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  1. Article ; Online: Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis

    Kristoffer Sahlin / Botond Sipos / Phillip L. James / Paul Medvedev

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 13

    Abstract: Nanopore sequencing technologies applied to transcriptome analysis suffer from high error rates, limiting them largely to reference-based analyses. Here, the authors develop a computational error correction method for transcriptome analysis that reduces ... ...

    Abstract Nanopore sequencing technologies applied to transcriptome analysis suffer from high error rates, limiting them largely to reference-based analyses. Here, the authors develop a computational error correction method for transcriptome analysis that reduces the median error rate from ~7% to ~1%.
    Keywords Science ; Q
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Comparison of the upper and lower airway microbiota in children with chronic lung diseases.

    Bushra Ahmed / Michael J Cox / Leah Cuthbertson / Phillip L James / William O C Cookson / Jane C Davies / Miriam F Moffatt / Andrew Bush

    PLoS ONE, Vol 13, Iss 8, p e

    2018  Volume 0201156

    Abstract: RATIONALE:The lower airway microbiota is important in normal immunological development and chronic lung diseases (CLDs). Young children cannot expectorate and because of the uncertainty whether upper airway samples reflect the lower airway microbiota, ... ...

    Abstract RATIONALE:The lower airway microbiota is important in normal immunological development and chronic lung diseases (CLDs). Young children cannot expectorate and because of the uncertainty whether upper airway samples reflect the lower airway microbiota, there have been few longitudinal paediatric studies to date. OBJECTIVES:To assess whether throat swabs (TS) and cough swabs (CS) are representative of the lower airway microbiota. METHODS:TS, CS, bronchoalveolar lavage and bronchial brushings were prospectively collected from 49 children undergoing fibreoptic bronchoscopy for CLDs. Bacterial DNA was extracted and the 16S rRNA gene V4 region sequenced using the Illumina MiSeq. RESULTS:5.97 million high quality reads were obtained from 168 samples (47 TS, 37 CS, 42 BALF and 42 bronchial brushings). CS sequenced poorly. At a community level, no difference in alpha diversity (richness, evenness or Shannon Diversity Index) was seen between lower airway samples and TS (P > 0.05). Less than 6.31% of beta diversity variation related to sampling method for TS (P = 0.001). Variation between pathologies and individual patients was greater (20%, 54% respectively P ≤ 0.001) than between TS and lower airway samples. There was strong correlation in the relative abundance of genera between samples (r = 0.78, P < 0.001). Similarity between upper and lower airway samples was observed to be less for individuals where one sample type was dominated by a single organism. CONCLUSIONS:At the community structure level, TS correlate with lower airway samples and distinguish between different CLDs. TS may be a useful sample for the study of the differences in longitudinal changes in the respiratory microbiota between different CLDs. Differences are too great however for TS to be used for clinical decision making.
    Keywords Medicine ; R ; Science ; Q
    Subject code 610
    Language English
    Publishing date 2018-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-cystic fibrosis bronchiectasis patients.

    Michael J Cox / Elena M Turek / Catherine Hennessy / Ghazala K Mirza / Phillip L James / Meg Coleman / Andrew Jones / Robert Wilson / Diana Bilton / William O C Cookson / Miriam F Moffatt / Michael R Loebinger

    PLoS ONE, Vol 12, Iss 2, p e

    2017  Volume 0170622

    Abstract: BACKGROUND:Bronchiectasis is accompanied by chronic bronchial infection that may drive disease progression. However, the evidence base for antibiotic therapy is limited. DNA based methods offer better identification and quantification of microbial ... ...

    Abstract BACKGROUND:Bronchiectasis is accompanied by chronic bronchial infection that may drive disease progression. However, the evidence base for antibiotic therapy is limited. DNA based methods offer better identification and quantification of microbial constituents of sputum than standard clinical culture and may help inform patient management strategies. Our study objective was to determine the longitudinal variability of the non-cystic fibrosis (CF) bronchiectasis microbiome in sputum with respect to clinical variables. Eighty-five patients with non-CF bronchiectasis and daily sputum production were recruited from outpatient clinics and followed for six months. Monthly sputum samples and clinical measurements were taken, together with additional samples during exacerbations. 16S rRNA gene sequencing of the sputum microbiota was successful for 381 samples from 76 patients and analysed in conjunction with clinical data. RESULTS:Microbial communities were highly individual in composition and stability, usually with limited diversity and often containing multiple pathogens. When compared to DNA sequencing, microbial culture had restricted sensitivity in identifying common pathogens such as Pseudomonas aeruginosa, Haemophilus influenzae, Moraxella catarrhalis. With some exceptions, community characteristics showed poor correlations with clinical features including underlying disease, antibiotic use and exacerbations, with the subject showing the strongest association with community structure. When present, the pathogens mucoid Pseudomonas aeruginosa and Haemophilus influenzae may also shape the structure of the rest of the microbial community. CONCLUSIONS:The use of microbial community analysis of sputum added to information from microbial culture. A simple model of exacerbations driven by bacterial overgrowth was not supported, suggesting a need for revision of principles for antibiotic therapy. In individual patients, the management of chronic bronchial infection may be improved by therapy specific to their ...
    Keywords Medicine ; R ; Science ; Q
    Subject code 610
    Language English
    Publishing date 2017-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

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  4. Article ; Online: Corticosteroid suppression of antiviral immunity increases bacterial loads and mucus production in COPD exacerbations

    Aran Singanayagam / Nicholas Glanville / Jason L. Girkin / Yee Man Ching / Andrea Marcellini / James D. Porter / Marie Toussaint / Ross P. Walton / Lydia J. Finney / Julia Aniscenko / Jie Zhu / Maria-Belen Trujillo-Torralbo / Maria Adelaide Calderazzo / Chris Grainge / Su-Ling Loo / Punnam Chander Veerati / Prabuddha S. Pathinayake / Kristy S. Nichol / Andrew T. Reid /
    Phillip L. James / Roberto Solari / Peter A. B. Wark / Darryl A. Knight / Miriam F. Moffatt / William O. Cookson / Michael R. Edwards / Patrick Mallia / Nathan W. Bartlett / Sebastian L. Johnston

    Nature Communications, Vol 9, Iss 1, Pp 1-

    2018  Volume 16

    Abstract: Corticosteroid therapy is frequently used for chronic obstructive pulmonary disease (COPD) but its use is associated with increased risk of pneumonia. Here the authors show that corticosteroid use impairs innate and adaptive immunity to rhinovirus ... ...

    Abstract Corticosteroid therapy is frequently used for chronic obstructive pulmonary disease (COPD) but its use is associated with increased risk of pneumonia. Here the authors show that corticosteroid use impairs innate and adaptive immunity to rhinovirus infection, which is restored by exogenous IFNβ.
    Keywords Science ; Q
    Language English
    Publishing date 2018-06-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

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  5. Article ; Online: Corticosteroid suppression of antiviral immunity increases bacterial loads and mucus production in COPD exacerbations

    Aran Singanayagam / Nicholas Glanville / Jason L. Girkin / Yee Man Ching / Andrea Marcellini / James D. Porter / Marie Toussaint / Ross P. Walton / Lydia J. Finney / Julia Aniscenko / Jie Zhu / Maria-Belen Trujillo-Torralbo / Maria Adelaide Calderazzo / Chris Grainge / Su-Ling Loo / Punnam Chander Veerati / Prabuddha S. Pathinayake / Kristy S. Nichol / Andrew T. Reid /
    Phillip L. James / Roberto Solari / Peter A. B. Wark / Darryl A. Knight / Miriam F. Moffatt / William O. Cookson / Michael R. Edwards / Patrick Mallia / Nathan W. Bartlett / Sebastian L. Johnston

    Nature Communications, Vol 9, Iss 1, Pp 1-

    2018  Volume 16

    Abstract: Corticosteroid therapy is frequently used for chronic obstructive pulmonary disease (COPD) but its use is associated with increased risk of pneumonia. Here the authors show that corticosteroid use impairs innate and adaptive immunity to rhinovirus ... ...

    Abstract Corticosteroid therapy is frequently used for chronic obstructive pulmonary disease (COPD) but its use is associated with increased risk of pneumonia. Here the authors show that corticosteroid use impairs innate and adaptive immunity to rhinovirus infection, which is restored by exogenous IFNβ.
    Keywords Science ; Q
    Language English
    Publishing date 2018-06-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

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