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77 results for “mitochondrial dynamics”
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>
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>
Molecular dynamic trajectory of calcium 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 calcium:</p> <p>50ns trajectory (ATPsynth_woh2o_Ca_wt.dcd) and corresponding psf file (ATPsynth_ca_wt.psf)</p> <p> </p>
Molecular dynamic trajectory of magnesium 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 magnesium:</p> <p>50ns trajectory (ATPsynth_woh2o_Mg_mut.dcd) and corresponding psf file (ATPsynth_mg_mut.psf)</p> <p> </p>
Raw data for the manuscript under the title "Mitochondrial RNA granules are fluid condensates, positioned by membrane dynamics".
<p><strong>This is the data-repository</strong> to contain all relevant raw-data used and referred to in the manuscript entitled:<br> "Mitochondrial RNA granules are fluid condensates, positioned by membrane dynamics"<br> [manuscript under revision, and thus not citable as published article]</p> <p>The repository is structured analogous to the manuscript. Find a more detailed description in the README.</p>
Data and source code from: Contingency and selection in mitochondrial genome dynamics
<p>Eukaryotic cells contain numerous copies of mitochondrial DNA (mtDNA), allowing for the coexistence of mutant and wild-type mtDNA in individual cells. The fate of mutant mtDNA depends on their relative replicative fitness within cells and the resulting cellular fitness within populations of cells. Yet the dynamics of the generation of mutant mtDNA and features that inform their fitness remain unaddressed. Here we utilize long read single-molecule sequencing to track mtDNA mutational trajectories in Saccharomyces cerevisiae. We show a previously unseen pattern that constrains subsequent excision events in mtDNA fragmentation. We also provide evidence for the generation of rare and contentious non-periodic mtDNA structures that lead to persistent diversity within individual cells. Finally, we show that measurements of relative fitness of mtDNA fit a phenomenological model that highlights important biophysical parameters governing mtDNA fitness. Altogether, our study provides techniques and insights into the dynamics of large structural changes in genomes that may be applicable in more complex organisms.</p>
Structural determinants of ligands recognition by the human mitochondrial basic amino acids transporter SLC25A29. Insights from molecular dynamics simulations of the c-state.
<p>Initial coordinates, molecular dynamics trajectories and representative snapshots resulting from the study "Structural determinants of ligands recognition by the human mitochondrial basic amino acids transporter SLC25A29. Insights from molecular dynamics simulations of the c-state." by Pasquadibisceglie and Polticelli.</p> <p>The MD folders contain the parameter/topology (parm7) and initial coordinates (rst7) for the molecular dynamics simulations. Moreover, a NetCDF trajectory "prod.nc" of the production phase is also included.<br> In detail:<br> - MD0 -> SLC25A29 in absence of ligands;<br> - MD1, MD3, MD4 -> SLC25A29-ARG complex;<br> - MD1-LYS, MD3-LYS, MD4-LYS -> SLC25A29-LYS complex.</p> <p>The folder PDB_figures contains the PDB files used to produce the figures presented in the manuscript.</p>
Data from: Spatial analysis of mitochondrial gene expression reveals dynamic translation hubs and remodeling in stress
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Effects of endurance flight on mitochondrial physiology, lean mass dynamics and flight muscle morphology in blackpoll warblers
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Data and source code from: Contingency and selection in mitochondrial genome dynamics
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Data from: The hitchhiker's guide to Europe: the infection dynamics of an ongoing Wolbachia invasion and mitochondrial selective sweep in Rhagoletis cerasi
Wolbachia is a maternally inherited and ubiquitous endosymbiont of insects. It can hijack host reproduction by manipulations such as cytoplasmic incompatibility (CI) to enhance vertical transmission. Horizontal transmission of Wolbachia can also result in the colonization of new mitochondrial lineages. In this study, we present a 15-year-long survey of Wolbachia in the cherry fruit fly Rhagoletis cerasi across Europe and the spatiotemporal distribution of two prevalent strains, wCer1 and wCer2, and associated mitochondrial haplotypes in Germany. Across most of Europe, populations consisted of either 100% singly (wCer1) infected individuals with haplotype HT1, or 100% doubly (wCer1&2) infected individuals with haplotype HT2, differentiated only by a single nucleotide polymorphism. In central Germany, singly infected populations were surrounded by transitional populations, consisting of both singly and doubly infected individuals, sandwiched between populations fixed for wCer1&2. Populations with fixed infection status showed perfect association of infection and mitochondria, suggesting a recent CI-driven selective sweep of wCer2 linked with HT2. Spatial analysis revealed a range expansion for wCer2 and a large transition zone in which wCer2 splashes appeared to coalesce into doubly infected populations. Unexpectedly, the transition zone contained a large proportion (22%) of wCer1&2 individuals with HT1, suggesting frequent intraspecific horizontal transmission. However, this horizontal transmission did not break the strict association between infection types and haplotypes in populations outside the transition zone, suggesting that this horizontally acquired Wolbachia infection may be transient. Our study provides new insights into the rarely studied Wolbachia invasion dynamics in field populations.
Haplotype analysis of the mitochondrial DNA d-loop region reveals the maternal origin and historical dynamics among the indigenous goat populations in east and west of the Democratic Republic of Congo (DRC)
<p><span>This study aimed at assessing haplotype diversity and population dynamics of three Congolese indigenous goat populations that included Kasai goat (KG), small goat (SG), and dwarf goat (DG) of the Democratic Republic of Congo (DRC). The 1,169 bp <em>d-loop</em> region of mitochondrial DNA (mtDNA) was sequenced for 339 Congolese indigenous goats. The total length of sequences was used to generate the haplotypes and evaluate their diversities, whereas the hypervariable region (HVI, 453 bp) was analyzed to define the maternal variation and the demographic dynamic. A total of 568 segregating sites that generated 192 haplotypes were observed from the entire <em>d-loop</em> region (1,169 bp <em>d-loop</em>). Phylogenetic analyses using reference haplotypes from the six globally defined goat mtDNA haplogroups showed that all the three Congolese indigenous goat populations studied clustered into the dominant haplogroup A, as revealed by the Neighbor-joining (NJ) tree and median-joining (MJ) network. Nine haplotypes were shared between the studied goats and goat populations from Pakistan (1 haplotype), Kenya, Ethiopia and Algeria (1 haplotype), Zimbabwe (1 haplotype), Cameroon (3 haplotypes), and Mozambique (3 haplotypes). The population pairwise analysis (<em>F<sub>ST</sub></em>) indicated a weak differentiation between the Congolese indigenous goat populations. Negative and significant (<em>p</em>-value < 0.05) values for <em>F</em>u's <em>F</em>s (-20.418) and Tajima's (-2.189) tests showed the expansion in the history of the three Congolese indigenous goat populations. These results suggest a weak differentiation and a single maternal origin for the studied goats. This information will contribute to the improvement of the management strategies and long-term conservation of indigenous goats in DRC</span><span>.</span></p>
Fig. 2 Mitochondrial haplotype network using the 590 in Differentiation of North African foxes and population genetic dynamics in the desert-insights into the evolutionary history of two sister taxa, Vulpes rueppellii and Vulpes vulpes
Fig. 2 Mitochondrial haplotype network using the 590-bp concatenated sequences from Cyt-b and D-loop and a total of 46 sequences (same as in Fig. 1, except for C. lupus not being used as an outgroup in the TCS network). a Neighbour-Net network based on uncorrected patristic distances as implemented in SPLITSTREE. Canis lupus (DQ480504) was used as an outgroup. Numbers indicate bootstrap values. Scale bar represents 0.01 sequence divergence. Highlighoed are the four species, the three V. vulpes clades and the location within the network of the V. vulpes sample from Egypt. Colour patterns are concordant with Fig. 1 and b. b Statistical parsimony network assuming a 95 % parsimony threshold, as constructed by TCS. Symbol size and branch lengths are proportional to the number of shared individuals per haplotype and the number of mutational steps amongst haplotypes, respectively. Numbers in black background also refer to the number of mutation steps between species and V. vulpes clades. Symbols and colours are concordant with Fig. 1 and a. Haplotype codes, sample origin and corresponding accession numbers are available in Online Resource Table S1
In silico analysis of the structural dynamics and substrate recognition determinants of the human mitochondrial carnitine/acylcarnitine SLC25A20 transporter
<p>Structural models and MD trajectories analyzed in the original article "In silico analysis of the structural dynamics and substrate recognition determinants of the human mitochondrial carnitine/acylcarnitine SLC25A20 transporter". Topologies and trajectories were stripped of the water molecules.</p> <p>- "alphafold2" contains the c-state and m-state models obtained with alphafold2 and colabfold_advanced, respectively;</p> <p>- "slc25a20_cstate" contains the parameter/topology file (slc25a20_cstate_nowat.parm7), the MD simulations of the c-model of the slc25a20 apo protein (prod1_nowat_skip10.nc, prod2_nowat_skip10.nc), and the representative structure used to analyzed the transmembrane helices (cstate1.pdb);</p> <p>- "slc25a20_mstate" contains the parameter/topology file (slc25a20_mstate_nowat.parm7), the MD simulations of the m-state model of the slc25a20 apo protein (prod1_nowat_skip10.nc, prod2_nowat_skip10.nc), and the representative structure used to analyzed the transmembrane helices (cstate2.pdb);</p> <p>- "slc25a20_car" contains the parameter/topology file (slc25a20_carn_nowat.parm7, slc25a20_carn2_nowat.parm7), the MD simulations of the slc25a20-carnitine complex (prod1_nowat_skip2.nc, prod2_nowat_skip2.nc), and a representative structure (snapshot_slc25a20-car.pdb);</p> <p>- "slc25a20_pcar" contains the parameter/topology file (slc25a20_pcarn_nowat.parm7, slc25a20_pcarn2_nowat.parm7), the MD simulations of the slc25a20-propionylcarnitine complex (prod1_nowat_skip2.nc, prod2_nowat_skip2.nc), and a representative structure (snapshot_slc25a20-pcar.pdb).</p> <p>If you include these data in your manuscript, please cite: Pasquadibisceglie A, Quadrotta V and Polticelli F "In silico analysis of the structural dynamics and substrate recognition determinants of the human mitochondrial carnitine/acylcarnitine SLC25A20 transporter"</p>
MITAORTA - Role of Mitochondrial Dynamic in Aneurysm and Dissection of Ascending Thoracic Aorta
ClinicalTrials.gov study NCT05434481. IPD Sharing: NO. Countries: 1. Publications: 6.
Data from: Mitochondrial DNA variants help monitor the dynamics of Wolbachia invasion into host populations
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Temporal dynamics of mildly deleterious nonsynonymous substitutions in mitochondrial gene sequences in rodents and moles
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Data from: The hitchhiker's guide to Europe: the infection dynamics of an ongoing Wolbachia invasion and mitochondrial selective sweep in Rhagoletis cerasi
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Haplotype analysis of the mitochondrial DNA d-loop region reveals the maternal origin and historical dynamics among the indigenous goat populations in east and west of the Democratic Republic of Congo (DRC)
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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