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56 results for “Nucleoid”
DATA and CARE model for the segmentation of bacterial nucleoids in SMLM data
<p>This dataset and CARE model is part of the publication "<strong>Transertion and cell geometry organize the <em>Escherichia coli</em> nucleoid during rapid growth</strong>".</p> <p>Data represents PAINT images of fixed <em>Escherichia coli </em>cells grown in LB Lennox to exponential phase. Cultures were treated with different antibiotics and fixed various treatment times (0 - 60 min).</p> <p>The strain (NO34) expresses a MreB<sup>sw</sup>-sfGFP fusion protein from the native chromosomal locus. It was a kind gift from Zemer Gitai (<a href="http://doi:10.1016/j.bpj.2016.07.017">Ouzounov et al., 2016</a>).</p> <p>The CARE 2D model was trained from scratch for 100 epochs (332 steps/epoch) on 736 paired image patches (image dimensions: (1024,1024), patch size: (256,256)) with a batch size of 4, an initial learning rate of 0.0004, 10% validation data and a laplace loss function, using the CARE 2D ZeroCostDL4Micnotebook. Data was augmented by a factor of two involving rotation and flipping and random zoom magnification.</p> <p>The model can currently not be used in CSBDeep Fiji plugin, but in the <a href="https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki">ZeroCostDL4Mic platform</a>.</p> <p> </p>
DeepBacs – Escherichia coli nucleoid denoising dataset and CARE model
<p>Training and test images of H-NS-mScarlet-I expressing <em>E. coli </em>cells for image denoising, as well as a trained CARE model.</p> <p>Additional information can be found on our <a href="https://github.com/HenriquesLab/DeepBacs/wiki">github wiki</a>.</p> <p>The example images show confocal images of labelled <em>E. coli</em> nucleoids at low and high SNR.</p> <p> </p> <p><strong>Training and test dataset</strong></p> <p><strong>Data type</strong>: Paired microscopy images (fluorescence)</p> <p><strong>Microscopy data type</strong>: Confocal fluorescence images</p> <p><strong>Microscope</strong>: Leica SP8 confocal microscope with a 1.40 NA 63x oil immersion objective </p> <p><strong>Cell type</strong>: <em>E. coli</em> strain CS01 expressing H-NS-mScarlet-I fusion protein (H-NS-mScarlet-I) in NO34 parental strain (MreB-sfGFPsw, kindly provided by Zemer Gitai) </p> <p><strong>File format</strong>: .tif (16-bit)</p> <p><strong>Image size</strong>: 512 x 512 px<sup>2</sup> (Pixel size: 45 nm)</p> <p> </p> <p><strong>CARE model</strong>:</p> <p>The CARE 2D model was generated using the ZeroCostDL4Mic platform (Chamier et al., 2021). It was trained from scratch for 100 epochs (600 steps/epoch) on 1400 paired image patches (image dimensions: (512 x 512 px²), patch size: (64 x 64 px²), 50 patches/image) with a batch size of 8 and a laplace loss function, using the CARE 2D ZeroCostDL4Mic notebook (v 1). Key python packages used include tensorflow (v 0.1.12), Keras (v2.3.1), csbdeep (v 0.6.2), numpy (v 1.19.5), cuda (v 11.0.221). The training was accelerated using a Tesla T4 GPU and data was augmented by a factor of 4 using rotation and flipping.</p> <p>The model weights can be used with the ZeroCostDL4Mic CARE 2D notebook and the CSBDeep Fiji plugin.</p> <p> </p> <p><strong>Author(s)</strong>: Christoph Spahn<sup>1,2</sup>, Mike Heilemann<sup>1,3</sup></p> <p><strong>Contact email</strong>: christoph.spahn@mpi-marburg.mpg.de</p> <p> </p> <p><strong>Affiliation(s)</strong>: </p> <p>1) Institute of Physical and Theoretical Chemistry, Max-von-Laue Str. 7, Goethe-University Frankfurt, 60439 Frankfurt, Germany</p> <p>2) ORCID: 0000-0001-9886-2263 </p> <p>3) ORCID: 0000-0002-9821-3578</p>
Image data for bioRxiv article named: mtFociCounter - Reproducible, open source and quantitative single-cell analysis of mitochondrial nucleoids and other foci
<p>Raw imaging data to reproduce and test the findings of the bioRxiv article: <strong>mtFociCounter </strong>- Reproducible, open source and quantitative single-cell analysis of mitochondrial nucleoids and other foci. It contains data from three imaging days and 2 or three technical replicates on each day.</p> <p> </p>
Uncharacterized protein C17orf80 concentrates in mitochondrial nucleoids following treatment with ddC
<p><strong>Dataset description:</strong> Immunofluorescence (IF) images demonstrating changes in c17orf80 IF signal upon 2',3'-dideoxycytidine (ddC) treatment in human osteosarcoma cells (U2OS). U2OS cells were treated or not with 100 µM ddC for 48 h. Co-immunostaining with c17orf80, TFAM (nucleoids), and DNA (nucleoids and nuclei) antibodies. Nuclei stained with DAPI (blue). The scale bar is 10 µm. Signals of TFAM and mtDNA in ddC-treated cells were reduced, whereas the nucleoid-specific signal of c17orf80 was increased.</p> <p><strong>Methods:</strong> U2OS cells (University of Helsinki, Finland) were grown in high-glucose DMEM (Lonza; BE12–604F) supplemented with 10% fetal bovine serum (FBS) (Gibco; 16000044) in a humidified 37 °C incubator at 5% CO2. To inhibit mtDNA replication, growth medium was supplemented with 100 µM of 2′,3′-dideoxycytidine (Sigma; D5782). For immunofluorescence detection, U2OS cells were grown on coverslips in six-well plates. The cells were fixed using 3.3% paraformaldehyde (PFA) in DMEM/10% FBS for 20 min, washed in phosphate-buffered saline (PBS), and permeabilized for 15 min with 0.5% Triton X-100 (TX-100) in PBS/10% FBS. The cells were then incubated for 1 h with primary antibodies diluted in PBS/10% FBS (Table 1). After washing, the cells were incubated for 45 min with the corresponding secondary antibodies labelled with Alexa Fluor diluted in PBS/10% FBS (1:1000; Invitrogen): goat-anti-rabbit IgG 488 nm, goat-anti-mouse IgG 568 nm, and goat-anti-mouse IgM 647 nm. After the final incubation and washing, coverslips were mounted using ProLong™ Gold Antifade reagent with DAPI (Invitrogen; P36935). Images were acquired using a Zeiss apotome system in apotome mode on an Axio Observer Z.1 with Colibri-led illumination and appropriate emission filters using the x40 or x63 oil immersion objectives. Images were processed using the ImageJ software. To compare control cells with cells treated with ddC, images for each channel were acquired with identical illumination and exposure settings and processed identically.</p>
Coarse-grain Models of HIV-1 Nucleoids
<p>These are PDB-format files that may be read by most molecular<br> graphics programs. The script JSmol.script will create a customized<br> view with appropriate radii, using JSmol. The PDB format is modified<br> in the following ways:<br> --coordinates are in nanometers<br> --RNA strands have atom name "P" and residue name "RNA"<br> --integrase subunits have atom name "CA" and residue name "IN"<br> --nucleocapsid subunits have atom name "N", and residue names<br> "NCO" for experimentally-observed positions and<br> "NCR" for randomly-placed positions</p> <p>Each file contains 25 instances of the nucleoid model.<br> Each model includes 2 gRNA strands, 2000 nucleocapsid subunits, and 140/0 integrase subunits.<br> Nine models are included in this release, exploring two types of variables:<br> 1) Three types of starting models: <br> "selfavoidingGag" assumes that the RNA forms a non-overlapping random walk on<br> the lattice of gag proteins in the immature virion<br> "overlappingGag" assumes a similar random walk, but the RNA strands may overlap<br> "random" assumes that RNA is released from gag and randomly fills the interior of<br> the virion before condensation <br> 2) Three assumptions about integrase interaction:<br> 35 integrase tetramers, 70 integrase dimers, and no integrase</p> <p>More information is available at:<br> http://ccsb.scripps.edu/latticenucleoid/HIVnucleoid</p>
mtKO_nucleoids dataset 05 - CYTB KO
<p>This is one of five imaging datasets to compare mtDNA mutant cell lines with isogenic wild-type cell lines by mtFociCounter.</p> <p>Images are <strong>Spinning Disk Confocal </strong>Images of unsorted 3t3 NIH mouse fibroblasts stably expressing <strong>mitochondrially</strong>targeted dsRed, immunofluorescence against dsDNA (mitochondrial <strong>nucleoids</strong>) and AlexaFluor 647, and stained <strong>nuclei</strong>with Hoechst.<br> Samples from the same day are 13mm coverslips processed in parallel (seeding of cells, fixation, immunofluorescence, microscopy) and mounted on the same glass slide (#1 on left, #2 centre, #3 right).</p> <p>This dataset contains data from <strong>WT</strong> cells and <strong>CYTB loss of function</strong> mutations from the following acquisition dates:<br> 20221217<br> 20221220<br> 20221221</p> <p>For further details, please do not hesitate to contact the author, timorey AT hotmail DOT com.<br> A preprint with experimental details and analysis will be available soon.</p>
mtKO_nucleoids dataset 02 - COXII KO
<p>This is one of five imaging datasets to compare mtDNA mutant cell lines with isogenic wild-type cell lines by mtFociCounter.</p> <p>Images are <strong>Spinning Disk Confocal </strong>Images of unsorted 3t3 NIH mouse fibroblasts stably expressing <strong>mitochondrially</strong>targeted dsRed, immunofluorescence against dsDNA (mitochondrial <strong>nucleoids</strong>) and AlexaFluor 647, and stained <strong>nuclei</strong>with Hoechst.<br> Samples from the same day are 13mm coverslips processed in parallel (seeding of cells, fixation, immunofluorescence, microscopy) and mounted on the same glass slide (#1 on left, #2 centre, #3 right).</p> <p>This dataset contains data from <strong>WT</strong> cells and <strong>COXII loss of function</strong> mutations from the following acquisition dates:<br> 20221022<br> 20221026<br> 20221029</p> <p>For further details, please do not hesitate to contact the author, timorey AT hotmail DOT com.<br> A preprint with experimental details and analysis will be available soon.</p>
mtKO_nucleoids dataset 03 - ATP8 KO
<p>This is one of five imaging datasets to compare mtDNA mutant cell lines with isogenic wild-type cell lines by mtFociCounter.</p> <p>Images are <strong>Spinning Disk Confocal </strong>Images of unsorted 3t3 NIH mouse fibroblasts stably expressing <strong>mitochondrially</strong>targeted dsRed, immunofluorescence against dsDNA (mitochondrial <strong>nucleoids</strong>) and AlexaFluor 647, and stained <strong>nuclei</strong>with Hoechst.<br> Samples from the same day are 13mm coverslips processed in parallel (seeding of cells, fixation, immunofluorescence, microscopy) and mounted on the same glass slide (#1 on left, #2 centre, #3 right).</p> <p>This dataset contains data from <strong>WT</strong> cells and <strong>ATP8 loss of function</strong> mutations from the following acquisition dates:<br> 20221210<br> 20221211<br> 20221212</p> <p>For further details, please do not hesitate to contact the author, timorey AT hotmail DOT com.<br> A preprint with experimental details and analysis will be available soon.</p>
Nucleoid as an Adjuvant Therapy After Radiofrequency Ablation for Hepatocellular Carcinoma
ClinicalTrials.gov study NCT00555334. IPD Sharing: Not stated. Countries: 1. Publications: 4.
SMC translocation is unaffected by an excess of nucleoid associated proteins in vivo
GEO Series GSE269767. Bacillus subtilis PY79. 54 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other.
Condensation of nucleoid during environmental adaptation is regulated by dynamic HU interactions
GEO Series GSE134667. Escherichia coli. 36 samples. Type: Expression profiling by high throughput sequencing.
Cooperative function of the three different kinds of nucleoid-associated proteins encoded on the IncP-7 plasmid pCAR1
GEO Series GSE53069. Pseudomonas; Pseudomonas putida; Pseudomonas putida KT2440. 12 samples. Type: Expression profiling by genome tiling array.
The Heparin-binding hemagglutinin protein of Mycobacterium tuberculosis is a nucleoid-associated protein
GEO Series GSE235293. Mycobacterium tuberculosis. 16 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq Analysis Identifies New Genes Regulated by the Histone-like Nucleoid Structuring Protein (H-NS) Affecting Vibrio cholerae Virulence, Stress Response and Chemotaxis
GEO Series GSE62785. Vibrio cholerae. 8 samples. Type: Expression profiling by high throughput sequencing.
Essential Nucleoid Associated Protein mIHF (Rv1388) controls virulence and housekeeping genes in Mycobacterium tuberculosis
GEO Series GSE111194. Mycobacterium tuberculosis. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
The nucleoid occlusion factor Noc controls DNA replication initiation in Staphylococcus aureus
GEO Series GSE100777. Staphylococcus aureus subsp. aureus NCTC 8325; Bacillus subtilis PY79. 37 samples. Type: Other; Genome binding/occupancy profiling by high throughput sequencing.
The nucleoid occlusion factor Noc controls DNA replication initiation in Staphylococcus aureus [ChIP-Seq]
GEO Series GSE93264. Bacillus subtilis PY79; Staphylococcus aureus subsp. aureus NCTC 8325. 20 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
The Nucleoid Protein Dps Binds Genomic DNA of Escherichia coli in a Non-random Manner
GEO Series GSE102091. Escherichia coli str. K-12 substr. MG1655. 4 samples. Type: Expression profiling by high throughput sequencing.
Virulence regulator EspR of Mycobacterium tuberculosis is a nucleoid-associated protein
GEO Series GSE35149. Mycobacterium tuberculosis. 3 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Single-nucleoid architecture reveals heterogeneous packaging of mitochondrial DNA [RNA-seq]
GEO Series GSE240902. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
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