A software pipeline for processing and identification of fungal ITS sequences

<p>Abstract</p> <p>Background</p> <p>Fungi from environmental samples are typically identified to species level through DNA sequencing of the nuclear ribosomal internal transcribed spacer (<it>ITS</it>) region for use in BLAST-based similarity searches in the International Nucleotide Sequence Databases. These searches are time-consuming and regularly require a significant amount of manual intervention and complementary analyses. We here present software – in the form of an identification pipeline for large sets of fungal <it>ITS </it>sequences – developed to automate the BLAST process and several additional analysis steps. The performance of the pipeline was evaluated on a dataset of 350 <it>ITS </it>sequences from fungi growing as epiphytes on building material.</p> <p>Results</p> <p>The pipeline was written in Perl and uses a local installation of NCBI-BLAST for the similarity searches of the query sequences. The variable subregion <it>ITS2 </it>of the <it>ITS </it>region is extracted from the sequences and used for additional searches of higher sensitivity. Multiple alignments of each query sequence and its closest matches are computed, and query sequences sharing at least 50% of their best matches are clustered to facilitate the evaluation of hypothetically conspecific groups. The pipeline proved to speed up the processing, as well as enhance the resolution, of the evaluation dataset considerably, and the fungi were found to belong chiefly to the <it>Ascomycota</it>, with <it>Penicillium </it>and <it>Aspergillus </it>as the two most common genera. The <it>ITS2 </it>was found to indicate a different taxonomic affiliation than did the complete <it>ITS </it>region for 10% of the query sequences, though this figure is likely to vary with the taxonomic scope of the query sequences.</p> <p>Conclusion</p> <p>The present software readily assigns large sets of fungal query sequences to their respective best matches in the international sequence databases and places them in a larger biological context. The output is highly structured to be easy to process, although it still needs to be inspected and possibly corrected for the impact of the incomplete and sometimes erroneously annotated fungal entries in these databases. The open source pipeline is available for UNIX-type platforms, and updated releases of the target database are made available biweekly. The pipeline is easily modified to operate on other molecular regions and organism groups.</p

The estimated prevalence of exposure to asthmagens in the Australian workforce

Background: There is very little information available on a national level as to the number of people exposed to specific asthmagens in workplaces. Methods: We conducted a national telephone survey in Australia to investigate the prevalence of current occupational exposure to 277 asthmagens, assembled into 27 groups. Demographic and current job information were obtained. A web-based tool, OccIDEAS, was used to collect job task information and assign exposure to each asthmagen group. Results: In the Australian Workplace Exposure Study – Asthma (AWES- Asthma) we interviewed 4878 participants (2441 male and 2437 female). Exposure to at least one asthmagen was more common among men (47 %) than women (40 %). Extrapolated to the Australian population, approximately 2.8 million men and 1.7 million women were estimated to be exposed. Among men, the most common exposures were bioaerosols (29 %) and metals (27 %), whilst the most common exposures among women were latex (25 %) and industrial cleaning and sterilising agents (20 %). Conclusions: This study provides information about the prevalence of exposure to asthmagens in Australian workplaces which will be useful in setting priorities for control and prevention of occupational asthma

Exposure to environmental tobacco smoke among South Korean adults: a cross-sectional study of the 2005 Korea National Health and Nutrition Examination Survey

<p>Abstract</p> <p>Background</p> <p>Studies have identified that environmental tobacco smoke exposure is associated with sociodemographic factors such as age, sex, and socioeconomic status, but few studies have been conducted in South Korea. In this study, the authors investigated the extent of environmental tobacco smoke exposure and factors related in a nationally representative sample of Korean adults.</p> <p>Methods</p> <p>The data of 7,801 adults aged 19 years and over collected during the 2005 Korea National Health and Nutrition Examination Survey were analyzed. Information on smoking habits and exposure to environmental tobacco smoke was obtained by self-reports using a standardized questionnaire. Risks of environmental tobacco smoke exposure conferred by sociodemographic variables and behavioral risk factors were evaluated using logistic regression methods.</p> <p>Results</p> <p>Overall, 36.1% of nonsmokers (defined as those not currently smoking) and 50.1% of current smokers were found to be exposed to environmental tobacco smoke either at work or at home. Among the nonsmokers, women were more likely to be exposed to environmental tobacco smoke at home (OR = 5.22, 95%CI, 4.08-6.67). Furthermore, an inverse relationship was found between education level and the risk of environmental tobacco smoke exposure at home (OR = 1.73, 95%CI, 1.38-2.17 for those with a high school education; OR = 2.30, 95%CI, 1.68-3.16 for those with a middle school education; and OR = 2.58, 95%CI, 1.85-3.59 for those with less than an elementary school education vs. those with a college education or more). In addition, those with office, sales service, or manual labor jobs were found to be at significantly higher risk of environmental tobacco smoke exposure at work than those with professional, administrative, or managerial jobs. Also, the risk of environmental tobacco smoke exposure in the workplace was significantly higher for alcohol drinkers than non-drinkers (OR = 1.23, 95%CI, 1.07-1.47). After adjusting for age, sex and education, it was found that those exposed to environmental tobacco smoke at home were more likely to have been admitted to hospital during the previous year (OR 1.29, 95%CI, 1.002-1.66).</p> <p>Conclusions</p> <p>In this study of Korean adults, exposure to environmental tobacco smoke at home or work was found to be affected by sex, age, marital status, educational level, and type of occupation. Accordingly, these factors should be given appropriate consideration by those developing policies or interventions designed to control exposure to environmental tobacco smoke.</p

Adult attention deficit hyperactivity disorder is associated with asthma

<p>Abstract</p> <p>Background</p> <p>Attention deficit hyperactivity disorder (ADHD) is increasingly recognized as a common disorder not only in children, but also in the adult population. Similarly, asthma also has a substantial prevalence among adults. Previous studies concerning a potential relationship between ADHD and asthma have not presented consistent results.</p> <p>Methods</p> <p>A cross-sectional study of 594 adult patients diagnosed with ADHD, compared with 719 persons from the general population. Information was collected between 1997 and 2005 using auto-questionnaires rating past and present symptoms of ADHD, co-morbid conditions, including asthma, and work status.</p> <p>Results</p> <p>The prevalence of asthma was significantly higher in the ADHD patient group compared to the controls, 24.4% vs. 11.3% respectively (OR = 2.54, 95% CI 1.89-3.44), and controls with asthma scored higher on ratings of both past and present symptoms of ADHD. Female ADHD patients had a significantly higher prevalence of asthma compared to male ADHD patients (30.9% vs. 18.2%, OR = 2.01, CI 1.36-2.95), but in controls a slight female preponderance was not statistically significant. In both ADHD patients and controls, having asthma was associated with an increased prevalence of symptoms of mood- and anxiety disorders.</p> <p>Conclusions</p> <p>The present findings point to a co-morbidity of ADHD and asthma, and these patients may represent a clinical and biological subgroup of adult patients with ADHD.</p

Mouse models to unravel the role of inhaled pollutants on allergic sensitization and airway inflammation

Air pollutant exposure has been linked to a rise in wheezing illnesses. Clinical data highlight that exposure to mainstream tobacco smoke (MS) and environmental tobacco smoke (ETS) as well as exposure to diesel exhaust particles (DEP) could promote allergic sensitization or aggravate symptoms of asthma, suggesting a role for these inhaled pollutants in the pathogenesis of asthma. Mouse models are a valuable tool to study the potential effects of these pollutants in the pathogenesis of asthma, with the opportunity to investigate their impact during processes leading to sensitization, acute inflammation and chronic disease. Mice allow us to perform mechanistic studies and to evaluate the importance of specific cell types in asthma pathogenesis. In this review, the major clinical effects of tobacco smoke and diesel exhaust exposure regarding to asthma development and progression are described. Clinical data are compared with findings from murine models of asthma and inhalable pollutant exposure. Moreover, the potential mechanisms by which both pollutants could aggravate asthma are discussed

Cleaning at home and at work in relation to lung function decline and airway obstruction

Rationale: Cleaning tasks may imply exposure to chemical agents with potential harmful effects to the respiratory system, and increased risk of asthma and respiratory symptoms among professional cleaners and in persons cleaning at home has been reported. Long-term consequences of cleaning agents on respiratory health are, however, not well described. Objectives: This study aimed to investigate long-term effects of occupational cleaning and cleaning at home on lung function decline and airway obstruction. Methods: The European Community Respiratory Health Survey (ECRHS) investigated a multicenter population-based cohort at three time points over 20 years. A total of 6,235 participants with at least one lung function measurement from 22 study centers, who in ECRHS II responded to questionnaire modules concerning cleaning activities between ECRHS I and ECRHS II, were included. The data were analyzed with mixed linear models adjusting for potential confounders. Measurements and Main Results: As compared with women not engaged in cleaning (ΔFEV1 = −18.5 ml/yr), FEV1 declined more rapidly in women responsible for cleaning at home (−22.1; P = 0.01) and occupational cleaners (−22.4; P = 0.03). The same was found for decline in FVC (ΔFVC = −8.8 ml/yr; −13.1, P = 0.02; and −15.9, P = 0.002; respectively). Both cleaning sprays and other cleaning agents were associated with accelerated FEV1 decline (−22.0, P = 0.04; and −22.9, P = 0.004; respectively). Cleaning was not significantly associated with lung function decline in men or with FEV1/FVC decline or airway obstruction. Conclusions: Women cleaning at home or working as occupational cleaners had accelerated decline in lung function, suggesting that exposures related to cleaning activities may constitute a risk to long-term respiratory health

Cleaning at home and at work in relation to lung function decline and airway obstruction

Rationale: Cleaning tasks may imply exposure to chemical agents with potential harmful effects to the respiratory system, and increased risk of asthma and respiratory symptoms among professional cleaners and in persons cleaning at home has been reported. Long-term consequences of cleaning agents on respiratory health are, however, not well described. Objectives: This study aimed to investigate long-term effects of occupational cleaning and cleaning at home on lung function decline and airway obstruction. Methods: The European Community Respiratory Health Survey (ECRHS) investigated a multicenter population-based cohort at three time points over 20 years. A total of 6,235 participants with at least one lung function measurement from 22 study centers, who in ECRHS II responded to questionnaire modules concerning cleaning activities between ECRHS I and ECRHS II, were included. The data were analyzed with mixed linear models adjusting for potential confounders. Measurements and Main Results: As compared with women not engaged in cleaning (ΔFEV1 = −18.5 ml/yr), FEV1 declined more rapidly in women responsible for cleaning at home (−22.1; P = 0.01) and occupational cleaners (−22.4; P = 0.03). The same was found for decline in FVC (ΔFVC = −8.8 ml/yr; −13.1, P = 0.02; and −15.9, P = 0.002; respectively). Both cleaning sprays and other cleaning agents were associated with accelerated FEV1 decline (−22.0, P = 0.04; and −22.9, P = 0.004; respectively). Cleaning was not significantly associated with lung function decline in men or with FEV1/FVC decline or airway obstruction. Conclusions: Women cleaning at home or working as occupational cleaners had accelerated decline in lung function, suggesting that exposures related to cleaning activities may constitute a risk to long-term respiratory health