[{"article_processing_charge":"No","volume":136,"date_updated":"2024-01-22T13:35:48Z","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"_id":"14827","pmid":1,"oa_version":"None","project":[{"name":"A mechano-chemical theory for stem cell fate decisions in organoid development","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","grant_number":"343-2022"}],"quality_controlled":"1","acknowledgement":"We thank Prisca Liberali and Edouard Hannezo for many inspiring discussions; Mehmet Can Uçar, Nicoletta I Petridou and Qiutan Yang for a critical reading of the manuscript, and Claudia Flandoli for the artwork in Figs 2 and 3. We would also like to thank The Company of Biologists for the opportunity to attend the 2023 workshop on Collective Cell Migration, and all workshop participants for discussions.\r\nC.S. was supported by a European Molecular Biology Organization (EMBO) Postdoctoral Fellowship (ALTF 660-2020) and Human Frontier Science Program (HFSP) Postdoctoral fellowship (LT000746/2021-L). D.B.B. was supported by the NOMIS Foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Schwayer, C., &#38; Brückner, D. (2023). Connecting theory and experiment in cell and tissue mechanics. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.261515\">https://doi.org/10.1242/jcs.261515</a>","ieee":"C. Schwayer and D. Brückner, “Connecting theory and experiment in cell and tissue mechanics,” <i>Journal of Cell Science</i>, vol. 136, no. 24. The Company of Biologists, 2023.","chicago":"Schwayer, Cornelia, and David Brückner. “Connecting Theory and Experiment in Cell and Tissue Mechanics.” <i>Journal of Cell Science</i>. The Company of Biologists, 2023. <a href=\"https://doi.org/10.1242/jcs.261515\">https://doi.org/10.1242/jcs.261515</a>.","ama":"Schwayer C, Brückner D. Connecting theory and experiment in cell and tissue mechanics. <i>Journal of Cell Science</i>. 2023;136(24). doi:<a href=\"https://doi.org/10.1242/jcs.261515\">10.1242/jcs.261515</a>","mla":"Schwayer, Cornelia, and David Brückner. “Connecting Theory and Experiment in Cell and Tissue Mechanics.” <i>Journal of Cell Science</i>, vol. 136, no. 24, jcs. 261515, The Company of Biologists, 2023, doi:<a href=\"https://doi.org/10.1242/jcs.261515\">10.1242/jcs.261515</a>.","short":"C. Schwayer, D. Brückner, Journal of Cell Science 136 (2023).","ista":"Schwayer C, Brückner D. 2023. Connecting theory and experiment in cell and tissue mechanics. Journal of Cell Science. 136(24), jcs. 261515."},"publication_status":"published","abstract":[{"lang":"eng","text":"Understanding complex living systems, which are fundamentally constrained by physical phenomena, requires combining experimental data with theoretical physical and mathematical models. To develop such models, collaborations between experimental cell biologists and theoreticians are increasingly important but these two groups often face challenges achieving mutual understanding. To help navigate these challenges, this Perspective discusses different modelling approaches, including bottom-up hypothesis-driven and top-down data-driven models, and highlights their strengths and applications. Using cell mechanics as an example, we explore the integration of specific physical models with experimental data from the molecular, cellular and tissue level up to multiscale input. We also emphasize the importance of constraining model complexity and outline strategies for crosstalk between experimental design and model development. Furthermore, we highlight how physical models can provide conceptual insights and produce unifying and generalizable frameworks for biological phenomena. Overall, this Perspective aims to promote fruitful collaborations that advance our understanding of complex biological systems."}],"author":[{"id":"3436488C-F248-11E8-B48F-1D18A9856A87","first_name":"Cornelia","orcid":"0000-0001-5130-2226","full_name":"Schwayer, Cornelia","last_name":"Schwayer"},{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","last_name":"Brückner","full_name":"Brückner, David","first_name":"David"}],"keyword":["Cell Biology"],"article_number":"jcs.261515","doi":"10.1242/jcs.261515","year":"2023","title":"Connecting theory and experiment in cell and tissue mechanics","external_id":{"pmid":["38149871"]},"publication":"Journal of Cell Science","issue":"24","day":"27","type":"journal_article","intvolume":"       136","status":"public","department":[{"_id":"EdHa"},{"_id":"CaHe"}],"date_created":"2024-01-17T12:46:55Z","month":"12","article_type":"original","date_published":"2023-12-27T00:00:00Z","scopus_import":"1","publisher":"The Company of Biologists","language":[{"iso":"eng"}]},{"date_created":"2023-07-23T22:01:12Z","department":[{"_id":"EdHa"}],"scopus_import":"1","publisher":"American Association for the Advancement of Science","language":[{"iso":"eng"}],"month":"06","article_type":"original","date_published":"2023-06-29T00:00:00Z","publication":"Science","issue":"6652","page":"1357-1362","intvolume":"       380","status":"public","day":"29","type":"journal_article","isi":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/science.adf5568"}],"title":"Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome","external_id":{"isi":["001106405600028"]},"doi":"10.1126/science.adf5568","year":"2023","publication_identifier":{"eissn":["1095-9203"]},"_id":"13261","oa_version":"Preprint","project":[{"grant_number":"343-2022","name":"A mechano-chemical theory for stem cell fate decisions in organoid development","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"}],"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported in part by the U.S. National Science Foundation, the Center for the Physics of Biological Function (grant PHY-1734030), and the National Institutes of Health (grants R01GM097275, U01DA047730, and U01DK127429). D.B.B. was supported by the NOMIS Foundation as a fellow and by an EMBO postdoctoral fellowship (ALTF 343-2022). H.C. was supported by a Charles H. Revson Biomedical Science Fellowship.","article_processing_charge":"No","date_updated":"2023-12-13T11:41:07Z","volume":380,"oa":1,"abstract":[{"lang":"eng","text":"Chromosomes in the eukaryotic nucleus are highly compacted. However, for many functional processes, including transcription initiation, the pairwise motion of distal chromosomal elements such as enhancers and promoters is essential and necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously measure the positions of pairs of enhancers and promoters and their transcriptional output while systematically varying the genomic separation between these two DNA loci. Our analysis reveals the coexistence of a compact globular organization and fast subdiffusive dynamics. These combined features cause an anomalous scaling of polymer relaxation times with genomic separation leading to long-ranged correlations. Thus, encounter times of DNA loci are much less dependent on genomic distance than predicted by existing polymer models, with potential consequences for eukaryotic gene expression."}],"author":[{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","last_name":"Brückner","full_name":"Brückner, David","first_name":"David"},{"first_name":"Hongtao","last_name":"Chen","full_name":"Chen, Hongtao"},{"full_name":"Barinov, Lev","last_name":"Barinov","first_name":"Lev"},{"first_name":"Benjamin","last_name":"Zoller","full_name":"Zoller, Benjamin"},{"first_name":"Thomas","full_name":"Gregor, Thomas","last_name":"Gregor"}],"citation":{"mla":"Brückner, David, et al. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA Loci on a Compacted Chromosome.” <i>Science</i>, vol. 380, no. 6652, American Association for the Advancement of Science, 2023, pp. 1357–62, doi:<a href=\"https://doi.org/10.1126/science.adf5568\">10.1126/science.adf5568</a>.","ama":"Brückner D, Chen H, Barinov L, Zoller B, Gregor T. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. <i>Science</i>. 2023;380(6652):1357-1362. doi:<a href=\"https://doi.org/10.1126/science.adf5568\">10.1126/science.adf5568</a>","short":"D. Brückner, H. Chen, L. Barinov, B. Zoller, T. Gregor, Science 380 (2023) 1357–1362.","ista":"Brückner D, Chen H, Barinov L, Zoller B, Gregor T. 2023. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science. 380(6652), 1357–1362.","apa":"Brückner, D., Chen, H., Barinov, L., Zoller, B., &#38; Gregor, T. (2023). Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adf5568\">https://doi.org/10.1126/science.adf5568</a>","ieee":"D. Brückner, H. Chen, L. Barinov, B. Zoller, and T. Gregor, “Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome,” <i>Science</i>, vol. 380, no. 6652. American Association for the Advancement of Science, pp. 1357–1362, 2023.","chicago":"Brückner, David, Hongtao Chen, Lev Barinov, Benjamin Zoller, and Thomas Gregor. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA Loci on a Compacted Chromosome.” <i>Science</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/science.adf5568\">https://doi.org/10.1126/science.adf5568</a>."},"publication_status":"published"}]