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64 results for “mito”
Three-color whole cell LLSM imaging data of ER, H2B, and Mito over 1000 time points during mitosis (Mito channel)
<p>This dataset includes the three-color whole cell lattice light-sheet microscopy (LLSM) data of ER, H2B, and Mitochondia over 1000 time points at 6 sec intervals in a HeLa cell stably expressing calnexin-mEmerald, H2B-mCherry and Mito-Halo during mitosis (only Mito channel here due to the file size restriction, other channels can be found in the same depository with different DOI), which was used to demonstrate SiS-rDL denoising algorithm in our Nature Biotechnology paper (DOI: 10.1038/s41587-022-01471-3). This dataset can be used for non-commercial purposes with proper citations of our NBT paper.</p>
Three-color whole cell LLSM imaging data of ER, H2B, and Mito over 1000 time points during mitosis (ER channel)
<p>This dataset includes the three-color whole cell lattice light-sheet microscopy (LLSM) data of ER, H2B, and Mitochondria over 1000 time points at 6 sec intervals in a HeLa cell stably expressing calnexin-mEmerald, H2B-mCherry and Mito-Halo during mitosis (only ER channel here due to the file size restriction, other channels can be found in the same depository with different DOI), which was used to demonstrate SiS-rDL denoising algorithm in our Nature Biotechnology paper (DOI: 10.1038/s41587-022-01471-3). This dataset can be used for non-commercial purposes with proper citations of our NBT paper.</p>
Three-color whole cell LLSM imaging data of ER, H2B, and Mito over 1000 time points during mitosis (H2B channel)
<p>This dataset includes the three-color whole cell lattice light-sheet microscopy (LLSM) data of ER, H2B, and Mitochondia over 1000 time points at 6 sec intervals in a HeLa cell stably expressing calnexin-mEmerald, H2B-mCherry and Mito-Halo during mitosis (only H2B channel here due to the file size restriction, other channels can be found in the same depository with different DOI), which was used to demonstrate SiS-rDL denoising algorithm in our Nature Biotechnology paper (DOI: 10.1038/s41587-022-01471-3). This dataset can be used for non-commercial purposes with proper citations of our NBT paper.</p>
Data from: Modeling the mito-nuclear compatibility and its role in species identification
<p>Mitochondrial genetic material (mtDNA) is widely used for phylogenetic reconstruction and as a barcode for species identification. The utility of mtDNA in these contexts derives from its particular molecular properties, including its high evolutionary rate, uniparental inheritance, and small size. But mtDNA may also play a fundamental role in speciation -- as suggested by recent observations of coevolution with the nuclear DNA, along with the fact that respiration depends on coordination of genes from both sources. Here we study how mito-nuclear interactions affect the accuracy of species identification by mtDNA, as well as the speciation process itself. We simulate the evolution of a population of individuals who carry a recombining nuclear genome and a mitochondrial genome inherited maternally. We compare a null model fitness landscape that lacks any mito-nuclear interaction against a scenario in which interactions influence fitness. Fitness is assigned to individuals according to their mito-nuclear compatibility, which drives the coevolution of the nuclear and mitochondrial genomes. Depending on the model parameters, the population breaks into distinct species and the model output then allows us to analyze the accuracy of mtDNA barcode for species identification. Remarkably, we find that species identification by mtDNA is equally accurate in the presence or absence of mito-nuclear coupling and that the success of the DNA barcode derives mainly from population geographical isolation during speciation. Nevertheless, selection imposed by mito-nuclear compatibility influences the diversification process and leaves signatures in the genetic content and spatial distribution of the populations, in three ways. First, speciation is delayed and the resulting phylogenetic trees are more balanced. Second, clades in the resulting phylogenetic tree correlate more strongly with the spatial distribution of species and clusters of more similar mtDNA's. Third, there is a substantial increase in the intraspecies mtDNA similarity, decreasing the number of alleles substitutions per locus and promoting the conservation of genetic information. We compare the evolutionary patterns observed in our model to empirical data from copepods (<em>T. californicus</em>). We find good qualitative agreement in the geographic patterns and the topology of the phylogenetic tree, provided the model includes selection based on mito-nuclear interactions. These results highlight the role of mito-nuclear compatibility in the speciation process and its reconstruction from genetic data.</p>
Presentador del libro Mitos y leyendas del Cerro Montecristi, del Coord. Olaff Durand Núñez
<p>Presentación del libro Mitos y leyendas del Cerro Montecristi, del Coord. Olaff Durand Núñez.</p>
Phylomitogenomics reveals mito-nuclear concordance in social wasps: the performance of mitochondrial markers and gene order for hymenopteran systematics.
<p>Mitochondrial (mtDNA) genes have served as widely utilized genetic loci for animal phylogenetics and phylogeography studies. However, the phylogenetic performance of many mtDNA genes has not been empirically evaluated across lineages within hymenopteran wasps. To address this question, we assembled and analyzed mitogenomic data from social wasps, representing the four recognized tribes of Polistinae and also all Epiponini genera. Additionally, we evaluated whether mtDNA gene order in Polistinae is congruent with its tribal classification. Using concatenation phylogenetic methods, we show phylogenetic congruence between mitogenomic and nuclear data. Statistically comparing the phylogenetic performance of individual mtDNA genes, we demonstrate that for social wasps the molecular markers COI, 16S, NAD5, and NAD2 perform best, while ATP6, COII, and 12S show the worst results. Finally, we verified that the tRNA cluster close to the noncoding region is a hotspot of rearrangement in Vespidae and can be used as additional information for the systematics of this group. Together, these results indicate that mitogenomes contain robust phylogenetic signal to elucidate the evolutionary history of Vespidae. Moreover, our study identifies the best choice of mitochondrial markers for systematic investigations of social wasps.</p>
Phylogenomics improves the phylogenetic resolution and provides strong evidence of mito-nuclear discordance in two genera of a New Zealand cicada (Hemiptera: Cicadidae) species radiation
<p>Rapid species radiations present difficulties for phylogenetic reconstruction due to lack of phylogenetic information and processes such as deep coalescence/incomplete lineage sorting and hybridization. Phylogenomic data can overcome some of these difficulties. In this study, we use Anchored Hybrid Enrichment (AHE) nuclear phylogenomic data and mitochondrial genomes recovered from AHE bycatch with several concatenated and coalescent approaches to reconstruct the poorly-resolved radiation of the New Zealand cicada species in the genera <em>Kikihia</em> Dugdale and <em>Maoricicada</em> Dugdale. Compared to previous studies using only three to five Sanger-sequenced genes, we find increased resolution across our phylogenies, but several branches remain unresolved due to topological conflict among genes. Some nodes that are strongly supported by traditional support measures like bootstraps and posterior probabilities still show significant gene and site concordance conflict. Additionally, we find strong mito-nuclear discordance; likely the result of interspecific hybridization events in the evolutionary history of <em>Kikihia</em> and <em>Maoricicada</em>.</p>
Efficacy/Safety of CPI-613 in Combination With HD Cyt. and Mito. vs HD Cyt. and Mito. in Older Patients With R/R AML
ClinicalTrials.gov study NCT03504410. IPD Sharing: NO. Countries: 9. Publications: 1.
A Long-term Extension of Study RP103-MITO-001 (NCT02023866) to Assess Cysteamine Bitartrate Delayed-release Capsules (RP103) in Children With Inherited Mitochondrial Disease
ClinicalTrials.gov study NCT02473445. IPD Sharing: UNDECIDED. Countries: 1. Publications: 4.
Data from: Modeling the mito-nuclear compatibility and its role in species identification
Open the record for dataset details and reuse information.
Phylogenomics improves the phylogenetic resolution and provides strong evidence of mito-nuclear discordance in two genera of a New Zealand cicada (Hemiptera: Cicadidae) species radiation
Open the record for dataset details and reuse information.
Data from: Mito-nuclear discord in six congeneric lineages of Holarctic ducks (genus Anas)
Many species have Holarctic distributions that extend across Europe, Asia, and North America. Most genetics research on these species has examined only mitochondrial (mt) DNA, which has revealed wide variance in divergence between Old World (OW) and New World (NW) populations, ranging from shallow, unstructured genealogies to deeply divergent lineages. In this study, we sequenced 20 nuclear introns to test for concordant patterns of OW-NW differentiation between mtDNA and nuclear (nu) DNA for six lineages of Holarctic ducks (genus Anas). Genetic differentiation for both marker types varied widely among these lineages (idiosyncratic population histories), but mtDNA and nuDNA divergence within lineages was not significantly correlated. Moreover, compared to the association between mtDNA and nuDNA divergence observed among different species, OW-NW nuDNA differentiation was generally lower than mtDNA divergence, at least for lineages with deeply divergent mtDNA. Furthermore, coalescent estimates indicated significantly higher rates of gene flow for nuDNA than mtDNA for four of the six lineages. Thus, Holarctic ducks show prominent mito-nuclear discord between OW and NW populations, and we reject differences in sorting rates as the sole cause of the within-species discord. Male-mediated intercontinental gene flow is likely a leading contributor to this discord, although selection could also cause elevated mtDNA divergence relative to weak nuDNA differentiation. The population genetics of these ducks contribute to growing evidence that mtDNA can be an unreliable indicator of stage of speciation, and that more holistic approaches are needed for species delimitation.
Data from: Evaluating summary statistics used to test for incomplete lineage sorting: mito-nuclear discordance in the reef sponge Callyspongia vaginalis
Conflicting patterns of population differentiation between the mitochondrial and nuclear genomes (mito-nuclear discordance) have become increasingly evident as multilocus datasets have become easier to generate. Incomplete lineage sorting (ILS) of nucDNA is often implicated as the cause of such discordance, stemming from the large effective population size of nucDNA relative to mtDNA. However, selection, sex-biased dispersal, and historical demography can also lead to mito-nuclear discordance. Here we compare patterns of genetic diversity and subdivision for six nuclear protein-coding gene regions to those for mtDNA in a common Caribbean coral reef sponge, Callyspongia vaginalis, along the Florida reef tract. We also evaluated a suite of summary statistics to determine which are effective metrics for comparing empirical and simulated data when testing drivers of mito-nuclear discordance in a statistical framework. While earlier work revealed three divergent and geographically subdivided mtDNA COI haplotypes separated by 2.4% sequence divergence, nuclear alleles were admixed with respect to mitochondrial clade and geography. Bayesian analysis showed substitution rates for the nuclear loci were up to 7 times faster than for mitochondrial COI. Coalescent simulations and neutrality tests suggested that mito-nuclear discordance in C. vaginalis is not the result of ILS in the nucDNA or selection on the mtDNA but is more likely caused by changes in population size. Sperm-mediated gene flow may also influence patterns of population subdivision in the nucDNA.
Data from: Divergent clades or cryptic species? Mito-nuclear discordance in a Daphnia species complex
Background: Genetically divergent cryptic species are frequently detected by molecular methods. These discoveries are often a byproduct of molecular barcoding studies in which fragments of a selected marker are used for species identification. Highly divergent mitochondrial lineages and putative cryptic species are even detected in intensively studied animal taxa, such as the crustacean genus Daphnia. Recently, eleven such lineages, exhibiting genetic distances comparable to levels observed among well-defined species, were recorded in the D. longispina species complex, a group that contains several key taxa of freshwater ecosystems. We tested if three of those lineages represent indeed distinct species, by analyzing patterns of variation of ten nuclear microsatellite markers in six populations. Results: We observed a discordant pattern between mitochondrial and nuclear DNA, as all individuals carrying one of the divergent mitochondrial lineages grouped at the nuclear level with widespread, well-recognized species coexisting at the same localities (Daphnia galeata, D. longispina, and D. cucullata). Conclusions: A likely explanation for this pattern is the introgression of the mitochondrial genome of undescribed taxa into the common species, either in the distant past or after long-distance dispersal. The occurrence of highly divergent but rare mtDNA lineages in the gene pool of widespread species would suggest that hybridization and introgression in the D. longispina species complex is frequent even across large phylogenetic distances, and that discoveries of such distinct clades must be interpreted with caution. However, maintenance of ancient polymorphisms through selection is another plausible alternative that may cause the observed discordance and cannot be entirely excluded.
Data from: Evidence for high dispersal ability and mito-nuclear discordance in the small brown planthopper, Laodelphax striatellus
Understanding dispersal ability in pest species is critical for both theoretical aspects of evolutionary and population biology and from a practical standpoint, such as implementing effective forecasting systems. The small brown planthopper (SBPH), Laodelphax striatellus (Fallén), is an economically important pest, but few data exist on its dispersal ability. Here, we used mitochondrial and nuclear markers to elucidate the population genetic structure of SBPH and of the parasitic bacterium Wolbachia throughout temperate and subtropical China. Our results showed that the SBPH populations in China lack significant differences in genetic structure, suggesting extensive gene flow. Multilocus sequence typing revealed that Wolbachia infection was systematic and due to the same strain (wStri) within and across populations. However, the mtDNA haplogroups had a nonrandom distribution across the sampling localities, which correlated to latitudinal and climatic gradients. We explain this mito-nuclear discordance as a result of historical population recolonization or mitochondria adaptation to climate.
Association of Peripheral Monocytic-Myeloid-Derived Suppressor Cells with Molecular Subtypes in Single Center Endometrial Cancer Patients Receiving Carboplatin + Paclitaxel/Avelumab (MITO END-3 Trial)
<p><span>The MITO-END3 trial compared carboplatin and paclitaxel (</span><span>CP</span><span>) with avelumab plus carboplatin and paclitaxel (</span><span>CPA)</span><span> as first-line treatment in endometrial cancer (EC) patients and </span><span>demonstrated a significant interaction between avelumab response and mismatch repair status. To investigate prognostic/predictive biomarker, </span><span>twenty-nine MITO-END3-EC patients were evaluated at pre-treatment (B1) and at the end of CP/CPA treatment (B2) for </span><span>peripheral Myeloid derived suppressor cells (MDSC) and Tregs. </span><span>At B2, <span>effector</span> Tregs frequency was significantly higher in patients treated with CPA as compared to CP (p=0.038). Both treatments (CP/CPA) induced significant decrease in peripheral M-MDSC (-5.41%) in TCGA 2-MSI-High as compared to TCGA-category 4 tumors (p=0.004). In accordance, both treatments induced M-MDSCs (+5.34%) in MSS patients as compared to MSI-High patients (p=0.001). Moreover, in a subgroup of patients, </span><span>primary tumors were highly infiltrated by M-MDSCs in MSS as compared to MSI-high ECs. </span><span>A post hoc analysis displayed higher frequeny of M-MDSCs (p=0.020) and lower frequency of CD4+ (p<0.005) at pretreatment in EC patients as compared to healthy donors. </span><span>In conclusion, </span><span>the</span><span> peripheral evaluation of MDSCs and Tregs correlated with molecular features in EC treated with CP/CPA and may add insights in identifying EC patients responder to first line chemo/chemo-immunotherapy. </span></p>
Reference data for MITOS
<p>Reference data for MITOS. Contains</p> <p>- fasta databases for the BLAST searches (RefSeq release 39)</p> <p>- automatically covariance models for ncRNA searches (for tRNAs the models are taken from MiTFi http://dx.doi.org/10.1093/nar/gkv746)</p> <p>As described in http://dx.doi.org/10.1016/j.ympev.2012.08.023</p>
Precise measurements of chromatin diffusion dynamics by modeling using Gaussian processes (Inter-Mito)
<p>Microscopy movies corresponding to interphase and mitotic cells in publication (add DOI when available).</p>
MITO training datasets for live cell anatomy segmentation
<p>Training dataset acquired from two microscopes for the segmentation of mitochondria.</p>
MITO-2: A Study Comparing 2 Chemotherapy Regimens (Carboplatin/Liposomal Doxorubicin vs Carboplatin/Paclitaxel) in Patients With Ovarian Cancer
ClinicalTrials.gov study NCT00326456. IPD Sharing: Not stated. Countries: 3. Publications: 3.
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International Brain Laboratory public data
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OpenNeuro
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