester, ABA and hormone signalling-related gene expression, and the expression of genes in several transcription factor families differentiated the effects of GLRaVs in berries from Cabernet Franc grapevines grafted to different rootstocks. These results support that ABA participates in the shared responses to GLRaV infection and differentiates the responses observed in grapevines grafted to different rootstocks

The genomic diversification of grapevine clones.

BACKGROUND:Vegetatively propagated clones accumulate somatic mutations. The purpose of this study was to better appreciate clone diversity and involved defining the nature of somatic mutations throughout the genome. Fifteen Zinfandel winegrape clone genomes were sequenced and compared to one another using a highly contiguous genome reference produced from one of the clones, Zinfandel 03. RESULTS:Though most heterozygous variants were shared, somatic mutations accumulated in individual and subsets of clones. Overall, heterozygous mutations were most frequent in intergenic space and more frequent in introns than exons. A significantly larger percentage of CpG, CHG, and CHH sites in repetitive intergenic space experienced transition mutations than in&nbsp;genic and non-repetitive intergenic spaces, likely because of higher levels of methylation in the region and&nbsp;because methylated cytosines often spontaneously deaminate. Of the minority of mutations that occurred in exons, larger proportions of these were putatively deleterious when they occurred in relatively few clones. CONCLUSIONS:These data support three major conclusions. First, repetitive intergenic space is a major driver of clone genome diversification. Second, clones accumulate putatively deleterious mutations. Third, the data suggest selection against deleterious variants in coding regions or some mechanism by which mutations are less frequent in coding than noncoding regions of the genome

Reliability and validity of spirituality questionnaire by Parsian and Dunning in the Spanish version Confiabilidad y validez del cuestionario de espiritualidad de Parsian y Dunning en versión española Validade e confiabilidade do Questionário de Espiritualidade de Parsian e Dunning em versão espanhola

The aim of this methodological study was to translate, culturally adapt and assess the internal consistency and validity of the Spanish version of the "Spirituality Questionnaire". The sample comprised 204 young people between 18 and 25 years of age from two universities in Bogotá. Cronbach's Alpha was used for reliability, while groups of experts and young people were used for construct validity. Exploratory and confirmatory factor analysis was used for construct validity. The reliability score of the total instrument was 0.88. The overall index of content validity corresponded to 0.90. Exploratory factor analysis showed that four factors explain 52.60% of the variance. The originally proposed theoretical model was confirmed and, in two dimensions, a different structure was proposed. In conclusion, the instrument "Spirituality Questionnaire" by Parsian and Dunning is reliable and valid in the Spanish version.<br>Se presenta un estudio de tipo metodológico, cuyo objetivo fue el de traducir, adaptar culturalmente, evaluar la consistencia interna y la validez de la versión en español del "Cuestionario de Espiritualidad". La muestra fue de 204 jóvenes de 18 a 25 años, de dos universidades en Bogotá. Se utilizó el Alpha de Cronbach para la confiablidad, mientras la validez de contenido fue por paneles de expertos y jóvenes. Para la validez de constructo se utilizó el análisis factorial exploratorio y confirmatorio. La confiablidad del instrumento total fue de 0.88. El índice global de validez de contenido de 0.90. El análisis factorial exploratorio arrojó que el 52.60% de la varianza está explicada por cuatro factores. Se confirmó el modelo teórico originalmente propuesto y en dos de las dimensiones se planteó una estructura diferente. Se concluye que el instrumento "Cuestionario de Espiritualidad" de Parsian y Dunning es confiable y válido en su versión en español.<br>Trata-se de estudo metodológico que objetivou traduzir, adaptar culturalmente, avaliar a consistência interna e validade da versão em espanhol do Questionário de Espiritualidade, de Parsian e Dunning. A amostra foi composta por 204 estudantes entre 18 e 25 anos, de duas universidades de Bogotá, Colômbia. Parar testar a confiabilidade utilizou-se o alpha de Cronbach. A validade de conteúdo foi realizada por um grupo de juízes e uma amostra de 12 estudantes. Para validade de construto foram realizadas análises fatoriais exploratória e confirmatória. A confiabilidade total obteve um alfa de 0,88. O índice total de validade de conteúdo observado foi de 0,90. O produto da análise fatorial evidenciou que 52,6% da variância foi explicada pelos quatro fatores. O modelo teórico proposto originalmente foi confirmado, observando-se diferença em duas das dimensões originais. Concluiu-se que o instrumento é confiável e válido em sua versão em língua espanhola