{"total":1346,"hits":[{"id":"https://idr.openmicroscopy.org/study/idr0167/","entry":{"id":"https://idr.openmicroscopy.org/study/idr0167/","type":["Dataset"],"name":"Predicting cell cycle stage from 3D single-cell nuclear-stained images","author":[{"id":"https://orcid.org/0000-0002-8501-8028","type":["Person"],"name":"Eva Nichols","affiliation":[],"email":"eknich@uw.edu","address":"Dept. of Genome Sciences, Foege South-303A, Box 355065, 3720 15th Ave NE, Seattle, WA 98105, USA","familyName":"Nichols","givenName":"Eva"}],"description":"The cell cycle governs proliferation of all eukaryotic cells. Profiling cell cycle dynamics is therefore central to basic and biomedical research. However, current approaches to cell cycle profiling involve complex interventions that may confound experimental interpretation. We developed CellCycleNet, a machine learning (ML) workflow, to simplify cell cycle staging from fluorescent microscopy data with minimal experimenter intervention and cost. CellCycleNet accurately predicts cell cycle phase using only a fluorescent nuclear stain (DAPI) in fixed interphase cells. Using the Fucci2a cell cycle reporter system as ground truth, we collected two benchmarking image datasets and trained 2D and 3D ML modelsÑof support vector machine (SVM) and deep neural network architectureÑto classify nuclei in the G1 or S/G2 phases. Our results show that 3D CellCycleNet outperforms SVM models on each dataset. When trained on two image datasets simultaneously, CellCycleNet achieves the highest classification accuracy (AUROC of 0.94-0.95). Overall, we found that using 3D features, rather than 2D features alone, significantly improves classification performance for all model architectures. We released our image data, models, and software as a community resource.","datePublished":"2026-03-30","license":"https://creativecommons.org/licenses/by/4.0/","publisher":{"id":"https://idr.openmicroscopy.org/","type":["Organization"],"name":"Image Data Resource","url":"https://idr.openmicroscopy.org/","address":null},"about":[{"id":"https://idr.openmicroscopy.org/study/idr0167/#experiment-biosample-1","type":["BioSample"],"name":"cell","description":"CellCycleNet 60x Confocal Dataset.","taxonomicRange":[{"id":"http://purl.obolibrary.org/obo/NCBITaxon_10090","type":["Taxon"],"scientificName":"Mus musculus","name":"Mus musculus","vernacularName":null}],"hasCellLine":[]},{"id":"https://idr.openmicroscopy.org/study/idr0167/#experiment-biosample-2","type":["BioSample"],"name":"cell","description":"CellCycleNet 40x Epifluorescent  Dataset.","taxonomicRange":[{"id":"http://purl.obolibrary.org/obo/NCBITaxon_10090","type":["Taxon"],"scientificName":"Mus musculus","name":"Mus musculus","vernacularName":null}],"hasCellLine":[]},{"id":"http://purl.obolibrary.org/obo/NCBITaxon_10090","type":["Taxon"],"scientificName":"Mus musculus","name":"Mus musculus","vernacularName":null}],"measurementMethod":[{"id":"https://idr.openmicroscopy.org/study/idr0167/#experiment-protocol-1-0","type":["LabProtocol"],"name":"confocal microscopy","description":"CellCycleNet 60x Confocal Dataset.","measurementTechnique":[{"id":"http://purl.obolibrary.org/obo/FBbi_00000251","type":["DefinedTerm"],"name":"confocal microscopy"}],"labEquipment":null},{"id":"https://idr.openmicroscopy.org/study/idr0167/#experiment-protocol-2-0","type":["LabProtocol"],"name":"wide-field epi-fluorescence microscopy","description":"CellCycleNet 40x Epifluorescent  Dataset.","measurementTechnique":[{"id":"http://purl.obolibrary.org/obo/FBbi_00000246","type":["DefinedTerm"],"name":"wide-field epi-fluorescence microscopy"}],"labEquipment":null},{"id":"https://idr.openmicroscopy.org/study/idr0167/#experiment-protocol-1-1","type":["LabProtocol"],"name":"Cell growth","description":"The Fucci (Fluorescent Ubiquitination-based Cell Cycle Indicator) 3T3 Fucci2a reporter cell line was a gracious gift from Richard Mort and were maintained in complete 3T3 complete cell culture media (high glucose 4.5 g/L DMEM with 2 mM L-glutamine, 10% FBS, and 1% pen/strep antibiotic) in the presence of 100-200 ug/mL hygromycin selection antibiotic. Prior to imaging experiments, ~70,000 cells were seeded in a 35 mm dish. Next day, cells were fixed in 4% PFA in 1xPBS for 10 minutes, followed by three washes in 1xPBS for one minute each prior to immunofluorescence staining.","measurementTechnique":[{"id":"http://www.ebi.ac.uk/efo/EFO_0003789","type":["DefinedTerm"],"name":"growth protocol"}],"labEquipment":null},{"id":"https://idr.openmicroscopy.org/study/idr0167/#experiment-protocol-1-2","type":["LabProtocol"],"name":"treatment protocol","description":"A tiled acquisition was obtained over approximately 21 square millimeters of the cell culture plate, at fixed z range of 30 µm and z-step of 0.2 µm. Each image consists of three fluorescent channels, using excitation light emitted at 30 percent maximal intensity from 405 nm, 488 nm, and 561 nm lasers housed in a Nikon LUNF 405/488/561/640NM 1F commercial launch. The nuclear stain DAPI was excited by the 405 nm laser line at 300 ms exposure; the mVenus-hGeminin-AF488 signal was excited by the 488 nm laser line at 300 ms exposure; the mCherry-hCdt1-AF555 signal was excited by the 561 nm laser line at 300 ms exposure. Laser excitation was conveyed through a single-mode optical fiber fed into the CSU-W1 SoRa unit and directed through a microlens array and ÕSoRaÕ disc containing 50 µm pinholes. A Nikon Plan Apochromat Lambda 60X air objective lens (NA 0.95/0.17 mm) was used to project the excitation and collects the emission light. Emission light was relayed by a 1x lens, through the pinhole disc, after which it was spectrally separated by a quad bandpass dichroic mirror (Semrock Di01-T405/488/568/647-13x15x0.5) and then filtered by one of three single bandpass filters (DAPI: Chroma ET455/50M; mVenus-hGeminin-AF488: Chroma ET525/36M; mCherry-hCdt1-AF555:Chroma ET605/50M). Emission light was then focused by a 1x relay lens onto an Andor Sona 4.2B-11 camera with a physical pixel size of 11 µm, resulting in an effective pixel size of 110 nm. The Andor Sona 4.2B-11 camera was operated in 16-bit mode with rolling shutter. The final dataset used for analysis and model training consists of 625 tiled z-stacks (150 images per z-stack) and 3 channels; each image is 1024x1024 pixels. The voxel size for each image in the dataset was 182nm*182nm*200nm (X*Y*Z).","measurementTechnique":[{"id":"http://www.ebi.ac.uk/efo/EFO_0003969","type":["DefinedTerm"],"name":"treatment protocol"}],"labEquipment":null},{"id":"https://idr.openmicroscopy.org/study/idr0167/#experiment-protocol-1-3","type":["LabProtocol"],"name":"image acquisition","description":"We performed instance segmentation and preprocessed the data prior to machine learning (ML) model training. Please see the manuscript and/or GitHub repository for details regarding CellCycleNet model training and/or implementation after preprocessing steps.","measurementTechnique":[],"labEquipment":null},{"id":"https://idr.openmicroscopy.org/study/idr0167/#experiment-protocol-1-4","type":["LabProtocol"],"name":"data analysis protocol","description":"data analysis protocol","measurementTechnique":[],"labEquipment":null},{"id":"https://idr.openmicroscopy.org/study/idr0167/#experiment-protocol-2-1","type":["LabProtocol"],"name":"Cell growth","description":"The Fucci (Fluorescent Ubiquitination-based Cell Cycle Indicator) 3T3 Fucci2a reporter cell line was a gracious gift from Richard Mort and were maintained in complete 3T3 complete cell culture media (high glucose 4.5 g/L DMEM with 2 mM L-glutamine, 10% FBS, and 1% pen/strep antibiotic) in the presence of 100-200 ug/mL hygromycin selection antibiotic. Prior to imaging experiments, ~70,000 cells were seeded in a 35 mm dish. Next day, cells were fixed in 4% PFA in 1xPBS for 10 minutes, followed by three washes in 1xPBS for one minute each prior to immunofluorescence staining.","measurementTechnique":[{"id":"http://www.ebi.ac.uk/efo/EFO_0003789","type":["DefinedTerm"],"name":"growth protocol"}],"labEquipment":null},{"id":"https://idr.openmicroscopy.org/study/idr0167/#experiment-protocol-2-2","type":["LabProtocol"],"name":"treatment protocol","description":"All images were acquired using the Keyence Plan Apochromatic 40x objective lens (model PZ-PA40, PlanApo NA 0.95/0.17 mm default). A tiled acquisition was obtained over approximately 5 square millimeters of the cell culture plate, at fixed z range of 35 µm, z-step of 0.5 µm, and optical sectioning width of 10. 100% excitation light (metal halide lamp) was used with no binning and monochromatic camera with a digital zoom of x1.0. Each image consists of three fluorescent channels: nuclear stain DAPI (using the DAPI filter cube; model OP-87762, 360/40 nm excitation filter, 400 nm longpass dichroic mirror, 460/50 nm emission filter; 1/1.2s exposure time), the mVenus-hGeminin-AF488 signal (via the GFP filter cube; model OP-87763, excitation wavelength 470/40 nm, emission wavelength 525/50 nm, dichroic mirror wavelength 495 nm; 1/2.3s exposure time), and the mCherry-hCdt1-AF555 signal (via the Cy3/TRITC filter cube; CHROMA model 49004, excitation wavelength 545/25 nm, emission wavelength 605/70 nm, dichroic mirror wavelength 565 nm; 1/7.5s exposure time). An integrated CCD camera was used in 14-bit mode, without binning and with a physical pixel size of 7.549 µm, resulting in an effective pixel size of 188.7 nm while imaging at 40x magnification. The final dataset used for analysis and model training consists of 19,170 total images over 90 tiled z-stacks (71 images per z-stack) and 3 channels; each image is 1440x1920 pixels. The voxel size for each image in the dataset was 188nm*188nm*500nm (X*Y*Z).","measurementTechnique":[{"id":"http://www.ebi.ac.uk/efo/EFO_0003969","type":["DefinedTerm"],"name":"treatment protocol"}],"labEquipment":null},{"id":"https://idr.openmicroscopy.org/study/idr0167/#experiment-protocol-2-3","type":["LabProtocol"],"name":"image acquisition","description":"We performed instance segmentation and preprocessed the data prior to machine learning (ML) model training. Please see the manuscript and/or GitHub repository for details regarding CellCycleNet model training and/or implementation after preprocessing steps.","measurementTechnique":[],"labEquipment":null},{"id":"https://idr.openmicroscopy.org/study/idr0167/#experiment-protocol-2-4","type":["LabProtocol"],"name":"data analysis protocol","description":"data analysis protocol","measurementTechnique":[],"labEquipment":null},{"id":"http://purl.obolibrary.org/obo/FBbi_00000251","type":["DefinedTerm"],"name":"confocal microscopy"},{"id":"http://purl.obolibrary.org/obo/FBbi_00000246","type":["DefinedTerm"],"name":"fluorescence microscopy"}],"thumbnailUrl":["https://idr.openmicroscopy.org/webgateway/render_thumbnail/15232834/"],"identifier":"idr0167","keywords":[],"funder":[],"seeAlso":[],"size":[],"copyrightNotice":"Li and Nichols et al, CC-BY-4.0, 2026","rdfs:seeAlso":{"@id":"https://doi.org/10.26508/lsa.202403067","@type":["ScholarlyArticle"],"name":"Predicting cell cycle stage from 3D single-cell nuclear-stained images"}},"score":1.0},{"id":"https://idr.openmicroscopy.org/study/idr0171/","entry":{"id":"https://idr.openmicroscopy.org/study/idr0171/","type":["Dataset"],"name":"Interdisciplinary Study on Drug-Induced-Phospholipidosis of Repurposing Libraries through Machine Learning and Experimental Evaluation in Different Cell Lines","author":[{"id":"https://orcid.org/0000-0001-8771-1865","type":["Person"],"name":"Maria Kuzikov","affiliation":[],"email":"maria.kuzikov@itmp.fraunhofer.de","address":"Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany","familyName":"Kuzikov","givenName":"Maria"}],"description":"Phospholipidosis (PLD) is a cellular adverse effect that is, among others, caused by numerous cationic amphiphilic drugs. Interest is raised within pharma discovery to predict this phenomenon, as it can impact the outcome of phenotypic cellular screens and significantly delay drug development processes. The development of accurate and validated machine learning models for predicting drug-induced PLD across different cell lines and research centers could provide a valuable early application tool for the pharmaceutical industry, potentially accelerating drug discovery and reducing the risk of late-stage failures. We report here the assembly, curation, testing and modeling of one of the largest datasets of repurposed drugs (5000+) tested for PLD induction on different cell lines. A machine-learning classification method was developed and validated to predict whether molecules are prone to induce PLD effects when applied in cell-based screens.","datePublished":"2026-03-30","license":"https://creativecommons.org/licenses/by/4.0/","publisher":{"id":"https://idr.openmicroscopy.org/","type":["Organization"],"name":"Image Data Resource","url":"https://idr.openmicroscopy.org/","address":null},"about":[{"id":"https://idr.openmicroscopy.org/study/idr0171/#screen-biosample-1","type":["BioSample"],"name":"cell","description":"Vero E-6 kidney cells treated with repurposed drugs for phospholipidosis induction.","taxonomicRange":[{"id":"http://purl.obolibrary.org/obo/NCBITaxon_9534","type":["Taxon"],"scientificName":"Chlorocebus aethiops","name":"Chlorocebus aethiops","vernacularName":null}],"hasCellLine":[]},{"id":"http://purl.obolibrary.org/obo/NCBITaxon_9534","type":["Taxon"],"scientificName":"Chlorocebus aethiops","name":"Chlorocebus aethiops","vernacularName":null}],"measurementMethod":[{"id":"https://idr.openmicroscopy.org/study/idr0171/#screen-protocol-1-0","type":["LabProtocol"],"name":"spinning disk confocal microscopy","description":"Vero E-6 kidney cells treated with repurposed drugs for phospholipidosis induction.","measurementTechnique":[{"id":"http://purl.obolibrary.org/obo/FBbi_00000253","type":["DefinedTerm"],"name":"spinning disk confocal microscopy"}],"labEquipment":null},{"id":"https://idr.openmicroscopy.org/study/idr0171/#screen-protocol-1-1","type":["LabProtocol"],"name":"growth protocol","description":"Vero-E6 cells were cultured in a complete medium: Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% FBS, 6 mM L-glutamine, and 1% penicillin/streptomycin. Cells were harvested at 80% confluence from a T175 cm² flask by washing once with 10 mL of RT PBS, followed by incubation with 5 mL of Trypsin 0.05% / EDTA 0.02% for 5 minutes. Cells were then resuspended in 10 mL of prewarmed culture medium. For plating, Vero-E6 cells were diluted to a concentration of 500,000 cells/mL in cell culture medium supplemented with 1:1000 dilution of HCS LipidTOX™ Red Phospholipidosis Detection Reagent (1000X). A volume of 20 µL of this cell suspension was added to each well of the 384-well plate, and cells were incubated for 24 hours at 37 °C in a 5% CO₂ environment. For fixation, 20 µL of 8% formaldehyde solution was added to each well and incubated for 30 minutes at room temperature. After incubation, the fixation buffer was then removed, and cells were washed with 50 µL/well of PBS. Cells were stained for 45 minutes with 20 µL/well of a solution containing CellMask™ Deep Red stain (1:3,000, Invitrogen #H32721) and Hoechst 33258 (1:10,000, Merck/Sigma-Aldrich #94403) diluted in PBS. Following staining, the solution was removed, and cells were washed three times with 50 µL/well of PBS.","measurementTechnique":[{"id":"http://www.ebi.ac.uk/efo/EFO_0003789","type":["DefinedTerm"],"name":"growth protocol"}],"labEquipment":null},{"id":"https://idr.openmicroscopy.org/study/idr0171/#screen-protocol-1-2","type":["LabProtocol"],"name":"treatment protocol","description":"Compounds (at 10 µM concentration) and controls (amiodarone 10 µM concentration; DMSO 0.1 v/v %) were added to clear bottom, 384-well plates (PhenoPlate 384-well, black, optically clear flat-bottom, tissue-culture treated, Revvity #6057302) using the Echo Liquid Handler (Labcyte).","measurementTechnique":[{"id":"http://www.ebi.ac.uk/efo/EFO_0003969","type":["DefinedTerm"],"name":"treatment protocol"}],"labEquipment":null},{"id":"https://idr.openmicroscopy.org/study/idr0171/#screen-protocol-1-3","type":["LabProtocol"],"name":"HCS library protocol","description":"Image acquisition was performed using the automated Operetta Phenix High Content Screening system (Revvity). Image analysis was performed using Columbus 2.9 image analysis software (PerkinElmer Inc).","measurementTechnique":[{"id":"http://www.ebi.ac.uk/efo/EFO_0007571","type":["DefinedTerm"],"name":"HCS library protocol"}],"labEquipment":null},{"id":"https://idr.openmicroscopy.org/study/idr0171/#screen-protocol-1-4","type":["LabProtocol"],"name":"HCS image acquisition and feature extraction protocol","description":"Results were normalized against the positive control (amiodarone at 10 µM, set at 100% PLD induction) and the negative control (DMSO at 0.1% v/v, set at 0% PLD induction). Compounds with >50% PLD induction were classified as primary hits.","measurementTechnique":[{"id":"http://www.ebi.ac.uk/efo/EFO_0007572","type":["DefinedTerm"],"name":"HCS image acquisition and feature extraction protocol"}],"labEquipment":null},{"id":"https://idr.openmicroscopy.org/study/idr0171/#screen-protocol-1-5","type":["LabProtocol"],"name":"HCS data analysis protocol","description":"HCS data analysis protocol","measurementTechnique":[{"id":"http://www.ebi.ac.uk/efo/EFO_0007573","type":["DefinedTerm"],"name":"HCS data analysis protocol"}],"labEquipment":null},{"id":"http://purl.obolibrary.org/obo/FBbi_00000253","type":["DefinedTerm"],"name":"spinning disk confocal microscopy"}],"thumbnailUrl":["https://idr.openmicroscopy.org/webgateway/render_thumbnail/15201742/"],"identifier":"idr0171","keywords":[],"funder":[],"seeAlso":[],"size":[],"copyrightNotice":"Kuzikov et al, CC-BY-4.0, 2026","rdfs:seeAlso":{"@id":"https://doi.org/10.1016/j.patter.2025.101453","@type":["ScholarlyArticle"],"name":"Experimental and machine learning-based exploration of repurposed drugs reveals chemical features underlying phospholipidosis"}},"score":1.0},{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000484/","entry":{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000484/","type":["Dataset"],"name":"Imaging data in the paper, \"Isotonic and minimally invasive optical clearing media for live cell imaging ex vivo and in vivo\" (Inagaki et al., 2025).","author":[{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000484/#auth-001","type":["Person"],"name":"Takeshi Imai","affiliation":[{"id":"https://ror.org/00p4k0j84","type":["Organization"],"name":"Kyushu Univerisity","url":null,"address":null}],"email":"imai.takeshi.457@m.kyushu-u.ac.jp","description":"Organization: Kyushu Univerisity"},{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000484/#auth-002","type":["Person"],"name":"Shigenori Inagaki","affiliation":[],"email":null}],"description":"Images of cultured cells, organoids, glia and neurons in brain slices and in the brains of mice.","datePublished":"2026-03-12","license":"https://creativecommons.org/licenses/by/4.0/","publisher":{"id":"https://ssbd.riken.jp/repository/","type":["Organization"],"name":"SSBD:repository","url":null,"address":null},"about":[{"id":"http://purl.obolibrary.org/obo/NCBITaxon_10090","type":["Taxon"],"scientificName":"Mus musculus","name":"Mus musculus","vernacularName":"mouse"},{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000484/#biosample-2","type":["BioSample"],"name":"Organism","description":"brain slice","taxonomicRange":[],"hasCellLine":[]},{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000484/#biosample-3","type":["BioSample"],"name":"Organism","description":"organoids)","taxonomicRange":[],"hasCellLine":[]},{"id":"http://purl.obolibrary.org/obo/NCBITaxon_9606","type":["Taxon"],"scientificName":"Homo sapiens","name":"Homo sapiens","vernacularName":"human"},{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000484/#biosample-1","type":["BioSample"],"name":"C57BL/6, ICR (Mus musculus)","description":"C57BL/6, ICR (Mus musculus)","taxonomicRange":[{"id":"http://purl.obolibrary.org/obo/NCBITaxon_10090","type":["Taxon"],"scientificName":"Mus musculus","name":"Mus musculus","vernacularName":"mouse"},{"id":"http://purl.obolibrary.org/obo/NCBITaxon_9606","type":["Taxon"],"scientificName":"Homo sapiens","name":"Homo sapiens","vernacularName":"human"}],"hasCellLine":[{"id":"http://purl.obolibrary.org/obo/CLO_0003684","type":["DefinedTerm"],"name":"HeLa cells"},{"id":"http://purl.obolibrary.org/obo/CLO_0001727","type":["DefinedTerm"],"name":"HeLa/Fucci2 cells"},{"id":"http://purl.obolibrary.org/obo/CLO_0037354","type":["DefinedTerm"],"name":"AAVpro 293T cells"}]},{"id":"http://purl.obolibrary.org/obo/CLO_0003684","type":["DefinedTerm"],"name":"HeLa cells"},{"id":"http://purl.obolibrary.org/obo/CLO_0001727","type":["DefinedTerm"],"name":"HeLa/Fucci2 cells"},{"id":"http://purl.obolibrary.org/obo/CLO_0037354","type":["DefinedTerm"],"name":"AAVpro 293T cells"}],"measurementMethod":[{"id":"http://purl.obolibrary.org/obo/FBbi_00000265","type":["DefinedTerm"],"name":"recorded image"}],"thumbnailUrl":[],"identifier":"ssbd-repos-000484","keywords":[],"funder":[],"seeAlso":[],"size":[{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000484/#total-dataset-size","type":["QuantitativeValue"],"value":393222467584,"unitText":"bytes","unitCode":"http://purl.obolibrary.org/obo/UO_0000233","description":"393.2 GB"},{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000484/#file-count","type":["QuantitativeValue"],"value":873,"unitText":"file count","unitCode":"http://purl.obolibrary.org/obo/UO_0000189"}],"rdfs:seeAlso":{"@id":"https://doi.org/10.1038/s41592-026-03023-y","@type":["ScholarlyArticle"],"datePublished":"2026","name":"Isotonic and minimally invasive optical clearing media for live cell imaging ex vivo and in vivo."}},"score":1.0},{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000495/","entry":{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000495/","type":["Dataset"],"name":"Intra- and extra-nuclear PML and SUMO","author":[{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000495/#auth-001","type":["Person"],"name":"Seishiro Hirano","affiliation":[{"id":"https://ror.org/02hw5fp67","type":["Organization"],"name":"National Institute for Environmental Studies","url":null,"address":null}],"email":"seishiro@nies.go.jp","description":"Organization: National Institute for Environmental Studies; Department: Center for Health and Environmental Risk Research"}],"description":"Promyelocytic leukemia (PML) proteins are known to form phase-separated nuclear punctate structures called PML-nuclear bodies (PML-NBs). The integrity disruption of PML-NBs is linked with the pathogenesis of acute promyelocytic leukemia (APL), and trivalent arsenic (As3+) has been used for the clinical treatment of APL to restore normal PML-NBs. As3+ is considered to bind to cysteine residues and enhances modification of PML with small-ubiquitin-like protein (SUMO). We exposed U-2OS and CHO-K1 cells stably overexpressing PML-VI to As3+ and found that the solubility of PML decreased and SUMOylation of PML increased after 2 h-exposure to 3 μM As3+. Contrary to As3+-induced remarkable biochemical changes including the solubility change and SUMOylation of PML, microscopic observation of PML-NBs was not changed clearly after a short-term exposure to As3+. The number of PML-NBs decreased and extranuclear PML bodies (EnPBs), which are remniscences of PML-NBs after nuclear membrane breakdown at mitosis, increased after exposure to As3+ for 24 - 72 h. The amount of SUMOylated PML decreased after prolonged exposure to As3+ while the solubility of PML was kept low, suggesting that As3+ stabilized EnPB without SUMOylation. The effects of As3+ on EnPBs were clearly observed at as low as 0.3 μM As3+ which corresponds to inorganic arsenic level in drinking water worldwide.\r\n\r\nKeywords: arsenic, small ubiquitin-like modifier (SUMO), solubility, phase separation, promyelocytic leukemia-nuclear body (PML-NB), extranuclear PML body (EnPB)","datePublished":"2026-03-03","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","publisher":{"id":"https://ssbd.riken.jp/repository/","type":["Organization"],"name":"SSBD:repository","url":null,"address":null},"about":[{"id":"http://purl.obolibrary.org/obo/NCBITaxon_9606","type":["Taxon"],"scientificName":"Homo sapiens","name":"Homo sapiens","vernacularName":"human"},{"id":"http://purl.obolibrary.org/obo/NCBITaxon_10029","type":["Taxon"],"scientificName":"Cricetulus griseus","name":"Cricetulus griseus","vernacularName":"chinese hamster"},{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000495/#biosample-1","type":["BioSample"],"name":"Cell line sample","description":"Cell line sample","taxonomicRange":[{"id":"http://purl.obolibrary.org/obo/NCBITaxon_9606","type":["Taxon"],"scientificName":"Homo sapiens","name":"Homo sapiens","vernacularName":"human"},{"id":"http://purl.obolibrary.org/obo/NCBITaxon_10029","type":["Taxon"],"scientificName":"Cricetulus griseus","name":"Cricetulus griseus","vernacularName":"chinese hamster"}],"hasCellLine":["U-2OS",{"id":"http://purl.obolibrary.org/obo/CLO_0002462","type":["DefinedTerm"],"name":"CHO-K1"}]},{"id":"http://purl.obolibrary.org/obo/CLO_0002462","type":["DefinedTerm"],"name":"CHO-K1"}],"measurementMethod":[{"id":"http://purl.obolibrary.org/obo/FBbi_00000265","type":["DefinedTerm"],"name":"recorded image"}],"thumbnailUrl":[],"identifier":"ssbd-repos-000495","keywords":[],"funder":[],"seeAlso":[],"size":[{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000495/#total-dataset-size","type":["QuantitativeValue"],"value":240402432,"unitText":"bytes","unitCode":"http://purl.obolibrary.org/obo/UO_0000233","description":"240.4 MB"},{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000495/#file-count","type":["QuantitativeValue"],"value":93,"unitText":"file count","unitCode":"http://purl.obolibrary.org/obo/UO_0000189"}],"rdfs:seeAlso":{"@id":"https://doi.org/10.64898/2026.01.25.701640","@type":["ScholarlyArticle"],"datePublished":"2026","name":"Biological differences in promyelocytic leukemia (PML) proteins between PML-nuclear bodies (PML-NBs) and extranuclear PML bodies (EnPBs) in arsenite-exposed cells"}},"score":1.0},{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000488/","entry":{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000488/","type":["Dataset"],"name":"Fluorescence images of myocytes in rat hearts cryo-fixed at different contractile state","author":[{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000488/#auth-001","type":["Person"],"name":"Kentaro Mochizuki","affiliation":[{"id":"https://ror.org/028vxwa22","type":["Organization"],"name":"Kyoto Prefectural University of Medicine","url":null,"address":null}],"email":"k-mochi@koto.kpu-m.ac.jp","description":"Organization: Kyoto Prefectural University of Medicine; Department: Department of Pathology and Cell Regulation"},{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000488/#auth-002","type":["Person"],"name":"Hideo Tanaka","affiliation":[],"email":null,"description":"Department: Graduate School of Medical Science"}],"description":"The dataset provides fluorescence images of myocytes in subepicardial myocardium of Langendorff-perfused rat hearts, which were rapidly-frozen (RF) during different contractile state including systole, diastole, and ventricular fibrillation (VF). The RF hearts were subsequently fixed with acetone and paraformaldehyde (PFA) by freeze-substitution procedure, then α-actinin in myocytes of them was immuno-stained with fluorescence labels. As control, hearts rapidly-frozen under mechanical relaxation induced by 2,3-butanedione monoxime (BDM), hearts fixed with PFA solely, hearts rapidly-frozen after PFA-fixation were also prepared.","datePublished":"2026-02-28","license":"https://creativecommons.org/licenses/by/4.0/","publisher":{"id":"https://ssbd.riken.jp/repository/","type":["Organization"],"name":"SSBD:repository","url":null,"address":null},"about":[{"id":"http://purl.obolibrary.org/obo/NCBITaxon_10116","type":["Taxon"],"scientificName":"Rattus norvegicus","name":"Rattus norvegicus","vernacularName":"rat"}],"measurementMethod":[{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000488/#imaging-protocol-1","type":["LabProtocol"],"name":"confocal laser scanning microscopy","description":"confocal laser scanning microscopy","measurementTechnique":[{"id":"http://purl.obolibrary.org/obo/FBbi_00000256","type":["DefinedTerm"],"name":"confocal laser scanning 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The authors visualized PGE2-induced protein kinase A (PKA) activation and quantitated PGE2 secreted from a single cell by combining fluorescence microscopy and a simulation model. For this purpose, they first prepared PGE2-producer cells that express either an optogenetic or a chemogenetic calcium channel stimulator: OptoSTIM1 (CRY2clust) or Gq-DREADD, respectively. Second, they prepared reporter cells expressing the Gs-coupled PGE2 reporter EP2 and the PKA biosensor Booster-PKA, which is based on the principle of Forster resonance FRET. Upon the stimulation-induced triggering of calcium transients, a single producer cell discharges PGE2 to stimulate PKA in the surrounding reporter cells. Due to the flow of the medium, the PKA-activated area exhibited a comet-like smear when HeLa cells were used. In contrast, radial PKA activation was observed when confluent MDCK cells were used, indicating that PGE2 diffusion was restricted to the basolateral space. By fitting the radius of the PKA-activated area to a simulation model based on simple diffusion, the authors estimated that a single HeLa cell secretes 0.25 fmol PGE2 upon a single calcium transient to activate PKA in more than 1000 neighboring cells. This model also predicts that the PGE2 discharge rate is comparable to the diffusion rate. Thus, their method quantitatively envisions that a single calcium transient affects more than 1000 neighboring cells via PGE2.","datePublished":"2026-01-21","license":"https://creativecommons.org/licenses/by/4.0/","publisher":{"id":"https://ssbd.riken.jp/database/","type":["Organization"],"name":"SSBD:database","url":null,"address":null},"about":[{"id":"https://ssbd.riken.jp/v3/project/389-Watabe-PGE2discharge#biosample-2","type":["BioSample"],"name":"Canis lupus familiaris (NCBI:txid9615) ~ MDCK cell","description":"Co-culture of the producer cells and the reporter cells.\nProducer cells; MDCK cells expressing OptoSTIM, R-GECO1 and  iRFP670.\nReporter cells; COX-1 and COX-2 (COX-DKO)-deficient MDCK cells which express Booster-PKA","taxonomicRange":[{"id":"https://www.ncbi.nlm.nih.gov/datasets/taxonomy/9615","type":["Taxon"],"scientificName":"Canis lupus familiaris","name":"Canis lupus familiaris","vernacularName":null,"identifier":"NCBITaxon:9615"}],"hasCellLine":[{"id":"http://purl.obolibrary.org/obo/CLO_0007646","type":["DefinedTerm"],"name":"MDCK cell"}]},{"id":"http://purl.obolibrary.org/obo/CLO_0007646","type":["DefinedTerm"],"name":"MDCK cell"},{"id":"https://ssbd.riken.jp/v3/project/389-Watabe-PGE2discharge#biosample-1","type":["BioSample"],"name":"Homo sapiens (NCBI:txid9606) ~ HeLa cell","description":"Co-culture of the producer cells and the reporter cells.\nProducer cells; HeLa cells expressing OptoSTIM, R-GECO1 and  iRFP670.\nReporter cells; COX-1 and COX-2 (COX-DKO)-deficient HeLa cells which express Gs-coupled EP2 receptor and Booster-PKA","taxonomicRange":[{"id":"https://www.ncbi.nlm.nih.gov/datasets/taxonomy/9606","type":["Taxon"],"scientificName":"Homo sapiens","name":"Homo sapiens","vernacularName":null,"identifier":"NCBITaxon:9606"}],"hasCellLine":[{"id":"http://purl.obolibrary.org/obo/CLO_0003684","type":["DefinedTerm"],"name":"HeLa cell"}]},{"id":"http://purl.obolibrary.org/obo/CLO_0003684","type":["DefinedTerm"],"name":"HeLa cell"},{"id":"https://www.ncbi.nlm.nih.gov/datasets/taxonomy/9606","type":["Taxon"],"scientificName":"Homo sapiens","name":"Homo sapiens","vernacularName":null,"identifier":"NCBITaxon:9606"},{"id":"https://www.ncbi.nlm.nih.gov/datasets/taxonomy/9615","type":["Taxon"],"scientificName":"Canis lupus familiaris","name":"Canis lupus familiaris","vernacularName":null,"identifier":"NCBITaxon:9615"}],"measurementMethod":[{"id":"https://ssbd.riken.jp/v3/project/389-Watabe-PGE2discharge#imaging-protocol-1","type":["LabProtocol"],"name":"recorded image","description":"recorded image","measurementTechnique":[{"id":"http://purl.obolibrary.org/obo/FBbi_00000265","type":["DefinedTerm"],"name":"recorded image","identifier":"FBbi:00000265"}],"labEquipment":null},{"id":"http://purl.obolibrary.org/obo/FBbi_00000265","type":["DefinedTerm"],"name":"recorded image","identifier":"FBbi:00000265"},{"id":"https://ssbd.riken.jp/v3/project/389-Watabe-PGE2discharge#imaging-protocol-2","type":["LabProtocol"],"name":"fluorescence microscopy","description":"fluorescence microscopy","measurementTechnique":[{"id":"http://purl.obolibrary.org/obo/FBbi_00000246","type":["DefinedTerm"],"name":"fluorescence microscopy","identifier":"FBbi:00000246"}],"labEquipment":null},{"id":"http://purl.obolibrary.org/obo/FBbi_00000246","type":["DefinedTerm"],"name":"fluorescence microscopy","identifier":"FBbi:00000246"},{"id":"https://ssbd.riken.jp/v3/project/389-Watabe-PGE2discharge#imaging-protocol-3","type":["LabProtocol"],"name":"time lapse microscopy","description":"time lapse microscopy","measurementTechnique":[{"id":"http://purl.obolibrary.org/obo/FBbi_00000249","type":["DefinedTerm"],"name":"time lapse microscopy","identifier":"FBbi:00000249"}],"labEquipment":null},{"id":"http://purl.obolibrary.org/obo/FBbi_00000249","type":["DefinedTerm"],"name":"time lapse microscopy","identifier":"FBbi:00000249"},{"id":"https://ssbd.riken.jp/v3/project/389-Watabe-PGE2discharge#imaging-protocol-4","type":["LabProtocol"],"name":"FRET","description":"FRET","measurementTechnique":[{"id":"http://purl.obolibrary.org/obo/FBbi_00000367","type":["DefinedTerm"],"name":"FRET","identifier":"FBbi:00000367"}],"labEquipment":null},{"id":"http://purl.obolibrary.org/obo/FBbi_00000367","type":["DefinedTerm"],"name":"FRET","identifier":"FBbi:00000367"}],"thumbnailUrl":["https://ssbd.riken.jp/ssbd-omero/v1/projects/1853/render_thumbnail/"],"identifier":"389-Watabe-PGE2discharge","keywords":["Madin Darby Canine Kidney Cells","Microscopy, Fluorescence,\nTime-Lapse Imaging,\nFluorescence Resonance Energy Transfer","Cell Communication","Cytoplasm","Signal Transduction"],"funder":[{"id":"https://ssbd.riken.jp/v3/project/389-Watabe-PGE2discharge#grant-001","type":["Grant"],"name":"Financial\nsupport was provided by JSPS KAKENHI grants (nos. 21K20773 to\nT.W., 21H02715 and 21H05226 to K.T., and 19H00993, 20H05898,\n22H04926 to M.M.), a JST Moonshot R&D grant (no. JPMJPS2022\nto M.M.), a grant from Fugaku Foundation to M.M., and Research\nGrants of Princess Takamatsu Cancer Research Fund to K.T.","identifier":null}],"seeAlso":[],"size":[{"id":"https://ssbd.riken.jp/v3/project/389-Watabe-PGE2discharge#total-dataset-size","type":["QuantitativeValue"],"value":308773461162,"unitText":"bytes","unitCode":"http://purl.obolibrary.org/obo/UO_0000233","description":"308.8 GB"},{"id":"https://ssbd.riken.jp/v3/project/389-Watabe-PGE2discharge#file-count","type":["QuantitativeValue"],"value":12063,"unitText":"file count","unitCode":"http://purl.obolibrary.org/obo/UO_0000189"}],"rdfs:seeAlso":{"@id":"https://doi.org/10.1247/csf.23047","@type":["ScholarlyArticle"],"datePublished":"2023","name":"Watabe T, Yamahira S, Matsuda M, Terai K. Visual quantification of prostaglandin E2 discharge from a single cell. Cell Struct Funct\n. 2023 Dec 7;48(2):241-249.","sameAs":["https://pubmed.ncbi.nlm.nih.gov/37813623/","https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11496778/"]}},"score":1.0},{"id":"https://ssbd.riken.jp/v3/project/454-Mizuta-PollenTubeGuidance","entry":{"id":"https://ssbd.riken.jp/v3/project/454-Mizuta-PollenTubeGuidance","type":["Dataset"],"name":"Dynamics of pollen tube in Arabidopsis thaliana","author":[{"id":"https://orcid.org/0000-0002-8086-2297","type":["Person"],"name":"Yoko Mizuta","affiliation":[{"id":"https://ssbd.riken.jp/v3/project/454-Mizuta-PollenTubeGuidance#affiliation-001","type":["Organization"],"name":"Nagoya University","url":null,"address":null}],"email":"mizuta.yoko.u6@f.mail.nagoya-u.ac.jp","description":"Organization: Nagoya University; Department: Institute of Transformative Bio-Molecules (WPI-ITbM), Institute for Advanced Research (IAR)","url":"https://researchmap.jp/ym72?lang=en"},{"id":"https://ssbd.riken.jp/v3/project/454-Mizuta-PollenTubeGuidance#auth-002","type":["Person"],"name":"Yoko Mizuta","affiliation":[{"id":"https://ssbd.riken.jp/v3/project/454-Mizuta-PollenTubeGuidance#affiliation-001","type":["Organization"],"name":"Nagoya University","url":null,"address":null}],"email":"mizuta.yoko.u6@f.mail.nagoya-u.ac.jp","description":"Organization: Nagoya University; Department: Institute of Transformative Bio-Molecules (WPI-ITbM), Institute for Advanced Research (IAR)","url":"https://researchmap.jp/ym72?lang=en"},{"id":"https://ssbd.riken.jp/v3/project/454-Mizuta-PollenTubeGuidance#auth-003","type":["Person"],"name":"Daigo Sakakibara","affiliation":[{"id":"https://ssbd.riken.jp/v3/project/454-Mizuta-PollenTubeGuidance#affiliation-001","type":["Organization"],"name":"Nagoya University","url":null,"address":null}],"email":"sakakibara.daigo.j0@s.mail.nagoya-u.ac.jp","description":"Organization: Nagoya University; Department: Division of Biological Sciences, Graduate School of Science"},{"id":"https://ssbd.riken.jp/v3/project/454-Mizuta-PollenTubeGuidance#auth-004","type":["Person"],"name":"Shiori Nagahara","affiliation":[{"id":"https://ssbd.riken.jp/v3/project/454-Mizuta-PollenTubeGuidance#affiliation-001","type":["Organization"],"name":"Nagoya University","url":null,"address":null}],"email":"nagahara.shiori.3n@kyoto-u.ac.jp","description":"Organization: Nagoya University; Department: Institute of Transformative Bio-Molecules (WPI-ITbM)"},{"id":"https://ssbd.riken.jp/v3/project/454-Mizuta-PollenTubeGuidance#auth-005","type":["Person"],"name":"Ikuma Kaneshiro","affiliation":[{"id":"https://ssbd.riken.jp/v3/project/454-Mizuta-PollenTubeGuidance#affiliation-001","type":["Organization"],"name":"Nagoya University","url":null,"address":null}],"email":"kaneshiro.ikuma.k2@f.mail.nagoya-u.ac.jp","description":"Organization: Nagoya University; Department: Institute of Transformative Bio-Molecules (WPI-ITbM)"}],"description":"In the pistil of flowering plants, each ovule usually associates with a single pollen tube for fertilization. This one-to-one pollen tube guidance, which contributes to polyspermy blocking and efficient seed production, is largely different from animal chemotaxis of many sperms to one egg. However, the functional mechanisms underlying the directional cues and polytubey blocks in the depths of the pistil remain unknown. Here, the authors develop a two-photon live imaging method to directly observe pollen tube guidance in the pistil of Arabidopsis thaliana, clarifying signaling and cellular behaviors in the one-to-one guidance. Ovules are suggested to emit multiple signals for pollen tubes, including an integument- dependent directional signal that reaches the inner surface of the septum and adhesion signals for emerged pollen tubes on the septum. Not only FERONIA in the septum but ovular gametophytic FERONIA and LORELEI, as well as FERONIA- and LORELEI- independent repulsion signal, are involved in polytubey blocks on the ovular funiculus. However, these funicular blocks are not strictly maintained in the first 45 min, explaining previous reports of polyspermy in flowering plants.","datePublished":"2026-01-21","license":"https://creativecommons.org/licenses/by/4.0/","publisher":{"id":"https://ssbd.riken.jp/database/","type":["Organization"],"name":"SSBD:database","url":null,"address":null},"about":[{"id":"https://ssbd.riken.jp/v3/project/454-Mizuta-PollenTubeGuidance#biosample-3","type":["BioSample"],"name":"Col-0 ~ ovary\nepidermal cell","description":"The dissected pistil of HDG11p::NLS-YFP Arabidopsis after hand pollination.","taxonomicRange":[{"id":"https://www.ncbi.nlm.nih.gov/datasets/taxonomy/3702","type":["Taxon"],"scientificName":"Arabidopsis thaliana","name":"Arabidopsis thaliana","vernacularName":null,"identifier":"NCBITaxon:3702"}],"hasCellLine":[]},{"id":"https://ssbd.riken.jp/v3/project/454-Mizuta-PollenTubeGuidance#biosample-2","type":["BioSample"],"name":"Col-0 ~ ovary\nsynergid cell","description":"The dissected pistil of MYB98p::GFP Arabidopsis after hand pollination.","taxonomicRange":[{"id":"https://www.ncbi.nlm.nih.gov/datasets/taxonomy/3702","type":["Taxon"],"scientificName":"Arabidopsis thaliana","name":"Arabidopsis thaliana","vernacularName":null,"identifier":"NCBITaxon:3702"}],"hasCellLine":[]},{"id":"https://ssbd.riken.jp/v3/project/454-Mizuta-PollenTubeGuidance#biosample-1","type":["BioSample"],"name":"Col-0 ~ ovary","description":"The dissected pistil of wild type Arabidopsis after hand pollination.","taxonomicRange":[{"id":"https://www.ncbi.nlm.nih.gov/datasets/taxonomy/3702","type":["Taxon"],"scientificName":"Arabidopsis thaliana","name":"Arabidopsis thaliana","vernacularName":null,"identifier":"NCBITaxon:3702"}],"hasCellLine":[]},{"id":"https://www.ncbi.nlm.nih.gov/datasets/taxonomy/3702","type":["Taxon"],"scientificName":"Arabidopsis thaliana","name":"Arabidopsis thaliana","vernacularName":null,"identifier":"NCBITaxon:3702"}],"measurementMethod":[{"id":"https://ssbd.riken.jp/v3/project/454-Mizuta-PollenTubeGuidance#imaging-protocol-1","type":["LabProtocol"],"name":"recorded image","description":"recorded image","measurementTechnique":[{"id":"http://purl.obolibrary.org/obo/FBbi_00000265","type":["DefinedTerm"],"name":"recorded image","identifier":"FBbi:00000265"}],"labEquipment":null},{"id":"http://purl.obolibrary.org/obo/FBbi_00000265","type":["DefinedTerm"],"name":"recorded image","identifier":"FBbi:00000265"},{"id":"https://ssbd.riken.jp/v3/project/454-Mizuta-PollenTubeGuidance#imaging-protocol-2","type":["LabProtocol"],"name":"two-photon laser scanning microscopy","description":"two-photon laser scanning microscopy","measurementTechnique":[{"id":"http://purl.obolibrary.org/obo/FBbi_00000254","type":["DefinedTerm"],"name":"two-photon laser scanning microscopy","identifier":"FBbi:00000254"}],"labEquipment":null},{"id":"http://purl.obolibrary.org/obo/FBbi_00000254","type":["DefinedTerm"],"name":"two-photon laser scanning microscopy","identifier":"FBbi:00000254"},{"id":"https://ssbd.riken.jp/v3/project/454-Mizuta-PollenTubeGuidance#imaging-protocol-3","type":["LabProtocol"],"name":"time lapse microscopy","description":"time lapse microscopy","measurementTechnique":[{"id":"http://purl.obolibrary.org/obo/FBbi_00000249","type":["DefinedTerm"],"name":"time lapse microscopy","identifier":"FBbi:00000249"}],"labEquipment":null},{"id":"http://purl.obolibrary.org/obo/FBbi_00000249","type":["DefinedTerm"],"name":"time lapse microscopy","identifier":"FBbi:00000249"}],"thumbnailUrl":["https://ssbd.riken.jp/ssbd-omero/v1/projects/1851/render_thumbnail/"],"identifier":"454-Mizuta-PollenTubeGuidance","keywords":["Ovary","Microscopy, Fluorescence, Multiphoton","Pollen Tube","Cytoplasm","Cell Nucleus"],"funder":[{"id":"https://ssbd.riken.jp/v3/project/454-Mizuta-PollenTubeGuidance#grant-001","type":["Grant"],"name":"This work was supported by grants from the Japan Science and Technology Agency (ERATO Grant no. JPMJER1004 to T.H., CREST Grant no. JPMJCR20E5 to T.H. and Y.M. and FOREST Program Grant no. JPMJFR204T to D.K.); the Japan Society for the Promotion of Science (nos. 18K14741, 20H05778 and 20H05779 to Y.M., no. 22H04668 to D.K., and nos. 16H06465 and 22H04980 to T.H.); the Program for Promoting the Enhancement of Research Universities (2022 to Y.M.); the Ohsumi Frontier Science Foundation (2023 to Y.M.); and the Sumitomo Basic Science Research Projects (2023 to Y.M.).","identifier":null}],"seeAlso":[],"size":[{"id":"https://ssbd.riken.jp/v3/project/454-Mizuta-PollenTubeGuidance#total-dataset-size","type":["QuantitativeValue"],"value":56443510172,"unitText":"bytes","unitCode":"http://purl.obolibrary.org/obo/UO_0000233","description":"56.4 GB"},{"id":"https://ssbd.riken.jp/v3/project/454-Mizuta-PollenTubeGuidance#file-count","type":["QuantitativeValue"],"value":77,"unitText":"file count","unitCode":"http://purl.obolibrary.org/obo/UO_0000189"}],"rdfs:seeAlso":{"@id":"https://doi.org/10.1038/s44319-024-00151-4","@type":["ScholarlyArticle"],"datePublished":"2024","name":"Mizuta Y, Sakakibara D, Nagahara S, Kaneshiro I, Nagae TT, Kurihara D, Higashiyama T. Deep imaging reveals dynamics and signaling in one-to-one pollen tube guidance. EMBO Rep. 2024 Jun;25(6):2529-2549.","sameAs":["https://pubmed.ncbi.nlm.nih.gov/38773320/","https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11169409/"]}},"score":1.0},{"id":"https://ssbd.riken.jp/v3/project/460-Tanaka-RadialAxisDyn","entry":{"id":"https://ssbd.riken.jp/v3/project/460-Tanaka-RadialAxisDyn","type":["Dataset"],"name":"Dynamics of radial axis formation in Arabidopsis thaliana zygote","author":[{"id":"https://orcid.org/0000-0002-6892-2744","type":["Person"],"name":"Minako Ueda","affiliation":[{"id":"https://ssbd.riken.jp/v3/project/460-Tanaka-RadialAxisDyn#affiliation-001","type":["Organization"],"name":"Tohoku University","url":null,"address":null}],"email":"minako.ueda.e7@tohoku.ac.jp","description":"Organization: Tohoku University; Department: Graduate School of Life Sciences; Laboratory: Laboratory of Plant Cell Dynamics"},{"id":"https://ssbd.riken.jp/v3/project/460-Tanaka-RadialAxisDyn#auth-002","type":["Person"],"name":"Sayuri Tanaka","affiliation":[{"id":"https://ssbd.riken.jp/v3/project/460-Tanaka-RadialAxisDyn#affiliation-002","type":["Organization"],"name":"Nagoya University","url":null,"address":null}],"email":null,"description":"Organization: Nagoya University"}],"description":"Plants develop along apical-basal and radial axes. In Arabidopsis thaliana, the radial axis becomes evident when the cells of the 8-cell proembryo divide periclinally, forming inner and outer cell layers. Although changes in cell polarity or morphology likely precede this oriented cell division, the initial events and the factors regulating radial axis formation remain elusive. Here, we report that three transcription factors belonging to the class IV homeodomain-leucine zipper (HD-ZIP IV) family redundantly regulate radial pattern formation:HOMEODOMAIN GLABROUS11 (HDG11), HDG12, and PROTODERMAL FACTOR2 (PDF2). The hdg11 hdg12 pdf2 triple mutant failed to undergo periclinal division at the 8-cell stage and cell differentiation along the radial axis. Live-cell imaging revealed that the mutant defect is already evident in the behavior of the embryo’s initial cell (apical cell), which is generated by zygote division. In the wild type, the apical cell grows longitudinally and then radially, and its nucleus remains at the bottom of the cell, where the vertical cell plate emerges. By contrast, the mutant apical cell elongates longitudinally, and its nucleus releases from its basal position, resulting in a transverse division. Computer simulations based on the live-cell imaging data confirmed the importance of the geometric rule (the minimal plane principle and nucleus-passing principle) in determining the cell division plane. We propose that HDG11, HDG12, and PDF2 promote apical cell polarization, i.e., radial cell growth and basal nuclear retention, and set proper radial axis formation during embryogenesis.","datePublished":"2026-01-21","license":"https://creativecommons.org/licenses/by/4.0/","publisher":{"id":"https://ssbd.riken.jp/database/","type":["Organization"],"name":"SSBD:database","url":null,"address":null},"about":[{"id":"https://ssbd.riken.jp/v3/project/460-Tanaka-RadialAxisDyn#biosample-1","type":["BioSample"],"name":"Col-0 ~ zygote","description":"The embryo nucleus of Arabidopsis vitro-cultivated WT ovules was labelld by the markers WOX2p::H2B-GFP and WOX2p::LTI-tdTomato.","taxonomicRange":[{"id":"https://www.ncbi.nlm.nih.gov/datasets/taxonomy/3702","type":["Taxon"],"scientificName":"NCBITaxon:3702","name":"NCBITaxon:3702","vernacularName":null,"identifier":"NCBITaxon:3702"}],"hasCellLine":[]},{"id":"https://www.ncbi.nlm.nih.gov/datasets/taxonomy/3702","type":["Taxon"],"scientificName":"NCBITaxon:3702","name":"NCBITaxon:3702","vernacularName":null,"identifier":"NCBITaxon:3702"}],"measurementMethod":[{"id":"https://ssbd.riken.jp/v3/project/460-Tanaka-RadialAxisDyn#imaging-protocol-1","type":["LabProtocol"],"name":"recorded image","description":"recorded image","measurementTechnique":[{"id":"http://purl.obolibrary.org/obo/FBbi_00000265","type":["DefinedTerm"],"name":"recorded image","identifier":"FBbi:00000265"}],"labEquipment":null},{"id":"http://purl.obolibrary.org/obo/FBbi_00000265","type":["DefinedTerm"],"name":"recorded image","identifier":"FBbi:00000265"},{"id":"https://ssbd.riken.jp/v3/project/460-Tanaka-RadialAxisDyn#imaging-protocol-2","type":["LabProtocol"],"name":"spinning disk confocal microscopy","description":"spinning disk confocal microscopy","measurementTechnique":[{"id":"https://ssbd.riken.jp/v3/project/460-Tanaka-RadialAxisDyn#imaging-technique-2","type":["DefinedTerm"],"name":"spinning disk confocal microscopy"}],"labEquipment":null},{"id":"https://ssbd.riken.jp/v3/project/460-Tanaka-RadialAxisDyn#imaging-technique-2","type":["DefinedTerm"],"name":"spinning disk confocal microscopy"},{"id":"https://ssbd.riken.jp/v3/project/460-Tanaka-RadialAxisDyn#imaging-protocol-3","type":["LabProtocol"],"name":"http://purl.obolibrary.org/obo/FBbi_00000253","description":"http://purl.obolibrary.org/obo/FBbi_00000253","measurementTechnique":[{"id":"http://purl.obolibrary.org/obo/FBbi_00000253","type":["DefinedTerm"],"name":"FBbi:00000253","identifier":"FBbi:00000253"}],"labEquipment":null},{"id":"http://purl.obolibrary.org/obo/FBbi_00000253","type":["DefinedTerm"],"name":"spinning disk confocal microscopy","identifier":"FBbi:00000253"}],"thumbnailUrl":["https://ssbd.riken.jp/ssbd-omero/v1/projects/1852/render_thumbnail/"],"identifier":"460-Tanaka-RadialAxisDyn","keywords":["Zygote","Microscopy, Confocal","Cell Nucleus","Embryonic Structures","Cell Membrane"],"funder":[{"id":"https://ssbd.riken.jp/v3/project/460-Tanaka-RadialAxisDyn#grant-001","type":["Grant"],"name":"This work was supported by the Japan Society for the Promotion of Science\n(a Grant-in-Aid for Scientific Research on Innovative Areas) (JP19H05670\nand JP19H05676 to M.U., JP22H04719 to K.F., and JP16H06280 [Advanced\nBioimaging Support]), a Grant-in-Aid for Scientific Research (B) (JP23H02494\nto M.U. and JP20H03289 to T. Higaki), International Leading Research KEPLR\n(JP22K21352 to T. Higashiyama and M.U.), the Japan Science and Technology\nAgency (CREST [JPMJCR2121 to M.U., T. Higaki, and K.F.]), the Suntory Rising\nStars Encouragement Program in Life Sciences (SunRiSE; to M.U.), and the\nToray Science Foundation (20-6102 to M.U.).","identifier":null}],"seeAlso":[],"size":[{"id":"https://ssbd.riken.jp/v3/project/460-Tanaka-RadialAxisDyn#total-dataset-size","type":["QuantitativeValue"],"value":26613851792,"unitText":"bytes","unitCode":"http://purl.obolibrary.org/obo/UO_0000233","description":"26.6 GB"},{"id":"https://ssbd.riken.jp/v3/project/460-Tanaka-RadialAxisDyn#file-count","type":["QuantitativeValue"],"value":19,"unitText":"file count","unitCode":"http://purl.obolibrary.org/obo/UO_0000189"}],"rdfs:seeAlso":{"@id":"https://doi.org/10.1016/j.cub.2024.08.038","@type":["ScholarlyArticle"],"datePublished":"2024","name":"Tanaka S, Matsushita Y, Hanaki Y, Higaki T, Kamamoto N, Matsushita K, Higashiyama T, Fujimoto K, Ueda M. HD-ZIP IV genes are essential for embryo initial cell polarization and the radial axis formation in Arabidopsis. Curr Biol. 2024 Oct 21;34(20):4639-4649.e4.","sameAs":["https://www.sciencedirect.com/science/article/pii/S0960982224011539?via%3Dihub","https://pubmed.ncbi.nlm.nih.gov/39303713/"]}},"score":1.0},{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2515","entry":{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2515","type":["Dataset"],"name":"High-content live-cell time-lapse imaging predicts cells about to die via apoptosis","author":[{"id":"https://orcid.org/0000-0002-8637-1448","type":["Person"],"name":"Michael J. Lippincott","affiliation":[{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2515#8ad0f668-6640-42c5-8125-7eea44ddbf51","type":["Organization"],"name":"Department of Biomedical Informatics, University of Colorado Anschutz","url":null,"address":null}],"email":"michael.lippincott@cuanschutz.edu"},{"id":"https://orcid.org/0000-0003-2676-5813","type":["Person"],"name":"Jenna Tomkinson","affiliation":[{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2515#8ad0f668-6640-42c5-8125-7eea44ddbf51","type":["Organization"],"name":"Department of Biomedical Informatics, University of Colorado Anschutz","url":null,"address":null}],"email":"enna.tomkinson@ucdenver.edu"},{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2515#80e6bf97-c53a-4fb1-9470-0d8043e98fd4","type":["Person"],"name":"Ibrahim Bilem","affiliation":[{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2515#45adb958-58a5-4ba4-b2f6-befd800ec2a2","type":["Organization"],"name":"Saguaro Biosciences","url":null,"address":null}],"email":"ibilem@saguarobio.com"},{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2515#1a130b97-32a5-406b-9684-a0d08e60506b","type":["Person"],"name":"Mahomi Suzuki","affiliation":[{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2515#4cf2caa0-a99a-4ec7-a2b2-67d987c27dd2","type":["Organization"],"name":"Life Business Headquarters, Yokogawa Electric Corporation","url":null,"address":null}],"email":"mahomi.suzuki@cellsignal.com"},{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2515#081d098a-f010-4706-89e6-91ea08cdfc61","type":["Person"],"name":"Akiko Nakde","affiliation":[{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2515#4cf2caa0-a99a-4ec7-a2b2-67d987c27dd2","type":["Organization"],"name":"Life Business Headquarters, Yokogawa Electric Corporation","url":null,"address":null}],"email":"Akiko.Nakade@yokogawa.com"},{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2515#76610d25-1c33-449f-b87d-482b69407856","type":["Person"],"name":"Toshiaki Endou","affiliation":[{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2515#4cf2caa0-a99a-4ec7-a2b2-67d987c27dd2","type":["Organization"],"name":"Life Business Headquarters, Yokogawa Electric Corporation","url":null,"address":null}],"email":"Toshiaki.Endou@yokogawa.com"},{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2515#b91e76b8-18e4-4ba4-900c-e0f3753ab271","type":["Person"],"name":"Simon Mathien","affiliation":[{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2515#463b862a-b554-4f5e-9c1a-42dd7ddc5902","type":["Organization"],"name":"Institute for Research in Immunology and Cancer, University of Montreal","url":null,"address":null}],"email":"simon.mathien.1@umontreal.ca"},{"id":"https://orcid.org/0000-0002-0934-8201","type":["Person"],"name":"Carla Basualto-Alarcon","affiliation":[{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2515#cb255077-2aea-49ce-9ed6-8938acbe5c47","type":["Organization"],"name":"Health Sciences Department, Universidad de Aysén, Universidad de Chile","url":null,"address":null}],"email":"carla.basualto@uaysen.cl"},{"id":"https://orcid.org/0000-0001-6041-3665","type":["Person"],"name":"Dave Bunten","affiliation":[{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2515#8ad0f668-6640-42c5-8125-7eea44ddbf51","type":["Organization"],"name":"Department of Biomedical Informatics, University of Colorado Anschutz","url":null,"address":null}],"email":"dave.bunten@cuanschutz.edu"},{"id":"https://orcid.org/0000-0002-0503-9348","type":["Person"],"name":"Gregory P. Way","affiliation":[{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2515#8ad0f668-6640-42c5-8125-7eea44ddbf51","type":["Organization"],"name":"Department of Biomedical Informatics, University of Colorado Anschutz","url":null,"address":null}],"email":"gregory.way@cuanschutz.edu"}],"description":"This dataset contains high-content, live-cell, time-lapse imaging of HeLa cells undergoing apoptosis across a 10-point dose response to the apoptosis inducer staurosporine. Using the ChromaLIVE™ Live Cell Painting assay, cells were imaged every 30 minutes over a six-hour period on the Yokogawa CellVoyager CQ1 spinning-disk confocal platform, capturing multiplexed fluorescence signals (Hoechst, ChromaLIVE 488_yellow, ChromaLIVE 488_red, and ChromaLIVE 561) across three z-planes at four fields of view per well. After live imaging, cells were fixed and stained with AnnexinV to provide a single-cell ground-truth readout of apoptosis.\n\nThe dataset includes raw and illumination-corrected images, cell segmentation masks, single-cell tracking outputs, and extracted morphological features generated using CellProfiler and scDINO deep-learning embeddings. In total, the dataset comprises over 188,000 single-cell observations and 20,677 cell tracks across time, with 2,336 curated morphology features per cell. These measurements quantify the dynamic morphological signatures preceding apoptosis and capture dose- and time-dependent phenotypic trajectories.\n\nThis resource enables the study of temporal morphology changes, benchmarking of image-based profiling pipelines, development of machine-learning models for early apoptosis prediction, and exploration of dynamic cell-state transitions. It supports future work such as profiling additional forms of regulated cell death and constructing temporal morphology atlases.\n","datePublished":"2026-01-21","license":"https://creativecommons.org/publicdomain/zero/1.0/","publisher":{"id":"https://www.ebi.ac.uk/bioimage-archive/","type":["Organization"],"name":"BioImage Archive","url":null,"address":null},"about":[{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2515#76a61d27-9feb-404f-b042-9e68e2c12236","type":["BioSample"],"name":"High-content live-cell time-lapse imaging of apoptosis in HeLa cells treated with staurosporine","description":"HeLa cell line (human cervical adenocarcinoma) - HeLa cells were exposed to a 10-point dose series of the apoptosis-inducing compound staurosporine and imaged over six hours using the ChromaLIVE™ Live Cell Painting assay. The study captures dynamic single-cell morphological changes during the onset and progression of apoptosis, with multiplexed fluorescence channels and terminal Annexin V staining used to establish ground-truth apoptotic states.","taxonomicRange":[{"id":"http://purl.obolibrary.org/obo/NCBITaxon_9606","type":["Taxon"],"scientificName":"Homo sapiens","name":"Homo sapiens","vernacularName":null}],"hasCellLine":[]},{"id":"http://purl.obolibrary.org/obo/NCBITaxon_9606","type":["Taxon"],"scientificName":"Homo sapiens","name":"Homo sapiens","vernacularName":null}],"measurementMethod":[{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2515#99f3eee4-8506-4a4a-94fb-867fa2cb7468","type":["LabProtocol"],"name":"Live-cell time-lapse imaging of ChromaLIVE™- and Hoechst-stained HeLa cells","description":"Images were acquired every 30 minutes for six hours.  \nFour fields of view (FOVs) per well were imaged, each with three z-slices spaced 3 µm apart.  \nChannels and exposure settings:  \n- CH1: Hoechst (excitation 405 nm; emission 447/60 nm; 300 ms exposure)  \n- CH2: ChromaLIVE 488_yellow (excitation 488 nm; emission 617/73 nm; 400 ms exposure)  \n- CH3: ChromaLIVE 488_red (excitation 488 nm; emission 685/40 nm; 400 ms exposure)  \n- CH4: ChromaLIVE 561 (excitation 561 nm; emission 617/73 nm; 400 ms exposure)  \n- CH5: Annexin V (terminal imaging only; excitation 640 nm; emission 685/40 nm; 400 ms exposure)\n","measurementTechnique":[],"labEquipment":"Yokogawa CellVoyager CQ1 spinning-disk confocal microscope with an Olympus UPLXAPO 20× dry lens (0.75 NA)"}],"thumbnailUrl":["https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD2515/f4a63b01-7924-46e0-b5d9-e9b4a128856b/static_display_512_512.png"],"identifier":"S-BIAD2515","keywords":["apoptosis","regulated cell death","time-lapse imaging","high-content imaging","live-cell imaging","morphological profiling","single-cell analysis","ChromaLIVE","Cell Painting","image-based profiling","cell tracking","Ultrack","CellProfiler","scDINO","deep learning embeddings","machine learning","staurosporine","dose-response","HeLa cells","Annexin V","phenotype dynamics","temporal morphology","bioimage analysis","fluorescence microscopy","cytometry by imaging","systems biology"],"funder":[],"seeAlso":[],"size":[{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2515#480bb0bc-db43-46e5-88ae-071380b9d63c","type":["https://www.ebi.ac.uk/biostudies/bioimages/studies/QuantitiveValue"],"value":45085609920,"unitText":"bytes","unitCode":"http://purl.obolibrary.org/obo/UO_0000233"},{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2515#1037e7dd-b10a-47a1-885c-1f3b2998ff1c","type":["https://www.ebi.ac.uk/biostudies/bioimages/studies/QuantitiveValue"],"value":6240,"unitText":"file count","unitCode":"http://purl.obolibrary.org/obo/UO_0000189"}]},"score":1.0},{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2807","entry":{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2807","type":["Dataset"],"name":"Alternative Splicing Directs PMCA2 to Lysosomes and is Linked to Neurodegeneration","author":[{"id":"https://orcid.org/0000-0003-4277-2079","type":["Person"],"name":"Maria Fernandez-Suarez","affiliation":[{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2807#4fd6f7d5-9a50-4f9b-8bac-2be37914c43e","type":["Organization"],"name":"University of Oxford","url":null,"address":null}],"email":"maria.fernandez-suarez@pharm.ox.ac.uk"}],"description":"Plasma membrane calcium ATPases (PMCAs) are believed to function exclusively at the plasma membrane where they expel calcium from the cytosol. We have unexpectedly identified a splice variant-dependent localisation of the PMCA isoform PMCA2 to the lysosome, where it forms an evolutionarily conserved complex with NPC1, the lysosomal membrane protein defective in the rare lysosomal storage disease Niemann-Pick disease type C (NPC). This interaction is required for lysosomal Ca2+ homeostasis and implicates PMCA2 as a mediator of Ca2+ uptake into lysosomes. Disruption of the NPC1-PMCA2 complex contributes to the pathophysiology of both Niemann-Pick disease type C and Parkinson’s disease, revealing an unrecognised intracellular function for PMCA2 and a shared mechanism linking lysosomal Ca2+ and lipid regulation in neurodegeneration. ","datePublished":"2026-01-21","license":"https://creativecommons.org/licenses/by/4.0/","publisher":{"id":"https://www.ebi.ac.uk/bioimage-archive/","type":["Organization"],"name":"BioImage Archive","url":null,"address":null},"about":[{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2807#a8cec56f-6c97-4493-a003-c33a586a9ac3","type":["BioSample"],"name":"PC12 cells","description":"PC12 cells","taxonomicRange":[{"id":"http://purl.obolibrary.org/obo/NCBITaxon_10116","type":["Taxon"],"scientificName":"Rattus norvegicus","name":"Rattus norvegicus","vernacularName":null}],"hasCellLine":[]},{"id":"http://purl.obolibrary.org/obo/NCBITaxon_10116","type":["Taxon"],"scientificName":"Rattus norvegicus","name":"Rattus norvegicus","vernacularName":null}],"measurementMethod":[{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2807#7bb2d3b8-87a5-43ad-a002-084e941abe39","type":["LabProtocol"],"name":"Filipin stained scramble and Atp2b2 knockdown PC12 cells","description":"405 laser,  LD 63X objective, Zoom: 2.","measurementTechnique":[{"id":"http://purl.obolibrary.org/obo/FBbi_00000251","type":["DefinedTerm"],"name":"confocal microscopy"}],"labEquipment":"Confocal images were acquired using a Leica-SP8 confocal microscope with an LD 63X objective."},{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2807#397dcc38-0a94-4b15-a3fd-5c00839647ff","type":["LabProtocol"],"name":"PMCA2-KD immunocytochemistry","description":"552 laser,  LD 63X objective, Zoom: 2.","measurementTechnique":[{"id":"http://purl.obolibrary.org/obo/FBbi_00000251","type":["DefinedTerm"],"name":"confocal microscopy"}],"labEquipment":"Confocal images were acquired using a Leica-SP8 confocal microscope with an LD 63X objective."},{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2807#01dae9da-49e0-4e51-a08b-64ce6d44131f","type":["LabProtocol"],"name":"GFP-PMCA2 expressing PC12 cells","description":"488 laser,  LD 63X objective, Zoom: 2.","measurementTechnique":[{"id":"http://purl.obolibrary.org/obo/FBbi_00000251","type":["DefinedTerm"],"name":"confocal microscopy"}],"labEquipment":"Live cell imaging was performed using a Leica-SP8 confocal microscope with an LD 63X objective."},{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2807#54a0704e-7d23-4d66-9879-a3dc98dca755","type":["LabProtocol"],"name":"Endogenous NPC1 and PMCA2 colocalisation in PC12 cells","description":"488 and 552 lasers,  LD 63X objective, Zoom: 2.","measurementTechnique":[{"id":"http://purl.obolibrary.org/obo/FBbi_00000251","type":["DefinedTerm"],"name":"confocal microscopy"}],"labEquipment":"Confocal images were acquired using a Leica-SP8 confocal microscope with an LD 63X objective."},{"id":"http://purl.obolibrary.org/obo/FBbi_00000251","type":["DefinedTerm"],"name":"confocal microscopy"}],"thumbnailUrl":["https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD2807/18d9935a-220a-48d2-aae7-60545ac478c1/static_display_512_512.png"],"identifier":"S-BIAD2807","keywords":["PMCA2","PMCA","NPC","Parkinson's","lysosomal calcium"],"funder":[],"seeAlso":[],"size":[{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2807#480bb0bc-db43-46e5-88ae-071380b9d63c","type":["https://www.ebi.ac.uk/biostudies/bioimages/studies/QuantitiveValue"],"value":3535248154,"unitText":"bytes","unitCode":"http://purl.obolibrary.org/obo/UO_0000233"},{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2807#1037e7dd-b10a-47a1-885c-1f3b2998ff1c","type":["https://www.ebi.ac.uk/biostudies/bioimages/studies/QuantitiveValue"],"value":644,"unitText":"file count","unitCode":"http://purl.obolibrary.org/obo/UO_0000189"}]},"score":1.0},{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000452/","entry":{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000452/","type":["Dataset"],"name":"Intracellular signaling observed using giant Dictyostelium cells","author":[{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000452/#auth-001","type":["Person"],"name":"Yusuke V. Morimoto","affiliation":[{"id":"https://ror.org/02278tr80","type":["Organization"],"name":"Kyushu Institute of Technology","url":null,"address":null}],"email":"yvm001@phys.kyutech.ac.jp","description":"Organization: Kyushu Institute of Technology; Department: Department of Physics and Information Technology"}],"description":"We developed a method to enlarge Dictyostelium discoideum cells by partial cytokinesis inhibition, generating multinucleated yet functional giant cells. These cells retained chemotactic signaling, polarity, and motility, enabling high-resolution live-cell imaging. Using fluorescent probes for cAMP and Ca2+, we uncovered a directional, front-to-rear propagation of cAMP signaling and a biphasic Ca2+ response coordinated with actin wave dynamics.","datePublished":"2026-01-21","license":"https://creativecommons.org/licenses/by/4.0/","publisher":{"id":"https://ssbd.riken.jp/repository/","type":["Organization"],"name":"SSBD:repository","url":null,"address":null},"about":[{"id":"http://purl.obolibrary.org/obo/NCBITaxon_44689","type":["Taxon"],"scientificName":"Dictyostelium discoideum","name":"Dictyostelium discoideum","vernacularName":"social amoeba"},{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000452/#biosample-1","type":["BioSample"],"name":"Dictyostelium discoideum, AX2","description":"Dictyostelium discoideum, AX2","taxonomicRange":[{"id":"http://purl.obolibrary.org/obo/NCBITaxon_44689","type":["Taxon"],"scientificName":"Dictyostelium discoideum","name":"Dictyostelium discoideum","vernacularName":"social amoeba"}],"hasCellLine":[]},{"id":"http://purl.obolibrary.org/obo/GO_0016477","type":["DefinedTerm"],"name":"cell migration"},{"id":"http://purl.obolibrary.org/obo/GO_0045168","type":["DefinedTerm"],"name":"cell"},{"id":"http://purl.obolibrary.org/obo/GO_0005737","type":["DefinedTerm"],"name":"cytoplasm"}],"measurementMethod":[{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000452/#imaging-protocol-1","type":["LabProtocol"],"name":"spinning disk confocal microscopy","description":"spinning disk confocal microscopy","measurementTechnique":[{"id":"http://purl.obolibrary.org/obo/FBbi_00000253","type":["DefinedTerm"],"name":"spinning disk confocal microscopy"}],"labEquipment":null},{"id":"http://purl.obolibrary.org/obo/FBbi_00000253","type":["DefinedTerm"],"name":"spinning disk confocal microscopy"},{"id":"http://purl.obolibrary.org/obo/FBbi_00000265","type":["DefinedTerm"],"name":"recorded image"}],"thumbnailUrl":[],"identifier":"ssbd-repos-000452","keywords":[],"funder":[{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000452/#grant-001","type":["Grant"],"name":"Japan Science and Technology Agency, JPMJSP2154, JPMJPR204B","identifier":null}],"seeAlso":[],"size":[{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000452/#total-dataset-size","type":["QuantitativeValue"],"value":4980424704,"unitText":"bytes","unitCode":"http://purl.obolibrary.org/obo/UO_0000233","description":"5.0 GB"},{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000452/#file-count","type":["QuantitativeValue"],"value":54,"unitText":"file count","unitCode":"http://purl.obolibrary.org/obo/UO_0000189"}],"rdfs:seeAlso":[{"@id":"https://doi.org/10.1038/s42003-025-09505-7","@type":["ScholarlyArticle"],"datePublished":"2026","name":"Establishing functional giant Dictyostelium cells reveals front–rear polarity in intracellular signaling"},{"@id":"https://doi.org/10.1101/2025.06.30.662253","@type":["ScholarlyArticle"],"datePublished":"2025","name":"Front–rear polarity of intracellular signaling uncovered via giant &lt;em&gt;Dictyostelium&lt;/em&gt; cells"}]},"score":1.0},{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000454/","entry":{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000454/","type":["Dataset"],"name":"Dynamics of pollen tube in Arabidopsis thaliana","author":[{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000454/#auth-001","type":["Person"],"name":"Yoko Mizuta","affiliation":[{"id":"https://ror.org/04chrp450","type":["Organization"],"name":"Nagoya University","url":null,"address":null}],"email":"mizuta.yoko.u6@f.mail.nagoya-u.ac.jp","description":"Organization: Nagoya University; Department: Institute of Transformative Bio-Molecules (WPI-ITbM)"}],"description":"In the pistil of flowering plants, each ovule usually associates with a single pollen tube for fertilization. This one-to-one pollen tube guidance, which contributes to polyspermy blocking and efficient seed production, is largely different from animal chemotaxis of many sperms to one egg. However, the functional mechanisms underlying the directional cues and polytubey blocks in the depths of the pistil remain unknown. Here, the authors develop a two-photon live imaging method to directly observe pollen tube guidance in the pistil of Arabidopsis thaliana, clarifying signaling and cellular behaviors in the one-to-one guidance. Ovules are suggested to emit multiple signals for pollen tubes, including an integument- dependent directional signal that reaches the inner surface of the septum and adhesion signals for emerged pollen tubes on the septum. Not only FERONIA in the septum but ovular gametophytic FERONIA and LORELEI, as well as FERONIA- and LORELEI- independent repulsion signal, are involved in polytubey blocks on the ovular funiculus. However, these funicular blocks are not strictly maintained in the first 45 min, explaining previous reports of polyspermy in flowering plants.","datePublished":"2026-01-21","license":"https://creativecommons.org/licenses/by/4.0/","publisher":{"id":"https://ssbd.riken.jp/repository/","type":["Organization"],"name":"SSBD:repository","url":null,"address":null},"about":[{"id":"http://purl.obolibrary.org/obo/NCBITaxon_3702","type":["Taxon"],"scientificName":"Arabidopsis thaliana","name":"Arabidopsis thaliana","vernacularName":"thale cress"}],"measurementMethod":[{"id":"http://purl.obolibrary.org/obo/FBbi_00000265","type":["DefinedTerm"],"name":"recorded image"}],"thumbnailUrl":[],"identifier":"ssbd-repos-000454","keywords":[],"funder":[],"seeAlso":[],"size":[{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000454/#total-dataset-size","type":["QuantitativeValue"],"value":18951815168,"unitText":"bytes","unitCode":"http://purl.obolibrary.org/obo/UO_0000233","description":"19.0 GB"},{"id":"https://ssbd.riken.jp/repository/ssbd-repos-000454/#file-count","type":["QuantitativeValue"],"value":33,"unitText":"file count","unitCode":"http://purl.obolibrary.org/obo/UO_0000189"}],"rdfs:seeAlso":{"@id":"https://doi.org/10.1038/s44319-024-00151-4","@type":["ScholarlyArticle"],"datePublished":"2024","name":"Deep imaging reveals dynamics and signaling in one-to-one pollen tube guidance."}},"score":1.0},{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2808","entry":{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2808","type":["Dataset"],"name":"MitoEM 2.0 - A Benchmark for Challenging 3D Mitochondria Instance Segmentation from EM Images","author":[{"id":"https://orcid.org/0000-0001-5437-1294","type":["Person"],"name":"peng liu","affiliation":[{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2808#4c14d27f-92a2-4d73-a64d-d121828b0e6d","type":["Organization"],"name":"Boston College","url":null,"address":null}],"email":"luckiepeng@gmail.com"}],"description":"We present MitoEM 2.0, a curated benchmark resource for training and evaluating three-dimensional (3D) mitochondria instance segmentation in volume electron microscopy (vEM). The collection assembles multiscale vEM datasets (FIB-SEM, SBF-SEM, and ssSEM) spanning diverse tissues and species, with expert-verified instance labels emphasizing biologically difficult scenarios, including dense mitochondrial packing, hyperfused networks, and thin filamentous connections with ambiguous boundaries.  All releases include native-resolution volumes and standardized processed versions, per-volume metadata (voxel size, modality, tissue, and data splits), and official train/validation/test partitions to enable reproducible benchmarking. Annotations follow a consistent protocol with quality checks and instance reindexing. Data are provided in NIfTI format with an nnU-Net–compatible layout, alongside machine-readable split files and checksums. 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T.","affiliation":[{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1474#0a743a52-cdcb-47f5-b997-22464b5cbd84","type":["Organization"],"name":"Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, Portugal","url":null,"address":null},{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1474#f720720f-f8d3-4520-9929-5a23fb5eac78","type":["Organization"],"name":"ABC-RI, Algarve Biomedical Center Research Institute, Portugal","url":null,"address":null},{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1474#58a0a468-45b5-428e-8a64-42b1a3f3a855","type":["Organization"],"name":"Faculdade de Ciências, Universidade de Lisboa, Portugal","url":null,"address":null}],"email":null},{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1474#506de223-656b-4453-a7bd-830dd915cf6d","type":["Person"],"name":"Martins, G. G.","affiliation":[{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1474#a47aa904-08f5-482b-b4e3-f47cae8892f5","type":["Organization"],"name":"Faculdade de Cências, Universidade de Lisboa, Portugal","url":null,"address":null},{"id":"https://ror.org/0346k0491","type":["Organization"],"name":"Gulbenkian Institute for Molecular Medicine","url":null,"address":null}],"email":null},{"id":"https://orcid.org/0000-0002-0397-5917","type":["Person"],"name":"Raquel P. Andrade","affiliation":[{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1474#0a743a52-cdcb-47f5-b997-22464b5cbd84","type":["Organization"],"name":"Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, Portugal","url":null,"address":null},{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1474#f720720f-f8d3-4520-9929-5a23fb5eac78","type":["Organization"],"name":"ABC-RI, Algarve Biomedical Center Research Institute, Portugal","url":null,"address":null}],"email":"rgandrade@ualg.pt"}],"description":"The chicken embryo has been a long-standing model for studying embryonic development. Its easy access for in vivo experiments, together with the development of ex ovo culture techniques, has made it a choice model system for elaborate experimental manipulations. Here we present a time-lapse imaging dataset of the developing chicken embryo in ex ovo culture covering a range of HH3 to HH14+ embryonic stages, with 3-6 min temporal resolution. ","datePublished":"2026-01-16","license":"https://creativecommons.org/licenses/by/4.0/","publisher":{"id":"https://www.ebi.ac.uk/bioimage-archive/","type":["Organization"],"name":"BioImage Archive","url":null,"address":null},"about":[{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1474#e7c7d3d8-1042-4600-aa1b-18f5689ccfd2","type":["BioSample"],"name":"Chicken Embryo","description":"Chicken embryos from HH3 to HH14+","taxonomicRange":[{"id":"http://purl.obolibrary.org/obo/NCBITaxon_9031","type":["Taxon"],"scientificName":"Gallus gallus","name":"Gallus gallus","vernacularName":null}],"hasCellLine":[]},{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1474#59fd060a-67a5-4394-9290-1743e15d7d1a","type":["BioSample"],"name":"Chicken Embryo","description":"Chicken embryos from HH3 to HH14+","taxonomicRange":[{"id":"http://purl.obolibrary.org/obo/NCBITaxon_9031","type":["Taxon"],"scientificName":"Gallus gallus","name":"Gallus 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","measurementTechnique":[{"id":"http://purl.obolibrary.org/obo/FBbi_00000243","type":["DefinedTerm"],"name":"bright-field microscopy"}],"labEquipment":"Lumar V12 (Zeiss) stereomicroscope coupled with a Zeiss Axiocam Mrc camera"},{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1474#907ee12b-9688-4145-ba73-77a10417b180","type":["LabProtocol"],"name":"Image Acquisition (6-min Interval)","description":"Time-lapse movies performed with 6-min interval ","measurementTechnique":[{"id":"http://purl.obolibrary.org/obo/FBbi_00000243","type":["DefinedTerm"],"name":"bright-field microscopy"}],"labEquipment":"Lumar V12 (Zeiss) stereomicroscope coupled with a Zeiss Axiocam Mrc camera"},{"id":"http://purl.obolibrary.org/obo/FBbi_00000243","type":["DefinedTerm"],"name":"bright-field microscopy"}],"thumbnailUrl":["https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD1474/3624b693-4c76-4c7d-8c4f-ad001b3514a7/static_display_512_512.png"],"identifier":"S-BIAD1474","keywords":["Embryo 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copies of the exocyst complex tether each secretory vesicle to\nthe plasma membrane (PM) in constitutive exocytosis. The exocyst higher-order structure\n(ExHOS) that coordinates the action of these multiple exocysts remains unexplored. We integrated particle tracking, super-resolution microscopy and cryo-electron tomography to time-\nresolve the continuum conformational landscape of the ExHOS and to functionally annotate its\ndifferent conformations. We found that 7 exocysts form flexible ring-shaped ExHOS that tether 2\nvesicles at <45 nm from the PM. The ExHOS rapidly expands while it pulls the vesicle towards the\nPM in a stepwise mechanism comprising three metastable states at 27, 18 and 5 nm from the\nPM. After fusion, Sec18 mediates the disassembly of the stationary ExHOS, an emergent function\nthat controls the rate of exocytosis. By resolving the biophysical principles of tethering we\nbridged the gap between static isolated structures and the dynamic and multimeric nature of\nexocytosis.\n\nThis datset contains in particular the correlative light and electorn microscopy images of lamellae that were subsequently used to target tomogram acqusition. 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We demonstrated its capability for (semi-)automatic biological analysis in two applications and made it available as an easy-to-use tool to enable novel data-driven insights into synapse organization and function.","datePublished":"2026-01-16","license":"https://creativecommons.org/publicdomain/zero/1.0/","publisher":{"id":"https://www.ebi.ac.uk/bioimage-archive/","type":["Organization"],"name":"BioImage Archive","url":null,"address":null},"about":[{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2534#7f0b6258-9e37-4484-b6e2-1386d990886b","type":["BioSample"],"name":"First biosample","description":"brain, hippocampus (organotypic slices), neuronal, synapses","taxonomicRange":[{"id":"http://purl.obolibrary.org/obo/NCBITaxon_10090","type":["Taxon"],"scientificName":"Mus musculus","name":"Mus musculus","vernacularName":"house mouse"}],"hasCellLine":[]},{"id":"http://purl.obolibrary.org/obo/NCBITaxon_10090","type":["Taxon"],"scientificName":"Mus musculus","name":"Mus musculus","vernacularName":"house mouse"}],"measurementMethod":[{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2534#dfe4813d-b957-4e6b-b641-d7c4a5e7c18d","type":["LabProtocol"],"name":"First acquisition","description":"Tilt-series (tilt range ± 60°; 1° angular increments) were acquired at ×30,000 magnifications using SerialEM (Mastronarde, 2005). 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We evaluated whether HDAP2, a mitochondria-targeted aromatic peptide designed to support mitochondrial membrane integrity, could preserve neuronal structure after optic nerve crush (ONC) in C57BL/6 mice (both sexes, n=31). Systemically administered HDAP2 penetrated the blood–retinal barrier and localized to RGCs and mitochondrial-rich retinal layers. Daily treatment significantly improved RGC survival compared to saline-treated ONC animals. RGC densities increased across central, midperipheral, and peripheral regions.\nTransmission electron microscopy revealed that HDAP2 substantially reduced mitochondrial loss within crushed optic nerve axons. Mitochondrial density in HDAP2-treated nerves approached levels observed in uninjured controls and was nearly 3-fold higher than untreated ONC nerves. Mitochondrial morphology was similar across groups, indicating that HDAP2 prevents mitochondrial loss rather than rescuing damaged organelles. HDAP2-treated nerves also exhibited a numerically higher density of structurally intact axons, consistent with reduced ultrastructural degeneration.\nThese findings demonstrate that HDAP2 limits mitochondrial loss and attenuates neuronal degeneration after ONC. Together, the results support HDAP2 as a promising therapeutic candidate for protecting CNS projection neurons by maintaining mitochondrial stability after axonal injury.\n","datePublished":"2026-01-15","license":"https://creativecommons.org/publicdomain/zero/1.0/","publisher":{"id":"https://www.ebi.ac.uk/bioimage-archive/","type":["Organization"],"name":"BioImage Archive","url":null,"address":null},"about":[{"id":"https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2789#8a271cca-aa5c-40af-899d-7aa11261bd16","type":["BioSample"],"name":"ONC C57BL/6 mice","description":"Retinal ganglion cells and optic nerve - Study of the retina and optic nerves in animals that received unilateral optic nerve crush.","taxonomicRange":[{"id":"http://purl.obolibrary.org/obo/NCBITaxon_10090","type":["Taxon"],"scientificName":"Mus musculus","name":"Mus musculus","vernacularName":null}],"hasCellLine":[]},{"id":"http://purl.obolibrary.org/obo/NCBITaxon_10090","type":["Taxon"],"scientificName":"Mus 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