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ledger re-read.", "claim_fit": "Selected chromosome-21 fixed-cell intervals; variable domain boundaries and cohesin-depleted HCT116 comparisons.", "limitations": "Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed." }, { "id": "ou2017", "doi": "10.1126/science.aag0025", "title": "ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells", "authors": "Ou HD, Phan S, Deerinck TJ, Thor A, Ellisman MH, O’Shea CC", "year": 2017, "journal": "Science 357:eaag0025", "source_type": "primary", "url": "https://doi.org/10.1126/science.aag0025", "access_depth": "Prior audit selected original body and captions; ledger re-read.", "claim_fit": "Disordered chromatin chains and heterogeneous packing in sampled human cellular preparations.", "limitations": "Fixed and processed structural specimen; not a live dynamics assay." }, { "id": "heintzman2009", "doi": "10.1038/nature07829", "title": "Histone modifications at human enhancers reflect global cell-type-specific gene expression", "authors": "Heintzman ND, Hon GC, Hawkins RD, et al.", "year": 2009, "journal": "Nature 459:108–112", "source_type": "primary", "url": "https://doi.org/10.1038/nature07829", "access_depth": "Consensus fetched original abstract inspected.", "claim_fit": "Multi-cell-type chromatin maps and enhancer activity associate enhancer signatures with cell-specific expression programs.", "limitations": "Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed." }, { "id": "soufi2015", "doi": "10.1016/j.cell.2015.03.017", "title": "Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming", "authors": "Soufi A, Garcia MF, Jaroszewicz A, Osman N, Pellegrini M, Zaret KS", "year": 2015, "journal": "Cell 161:555–568", "source_type": "primary", "url": "https://doi.org/10.1016/j.cell.2015.03.017", "access_depth": "Original abstract in Consensus search read; fetched record confirms identity but contains takeaway only.", "claim_fit": "Purified Oct4, Sox2 and Klf4 nucleosome binding and cellular targeting of nucleosome-enriched silent sites.", "limitations": "Full Results not appraised; c-Myc must not be grouped with the three factors as an equally demonstrated nucleosome-binding pioneer." }, { "id": "basurto2024", "doi": "10.1016/j.celrep.2024.113855", "title": "SWI/SNF-dependent genes are defined by their chromatin landscape", "authors": "Basurto-Cayuela L, Guerrero-Martínez JA, Gómez-Marín E, et al.", "year": 2024, "journal": "Cell Reports 43:113855", "source_type": "primary", "url": "https://doi.org/10.1016/j.celrep.2024.113855", "access_depth": "Prior audit fetched original Consensus abstract; identity checked against indexed DOI metadata.", "claim_fit": "Chromatin landscape association with gene-specific SWI/SNF dependence; claims restricted to original abstract.", "limitations": "No complete original main Results or supplementary analysis inspected." }, { "id": "alabert2015", "doi": "10.1101/gad.256354.114", "title": "Two distinct modes for propagation of histone PTMs across the cell cycle", "authors": "Alabert C, Barth TK, Reverón-Gómez N, et al.", "year": 2015, "journal": "Genes & Development 29:585–590", "source_type": "primary", "url": "https://doi.org/10.1101/gad.256354.114", "access_depth": "Prior audit original main Results, Figures 1–4 and Discussion; ledger re-read.", "claim_fit": "Nascent-chromatin isotope/mass-spectrometry study distinguishes parental and new histone modification kinetics.", "limitations": "Population peptides, not genomic address or every pair of modifications on one nucleosome; supplementary cell-line details not appraised." }, { "id": "liu2023", "doi": "10.1038/s41467-023-39846-y", "title": "Histone H1 facilitates restoration of H3K27me3 during DNA replication by chromatin compaction", "authors": "Liu C, Yu J, Song A, et al.", "year": 2023, "journal": "Nature Communications 14:4081", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-023-39846-y", "access_depth": "Prior audit original selected Results and Discussion; ledger re-read.", "claim_fit": "mESC H1c/d/e-depleted comparison, chromatin compaction and delayed H3K27me3 restoration on replicated DNA.", "limitations": "Ensemble occupancy and fitted restoration rates; chronic depletion may have indirect effects." }, { "id": "charlton2024", "doi": "10.1016/j.cell.2024.07.017", "title": "The fork protection complex promotes parental histone recycling and epigenetic memory", "authors": "Charlton SJ, Flury V, Kanoh Y, et al.", "year": 2024, "journal": "Cell 187:5029–5047.e21", "source_type": "primary", "url": "https://doi.org/10.1016/j.cell.2024.07.017", "access_depth": "Prior audit fetched original abstract and selected main Results/Figure 1; ledger re-read.", "claim_fit": "Fork-protection-complex contribution to parental histone recycling and epigenetic-memory maintenance.", "limitations": "Main-text or abstract findings only; supplements and raw data have not been independently reanalyzed." } ], "word_path": "Reviews_useredit/current_2026-10-12/euchromatin.docx", "word_sha256": "a39f1a23f6a95ba460ba1a71307a876a009f194c194aa2eeca7abd14ebc958e8", "edition_slug": "euchromatin", "scope": "This narrative integrates foundational and recent primary studies available by 12 October 2026. 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ledger re-read.", "claim_fit": "Mouse fibroblast chromocenter compaction and HP1 partition/perturbation measurements; absence of tested HP1-liquid hallmarks.", "limitations": "Specific pericentric foci, not every heterochromatin domain or every chromatin-condensation mechanism." }, { "id": "hou2023", "doi": "10.1038/s41467-023-42072-1", "title": "Structure of native chromatin fibres revealed by Cryo-ET in situ", "authors": "Hou Z, Nightingale F, Zhu Y, MacGregor-Chatwin C, Zhang P", "year": 2023, "journal": "Nature Communications 14:6324", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-023-42072-1", "access_depth": "Prior audit original selected Results and Methods; ledger re-read.", "claim_fit": "Cryo-ET in interphase CEM cells reveals heterogeneous local zigzag organization near the envelope.", "limitations": "Limited cryogenic volumes and cellular model; local arrangements do not define a genome-wide polymer conformation." }, { "id": "kreysing2026", "doi": "10.1038/s41467-026-75087-5", "title": "Molecular architecture of heterochromatin at the nuclear periphery of primary human cells", "authors": "Kreysing JP, Cruz-León S, Betz J, et al.", "year": 2026, "journal": "Nature Communications 17:5844", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-026-75087-5", "access_depth": "Prior audit original publisher Results and Methods; ledger re-read.", "claim_fit": "Resting primary human CD4+ T-cell peripheral chromatin, heterogeneous elongated arrangement and frequent nucleosome stacking.", "limitations": "Selected cellular region and quiescent state; observed envelope width is not proof of canonical fiber periodicity." }, { "id": "xie2026", "doi": "10.1093/nsr/nwaf451", "title": "MINFLUX dissects nucleosome and compacting chromatin structures in living cells", "authors": "Xie H, Hu Y, Cheng R, et al.", "year": 2026, "journal": "National Science Review 13:nwaf451; online 21 October 2025", "source_type": "primary", "url": "https://doi.org/10.1093/nsr/nwaf451", "access_depth": "Prior audit indexed original Introduction, Results and Discussion; ledger re-read.", "claim_fit": "DNA-probe MINFLUX localizations, selected living-U2OS fiber-like domains and probe/sampling limits.", "limitations": "AT-preferring probe, selected trajectories and possible probe stabilization; localization precision differs from structural resolution." }, { "id": "brackley2013", "doi": "10.1073/pnas.1302950110", "title": "Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization", "authors": "Brackley CA, Taylor S, Papantonis A, Cook PR, Marenduzzo D", "year": 2013, "journal": "PNAS 110:E3605–E3611", "source_type": "primary", "url": "https://doi.org/10.1073/pnas.1302950110", "access_depth": "Prior audit selected original model Results and Methods; ledger re-read.", "claim_fit": "Brownian bead-spring polymer with reversible multivalent bridging can form clusters without direct protein attraction.", "limitations": "Coarse-grained equilibrium model; not proof that a specific nuclear assembly is produced by bridging." }, { "id": "larson2017", "doi": "10.1038/nature22822", "title": "Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin", "authors": "Larson AG, Elnatan D, Keenen MM, et al.", "year": 2017, "journal": "Nature 547:236–240", "source_type": "primary", "url": "https://doi.org/10.1038/nature22822", "access_depth": "Prior audit original abstract and selected Methods; ledger re-read.", "claim_fit": "Purified human HP1α, DNA, phosphorylation and partner partitioning demonstrate context-dependent droplet capacity.", "limitations": "In-vitro capacity is distinguished from a general mammalian cellular mechanism." }, { "id": "strom2017", "doi": "10.1038/nature22989", "title": "Phase separation drives heterochromatin domain formation", "authors": "Strom AR, Emelyanov AV, Mir M, et al.", "year": 2017, "journal": "Nature 547:241–245", "source_type": "primary", "url": "https://doi.org/10.1038/nature22989", "access_depth": "Prior audit original abstract; 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Adam et al.", "year": 2017, "journal": "Molecular Biology of the Cell", "source_type": "primary", "url": "https://doi.org/10.1091/mbc.E16-09-0653", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Chromatin and lamins contribute in separate isolated-nucleus extension regimes; spring constants are not universal moduli or viscosity.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "feric", "doi": "10.1016/j.cell.2016.04.047", "title": "Coexisting Liquid Phases Underlie Nucleolar Subcompartments", "authors": "Marina Feric, Nilesh Vaidya, Tyler S. Harmon et al.", "year": 2016, "journal": "Cell", "source_type": "primary", "url": "https://doi.org/10.1016/j.cell.2016.04.047", "access_depth": "Primary main-text Results subsection on in-vitro viscoelasticity, Fig2E and main Experimental Procedures, independently checked in root browser; source detail received as collaborator evidence. No supplements/raw-data reanalysis.", "claim_fit": "Component-specific nucleolar coexistence and dynamics; in-vitro 50nm-radius tracer values belong to reconstituted NPM1/FIB1 droplets.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "denais", "doi": "10.1126/science.aad7297", "title": "Nuclear envelope rupture and repair during cancer cell migration", "authors": "Céline Denais, Rachel M. Gilbert, Philipp Isermann et al.", "year": 2016, "journal": "Science", "source_type": "primary", "url": "https://doi.org/10.1126/science.aad7297", "access_depth": "Primary author-manuscript main Abstract/Results pages1–4 and Figures1/2/4; supplementary Methods and raw data not reanalysed.", "claim_fit": "NLS-reporter rupture, defined in-vitro and mouse-dermis models, deformation-associated damage foci and ESCRT-III-dependent resealing independently match primary main Results/Figures. Mixed-topic Scite opening excluded.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "rashid", "doi": "10.1016/j.celrep.2024.114462", "title": "Mechanomemory of nucleoplasm and RNA polymerase II after chromatin stretching by a microinjected magnetic nanoparticle force", "authors": "Fazlur Rashid, Sadia Amin Kabbo, Ning Wang", "year": 2024, "journal": "Cell Reports", "source_type": "primary", "url": "https://doi.org/10.1016/j.celrep.2024.114462", "access_depth": "Primary manuscript main Summary, Results on microrheology and mechanomemory, Figures 1–5 and Discussion read; supplemental figures and raw measurements not reanalysed.", "claim_fit": "200-nm-diameter targeted magnetic particles in CHO DHFR reporter nuclei; 0.1–5 Hz force response and separate hiPSC Pol II arm; local perturbation and injection limitations.", "limitations": "No independent experimental replication or raw-data reanalysis. 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Source interpretation confined to the stated access depth." }, { "id": "bergamaschi", "doi": "10.1016/j.celrep.2024.114852", "title": "Heterogeneous force response of chromatin in isolated nuclei.", "authors": "G. Bergamaschi, A. Biebricher, Hannes Witt, F. Byfield, Xamanie M R Seymonson, Cornelis Storm, P. Janmey, G. Wuite", "year": 2024, "journal": "Cell Reports", "source_type": "primary", "url": "https://doi.org/10.1016/j.celrep.2024.114852", "access_depth": "Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.", "claim_fit": "Bergamaschi and colleagues measured isolated-nucleus force responses together with chromatin and nuclear-envelope deformation. Chromatin was more compliant than the envelope below the reported 30% strain regime, and chromatin digestion softened nuclei. 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New records lacked complete Scite notice check after monthly quota." }, { "id": "lewis", "doi": "10.1038/s41556-025-01822-7", "title": "LBR and LAP2 mediate heterochromatin tethering to the nuclear periphery to preserve genome homeostasis", "authors": "Renard Lewis, Virginia Sinigiani, Noura Maziak et al.", "year": 2026, "journal": "Nature Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1038/s41556-025-01822-7", "access_depth": "Publisher primary Abstract and main Results through heterochromatin-tether deconvolution, membrane LAP2 rescue and short/long-term transcription effects read; complete Methods and supplements not appraised. Published 24 February 2026.", "claim_fit": "Redundant LBR/membrane LAP2 tethering in mammalian cell models, distinction between short-term release and persistent loss; not universal instant repression by peripheral position.", "limitations": "No independent experimental replication or raw-data reanalysis. 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Source interpretation confined to the stated access depth." }, { "id": "panexm", "doi": "10.1083/jcb.202409120", "title": "Visualizing nuclear pore complex plasticity with pan-expansion microscopy", "authors": "Kimberly J. Morgan, Emma Carley, Alyssa N. Coyne, Jeffrey D. Rothstein, C. Patrick Lusk, Megan C. King", "year": 2025, "journal": "Journal of Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1083/jcb.202409120", "access_depth": "Fetched primary abstract and publication record; full Methods and Results not yet appraised.", "claim_fit": "Expanded fixed-cell NPC diameter distributions, nuclear-surface bias, hyperosmotic constriction and LINC perturbation; one patient-derived neuronal comparison does not establish all ALS.", "limitations": "No independent experimental replication or raw-data reanalysis. 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New records lacked complete Scite notice check after monthly quota." }, { "id": "erdel", "doi": "10.1088/0953-8984/27/6/064115", "title": "The viscoelastic properties of chromatin and the nucleoplasm revealed by scale-dependent protein mobility", "authors": "Fabian Erdel, Michael Baum, Karsten Rippe", "year": 2015, "journal": "Journal of Physics: Condensed Matter", "source_type": "primary", "url": "https://doi.org/10.1088/0953-8984/27/6/064115", "access_depth": "Published identity and primary abstract from author-manuscript repository; full main text not appraised.", "claim_fit": "Differently sized inert GFP probes and polymer simulations; size-dependent intermediate-scale viscoelastic behavior and obstacle-network model; not universal fixed fractal organization.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "turgay", "doi": "10.1038/nature21382", "title": "The molecular architecture of lamins in somatic cells", "authors": "Yagmur Turgay, Matthias Eibauer, Anne E. Goldman et al.", "year": 2017, "journal": "Nature", "source_type": "primary", "url": "https://doi.org/10.1038/nature21382", "access_depth": "Selected indexed primary main text (opening8000chars; not complete article), plus metadata.", "claim_fit": "Prepared vimentin-null mouse-fibroblast lamina filament structure; approximately3.5nm filaments are not live-lamina thickness.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "linker", "doi": "10.1126/science.abm9798", "title": "Architecture of the linker-scaffold in the nuclear pore", "authors": "Stefan Petrovic, Dipanjan Samanta, Thibaud Perriches et al.", "year": 2022, "journal": "Science", "source_type": "primary", "url": "https://doi.org/10.1126/science.abm9798", "access_depth": "Selected indexed primary main text (opening8000chars; not complete article), plus metadata.", "claim_fit": "Linker/scaffold structural integration and flexible ring-spoke models; model architecture not universal transport threshold.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "cytoplasmic", "doi": "10.1126/science.abm9129", "title": "Architecture of the cytoplasmic face of the nuclear pore", "authors": "Christopher J. Bley, Si Nie, George W. Mobbs et al.", "year": 2022, "journal": "Science", "source_type": "primary", "url": "https://doi.org/10.1126/science.abm9129", "access_depth": "Selected indexed primary main text (opening8000chars; not complete article), plus metadata.", "claim_fit": "Composite human/fungal cytoplasmic-face architecture and approximate composition; not one atomic image of a functioning pore.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "guelen", "doi": "10.1038/nature06947", "title": "Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions", "authors": "Lars Guelen, Ludo Pagie, Émilie Brasset et al.", "year": 2008, "journal": "Nature", "source_type": "primary", "url": "https://doi.org/10.1038/nature06947", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "LAD association map, domain scales and low expression in human fibroblasts; no universal permanent tether or repression causality.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "guelen-corr", "doi": "10.1038/nature12316", "title": "Correction: Corrigendum: Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions", "authors": "Lars Guelen, Ludo Pagie, Émilie Brasset et al.", "year": 2013, "journal": "Nature", "source_type": "editorial_notice", "url": "https://doi.org/10.1038/nature12316", "access_depth": "Primary correction abstract/citation record containing full correction statements; original full Methods not reappraised.", "claim_fit": "Official corrected H3K9me3 identity and Methods data sources; no inferred change to uncorrected abstract-level LAD conclusions.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "bancaud", "doi": "10.1038/emboj.2009.340", "title": "Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin", "authors": "Aurélien Bancaud, Sébastien Huet, Nathalie Daigle et al.", "year": 2009, "journal": "The EMBO Journal", "source_type": "primary", "url": "https://doi.org/10.1038/emboj.2009.340", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Tracer exclusion/hindrance and transient chromatin-protein trapping; fractal interpretation remains model dependent.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "frap", "doi": "10.1529/biophysj.103.026765", "title": "Analysis of Binding Reactions by Fluorescence Recovery after Photobleaching", "authors": "Brian L. Sprague, Robert L. Pego, Diana A. Stavreva et al.", "year": 2004, "journal": "Biophysical Journal", "source_type": "primary", "url": "https://doi.org/10.1529/biophysj.103.026765", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Reaction-diffusion FRAP solutions constrain binding inference; not every recovery curve identifies every parameter.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "spoton", "doi": "10.7554/eLife.33125", "title": "Robust model-based analysis of single-particle tracking experiments with Spot-On", "authors": "Anders S. Hansen, Maxime Woringer, Jonathan B. Grimm et al.", "year": 2018, "journal": "eLife", "source_type": "primary", "url": "https://doi.org/10.7554/eLife.33125", "access_depth": "Primary indexed main Introduction and selected Results/model/simulation evaluation, first8000char source excerpt; not complete article.", "claim_fit": "Spot-On model/testing distinguishes localization, defocalization, density and motion-blur biases with steady-state Brownian populations.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "squires", "doi": "10.1146/annurev-fluid-121108-145608", "title": "Fluid Mechanics of Microrheology", "authors": "Todd M. Squires, Thomas G. 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no raw-data reanalysis or independent reproduction of experiments." }, { "id": "ilik", "doi": "10.7554/eLife.60579", "title": "SON and SRRM2 are essential for nuclear speckle formation", "authors": "Ilik et al.", "year": 2020, "journal": "eLife", "source_type": "primary", "url": "https://doi.org/10.7554/eLife.60579", "access_depth": "Scite main body and targeted primary Results/figure excerpts", "claim_fit": "SON/SRRM2 combination disperses speckle proteins in HAP1/HEK293 models; monoclonal SC35 principal speckle target is SRRM2, historic SRSF2 attribution inappropriate", "limitations": "Study-specific findings; no raw-data reanalysis or independent reproduction of experiments." }, { "id": "sahin", "doi": "10.1083/jcb.201305148", "title": "Oxidative stress-induced assembly of PML nuclear bodies controls sumoylation of partner proteins", "authors": "Sahin et al.", "year": 2014, "journal": "Journal of Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1083/jcb.201305148", "access_depth": "Scite identity; 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no universal visible-body necessity", "limitations": "Study-specific findings; no raw-data reanalysis or independent reproduction of experiments." }, { "id": "strzelecka_function", "doi": "10.1038/nsmb.1783", "title": "Coilin-dependent snRNP assembly is essential for zebrafish embryogenesis", "authors": "Strzelecka et al.", "year": 2010, "journal": "Nature Structural & Molecular Biology", "source_type": "primary", "url": "https://doi.org/10.1038/nsmb.1783", "access_depth": "Publisher primary abstract, Fig1–7 descriptions and 4 April 2010 inline correction notice", "claim_fit": "Coilin depletion, developmental and spliced-RNA deficits, rescue by assembled human snRNPs.", "limitations": "Study-specific findings; no raw-data reanalysis or independent reproduction of experiments." }, { "id": "bhat", "doi": "10.1038/s41586-024-07429-6", "title": "Genome organization around nuclear speckles drives mRNA splicing efficiency", "authors": "Bhat et al.", "year": 2024, "journal": "Nature", "source_type": "primary", "url": "https://doi.org/10.1038/s41586-024-07429-6", "access_depth": "Consensus fetched primary abstract; 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complete body not appraised.", "claim_fit": "Bergamaschi and colleagues combined optical-tweezer deformation of isolated nuclei with fluorescence imaging. Chromatin deformed more readily than the nuclear envelope below the reported 30% strain regime, and nuclease treatment softened nuclei. These measurements help resolve component contributions in that preparation. They do not turn a nuclear-shape change in a patient image into a calibrated mechanical measurement or a disease prognosis. Bergamaschi et al. (2024) .", "access_limit": "" }, { "doi": "10.1038/6799", "url": "https://doi.org/10.1038/6799", "title": "Mutations in the gene encoding lamin A/C cause autosomal dominant Emery-Dreifuss muscular dystrophy", "source_type": "primary_study", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Four LMNA variants co-segregated with EDMD in five families; genetics alone does not identify one mechanical defect.", "access_limit": "" }, { "doi": "10.1038/nature01629", "url": "https://doi.org/10.1038/nature01629", "title": "Recurrent de novo point mutations in lamin A cause Hutchinson–Gilford progeria syndrome", "source_type": "primary_study", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Recurrent G608G in18/20 classical HGPS cases, cryptic splice consequence and50-amino-acid deletion; not ordinary-ageing equivalence.", "access_limit": "" }, { "doi": "10.1091/mbc.E16-09-0653", "url": "https://doi.org/10.1091/mbc.E16-09-0653", "title": "Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus", "source_type": "primary_study", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Chromatin and lamins contribute in separate isolated-nucleus extension regimes; spring constants are not universal moduli or viscosity.", "access_limit": "" }, { "doi": "10.1126/science.aad7297", "url": "https://doi.org/10.1126/science.aad7297", "title": "Nuclear envelope rupture and repair during cancer cell migration", "source_type": "primary_study", "access_depth": "Primary author-manuscript main Abstract/Results pages1–4 and Figures1/2/4; supplementary Methods and raw data not reanalysed.", "claim_fit": "NLS-reporter rupture, defined in-vitro and mouse-dermis models, deformation-associated damage foci and ESCRT-III-dependent resealing independently match primary main Results/Figures. Mixed-topic Scite opening excluded.", "access_limit": "" }, { "doi": "10.1172/JCI19670", "url": "https://doi.org/10.1172/JCI19670", "title": "Lamin A/C deficiency causes defective nuclear mechanics and mechanotransduction", "source_type": "primary_study", "access_depth": "Primary publisher main Abstract/selected Results and Methods, including cell strain and surface-bead controls, independently read; Scite truncated abstract insufficient alone.", "claim_fit": "LaminA/C-null mouse-cell strain/deformation, viability and selected signaling; surface-bead cytoskeletal controls not intranuclear rheology.", "access_limit": "" } ] }, { "path": "nuclear_biology_reviews/reviews/nuclear_metabolism_standardized_review.html", "title": "Nuclear Metabolism: Acetyl-CoA and Local ATP Evidence", "kind": "research", "audit_date": "2026-10-12", "status": "Scientific text and references appraised at recorded source depth", "sha256": "f1c06d4aeddb5ebd0e223c22849450788a7c0098c5193c8133300bfe22b04d94", "findings": [ "Nuclear position and mitochondrial proximity provide distinct recent examples", "Retained narrative separates measurement, model and biological/clinical inference; citations interpreted at stated access depth." ], "limitations": [ "No raw-data reanalysis, independent experimental replication, exhaustive literature coverage or archived Word-document validation.", "New source claims confined to listed access depth; connector quota prevented complete new-source Scite editorial/fulltext checks." ], "references": [ { "doi": "10.1016/j.cell.2014.04.046", "url": "https://doi.org/10.1016/j.cell.2014.04.046", "title": "A Nuclear Pyruvate Dehydrogenase Complex Is Important for the Generation of Acetyl-CoA and Histone Acetylation", "source_type": "primary_study", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Functional nuclear PDC and reduced acetyl-CoA/histone acetylation after perturbation; abundance redistribution is not directly tracked translocation.", "access_limit": "" }, { "doi": "10.1038/s41467-025-61787-x", "url": "https://doi.org/10.1038/s41467-025-61787-x", "title": "Mitochondria-derived nuclear ATP surge protects against confinement-induced proliferation defects", "source_type": "primary_study", "access_depth": "Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.", "claim_fit": "The Ghose et al. (2025) reported mitochondrial repositioning toward the nuclear periphery and a nuclear ATP rise sensitive to mitochondrial ATP production and actin organization. This offers a mitochondria-associated route alongside the stimulus-specific NUDIX5 route above. It does not establish that one source supplies most ATP in every nuclear compartment. Ghose et al. (2025) .", "access_limit": "" }, { "doi": "10.1038/s41586-024-07471-4", "url": "https://doi.org/10.1038/s41586-024-07471-4", "title": "Nuclear position and local acetyl-CoA production regulate chromatin state", "source_type": "primary_study", "access_depth": "Bibliographic metadata and primary abstract via SciSpace/discovery where available; full-text retrieval failed after Scite quota.", "claim_fit": "A Willnow and Teleman (2024) linked nuclear position near the epithelial surface with increased acetyl-CoA synthase and histone acetylation. Fatty-acid oxidation contributed to that tissue pattern. These spatial and metabolic perturbations provide a defined tissue context; they do not establish an autonomous metabolic circuit in every nucleus. Willnow and Teleman (2024) .", "access_limit": "" }, { "doi": "10.1126/science.1164097", "url": "https://doi.org/10.1126/science.1164097", "title": "ATP-Citrate Lyase Links Cellular Metabolism to Histone Acetylation", "source_type": "primary_study", "access_depth": "Selected indexed primary main text (opening8000chars; not complete article), plus metadata.", "claim_fit": "ACLY-associated cellular carbon supply/histone acetylation in mammalian models; no autonomous nuclear metabolic circuit.", "access_limit": "" }, { "doi": "10.1126/science.aad9335", "url": "https://doi.org/10.1126/science.aad9335", "title": "ADP-ribose–derived nuclear ATP synthesis by NUDIX5 is required for chromatin remodeling", "source_type": "primary_study", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Progestin-responsive breast-cell ADP-ribose/NUDIX5 ATP route; not dominant nuclear ATP source in every cell.", "access_limit": "" } ] }, { "path": "nuclear_biology_reviews/reviews/nuclear-microrheology-enhanced-graphics.html", "title": "Nuclear Microrheology: Measuring Local Response in a Living Composite", "kind": "research", "audit_date": "2026-10-12", "status": "Complete rewritten narrative and matching current Word edition", "sha256": "2451d13e693c596f4e14e2ad48f2b8d3a78d114e446cfbf312b360a327811b4f", "findings": [ "Replaced the earlier narrative with a complete current scientific review.", "Word and web scientific text, comparison tables and bibliography share one source.", "All factual blocks cite primary studies or selected seminal reviews." ], "limitations": [ "This review integrates published primary research with a foundational methods review where needed. Source access ranges from primary abstracts to the selected main Results and Methods identified in each reference record. It is a scholarly synthesis rather than an independent reanalysis of experimental data. Conclusions retain the biological system, measurement scale and model assumptions of the cited studies." ], "references": [ { "id": "mason", "doi": "10.1103/PhysRevLett.74.1250", "title": "Optical Measurements of Frequency-Dependent Linear Viscoelastic Moduli of Complex Fluids", "authors": "Thomas G. Mason, David A. Weitz", "year": 1995, "journal": "Physical Review Letters", "source_type": "primary", "url": "https://doi.org/10.1103/PhysRevLett.74.1250", "access_depth": "Primary citation identity and primary abstract through author/index record; complete experimental text not read.", "claim_fit": "Thermal probe fluctuations related to linear viscoelastic response in tested complex fluids; extrapolation to actively driven nuclei requires additional assumptions.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "dross", "doi": "10.1371/journal.pone.0005041", "title": "Mapping eGFP Oligomer Mobility in Living Cell Nuclei", "authors": "Nicolas Dross, Corentin Spriet, Monika Zwerger et al.", "year": 2009, "journal": "PLOS ONE", "source_type": "primary", "url": "https://doi.org/10.1371/journal.pone.0005041", "access_depth": "Primary PLOS main Abstract, Methods data analysis/acquisition/calibration and selected Results/Discussion; no raw data reanalysis.", "claim_fit": "eGFP oligomer FCS outside nucleoli: calibrated two-normal-diffusion components plus triplet term; cell/model/probe constraints retained.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "rashid", "doi": "10.1016/j.celrep.2024.114462", "title": "Mechanomemory of nucleoplasm and RNA polymerase II after chromatin stretching by a microinjected magnetic nanoparticle force", "authors": "Fazlur Rashid, Sadia Amin Kabbo, Ning Wang", "year": 2024, "journal": "Cell Reports", "source_type": "primary", "url": "https://doi.org/10.1016/j.celrep.2024.114462", "access_depth": "Primary manuscript main Summary, Results on microrheology and mechanomemory, Figures 1–5 and Discussion read; supplemental figures and raw measurements not reanalysed.", "claim_fit": "200-nm-diameter targeted magnetic particles in CHO DHFR reporter nuclei; 0.1–5 Hz force response and separate hiPSC Pol II arm; local perturbation and injection limitations.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "afm", "doi": "10.1098/rsif.2024.0885", "title": "Viscoelastic differences between isolated and live MCF7 cancer cell nuclei resolved with AFM microrheology", "authors": "Ellen Juel Pørtner, Anna Mularski, Tobias William Jarrett, Stine Lauritzen Sønder, Jesper Nylandsted, Adam Cohen Simonsen", "year": 2025, "journal": "Journal of the Royal Society Interface", "source_type": "primary", "url": "https://doi.org/10.1098/rsif.2024.0885", "access_depth": "Root independently read primary PMC12173521 Abstract and selected main Methods/Results paragraphs, including oscillatory preparation, hydrodynamic drag correction, morphology and Jeffreys analysis; primary Scite webpage identity corroborated. Supplement and raw-data reanalysis excluded.", "claim_fit": "Oscillatory AFM on live and isolated MCF7 nuclei, hydrodynamic-drag validation, modulus/loss-tangent distinction and Jeffreys model. The published author list supersedes incomplete Consensus authors.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "byfield", "doi": "10.1016/j.bpj.2024.11.3322", "title": "Metabolically intact nuclei are fluidized by the activity of the chromatin remodeling motor BRG1", "authors": "Fitzroy J. Byfield, Behnaz Eftekhari, Kaeli Kaymak-Loveless et al.", "year": 2025, "journal": "Biophysical Journal", "source_type": "primary", "url": "https://doi.org/10.1016/j.bpj.2024.11.3322", "access_depth": "Published PDF front matter, main preparation/treatment Methods, Results around Figure 9 and Discussion read; supplementary data not appraised.", "claim_fit": "Metabolically active karyoplast compression/dissipation and BRM-014 inhibition; BRM-014 inhibits BRM and BRG1, so pharmacology is not exclusive genetic proof for BRG1. Karyoplasts are not bare detergent-isolated nuclei.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "bergamaschi", "doi": "10.1016/j.celrep.2024.114852", "title": "Heterogeneous force response of chromatin in isolated nuclei.", "authors": "G. Bergamaschi, A. Biebricher, Hannes Witt, F. Byfield, Xamanie M R Seymonson, Cornelis Storm, P. Janmey, G. Wuite", "year": 2024, "journal": "Cell Reports", "source_type": "primary", "url": "https://doi.org/10.1016/j.celrep.2024.114852", "access_depth": "Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.", "claim_fit": "Bergamaschi and colleagues measured isolated-nucleus force responses together with chromatin and nuclear-envelope deformation. Chromatin was more compliant than the envelope below the reported 30% strain regime, and chromatin digestion softened nuclei. The joint readouts strengthen component interpretation in the tested preparation without defining one elastic modulus or viscosity for every nucleus. Bergamaschi et al. (2024) .", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "erdel", "doi": "10.1088/0953-8984/27/6/064115", "title": "The viscoelastic properties of chromatin and the nucleoplasm revealed by scale-dependent protein mobility", "authors": "Fabian Erdel, Michael Baum, Karsten Rippe", "year": 2015, "journal": "Journal of Physics: Condensed Matter", "source_type": "primary", "url": "https://doi.org/10.1088/0953-8984/27/6/064115", "access_depth": "Published identity and primary abstract from author-manuscript repository; full main text not appraised.", "claim_fit": "Differently sized inert GFP probes and polymer simulations; size-dependent intermediate-scale viscoelastic behavior and obstacle-network model; not universal fixed fractal organization.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "stephens", "doi": "10.1091/mbc.E16-09-0653", "title": "Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus", "authors": "Andrew D. Stephens, Edward J. Banigan, Stephen A. Adam et al.", "year": 2017, "journal": "Molecular Biology of the Cell", "source_type": "primary", "url": "https://doi.org/10.1091/mbc.E16-09-0653", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Chromatin and lamins contribute in separate isolated-nucleus extension regimes; spring constants are not universal moduli or viscosity.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "squires", "doi": "10.1146/annurev-fluid-121108-145608", "title": "Fluid Mechanics of Microrheology", "authors": "Todd M. Squires, Thomas G. Mason", "year": 2010, "journal": "Annual Review of Fluid Mechanics", "source_type": "seminal_review", "url": "https://doi.org/10.1146/annurev-fluid-121108-145608", "access_depth": "Publisher bibliographic identity and abstract; established mathematical relationships independently checked dimensionally. Detailed review body not appraised.", "claim_fit": "Foundational synthesis of probe/bulk coupling, passive thermal-fluctuation and active-force microrheology assumptions; not a nuclear measurement.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth.", "seminal_reason": "Foundational review of the physical inference framework underlying particle microrheology, retained for definitions and assumptions rather than claims of nuclear experimental findings." }, { "id": "feric", "doi": "10.1016/j.cell.2016.04.047", "title": "Coexisting Liquid Phases Underlie Nucleolar Subcompartments", "authors": "Marina Feric, Nilesh Vaidya, Tyler S. Harmon et al.", "year": 2016, "journal": "Cell", "source_type": "primary", "url": "https://doi.org/10.1016/j.cell.2016.04.047", "access_depth": "Primary main-text Results subsection on in-vitro viscoelasticity, Fig2E and main Experimental Procedures, independently checked in root browser; source detail received as collaborator evidence. No supplements/raw-data reanalysis.", "claim_fit": "Component-specific nucleolar coexistence and dynamics; in-vitro 50nm-radius tracer values belong to reconstituted NPM1/FIB1 droplets.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "spoton", "doi": "10.7554/eLife.33125", "title": "Robust model-based analysis of single-particle tracking experiments with Spot-On", "authors": "Anders S. Hansen, Maxime Woringer, Jonathan B. Grimm et al.", "year": 2018, "journal": "eLife", "source_type": "primary", "url": "https://doi.org/10.7554/eLife.33125", "access_depth": "Primary indexed main Introduction and selected Results/model/simulation evaluation, first8000char source excerpt; not complete article.", "claim_fit": "Spot-On model/testing distinguishes localization, defocalization, density and motion-blur biases with steady-state Brownian populations.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "bancaud", "doi": "10.1038/emboj.2009.340", "title": "Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin", "authors": "Aurélien Bancaud, Sébastien Huet, Nathalie Daigle et al.", "year": 2009, "journal": "The EMBO Journal", "source_type": "primary", "url": "https://doi.org/10.1038/emboj.2009.340", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Tracer exclusion/hindrance and transient chromatin-protein trapping; fractal interpretation remains model dependent.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "frap", "doi": "10.1529/biophysj.103.026765", "title": "Analysis of Binding Reactions by Fluorescence Recovery after Photobleaching", "authors": "Brian L. Sprague, Robert L. Pego, Diana A. Stavreva et al.", "year": 2004, "journal": "Biophysical Journal", "source_type": "primary", "url": "https://doi.org/10.1529/biophysj.103.026765", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Reaction-diffusion FRAP solutions constrain binding inference; not every recovery curve identifies every parameter.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "attar", "doi": "10.1093/nar/gkaf763", "title": "Peripheral heterochromatin tethering is required for chromatin-based nuclear mechanical response", "authors": "A. G. Attar, J. Paturej, Ozan S. Sarıyer, E. Banigan, A. Erbaş", "year": 2025, "journal": "Nucleic Acids Research", "source_type": "primary", "url": "https://doi.org/10.1093/nar/gkaf763", "access_depth": "Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.", "claim_fit": "Attar and colleagues used polymer simulations compared with micromechanical and chromosome-contact measurements. In that model, peripheral chromatin attachment transmitted imposed nuclear forces to chromatin, and internal crosslinks stiffened the nucleus only when that peripheral coupling was present. This is a model-constrained account of load transfer; a mapped lamina association by itself does not establish the strength or permanence of every molecular tether. Attar et al. (2025) .", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." } ], "word_path": "Reviews_useredit/current_2026-10-12/nuclear-microrheology.docx", "word_sha256": "254b53b4b1cb8cbb31d261a679955fe744e428ff2e165afe3aaecf33bdc0a834", "edition_slug": "nuclear-microrheology", "scope": "This review integrates published primary research with a foundational methods review where needed. Source access ranges from primary abstracts to the selected main Results and Methods identified in each reference record. It is a scholarly synthesis rather than an independent reanalysis of experimental data. Conclusions retain the biological system, measurement scale and model assumptions of the cited studies." }, { "path": "nuclear_biology_reviews/reviews/nuclear_pore_complex_standardized_review.html", "title": "Nuclear Pore Complexes: Architecture, Selective Transport and Plasticity", "kind": "research", "audit_date": "2026-10-12", "status": "Complete rewritten narrative and matching current Word edition", "sha256": "f071433f7bef66651399dbe9d061ed045fa7d8deeea0dd353e3cc1ea79b29b95", "findings": [ "Replaced the earlier narrative with a complete current scientific review.", "Word and web scientific text, comparison tables and bibliography share one source.", "All factual blocks cite primary studies or selected seminal reviews." ], "limitations": [ "This review integrates published primary research with a foundational methods review where needed. Source access ranges from primary abstracts to the selected main Results and Methods identified in each reference record. It is a scholarly synthesis rather than an independent reanalysis of experimental data. Conclusions retain the biological system, measurement scale and model assumptions of the cited studies." ], "references": [ { "id": "linker", "doi": "10.1126/science.abm9798", "title": "Architecture of the linker-scaffold in the nuclear pore", "authors": "Stefan Petrovic, Dipanjan Samanta, Thibaud Perriches et al.", "year": 2022, "journal": "Science", "source_type": "primary", "url": "https://doi.org/10.1126/science.abm9798", "access_depth": "Selected indexed primary main text (opening8000chars; not complete article), plus metadata.", "claim_fit": "Linker/scaffold structural integration and flexible ring-spoke models; model architecture not universal transport threshold.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "cytoplasmic", "doi": "10.1126/science.abm9129", "title": "Architecture of the cytoplasmic face of the nuclear pore", "authors": "Christopher J. Bley, Si Nie, George W. Mobbs et al.", "year": 2022, "journal": "Science", "source_type": "primary", "url": "https://doi.org/10.1126/science.abm9129", "access_depth": "Selected indexed primary main text (opening8000chars; not complete article), plus metadata.", "claim_fit": "Composite human/fungal cytoplasmic-face architecture and approximate composition; not one atomic image of a functioning pore.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "timney", "doi": "10.1083/jcb.201601004", "title": "Simple rules for passive diffusion through the nuclear pore complex", "authors": "Benjamin L. Timney, Barak Raveh, Roxana Mironska et al.", "year": 2016, "journal": "Journal of Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1083/jcb.201601004", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Gradual size-dependent passive NPC reporter exchange in yeast; not a hard universal mass cutoff or whole-nucleoplasm diffusion law.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "ran", "doi": "10.1093/emboj/16.21.6535", "title": "The asymmetric distribution of the constituents of the Ran system is essential for transport into and out of the nucleus", "authors": "Elisa Izaurralde, Ulrike Kutay, Cayetano von Kobbe et al.", "year": 1997, "journal": "The EMBO Journal", "source_type": "primary", "url": "https://doi.org/10.1093/emboj/16.21.6535", "access_depth": "Selected indexed primary main text (opening8000chars; not complete article), plus metadata.", "claim_fit": "Ran-system asymmetry regulates particular import/export reporters; not all cargo uses the same energy mechanism.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "dbp5", "doi": "10.1101/gad.2040611", "title": "The Dbp5 cycle at the nuclear pore complex during mRNA export II: nucleotide cycling and mRNP remodeling by Dbp5 are controlled by Nup159 and Gle1", "authors": "Kristen N. Noble, Elizabeth Tran, Abel R. Alcázar-Román et al.", "year": 2011, "journal": "Genes & Development", "source_type": "primary", "url": "https://doi.org/10.1101/gad.2040611", "access_depth": "Selected indexed primary main text (opening8000chars; not complete article), plus metadata.", "claim_fit": "Nup159/Gle1-IP6 regulation of Dbp5 nucleotide/remodeling cycles; distinct from general Ran-mediated traffic.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "hoffmann", "doi": "10.1016/j.molcel.2024.11.038", "title": "Nuclear pore permeability and fluid flow are modulated by its dilation state", "authors": "Patrick C. Hoffmann, Hyuntae Kim, Aleksandra Obarska-Kosińska et al.", "year": 2024, "journal": "Molecular Cell", "source_type": "primary", "url": "https://doi.org/10.1016/j.molcel.2024.11.038", "access_depth": "Consensus fetched primary record and search-returned primary abstract; full Results inaccessible. Online 2024; issue year should not replace online publication date.", "claim_fit": "Dictyostelium osmotic adaptation, dilation-dependent pressure-driven nucleocytosolic fluid flow and viral blockage; not identical to diffusion or receptor-driven transport.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "panexm", "doi": "10.1083/jcb.202409120", "title": "Visualizing nuclear pore complex plasticity with pan-expansion microscopy", "authors": "Kimberly J. Morgan, Emma Carley, Alyssa N. Coyne, Jeffrey D. Rothstein, C. Patrick Lusk, Megan C. King", "year": 2025, "journal": "Journal of Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1083/jcb.202409120", "access_depth": "Fetched primary abstract and publication record; full Methods and Results not yet appraised.", "claim_fit": "Expanded fixed-cell NPC diameter distributions, nuclear-surface bias, hyperosmotic constriction and LINC perturbation; one patient-derived neuronal comparison does not establish all ALS.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "kozai", "doi": "10.1038/s41556-025-01812-9", "title": "Karyopherins remodel the dynamic organization of the nuclear pore complex transport barrier", "authors": "Toshiya Kozai, Javier Fernandez-Martinez, Larisa E. Kapinos et al.", "year": 2025, "journal": "Nature Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1038/s41556-025-01812-9", "access_depth": "Publisher primary Abstract, opening Results on isolated yeast NPCs, selected DNA-origami Results and Discussion read; entire Methods and supplements not appraised.", "claim_fit": "High-speed AFM of isolated yeast NPCs and orthogonal approaches; transport-factor-dependent FG organization, mobile central cluster, altered FG mutants, and contrast with hydrogels.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "eibauer", "doi": "10.1038/ncomms8532", "title": "Structure and gating of the nuclear pore complex", "authors": "Matthias Eibauer, Mauro Pellanda, Yagmur Turgay et al.", "year": 2015, "journal": "Nature Communications", "source_type": "primary", "url": "https://doi.org/10.1038/ncomms8532", "access_depth": "Selected indexed primary main text (opening8000chars; not complete article), plus metadata.", "claim_fit": "Xenopus oocyte NPC cryo-tomographic scaffold/channel structure; not direct universal transport kinetics.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "dickson", "doi": "10.1038/s41586-023-06969-7", "title": "The HIV capsid mimics karyopherin engagement of FG-nucleoporins", "authors": "Claire F. Dickson, Sophie Hertel, Andrew Tuckwell et al.", "year": 2024, "journal": "Nature", "source_type": "primary", "url": "https://doi.org/10.1038/s41586-023-06969-7", "access_depth": "Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.", "claim_fit": "The Dickson et al. (2024) used an in-vitro dissection of the nuclear barrier and identified a capsid pocket engaging FG motifs from several nucleoporins. Capsids penetrated tested FG condensates, supporting a karyopherin-mimicry interpretation for a large viral cargo. This illustrates why interaction chemistry matters alongside size. Reconstituted-condensate entry is not identical to passage kinetics through an intact, mechanically changing NPC in a living human cell. Dickson et al. (2024) .", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "stoichiometry", "doi": "10.1038/msb.2013.4", "title": "Cell type‐specific nuclear pores: a case in point for context‐dependent stoichiometry of molecular machines", "authors": "Alessandro Ori‬‬, Niccolò Banterle, Murat Iskar et al.", "year": 2013, "journal": "Molecular Systems Biology", "source_type": "primary", "url": "https://doi.org/10.1038/msb.2013.4", "access_depth": "Selected indexed primary main text (opening8000chars; not complete article), plus metadata.", "claim_fit": "NPC stoichiometry comparisons across human cell lines and calibrated counting; no invariant universal composition.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "dangelo", "doi": "10.1016/j.cell.2008.11.037", "title": "Age-Dependent Deterioration of Nuclear Pore Complexes Causes a Loss of Nuclear Integrity in Postmitotic Cells", "authors": "Maximiliano A. D’Angelo, Marcela Raı́ces, Siler H. Panowski et al.", "year": 2009, "journal": "Cell", "source_type": "primary", "url": "https://doi.org/10.1016/j.cell.2008.11.037", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Long-lived scaffold components and age-associated permeability loss in defined postmitotic models; not all human ageing or every NPC component.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "mohr", "doi": "10.1038/emboj.2009.200", "title": "Characterisation of the passive permeability barrier of nuclear pore complexes", "authors": "Dagmar Mohr, Steffen Frey, Torsten Fischer et al.", "year": 2009, "journal": "The EMBO Journal", "source_type": "primary", "url": "https://doi.org/10.1038/emboj.2009.200", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Probe passage in permeabilized nuclei and barrier perturbations; distinct from living-yeast passive exchange.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "osutsumi", "doi": "10.7554/eLife.19071", "title": "Nuclear pore assembly proceeds by an inside-out extrusion of the nuclear envelope", "authors": "Shotaro Otsuka, Khanh Huy Bui, Martin Schorb et al.", "year": 2016, "journal": "eLife", "source_type": "primary", "url": "https://doi.org/10.7554/eLife.19071", "access_depth": "Selected indexed primary main text (opening8000chars; not complete article), plus metadata.", "claim_fit": "Correlative main-text interphase NPC membrane intermediates; not a full mitotic assembly account.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "olmos", "doi": "10.1038/nature14503", "title": "ESCRT-III controls nuclear envelope reformation", "authors": "Yolanda Olmos, Lorna Hodgson, Judith Mantell, Paul Verkade, Jeremy G. Carlton", "year": 2015, "journal": "Nature", "source_type": "primary", "url": "https://doi.org/10.1038/nature14503", "access_depth": "Fetched primary abstract and identity; full Methods not accessible.", "claim_fit": "CHMP2A/CHMP4B/UFD1-dependent postmitotic envelope sealing and compartmentalization in human cells, not all envelope-repair routes.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "lem2", "doi": "10.1038/s41586-020-2232-x", "title": "LEM2 phase separation governs ESCRT-mediated nuclear envelope reformation", "authors": "Alexander von Appen, Dollie LaJoie, Isabel E. Johnson et al.", "year": 2020, "journal": "Nature", "source_type": "primary", "url": "https://doi.org/10.1038/s41586-020-2232-x", "access_depth": "Fetched primary abstract and identity plus selected primary Results excerpts; complete Methods/supplements not appraised.", "claim_fit": "LEM2 chromatin/microtubule targeting and CHMP7 activation in postmitotic reformation; O-ring is mechanistic model, not every membrane-less-body mechanism.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "yap", "doi": "10.1016/j.cell.2017.10.008", "title": "Force Triggers YAP Nuclear Entry by Regulating Transport across Nuclear Pores", "authors": "Alberto Elosegui-Artola, Ion Andreu, Amy E. M. 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New records lacked complete Scite notice check after monthly quota." }, { "id": "osutsumi", "doi": "10.7554/eLife.19071", "title": "Nuclear pore assembly proceeds by an inside-out extrusion of the nuclear envelope", "authors": "Shotaro Otsuka, Khanh Huy Bui, Martin Schorb et al.", "year": 2016, "journal": "eLife", "source_type": "primary", "url": "https://doi.org/10.7554/eLife.19071", "access_depth": "Selected indexed primary main text (opening8000chars; not complete article), plus metadata.", "claim_fit": "Correlative main-text interphase NPC membrane intermediates; not a full mitotic assembly account.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "olmos", "doi": "10.1038/nature14503", "title": "ESCRT-III controls nuclear envelope reformation", "authors": "Yolanda Olmos, Lorna Hodgson, Judith Mantell, Paul Verkade, Jeremy G. 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New records lacked complete Scite notice check after monthly quota." }, { "id": "linker", "doi": "10.1126/science.abm9798", "title": "Architecture of the linker-scaffold in the nuclear pore", "authors": "Stefan Petrovic, Dipanjan Samanta, Thibaud Perriches et al.", "year": 2022, "journal": "Science", "source_type": "primary", "url": "https://doi.org/10.1126/science.abm9798", "access_depth": "Selected indexed primary main text (opening8000chars; not complete article), plus metadata.", "claim_fit": "Linker/scaffold structural integration and flexible ring-spoke models; model architecture not universal transport threshold.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "timney", "doi": "10.1083/jcb.201601004", "title": "Simple rules for passive diffusion through the nuclear pore complex", "authors": "Benjamin L. 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New records lacked complete Scite notice check after monthly quota." }, { "id": "mohr", "doi": "10.1038/emboj.2009.200", "title": "Characterisation of the passive permeability barrier of nuclear pore complexes", "authors": "Dagmar Mohr, Steffen Frey, Torsten Fischer et al.", "year": 2009, "journal": "The EMBO Journal", "source_type": "primary", "url": "https://doi.org/10.1038/emboj.2009.200", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Probe passage in permeabilized nuclei and barrier perturbations; distinct from living-yeast passive exchange.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "dbp5", "doi": "10.1101/gad.2040611", "title": "The Dbp5 cycle at the nuclear pore complex during mRNA export II: nucleotide cycling and mRNP remodeling by Dbp5 are controlled by Nup159 and Gle1", "authors": "Kristen N. Noble, Elizabeth Tran, Abel R. Alcázar-Román et al.", "year": 2011, "journal": "Genes & Development", "source_type": "primary", "url": "https://doi.org/10.1101/gad.2040611", "access_depth": "Selected indexed primary main text (opening8000chars; not complete article), plus metadata.", "claim_fit": "Nup159/Gle1-IP6 regulation of Dbp5 nucleotide/remodeling cycles; distinct from general Ran-mediated traffic.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "cytoplasmic", "doi": "10.1126/science.abm9129", "title": "Architecture of the cytoplasmic face of the nuclear pore", "authors": "Christopher J. Bley, Si Nie, George W. Mobbs et al.", "year": 2022, "journal": "Science", "source_type": "primary", "url": "https://doi.org/10.1126/science.abm9129", "access_depth": "Selected indexed primary main text (opening8000chars; not complete article), plus metadata.", "claim_fit": "Composite human/fungal cytoplasmic-face architecture and approximate composition; not one atomic image of a functioning pore.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "lem2", "doi": "10.1038/s41586-020-2232-x", "title": "LEM2 phase separation governs ESCRT-mediated nuclear envelope reformation", "authors": "Alexander von Appen, Dollie LaJoie, Isabel E. 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New records lacked complete Scite notice check after monthly quota." }, { "id": "guelen-corr", "doi": "10.1038/nature12316", "title": "Correction: Corrigendum: Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions", "authors": "Lars Guelen, Ludo Pagie, Émilie Brasset et al.", "year": 2013, "journal": "Nature", "source_type": "editorial_notice", "url": "https://doi.org/10.1038/nature12316", "access_depth": "Primary correction abstract/citation record containing full correction statements; original full Methods not reappraised.", "claim_fit": "Official corrected H3K9me3 identity and Methods data sources; no inferred change to uncorrected abstract-level LAD conclusions.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "lammerding", "doi": "10.1172/JCI19670", "title": "Lamin A/C deficiency causes defective nuclear mechanics and mechanotransduction", "authors": "Jan Lammerding, Paul Christian Schulze, Tomosaburo Takahashi et al.", "year": 2004, "journal": "Journal of Clinical Investigation", "source_type": "primary", "url": "https://doi.org/10.1172/JCI19670", "access_depth": "Primary publisher main Abstract/selected Results and Methods, including cell strain and surface-bead controls, independently read; Scite truncated abstract insufficient alone.", "claim_fit": "LaminA/C-null mouse-cell strain/deformation, viability and selected signaling; surface-bead cytoskeletal controls not intranuclear rheology.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "stephens", "doi": "10.1091/mbc.E16-09-0653", "title": "Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus", "authors": "Andrew D. Stephens, Edward J. Banigan, Stephen A. Adam et al.", "year": 2017, "journal": "Molecular Biology of the Cell", "source_type": "primary", "url": "https://doi.org/10.1091/mbc.E16-09-0653", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Chromatin and lamins contribute in separate isolated-nucleus extension regimes; spring constants are not universal moduli or viscosity.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "dangelo", "doi": "10.1016/j.cell.2008.11.037", "title": "Age-Dependent Deterioration of Nuclear Pore Complexes Causes a Loss of Nuclear Integrity in Postmitotic Cells", "authors": "Maximiliano A. D’Angelo, Marcela Raı́ces, Siler H. Panowski et al.", "year": 2009, "journal": "Cell", "source_type": "primary", "url": "https://doi.org/10.1016/j.cell.2008.11.037", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Long-lived scaffold components and age-associated permeability loss in defined postmitotic models; not all human ageing or every NPC component.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. 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New records lacked complete Scite notice check after monthly quota." }, { "id": "stephens", "doi": "10.1091/mbc.E16-09-0653", "title": "Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus", "authors": "Andrew D. Stephens, Edward J. Banigan, Stephen A. Adam et al.", "year": 2017, "journal": "Molecular Biology of the Cell", "source_type": "primary", "url": "https://doi.org/10.1091/mbc.E16-09-0653", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Chromatin and lamins contribute in separate isolated-nucleus extension regimes; spring constants are not universal moduli or viscosity.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "bonne", "doi": "10.1038/6799", "title": "Mutations in the gene encoding lamin A/C cause autosomal dominant Emery-Dreifuss muscular dystrophy", "authors": "Gisèle Bonne, Marina Raffaele di Barletta, Shaïda Varnous et al.", "year": 1999, "journal": "Nature Genetics", "source_type": "primary", "url": "https://doi.org/10.1038/6799", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Four LMNA variants co-segregated with EDMD in five families; genetics alone does not identify one mechanical defect.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "eriksson", "doi": "10.1038/nature01629", "title": "Recurrent de novo point mutations in lamin A cause Hutchinson–Gilford progeria syndrome", "authors": "Maria Eriksson, William Ted Brown, Leslie B. Gordon et al.", "year": 2003, "journal": "Nature", "source_type": "primary", "url": "https://doi.org/10.1038/nature01629", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Recurrent G608G in18/20 classical HGPS cases, cryptic splice consequence and50-amino-acid deletion; not ordinary-ageing equivalence.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "lewis", "doi": "10.1038/s41556-025-01822-7", "title": "LBR and LAP2 mediate heterochromatin tethering to the nuclear periphery to preserve genome homeostasis", "authors": "Renard Lewis, Virginia Sinigiani, Noura Maziak et al.", "year": 2026, "journal": "Nature Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1038/s41556-025-01822-7", "access_depth": "Publisher primary Abstract and main Results through heterochromatin-tether deconvolution, membrane LAP2 rescue and short/long-term transcription effects read; complete Methods and supplements not appraised. Published 24 February 2026.", "claim_fit": "Redundant LBR/membrane LAP2 tethering in mammalian cell models, distinction between short-term release and persistent loss; not universal instant repression by peripheral position.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "attar", "doi": "10.1093/nar/gkaf763", "title": "Peripheral heterochromatin tethering is required for chromatin-based nuclear mechanical response", "authors": "A. G. Attar, J. Paturej, Ozan S. Sarıyer, E. Banigan, A. Erbaş", "year": 2025, "journal": "Nucleic Acids Research", "source_type": "primary", "url": "https://doi.org/10.1093/nar/gkaf763", "access_depth": "Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.", "claim_fit": "Attar and colleagues used polymer simulations compared with micromechanical and chromosome-contact measurements. In that model, peripheral chromatin attachment transmitted imposed nuclear forces to chromatin, and internal crosslinks stiffened the nucleus only when that peripheral coupling was present. This is a model-constrained account of load transfer; a mapped lamina association by itself does not establish the strength or permanence of every molecular tether. Attar et al. (2025) .", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "lammerding", "doi": "10.1172/JCI19670", "title": "Lamin A/C deficiency causes defective nuclear mechanics and mechanotransduction", "authors": "Jan Lammerding, Paul Christian Schulze, Tomosaburo Takahashi et al.", "year": 2004, "journal": "Journal of Clinical Investigation", "source_type": "primary", "url": "https://doi.org/10.1172/JCI19670", "access_depth": "Primary publisher main Abstract/selected Results and Methods, including cell strain and surface-bead controls, independently read; Scite truncated abstract insufficient alone.", "claim_fit": "LaminA/C-null mouse-cell strain/deformation, viability and selected signaling; surface-bead cytoskeletal controls not intranuclear rheology.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "freund", "doi": "10.1091/mbc.E11-10-0884", "title": "Lamin B1 loss is a senescence-associated biomarker", "authors": "Adam Freund, Rémi-Martin Laberge, Marco Demaria et al.", "year": 2012, "journal": "Molecular Biology of the Cell", "source_type": "primary", "url": "https://doi.org/10.1091/mbc.E11-10-0884", "access_depth": "Selected indexed primary main text (opening8000chars; not complete article), plus metadata.", "claim_fit": "LaminB1 decrease in defined fibroblast senescence states and irradiated-mouse tissue; no standalone individual-cell diagnosis or ordinary ageing equivalence.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "linc", "doi": "10.1083/jcb.200509124", "title": "Coupling of the nucleus and cytoplasm: role of the LINC complex", "authors": "Melissa Crisp, Qian Liu, Kyle Roux et al.", "year": 2006, "journal": "Journal of Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1083/jcb.200509124", "access_depth": "Primary abstract and bibliographic identity through author institutional repository; full Methods not appraised.", "claim_fit": "SUN1/SUN2–nesprin2 localization and depletion/overexpression in HeLa cells, perinuclear spacing and LINC model.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "guelen-corr", "doi": "10.1038/nature12316", "title": "Correction: Corrigendum: Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions", "authors": "Lars Guelen, Ludo Pagie, Émilie Brasset et al.", "year": 2013, "journal": "Nature", "source_type": "editorial_notice", "url": "https://doi.org/10.1038/nature12316", "access_depth": "Primary correction abstract/citation record containing full correction statements; original full Methods not reappraised.", "claim_fit": "Official corrected H3K9me3 identity and Methods data sources; no inferred change to uncorrected abstract-level LAD conclusions.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "bergamaschi", "doi": "10.1016/j.celrep.2024.114852", "title": "Heterogeneous force response of chromatin in isolated nuclei.", "authors": "G. Bergamaschi, A. Biebricher, Hannes Witt, F. Byfield, Xamanie M R Seymonson, Cornelis Storm, P. Janmey, G. Wuite", "year": 2024, "journal": "Cell Reports", "source_type": "primary", "url": "https://doi.org/10.1016/j.celrep.2024.114852", "access_depth": "Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.", "claim_fit": "Bergamaschi and colleagues measured isolated-nucleus force responses together with chromatin and nuclear-envelope deformation. Chromatin was more compliant than the envelope below the reported 30% strain regime, and chromatin digestion softened nuclei. The joint readouts strengthen component interpretation in the tested preparation without defining one elastic modulus or viscosity for every nucleus. Bergamaschi et al. (2024) .", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "byfield", "doi": "10.1016/j.bpj.2024.11.3322", "title": "Metabolically intact nuclei are fluidized by the activity of the chromatin remodeling motor BRG1", "authors": "Fitzroy J. Byfield, Behnaz Eftekhari, Kaeli Kaymak-Loveless et al.", "year": 2025, "journal": "Biophysical Journal", "source_type": "primary", "url": "https://doi.org/10.1016/j.bpj.2024.11.3322", "access_depth": "Published PDF front matter, main preparation/treatment Methods, Results around Figure 9 and Discussion read; supplementary data not appraised.", "claim_fit": "Metabolically active karyoplast compression/dissipation and BRM-014 inhibition; BRM-014 inhibits BRM and BRG1, so pharmacology is not exclusive genetic proof for BRG1. Karyoplasts are not bare detergent-isolated nuclei.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "afm", "doi": "10.1098/rsif.2024.0885", "title": "Viscoelastic differences between isolated and live MCF7 cancer cell nuclei resolved with AFM microrheology", "authors": "Ellen Juel Pørtner, Anna Mularski, Tobias William Jarrett, Stine Lauritzen Sønder, Jesper Nylandsted, Adam Cohen Simonsen", "year": 2025, "journal": "Journal of the Royal Society Interface", "source_type": "primary", "url": "https://doi.org/10.1098/rsif.2024.0885", "access_depth": "Root independently read primary PMC12173521 Abstract and selected main Methods/Results paragraphs, including oscillatory preparation, hydrodynamic drag correction, morphology and Jeffreys analysis; primary Scite webpage identity corroborated. Supplement and raw-data reanalysis excluded.", "claim_fit": "Oscillatory AFM on live and isolated MCF7 nuclei, hydrodynamic-drag validation, modulus/loss-tangent distinction and Jeffreys model. The published author list supersedes incomplete Consensus authors.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "denais", "doi": "10.1126/science.aad7297", "title": "Nuclear envelope rupture and repair during cancer cell migration", "authors": "Céline Denais, Rachel M. Gilbert, Philipp Isermann et al.", "year": 2016, "journal": "Science", "source_type": "primary", "url": "https://doi.org/10.1126/science.aad7297", "access_depth": "Primary author-manuscript main Abstract/Results pages1–4 and Figures1/2/4; supplementary Methods and raw data not reanalysed.", "claim_fit": "NLS-reporter rupture, defined in-vitro and mouse-dermis models, deformation-associated damage foci and ESCRT-III-dependent resealing independently match primary main Results/Figures. Mixed-topic Scite opening excluded.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." } ], "word_path": "Reviews_useredit/current_2026-10-12/nuclear-lamina.docx", "word_sha256": "ef7bd9fe398781ddbf5aeb7432a5201d994c76e3ec8a22186f982b76d5853b7c", "edition_slug": "nuclear-lamina", "scope": "This review integrates published primary research with a foundational methods review where needed. Source access ranges from primary abstracts to the selected main Results and Methods identified in each reference record. It is a scholarly synthesis rather than an independent reanalysis of experimental data. Conclusions retain the biological system, measurement scale and model assumptions of the cited studies." }, { "path": "nuclear_biology_reviews/reviews/nuclear-transport-compartment-dynamics.html", "title": "Nuclear Transport and Compartment Dynamics: Gates, Search and Processing", "kind": "research", "audit_date": "2026-10-12", "status": "Complete rewritten narrative and matching current Word edition", "sha256": "3973208d80d8c312a784d402801f53d67c2bda7961bcc8a14d0a21866dff8d34", "findings": [ "Replaced the earlier narrative with a complete current scientific review.", "Word and web scientific text, comparison tables and bibliography share one source.", "All factual blocks cite primary studies or selected seminal reviews." ], "limitations": [ "This review integrates published primary research with a foundational methods review where needed. Source access ranges from primary abstracts to the selected main Results and Methods identified in each reference record. It is a scholarly synthesis rather than an independent reanalysis of experimental data. Conclusions retain the biological system, measurement scale and model assumptions of the cited studies." ], "references": [ { "id": "timney", "doi": "10.1083/jcb.201601004", "title": "Simple rules for passive diffusion through the nuclear pore complex", "authors": "Benjamin L. Timney, Barak Raveh, Roxana Mironska et al.", "year": 2016, "journal": "Journal of Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1083/jcb.201601004", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Gradual size-dependent passive NPC reporter exchange in yeast; not a hard universal mass cutoff or whole-nucleoplasm diffusion law.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "ran", "doi": "10.1093/emboj/16.21.6535", "title": "The asymmetric distribution of the constituents of the Ran system is essential for transport into and out of the nucleus", "authors": "Elisa Izaurralde, Ulrike Kutay, Cayetano von Kobbe et al.", "year": 1997, "journal": "The EMBO Journal", "source_type": "primary", "url": "https://doi.org/10.1093/emboj/16.21.6535", "access_depth": "Selected indexed primary main text (opening8000chars; not complete article), plus metadata.", "claim_fit": "Ran-system asymmetry regulates particular import/export reporters; not all cargo uses the same energy mechanism.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "dbp5", "doi": "10.1101/gad.2040611", "title": "The Dbp5 cycle at the nuclear pore complex during mRNA export II: nucleotide cycling and mRNP remodeling by Dbp5 are controlled by Nup159 and Gle1", "authors": "Kristen N. Noble, Elizabeth Tran, Abel R. Alcázar-Román et al.", "year": 2011, "journal": "Genes & Development", "source_type": "primary", "url": "https://doi.org/10.1101/gad.2040611", "access_depth": "Selected indexed primary main text (opening8000chars; not complete article), plus metadata.", "claim_fit": "Nup159/Gle1-IP6 regulation of Dbp5 nucleotide/remodeling cycles; distinct from general Ran-mediated traffic.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "dross", "doi": "10.1371/journal.pone.0005041", "title": "Mapping eGFP Oligomer Mobility in Living Cell Nuclei", "authors": "Nicolas Dross, Corentin Spriet, Monika Zwerger et al.", "year": 2009, "journal": "PLOS ONE", "source_type": "primary", "url": "https://doi.org/10.1371/journal.pone.0005041", "access_depth": "Primary PLOS main Abstract, Methods data analysis/acquisition/calibration and selected Results/Discussion; no raw data reanalysis.", "claim_fit": "eGFP oligomer FCS outside nucleoli: calibrated two-normal-diffusion components plus triplet term; cell/model/probe constraints retained.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "frap", "doi": "10.1529/biophysj.103.026765", "title": "Analysis of Binding Reactions by Fluorescence Recovery after Photobleaching", "authors": "Brian L. Sprague, Robert L. Pego, Diana A. Stavreva et al.", "year": 2004, "journal": "Biophysical Journal", "source_type": "primary", "url": "https://doi.org/10.1529/biophysj.103.026765", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Reaction-diffusion FRAP solutions constrain binding inference; not every recovery curve identifies every parameter.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "feric", "doi": "10.1016/j.cell.2016.04.047", "title": "Coexisting Liquid Phases Underlie Nucleolar Subcompartments", "authors": "Marina Feric, Nilesh Vaidya, Tyler S. Harmon et al.", "year": 2016, "journal": "Cell", "source_type": "primary", "url": "https://doi.org/10.1016/j.cell.2016.04.047", "access_depth": "Primary main-text Results subsection on in-vitro viscoelasticity, Fig2E and main Experimental Procedures, independently checked in root browser; source detail received as collaborator evidence. No supplements/raw-data reanalysis.", "claim_fit": "Component-specific nucleolar coexistence and dynamics; in-vitro 50nm-radius tracer values belong to reconstituted NPM1/FIB1 droplets.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "quinodoz", "doi": "10.1038/s41586-025-09207-4", "title": "Mapping and engineering RNA-driven architecture of the multiphase nucleolus", "authors": "Sofia A. Quinodoz, Lifei Jiang, Aya A. Abu-Alfa et al.", "year": 2025, "journal": "Nature", "source_type": "primary", "url": "https://doi.org/10.1038/s41586-025-09207-4", "access_depth": "Fetched Consensus primary abstract/record, cross-checked with SciSpace where available; complete body not appraised.", "claim_fit": "Quinodoz and colleagues spatially mapped rRNA maturation and engineered nucleoli with processing defects. Disrupting small-subunit processing reordered nucleolar layers and blocked normal rRNA outflux. This provides a substrate-linked perturbation of multiphase architecture, complementary to earlier material measurements. It does not establish that every nuclear body contains a permanent solid core or that all RNA-protein assemblies use the same phase mechanism. Quinodoz et al. (2025) .", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "kozai", "doi": "10.1038/s41556-025-01812-9", "title": "Karyopherins remodel the dynamic organization of the nuclear pore complex transport barrier", "authors": "Toshiya Kozai, Javier Fernandez-Martinez, Larisa E. Kapinos et al.", "year": 2025, "journal": "Nature Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1038/s41556-025-01812-9", "access_depth": "Publisher primary Abstract, opening Results on isolated yeast NPCs, selected DNA-origami Results and Discussion read; entire Methods and supplements not appraised.", "claim_fit": "High-speed AFM of isolated yeast NPCs and orthogonal approaches; transport-factor-dependent FG organization, mobile central cluster, altered FG mutants, and contrast with hydrogels.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "hoffmann", "doi": "10.1016/j.molcel.2024.11.038", "title": "Nuclear pore permeability and fluid flow are modulated by its dilation state", "authors": "Patrick C. Hoffmann, Hyuntae Kim, Aleksandra Obarska-Kosińska et al.", "year": 2024, "journal": "Molecular Cell", "source_type": "primary", "url": "https://doi.org/10.1016/j.molcel.2024.11.038", "access_depth": "Consensus fetched primary record and search-returned primary abstract; full Results inaccessible. Online 2024; issue year should not replace online publication date.", "claim_fit": "Dictyostelium osmotic adaptation, dilation-dependent pressure-driven nucleocytosolic fluid flow and viral blockage; not identical to diffusion or receptor-driven transport.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "biswas", "doi": "10.1038/s41467-025-62605-0", "title": "Conserved nucleocytoplasmic density homeostasis drives cellular organization across eukaryotes", "authors": "Abin Biswas, Omar Muñoz, Kyoohyun Kim et al.", "year": 2025, "journal": "Nature Communications", "source_type": "primary", "url": "https://doi.org/10.1038/s41467-025-62605-0", "access_depth": "Fetched primary abstract and publisher Results excerpts on Xenopus assembly and density model; Crossmark publication date and author metadata checked. Complete body and supplements not appraised.", "claim_fit": "Nuclear/cytoplasmic density differences and pressure-balance model constrained by transport, chromatin and embryo observations. Erroneous2023 provider year corrected to publisher15August2025.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "mohr", "doi": "10.1038/emboj.2009.200", "title": "Characterisation of the passive permeability barrier of nuclear pore complexes", "authors": "Dagmar Mohr, Steffen Frey, Torsten Fischer et al.", "year": 2009, "journal": "The EMBO Journal", "source_type": "primary", "url": "https://doi.org/10.1038/emboj.2009.200", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Probe passage in permeabilized nuclei and barrier perturbations; distinct from living-yeast passive exchange.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "erdel", "doi": "10.1088/0953-8984/27/6/064115", "title": "The viscoelastic properties of chromatin and the nucleoplasm revealed by scale-dependent protein mobility", "authors": "Fabian Erdel, Michael Baum, Karsten Rippe", "year": 2015, "journal": "Journal of Physics: Condensed Matter", "source_type": "primary", "url": "https://doi.org/10.1088/0953-8984/27/6/064115", "access_depth": "Published identity and primary abstract from author-manuscript repository; full main text not appraised.", "claim_fit": "Differently sized inert GFP probes and polymer simulations; size-dependent intermediate-scale viscoelastic behavior and obstacle-network model; not universal fixed fractal organization.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "bancaud", "doi": "10.1038/emboj.2009.340", "title": "Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin", "authors": "Aurélien Bancaud, Sébastien Huet, Nathalie Daigle et al.", "year": 2009, "journal": "The EMBO Journal", "source_type": "primary", "url": "https://doi.org/10.1038/emboj.2009.340", "access_depth": "Primary abstract and bibliographic metadata; complete body unavailable through connector.", "claim_fit": "Tracer exclusion/hindrance and transient chromatin-protein trapping; fractal interpretation remains model dependent.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "spoton", "doi": "10.7554/eLife.33125", "title": "Robust model-based analysis of single-particle tracking experiments with Spot-On", "authors": "Anders S. Hansen, Maxime Woringer, Jonathan B. Grimm et al.", "year": 2018, "journal": "eLife", "source_type": "primary", "url": "https://doi.org/10.7554/eLife.33125", "access_depth": "Primary indexed main Introduction and selected Results/model/simulation evaluation, first8000char source excerpt; not complete article.", "claim_fit": "Spot-On model/testing distinguishes localization, defocalization, density and motion-blur biases with steady-state Brownian populations.", "limitations": "No indexed notice in retrieved result is not a guarantee of no correction/retraction. New records lacked complete Scite notice check after monthly quota." }, { "id": "yap", "doi": "10.1016/j.cell.2017.10.008", "title": "Force Triggers YAP Nuclear Entry by Regulating Transport across Nuclear Pores", "authors": "Alberto Elosegui-Artola, Ion Andreu, Amy E. M. Beedle et al.", "year": 2017, "journal": "Cell", "source_type": "primary", "url": "https://doi.org/10.1016/j.cell.2017.10.008", "access_depth": "Publisher primary selected Results on force application and import/export plus AFM Methods excerpt read; complete body and supplements not appraised.", "claim_fit": "Force-dependent YAP entry in defined fibroblast/MCF10A systems, nuclear deformation and import-rate assays; not all cargo or universal pore-mechanics explanation.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "rashid", "doi": "10.1016/j.celrep.2024.114462", "title": "Mechanomemory of nucleoplasm and RNA polymerase II after chromatin stretching by a microinjected magnetic nanoparticle force", "authors": "Fazlur Rashid, Sadia Amin Kabbo, Ning Wang", "year": 2024, "journal": "Cell Reports", "source_type": "primary", "url": "https://doi.org/10.1016/j.celrep.2024.114462", "access_depth": "Primary manuscript main Summary, Results on microrheology and mechanomemory, Figures 1–5 and Discussion read; supplemental figures and raw measurements not reanalysed.", "claim_fit": "200-nm-diameter targeted magnetic particles in CHO DHFR reporter nuclei; 0.1–5 Hz force response and separate hiPSC Pol II arm; local perturbation and injection limitations.", "limitations": "No independent experimental replication or raw-data reanalysis. Source interpretation confined to the stated access depth." }, { "id": "panexm", "doi": "10.1083/jcb.202409120", "title": "Visualizing nuclear pore complex plasticity with pan-expansion microscopy", "authors": "Kimberly J. Morgan, Emma Carley, Alyssa N. Coyne, Jeffrey D. Rothstein, C. Patrick Lusk, Megan C. King", "year": 2025, "journal": "Journal of Cell Biology", "source_type": "primary", "url": "https://doi.org/10.1083/jcb.202409120", "access_depth": "Fetched primary abstract and publication record; full Methods and Results not yet appraised.", "claim_fit": "Expanded fixed-cell NPC diameter distributions, nuclear-surface bias, hyperosmotic constriction and LINC perturbation; one patient-derived neuronal comparison does not establish all ALS.", "limitations": "No independent experimental replication or raw-data reanalysis. 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Experiments and models retain their organism, construct and perturbation context; raw data and supplementary material have not been comprehensively reanalysed." ], "references": [ { "id": "mccracken", "doi": "10.1038/385357a0", "title": "The C-terminal domain of RNA polymerase II couples mRNA processing to transcription", "authors": "McCracken et al.", "year": 1997, "journal": "Nature", "source_type": "primary", "url": "https://doi.org/10.1038/385357a0", "access_depth": "Primary publication abstract and bibliographic record", "claim_fit": "CTD truncation inhibits efficient splicing, 3′ processing and termination in tested cellular context.", "limitations": "Study-specific findings; no raw-data reanalysis or independent reproduction of experiments." }, { "id": "liu", "doi": "10.1371/journal.pcbi.1008999", "title": "Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage", "authors": "Liu et al.", "year": 2021, "journal": "PLOS Computational Biology", "source_type": "primary", "url": "https://doi.org/10.1371/journal.pcbi.1008999", "access_depth": "Scite primary body introduction plus targeted Results/Discussion excerpts", "claim_fit": "Engineered fly reporter, effective Bayesian parameters, 355 cells/7 embryos, initial 18-minute window, model assumptions and limited burst applicability", "limitations": "Study-specific findings; no raw-data reanalysis or independent reproduction of experiments." }, { "id": "muller", "doi": "10.1371/journal.pcbi.1012059", "title": "Nuclear export is a limiting factor in eukaryotic mRNA metabolism", "authors": "Müller et al.", "year": 2024, "journal": "PLOS Computational Biology", "source_type": "primary", "url": "https://doi.org/10.1371/journal.pcbi.1012059", "access_depth": "SciSpace original publication abstract and journal/author/DOI metadata", "claim_fit": "Compartmental SLAM-seq and model estimate synthesis, export and degradation in human cancer cells.", "limitations": "Study-specific findings; no raw-data reanalysis or independent reproduction of experiments." }, { "id": "ietswaart", "doi": "10.1016/j.molcel.2024.06.008", "title": "Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle", "authors": "Ietswaart et al.", "year": 2024, "journal": "Molecular Cell", "source_type": "primary", "url": "https://doi.org/10.1016/j.molcel.2024.06.008", "access_depth": "SciSpace original publication abstract and metadata", "claim_fit": "Subcellular TimeLapse-seq in human and mouse cells; modeled RNA flow and retained-intron/exosome dependency.", "limitations": "Study-specific findings; no raw-data reanalysis or independent reproduction of experiments." }, { "id": "bhat", "doi": "10.1038/s41586-024-07429-6", "title": "Genome organization around nuclear speckles drives mRNA splicing efficiency", "authors": "Bhat et al.", "year": 2024, "journal": "Nature", "source_type": "primary", "url": "https://doi.org/10.1038/s41586-024-07429-6", "access_depth": "Consensus fetched primary abstract; publisher abstract and figure-caption descriptions", "claim_fit": "Speckle-proximal spliceosome binding and splicing; directed RNA recruitment tests spatial sufficiency.", "limitations": "Study-specific findings; no raw-data reanalysis or independent reproduction of experiments." }, { "id": "malszycki", "doi": "10.1016/j.cell.2026.01.011", "title": "Nuclear speckles enable processing of RNA from GC-rich isochores", "authors": "Małszycki et al.", "year": 2026, "journal": "Cell", "source_type": "primary", "url": "https://doi.org/10.1016/j.cell.2026.01.011", "access_depth": "Consensus fetched identity; 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