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4,498 results for “mitochondrial”
A novel approach to the detection of unusual mitochondrial protein change suggests hypometabolism of ancestral simians: Supplemental Files
<p><strong>Supplementary Fig. S1</strong>: θ<sub>evo</sub> calculated for each analyzed edge for specific OXPHOS complexes. Analyses were performed as in fig. 1F, except that SPCSs calculated from mtDNA-encoded protein positions in Complex I, Complex III, Complex IV, or Complex V were used to generate θevo values.</p> <p><strong>Supplementary Fig. S2</strong>: Mammalian orders differ in their propensity for potentially efficacious mitochondrial protein substitutions within specific OXPHOS complexes (median calculations). Analysis was performed as in fig. 2A, except that θ<sub>evo</sub> values were obtained by analysis of mtDNA-encoded Complex I, Complex III, Complex IV, or Complex V polypeptides.</p> <p><strong>Supplementary Fig. S3</strong>: Mammalian orders differ in their propensity for potentially efficacious mitochondrial protein substitutions within specific OXPHOS complexes (median confidence intervals). Analysis was performed as in (<em>A</em>) fig. 2B or (<em>B</em>) fig. 2C, except that θ<sub>evo</sub> values were obtained by analysis of mtDNA-encoded Complex I, Complex III, Complex IV, or Complex V proteins.</p> <p><strong>Supplementary Fig. S4</strong>: Mammalian families differ in their propensity for potentially efficacious mitochondrial protein substitutions at specific OXPHOS complexes (median calculations). Analysis was performed as in fig. 3A, except that θ<sub>evo</sub> values were obtained by analysis of mtDNA-encoded Complex I, Complex III, Complex IV, or Complex V subunits.</p> <p><strong>Supplementary Fig. S5</strong>: Mammalian families differ in their propensity for potentially efficacious mitochondrial protein substitutions at specific OXPHOS complexes (median confidence intervals ordered by lower 90% median confidence limit). Analysis was performed as in fig. 3B, except that θ<sub>evo</sub> values were obtained by analysis of mtDNA-encoded Complex I, Complex III, Complex IV, or Complex V proteins.</p> <p><strong>Supplementary Fig. S6</strong>: Mammalian families differ in their propensity for potentially efficacious mitochondrial protein substitutions at specific OXPHOS complexes (median confidence intervals ordered by upper 90% median confidence limit). Analysis was performed as in fig. 3C, except that θ<sub>evo</sub> values were obtained by analysis of mtDNA-encoded Complex I, Complex III, Complex IV, or Complex V polypeptides.</p> <p>---</p> <p><strong>Supplementary File 1</strong>: All predicted protein substitutions along all edges at positions containing less than 2% gaps across input and ancestral sequences are listed, along with associated taxonomy information, TSS, and branch length. All alignment positions refer to Bos taurus reference sequences.</p> <p><strong>Supplementary File 2</strong>: The TSS calculated for each mitochondrial protein alignment position. All alignment positions refer to Bos taurus reference sequences.</p> <p><strong>Supplementary File 3</strong>: SPCS and θevo outputs are provided for analyses across all mitochondria-encoded positions, as well as for focused analyses of specific OXPHOS complexes and individual proteins.</p> <p><strong>Supplementary File 4</strong>: A GenBank flat file containing RefSeq entries for mammalian mtDNAs, as well as the entry for the reptile Anolis punctatus.</p> <p><strong>Supplementary File 5</strong>: A maximum likelihood inferred tree generated by a RAxML-NG analysis of concatenated and aligned protein coding sequences from mammalian and Anolis punctatusmtDNAs.</p> <p><strong>Supplementary File 6</strong>: Bootstrap replicates were generated from the alignment of concatenated protein coding sequences. Felsenstein’s Bootstrap Proportions (Felsenstein 1985) were calculated and used to label the maximum likelihood inferred tree of mammalian mtDNAs.</p> <p><strong>Supplementary File 7</strong>: Bootstrap replicates were generated using concatenated mammalian mtDNA coding sequences. Transfer Bootstrap Expectations (Lemoine 2018) were calculated and used to label the maximum likelihood inferred tree of mammalian mtDNAs.</p> <p><strong>Supplementary File 8</strong>: PAGAN tree output produced using aligned amino acid sequences and the rooted maximum likelihood inferred tree as input.</p>
Phylogeny of "Philoceanus complex" seabird lice (Phthiraptera: Ischnocera) inferred from mitochondrial DNA sequences
<p>Data from "Phylogeny of “<em>Philoceanus </em>complex” seabird lice (Phthiraptera: Ischnocera) inferred from mitochondrial DNA sequences". See the file index.html for details. Data includes NEXUS files for sequences, tree files output by MrBayes and PAUP, and host-parasite association files for TreeMap.</p>
Inter-Chemical Correlation results for the study: HHEARx2017-1740 (Mitochondrial DNA biomarkers of prenatal metal mixture exposure: intergenerational inheritance and infant growth)
Title: Mitochondrial DNA biomarkers of prenatal metal mixture exposure: intergenerational inheritance and infant growth <br>Species: Homo sapiens <br>Number of samples: 1423 <br>Number of named analytes: 20 <br>Datasource url: https://hheardatacenter.mssm.edu/PublicFile/ViewPublicFile?projectid=19 <br>
Data and software supporting the manuscript 'The population frequency of human mitochondrial DNA variants is highly dependent upon mutational bias'
<p>Next-generation sequencing can quickly reveal genetic variation potentially linked to heritable disease. As databases encompassing human variation continue to expand, rare variants have been of high interest, since the frequency of a variant is expected to be low if the genetic change leads to a loss of fitness or fecundity. However, the use of variant frequency when seeking genomic changes linked to disease remains very challenging. Here, we explore the role of selection in controlling human variant frequency using the HelixMT database, which encompasses hundreds of thousands of mitochondrial DNA (mtDNA) samples. We find that a substantial number of synonymous substitutions, which have no effect on protein sequence, were never encountered in this large study, while many other synonymous changes are found at very low frequencies. Further analyses of human and mammalian mtDNA datasets indicate that the population frequency of synonymous variants is predominantly determined by mutational biases rather than by strong selection acting upon nucleotide choice. Our work has important implications that extend to the interpretation of variant frequency for non-synonymous substitutions. </p> <p> </p>
Systematic investigation of mitochondrial transfer between cancer and T cells at singlecell level
<p>The benmark datasets about MT transfer, including mtSNV profile, coverage information, cell information and expression information.</p>
Datasets associated with Agostini, S., Houlbreque, F., Biscéré, T., Harvey, B. P., Heitzman, J. M., Takimoto, R., et al. (2020). Greater mitochondrial energy production provides resistance to ocean acidification in 'winning' hermatypic corals. Front. Mar. Sci. 7. doi:10.3389/fmars.2020.600836.
<p>Datasets associated with Agostini, S., Houlbreque, F., Biscéré, T., Harvey, B. P., Heitzman, J. M., Takimoto, R., et al. (2020). Greater mitochondrial energy production provides resistance to ocean acidification in ‘winning’ hermatypic corals. Front. Mar. Sci. 7. doi:10.3389/fmars.2020.600836.</p>
Time-lapse 3D confocal microscopy videos of mitochondrial dynamics in human alveolar epithelial cells (A549-DsRed) infected with Mycobacterium marinum (Mmar) strains
<div>The dataset consists of time-lapse, 3D confocal images of mitochondrial dynamics in human alveolar epithelial cells (A549-DsRed) infected with Mycobacterium marinum (Mmar) strains. Images were captured at 60X magnification in an environmental chamber at 35°C for live-cell imaging. Host cell mitochondria were labeled with red fluorescent protein (RFP) and infected with both wildtype (wt) and ESAT-6 operon knockout mutant labeled with green fluorescent protein (GFP) at MOI of 100 for 24 hours at 35°C. Infected cells were identified and analyzed to explore the effect of pathogenic mycobacteria on mitochondrial morphology over time.</div> <div> </div> <div>More details available in this preprint: <a href="https://doi.org/10.48550/arXiv.2411.06035">https://doi.org/10.48550/arXiv.2411.06035</a></div>
Metabolomics data associated with "Glial swip-10 controls systemic mitochondrial function, oxidative stress, and neuronal viability via copper ion homeostasis"
<p>Raw feature tables used for metabolomic analysis of the <em>Caenorhabditis elegans</em> mutant <em>swip-10</em>. The data were generated using liquid chromatography coupled high-resolution mass spectrometry. Two different columns were used: HILIC (+ ESI) and C18 (-ESI), coupled to a Thermo Q-Exactive Orbitrap mass spectrometer. The feature tables were generated using open-source peak peaking and alignment R packages: apLCMS and xMAanalyzer. See more details in the associated manuscript.</p>
Supplementary Materials associated with paper 'Complete linear mitochondrial genomes for Cephea cephea and Mastigias albipunctata (Scyphozoa: Rhizostomeae), with an analysis of phylogenetic relationships'
<p>This is a repository for coverage depth graphs and ML-phylogenetic trees that are associated with the paper 'Complete linear mitochondrial genomes for Cephea cephea and Mastigias albipunctata (Scyphozoa: Rhizostomeae), with an analysis of phylogenetic relationships' by Tan KC, Collins AG and Ames CL.</p>
Bioenergetic cluster analysis – mitochondrial respiratory control in human fibroblasts
<p>Gnaiger E (2021) Bioenergetic cluster analysis – mitochondrial respiratory control in human fibroblasts. MitoFit Preprints 2021.8. doi:10.26124/mitofit:2021-0008 - https://www.mitofit.org/index.php/Gnaiger_2021_MitoFit_BCA</p> <p>All respirometric data that were used for meta-analysis are obtained from the original publications, were converted to SI units, and are available here as a basis for bioenergetic cluster analysis. Inverted regression analysis is illustrated by an example (Figures 1c and d).</p>
Mitochondrial genome sequencing and analysis of the invasive Microstegium vimineum: a resource for systematics, invasion history, and management
<p>Table S1: Accession data for Microstegium samples included in this study.</p> <p>File S1: Alignment of Mitochondrial CDS for Poales mitochondrial sequences.</p> <p>File S2: SNP data for Microstegium vimineum mitochondrial variants.</p> <p>Figure S1: Transposable element content in the Microstegium vimineum mitogenome.</p> <p>Figure S2: Summary of Kraken2 output.</p> <p> </p>
Mitochondrial COXI sequences and associated metazoan abundances in soils collected from the McMurdo Dry Valleys, Antarctica from 1995 to 2022
As part of an ongoing long-term sampling effort conducted by the McMurdo Dry Valleys Long Term Ecological Research (LTER) project, the top 10 cm of soil was collected from sampling sites across the McMurdo Dry Valleys region of Antarctica. A subset of these samples representing each valley and a differing disturbance legacy from the last glacial maximum were analyzed for this data package. Samples were collected between 1995 and 2022. In each sample, the abundances of three genera of nematodes (Scottnema, Eudorylaimus, and Plectus), tardigrades, and rotifers were calculated. Following metazoan extractions, individual Scottnema lindsayae were selected for mitochondrial Cytochrome c oxidase I (COX1) Sanger dideoxy sequencing. Sequencing resulted in 249 assembled sequences of 285 base pairs after alignment and trimming.
Fig. 5 in First insights into past biodiversity of giraffes based on mitochondrial sequences from museum specimens
Fig. 5. Giraffe subspecies of the Nile region. The map (extracted from Google Earth; https://www.google.com/intl/de/earth/) shows the geographical barriers (rivers and mountains) that may have isolated (at least temporarily) the subspecies Giraffa camelopardalis camelopardalis (Linnaeus, 1758) (red), G. c. antiquorum (Jardine, 1835) (yellow), G. c. rothschildi Lydekker, 1903 (green) and G. c. reticulata de Winton, 1899 (magenta). The question mark refers to the uncertain geographic origin of Zarafa (left) and the two specimens from Abyssinia (right) (see Discussion for more details).
Fig. 2 in First insights into past biodiversity of giraffes based on mitochondrial sequences from museum specimens
Fig. 2. Illustrations of historical giraffe specimens. A. The ʻGiraffe of Levaillantʼ, anonymous painting made in the late 18th century and early 19th century, exhibited in ʻhôtel de Magnyʼ, Jardin des Plantes in Paris (France). B. The ʻGiraffe from Sennaarʼ, representing a lithography of Zarafa (MNHN-1845-211) and the skull of a giraffe from the Cape region (Geoffroy Saint-Hilaire 1827). C. Drawing of the holotype of Giraffa camelopardalis congoensis Lydekker, 1903 (RMCA-452), housed in the Royal Museum of Central Africa, Tervuren (Belgium) (Lydekker 1904). D. Head drawings of the holotypes of G. c. cottoni Lydekker, 1904 (NHMUK-1904.1.21.1, left) and G. g. wardi Lydekker, 1904 (NHMUK-1903.11.18.1, right) (Lydekker 1914).
Figure 1 in Evaluation of the taxonomy of Helix cincta (Muller, 1774) and Helix nucula (Mousson, 1854); insights using mitochondrial DNA sequence data
Figure 1. Map showing the localities of samples used in the present study representing the morphologically defined species and the distribution of Helix cincta (dash line, light grey) and Helix nucula (continuous line, dark grey).
Heteroplasmy Benchmark Dataset - mitochondrial DNA mixture model - MiSeq - U5-H1-M1-M2-M3-M4-M5 - FASTQ
<p>mtDNA mixture model of 2 mtDNA sequences belonging to haplogroups U5 and H1. Run on Illumina MiSeq with 3 different polymerases (Clontech, Herculase, NEB Taq), and different DNA extraction protocols - Paired-end Fastq files</p> <p>M1 = Mixture 1:2 i.e. 50%</p> <p>M2 = Mixture 1:10 i.e. 10%</p> <p>M3 = Mixture 1:50 i.e. 2%</p> <p>M4 = Mixture 1:100 i.e. 1%</p> <p>M5 = Mixture 1:200 i.e. 0.5%</p>
mRNA expression data of genes related to mitochondrial quality control in hepatopancreas of the two marine bivalves, Mytilus edulis and Crassostrea gigas, during short-term hypoxia/reoxygenation stress
<p>Coastal environments commonly experience strong oxygen fluctuations. Resulting hypoxia/reoxygenation stress can negatively affect mitochondrial functions, since oxygen deficiency impairs ATP generation, whereas a surge of oxygen causes mitochondrial damage by oxidative stress mechanisms. Marine intertidal bivalves are adapted to fluctuating oxygen conditions, yet the underlying molecular mechanisms that sustain mitochondrial integrity and function during oxygen fluctuations are not yet well understood. We used targeted mRNA expression analysis to determine the potential involvement of the mitochondrial quality control mechanisms in responses to short-term hypoxia (24 h at <0.01% O<sub>2</sub>) and subsequent reoxygenation (1.5 h at 21% O<sub>2</sub>) in two hypoxia-tolerant marine bivalves, the Pacific oysters <em>Crassostrea gigas</em> and the blue mussels <em>Mytilus edulis</em>. To test these hypotheses, We focused on the transcript levels of the following marker genes: for mitochondrial fission and fusion - <em>mfn</em>2 (encoding mitofusin 2), <em>opa</em>1 (mitochondrial dynamin-like 120kDa protein), <em>dnm</em>1<em>l </em>(dynamin-1-like protein), <em>mff</em> (mitochondrial fission factor), <em>fis</em>1 (mitochondrial fission protein 1); for protein and DNA quality control - <em>tsfm</em> (encoding mitochondrial translation elongation factor Ts), <em>lonp</em>1 (mitochondrial Lon protease), <em>spg</em>7 (paraplegin), <em>oma</em>1 (mitochondrial metalloendopeptidase OMA1), <em>clpB</em> (mitochondrial caseinolytic matrix peptidase chaperone subunit B), <em>atp</em>23 (mitochondrial inner membrane protease ATP23), <em>twnk</em> (mitochondrial twinkle mtDNA helicase); and for mitophagy - <em>mieap</em> (encoding mitochondrial eating protein), <em>hyou</em>1 (hypoxia upregulated protein 1), <em>prkn</em> (parkin), <em>pink</em>1 (PTEN- induced kinase 1), and <em>pgam</em>5 (mitochondrial serine/threonine protein phosphatase PGAM5). The revealed species-specific differences in the expression of the mitochondrial quality control pathways shed light on the potentially important mechanisms of mitochondrial protection against H/R-induced damage that might contribute to hypoxia tolerance in marine bivalves. </p>
Fig. 7. Maximum-likelihood tree for the mitochondrial DNA gene Cytochrome Oxidase C subunit 1 in A new species of the catfish Neoplecostomus (Loricariidae: Neoplecostominae) from a coastal drainage in southeastern Brazil
Fig. 7. Maximum-likelihood tree for the mitochondrial DNA gene Cytochrome Oxidase C subunit 1 for specimens of Neoplecostomus microps from rio Paraíba do Sul, rio Guapi- Açu and rio Macaé, and of Neoplecostomus paraty, using TN93+G model (n=21). Neoplecostomus paranensis and Neoplecostomus ribeirensis were used as outgroups.
Molecular dynamic trajectory of magnesium binding wild type for the article "Ca 2+ binding to F-ATP synthase β subunit triggers the mitochondrial permeability transition"
<p>ATP synthase molecular dynamics simulations files for wild type of the beta subunit binding magnesium:</p> <p>50ns trajectory (ATPsynth_woh2o_Mg_wt.dcd) and corresponding psf file (ATPsynth_mg_wt.psf)</p>
Molecular dynamic trajectory of calcium binding T163S mutant for the article "Ca 2+ binding to F-ATP synthase β subunit triggers the mitochondrial permeability transition"
<p>ATP synthase molecular dynamics simulations files for T163S mutants of the beta subunit binding calcium:</p> <p>50ns trajectory (ATPsynth_woh2o_Ca_mut.dcd) and corresponding psf file (ATPsynth_ca_mut.psf)</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.