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974 results for “mycobacterium”
Human memory CD4+ T cells recognize <em>Mycobacterium tuberculosis</em>-infected macrophages amid broader pathogen-specific responses
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Whole genome sequence data of Mycobacterium tuberculosis and Mycolicibacterium smegmatis mutants of the riboflavin biosynthetic pathway- Part 2
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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>
Plasticity, ligand conformation and enzyme action of Mycobacterium smegmatis MutT1
<p><em>Mycobacterium smegmatis</em> MutT1 (<em>Ms</em>MutT1) is a sanitation enzyme made up of an N-terminal Nudix hydrolase domain and a C-terminal domain resembling a histidine phosphatase. It has been established that the action of MutT1 on 8-oxo-dGTP, 8-oxo-GTP and diadenosine polyphosphates is modulated by intermolecular interactions. In order to further explore this and to elucidate the structural basis of its differential action on 8-oxo-NTPs and unsubstituted NTPs, the crystal structures of complexes of <em>Ms</em>MutT1 with 8-oxo-dGTP, GMPPNP and GMPPCP have been determined. Replacement soaking was used in order to ensure that the complexes were isomorphous to one another. Analysis of the structural data led to the elucidation of a relationship between the arrangements of molecules observed in the crystals, molecular plasticity and the action of the enzyme on nucleotides. The dominant mode of arrangement involving a head-to-tail sequence predominantly leads to the generation of NDPs. The other mode of packing arrangement appears to preferentially generate NMPs. This work also provides interesting insights into the dependence of enzyme action on the conformation of the ligand. The possibility of modulating the enzyme action through differences in intermolecular interactions and ligand conformations makes <em>Ms</em>MutT1 a versatile enzyme.</p>
Plasticity, ligand conformation and enzyme action of Mycobacterium smegmatis MutT1
<p><em>Mycobacterium smegmatis</em> MutT1 (<em>Ms</em>MutT1) is a sanitation enzyme made up of an N-terminal Nudix hydrolase domain and a C-terminal domain resembling a histidine phosphatase. It has been established that the action of MutT1 on 8-oxo-dGTP, 8-oxo-GTP and diadenosine polyphosphates is modulated by intermolecular interactions. In order to further explore this and to elucidate the structural basis of its differential action on 8-oxo-NTPs and unsubstituted NTPs, the crystal structures of complexes of <em>Ms</em>MutT1 with 8-oxo-dGTP, GMPPNP and GMPPCP have been determined. Replacement soaking was used in order to ensure that the complexes were isomorphous to one another. Analysis of the structural data led to the elucidation of a relationship between the arrangements of molecules observed in the crystals, molecular plasticity and the action of the enzyme on nucleotides. The dominant mode of arrangement involving a head-to-tail sequence predominantly leads to the generation of NDPs. The other mode of packing arrangement appears to preferentially generate NMPs. This work also provides interesting insights into the dependence of enzyme action on the conformation of the ligand. The possibility of modulating the enzyme action through differences in intermolecular interactions and ligand conformations makes <em>Ms</em>MutT1 a versatile enzyme.</p>
Plasticity, ligand conformation and enzyme action of Mycobacterium smegmatis MutT1
<p><em>Mycobacterium smegmatis</em> MutT1 (<em>Ms</em>MutT1) is a sanitation enzyme made up of an N-terminal Nudix hydrolase domain and a C-terminal domain resembling a histidine phosphatase. It has been established that the action of MutT1 on 8-oxo-dGTP, 8-oxo-GTP and diadenosine polyphosphates is modulated by intermolecular interactions. In order to further explore this and to elucidate the structural basis of its differential action on 8-oxo-NTPs and unsubstituted NTPs, the crystal structures of complexes of <em>Ms</em>MutT1 with 8-oxo-dGTP, GMPPNP and GMPPCP have been determined. Replacement soaking was used in order to ensure that the complexes were isomorphous to one another. Analysis of the structural data led to the elucidation of a relationship between the arrangements of molecules observed in the crystals, molecular plasticity and the action of the enzyme on nucleotides. The dominant mode of arrangement involving a head-to-tail sequence predominantly leads to the generation of NDPs. The other mode of packing arrangement appears to preferentially generate NMPs. This work also provides interesting insights into the dependence of enzyme action on the conformation of the ligand. The possibility of modulating the enzyme action through differences in intermolecular interactions and ligand conformations makes <em>Ms</em>MutT1 a versatile enzyme.</p>
Plasticity, ligand conformation and enzyme action of Mycobacterium smegmatis MutT1
<p><em>Mycobacterium smegmatis</em> MutT1 (<em>Ms</em>MutT1) is a sanitation enzyme made up of an N-terminal Nudix hydrolase domain and a C-terminal domain resembling a histidine phosphatase. It has been established that the action of MutT1 on 8-oxo-dGTP, 8-oxo-GTP and diadenosine polyphosphates is modulated by intermolecular interactions. In order to further explore this and to elucidate the structural basis of its differential action on 8-oxo-NTPs and unsubstituted NTPs, the crystal structures of complexes of <em>Ms</em>MutT1 with 8-oxo-dGTP, GMPPNP and GMPPCP have been determined. Replacement soaking was used in order to ensure that the complexes were isomorphous to one another. Analysis of the structural data led to the elucidation of a relationship between the arrangements of molecules observed in the crystals, molecular plasticity and the action of the enzyme on nucleotides. The dominant mode of arrangement involving a head-to-tail sequence predominantly leads to the generation of NDPs. The other mode of packing arrangement appears to preferentially generate NMPs. This work also provides interesting insights into the dependence of enzyme action on the conformation of the ligand. The possibility of modulating the enzyme action through differences in intermolecular interactions and ligand conformations makes <em>Ms</em>MutT1 a versatile enzyme.</p>
Data from: Bacteriophage infection and killing of intracellular Mycobacterium abscessus
<p><em>Mycobacterium</em> <em>abscessus</em> is a nontuberculous mycobacterium (NTM) that contributes to the decline and death of patients with lung diseases such as cystic fibrosis and other muco-obstructive airway diseases. <em>M. abscessus</em> is challenging to treat due to its extensive antibiotic resistance and ability to survive inside mammalian cells. An alternative to antibiotics is the therapeutic use of bacteriophages (phages). There are recent cases of phage therapy being used to treat <em>M. abscessus</em> infections in people under compassionate-use conditions. However, little is known about the ability of phages to kill bacteria, such as <em>M. abscessus</em>, that reside in an intracellular environment. Here, we used <em>M. abscessus</em> strains and phages from recent phage therapy cases to determine if phages can enter mammalian cells and if they can infect and kill intracellular <em>M. abscessus</em>. Using fluorescence microscopy, we demonstrate phage uptake by macrophages and lung epithelial cells, and we further demonstrate phage infection of intracellular <em>M. abscessus</em> with fluorescent reporter phages. Transmission electron microscopy was additionally used to image phage infection of intracellular <em>M. abscessus</em>. Together, these findings provide the first visualizations of phage-<em>M. abscessus</em> interactions in an intracellular environment. Finally, we show that phage treatment can significantly reduce the intracellular burden of <em>M. abscessus</em> in a manner that depends on both the specific phage and mammalian cell type involved. These results demonstrate the potential to use phage therapy to treat intracellular bacteria, specifically <em>M. abscessus</em>, while also highlighting the importance of prescreening phage therapy candidates for activity in an intracellular environment.</p>
GENOMIC INSIGHTS INTO THE GLOBAL EVOLUTION AND ANTIBIOTIC RESISTANCE OF THE MYCOBACTERIUM TUBERCULOSIS COMPLEX
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Genome of the inferred most recent common ancestor of the Mycobacterium tuberculosis complex
<p>Genome of the inferred most recent common ancestor of the <em>Mycobacterium tuberculosis</em> complex (MTBC) as described in <em>Human T cell epitopes of </em>Mycobacterium tuberculosis<em> are evolutionarily hyperconserved</em>. Comas et al 2010; Nature Genetics (doi:10.1038/ng.590).</p> <p>Mapping to the inferred MTBC ancestor instead of an extant, Lineage 4/LAM strain, allows to better distinguish between ancestral and derived mutations. This is exemplified by the number of single-nucleotide polymorphisms called for strains from different MTBC lineages (Figure 1).</p> <p>Figure 1 shows the number of fixed SNPs (fSNPs; allele frequency >= 90%), called for <em>Mycobacterium tuberculosis</em> isolates from different MTBC lineages when aligning to the reference strain H37Rv or to the MTBC ancestor. Each dot is an isolate. When aligning to the MTBC ancestor, some isolates appear as "outliers", with less fSNPs than the average. These are mixed infections.</p>
Drug sensitive and multidrug-resistant Mycobacterium tuberculosis genotypes from Bulgaria
<p>Dataset of drug sensitive and multidrug-resistant Mycobacteium tuberculosis spoligo- and MIRU-VNTR genotypes from Bulgaria collected between 2008 till 2019.</p>
Mycobacterium tuberculosis complex NGS made easy: data analysis step-by-step (datasets)
<p>Datasets used in the workshop "<em>Mycobacterium tuberculosis</em> complex NGS made easy: data analysis step-by-step". A capacity development initiative by TB-CAPT, PanACEA and Seq&Treat.</p>
Substrate recognition and cryo-EM structure of the ribosome-bound TAC toxin of Mycobacterium tuberculosis
<p>Datasets for the Figures 2 and S2 of the manuscript "Substrate recognition and cryo-EM structure of the ribosome-bound TAC toxin of Mycobacterium tuberculosis".</p> <p> </p> <p>The HTML files describe the analysis and the raw counts after nEMOTE-conv treatment.</p> <p>There are 5 files for each MMEMOTExx dataset:</p> <p>EmoteBarcodesReport.csv = summary<br> UnambNegTable.csv = counts of unique cuts on the reverse strand<br> UnambPosTable.csv = counts of unique cuts on the forward strand<br> AmbPosTable.csv = counts of all cuts on the forward strand<br> AmbNegTable.csv = counts of all cuts on the reverse strand</p> <p> </p>
Role of Alkylhydroperoxidase Rv2159c in the Oxidative Stress Response and Virulence of Mycobacterium tuberculosis
<p><em>Mycobacterium tuberculosis</em>, which causes tuberculosis, is one of the leading infectious agents worldwide with a high rate of mortality. Following aerosol inhalation, <em>M. tuberculosis</em> primarily infects the alveolar macrophages, which results in a host immune response that gradually activates various antimicrobial mechanisms, including the production of reactive oxygen species (ROS), within the phagocytes to neutralize the bacteria. <em>OxyR</em> is the master regulator of oxidative stress response in several bacterial species. However, due to the absence of a functional <em>oxyR </em>locus in <em>M. tuberculosis,</em> the peroxidase stress is controlled by alkylhydroperoxidases. <em>M. tuberculosis </em>expresses alkylhydroperoxide reductase to counteract the toxic effects of ROS. In the current study, we report the functional characterization of an ortholgue of alkylhydroperoxidase family member, Rv2159c, a conserved protein with putative peroxidase activity, during stress response and virulence of <em>M. tuberculosis</em><em>. </em>We generated a gene knockout mutant of <em>M. tuberculosis </em>Rv2159c (MtbΔ2159) by specialized transduction. The MtbΔ2159 was sensitive to oxidative stress and exposure to toxic transition metals. In a human monocyte (THP-1) cell infection model, MtbΔ2159 showed reduced intracellular survival and increased expression of pro-inflammatory molecules, includingIL-1β, IP-10 and MIP-1α, compared to the wild type <em>M. tuberculosis</em> and Rv2159c-complemented MtbΔ2159 strains. Similarly, in a guinea pig model of pulmonary infection, MtbΔ2159 displayed growth attenuation in the lungs, compared to the wild type <em>M. tuberculosis</em> and Rv2159c-complemented MtbΔ2159 strains<em>. </em>Our study suggests that Rv2159c has a significant role in maintaining the cellular homeostasis during stress and virulence of <em>M. tuberculosis</em>. </p>
MR1-restricted T-cell clonotypes are associated with 'resistance' to Mycobacterium Tuberculosis infection - TRA/D immunoSEQ
<p><strong>Summary</strong></p> <ul> <li>Number of files: 39</li> <li>Data format: tsv</li> <li>Data type: TCRA/D immunoSEQ (Adaptive Biotechnologies)</li> <li>immunoSEQ version: v2</li> <li>Sample type: peripheral blood mononuclear cells (PBMCs)</li> <li>Genomic DNA extraction protocol: QIAGEN DNeasy Blood and Tissue kit</li> </ul> <p><strong>Sample description</strong></p> <p>Peripheral blood samples were collected from participants enrolled in a longitudinal cohort study based in Uganda. Donors were classified as either "resistors" (RSTRs, n = 19, defined as concordantly negative for tuberculin skin test and IFNg release assay despite high environmental exposure) or latently infected with M. Tuberculosis (LTBI, n = 20, concordantly as longitudinally positive for tuberculin skin test and IFNg release assay). Genomic DNA (gDNA) was extracted from cryopreserved PBMCs without stimulation or enrichment of T-cells using the Quiagen DNeasy Blood and Tissue kit. Protocol can be found at: https://www.qiagen.com/us/products/discovery-and-translational-research/dna-rna-purification/dna-purification/genomic-dna/dneasy-blood-and-tissue-kit </p>
Single Crystal X-ray diffraction data for Mycobacterium tuberculosis BioA
<p>Single crystal X-ray diffraction data for MtBioA related to PDBID: xxxx</p> <p>Data collected at Diamond Light Source, UK</p> <p>Beamline I03</p>
Simulation dataset for "Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters"
<p>Simulated Illumina reads for SNP distance method evaluation and comparison used in the article "Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters".</p> <p>Details for simulation can be found at https://gitlab.com/rki_bioinformatics/panpasco/tree/master/simulation_dataset.</p>
Confocal imaging raw data files of autophagy analysis in optn and p62 zebrafish mutants during Mycobacterium marinum infection
<p>Association of fluorescent Mycobacterium marinum bacteria with Ubiquitin immunolabelling and GFP-Lc3 signal in zebrafish larvae carrying mutations in the selective autophagy receptors optnineurin and p62. Data deposited are Leica LIF files belonging bioRxiv 415463; doi: https://doi.org/10.1101/415463</p>
Monoclonal antibodies from humans with Mycobacterium tuberculosis exposure or latent infection recognize distinct arabinomannan epitopes
<p>The surface polysacharide arabinomannan (AM) and related glycolipid lipoarabinomannan (LAM) play critical roles in tuberculosis pathogenesis. Human antibody responses to AM/LAM are heterogenous and knowledge of reactivity to specific glycan epitopes at the monoclonal level is limited, especially in individuals who can control <i><span>M. tuberculosis</span></i> infection<span>. </span>We generated human IgG mAbs to AM/LAM from B cells of two asymptomatic individuals exposed to or latently infected with <i><span>M. tuberculosis</span></i>. We here show that two of these mAbs have high affinity to AM/LAM, are non-competing, and recognize different glycan epitopes <span>distinct from other anti-AM/LAM mAbs reported. Both mAbs recognize virulent </span><i><span>M. tuberculosis</span></i><span> and nontuberculous mycobacteria with marked differences, can be used for the detection of urinary LAM, and can detect </span><i><span>M. tuberculosis</span></i><span> and LAM in infected lungs. These mAbs enhance our understanding of the spectrum of antibodies to AM/LAM epitopes </span>in humans <span>and</span> are valuable for <span>tuberculosis</span> diagnostic and research applications.</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>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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.