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50 results for “Mycobacterium bovis”
Defining the genes required for survival of Mycobacterium bovis in the bovine host offers novel insights into the genetic basis of survival of pathogenic mycobacteria
<p>Supplementary dataset from "<strong><em>Defining the genes required for survival of Mycobacterium bovis in the bovine host offers novel insights into the genetic basis of survival of pathogenic mycobacteria</em></strong>"</p> <p> </p> <p><strong>Supplementary Figure legends</strong></p> <p><strong>Figure S1. Illustration of the transposon insertions around the <em>M. bovis </em>genome. </strong>Sequencing of the input library showed that transposon insertions were evenly distributed around the genome and 27,419 of the permissible 66,931 thymine–adenine dinucleotide (TA) sites contained an insertion representing an insertion density of ~41%. The outer ring are the genomic coordinates, the blue lines represent transposon insertions and the gray boxes indicate regions of that did not have any insertions. Plot made with Circlize (Gu et al, 2014).</p> <p> </p> <p><strong>Figure S2. Diversity of the output library isolated from lung and thoracic lymph node lesions compared to the input library. </strong>On average, libraries recovered from lung lesions contained 14,456 unique mutants and those recovered from the lymph nodes contained an average of 16,210 unique mutants. Insertion density is represented as a proportion of the TA sites that contained insertions. The numbers on the x-axis refer to the sequencing file from that sample and come from individual animals (Bioproject ID: PRJNA816175, Submission ID: SUB11067380).</p> <p> </p> <p><strong>Figure S3. Volcano plots showing the distribution of log<sub>2</sub> fold-changes and -log<sub>10</sub> of adjusted p-values for representative lung (A) and lymph node (B) samples. </strong>Adjusted p-values (BH-fdr correction) < 0.000001 cluster at the limits of the plot and precision reflects the number of resampling iterations (10,000).</p> <p> </p> <p><strong>Figure S4. Scatterplot of mean log<sub>2</sub> fold change per gene for all lung samples against all thoracic lymph node samples</strong>. Correlation between mean log<sub>2</sub> fold change among genes between the tissues was calculated with Spearman's ranked correlation, = 0.878, p-value < 2.2e-16.</p> <p> </p> <p><strong>Figure S5. Fold-changes caused by transposon insertions in <em>RD1<sup>BCG</sup></em> and <em>RD1<sup>MIC</sup> </em>in the lungs and lymph nodes of infected cattle. </strong>Boxplot for log<sub>2 </sub>fold-changes in genes of the RD1<sup>BCG</sup> region. Samples with adjusted p-values (BH-fdr corrected) <0.05 are indicated with purple points. Gene names highlighted in magenta have fewer than 5 TA sites located in the gene; too few to determine the statistical significance of changes in insertion levels with this method.</p> <p> </p> <p><strong>Supplementary Tables </strong></p> <p><strong>Table S1. Sequencing statistics of the input and output transposon libraries. </strong>The numbers in the column labelled “filename” refers to the sequencing file from that sample and come from individual animals (Bioproject ID: PRJNA816175, Submission ID: SUB11067380).</p> <p> </p> <p><strong>Table S2. Tissues collected and scored for gross pathology. </strong>Tissues from head and neck lymph nodes (from the right and left sub-mandibular lymph nodes, the right and left medial retropharyngeal lymph nodes), thoracic lymph nodes (the right and left bronchial lymph nodes, the cranial tracheobronchial lymph nodes, the cranial and caudal mediastinal lymph nodes) and from lung lesions, were collected and scored.</p> <p> </p> <p><strong>Table S3. Log<sub>2</sub> fold-changes for insertions across the entire genome of <em>M. bovis</em> AF2122/97. </strong>Cells are coloured according to log<sub>2</sub> fold-change. Refer to the text for the gene groups in individual tabs.</p> <p> </p> <p><strong>Table S4. </strong>Custom transposon sequencing primers and adaptors used in sequencing of the transposon libraries.</p> <p> </p>
Supplementary material for journal article "Challenge dose titration in a Mycobacterium bovis infection model in goats"
<p>Supplementary Figure and Table to Journal article. Figure shows daily rectal temperature of each animal after inoculation. Table 1 shows number and volume of pulmonary lesions for each animal as detected by computed tomography imaging. Table 2 gives details about scoring used at clinical examination.</p>
Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome - datasets
<p>This is an archive of the repository held under https://github.com/dmnfarrell/gordon-group/tree/master/mbovis_annotation</p> <p>It contains a notebook and required input files for updating the MTB/Mbovis AF2122/97 genomes with new protein product annotations from literature.</p> <p>D Farrell UCD February 2020</p> <p>Updates to M.bovis genome (Aug 2019):<br> added 611 product annotations<br> added 689 gene names<br> added 5 manually edited entries from pdb hits<br> removed locus_tags for repeat_region features<br> added prefix to tRNA and mobile_element features for consistency</p> <p><br> References<br> Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome (https://www.biorxiv.org/content/10.1101/757823v1)</p>
Appendix of the thesis "Acquisition of new genetic knowledge on strains of Mycobacterium bovis, circulating in France, by the whole genome sequencing approach." Ciriac CHARLES
<p>Appendix 1 Table showing the <em>Mycobacterium bovis </em>genome information used in this study in panel 1 The 87 genomes are from previous work (Hauer et al., 2019). The names of the genomes are highlighted with color to distinguish them within a previously defined M. bovis cluster. In Yellow Cluster I/Clonal Complex Eu3. In orange Cluster G/Family F9. In brown Cluster C/Family SB0134. In purple Cluster D/Clonal Complex Eu1. In pink the Cluster A/Family F4. In blue the Cluster F/Clonal Complex Eu2. In grey, the others.</p> <p>Appendix 2 Table showing the <em>Mycobacterium bovis </em>genome information used in this study in panel 3. The 187 genomes are of genotypes F7 and F15 (SB0821 and SB0832 respectively) which are two closely related genotypes. These genomes had already been sequenced before the start of the thesis work. Some were published with the work of Duault and collaborators and others have not yet been published (noted NA) (Duault et al., 2022).</p> <p>Appendix 3 Table showing the <em>Mycobacterium bovis </em>genome information used in this study in panel 4. The 227 genomes are of genotype SB0120-DHV. These genomes had already been sequenced before the start of the thesis work but are currently unpublished (noted NA in the columns "Date of deposit" and "Genbank biosample").</p> <p>Appendix 4 Position of IS<em>6110</em> insertion sites in the panel of <em>Mycobacterium bovis </em>strains from Pyrénées-Atlantiques (SB0821 and SB0832). The position of the start and end of IS<em>6110</em> are determined with the ISMapper tool and the reference genome AF2122/97.</p> <p>Appendix 5 Position of IS<em>6110</em> insertion sites in the <em>Mycobacterium bovis </em>strain panel of SB0120-DHV. Position of the start and end of IS<em>6110</em> are determined with the ISMapper tool and the Mb3601 reference genome.</p> <p>Appendix 6 This figure from the Modenesi internship report represents a circular consensus phylogenetic tree of 300 strains of SB0120-DHV (Modenesi 2019). The strains in panel 3 are part of these 300 strains and were selected according to their sequencing quality, which explains the smaller number of strains retained (227). This tree is divided into 11 different colored clades. The posterior probability values (which correspond to the probability that these clades are true) determined with Beast (Drummond and Rambaut, 2007) are represented inside the tree.</p>
Appendix of the thesis "Acquisition of new genetic knowledge on Mycobacterium bovis strains, circulating in France, by the whole genome sequencing approach", part "4. Sequencing of new complete genomes", Ciriac CHARLES
<p>Annex S1: Sequencing metric of the 10 new genomes and obtained with fastqc. A: Metric provide to Illumina metric. B: metric provide to MinION metric.</p> <p>Annex S2: Pan-genomic study performed on 12 <em>M. bovis</em> complete genomes. The table indicates the genes accessory. “1” shows the presence of CDS and “0” his absence.</p> <p>Annex S3: Indels between the ten new complete genomes and Mb3601 using progressiveMauve. Annotation of these indels was performed with reference genome comparison for gap or with the annotation (with Prokka) of the new complete genome studied for insertion. IS<em>6110</em> is marked in green. "Indel distribution" sheet shows the indel distribution on the <em>M. bovis</em> genome for the ten new complete genomes. Black arrows show the genomic region with the most of indel found.</p> <p>Annex S4: WgSNP analysis performed on 98 <em>M. bovis</em>. SNPs were annotated and selected according to their specificity to an <em>M. bovis</em> group described in Fig 5. The last common give information on the genetic impact of the SNP. The last sheet presents a graph of SNP number in genomic position.</p> <p>Annex S5: Alignments of the 12 <em>M. bovis </em>complete genomes.</p>
Data used by Calenge et al. in "Assessing the dynamics of Mycobacterium bovis infection in three French badger populations"
<p>The zip file contains the raw dataset used by Calenge et al. in their model of the <em>Mycobacterium bovis</em> infection in three French badger populations. The README file explains the content of this dataset.</p>
Safety, Immunogenicity, and Efficacy of Therapeutic Mycobacterium Bovis BCG (BOOST)
ClinicalTrials.gov study NCT07094711. IPD Sharing: NO. Countries: 1. Publications: 29.
Data from: Revaccination of cattle with Bacille Calmette-Guérin two years after first vaccination when immunity has waned, boosted protection against challenge with Mycobacterium bovis
Open the record for dataset details and reuse information.
Raw Raman data of Mycobacterium bovis BCG, Rhodococcus erythropolis, & Corynebacterium glutamicum
<p>Even in the face of the COVID-19 pandemic, Tuberculosis (TB) continues to be a major public health problem and the 2nd biggest infectious cause of death worldwide. There is, therefore, an urgent need to develop effective TB diagnostic methods, which are cheap, portable, sensitive and specific. Raman spectroscopy is a potential spectroscopic technique for this purpose, however, so far, research efforts have focused primarily on the characterisation of Mycobacterium tuberculosis and other Mycobacteria, neglecting bacteria within the microbiome and thus, failing to consider the bigger picture. It is paramount to characterise relevant Mycobacteriales and develop suitable analytical tools to discriminate them from each other. Herein, through the combined use of Raman spectroscopy and the self-optimising Kohonen index network and further multivariate tools, we have successfully undertaken the spectral analysis of Mycobacterium bovis BCG, Corynebacterium glutamicum and Rhodoccocus erythropolis. This has led to development of a useful tool set, which can readily discern spectral differences between these three closely related bacteria as well as generate a unique spectral barcode for each species. Further optimisation and refinement of the developed method will enable its application to other bacteria inhabiting the microbiome and ultimately lead to advanced diagnostic technologies, which can save many lives. </p>
Raw Raman data of Mycobacterium bovis BCG, Rhodococcus erythropolis, & Corynebacterium glutamicum
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MicroRNA analysis of the bovine alveolar macrophage response to Mycobacterium bovis infection suggests pathogen survival is enhanced by miRNA regulation of endocytosis and lysosome trafficking
GEO Series GSE58883. Bos taurus. 88 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Phase variation in Mycobacterium bovis frd operon disrupts the succinate/HIF-1α/IL-1β axis to drive immunometabolic rewiring and enhance pathogenicity [RNA-seq]
GEO Series GSE291007. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Comparative transcriptomics of Mycobacterium bovis and Mycobacterium marinum
GEO Series GSE51881. Mycobacterium marinum; Mycobacterium tuberculosis variant bovis. 8 samples. Type: Expression profiling by high throughput sequencing; Other.
Amino acid metabolism regulated by DNA Methylation in Mycobacterium bovis BCG str. Tokyo 172 induced by vitamins
GEO Series GSE141513. Mycobacterium tuberculosis variant bovis. 6 samples. Type: Expression profiling by high throughput sequencing.
Characterization of the global bovine microRNAome of peripheral blood mononuclear cells isolated from Mycobacterium bovis exposed cattle
GEO Series GSE285119. Bos taurus. 12 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Comparative transcriptomic signatures of virulent and attenuated Mycobacterium bovis growing in vitro and in mice
GEO Series GSE308287. Mycobacterium. 12 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis
GEO Series GSE60265. Bos taurus. 16 samples. Type: Expression profiling by high throughput sequencing.
Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro
GEO Series GSE45439. Bos taurus. 14 samples. Type: Expression profiling by high throughput sequencing.
The bovine alveolar macrophage (bAM) DNA methylome is resilient to infection with Mycobacterium bovis
GEO Series GSE110412. Bos taurus. 16 samples. Type: Methylation profiling by high throughput sequencing.
Annexe de la thèse "Acquisition de nouvelles connaissances génétiques sur les souches de Mycobacterium bovis, circulant en France, par l'approche du séquençage du génome complet." Ciriac CHARLES
<p>Annexe 1 : Tableau présentant les informations des génomes de <em>Mycobacterium bovis</em> utilisés dans cette étude dans le panel 1 Les 87 génomes proviennent d’un travail précédent (Hauer et al., 2019). Le nom des génomes est surligné d’une couleur permettant de les distinguer à l’intérieur d’un groupe de M. bovis précédemment défini. En Jaune le Cluster I/Complexe clonal Eu3. En orange le Cluster G/Famille F9. En marron le Cluster C/Famille SB0134. En violet le Cluster D/Complexe clonal Eu1. En rose le Cluster A/Famille F4. En bleu le Cluster F/Complexe clonal Eu2. En gris, les autres.</p> <p>Annexe 2 : Tableau présentant les informations des génomes de <em>Mycobacterium bovis</em> utilisés dans cette étude dans le panel 3. Les 187 génomes sont de génotypes F7 et F15 (respectivement SB0821 et SB0832) qui sont deux génotypes très proches. Ces génomes avaient déjà été séquencés avant le début du travail de thèse. Certains ont été publiés avec le travail de Duault et collaborateur et d’autres ne l’ont pas encore été (noté NA) (Duault et al., 2022).</p> <p>Annexe 3 : Tableau présentant les informations des génomes de <em>Mycobacterium bovis</em> utilisés dans cette étude dans le panel 4. Les 227 génomes sont de génotypes SB0120-DHV. Ces génomes avaient déjà été séquencés avant le début du travail de thèse, mais ne sont actuellement pas publiés (noté NA dans les colonnes "Date de dépot" et "Bio-échantillon Genbank").</p> <p>Annexe 4 : Position des sites d’insertions IS<em>6110</em> dans le panel de souche de <em>Mycobacterium bovis</em> de Pyrénées-Atlantiques (SB0821 et SB0832). Position du début et de la fin de l’IS<em>6110</em> sont déterminés avec l’outil ISMapper et le génome de référence AF2122/97.</p> <p>Annexe 5 : Position des sites d’insertions IS<em>6110</em> dans le panel de souche de <em>Mycobacterium bovis </em>de SB0120-DHV. Position du début et de la fin de l’IS<em>6110</em> sont déterminés avec l’outil ISMapper et le génome de référence Mb3601.</p> <p>Annexe 6 : Cette figure provenant du rapport de stage de Modenesi représente un arbre phylogénétique consensus circulaire de 300 souches de SB0120-DHV (Modenesi 2019). Les souches du panel 3 font parties de ces 300 souches et ont été sélectionné selon la qualité de séquençage de celle-ci ce qui explique le nombre plus petit de souches retenues (227). Cet arbre est divisé en 11 clades de couleur différente. Les valeurs de probabilité postérieures (qui correspondent à la probabilité que ces clades soient vrais) déterminées avec Beast (Drummond and Rambaut, 2007) sont représentées à l’intérieur de l’arbre.</p>
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International Brain Laboratory public data
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.