@article {Naik2025,
	author = {Naik, Suyash and Keta, Yann-Edwin and Pranjic-Ferscha, Kornelija and Hannezo, {\'E}douard and Henkes, Silke and Heisenberg, Carl-Philipp},
	title = {Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties},
	elocation-id = {2025.02.14.638262},
	year = {2025},
	doi = {10.1101/2025.02.14.638262},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {For tissues to spread, they must be deformable while maintaining their structural integrity. How these opposing requirements are balanced within spreading tissues is not yet well understood. Here, we show that keratin intermediate filaments function in epithelial spreading by adapting tissue mechanical resilience to the stresses arising in the tissue during the spreading process. By analysing the expansion of the enveloping cell layer (EVL) over the large yolk cell in early zebrafish embryos in vivo, we found that keratin network maturation in EVL cells is promoted by stresses building up within the spreading tissue. Through genetic interference and tissue rheology experiments, complemented by a vertex model with mechanochemical feedback, we demonstrate that stress-induced keratin network maturation in the EVL increases tissue viscosity, which is essential for preventing tissue rupture. Interestingly, keratins are also required in the yolk cell for mechanosensitive actomyosin network contraction and flow, the force-generating processes pulling the EVL. These dual mechanosensitive functions of keratins enable a balance between pulling force production in the yolk cell and the mechanical resilience of the EVL against stresses generated by these pulling forces, thereby ensuring uniform and robust tissue spreading.Competing Interest StatementThe authors have declared no competing interest.},
	URL = {https://www.biorxiv.org/content/early/2025/02/17/2025.02.14.638262},
	eprint = {https://www.biorxiv.org/content/early/2025/02/17/2025.02.14.638262.full.pdf},
        volume={12},
	journal = {bioRxiv}
}

@Article{Turing1952,
  title={A theory of morphogenesis},
  author={Turing, AM},
  journal={Phil. Trans. B},
  volume={12},
  year={1952}
}
@article{holtfreter1943study,
  title={A study of the mechanics of gastrulation. Part I},
  author={Holtfreter, Johannes},
  journal={Journal of experimental zoology},
  volume={94},
  number={3},
  pages={261--318},
  year={1943},
  publisher={Wiley Online Library}
}
@article{holtfreter1944study,
  title={A study of the mechanics of gastrulation},
  author={Holtfreter, Johannes},
  journal={Journal of experimental zoology},
  volume={95},
  number={2},
  pages={171--212},
  year={1944},
  publisher={Wiley Online Library}
}
@article{steinert1983Completeaminoacid,
  title = {Complete Amino Acid Sequence of a Mouse Epidermal Keratin Subunit and Implications for the Structure of Intermediate Filaments},
  author = {Steinert, Peter M. and Rice, Robert H. and Roop, Dennis R. and Trus, Benes L. and Steven, Alasdair C.},
  year = {1983},
  month = apr,
  journal = {Nature},
  volume = {302},
  number = {5911},
  pages = {794--800},
  publisher = {Nature Publishing Group},
  issn = {1476-4687},
  doi = {10.1038/302794a0},
  urldate = {2025-05-23},
  abstract = {We have determined the complete primary structure of an intermediate filament subunit, the 59,000 molecular weight subunit of mouse epidermal keratin, from the nucleotide sequence of cDNA clones. The central portion of the sequence forms extended tracts of a coiled-coil {$\alpha$}-helical conformation. This is flanked at both termini by similar non-{$\alpha$}-helical sequences that are extremely rich in glycine residues, frequently configured in tandem peptide repeats. Limited chymotryptic digestion of keratin filaments containing this protein suggests a structural organization whereby the terminal glycine-rich sequences protrude from a conserved core structure into which the coiled-coil {$\alpha$}-helical segments are packed.},
  copyright = {1983 Springer Nature Limited},
  langid = {english},
  keywords = {Humanities and Social Sciences,multidisciplinary,Science},
  file = {/Users/snaik/Zotero/storage/QJM7GZ35/Steinert et al. - 1983 - Complete amino acid sequence of a mouse epidermal keratin subunit and implications for the structure.pdf}
}

@article{Saias2015DecreaseCellVolume,
  author  = {Saias, Laurent and Swoger, James and D’Angelo, Andrea and Hayes, Patrick and Colombelli, Julien and Sharpe, James and Salbreux, Guillaume and Solon, Julia},
  title   = {Decrease in Cell Volume Generates Contractile Forces Driving Dorsal Closure},
  journal = {Developmental Cell},
  year    = {2015},
  volume  = {33},
  pages   = {611--621},
  doi     = {10.1016/j.devcel.2015.03.016}
}

@article{Young1993NonmuscleMyosinNeeded,
  author  = {Young, P. E. and Richman, A. M. and Ketchum, A. S. and Kiehart, D. P.},
  title   = {Morphogenesis in \textit{Drosophila} requires nonmuscle myosin heavy chain function},
  journal = {Genes \& Development},
  year    = {1993},
  volume  = {7},
  pages   = {29--41},
  doi     = {10.1101/gad.7.1.29}
}

@article{Jacinto2000DynamicActinAdhesion,
  author  = {Jacinto, Antonio and Wood, Will and Balayo, Torsten and Turmaine, Mark and Martinez-Arias, Alfonso and Martin, Paul},
  title   = {Dynamic actin-based epithelial adhesion and cell matching during \textit{Drosophila} dorsal closure},
  journal = {Current Biology},
  year    = {2000},
  volume  = {10},
  pages   = {1420--1426},
  doi     = {10.1016/S0960-9822(00)00796-X}
}

@article{Losick2013PolyploidFusionWound,
  author  = {Losick, V. P. and Fox, D. T. and Spradling, A. C.},
  title   = {Polyploidization and cell fusion contribute to wound healing in the adult \textit{Drosophila} epithelium},
  journal = {Current Biology},
  year    = {2013},
  volume  = {23},
  pages   = {2224--2232},
  doi     = {10.1016/j.cub.2013.09.029}
}

@article{Brown1981CornealSpreading,
  author  = {Brown, R. M. and Middleton, C. A.},
  title   = {Contact-induced spreading in cultures of corneal epithelial cells},
  journal = {Journal of Cell Science},
  year    = {1981},
  volume  = {51},
  pages   = {143--152},
  doi     = {10.1242/jcs.51.1.143}
}

@article{Lecuit2007OrchestratingSizeShape,
  author  = {Lecuit, Thomas and Le Goff, Lo{\"i}c},
  title   = {Orchestrating size and shape during morphogenesis},
  journal = {Nature},
  year    = {2007},
  volume  = {450},
  pages   = {189--192},
  doi     = {10.1038/nature06304}
}

@article{Kimmel1995ZebrafishStages,
  author  = {Kimmel, C. B. and Ballard, W. W. and Kimmel, S. R. and Ullmann, B. and Schilling, T. F.},
  title   = {Stages of embryonic development of the zebrafish},
  journal = {Developmental Dynamics},
  year    = {1995},
  volume  = {203},
  pages   = {253--310},
  doi     = {10.1002/aja.1002030302}
}

@article{Bruce2016ZebrafishEpibolyReview,
  author  = {Bruce, A. E. E.},
  title   = {Zebrafish epiboly: Spreading thin over the yolk},
  journal = {Developmental Dynamics},
  year    = {2016},
  volume  = {245},
  pages   = {244--258},
  doi     = {10.1002/dvdy.24353}
}

@article{Lepage2010ZebrafishEpibolyMech,
  author  = {Lepage, S. and Bruce, A.},
  title   = {Zebrafish epiboly: Mechanics and mechanisms},
  journal = {The International Journal of Developmental Biology},
  year    = {2010},
  volume  = {54},
  pages   = {1213--1228},
  doi     = {10.1387/ijdb.093028sl}
}

@article{Behrndt2012ForcesEpithelialSpreading,
  author  = {Behrndt, M. and Salbreux, G. and Campinho, P. and Hauschild, R. and Oswald, F. and Roensch, J. and Grill, S. W. and Heisenberg, C.-P.},
  title   = {Forces Driving Epithelial Spreading in Zebrafish Gastrulation},
  journal = {Science},
  year    = {2012},
  volume  = {338},
  pages   = {257--260},
  doi     = {10.1126/science.1224143}
}

@article{Schwayer2019ZO1PhaseSeparation,
  author  = {Schwayer, Christian and Shamipour, Shayan and Pranjic-Ferscha, Katharina and Schauer, Alexandra and Balda, M{\"o}nica and Tada, Masazumi and Matter, Karl and Heisenberg, Carl-Philipp},
  title   = {Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow},
  journal = {Cell},
  year    = {2019},
  volume  = {179},
  pages   = {937--952.e18},
  doi     = {10.1016/j.cell.2019.10.006}
}

@article{Morita2017PhysicalBasisSpreading,
  author  = {Morita, Hidenori and Grigolon, Silvia and Bock, Martin and Krens, Sander F. G. and Salbreux, Guillaume and Heisenberg, Carl-Philipp},
  title   = {The Physical Basis of Coordinated Tissue Spreading in Zebrafish Gastrulation},
  journal = {Developmental Cell},
  year    = {2017},
  volume  = {40},
  pages   = {354--366.e4},
  doi     = {10.1016/j.devcel.2017.01.010}
}

@article{Campinho2013TensionOrientedDivisions,
  author  = {Campinho, Pedro and Behrndt, Martin and Ranft, Jonas and Risler, Thomas and Minc, Nicolas and Heisenberg, Carl-Philipp},
  title   = {Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly},
  journal = {Nature Cell Biology},
  year    = {2013},
  volume  = {15},
  pages   = {1405--1414},
  doi     = {10.1038/ncb2869}
}

@article{Petridou2019TissueRheologyEmbryos,
  author  = {Petridou, Nicoletta I. and Heisenberg, Carl-Philipp},
  title   = {Tissue rheology in embryonic organization},
  journal = {The EMBO Journal},
  year    = {2019},
  volume  = {38},
  pages   = {e102497},
  doi     = {10.15252/embj.2019102497}
}

@article{Laly2021KeratinRigiditySensing,
  author  = {Laly, Antoine C. and Sliogeryte, Kristina and Pundel, Olivier J. and Ross, Ruth and Keeling, Michelle C. and Avisetti, Divya and Waseem, Alykhan and Gavara, Nicolas and Connelly, John T.},
  title   = {The keratin network of intermediate filaments regulates keratinocyte rigidity sensing and nuclear mechanotransduction},
  journal = {Science Advances},
  year    = {2021},
  volume  = {7},
  pages   = {eabd6187},
  doi     = {10.1126/sciadv.abd6187}
}

@article{Loschke2015KeratinNetworkRegulation,
  author  = {Loschke, Franziska and Seltmann, Katharina and Bouameur, Jean{-}Emmanuel and Magin, Thomas M.},
  title   = {Regulation of keratin network organization},
  journal = {Current Opinion in Cell Biology},
  year    = {2015},
  volume  = {32},
  pages   = {56--64},
  doi     = {10.1016/j.ceb.2014.12.006}
}

@article{Herrmann1999EarlyIFAssemblyUnits,
  author  = {Herrmann, Harald and H{\"a}ner, Markus and Brettel, Manfred and Ku, Nam-On and Aebi, Ueli},
  title   = {Characterization of distinct early assembly units of different intermediate filament proteins},
  journal = {Journal of Molecular Biology},
  year    = {1999},
  volume  = {286},
  pages   = {1403--1420},
  doi     = {10.1006/jmbi.1999.2528}
}

@article{Herrmann2007IFsToNanomechanics,
  author  = {Herrmann, Harald and B{\"a}r, Harald and Kreplak, Laurent and Strelkov, Sergei V. and Aebi, Ueli},
  title   = {Intermediate filaments: from cell architecture to nanomechanics},
  journal = {Nature Reviews Molecular Cell Biology},
  year    = {2007},
  volume  = {8},
  pages   = {562--573},
  doi     = {10.1038/nrm2197}
}

@article{Lorenz2019LateralCouplingIFMechanics,
  author  = {Lorenz, Christoph and Forsting, Jens and Schepers, Annika V. and Kraxner, Johannes and Bauch, Sabine and Witt, Holger and Klumpp, Stefan and K{\"o}ster, Sarah},
  title   = {Lateral Subunit Coupling Determines Intermediate Filament Mechanics},
  journal = {Physical Review Letters},
  year    = {2019},
  volume  = {123},
  pages   = {188102},
  doi     = {10.1103/PhysRevLett.123.188102}
}

@article{Kreplak2004IFAssemblyMechanisms,
  author  = {Kreplak, Laurent and Aebi, Ueli and Herrmann, Harald},
  title   = {Molecular mechanisms underlying the assembly of intermediate filaments},
  journal = {Experimental Cell Research},
  year    = {2004},
  volume  = {301},
  pages   = {77--83},
  doi     = {10.1016/j.yexcr.2004.08.021}
}

@article{Bragulla2009KeratinStructureFunctions,
  author  = {Bragulla, Hermann H. and Homberger, Dominique G.},
  title   = {Structure and functions of keratin proteins in simple, stratified, keratinized and cornified epithelia},
  journal = {Journal of Anatomy},
  year    = {2009},
  volume  = {214},
  pages   = {516--559},
  doi     = {10.1111/j.1469-7580.2009.01066.x}
}

@article{Quinlan2017RimSpokeIFHypothesis,
  author  = {Quinlan, Roy A. and Schwarz, Nina and Windoffer, Reinhard and Richardson, Clare and Hawkins, Tavia and Broussard, Jennifer A. and Green, Kathleen J. and Leube, Rudolf E.},
  title   = {A rim-and-spoke hypothesis to explain the biomechanical roles for cytoplasmic intermediate filament networks},
  journal = {Journal of Cell Science},
  year    = {2017},
  volume  = {130},
  pages   = {3437--3445},
  doi     = {10.1242/jcs.202168}
}

@article{Acehan2008PlakoglobinIFAnchorage,
  author  = {Acehan, Derya and Petzold, Christian and Gumper, Ingo and Sabatini, Diego D. and M{\"u}ller, Eva J. and Cowin, Pamela and Stokes, David L.},
  title   = {Plakoglobin Is Required for Effective Intermediate Filament Anchorage to Desmosomes},
  journal = {Journal of Investigative Dermatology},
  year    = {2008},
  volume  = {128},
  pages   = {2665--2675},
  doi     = {10.1038/jid.2008.141}
}

@article{Kroger2013KeratinsAdhesionPKC,
  author  = {Kr{\"o}ger, Claudia and Loschke, Franziska and Schwarz, Nina and Windoffer, Reinhard and Leube, Rudolf E. and Magin, Thomas M.},
  title   = {Keratins control intercellular adhesion involving PKC-\(\alpha\)–mediated desmoplakin phosphorylation},
  journal = {Journal of Cell Biology},
  year    = {2013},
  volume  = {201},
  pages   = {681--692},
  doi     = {10.1083/jcb.201208162}
}

@article{Windoffer2021QuantitativeKeratin3D,
  author  = {Windoffer, Reinhard and Schwarz, Nina and Yoon, Sun and Piskova, Tereza and Scholkemper, Matthias and Stegmaier, Johannes and B{\"o}nsch, Alexander and Russo, Jos{\'e} D. and Leube, Rudolf E.},
  title   = {Quantitative Mapping of Keratin Networks in 3D},
  journal = {bioRxiv},
  year    = {2021},
  doi     = {10.1101/2021.12.06.470977}
}

@article{Salas2016KeratinBarrierPolarity,
  author  = {Salas, Pablo J. and Forteza, Rosana and Mashukova, Anastasiya},
  title   = {Multiple roles for keratin intermediate filaments in the regulation of epithelial barrier function and apico-basal polarity},
  journal = {Tissue Barriers},
  year    = {2016},
  volume  = {4},
  pages   = {e1178368},
  doi     = {10.1080/21688370.2016.1178368}
}

@article{Kayser2012AssemblyKineticsKeratin,
  author  = {Kayser, Jan and Grabmayr, Harald and Harasim, Michael and Herrmann, Harald and Bausch, Andreas R.},
  title   = {Assembly kinetics determine the structure of keratin networks},
  journal = {Soft Matter},
  year    = {2012},
  volume  = {8},
  pages   = {8873--8879},
  doi     = {10.1039/C2SM26032H}
}

@article{Latorre2018ActiveSuperelasticity,
  author  = {Latorre, Eduardo and Kale, Sagar and Casares, Luis and G{\'o}mez-Gonz{\'a}lez, Mar{\'i}a and Uroz, Miguel and Valon, Laurent and Nair, Raghavan V. and Garreta, Elisa and Montserrat, Nuria and del Campo, Agust{\'i}n and others},
  title   = {Active superelasticity in three-dimensional epithelia of controlled shape},
  journal = {Nature},
  year    = {2018},
  volume  = {563},
  pages   = {203--208},
  doi     = {10.1038/s41586-018-0671-4}
}

@article{Duque2024RuptureStrengthMonolayers,
  author  = {Duque, Javier and Bonfanti, Andrea and Fouchard, J{\'e}r{\'e}my and Baldauf, Lukas and Azenha, S{\'e}rgio R. and Ferber, Eugen and Harris, Adam and Barriga, Eva H. and Kabla, Alexandre J. and Charras, Guillaume},
  title   = {Rupture strength of living cell monolayers},
  journal = {Nature Materials},
  year    = {2024},
  volume  = {23},
  pages   = {1563--1574},
  doi     = {10.1038/s41563-024-02027-3}
}

@article{Lim2020KeratinsAsymmetricInheritance,
  author  = {Lim, Harry Y. G. and Alvarez, Yann D. and Gasnier, Morgan and Wang, Ye and Tetlak, Paul and Bissiere, Sophie and Wang, Hao and Biro, Mat{\'e} and Plachta, Nicolas},
  title   = {Keratins are asymmetrically inherited fate determinants in the mammalian embryo},
  journal = {Nature},
  year    = {2020},
  volume  = {585},
  pages   = {404--409},
  doi     = {10.1038/s41586-020-2647-4}
}

@article{Nahaboo2022KeratinMembranesMouse,
  author  = {Nahaboo, Wahbi and Eski, Selma E. and Despin-Guitard, Emilie and Vermeersch, Marijn and Versaevel, Maxime and Saykali, Batoul and Monteyne, Delphine and Gabriele, Sylvain and Magin, Thomas M. and Schwarz, Nina and others},
  title   = {Keratin filaments mediate the expansion of extra-embryonic membranes in the post-gastrulation mouse embryo},
  journal = {The EMBO Journal},
  year    = {2022},
  volume  = {41},
  pages   = {e108747},
  doi     = {10.15252/embj.2021108747}
}

@article{Fuchs1995KeratinsSkin,
  author  = {Fuchs, Elaine},
  title   = {Keratins and the Skin},
  journal = {Annual Review of Cell and Developmental Biology},
  year    = {1995},
  volume  = {11},
  pages   = {123--154},
  doi     = {10.1146/annurev.cb.11.110195.001011}
}

@incollection{Homberg2014IRCMBBeyondExpectations,
  author    = {Homberg, Markus and Magin, Thomas M.},
  title     = {Beyond Expectations: Novel Insights into Epidermal Keratin Function and Regulation},
  booktitle = {International Review of Cell and Molecular Biology},
  editor    = {Jeon, Kwang W.},
  publisher = {Academic Press},
  year      = {2014},
  pages     = {265--306},
  doi       = {10.1016/B978-0-12-800179-0.00007-6}
}

@article{Pan2013ExpandingSignificanceKeratin,
  author  = {Pan, Xian and Hobbs, Robin P. and Coulombe, Pierre A.},
  title   = {The expanding significance of keratin intermediate filaments in normal and diseased epithelia},
  journal = {Current Opinion in Cell Biology},
  year    = {2013},
  volume  = {25},
  pages   = {47--56},
  doi     = {10.1016/j.ceb.2012.10.018}
}

@article{Ho2022KeratinGeneUpdate,
  author  = {Ho, Michael and Thompson, Beth and Fisk, Jeffrey N. and Nebert, Daniel W. and Bruford, Elspeth A. and Vasiliou, Vasilis and Bunick, Christopher G.},
  title   = {Update of the keratin gene family: evolution, tissue-specific expression patterns, and relevance to clinical disorders},
  journal = {Human Genomics},
  year    = {2022},
  volume  = {16},
  pages   = {1},
  doi     = {10.1186/s40246-021-00374-9}
}

@article{Farrell2018SingleCellTrajectoriesZfish,
  author  = {Farrell, Jacob A. and Wang, Yuanhao and Riesenfeld, Samantha J. and Shekhar, Karthik and Regev, Aviv and Schier, Alexander F.},
  title   = {Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis},
  journal = {Science},
  year    = {2018},
  volume  = {360},
  pages   = {eaar3131},
  doi     = {10.1126/science.aar3131}
}

@article{Pei2007MaternalFoxH1Zfish,
  author  = {Pei, Wei and Noushmehr, Houtan and Costa, Joaquim and Ouspenskaia, Maria V. and Elkahloun, Abbas G. and Feldman, Brian},
  title   = {An Early Requirement for Maternal FoxH1 during Zebrafish Gastrulation},
  journal = {Developmental Biology},
  year    = {2007},
  volume  = {310},
  pages   = {10--22},
  doi     = {10.1016/j.ydbio.2007.07.011}
}

@article{Sivaramakrishnan2009ShearStressKeratinPKCz,
  author  = {Sivaramakrishnan, Sundarapandiyan and Schneider, Joseph L. and Sitikov, Alexander and Goldman, Robert D. and Ridge, Karen M.},
  title   = {Shear stress induced reorganization of the keratin intermediate filament network requires phosphorylation by protein kinase C zeta},
  journal = {Molecular Biology of the Cell},
  year    = {2009},
  volume  = {20},
  pages   = {2755--2765},
  doi     = {10.1091/mbc.e08-10-1028}
}

@article{HernandezVega2017PolarizedCorticalTension,
  author  = {Hern{\'a}ndez{-}Vega, A. and Marsal, M. and Pouille, P. and Tosi, S. and Colombelli, J. and Luque, T. and Navajas, D. and Pagonabarraga, I. and Mart{\'i}n{-}Blanco, E.},
  title   = {Polarized cortical tension drives zebrafish epiboly movements},
  journal = {The EMBO Journal},
  year    = {2017},
  volume  = {36},
  pages   = {25--41},
  doi     = {10.15252/embj.201694264}
}

@article{Jayashankar2013PP1bZfishMyosinPhosphatase,
  author  = {Jayashankar, Varsha and Nguyen, Michael J. and Carr, Bethany W. and Zheng, Daniel C. and Rosales, Jose B. and Rosales, Jocelyn B. and Weiser, Daniel C.},
  title   = {Protein Phosphatase 1 \(\beta\) Paralogs Encode the Zebrafish Myosin Phosphatase Catalytic Subunit},
  journal = {PLoS ONE},
  year    = {2013},
  volume  = {8},
  pages   = {e75766},
  doi     = {10.1371/journal.pone.0075766}
}

@article{Chanet2017ActomyosinMechanosensingShape,
  author  = {Chanet, Sylvain and Miller, Christopher J. and Vaishnav, Evan D. and Ermentrout, Bard and Davidson, Lance A. and Martin, Adam C.},
  title   = {Actomyosin meshwork mechanosensing enables tissue shape to orient cell force},
  journal = {Nature Communications},
  year    = {2017},
  volume  = {8},
  pages   = {15014},
  doi     = {10.1038/ncomms15014}
}

@article{He2016FlowDependentMyosinRecruitment,
  author  = {He, Binyue and Martin, Adam and Wieschaus, Eric},
  title   = {Flow-dependent myosin recruitment during \textit{Drosophila} cellularization requires zygotic \textit{dunk} activity},
  journal = {Development},
  year    = {2016},
  volume  = {143},
  pages   = {2417--2430},
  doi     = {10.1242/dev.131334}
}

@article{Chang2014ActinPerturbationKeratinMSCs,
  author  = {Chang, T.-H. and Huang, H.-D. and Ong, W.-K. and Fu, Y.-J. and Lee, O. K. and Chien, S. and Ho, J. H.},
  title   = {The effects of actin cytoskeleton perturbation on keratin intermediate filament formation in mesenchymal stem/stromal cells},
  journal = {Biomaterials},
  year    = {2014},
  volume  = {35},
  pages   = {3934--3944},
  doi     = {10.1016/j.biomaterials.2014.01.028}
}

@article{Kolsch2009ActinDependentKeratinPrecursors,
  author  = {K{\"o}lsch, Annette and Windoffer, Reinhard and Leube, Rudolf E.},
  title   = {Actin-dependent dynamics of keratin filament precursors},
  journal = {Cell Motility and the Cytoskeleton},
  year    = {2009},
  volume  = {66},
  pages   = {976--985},
  doi     = {10.1002/cm.20395}
}

@article{Werner2004EBSMutationsKeratinDynamics,
  author  = {Werner, N. Sabine and Windoffer, Reinhard and Strnad, Peter and Grund, Christian and Leube, Rudolf E. and Magin, Thomas M.},
  title   = {Epidermolysis Bullosa Simplex-Type Mutations Alter the Dynamics of the Keratin Cytoskeleton and Reveal a Contribution of Actin to the Transport of Keratin Subunits},
  journal = {Molecular Biology of the Cell},
  year    = {2004},
  volume  = {15},
  pages   = {990--1002},
  doi     = {10.1091/mbc.E03-09-0687}
}

@article{Solon2009PulsedForcesRatchet,
  author  = {Solon, J. and Kaya-\c{C}opur, A. and Colombelli, J. and Brunner, D.},
  title   = {Pulsed Forces Timed by a Ratchet-like Mechanism Drive Directed Tissue Movement during Dorsal Closure},
  journal = {Cell},
  year    = {2009},
  volume  = {137},
  pages   = {1331--1342},
  doi     = {10.1016/j.cell.2009.03.050}
}

@article{Colombelli2013LaserNanosurgeryReview,
  author  = {Colombelli, Julien and Solon, Julia},
  title   = {Force communication in multicellular tissues addressed by laser nanosurgery},
  journal = {Cell and Tissue Research},
  year    = {2013},
  volume  = {352},
  pages   = {133--147},
  doi     = {10.1007/s00441-012-1445-1}
}

@article{Bi2016MotilityDrivenGlass,
  author  = {Bi, Dapeng and Yang, Xiang and Marchetti, M. Cristina and Manning, M. Lisa},
  title   = {Motility-Driven Glass and Jamming Transitions in Biological Tissues},
  journal = {Physical Review X},
  year    = {2016},
  volume  = {6},
  pages   = {021011},
  doi     = {10.1103/PhysRevX.6.021011}
}

@article{Farhadifar2007EpithelialPacking,
  author  = {Farhadifar, Reza and R{\"o}per, Jens{-}Christian and Aigouy, Benoit and Eaton, Suzanne and J{\"u}licher, Frank},
  title   = {The Influence of Cell Mechanics, Cell-Cell Interactions, and Proliferation on Epithelial Packing},
  journal = {Current Biology},
  year    = {2007},
  volume  = {17},
  pages   = {2095--2104},
  doi     = {10.1016/j.cub.2007.11.049}
}

@misc{YketaHenkesCellsGitHub,
  author = {Keta, Yassine{-}Eddine and Henkes, Silke},
  title  = {cells},
  howpublished = {\url{https://github.com/yketa/cells}},
  note   = {GitHub repository, MIT License}
}

@article{Wang2018Keratin6CollectiveMigration,
  author  = {Wang, Fang and Chen, Shun and Liu, Hong and Parent, Carine and Coulombe, Pierre},
  title   = {Keratin 6 regulates collective keratinocyte migration by altering cell–cell and cell–matrix adhesion},
  journal = {Journal of Cell Biology},
  year    = {2018},
  volume  = {217},
  pages   = {jcb.201712130},
  doi     = {10.1083/jcb.201712130}
}

@article{Nanes2024KeratinIsoformShifts,
  author  = {Nanes, Benjamin A. and Bhatt, Kunal and Boujemaa-Paterski, Radiah and Azarova, Ekaterina and Munawar, Saad and Rajendran, Deepa and Isogai, Tetsuya and Dean, Kevin M. and Medalia, Ohad and Danuser, Gaudenz},
  title   = {Keratin isoform shifts modulate motility signals during wound healing},
  journal = {bioRxiv},
  year    = {2024},
  doi     = {10.1101/2023.05.04.538989}
}

@article{Karsch2020KeratinNetworkIntegrity,
  author  = {Karsch, Sebastian and B{\"u}chau, Florian and Magin, Thomas M. and Janshoff, Andreas},
  title   = {An intact keratin network is crucial for mechanical integrity and barrier function in keratinocyte cell sheets},
  journal = {Cellular and Molecular Life Sciences},
  year    = {2020},
  volume  = {77},
  pages   = {4397--4411},
  doi     = {10.1007/s00018-019-03424-7}
}

@article{Lulevich2010SingleCellMechanicsKeratinocytes,
  author  = {Lulevich, Valentin and Yang, Hong and Isseroff, Rivkah and Liu, Gang-yu},
  title   = {Single cell mechanics of keratinocyte cells},
  journal = {Ultramicroscopy},
  year    = {2010},
  volume  = {110},
  pages   = {1435--1442},
  doi     = {10.1016/j.ultramic.2010.07.009}
}

@article{Wong2003K6WoundRepair,
  author  = {Wong, Ping and Coulombe, Pierre A.},
  title   = {Loss of keratin 6 (K6) proteins reveals a function for intermediate filaments during wound repair},
  journal = {Journal of Cell Biology},
  year    = {2003},
  volume  = {163},
  pages   = {327--337},
  doi     = {10.1083/jcb.200305032}
}

@article{Stenvall2021K8DeletionColon,
  author  = {Stenvall, Carl{-}Gustaf A. and Tayyab, Muhammad and Gr{\"o}nroos, Teemu J. and Ilom{\"a}ki, Miia A. and Viiri, Kirsi and Ridge, Karen M. and Polari, Leo and Toivola, Diana M.},
  title   = {Targeted deletion of keratin 8 in intestinal epithelial cells disrupts tissue integrity and predisposes to tumorigenesis in the colon},
  journal = {Cellular and Molecular Life Sciences},
  year    = {2021},
  volume  = {79},
  pages   = {10},
  doi     = {10.1007/s00018-021-04081-5}
}

@article{Deek2016MechanicsSoftKeratinNetworks,
  author  = {Deek, Joanna and Hecht, Florian and Rossetti, Livia and Wi{\ss}miller, Katharina and Bausch, Andreas R.},
  title   = {Mechanics of soft epithelial keratin networks depend on modular filament assembly kinetics},
  journal = {Acta Biomaterialia},
  year    = {2016},
  volume  = {43},
  pages   = {218--229},
  doi     = {10.1016/j.actbio.2016.07.010}
}

@article{Buchau2022DesmosomeHyperadhesionKeratin,
  author  = {B{\"u}chau, Florian and Vielmuth, Franziska and Waschke, Jens and Magin, Thomas M.},
  title   = {Bidirectional regulation of desmosome hyperadhesion by keratin isotypes and desmosomal components},
  journal = {Cellular and Molecular Life Sciences},
  year    = {2022},
  volume  = {79},
  pages   = {223},
  doi     = {10.1007/s00018-022-04244-y}
}

@incollection{Kowalczyk1998DesmosomesReview,
  author    = {Kowalczyk, Andrew P. and Bornslaeger, Elisabeth A. and Norvell, Staci M. and Palka, Heather L. and Green, Kathleen J.},
  title     = {Desmosomes: Intercellular Adhesive Junctions Specialized for Attachment of Intermediate Filaments},
  booktitle = {International Review of Cytology},
  editor    = {Jeon, Kwang W.},
  publisher = {Academic Press},
  year      = {1998},
  pages     = {237--302},
  doi       = {10.1016/S0074-7696(08)60153-9}
}

@article{Kim2012ModelingActinKeratinSpreading,
  author  = {Kim, Jin Sun and Lee, Chan{-}Ho and Su, Bryan Y. and Coulombe, Pierre A.},
  title   = {Mathematical Modeling of the Impact of Actin and Keratin Filaments on Keratinocyte Cell Spreading},
  journal = {Biophysical Journal},
  year    = {2012},
  volume  = {103},
  pages   = {1828--1838},
  doi     = {10.1016/j.bpj.2012.09.016}
}

@article{Bouameur2014PlakinsReview,
  author  = {Bouameur, Jean{-}Emmanuel and Favre, Beatrice and Borradori, Luca},
  title   = {Plakins, a Versatile Family of Cytolinkers: Roles in Skin Integrity and in Human Diseases},
  journal = {Journal of Investigative Dermatology},
  year    = {2014},
  volume  = {134},
  pages   = {885--894},
  doi     = {10.1038/jid.2013.498}
}

@article{Inaba2020KeratinsPlakinsMicroridges,
  author  = {Inaba, Yutaka and Chauhan, Vishakha and van Loon, A. Peter and Choudhury, Lokeshwar S. and Sagasti, Alvaro},
  title   = {Keratins and plakin family cytolinker proteins control the length of epithelial microridge protrusions},
  journal = {eLife},
  year    = {2020},
  volume  = {9},
  pages   = {e58149},
  doi     = {10.7554/eLife.58149}
}

@article{Weber2012CadherinKeratinMechano,
  author  = {Weber, Gregory F. and Bjerke, Margaret A. and DeSimone, Douglas W.},
  title   = {A Mechanoresponsive Cadherin-Keratin Complex Directs Polarized Protrusive Behavior and Collective Cell Migration},
  journal = {Developmental Cell},
  year    = {2012},
  volume  = {22},
  pages   = {104--115},
  doi     = {10.1016/j.devcel.2011.10.013}
}

@article{Herrmann2011IFHistoryInsects,
  author  = {Herrmann, Harald and Strelkov, Sergei V.},
  title   = {History and phylogeny of intermediate filaments: Now in insects},
  journal = {BMC Biology},
  year    = {2011},
  volume  = {9},
  pages   = {16},
  doi     = {10.1186/1741-7007-9-16}
}

@article{Jain2020FluidizationGapClosureInsect,
  author  = {Jain, Akanksha and Ulman, Vladim{\'\i}r and Mukherjee, Arghyadip and Prakash, Manoj and Cuenca, Marco B. and Pimpale, Leena G. and M{\"u}nster, S{\"o}ren and Haase, Rainer and Panfilio, Kristen A. and Jug, Florian and others},
  title   = {Regionalized tissue fluidization is required for epithelial gap closure during insect gastrulation},
  journal = {Nature Communications},
  year    = {2020},
  volume  = {11},
  pages   = {5604},
  doi     = {10.1038/s41467-020-19356-x}
}

@book{Westerfield2007ZebrafishBook,
  author    = {Westerfield, Monte},
  title     = {The Zebrafish Book: A Guide for the Laboratory Use of Zebrafish (\textit{Danio rerio})},
  year      = {2007},
  publisher = {University of Oregon Press}
}

@article{McCurley2008HousekeepingGenesZfish,
  author  = {McCurley, Amy T. and Callard, Glenn V.},
  title   = {Characterization of housekeeping genes in zebrafish: male-female differences and effects of tissue type, developmental stage and chemical treatment},
  journal = {BMC Molecular Biology},
  year    = {2008},
  volume  = {9},
  pages   = {102},
  doi     = {10.1186/1471-2199-9-102}
}

@article{Zhang2020MaternalZygoticMutantsZfish,
  author  = {Zhang, Fan and Li, Xiaojie and He, Ming and Ye, Dong and Xiong, Fang and Amin, Gulam and Zhu, Zhu and Sun, Yong},
  title   = {Efficient generation of zebrafish maternal-zygotic mutants through transplantation of ectopically induced and Cas9/gRNA targeted primordial germ cells},
  journal = {Journal of Genetics and Genomics},
  year    = {2020},
  volume  = {47},
  pages   = {37--47},
  doi     = {10.1016/j.jgg.2019.12.004}
}

@article{Pachitariu2022Cellpose2,
  author  = {Pachitariu, Marius and Stringer, Carsen},
  title   = {Cellpose 2.0: how to train your own model},
  journal = {Nature Methods},
  year    = {2022},
  volume  = {19},
  pages   = {1634--1641},
  doi     = {10.1038/s41592-022-01663-4}
}

@article{Stringer2021Cellpose,
  author  = {Stringer, Carsen and Wang, Tim and Michaelos, Michalis and Pachitariu, Marius},
  title   = {Cellpose: a generalist algorithm for cellular segmentation},
  journal = {Nature Methods},
  year    = {2021},
  volume  = {18},
  pages   = {100--106},
  doi     = {10.1038/s41592-020-01018-x}
}

@incollection{Biro2015DualPipetteAspiration,
  author    = {Bir{\'o}, Mat{\'e} and Ma{\^\i}tre, Jean{-}L{\'e}on},
  title     = {Dual pipette aspiration: A unique tool for studying intercellular adhesion},
  booktitle = {Methods in Cell Biology: Biophysical Methods in Cell Biology},
  editor    = {Paluch, Ewa K.},
  publisher = {Academic Press},
  year      = {2015},
  volume    = {125},
  pages     = {255--267},
  doi       = {10.1016/bs.mcb.2014.10.007}
}

@article{Guevorkian2010AspirationViscoelasticDrops,
  author  = {Guevorkian, Karine and Colbert, Marc{-}J. and Durth, Martine and Dufour, S{\'e}verine and Brochard{-}Wyart, Fran{\c c}oise},
  title   = {Aspiration of Biological Viscoelastic Drops},
  journal = {Physical Review Letters},
  year    = {2010},
  volume  = {104},
  pages   = {218101},
  doi     = {10.1103/PhysRevLett.104.218101}
}

@incollection{Guevorkian2017MicropipetteAspirationInVivo,
  author    = {Guevorkian, Karine and Ma{\^\i}tre, Jean{-}L{\'e}on},
  title     = {Micropipette aspiration: A unique tool for exploring cell and tissue mechanics in vivo},
  booktitle = {Methods in Cell Biology: Cell Polarity and Morphogenesis},
  editor    = {Lecuit, Thomas},
  publisher = {Academic Press},
  year      = {2017},
  volume    = {139},
  pages     = {187--201},
  doi       = {10.1016/bs.mcb.2016.11.012}
}

@misc{Thielicke2021PIVlabMATLAB,
  author = {Thielicke, William and Sonntag, Rainer},
  title  = {Particle Image Velocimetry for MATLAB: Accuracy and enhanced algorithms in PIVlab},
  year   = {2021},
  note   = {Software methods paper; details as provided by authors}
}

@article{Saha2016CellCortexProperties,
  author  = {Saha, Arnab and Nishikawa, Masashi and Behrndt, Martin and Heisenberg, Carl{-}Philipp and J{\"u}licher, Frank and Grill, Stephan W.},
  title   = {Determining Physical Properties of the Cell Cortex},
  journal = {Biophysical Journal},
  year    = {2016},
  volume  = {110},
  pages   = {1421--1429},
  doi     = {10.1016/j.bpj.2016.02.013}
}


@article{eldiranyRecentInsightIntermediate2021,
  title = {Recent Insight into Intermediate Filament Structure},
  author = {Eldirany, Sherif A. and Lomakin, Ivan B. and Ho, Minh and Bunick, Christopher G.},
  year = {2021},
  month = feb,
  journal = {Current Opinion in Cell Biology},
  volume = {68},
  pages = {132--143},
  issn = {0955-0674},
  doi = {10.1016/j.ceb.2020.10.001},
  urldate = {2020-12-18},
  abstract = {Intermediate filaments (IFs) are key players in multiple cellular processes throughout human tissues. Their biochemical and structural properties are important for understanding filament assembly mechanisms, for interactions between IFs and binding partners, and for developing pharmacological agents that target IFs. IF proteins share a conserved coiled-coil central-rod domain flanked by variable N-terminal `head' and C-terminal `tail' domains. There have been several recent advances in our understanding of IF structure from the study of keratins, glial fibrillary acidic protein, and lamin. These include discoveries of~(i) a knob--pocket tetramer assembly mechanism in coil 1B; (ii) a lamin-specific coil 1B insert providing a one-half superhelix turn; (iii) helical, yet flexible, linkers within the rod domain; and (iv) the identification of coil 2B residues required for mature filament assembly. Furthermore, the head and tail domains of some IFs contain low-complexity aromatic-rich kinked segments, and structures of IFs with binding partners show electrostatic surfaces are a major contributor to complex formation. These new data advance the connection between IF structure, pathologic mutations, and clinical diseases in humans.},
  langid = {english},
  keywords = {Assembly,Binding,Crystallography,Intermediate filament,Keratin,Lamin,Review,Structure,Vimentin},
  file = {/Users/snaik/Zotero/storage/E9DYBRT8/Eldirany et al_2021_Recent insight into intermediate filament structure.pdf;/Users/snaik/Zotero/storage/PWYNJ6J3/S0955067420301368.html}
}
@article{conlon1999SizeControlAnimal,
  title = {Size {{Control}} in {{Animal Development}}},
  author = {Conlon, Ian and Raff, Martin},
  year = {1999},
  month = jan,
  journal = {Cell},
  volume = {96},
  number = {2},
  pages = {235--244},
  publisher = {Elsevier},
  issn = {0092-8674, 1097-4172},
  doi = {10.1016/S0092-8674(00)80563-2},
  urldate = {2025-05-25},
  langid = {english},
  pmid = {9988218},
  file = {/Users/snaik/Zotero/storage/85YVGH6D/Conlon and Raff - 1999 - Size Control in Animal Development.pdf}
}
@article{horejs2014Biologicallyactivelaminin111fragment,
  title = {Biologically-Active Laminin-111 Fragment That Modulates the Epithelial-to-Mesenchymal Transition in Embryonic Stem Cells},
  author = {Horejs, Christine-Maria and Serio, Andrea and Purvis, Alan and Gormley, Adam J. and Bertazzo, Sergio and Poliniewicz, Anna and Wang, Alex J. and DiMaggio, Peter and Hohenester, Erhard and Stevens, Molly M.},
  year = {2014},
  month = apr,
  journal = {Proceedings of the National Academy of Sciences},
  volume = {111},
  number = {16},
  pages = {5908--5913},
  publisher = {Proceedings of the National Academy of Sciences},
  doi = {10.1073/pnas.1403139111},
  urldate = {2025-05-29},
  abstract = {The dynamic interplay between the extracellular matrix and embryonic stem cells (ESCs) constitutes one of the key steps in understanding stem cell differentiation in vitro. Here we report a biologically-active laminin-111 fragment generated by matrix metalloproteinase 2 (MMP2) processing, which is highly up-regulated during differentiation. We show that the {$\beta$}1-chain--derived fragment interacts via {$\alpha$}3{$\beta$}1-integrins, thereby triggering the down-regulation of MMP2 in mouse and human ESCs. Additionally, the expression of MMP9 and E-cadherin is up-regulated in mouse ESCs---key players in the epithelial-to-mesenchymal transition. We also demonstrate that the fragment acts through the {$\alpha$}3{$\beta$}1-integrin/extracellular matrix metalloproteinase inducer complex. This study reveals a previously unidentified role of laminin-111 in early stem cell differentiation that goes far beyond basement membrane assembly and a mechanism by which an MMP2-cleaved laminin fragment regulates the expression of E-cadherin, MMP2, and MMP9.},
  file = {/Users/snaik/Zotero/storage/YWCKS9CA/Horejs et al. - 2014 - Biologically-active laminin-111 fragment that modulates the epithelial-to-mesenchymal transition in.pdf}
}
@article{hartsock2008AdherensTightJunctions,
  title = {Adherens and {{Tight Junctions}}: {{Structure}}, {{Function}} and {{Connections}} to the {{Actin Cytoskeleton}}},
  shorttitle = {Adherens and {{Tight Junctions}}},
  author = {Hartsock, Andrea and Nelson, W. James},
  year = {2008},
  month = mar,
  journal = {Biochimica et biophysica acta},
  volume = {1778},
  number = {3},
  pages = {660--669},
  issn = {0006-3002},
  doi = {10.1016/j.bbamem.2007.07.012},
  urldate = {2025-05-29},
  abstract = {Adherens juctions and Tight junctions comprise two modes of cell-cell adhesion that provide different functions. Both junctional complexes are proposed to associate with the actin cytoskeleton, and formation and maturation of cell-cell contacts involves reorganization of the actin cytoskeleton. Adherens junctions initiate cell-cell contacts, and mediate the maturation and maintenance of the contact. Adherens junctions consist of the transmembrane protein E-cadherin, and intracellular components, p120-catenin, {$\beta$}-catenin and {$\alpha$}-catenin. Tight junctions regulate the paracellular pathway for the movement of ions and solutes in-between cells. Tight junctions consist of the transmembrane proteins occludin and claudin, and the cytoplasmic scaffolding proteins ZO-1,-2, and -3. This review discusses the binding interactions of the most studied proteins that occur within each of these two junctional complexes and possible modes of regulation of these interactions, and the different mechanisms that connect and regulate interactions with the actin cytoskeleton.},
  pmcid = {PMC2682436},
  pmid = {17854762},
  file = {/Users/snaik/Zotero/storage/FHWQULWN/Hartsock and Nelson - 2008 - Adherens and Tight Junctions Structure, Function and Connections to the Actin Cytoskeleton.pdf}
}
@article{manning2010Coactionintercellularadhesion,
  title = {Coaction of Intercellular Adhesion and Cortical Tension Specifies Tissue Surface Tension},
  author = {Manning, M. Lisa and Foty, Ramsey A. and Steinberg, Malcolm S. and Schoetz, Eva-Maria},
  year = {2010},
  month = jul,
  journal = {Proceedings of the National Academy of Sciences},
  volume = {107},
  number = {28},
  pages = {12517--12522},
  publisher = {Proceedings of the National Academy of Sciences},
  doi = {10.1073/pnas.1003743107},
  urldate = {2025-05-30},
  abstract = {In the course of animal morphogenesis, large-scale cell movements occur, which involve the rearrangement, mutual spreading, and compartmentalization of cell populations in specific configurations. Morphogenetic cell rearrangements such as cell sorting and mutual tissue spreading have been compared with the behaviors of immiscible liquids, which they closely resemble. Based on this similarity, it has been proposed that tissues behave as liquids and possess a characteristic surface tension, which arises as a collective, macroscopic property of groups of mobile, cohering cells. But how are tissue surface tensions generated? Different theories have been proposed to explain how mesoscopic cell properties such as cell--cell adhesion and contractility of cell interfaces may underlie tissue surface tensions. Although recent work suggests that both may be contributors, an explicit model for the dependence of tissue surface tension on these mesoscopic parameters has been missing. Here we show explicitly that the ratio of adhesion to cortical tension determines tissue surface tension. Our minimal model successfully explains the available experimental data and makes predictions, based on the feedback between mechanical energy and geometry, about the shapes of aggregate surface cells, which we verify experimentally. This model indicates that there is a crossover from adhesion dominated to cortical-tension dominated behavior as a function of the ratio between these two quantities.},
  file = {/Users/snaik/Zotero/storage/DUU2GNVP/Manning et al. - 2010 - Coaction of intercellular adhesion and cortical tension specifies tissue surface tension.pdf}
}
@article{olson2022ActinMyosinCytoskeletonRegulation,
  title = {Actin-{{Myosin Cytoskeleton Regulation}} and {{Function}}},
  author = {Olson, Michael F.},
  year = {2022},
  month = dec,
  journal = {Cells},
  volume = {12},
  number = {1},
  pages = {9},
  issn = {2073-4409},
  doi = {10.3390/cells12010009},
  urldate = {2025-05-31},
  pmcid = {PMC9818783},
  pmid = {36611802},
  file = {/Users/snaik/Zotero/storage/4VSYYYV6/Olson - 2022 - Actin-Myosin Cytoskeleton Regulation and Function.pdf}
}
@article{yang2010InhibitionCellMigration,
  title = {Inhibition of {{Cell Migration}} and {{Cell Division Correlates}} with {{Distinct Effects}} of {{Microtubule Inhibiting Drugs}}},
  author = {Yang, Hailing and Ganguly, Anutosh and Cabral, Fernando},
  year = {2010},
  month = oct,
  journal = {The Journal of Biological Chemistry},
  volume = {285},
  number = {42},
  pages = {32242--32250},
  issn = {0021-9258},
  doi = {10.1074/jbc.M110.160820},
  urldate = {2025-05-31},
  abstract = {Drugs that target microtubules are thought to inhibit cell division and cell migration by suppressing dynamic instability, a ``search and capture'' behavior that allows microtubules to probe their environment. Here, we report that subtoxic drug concentrations are sufficient to inhibit plus-end microtubule dynamic instability and cell migration without affecting cell division or microtubule assembly. The higher drug concentrations needed to inhibit cell division act through a novel mechanism that generates microtubule fragments by stimulating microtubule minus-end detachment from their organizing centers. The frequency of microtubule detachment in untreated cells increases at prophase suggesting that it is a regulated cellular process important for spindle assembly and function. We conclude that drugs produce differential dose-dependent effects at microtubule plus and minus-ends to inhibit different microtubule-mediated functions.},
  pmcid = {PMC2952225},
  pmid = {20696757}
}
@article{janshoff2021viscoelastic,
  title={Viscoelastic properties of epithelial cells},
  author={Janshoff, Andreas},
  journal={Biochemical society transactions},
  volume={49},
  number={6},
  pages={2687--2695},
  year={2021},
  publisher={Portland Press Ltd.}
}
@article{carmona2023TubulinPostTranslationalModifications,
  title = {Tubulin {{Post-Translational Modifications}}: {{The Elusive Roles}} of {{Acetylation}}},
  shorttitle = {Tubulin {{Post-Translational Modifications}}},
  author = {Carmona, Bruno and Marinho, H. Susana and Matos, Catarina Lopes and Nolasco, Sofia and Soares, Helena},
  year = {2023},
  month = apr,
  journal = {Biology},
  volume = {12},
  number = {4},
  pages = {561},
  issn = {2079-7737},
  doi = {10.3390/biology12040561},
  urldate = {2025-05-31},
  abstract = {Simple Summary Microtubules (MTs) are dynamic structures that compose part of the cell cytoskeleton. They play important roles in various cellular functions, such as intracellular transport, cell division, and cell movement. MTs are made up of {$\alpha$}/{$\beta$}-tubulin heterodimers that present a diversity due to the existence of different isotypes and post-translational modifications (PTMs). One specific PTM, tubulin-acetylation, occurs inside the MT lumen and has been found to enhance MT flexibility and prevent structural damage. This PTM is also associated with cellular responses to stress and various human pathologies. The regulation of enzymes involved in tubulin acetylation and deacetylation is important for maintaining proper cell physiology. While the role of tubulin-acetylation in MT stability remains debatable, it is clear that PTMs contribute to the unique biochemical and biophysical properties of MTs, creating a code that allows for cellular responses to different environmental cues. Abstract Microtubules (MTs), dynamic polymers of {$\alpha$}/{$\beta$}-tubulin heterodimers found in all eukaryotes, are involved in cytoplasm spatial organization, intracellular transport, cell polarity, migration and division, and in cilia biology. MTs functional diversity depends on the differential expression of distinct tubulin isotypes and is amplified by a vast number of different post-translational modifications (PTMs). The addition/removal of PTMs to {$\alpha$}- or {$\beta$}-tubulins is catalyzed by specific enzymes and allows combinatory patterns largely enriching the distinct biochemical and biophysical properties of MTs, creating a code read by distinct proteins, including microtubule-associated proteins (MAPs), which allow cellular responses. This review is focused on tubulin-acetylation, whose cellular roles continue to generate debate. We travel through the experimental data pointing to {$\alpha$}-tubulin Lys40 acetylation role as being a MT stabilizer and a typical PTM of long lived MTs, to the most recent data, suggesting that Lys40 acetylation enhances MT flexibility and alters the mechanical properties of MTs, preventing MTs from mechanical aging characterized by structural damage. Additionally, we discuss the regulation of tubulin acetyltransferases/desacetylases and their impacts on cell physiology. Finally, we analyze how changes in MT acetylation levels have been found to be a general response to stress and how they are associated with several human pathologies.},
  pmcid = {PMC10136095},
  pmid = {37106761},
  file = {/Users/snaik/Zotero/storage/M9STHCS2/Carmona et al. - 2023 - Tubulin Post-Translational Modifications The Elusive Roles of Acetylation.pdf}
}

@article{laevsky2003Crosslinkingactinfilaments,
  title = {Cross-Linking of Actin Filaments by Myosin {{II}} Is a Major Contributor to Cortical Integrity and Cell Motility in Restrictive Environments},
  author = {Laevsky, Gary and Knecht, David A.},
  year = {2003},
  month = sep,
  journal = {Journal of Cell Science},
  volume = {116},
  number = {Pt 18},
  pages = {3761--3770},
  issn = {0021-9533},
  doi = {10.1242/jcs.00684},
  abstract = {Cells are frequently required to move in a local environment that physically restricts locomotion, such as during extravasation or metastatic invasion. In order to model these events, we have developed an assay in which vegetative Dictyostelium amoebae undergo chemotaxis under a layer of agarose toward a source of folic acid [Laevsky, G. and Knecht, D. A. (2001). Biotechniques 31, 1140-1149]. As the concentration of agarose is increased from 0.5\% to 3\% the cells are increasingly inhibited in their ability to move under the agarose. The contribution of myosin II and actin cross-linking proteins to the movement of cells in this restrictive environment has now been examined. Cells lacking myosin II heavy chain (mhcA-) are unable to migrate under agarose overlays of greater than 0.5\%, and even at this concentration they move only a short distance from the trough. While attempting to move, the cells become stretched and fragmented due to their inability to retract their uropods. At higher agarose concentrations, the mhcA- cells protrude pseudopods under the agarose, but are unable to pull the cell body underneath. Consistent with a role for myosin II in general cortical stability, GFP-myosin dynamically localizes to the lateral and posterior cortex of cells moving under agarose. Cells lacking the essential light chain of myosin II (mlcE-), have no measurable myosin II motor activity, yet were able to move normally under all agarose concentrations. Mutants lacking either ABP-120 or alpha-actinin were also able to move under agarose at rates similar to wild-type cells. We hypothesize that myosin stabilizes the actin cortex through its cross-linking activity rather than its motor function and this activity is necessary and sufficient for the maintenance of cortical integrity of cells undergoing movement in a restrictive environment. The actin cross-linkers alpha-actinin and ABP-120 do not appear to play as major a role as myosin II in providing this cortical integrity.},
  langid = {english},
  pmid = {12890752},
  keywords = {Actin Cytoskeleton,Actinin,Animals,Carrier Proteins,Cell Movement,Chemotaxis,Cross-Linking Reagents,Dictyostelium,Green Fluorescent Proteins,Luminescent Proteins,Microfilament Proteins,Mutation,Myosin Light Chains,Myosin Type II,Recombinant Fusion Proteins,Sepharose}
}

@article{kowalczyk2013StructureFunctionRegulation,
  title = {Structure, {{Function}} and {{Regulation}} of {{Desmosomes}}},
  author = {Kowalczyk, Andrew P. and Green, Kathleen J.},
  year = {2013},
  journal = {Progress in molecular biology and translational science},
  volume = {116},
  pages = {95--118},
  issn = {1877-1173},
  doi = {10.1016/B978-0-12-394311-8.00005-4},
  urldate = {2025-05-29},
  abstract = {Desmosomes are adhesive intercellular junctions that mechanically integrate adjacent cells by coupling adhesive interactions mediated by desmosomal cadherins to the intermediate filament cytoskeletal network. Desmosomal cadherins are connected to intermediate filaments by densely clustered cytoplasmic plaque proteins comprising members of the armadillo gene family, including plakoglobin and plakophilins, and members of the plakin family of cytolinkers, such as desmoplakin. The importance of desmosomes in tissue integrity is highlighted by human diseases caused by mutations in desmosomal genes, autoantibody attack of desmosomal cadherins, and bacterial toxins that selectively target desmosomal cadherins. In addition to reviewing the well-known roles of desmosomal proteins in tissue integrity, this chapter also highlights the growing appreciation for how desmosomal proteins are integrated with cell signaling pathways to contribute to vertebrate tissue organization and differentiation.},
  pmcid = {PMC4336551},
  pmid = {23481192},
  file = {/Users/snaik/Zotero/storage/UICD53KK/Kowalczyk and Green - 2013 - Structure, Function and Regulation of Desmosomes.pdf}
}

@article{balachandra2022NucleartoCytoplasmicRatioCoupling,
  title = {The {{Nuclear-to-Cytoplasmic Ratio}}: {{Coupling DNA Content}} to {{Cell Size}}, {{Cell Cycle}}, and {{Biosynthetic Capacity}}},
  shorttitle = {The {{Nuclear-to-Cytoplasmic Ratio}}},
  author = {Balachandra, Shruthi and Sarkar, Sharanya and Amodeo, Amanda A.},
  year = {2022},
  month = nov,
  journal = {Annual Review of Genetics},
  volume = {56},
  number = {1},
  pages = {165--185},
  issn = {0066-4197, 1545-2948},
  doi = {10.1146/annurev-genet-080320-030537},
  urldate = {2025-05-25},
  abstract = {Though cell size varies between different cells and across species, the nuclear-to-cytoplasmic (N/C) ratio is largely maintained across species and within cell types. A cell maintains a relatively constant N/C ratio by coupling DNA content, nuclear size, and cell size. We explore how cells couple cell division and growth to DNA content. In some cases, cells use DNA as a molecular yardstick to control the availability of cell cycle regulators. In other cases, DNA sets a limit for biosynthetic capacity. Developmentally programmed variations in the N/C ratio for a given cell type suggest that a specific N/C ratio is required to respond to given physiological demands. Recent observations connecting decreased N/C ratios with cellular senescence indicate that maintaining the proper N/C ratio is essential for proper cellular functioning. Together, these findings suggest a causative, not simply correlative, role for the N/C ratio in regulating cell growth and cell cycle progression.},
  langid = {english},
  file = {/Users/snaik/Zotero/storage/CDXZIBXK/Balachandra et al. - 2022 - The Nuclear-to-Cytoplasmic Ratio Coupling DNA Content to Cell Size, Cell Cycle, and Biosynthetic Ca.pdf}
}

 @article{herrmann2016IntermediateFilamentsStructure,
  title = {Intermediate {{Filaments}}: {{Structure}} and {{Assembly}}},
  author = {Herrmann, Harald and Aebi, Ueli},
  year = {2016},
  month = nov,
  journal = {Cold Spring Harbor Perspectives in Biology},
  volume = {8},
  number = {11},
  publisher = {Cold Spring Harbor Laboratory Press},
  issn = {19430264},
  doi = {10.1101/CSHPERSPECT.A018242},
  urldate = {2023-02-13},
  abstract = {Proteins of the intermediate filament (IF) supergene family are ubiquitous structural components that comprise, in a cell type-specific manner, the cytoskeleton proper in animal tissues. All IF proteins show a distinctly organized, extended {$\alpha$}-helical conformation prone to form two-stranded coiled coils, which are the basic building blocks of these highly flexible, stressresistant cytoskeletal filaments. IF proteins are highly charged, thus representing versatile polyampholytes with multiple functions. Taking vimentin, keratins, and the nuclear lamins as our prime examples, we present an overview of their molecular and structural parameters. These, in turn, document the ability of IF proteins to form distinct, highly diverse supramolecular assemblies and biomaterials found, for example, at the inner nuclear membrane, throughout the cytoplasm, and in highly complex extracellular appendages, such as hair and nails, of vertebrate organisms. Ultimately, our aim is to set the stage for a more rational understanding of the immediate effects that missense mutations in IF genes have on cellular functions and for their far-reaching impact on the development of the numerous IF diseases caused by them.},
  pmid = {27803112},
  file = {/Users/snaik/Zotero/storage/TI2TRS6B/full-text.pdf}
}

@article{spemann1938embryonic,
  title={Embryonic development and induction New Haven Yale Univ},
  author={Spemann, H},
  journal={Press (ed)},
  pages={371--372},
  year={1938}
}
@article{teng2011apoptotic,
  title={Apoptotic force: active mechanical function of cell death during morphogenesis},
  author={Teng, Xiang and Toyama, Yusuke},
  journal={Development, growth \& differentiation},
  volume={53},
  number={2},
  pages={269--276},
  year={2011},
  publisher={Wiley Online Library}
}
@article{fristrom1988,
  title={The cellular basis of epithelial morphogenesis. A review},
  author={Fristrom, Dianne},
  journal={Tissue and Cell},
  volume={20},
  number={5},
  pages={645--690},
  year={1988},
  publisher={Elsevier}
}
@article{rosenblatt2001epithelial,
  title={An epithelial cell destined for apoptosis signals its neighbors to extrude it by an actin-and myosin-dependent mechanism},
  author={Rosenblatt, Jody and Raff, Martin C and Cramer, Louise P},
  journal={Current biology},
  volume={11},
  number={23},
  pages={1847--1857},
  year={2001},
  publisher={Elsevier}
}
@article{gu2011epithelial,
  title={Epithelial cell extrusion requires the sphingosine-1-phosphate receptor 2 pathway},
  author={Gu, Yapeng and Forostyan, Tetyana and Sabbadini, Roger and Rosenblatt, Jody},
  journal={Journal of Cell Biology},
  volume={193},
  number={4},
  pages={667--676},
  year={2011},
  publisher={The Rockefeller University Press}
}
@article{van2008cell,
  title={The cell-cell adhesion molecule E-cadherin},
  author={Van Roy, Frans and Berx, Geert},
  journal={Cellular and molecular life sciences},
  volume={65},
  pages={3756--3788},
  year={2008},
  publisher={Springer}
}
@book{hay2013cell,
  title={Cell biology of extracellular matrix},
  author={Hay, Elizabeth D},
  year={2013},
  publisher={Springer Science \& Business Media}
}
@article{gumbiner1996cell,
  title={Cell adhesion: the molecular basis of tissue architecture and morphogenesis},
  author={Gumbiner, Barry M},
  journal={Cell},
  volume={84},
  number={3},
  pages={345--357},
  year={1996},
  publisher={Elsevier}
}
@article{pei2007early,
  title={An early requirement for maternal FoxH1 during zebrafish gastrulation},
  author={Pei, Wuhong and Noushmehr, Houtan and Costa, Justin and Ouspenskaia, Maia V and Elkahloun, Abdel G and Feldman, Benjamin},
  journal={Developmental biology},
  volume={310},
  number={1},
  pages={10--22},
  year={2007},
  publisher={Elsevier}
}
@article{heisenberg2013forces,
  title={Forces in tissue morphogenesis and patterning},
  author={Heisenberg, Carl-Philipp and Bella{\"\i}che, Yohanns},
  journal={Cell},
  volume={153},
  number={5},
  pages={948--962},
  year={2013},
  publisher={Elsevier}
}
@article{demoulin2014power,
  title={Power transduction of actin filaments ratcheting in vitro against a load},
  author={D{\'e}moulin, Damien and Carlier, Marie-France and Bibette, J{\'e}r{\^o}me and Baudry, Jean},
  journal={Proceedings of the National Academy of Sciences},
  volume={111},
  number={50},
  pages={17845--17850},
  year={2014},
  publisher={National Academy of Sciences}
}
@article{blanchoin2014actin,
  title={Actin dynamics, architecture, and mechanics in cell motility},
  author={Blanchoin, Laurent and Boujemaa-Paterski, Rajaa and Sykes, C{\'e}cile and Plastino, Julie},
  journal={Physiological reviews},
  volume={94},
  number={1},
  pages={235--263},
  year={2014},
  publisher={American Physiological Society Bethesda, MD}
}
@article{schwayer2016actin,
  title={Actin rings of power},
  author={Schwayer, Cornelia and Sikora, Mateusz and Slov{\'a}kov{\'a}, Jana and Kardos, Roland and Heisenberg, Carl-Philipp},
  journal={Developmental cell},
  volume={37},
  number={6},
  pages={493--506},
  year={2016},
  publisher={Elsevier}
}
@article{svitkina2020actin,
  title={Actin cell cortex: structure and molecular organization},
  author={Svitkina, Tatyana M},
  journal={Trends in cell biology},
  volume={30},
  number={7},
  pages={556--565},
  year={2020},
  publisher={Elsevier}
}
@article{westerfield2007zebrafish,
  title={The Zebrafish Book; A guide for the laboratory use of zebrafish (Danio rerio)},
  author={Westerfield, Monte},
  journal={(No Title)},
  year={2007}
}
@article{hopyan2011budding,
  title={Budding behaviors: Growth of the limb as a model of morphogenesis},
  author={Hopyan, Sevan and Sharpe, James and Yang, Yingzi},
  journal={Developmental Dynamics},
  volume={240},
  number={5},
  pages={1054--1062},
  year={2011},
  publisher={Wiley Online Library}
}
@misc{thomson1917growth,
  title={On growth and form},
  author={Thomson, J Arthur},
  year={1917},
  publisher={Nature Publishing Group UK London}
}

@article{kreplakExploringMechanicalBehavior2005,
	title = {Exploring the {Mechanical} {Behavior} of {Single} {Intermediate} {Filaments}},
	volume = {354},
	issn = {0022-2836},
	url = {https://www.sciencedirect.com/science/article/pii/S0022283605012088},
	doi = {10.1016/j.jmb.2005.09.092},
	abstract = {Intermediate filaments (IFs) are structural elements of eukaryotic cells with distinct mechanical properties. Tissue integrity is severely impaired, in particular in skin and muscle, when IFs are either absent or malfunctioning due to mutations. Our knowledge on the mechanical properties of IFs is mainly based on tensile testing of macroscopic fibers and on the rheology of IF networks. At the single filament level, the only piece of data available is a measure of the persistence length of vimentin IFs. Here, we have employed an atomic force microscopy (AFM) based protocol to directly probe the mechanical properties of single cytoplasmic IFs when adsorbed to a solid support in physiological buffer environment. Three IF types were studied in vitro: recombinant murine desmin, recombinant human keratin K5/K14 and neurofilaments isolated from rat brains, which are composed of the neurofilament triplet proteins NF-L, NF-M and NF-H. Depending on the experimental conditions, the AFM tip was used to laterally displace or to stretch single IFs on the support they had been adsorbed to. Upon applying force, IFs were stretched on average 2.6-fold. The maximum stretching that we encountered was 3.6-fold. A large reduction of the apparent filament diameter was observed concomitantly. The observed mechanical properties therefore suggest that IFs may indeed function as mechanical shock absorbers in vivo.},
	number = {3},
	urldate = {2025-04-13},
	journal = {Journal of Molecular Biology},
	author = {Kreplak, L. and Bär, H. and Leterrier, J. F. and Herrmann, H. and Aebi, U.},
	month = dec,
	year = {2005},
	keywords = {AFM, desmin, keratin, neurofilament, stretching},
	pages = {569--577},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\Suyash\\Zotero\\storage\\D4KVU8HQ\\Kreplak et al. - 2005 - Exploring the Mechanical Behavior of Single Intermediate Filaments.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Suyash\\Zotero\\storage\\29P2PLRG\\S0022283605012088.html:text/html},
}

@article{stenvallCytoplasmicKeratinsCouple2022,
	title = {Cytoplasmic keratins couple with and maintain nuclear envelope integrity in colonic epithelial cells},
	volume = {33},
	issn = {1059-1524},
	url = {https://www.molbiolcell.org/doi/10.1091/mbc.E20-06-0387},
	doi = {10.1091/mbc.E20-06-0387},
	abstract = {Keratin intermediate filaments convey mechanical stability and protection against stress to epithelial cells. Keratins are essential for colon health, as seen in keratin 8 knockout (K8−/−) mice exhibiting a colitis phenotype. We hypothesized that keratins support the nuclear envelope and lamina in colonocytes. K8−/− colonocytes in vivo exhibit significantly decreased levels of lamins A/C, B1, and B2 in a colon-specific and cell-intrinsic manner. CRISPR/Cas9- or siRNA-mediated K8 knockdown in Caco-2 cells similarly decreased lamin levels, which recovered after reexpression of K8 following siRNA treatment. Nuclear area was not decreased, and roundness was only marginally increased in cells without K8. Down-regulation of K8 in adult K8flox/flox;Villin-CreERt2 mice following tamoxifen administration significantly decreased lamin levels at day 4 when K8 levels had reduced to 40\%. K8 loss also led to reduced levels of plectin, LINC complex, and lamin-associated proteins. While keratins were not seen in the nucleoplasm without or with leptomycin B treatment, keratins were found intimately located at the nuclear envelope and complexed with SUN2 and lamin A. Furthermore, K8 loss in Caco-2 cells compromised nuclear membrane integrity basally and after shear stress. In conclusion, colonocyte K8 helps maintain nuclear envelope and lamina composition and contributes to nuclear integrity.},
	number = {13},
	urldate = {2025-04-14},
	journal = {Molecular Biology of the Cell},
	author = {Stenvall, Carl-Gustaf A. and Nyström, Joel H. and Butler-Hallissey, Ciarán and Jansson, Theresia and Heikkilä, Taina R. H. and Adam, Stephen A. and Foisner, Roland and Goldman, Robert D. and Ridge, Karen M. and Toivola, Diana M.},
	month = nov,
	year = {2022},
	note = {Publisher: American Society for Cell Biology (mboc)},
	pages = {ar121},
	file = {Full Text PDF:C\:\\Users\\Suyash\\Zotero\\storage\\6VZBWZL7\\Stenvall et al. - 2022 - Cytoplasmic keratins couple with and maintain nuclear envelope integrity in colonic epithelial cells.pdf:application/pdf},
}

@article{nahabooKeratinFilamentsMediate2022,
	title = {Keratin filaments mediate the expansion of extra-embryonic membranes in the post-gastrulation mouse embryo},
	volume = {41},
	issn = {1460-2075},
	doi = {10.15252/embj.2021108747},
	abstract = {Mesoderm arises at gastrulation and contributes to both the mouse embryo proper and its extra-embryonic membranes. Two-photon live imaging of embryos bearing a keratin reporter allowed recording filament nucleation and elongation in the extra-embryonic region. Upon separation of amniotic and exocoelomic cavities, keratin 8 formed apical cables co-aligned across multiple cells in the amnion, allantois, and blood islands. An influence of substrate rigidity and composition on cell behavior and keratin content was observed in mesoderm explants. Embryos lacking all keratin filaments displayed a deflated extra-embryonic cavity, a narrow thick amnion, and a short allantois. Single-cell RNA sequencing of sorted mesoderm cells and micro-dissected amnion, chorion, and allantois, provided an atlas of transcriptomes with germ layer and regional information. It defined the cytoskeleton and adhesion expression profile of mesoderm-derived keratin 8-enriched cells lining the exocoelomic cavity. Those findings indicate a novel role for keratin filaments in the expansion of extra-embryonic structures and suggest mechanisms of mesoderm adaptation to the environment.},
	language = {eng},
	number = {7},
	journal = {The EMBO journal},
	author = {Nahaboo, Wallis and Eski, Sema Elif and Despin-Guitard, Evangéline and Vermeersch, Marjorie and Versaevel, Marie and Saykali, Bechara and Monteyne, Daniel and Gabriele, Sylvain and Magin, Thomas M. and Schwarz, Nicole and Leube, Rudolf E. and Zwijsen, An and Perez-Morga, David and Singh, Sumeet Pal and Migeotte, Isabelle},
	month = apr,
	year = {2022},
	pmid = {35266581},
	pmcid = {PMC8982622},
	keywords = {Animals, Keratins, intermediate filaments, Gastrulation, gastrulation, Embryo, Mammalian, extra-embryonic membranes, Extraembryonic Membranes, live imaging, Mesoderm, Mice, mouse embryo},
	pages = {e108747},
	file = {2022_Keratin filaments mediate the expansion of extra-embryonic membranes in the.pdf:C\:\\Users\\Suyash\\Zotero\\storage\\RFPVML2X\\2022_Keratin filaments mediate the expansion of extra-embryonic membranes in the.pdf:application/pdf},
}

@article{martin2009plakoglobin,
  title={Plakoglobin has both structural and signalling roles in zebrafish development},
  author={Martin, Eva D and Moriarty, Miriam A and Byrnes, Lucy and Grealy, Maura},
  journal={Developmental biology},
  volume={327},
  number={1},
  pages={83--96},
  year={2009},
  publisher={Elsevier}
}

@article{giuliodoriLossCardiacWnt2018,
	title = {Loss of cardiac {Wnt} beta-catenin signalling in desmoplakin-deficient {AC8} zebrafish models is rescuable by genetic and pharmacological intervention},
	volume = {114},
	issn = {0008-6363},
	url = {https://doi.org/10.1093/cvr/cvy057},
	doi = {10.1093/cvr/cvy057},
	number = {8},
	urldate = {2021-07-22},
	journal = {Cardiovascular Research},
	author = {Giuliodori, Alice and Beffagna, Giorgia and Marchetto, Giulia and Fornetto, Chiara and Vanzi, Francesco and Toppo, Stefano and Facchinello, Nicola and Santimaria, Mattia and Vettori, Andrea and Rizzo, Stefania and Della Barbera, Mila and Pilichou, Kalliopi and Argenton, Francesco and Thiene, Gaetano and Tiso, Natascia and Basso, Cristina},
	month = jul,
	year = {2018},
	pages = {1082--1097},
	file = {Snapshot:C\:\\Users\\Suyash\\Zotero\\storage\\ZYBXP948\\4924336.html:text/html},
}

@article{loschkeKeratinIsotypesControl2016,
	title = {Keratin {Isotypes} {Control} {Desmosome} {Stability} and {Dynamics} through {PKCalpha}},
	volume = {136},
	issn = {0022202X},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0022202X15000433},
	doi = {10.1038/JID.2015.403},
	language = {en},
	number = {1},
	urldate = {2025-04-17},
	journal = {Journal of Investigative Dermatology},
	author = {Loschke, Fanny and Homberg, Melanie and Magin, Thomas M.},
	month = jan,
	year = {2016},
	pages = {202--213},
	}

@article{buchauBidirectionalRegulationDesmosome2022,
	title = {Bidirectional regulation of desmosome hyperadhesion by keratin isotypes and desmosomal components},
	volume = {79},
	issn = {1420-682X},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8983532/},
	doi = {10.1007/s00018-022-04244-y},
	abstract = {Desmosomes are intercellular junctions which mediate cohesion and communication in tissues exposed to mechanical strain by tethering the intermediate filament cytoskeleton to the plasma membrane. While mature desmosomes are characterized by a hyperadhesive, Ca2+-independent state, they transiently loose this state during wound healing, pathogenesis and tissue regeneration. The mechanisms controlling the hyperadhesive state remain incompletely understood. Here, we show that upon Ca2+-induced keratinocyte differentiation, expression of keratin 17 (K17) prevents the formation of stable and hyperadhesive desmosomes, accompanied by a significant reduction of desmoplakin (DP), plakophilin-1 (PKP1), desmoglein-1 (Dsg1) and -3 (Dsg3) at intercellular cell borders. Atomic force microscopy revealed that both increased binding strength of desmoglein-3 molecules and amount of desmoglein-3 oligomers, known hallmarks of hyperadhesion, were reduced in K17- compared to K14-expressing cells. Importantly, overexpression of Dsg3 or DPII enhanced their localization at intercellular cell borders and increased the formation of Dsg3 oligomers, resulting in stable, hyperadhesive desmosomes despite the presence of K17. Notably, PKP1 was enriched in these desmosomes. Quantitative image analysis revealed that DPII overexpression contributed to desmosome hyperadhesion by increasing the abundance of K5/K17-positive keratin filaments in the proximity of desmosomes enriched in desmoglein-3. Thus, our data show that hyperadhesion can result from recruitment of keratin isotypes K5/K17 to desmosomes or from enhanced expression of DP and Dsg3 irrespective of keratin composition. The notion that hyperadhesive desmosomes failed to form in the absence of keratins underscores the essential role of keratins and suggest bidirectional control mechanisms at several levels.},
	number = {5},
	urldate = {2025-04-17},
	journal = {Cellular and Molecular Life Sciences: CMLS},
	author = {Büchau, Fanny and Vielmuth, Franziska and Waschke, Jens and Magin, Thomas M.},
	month = apr,
	year = {2022},
	pmid = {35380280},
	pmcid = {PMC8983532},
	pages = {223},
	file = {PubMed Central Full Text PDF:C\:\\Users\\Suyash\\Zotero\\storage\\EERJ6Z7Z\\Büchau et al. - 2022 - Bidirectional regulation of desmosome hyperadhesion by keratin isotypes and desmosomal components.pdf:application/pdf},
}
@article {Naik2025.02.14.638262,
	author = {Naik, Suyash and Keta, Yann-Edwin and Pranjic-Ferscha, Kornelija and Hannezo, {\'E}douard and Henkes, Silke and Heisenberg, Carl-Philipp},
	title = {Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties},
	elocation-id = {2025.02.14.638262},
	year = {2025},
	doi = {10.1101/2025.02.14.638262},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {For tissues to spread, they must be deformable while maintaining their structural integrity. How these opposing requirements are balanced within spreading tissues is not yet well understood. Here, we show that keratin intermediate filaments function in epithelial spreading by adapting tissue mechanical resilience to the stresses arising in the tissue during the spreading process. By analysing the expansion of the enveloping cell layer (EVL) over the large yolk cell in early zebrafish embryos in vivo, we found that keratin network maturation in EVL cells is promoted by stresses building up within the spreading tissue. Through genetic interference and tissue rheology experiments, complemented by a vertex model with mechanochemical feedback, we demonstrate that stress-induced keratin network maturation in the EVL increases tissue viscosity, which is essential for preventing tissue rupture. Interestingly, keratins are also required in the yolk cell for mechanosensitive actomyosin network contraction and flow, the force-generating processes pulling the EVL. These dual mechanosensitive functions of keratins enable a balance between pulling force production in the yolk cell and the mechanical resilience of the EVL against stresses generated by these pulling forces, thereby ensuring uniform and robust tissue spreading.Competing Interest StatementThe authors have declared no competing interest.},
	URL = {https://www.biorxiv.org/content/early/2025/02/17/2025.02.14.638262},
	eprint = {https://www.biorxiv.org/content/early/2025/02/17/2025.02.14.638262.full.pdf},
	journal = {bioRxiv}
}

@article{strelkov2003Moleculararchitectureintermediate,
  title = {Molecular Architecture of Intermediate Filaments},
  author = {Strelkov, Sergei V. and Herrmann, Harald and Aebi, Ueli},
  year = {2003},
  journal = {BioEssays},
  volume = {25},
  number = {3},
  pages = {243--251},
  issn = {1521-1878},
  doi = {10.1002/bies.10246},
  urldate = {2025-04-22},
  abstract = {Together with microtubules and actin microfilaments, {$\sim$}11 nm wide intermediate filaments (IFs) constitute the integrated, dynamic filament network present in the cytoplasm of metazoan cells. This network is critically involved in division, motility and other cellular processes. While the structures of microtubules and microfilaments are known in atomic detail, IF architecture is presently much less understood. The elementary `building block' of IFs is a highly elongated, rod-like dimer based on an {$\alpha$}-helical coiled-coil structure. Assembly of cytoplasmic IF proteins, such as vimentin, begins with a lateral association of dimers into tetramers and gradually into the so-called unit-length filaments (ULFs). Subsequently ULFs start to anneal longitudinally, ultimately yielding mature IFs after a compaction step. For nuclear lamins, however, assembly starts with a head-to-tail association of dimers. Recently, X-ray crystallographic data were obtained for several fragments of the vimentin dimer. Based on the dimer structure, molecular models of the tetramer and the entire filament are now a possibility. BioEssays 25:243--251, 2003. {\copyright} 2003 Wiley Periodicals, Inc.},
  copyright = {Copyright {\copyright} 2003 Wiley Periodicals, Inc.},
  langid = {english},
  file = {/Users/snaik/Zotero/storage/K7B7U9M3/Strelkov et al. - 2003 - Molecular architecture of intermediate filaments.pdf;/Users/snaik/Zotero/storage/U8LA7P49/bies.html}
}
@article{wu2006MorphoregulationAvianBeaks,
  title = {Morphoregulation of {{Avian Beaks}}: {{Comparative Mapping}} of {{Growth Zone Activities}} and {{Morphological Evolution}}},
  shorttitle = {Morphoregulation of {{Avian Beaks}}},
  author = {Wu, Ping and Jiang, Ting-Xin and Shen, Jen-Yee and Widelitz, Randall Bruce and Chuong, Cheng-Ming},
  year = {2006},
  month = may,
  journal = {Developmental dynamics : an official publication of the American Association of Anatomists},
  volume = {235},
  number = {5},
  pages = {1400--1412},
  issn = {1058-8388},
  doi = {10.1002/dvdy.20825},
  urldate = {2025-04-30},
  abstract = {Avian beak diversity is a classic example of morphological evolution. Recently, we showed that localized cell proliferation mediated by bone morphogenetic protein 4 (BMP4) can explain the different shapes of chicken and duck beaks ( Science 305:1465). Here, we compare further growth activities among chicken (conical and slightly curved), duck (straight and long), and cockatiel (highly curved) developing beak primordia. We found differential growth activities among different facial prominences and within one prominence. The duck has a wider frontal nasal mass (FNM), and more sustained fibroblast growth factor 8 activity. The cockatiel has a thicker FNM that grows more vertically and a relatively reduced mandibular prominence. In each prominence the number, size, and position of localized growth zones can vary: it is positioned more rostrally in the duck and more posteriorly in the cockatiel FNM, correlating with beak curvature. BMP4 is enriched in these localized growth zones. When BMP activity is experimentally altered in all prominences, beak size was enlarged or reduced proportionally. When only specific prominences were altered, the prototypic conical shaped chicken beaks were converted into an array of beak shapes mimicking those in nature. These results suggest that the size of beaks can be modulated by the overall activity of the BMP pathway, which mediates the growth. The shape of the beaks can be fine-tuned by localized BMP activity, which mediates the range, level, and duration of locally enhanced growth. Implications of topobiology vs. molecular blueprint concepts in the Evo--Devo of avian beak forms are discussed.},
  pmcid = {PMC4381996},
  pmid = {16586442}
}

@article{langdon2011MaternalZygoticControl,
  title = {Maternal and {{Zygotic Control}} of {{Zebrafish Dorsoventral Axial Patterning}}},
  author = {Langdon, Yvette G. and Mullins, Mary C.},
  year = {2011},
  month = dec,
  journal = {Annual Review of Genetics},
  volume = {45},
  number = {Volume 45, 2011},
  pages = {357--377},
  publisher = {Annual Reviews},
  issn = {0066-4197, 1545-2948},
  doi = {10.1146/annurev-genet-110410-132517},
  urldate = {2025-05-04},
  abstract = {Vertebrate development begins with precise molecular, cellular, and morphogenetic controls to establish the basic body plan of the embryo. In zebrafish, these tightly regulated processes begin during oogenesis and proceed through gastrulation to establish and pattern the axes of the embryo. During oogenesis a maternal factor is localized to the vegetal pole of the oocyte that is a determinant of dorsal tissues. Following fertilization this vegetally localized dorsal determinant is asymmetrically translocated in the egg and initiates formation of the dorsoventral axis. Dorsoventral axis formation and patterning is then mediated by maternal and zygotic factors acting through Wnt, BMP (bone morphogenetic protein), Nodal, and FGF (fibroblast growth factor) signaling pathways, each of which is required to establish and/or pattern the dorsoventral axis. This review addresses recent advances in our understanding of the molecular factors and mechanisms that establish and pattern the dorsoventral axis of the zebrafish embryo, including establishment of the animal-vegetal axis as it relates to formation of the dorsoventral axis.},
  langid = {english},
  file = {/Users/snaik/Zotero/storage/WKV9CM2R/annurev-genet-110410-132517.html}
}
@incollection{kowalczyk1998DesmosomesIntercellularAdhesive,
  title = {Desmosomes: {{Intercellular Adhesive Junctions Specialized}} for {{Attachment}} of {{Intermediate Filaments}}},
  shorttitle = {Desmosomes},
  booktitle = {International {{Review}} of {{Cytology}}},
  author = {Kowalczyk, Andrew P. and Bornslaeger, Elayne A. and Norvell, Suzanne M. and Palka, Helena L. and Green, Kathleen J.},
  editor = {Jeon, Kwang W.},
  year = {1998},
  month = jan,
  volume = {185},
  pages = {237--302},
  publisher = {Academic Press},
  doi = {10.1016/S0074-7696(08)60153-9},
  urldate = {2025-05-05},
  abstract = {Cell-cell adhesion is thought to play important roles in development, in tissue morphogenesis, and in the regulation of cell migration and proliferation. Desmosomes are adhesive intercellular junctions that anchor the intermediate filament network to the plasma membrane. By functioning both as an adhesive complex and as a cell-surface attachment site for intermediate filaments, desmosomes integrate the intermediate filament cytoskeleton between cells and play an important role in maintaining tissue integrity. Recent observations indicate that tissue integrity is severely compromised in autoimmune and genetic diseases in which the function of desmosomal molecules is impaired. In addition, the structure and function of many of the desmosomal molecules have been determined, and a number of the molecular interactions between desmosomal proteins have now been elucidated. Finally, the molecular constituents of desmosomes and other adhesive complexes are now known to function not only in cell adhesion, but also in the transduction of intracellular signals that regulate cell behavior.},
  keywords = {Cadherins,Catenins,Cell adhesion,Cytoskeleton,Desmoplakin,Plakoglobin},
  file = {/Users/snaik/Zotero/storage/TMLQBNFM/S0074769608601539.html}
}

@article{neufeld1998CoordinationGrowthCell,
  title = {Coordination of {{Growth}} and {{Cell Division}} in the {{Drosophila Wing}}},
  author = {Neufeld, Thomas P. and de la Cruz, Aida Flor A. and Johnston, Laura A. and Edgar, Bruce A.},
  year = {1998},
  month = jun,
  journal = {Cell},
  volume = {93},
  number = {7},
  pages = {1183--1193},
  publisher = {Elsevier},
  issn = {0092-8674, 1097-4172},
  doi = {10.1016/S0092-8674(00)81462-2},
  urldate = {2025-05-05},
  langid = {english},
  pmid = {9657151},
  file = {/Users/snaik/Zotero/storage/8TP6X9HB/Neufeld et al. - 1998 - Coordination of Growth and Cell Division in the Drosophila Wing.pdf}
}

@article{lecuitOrchestratingSizeShape2007,
  title = {Orchestrating Size and Shape during Morphogenesis},
  author = {Lecuit, Thomas and Le Goff, Lo{\"i}c},
  year = {2007},
  month = nov,
  journal = {Nature},
  volume = {450},
  number = {7167},
  pages = {189--192},
  publisher = {Nature Publishing Group},
  issn = {1476-4687},
  doi = {10.1038/nature06304},
  urldate = {2024-09-26},
  abstract = {This issue includes a landmark collection of papers on the stalwart of the genetics lab, the Drosophila fruit fly. The centrepiece is the publication by the Drosophila 12 Genomes Consortium of the genomic sequence for ten Drosophila species. The paper compares the newly sequenced genomes (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi species), with the two previously known sequences for D. melanogaster and D. pseudoobscura. The resulting database of genetic variation will be invaluable for the study of the forces of evolutionary change. A second major collaboration has mined the dozen Drosophila genome sequences for conserved elements, and reports the relationship between conservation and function for many specific sequence motifs. A detailed regulatory network emerges, identifying protein-coding genes and exons, RNA genes, microRNAs and their targets. These papers are discussed in News and Views. Two further research papers use the new genomic data to study gene expression, first for genes with male-biased expression and those unique to each species and second, to track the evolution of gene dosage compensation on Drosophila sex chromosomes. Four new reviews focus on how the latest work on Drosophila is taking this genetically pliant lab model into exciting new fields. Pierre Leopold and Norbert Perrimon review advances in the study of endocrinology and homeostasis that are establishing Drosophila as a model for mammalian physiology. Drosophila has proved a powerful system in which to study the pathways controlling cell shape in growing tissue, as reported by Thomas Lecuit and Lo{\"i}c Le Goff. Leslie Vosshall reviews the remarkable work linking neural circuits and behaviour and John Lis reviews work on Drosophila that has rewritten the textbook view of gene transcription. The cover shows anaesthetized individuals of all twelve Drosophila species.},
  copyright = {2007 Springer Nature Limited},
  langid = {english},
  keywords = {Humanities and Social Sciences,multidisciplinary,Science},
  file = {/Users/snaik/Zotero/storage/EFX7P4IF/Lecuit and Le Goff - 2007 - Orchestrating size and shape during morphogenesis.pdf}
}

@article{santos-duran2025Selforganizedpatterningcrocodile,
  title = {Self-Organized Patterning of Crocodile Head Scales by Compressive Folding},
  author = {{Santos-Dur{\'a}n}, Gabriel N. and Cooper, Rory L. and Jahanbakhsh, Ebrahim and Timin, Grigorii and Milinkovitch, Michel C.},
  year = {2025},
  month = jan,
  journal = {Nature},
  volume = {637},
  number = {8045},
  pages = {375--383},
  publisher = {Nature Publishing Group},
  issn = {1476-4687},
  doi = {10.1038/s41586-024-08268-1},
  urldate = {2025-04-30},
  abstract = {Amniote integumentary appendages constitute a diverse group of micro-organs, including feathers, hair and scales. These structures typically develop as genetically controlled units1, the spatial patterning of which emerges from a self-organized chemical Turing system2,3 with integrated mechanical feedback4,5. The seemingly purely mechanical patterning of polygonal crocodile head scales provides an exception to this paradigm6. However, the nature and origin of the mechanical stress field driving this patterning remain unclear. Here, using precise in ovo intravenous injections of epidermal growth factor protein, we generate Nile crocodile embryos with substantially convoluted head skin, as well as hatchlings with smaller polygonal head scales resembling those of caimans. We then use light-sheet fluorescence microscopy to quantify embryonic tissue-layer geometry, collagen architecture and the spatial distribution of proliferating cells. Using these data, we build a phenomenological three-dimensional mechanical growth model that recapitulates both normal and experimentally modified patterning of crocodile head scales. Our experiments and numerical simulations demonstrate that crocodile head scales self-organize through compressive folding, originating from near-homogeneous skin growth with differential stiffness of the dermis versus the~epidermis. Our experiments and theoretical morphospace analyses indicate that variation in embryonic growth and material properties of skin layers provides a simple evolutionary mechanism that produces a diversity of head-scale patterns among crocodilian species.},
  copyright = {2024 The Author(s)},
  langid = {english},
  keywords = {Computational biophysics,Dynamical systems,Evolutionary developmental biology,Morphogenesis,Pattern formation},
  file = {/Users/snaik/Zotero/storage/3STYQQP7/Santos-Durán et al. - 2025 - Self-organized patterning of crocodile head scales by compressive folding.pdf}
}

@article{kolschActindependentDynamicsKeratin2009,
	title = {Actin-dependent dynamics of keratin filament precursors},
	volume = {66},
	copyright = {Copyright © 2009 Wiley-Liss, Inc.},
	issn = {1097-0169},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cm.20395},
	doi = {10.1002/cm.20395},
	abstract = {Actin filament and microtubule growth characteristics are defined by their different plus and minus ends. In contrast, intermediate filaments lack this type of polarity. Yet, intermediate filament network growth occurs by selective addition of newly formed and polymerizing keratin particles at peripheral network domains thereby allowing polarized network reorganization. To examine this process at high resolution in living cells, mammary epithelium-derived, immortalized EpH4-cells were infected with retroviral cDNA constructs coding for human keratin 18-fluorescent protein hybrids. Several stable cell lines were established presenting characteristic fluorescent keratin filament (KF) networks. These cells contain particularly large and abundant lamellipodia in which nascent keratin particle dynamics are easily detected by time-lapse fluorescence microscopy. These keratin particles originate close to the plasma membrane, translocate continuously toward the cell center, and integrate end-on into the peripheral KF network. We show that this inward-directed transport relies on intact actin filaments. After treatment with the actin filament-disrupting drug cytochalasin newly polymerizing keratin assemblies still appear in the peripheral cytoplasm but remain stationary. On the other hand, nocodazole-mediated disruption of microtubules does not affect the centripetal KF precursor transport. From these and other observations a model is deduced which postulates that focal adhesion-dependent keratin polymerization occurs in forming lamellipodia and that transport of newly formed keratin particles is mediated by actin filaments until network integration. This mechanism allows extension of the KF network toward the leading edge in migrating cells and may be of relevance for tissue development and regeneration. Cell Motil. Cytoskeleton 66: 976–985, 2009. © 2009 Wiley-Liss, Inc.},
	language = {en},
	number = {11},
	urldate = {2024-10-02},
	journal = {Cell Motility},
	author = {Kölsch, Anne and Windoffer, Reinhard and Leube, Rudolf E.},
	year = {2009},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/cm.20395},
	keywords = {cytoskeleton, intermediate filament, assembly, live cell imaging, transport},
	pages = {976--985},
	file = {Snapshot:C\:\\Users\\Suyash\\Zotero\\storage\\K4ZMTLAA\\cm.html:text/html},
}

@article{delvaDesmosome2009,
	title = {The {Desmosome}},
	volume = {1},
	issn = {, 1943-0264},
	url = {http://cshperspectives.cshlp.org/content/1/2/a002543},
	doi = {10.1101/cshperspect.a002543},
	abstract = {Desmosomes are intercellular junctions that tether intermediate filaments to the plasma membrane. Desmogleins and desmocollins, members of the cadherin superfamily, mediate adhesion at desmosomes. Cytoplasmic components of the desmosome associate with the desmosomal cadherin tails through a series of protein interactions, which serve to recruit intermediate filaments to sites of desmosome assembly. These desmosomal plaque components include plakoglobin and the plakophilins, members of the armadillo gene family. Linkage to the cytoskeleton is mediated by the intermediate filament binding protein, desmoplakin, which associates with both plakoglobin and plakophilins. Although desmosomes are critical for maintaining stable cell–cell adhesion, emerging evidence indicates that they are also dynamic structures that contribute to cellular processes beyond that of cell adhesion. This article outlines the structure and function of the major desmosomal proteins, and explores the contributions of this protein complex to tissue architecture and morphogenesis.},
	language = {en},
	number = {2},
	urldate = {2021-03-18},
	journal = {Cold Spring Harbor Perspectives in Biology},
	author = {Delva, Emmanuella and Tucker, Dana K. and Kowalczyk, Andrew P.},
	month = jan,
	year = {2009},
	pmid = {20066089},
	note = {Company: Cold Spring Harbor Laboratory Press
Distributor: Cold Spring Harbor Laboratory Press
Institution: Cold Spring Harbor Laboratory Press
Label: Cold Spring Harbor Laboratory Press
Publisher: Cold Spring Harbor Lab},
	pages = {a002543},
	file = {Delva et al_2009_The Desmosome.pdf:C\:\\Users\\Suyash\\Zotero\\storage\\6TK4U6WB\\Delva et al_2009_The Desmosome.pdf:application/pdf;Snapshot:C\:\\Users\\Suyash\\Zotero\\storage\\SGFBMUIS\\a002543.html:text/html},
}

@article{moll2008human,
  title={The human keratins: biology and pathology},
  author={Moll, Roland and Divo, Markus and Langbein, Lutz},
  journal={Histochemistry and cell biology},
  volume={129},
  pages={705--733},
  year={2008},
  publisher={Springer}
}
@article{inaba2020keratins,
  title={Keratins and plakin family cytolinker proteins control the length of epithelial microridge protrusions},
  author={Inaba, Yasuko and Chauhan, Vasudha and van Loon, Aaron Paul and Choudhury, Lamia Saiyara and Sagasti, Alvaro},
  journal={Elife},
  volume={9},
  pages={e58149},
  year={2020},
  publisher={eLife Sciences Publications, Ltd}
}

@article{kageyamaCELLULARBASISEPIBOLY1980,
	title = {{CELLULAR} {BASIS} {OF} {EPIBOLY} {OF} {THE} {ENVELOPING} {LAYER} {IN} {THE} {EMBRYO} {OF} {MEDAKA}, {ORYZIAS} {LATIPES}. {I}. {CELL} {ARCHITECTURE} {REVEALED} {BY} {SILVER} {STAINING} {METHOD}},
	volume = {22},
	copyright = {http://doi.wiley.com/10.1002/tdm\_license\_1.1},
	issn = {0012-1592, 1440-169X},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1440-169X.1980.00659.x},
	doi = {10.1111/j.1440-169X.1980.00659.x},
	language = {en},
	number = {4},
	urldate = {2025-04-13},
	journal = {Development, Growth and Differentiation},
	author = {Kageyama, Tetsuo},
	month = aug,
	year = {1980},
	pages = {659--668},
}

@article{kalabushevaKaleidoscopeKeratinGene2023,
	title = {A {Kaleidoscope} of {Keratin} {Gene} {Expression} and the {Mosaic} of {Its} {Regulatory} {Mechanisms}},
	volume = {24},
	issn = {1422-0067},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10052683/},
	doi = {10.3390/ijms24065603},
	abstract = {Keratins are a family of intermediate filament-forming proteins highly specific to epithelial cells. A combination of expressed keratin genes is a defining property of the epithelium belonging to a certain type, organ/tissue, cell differentiation potential, and at normal or pathological conditions. In a variety of processes such as differentiation and maturation, as well as during acute or chronic injury and malignant transformation, keratin expression undergoes switching: an initial keratin profile changes accordingly to changed cell functions and location within a tissue as well as other parameters of cellular phenotype and physiology. Tight control of keratin expression implies the presence of complex regulatory landscapes within the keratin gene loci. Here, we highlight patterns of keratin expression in different biological conditions and summarize disparate data on mechanisms controlling keratin expression at the level of genomic regulatory elements, transcription factors (TFs), and chromatin spatial structure.},
	number = {6},
	urldate = {2024-09-29},
	journal = {International Journal of Molecular Sciences},
	author = {Kalabusheva, Ekaterina P. and Shtompel, Anastasia S. and Rippa, Alexandra L. and Ulianov, Sergey V. and Razin, Sergey V. and Vorotelyak, Ekaterina A.},
	month = mar,
	year = {2023},
	pmid = {36982676},
	pmcid = {PMC10052683},
	pages = {5603},
	file = {PubMed Central Full Text PDF:C\:\\Users\\Suyash\\Zotero\\storage\\DG5J6YNF\\Kalabusheva et al. - 2023 - A Kaleidoscope of Keratin Gene Expression and the .pdf:application/pdf},
}

@article{shahbazi2020mechanisms,
  title={Mechanisms of human embryo development: from cell fate to tissue shape and back},
  author={Shahbazi, Marta N},
  journal={Development},
  volume={147},
  number={14},
  pages={dev190629},
  year={2020},
  publisher={The Company of Biologists Ltd}
}
@article{kimmel1995stages,
  title={Stages of embryonic development of the zebrafish},
  author={Kimmel, Charles B and Ballard, William W and Kimmel, Seth R and Ullmann, Bonnie and Schilling, Thomas F},
  journal={Developmental dynamics},
  volume={203},
  number={3},
  pages={253--310},
  year={1995},
  publisher={Wiley Online Library}
}
@article{hong2010pGasgene,
  title={Pre-gastrula expression of zebrafish extraembryonic genes},
  author={Hong, Sung-Kook and Levin, Carly S and Brown, Jamie L and Wan, Haiyan and Sherman, Brad T and Huang, Da Wei and Lempicki, Richard A and Feldman, Benjamin},
  journal={BMC Developmental Biology},
  volume={10},
  number={1},
  pages={1--11},
  year={2010},
  publisher={BioMed Central}
}
@article{bruce2016zebrafish,
  title={Zebrafish epiboly: Spreading thin over the yolk},
  author={Bruce, Ashley EE},
  journal={Developmental Dynamics},
  volume={245},
  number={3},
  pages={244--258},
  year={2016},
  publisher={Wiley Online Library}
}
@article{iwamatsu2004stages,
  title={Stages of normal development in the medaka Oryzias latipes},
  author={Iwamatsu, Takashi},
  journal={Mechanisms of development},
  volume={121},
  number={7-8},
  pages={605--618},
  year={2004},
  publisher={Elsevier}
}
@article{behrndt2012forces,
  title={Forces driving epithelial spreading in zebrafish gastrulation},
  author={Behrndt, Martin and Salbreux, Guillaume and Campinho, Pedro and Hauschild, Robert and Oswald, Felix and Roensch, Julia and Grill, Stephan W and Heisenberg, Carl-Philipp},
  journal={Science},
  volume={338},
  number={6104},
  pages={257--260},
  year={2012},
  publisher={American Association for the Advancement of Science}
}
@article{bruce2020mechanisms,
  title={Mechanisms of zebrafish epiboly: A current view},
  author={Bruce, Ashley EE and Heisenberg, Carl-Philipp},
  journal={Current topics in developmental biology},
  volume={136},
  pages={319--341},
  year={2020},
  publisher={Elsevier}
}
@article{kondo1997introduction,
  title={Introduction of cyclin B induces activation of the maturation-promoting factor and breakdown of germinal vesicle in growing zebrafish oocytes unresponsive to the maturation-inducing hormone},
  author={Kondo, Tomoko and Yanagawa, Toshiharu and Yoshida, Noriyuki and Yamashita, Masakane},
  journal={Developmental biology},
  volume={190},
  number={1},
  pages={142--152},
  year={1997},
  publisher={Elsevier}
}
@article{fuentes2010ooplasmic,
  title={Ooplasmic segregation in the zebrafish zygote and early embryo: pattern of ooplasmic movements and transport pathways},
  author={Fuentes, Ricardo and Fern{\'a}ndez, Juan},
  journal={Developmental Dynamics},
  volume={239},
  number={8},
  pages={2172--2189},
  year={2010},
  publisher={Wiley Online Library}
}
@article{shamipour2019bulk,
  title={Bulk actin dynamics drive phase segregation in zebrafish oocytes},
  author={Shamipour, Shayan and Kardos, Roland and Xue, Shi-Lei and Hof, Bj{\"o}rn and Hannezo, Edouard and Heisenberg, Carl-Philipp},
  journal={Cell},
  volume={177},
  number={6},
  pages={1463--1479},
  year={2019},
  publisher={Elsevier}
}
@article{xia2019lateral,
  title={Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity},
  author={Xia, Peng and G{\"u}tl, Daniel and Zheden, Vanessa and Heisenberg, Carl-Philipp},
  journal={Cell},
  volume={176},
  number={6},
  pages={1379--1392},
  year={2019},
  publisher={Elsevier}
}
@article{mishra2025geometry,
  title={Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo},
  author={Mishra, Nikhil and Li, Yuting I and Hannezo, Edouard and Heisenberg, Carl-Philipp},
  journal={bioRxiv},
  pages={2025--02},
  year={2025},
  publisher={Cold Spring Harbor Laboratory}
}
@article{marlow2008bucky,
  title={Bucky ball functions in Balbiani body assembly and animal--vegetal polarity in the oocyte and follicle cell layer in zebrafish},
  author={Marlow, Florence L and Mullins, Mary C},
  journal={Developmental biology},
  volume={321},
  number={1},
  pages={40--50},
  year={2008},
  publisher={Elsevier}
}
@article{sagerstrom1998determination,
  title={Determination of the enveloping layer and lack of autoneutralization in zebrafish embryos},
  author={Sagerstrom, CG and Gammill, LS and Veale, RV and Sive, HL},
  journal={EMBL/GenBank/DDBJ databases, accesion number AF084461},
  year={1998}
}
@article{lachnit2008alterations,
  title={Alterations of the cytoskeleton in all three embryonic lineages contribute to the epiboly defect of Pou5f1/Oct4 deficient MZspg zebrafish embryos},
  author={Lachnit, Martina and Kur, Esther and Driever, Wolfgang},
  journal={Developmental biology},
  volume={315},
  number={1},
  pages={1--17},
  year={2008},
  publisher={Elsevier}
}
@article{sabel2009maternal,
  title={Maternal Interferon Regulatory Factor 6 is required for the differentiation of primary superficial epithelia in Danio and Xenopus embryos},
  author={Sabel, Jaime L and d'Alen{\c{c}}on, Claudia and O'Brien, Erin K and Van Otterloo, Eric and Lutz, Katie and Cuykendall, Tawny N and Schutte, Brian C and Houston, Douglas W and Cornell, Robert A},
  journal={Developmental biology},
  volume={325},
  number={1},
  pages={249--262},
  year={2009},
  publisher={Elsevier}
}
@article{hongPregastrulaExpressionZebrafish2010,
	title = {Pre-gastrula expression of zebrafish extraembryonic genes},
	volume = {10},
	issn = {1471-213X},
	url = {https://doi.org/10.1186/1471-213X-10-42},
	doi = {10.1186/1471-213X-10-42},
	abstract = {Many species form extraembryonic tissues during embryogenesis, such as the placenta of humans and other viviparous mammals. Extraembryonic tissues have various roles in protecting, nourishing and patterning embryos. Prior to gastrulation in zebrafish, the yolk syncytial layer - an extraembryonic nuclear syncytium - produces signals that induce mesoderm and endoderm formation. Mesoderm and endoderm precursor cells are situated in the embryonic margin, an external ring of cells along the embryo-yolk interface. The yolk syncytial layer initially forms below the margin, in a domain called the external yolk syncytial layer (E-YSL).},
	number = {1},
	urldate = {2024-02-26},
	journal = {BMC Developmental Biology},
	author = {Hong, Sung-Kook and Levin, Carly S. and Brown, Jamie L. and Wan, Haiyan and Sherman, Brad T. and Huang, Da Wei and Lempicki, Richard A. and Feldman, Benjamin},
	month = apr,
	year = {2010},
	keywords = {Embryonic Cell, Extraembryonic Tissue, Maternal Gene, Nodal Signaling, Yolk Syncytial Layer},
	pages = {42},
	file = {Full Text PDF:C\:\\Users\\Suyash\\Zotero\\storage\\UKR7E77C\\Hong et al. - 2010 - Pre-gastrula expression of zebrafish extraembryoni.pdf:application/pdf;Snapshot:C\:\\Users\\Suyash\\Zotero\\storage\\IHPV3YTW\\1471-213X-10-42.html:text/html},
}

@article{peterEvolutionaryAspectsIntermediate2015,
	title = {Evolutionary aspects in intermediate filament proteins},
	volume = {32},
	issn = {0955-0674},
	doi = {10.1016/J.CEB.2014.12.009},
	abstract = {Intermediate filament (IF) proteins, together with tubulins and actins, constitute the majority of cytoskeletal proteins in metazoans. Proteins of the IF family fulfil increasingly diverse functions but share common structural features. Phylogenetic analysis within the metazoan lineage traces back their origin to a common lamin-like ancestor. Major steps in lamin evolution occurred at the base of the vertebrate radiation, while cytoplasmic IF protein subfamilies evolved independently in the major metazoan lineages.},
	urldate = {2023-02-01},
	journal = {Current Opinion in Cell Biology},
	author = {Peter, Annette and Stick, Reimer},
	month = feb,
	year = {2015},
	pmid = {25576801},
	note = {Publisher: Elsevier Current Trends},
	pages = {48--55},
	file = {PDF:C\:\\Users\\Suyash\\Zotero\\storage\\4KIEHIM3\\full-text.pdf:application/pdf},
}

@article{leeStructuralBasisHeteromeric2012a,
	title = {Structural basis for heteromeric assembly and perinuclear organization of keratin filaments},
	volume = {19},
	copyright = {2012 Springer Nature America, Inc.},
	issn = {1545-9985},
	url = {https://www.nature.com/articles/nsmb.2330},
	doi = {10.1038/nsmb.2330},
	abstract = {Keratins form heterodimers that assemble into intermediate filaments. The structure of a central coiled-coil region formed between keratins 5 and 14 provides a new understanding of intermediate-filament architecture and assembly. Cellular data suggest a role for disulfide bridges in filament organization.},
	language = {en},
	number = {7},
	urldate = {2025-06-19},
	journal = {Nature Structural \& Molecular Biology},
	author = {Lee, Chang-Hun and Kim, Min-Sung and Chung, Byung Min and Leahy, Daniel J. and Coulombe, Pierre A.},
	month = jul,
	year = {2012},
	note = {Publisher: Nature Publishing Group},
	keywords = {Intermediate filaments, Structural biology},
	pages = {707--715},
	file = {Full Text PDF:C\:\\Users\\Suyash\\Zotero\\storage\\PGZLYA8G\\Lee et al. - 2012 - Structural basis for heteromeric assembly and perinuclear organization of keratin filaments.pdf:application/pdf},
}


@misc{meyerKeratinCortexStabilizes2025a,
	title = {The keratin cortex stabilizes cells at high strains},
	copyright = {© 2025, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/},
	url = {https://www.biorxiv.org/content/10.1101/2025.02.24.639846v1},
	doi = {10.1101/2025.02.24.639846},
	abstract = {The eukaryotic cytoskeleton consists of three filament types: actin filaments, microtubules and intermediate filaments (IFs). IF proteins are expressed in a cell-type specific manner, and keratins are found in epithelial cells. In certain cell types, the keratins form a layer close to the membrane which may be referred to as an “IF-cortex”. It is hypothesized that this IF-cortex arranges with radial bundles in a “rim-and-spokes” structure in epithelia. Based on this hypothesis, IFs and actin filaments might add complementary mechanical properties to the cortex. It was previously shown that single IFs in vitro remain undamaged at high strains. We now ask the question of whether this unique force-extension behavior of single IFs is also relevant in the filament network within a cell. Here, we show the influence of equibiaxial strain on wild-type (WT) and keratin-deficient (KO) cells comparing the viscoelastic properties close to the cell membrane using atomic force microscopy, in a spatially resolved manner. We find that cells without keratin exhibit a higher pre-stress than the WT cells. The compressibility modulus is increased at the cell rim, compared to the inside region, due to the geometry of the cell layer. Interestingly, both the pre-stress and the fluidity of the KO cells are altered already at low strains, whereas the WT cells show a response only at large strain. Our results indicate that KO cells compensate for the missing keratin, but are nevertheless very sensitive to external strain, whereas the intricate interplay between the actin and keratin cortices preserves the mechanical state and cell stability.},
	language = {en},
	urldate = {2025-06-19},
	publisher = {bioRxiv},
	author = {Meyer, Ruth and Rölleke, Ulrike and Schwarz, Nicole and Perez-Tirado, Amaury and Schepers, Anna V. and Janshoff, Andreas and Köster, Sarah},
	month = feb,
	year = {2025},
	note = {Pages: 2025.02.24.639846
Section: New Results},
}

@article{ettensohnMechanismsEpithelialInvagination1985,
	title = {Mechanisms of epithelial invagination},
	volume = {60},
	issn = {0033-5770},
	doi = {10.1086/414426},
	abstract = {This review is concerned with the mechanical forces that cause epithelial sheets to invaginate during morphogenesis. Interest in this problem is currently increasing and a variety of models, each with a different emphasis, have been formulated to explain mechanical aspects of epithelial folding. A critical evaluation of the experimental evidence bearing on this problem leads to the following conclusions. (1) The most popular model of invagination, one based on microfilament-mediated cell shape change, should be re-examined, given the limitations of the experimental evidence usually offered in its support. Recent experiments with permeabilized epithelia offer a promising approach for confirming the validity of this model. (2) Current hypotheses based on disparities in the adhesive properties of epithelial cells are consistent with available data, but appear to be impossible to test directly at this time. (3) There is evidence that suggests that cell growth and division are involved in invagination during the branching morphogenesis of some epithelio-mesenchymal organs, but it has been shown that these processes are not involved in other cases. (4) Recent studies demonstrate that some epithelial invaginations are accompanied by movements of cells, both in the form of rearrangement (exchange of nearest neighbors) and involution (flow of surrounding cells into the invaginating region). (5) A general conclusion that may be drawn from the data now available is that several different mechanisms of epithelial folding operate during morphogenesis.},
	language = {eng},
	number = {3},
	journal = {The Quarterly Review of Biology},
	author = {Ettensohn, C. A.},
	month = sep,
	year = {1985},
	pmid = {3901078},
	keywords = {Morphogenesis, Animals, Actin Cytoskeleton, Epithelial Cells, Cell Adhesion, Models, Biological, Cell Movement, Cell Division, Epithelium},
	pages = {289--307},
}

@misc{liEpithelialInvaginationVertical2019,
	title = {Epithelial invagination by vertical telescoping},
	copyright = {© 2019, Posted by Cold Spring Harbor Laboratory. The copyright holder for this pre-print is the author. All rights reserved. The material may not be redistributed, re-used or adapted without the author's permission.},
	url = {https://www.biorxiv.org/content/10.1101/515981v2},
	doi = {10.1101/515981},
	abstract = {Epithelial bending is a fundamental process that shapes organs during development. All currently known mechanisms involve cells locally changing shape from columnar to wedge-shaped. Often this shape change occurs by cytoskeletal contraction at cell apices (“apical constriction”) but mechanisms such as basal nuclear positioning (“basal wedging”) or extrinsic compression are also known. Here we demonstrate a completely different mechanism which occurs without cell wedging. In mammalian salivary glands and teeth, we show that initial invagination occurs through coordinated vertical cell movement. Specifically, we show that cells towards the periphery of the placode move vertically upwards while their more central neighbours move downwards to create the invagination. We further show that this occurs by active cell-on-cell migration: outer cells migrate with an apical leading edge protrusion, depressing the central cells to “telescope” the epithelium downwards into the underlaying mesenchyme. Cells remain basally attached to the underlying lamina while their apical protrusions are dynamic and planar polarised centripetally. These protrusions depend on the actin cytoskeleton, and inhibition of the branching molecule Arp2/3 inhibits them and the invagination. FGF and Hedgehog morphogen signals are also required, with FGF providing a directional cue. These findings show that epithelial bending can be achieved by novel morphogenetic mechanism of coordinated cell rearrangement quite distinct from previously recognised invagination processes.},
	language = {en},
	urldate = {2025-06-19},
	publisher = {bioRxiv},
	author = {Li, Jingjing and Economou, Andrew D. and Green, Jeremy B. A.},
	month = sep,
	year = {2019},
	note = {Pages: 515981
Section: New Results},
	file = {Full Text PDF:C\:\\Users\\Suyash\\Zotero\\storage\\7C6M68AK\\Li et al. - 2019 - Epithelial invagination by vertical telescoping.pdf:application/pdf},
}

@article{rauziCellIntercalationSimple2020,
	title = {Cell intercalation in a simple epithelium},
	volume = {375},
	url = {https://royalsocietypublishing.org/doi/full/10.1098/rstb.2019.0552},
	doi = {10.1098/rstb.2019.0552},
	abstract = {Cell intercalation is a key topological transformation driving tissue morphogenesis, homeostasis and diseases such as cancer cell invasion. In recent years, much work has been undertaken to better elucidate the fundamental mechanisms controlling intercalation. Cells often use protrusions to propel themselves in between cell neighbours, resulting in topology changes. Nevertheless, in simple epithelial tissues, formed by a single layer of densely packed prism-shaped cells, topology change takes place in an astonishing fashion: cells exchange neighbours medio-laterally by conserving their apical–basal architecture and by maintaining an intact epithelial layer. Medio-lateral cell intercalation in simple epithelia is thus an exemplary case of both robustness and plasticity. Interestingly, in simple epithelia, cells use a combinatory set of mechanisms to ensure a topological transformation at the apical and basal sides.
This article is part of the discussion meeting issue ‘Contemporary morphogenesis’.},
	number = {1809},
	urldate = {2025-06-19},
	journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
	author = {Rauzi, Matteo},
	month = aug,
	year = {2020},
	note = {Publisher: Royal Society},
	keywords = {actomyosin flow, actomyosin tension, E-cadherin adhesion, junction remodelling},
	pages = {20190552},
	file = {Full Text PDF:C\:\\Users\\Suyash\\Zotero\\storage\\6UF2AJRS\\Rauzi - 2020 - Cell intercalation in a simple epithelium.pdf:application/pdf},
}


@article{sknepnekGeneratingActiveT12023,
	title = {Generating active {T1} transitions through mechanochemical feedback},
	volume = {12},
	issn = {2050-084X},
	url = {https://doi.org/10.7554/eLife.79862},
	doi = {10.7554/eLife.79862},
	abstract = {Convergence–extension in embryos is controlled by chemical and mechanical signalling. A key cellular process is the exchange of neighbours via T1 transitions. We propose and analyse a model with positive feedback between recruitment of myosin motors and mechanical tension in cell junctions. The model produces active T1 events, which act to elongate the tissue perpendicular to the main direction of tissue stress. Using an idealised tissue patch comprising several active cells embedded in a matrix of passive hexagonal cells, we identified an optimal range of mechanical stresses to trigger an active T1 event. We show that directed stresses also generate tension chains in a realistic patch made entirely of active cells of random shapes and leads to convergence–extension over a range of parameters. Our findings show that active intercalations can generate stress that activates T1 events in neighbouring cells, resulting in tension-dependent tissue reorganisation, in qualitative agreement with experiments on gastrulation in chick embryos.},
	urldate = {2023-11-10},
	journal = {eLife},
	author = {Sknepnek, Rastko and Djafer-Cherif, Ilyas and Chuai, Manli and Weijer, Cornelis and Henkes, Silke},
	editor = {Kruse, Karsten and Walczak, Aleksandra M},
	month = apr,
	year = {2023},
	note = {Publisher: eLife Sciences Publications, Ltd},
	keywords = {vertex model, tissue mechanics, activity},
	pages = {e79862},
	file = {Full Text:C\:\\Users\\Suyash\\Zotero\\storage\\4JB2SI5T\\Sknepnek et al. - 2023 - Generating active T1 transitions through mechanoch.pdf:application/pdf},
}

@article{xiongInterplayCellShape2014,
	title = {Interplay of {Cell} {Shape} and {Division} {Orientation} {Promotes} {Robust} {Morphogenesis} of {Developing} {Epithelia}},
	volume = {159},
	issn = {0092-8674},
	url = {https://www.sciencedirect.com/science/article/pii/S0092867414011556},
	doi = {10.1016/j.cell.2014.09.007},
	abstract = {Epithelial cells acquire functionally important shapes (e.g., squamous, cuboidal, columnar) during development. Here, we combine theory, quantitative imaging, and perturbations to analyze how tissue geometry, cell divisions, and mechanics interact to shape the presumptive enveloping layer (pre-EVL) on the zebrafish embryonic surface. We find that, under geometrical constraints, pre-EVL flattening is regulated by surface cell number changes following differentially oriented cell divisions. The division pattern is, in turn, determined by the cell shape distribution, which forms under geometrical constraints by cell-cell mechanical coupling. An integrated mathematical model of this shape-division feedback loop recapitulates empirical observations. Surprisingly, the model predicts that cell shape is robust to changes of tissue surface area, cell volume, and cell number, which we confirm in vivo. Further simulations and perturbations suggest the parameter linking cell shape and division orientation contributes to epithelial diversity. Together, our work identifies an evolvable design logic that enables robust cell-level regulation of tissue-level development.},
	language = {en},
	number = {2},
	urldate = {2023-01-11},
	journal = {Cell},
	author = {Xiong, Fengzhu and Ma, Wenzhe and Hiscock, Tom W. and Mosaliganti, Kishore R. and Tentner, Andrea R. and Brakke, Kenneth A. and Rannou, Nicolas and Gelas, Arnaud and Souhait, Lydie and Swinburne, Ian A. and Obholzer, Nikolaus D. and Megason, Sean G.},
	month = oct,
	year = {2014},
	pages = {415--427},
	file = {Xiong et al_2014_Interplay of Cell Shape and Division Orientation Promotes Robust Morphogenesis.pdf:C\:\\Users\\Suyash\\Zotero\\storage\\SK4XWWCA\\Xiong et al_2014_Interplay of Cell Shape and Division Orientation Promotes Robust Morphogenesis.pdf:application/pdf},
}

@article{dasMolecularMechanotransductionPathway2015,
	title = {A molecular mechanotransduction pathway regulates collective migration of epithelial cells},
	volume = {17},
	copyright = {2014 Springer Nature Limited},
	issn = {1476-4679},
	url = {https://www.nature.com/articles/ncb3115},
	doi = {10.1038/ncb3115},
	abstract = {Collective movement of epithelial cells drives essential multicellular organization during various fundamental physiological processes encompassing embryonic morphogenesis, cancer and wound healing. Yet the molecular mechanism that ensures the coordinated movement of many cells remains elusive. Here we show that a tumour suppressor protein, merlin, coordinates collective migration of tens of cells, by acting as a mechanochemical transducer. In a stationary epithelial monolayer and also in three-dimensional human skin, merlin localizes to cortical cell–cell junctions. During migration initiation, a fraction of cortical merlin relocalizes to the cytoplasm. This relocalization is triggered by the intercellular pulling force of the leading cell and depends on the actomyosin-based cell contractility. Then in migrating cells, taking its cue from the intercellular pulling forces, which show long-distance ordering, merlin coordinates polarized Rac1 activation and lamellipodium formation on the multicellular length scale. Together, these results provide a distinct molecular mechanism linking intercellular forces to collective cell movements in migrating epithelia.},
	language = {en},
	number = {3},
	urldate = {2025-06-20},
	journal = {Nature Cell Biology},
	author = {Das, Tamal and Safferling, Kai and Rausch, Sebastian and Grabe, Niels and Boehm, Heike and Spatz, Joachim P.},
	month = mar,
	year = {2015},
	note = {Publisher: Nature Publishing Group},
	keywords = {Mechanotransduction, Cell polarity, Collective cell migration, RHO signalling},
	pages = {276--287},
	file = {Full Text PDF:C\:\\Users\\Suyash\\Zotero\\storage\\DZAYNGEB\\Das et al. - 2015 - A molecular mechanotransduction pathway regulates collective migration of epithelial cells.pdf:application/pdf},
}

@article{tambeCollectiveCellGuidance2011,
	title = {Collective cell guidance by cooperative intercellular forces},
	volume = {10},
	copyright = {2011 Springer Nature Limited},
	issn = {1476-4660},
	url = {https://www.nature.com/articles/nmat3025},
	doi = {10.1038/nmat3025},
	abstract = {Cells comprising a tissue migrate as part of a collective. How collective processes are coordinated over large multi-cellular assemblies has remained unclear, however, because mechanical stresses exerted at cell–cell junctions have not been accessible experimentally. We report here maps of these stresses within and between cells comprising a monolayer. Within the cell sheet there arise unanticipated fluctuations of mechanical stress that are severe, emerge spontaneously, and ripple across the monolayer. Within that stress landscape, local cellular migrations follow local orientations of maximal principal stress. Migrations of both endothelial and epithelial monolayers conform to this behaviour, as do breast cancer cell lines before but not after the epithelial–mesenchymal transition. Collective migration in these diverse systems is seen to be governed by a simple but unifying physiological principle: neighbouring cells join forces to transmit appreciable normal stress across the cell–cell junction, but migrate along orientations of minimal intercellular shear stress.},
	language = {en},
	number = {6},
	urldate = {2025-06-20},
	journal = {Nature Materials},
	author = {Tambe, Dhananjay T. and Corey Hardin, C. and Angelini, Thomas E. and Rajendran, Kavitha and Park, Chan Young and Serra-Picamal, Xavier and Zhou, Enhua H. and Zaman, Muhammad H. and Butler, James P. and Weitz, David A. and Fredberg, Jeffrey J. and Trepat, Xavier},
	month = jun,
	year = {2011},
	note = {Publisher: Nature Publishing Group},
	keywords = {Collective cell migration, Mechanical properties},
	pages = {469--475},
	file = {Full Text PDF:C\:\\Users\\Suyash\\Zotero\\storage\\L6AGZMKY\\Tambe et al. - 2011 - Collective cell guidance by cooperative intercellular forces.pdf:application/pdf},
}

@article{tetleyTissueFluidityPromotes2019,
	title = {Tissue fluidity promotes epithelial wound healing},
	volume = {15},
	copyright = {2019 The Author(s), under exclusive licence to Springer Nature Limited},
	issn = {1745-2481},
	url = {http://www.nature.com/articles/s41567-019-0618-1},
	doi = {10.1038/s41567-019-0618-1},
	abstract = {The collective behaviour of cells in epithelial tissues is dependent on their mechanical properties. However, the contribution of tissue mechanics to wound healing in vivo remains poorly understood. Here, we investigate the relationship between tissue mechanics and wound healing in live Drosophila wing imaginal discs and show that by tuning epithelial cell junctional tension, we can systematically alter the rate of wound healing. Coincident with the contraction of an actomyosin purse string, we observe cells flowing past each other at the wound edge by intercalating, reminiscent of molecules in a fluid, resulting in seamless wound closure. Using a cell-based physical model, we predict that a reduction in junctional tension fluidizes the tissue through an increase in intercalation rate and corresponding reduction in bulk viscosity, in the manner of an unjamming transition. The resultant fluidization of the tissue accelerates wound healing. Accordingly, when we experimentally reduce tissue tension in wing discs, the intercalation rate increases and wounds repair in less time.},
	language = {en},
	number = {11},
	urldate = {2021-02-03},
	journal = {Nature Physics},
	author = {Tetley, Robert J. and Staddon, Michael F. and Heller, Davide and Hoppe, Andreas and Banerjee, Shiladitya and Mao, Yanlan},
	month = nov,
	year = {2019},
	note = {Number: 11
Publisher: Nature Publishing Group},
	pages = {1195--1203},
	file = {Accepted Version:C\:\\Users\\Suyash\\Zotero\\storage\\H8KQJRL9\\Tetley et al. - 2019 - Tissue fluidity promotes epithelial wound healing.pdf:application/pdf;Snapshot:C\:\\Users\\Suyash\\Zotero\\storage\\S6Q9ZFVU\\s41567-019-0618-1.html:text/html;Snapshot:C\:\\Users\\Suyash\\Zotero\\storage\\422NDV87\\s41567-019-0618-1.html:text/html;Tetley et al_2019_Tissue fluidity promotes epithelial wound healing.pdf:C\:\\Users\\Suyash\\Zotero\\storage\\Z5J82NRQ\\Tetley et al_2019_Tissue fluidity promotes epithelial wound healing.pdf:application/pdf},
}

@article{davidsonNoStringsAttached2012,
	title = {No strings attached: new insights into epithelial morphogenesis},
	volume = {10},
	issn = {1741-7007},
	shorttitle = {No strings attached},
	url = {https://doi.org/10.1186/1741-7007-10-105},
	doi = {10.1186/1741-7007-10-105},
	abstract = {The dramatic ingression of tissue sheets that accompanies many morphogenetic processes, most notably gastrulation, has been largely attributed to contractile circum-apical actomyosin 'purse-strings' in the infolding cells. Recent studies, however, including one in BMC Biology, expose mechanisms that rely less on actomyosin contractility of purse-string bundles and more on dynamics in the global cortical actomyosin network of the cells. These studies illustrate how punctuated actomyosin contractions and flow of these networks can remodel both epithelial and planarly organized mesenchymal sheets.},
	number = {1},
	urldate = {2025-06-19},
	journal = {BMC Biology},
	author = {Davidson, Lance A.},
	month = dec,
	year = {2012},
	keywords = {Cell Sheet, Epithelial Morphogenesis, Epithelial Sheet, Retinal Pigment Epithelium},
	pages = {105},
	file = {Full Text PDF:C\:\\Users\\Suyash\\Zotero\\storage\\YF6W7Q7K\\Davidson - 2012 - No strings attached new insights into epithelial morphogenesis.pdf:application/pdf;Snapshot:C\:\\Users\\Suyash\\Zotero\\storage\\YZLAI8MK\\1741-7007-10-105.html:text/html},
}

@article{peterEvolutionLaminProtein2012,
	title = {Evolution of the lamin protein family: {What} introns can tell},
	volume = {3},
	issn = {19491042},
	url = {https://www.tandfonline.com/doi/abs/10.4161/nucl.18927},
	doi = {10.4161/NUCL.18927/SUPPL_FILE/KNCL_A_10918927_SM0001.ZIP},
	abstract = {Lamins are the major components of the nuclear lamina, a filamentous layer found at the interphase between chromatin and the inner nuclear membrane. The lamina supports the nuclear envelope and provides anchorage sites for chromatin. Lamins and their associated proteins are required for most nuclear activities, mitosis, and for linking the nucleoskeleton to the network of cytoskeletal filaments. Mutations in lamins and their associated proteins give rise to a wide range of diseases, collectively called laminopathies. This review focuses on the evolution of the lamin protein family. Evolution from basal metazoans to man will be described on the basis of protein sequence comparisons and analyses of their gene structure. Lamins are the founding members of the family of intermediate filament proteins. How genes encoding cytoplasmic IF proteins could have arisen from the archetypal lamin gene progenitor, can be inferred from a comparison of the respective gene structures. The lamin/IF protein family seems to be restricted to the metazoans. In general, invertebrate genomes harbor only a single lamin gene encoding a B-type lamin. The archetypal lamin gene structure found in basal metazoans is conserved up to the vertebrate lineage. The completely different structure of lamin genes in Caenorhabditis and Drosophila are exceptions rather than the rule within their systematic groups. However, variation in the length of the coiled-coil forming central domain might be more common than previously anticipated. The increase in the number of lamin genes in vertebrates can be explained by two rounds of genome duplication. The origin of lamin A by exon shuffling might explain the processing of prelamin A to the mature non-isoprenylated form of lamin A. By alternative splicing the number of vertebrate lamin proteins has increased even further. Lamin C, an alternative splice form of the LMNA gene, is restricted to mammals. Amphibians and mammals express germline-specific lamins that differ in their protein structure from that of somatic lamins. Evidence is provided that there exist lamin-like proteins outside the metazoan lineage. © 2012 Landes Bioscience.},
	number = {1},
	urldate = {2023-04-19},
	journal = {Nucleus},
	author = {Peter, Annette and Stick, Reimer},
	year = {2012},
	pmid = {22156746},
	note = {Number: 1
Publisher: Taylor and Francis Inc.},
	keywords = {Lamins, Evolution, Intron/exon pattern, Metazoans, Nuclear lamina},
	pages = {44--59},
	file = {PDF:C\:\\Users\\Suyash\\Zotero\\storage\\B5SQBZPB\\full-text.pdf:application/pdf},
}

@article{galouImportanceIntermediateFilaments1997,
	title = {The importance of intermediate filaments in the adaptation of tissues to mechanical stress: {Evidence} from gene knockout studies},
	volume = {89},
	copyright = {1997 Société Française des Microscopies and Société Biologie Cellulaire de France},
	issn = {1768-322X},
	shorttitle = {The importance of intermediate filaments in the adaptation of tissues to mechanical stress},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1768-322X.1997.tb00997.x},
	doi = {10.1111/j.1768-322X.1997.tb00997.x},
	abstract = {Research over the past few years on the function of intermediate filaments in cells in culture has not produced convincing results, because the key role of intermediate filaments is within tissues and at certain periods of development. Only recently the technique of gene knockout has been used to examine intermediate filaments in mice and has provided the first evidence that intermediate filaments are directly involved in cell resilience and the maintenance of tissue integrity. Knockout of the gene encoding keratin K8 is lethal in the embryo, and results in hepatic or intestinal lesions, while knockout of the K14 or K10 genes leads to rupture of stratified epithelia. Knockout of the gene encoding desmin causes the rupture of skeletal and cardiac muscle, and collapse of blood vessel walls. Knockout of the gene coding for GFAP leads to a loss of cerebral white matter, and knockout of the gene coding for vimentin causes degeneration of the cerebellar Purkinje cells. The results reveal the lack of compensation by another intermediate filament. Tissues without intermediate filaments fall apart; they are mechanically unstable, unable to resist physical stress, and this leads to cell degeneration. By maintaining the shape and plasticity of the cell, the intermediate filament network acts as an integrator within the cell space. The state of mechanical force imposed on a tissue or a cell can alter the shape of certain elements of the cytoskeleton and thus participate to the control of cell functions.},
	language = {en},
	number = {2},
	urldate = {2025-06-19},
	journal = {Biology of the Cell},
	author = {Galou, Maria and Gao, Jie and Humbert, Jeanne and Mericskay, Mathias and Li, Zhenlin and Paulin, Denise and Vicart, Patrick},
	year = {1997},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1768-322X.1997.tb00997.x},
	keywords = {intermediate filaments, desmin, cytoskeleton, knockout, stress},
	pages = {85--97},
	file = {Snapshot:C\:\\Users\\Suyash\\Zotero\\storage\\NPPI3NR8\\j.1768-322X.1997.tb00997.html:text/html},
}

@article{wragg2016transcriptional,
  title={Transcriptional regulation during zygotic genome activation in zebrafish and other anamniote embryos},
  author={Wragg, Joseph and M{\"u}ller, Ferenc},
  journal={Advances in Genetics},
  volume={95},
  pages={161--194},
  year={2016},
  publisher={Elsevier}
}
@article{schauer2020zebrafish,
  title={Zebrafish embryonic explants undergo genetically encoded self-assembly},
  author={Schauer, Alexandra and Pinheiro, Diana and Hauschild, Robert and Heisenberg, Carl-Philipp},
  journal={Elife},
  volume={9},
  pages={e55190},
  year={2020},
  publisher={eLife Sciences Publications, Ltd}
}
@article{schauer2024robust,
  title={Robust axis elongation by Nodal-dependent restriction of BMP signaling},
  author={Schauer, Alexandra and Pranjic-Ferscha, Kornelija and Hauschild, Robert and Heisenberg, Carl-Philipp},
  journal={Development},
  volume={151},
  number={4},
  year={2024},
  publisher={The Company of Biologists}
}
@article{quintin2008epithelial,
  title={Epithelial morphogenesis in embryos: asymmetries, motors and brakes},
  author={Quintin, Sophie and Gally, Christelle and Labouesse, Michel},
  journal={Trends in genetics},
  volume={24},
  number={5},
  pages={221--230},
  year={2008},
  publisher={Elsevier}
}
@article{belahbib2018new,
  title={New genomic data and analyses challenge the traditional vision of animal epithelium evolution},
  author={Belahbib, Hassiba and Renard, Emmanuelle and Santini, S{\'e}bastien and Jourda, Cyril and Claverie, Jean-Michel and Borchiellini, Carole and Le Bivic, Andr{\'e}},
  journal={BMC genomics},
  volume={19},
  pages={1--15},
  year={2018},
  publisher={Springer}
}
@article{leys2012epithelia,
  title={Epithelia, an evolutionary novelty of metazoans},
  author={Leys, Sally P and Riesgo, Ana},
  journal={Journal of Experimental Zoology Part B: Molecular and Developmental Evolution},
  volume={318},
  number={6},
  pages={438--447},
  year={2012},
  publisher={Wiley Online Library}
}
@article{gibson2003apicobasal,
  title={Apicobasal polarization: epithelial form and function},
  author={Gibson, Matthew C and Perrimon, Norbert},
  journal={Current opinion in cell biology},
  volume={15},
  number={6},
  pages={747--752},
  year={2003},
  publisher={Elsevier}
}
@article{buckley2022apical,
  title={Apical--basal polarity and the control of epithelial form and function},
  author={Buckley, Clare E and St Johnston, Daniel},
  journal={Nature reviews Molecular cell biology},
  volume={23},
  number={8},
  pages={559--577},
  year={2022},
  publisher={Nature Publishing Group UK London}
}
@article{campanale2017development,
  title={Development and dynamics of cell polarity at a glance},
  author={Campanale, Joseph P and Sun, Thomas Y and Montell, Denise J},
  journal={Journal of cell science},
  volume={130},
  number={7},
  pages={1201--1207},
  year={2017},
  publisher={The Company of Biologists Ltd}
}
@article{vasquez2021cells,
  title={How cells tell up from down and stick together to construct multicellular tissues--interplay between apicobasal polarity and cell--cell adhesion},
  author={Vasquez, Claudia G and de la Serna, Eva L and Dunn, Alexander R},
  journal={Journal of cell science},
  volume={134},
  number={21},
  pages={jcs248757},
  year={2021},
  publisher={The Company of Biologists Ltd}
}
@article{zeng2017polarized,
  title={Polarized exocytosis},
  author={Zeng, Jingwen and Feng, Shanshan and Wu, Bin and Guo, Wei},
  journal={Cold Spring Harbor Perspectives in Biology},
  volume={9},
  number={12},
  pages={a027870},
  year={2017},
  publisher={Cold Spring Harbor Lab}
}
@article{matter2003signalling,
  title={Signalling to and from tight junctions},
  author={Matter, Karl and Balda, Maria S},
  journal={Nature reviews Molecular cell biology},
  volume={4},
  number={3},
  pages={225--237},
  year={2003},
  publisher={Nature Publishing Group UK London}
}
@article{pickett2019polarizing,
  title={A polarizing issue: diversity in the mechanisms underlying apico-basolateral polarization in vivo},
  author={Pickett, Melissa A and Naturale, Victor F and Feldman, Jessica L},
  journal={Annual Review of Cell and Developmental Biology},
  volume={35},
  number={1},
  pages={285--308},
  year={2019},
  publisher={Annual Reviews}
}
@article{shin2006tight,
  title={Tight junctions and cell polarity},
  author={Shin, Kunyoo and Fogg, Vanessa C and Margolis, Ben},
  journal={Annu. Rev. Cell Dev. Biol.},
  volume={22},
  number={1},
  pages={207--235},
  year={2006},
  publisher={Annual Reviews}
}
@article{godsel2004molecular,
  title={The molecular composition and function of desmosomes},
  author={Godsel, LM and Getsios, S and Huen, AC and Green, KJ},
  journal={Cell adhesion},
  pages={137--193},
  year={2004},
  publisher={Springer}
}
@article{stanley1982structure,
  title={Structure and function of basement membrane},
  author={Stanley, John R and Woodley, David T and Katz, Stephen I and Martin, George R},
  journal={Journal of Investigative Dermatology},
  volume={79},
  number={1},
  pages={69--72},
  year={1982},
  publisher={Elsevier}
}
@article{pachitariu2022cellpose,
  title={Cellpose 2.0: how to train your own model},
  author={Pachitariu, Marius and Stringer, Carsen},
  journal={Nature methods},
  volume={19},
  number={12},
  pages={1634--1641},
  year={2022},
  publisher={Nature Publishing Group US New York}
}
@incollection{guevorkian2017micropipette,
  title={Micropipette aspiration: A unique tool for exploring cell and tissue mechanics in vivo},
  author={Guevorkian, Karine and Ma{\^\i}tre, J-L},
  booktitle={Methods in cell biology},
  volume={139},
  pages={187--201},
  year={2017},
  publisher={Elsevier}
}
@article{thielicke2021particle,
  title={Particle Image Velocimetry for MATLAB: Accuracy and enhanced algorithms in PIVlab},
  author={Thielicke, William and Sonntag, Ren{\'e}},
  year={2021}
}
@article{herbert2021localzprojector,
  title={LocalZProjector and DeProj: a toolbox for local 2D projection and accurate morphometrics of large 3D microscopy images},
  author={Herbert, S{\'e}bastien and Valon, L{\'e}o and Mancini, Laure and Dray, Nicolas and Caldarelli, Paolo and Gros, J{\'e}r{\^o}me and Esposito, Elric and Shorte, Spencer L and Bally-Cuif, Laure and Aulner, Nathalie and others},
  journal={BMC biology},
  volume={19},
  pages={1--13},
  year={2021},
  publisher={Springer}
}
@article{arslan2024adhesion,
  title={Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts},
  author={Arslan, Feyza Nur and Hannezo, Edouard and Merrin, Jack and Loose, Martin and Heisenberg, Carl-Philipp},
  journal={Current Biology},
  volume={34},
  number={1},
  pages={171--182},
  year={2024},
  publisher={Elsevier}
}
@article{ramms2013keratins,
  title={Keratins as the main component for the mechanical integrity of keratinocytes},
  author={Ramms, Lena and Fabris, Gloria and Windoffer, Reinhard and Schwarz, Nicole and Springer, Ronald and Zhou, Chen and Lazar, Jaroslav and Stiefel, Simone and Hersch, Nils and Schnakenberg, Uwe and others},
  journal={Proceedings of the National Academy of Sciences},
  volume={110},
  number={46},
  pages={18513--18518},
  year={2013},
  publisher={National Academy of Sciences}
}
@article{lim2020keratins,
  title={Keratins are asymmetrically inherited fate determinants in the mammalian embryo},
  author={Lim, Hui Yi Grace and Alvarez, Yanina D and Gasnier, Maxime and Wang, Yiming and Tetlak, Piotr and Bissiere, Stephanie and Wang, Hongmei and Biro, Mat{\'e} and Plachta, Nicolas},
  journal={Nature},
  volume={585},
  number={7825},
  pages={404--409},
  year={2020},
  publisher={Nature Publishing Group UK London}
}
@article{bohnekamp2015drosophila,
  title={A Drosophila model of epidermolysis bullosa simplex},
  author={Bohnekamp, Jens and Cryderman, Diane E and Paululat, Achim and Baccam, Gabriel C and Wallrath, Lori L and Magin, Thomas M},
  journal={Journal of Investigative Dermatology},
  volume={135},
  number={8},
  pages={2031--2039},
  year={2015},
  publisher={Elsevier}
}
@article{de2018intermediate,
  title={Intermediate filaments control collective migration by restricting traction forces and sustaining cell--cell contacts},
  author={De Pascalis, Chiara and P{\'e}rez-Gonz{\'a}lez, Carlos and Seetharaman, Shailaja and Bo{\"e}da, Batiste and Vianay, Benoit and Burute, Mithila and Leduc, C{\'e}cile and Borghi, Nicolas and Trepat, Xavier and Etienne-Manneville, Sandrine},
  journal={Journal of cell biology},
  volume={217},
  number={9},
  pages={3031--3044},
  year={2018},
  publisher={Rockefeller University Press}
}
@article{goonesinghe2012desmosomal,
  title={Desmosomal cadherins in zebrafish epiboly and gastrulation},
  author={Goonesinghe, Alexander and Luan, Xing-Ming and Hurlstone, Adam and Garrod, David},
  journal={BMC Developmental Biology},
  volume={12},
  pages={1--16},
  year={2012},
  publisher={Springer}
}
@article{lulevich2010single,
  title={Single cell mechanics of keratinocyte cells},
  author={Lulevich, Valentin and Yang, Hsin-ya and Isseroff, R Rivkah and Liu, Gang-yu},
  journal={Ultramicroscopy},
  volume={110},
  number={12},
  pages={1435--1442},
  year={2010},
  publisher={Elsevier}
}
@article{sanghvi-shahIntermediateFilamentsJunction2017b,
  title = {Intermediate {{Filaments}} at the {{Junction}} of {{Mechanotransduction}}, {{Migration}}, and {{Development}}},
  author = {{Sanghvi-Shah}, Rucha and Weber, Gregory F.},
  year = {2017},
  month = sep,
  journal = {Frontiers in Cell and Developmental Biology},
  volume = {5},
  pages = {81},
  issn = {2296-634X},
  doi = {10.3389/fcell.2017.00081},
  urldate = {2023-09-27},
  pmcid = {PMC5603733},
  pmid = {28959689},
  file = {/Users/snaik/Zotero/storage/L9R5HXMF/Sanghvi-Shah and Weber - 2017 - Intermediate Filaments at the Junction of Mechanot.pdf}
}
@article{yoon2019Keratinintermediatefilaments,
  title = {Keratin Intermediate Filaments: Intermediaries of Epithelial Cell Migration},
  shorttitle = {Keratin Intermediate Filaments},
  author = {Yoon, Sungjun and Leube, Rudolf~E.},
  year = {2019},
  month = oct,
  journal = {Essays in Biochemistry},
  volume = {63},
  number = {5},
  pages = {521--533},
  issn = {0071-1365},
  doi = {10.1042/EBC20190017},
  urldate = {2022-09-04},
  abstract = {Migration of epithelial cells is fundamental to multiple developmental processes, epithelial tissue morphogenesis and maintenance, wound healing and metastasis. While migrating epithelial cells utilize the basic acto-myosin based machinery as do other non-epithelial cells, they are distinguished by their copious keratin intermediate filament (KF) cytoskeleton, which comprises differentially expressed members of two large multigene families and presents highly complex patterns of post-translational modification. We will discuss how the unique mechanophysical and biochemical properties conferred by the different keratin isotypes and their modifications serve as finely tunable modulators of epithelial cell migration. We will furthermore argue that KFs together with their associated desmosomal cell--cell junctions and hemidesmosomal cell--extracellular matrix (ECM) adhesions serve as important counterbalances to the contractile acto-myosin apparatus either allowing and optimizing directed cell migration or preventing it. The differential keratin expression in leaders and followers of collectively migrating epithelial cell sheets provides a compelling example of isotype-specific keratin functions. Taken together, we conclude that the expression levels and specific combination of keratins impinge on cell migration by conferring biomechanical properties on any given epithelial cell affecting cytoplasmic viscoelasticity and adhesion to neighboring cells and the ECM.},
  file = {/Users/snaik/Zotero/storage/4S4NFDMT/Yoon_Leube_2019_Keratin intermediate filaments.pdf;/Users/snaik/Zotero/storage/QYBMW2W7/Yoon and Leube - 2019 - Keratin intermediate filaments intermediaries of epithelial cell migration.pdf;/Users/snaik/Zotero/storage/RV5PECGF/Keratin-intermediate-filaments-intermediaries-of.html}
}
@article{cheung2013collective,
  title={Collective invasion in breast cancer requires a conserved basal epithelial program},
  author={Cheung, Kevin J and Gabrielson, Edward and Werb, Zena and Ewald, Andrew J},
  journal={Cell},
  volume={155},
  number={7},
  pages={1639--1651},
  year={2013},
  publisher={Elsevier}
}
@article{roberts2011Desmosomedynamicsmigrating,
  title = {Desmosome Dynamics in Migrating Epithelial Cells Requires the Actin Cytoskeleton},
  author = {Roberts, Brett J. and Pashaj, Anjeza and Johnson, Keith R. and Wahl, James K.},
  year = {2011},
  month = dec,
  journal = {Experimental Cell Research},
  volume = {317},
  number = {20},
  pages = {2814--2822},
  issn = {0014-4827},
  doi = {10.1016/j.yexcr.2011.09.003},
  urldate = {2025-04-11},
  abstract = {Re-modeling of epithelial tissues requires that the cells in the tissue rearrange their adhesive contacts in order to allow cells to migrate relative to neighboring cells. Desmosomes are prominent adhesive structures found in a variety of epithelial tissues that are believed to inhibit cell migration and invasion. Mechanisms regulating desmosome assembly and stability in migrating cells are largely unknown. In this study we established a cell culture model to examine the fate of desmosomal components during scratch wound migration. Desmosomes are rapidly assembled between epithelial cells at the lateral edges of migrating cells and structures are transported in a retrograde fashion while the structures become larger and mature. Desmosome assembly and dynamics in this system are dependent on the actin cytoskeleton prior to being associated with the keratin intermediate filament cytoskeleton. These studies extend our understanding of desmosome assembly and provide a system to examine desmosome assembly and dynamics during epithelial cell migration.},
  keywords = {Actin,Desmocollin,Desmosome,Live cell microscopy,Motility,Plakophilin-3},
  file = {/Users/snaik/Zotero/storage/BF2GKSL4/Roberts et al. - 2011 - Desmosome dynamics in migrating epithelial cells requires the actin cytoskeleton.pdf;/Users/snaik/Zotero/storage/AIXDUI4M/S0014482711003624.html}
}
@article{zhang2011tensioninducedmechanotransductionpathway,
  title = {A Tension-Induced Mechanotransduction Pathway Promotes Epithelial Morphogenesis},
  author = {Zhang, Huimin and Landmann, Fr{\'e}d{\'e}ric and Zahreddine, Hala and Rodriguez, David and Koch, Marc and Labouesse, Michel},
  year = {2011},
  month = mar,
  journal = {Nature},
  volume = {471},
  number = {7336},
  pages = {99--103},
  publisher = {Nature Publishing Group},
  issn = {1476-4687},
  doi = {10.1038/nature09765},
  urldate = {2025-04-11},
  abstract = {The development and function of many organs depend not only on biochemical signals, but also on the ability of cells and tissues to respond biochemically to mechanical forces --- mechanotransduction. Here, Michel Labouesse and colleagues describe a mechanotransduction pathway that links the body wall with the epidermis in the roundworm Caenorhabditis elegans. The pathway involves the p21-activated kinase PAK-1, an adaptor GIT-1 and its partner PIX-1. Tension exerted by muscles or external pressure keeps GIT-1 on station at hemidesmosomes --- the small rivet-like bodies that attach epidermal cells to the underlying musculature --- and stimulates PAK-1 through PIX-1 and Rac GTPase. The C. elegans hemidesmosome is therefore more than a passive attachment structure --- it is a sensor that responds to tension by triggering signalling processes.},
  copyright = {2011 Springer Nature Limited},
  langid = {english},
  keywords = {Mechanotransduction,Morphogenesis,Muscle},
  file = {/Users/snaik/Zotero/storage/5YBZ5TE7/Zhang et al. - 2011 - A tension-induced mechanotransduction pathway promotes epithelial morphogenesis.pdf}
}
@article{mueller1983Biochemicalimmunologicalcharacterization,
  title = {Biochemical and Immunological Characterization of Desmoplakins {{I}} and {{II}}, the Major Polypeptides of the Desmosomal Plaque},
  author = {Mueller, Helga and Franke, Werner W.},
  year = {1983},
  month = feb,
  journal = {Journal of Molecular Biology},
  volume = {163},
  number = {4},
  pages = {647--671},
  issn = {0022-2836},
  doi = {10.1016/0022-2836(83)90116-X},
  urldate = {2025-04-15},
  abstract = {Epithelial cells contain complexes of cytokeratin filaments (tonofilaments) with specific domains of the plasma membrane that appear as symmetric junctions, i.e. desmosomes, or as asymmetric hemi-desmosomes. These regions of filament-membrane-attachment are characterized by 14 to 20 nm thick dense plaques (desmosomal plaque). In isolated desmosome-tonofilament complexes or other desmosomal fractions from various stratified squamous epithelia (e.g. bovine muzzle epidermis and tongue mucosa) desmosomal plaque structures are recognized and show a relatively high resistance to various extraction buffers and detergents. Such fractions enriched in desmosomal plaque material are also enriched in two prominent polypeptide bands of apparent molecular weights 250,000 (desmoplakin{\dag}{\dag}Constructed from the Greek words {$\delta\epsilon\sigma\mu$}{\'o}s, for link, tie, bond, connection, anchorage, and {$\pi\lambda$}{\'{\textbackslash}}ga{$\xi$}, {$\pi\lambda\alpha\kappa$}{\'o}s, for plate, plaque, board. I) and 215,000 (desmoplakin II) which appear, on two-dimensional gel electrophoresis, as two distinct polypeptides isoelectric near neutral pH. These two polypeptides are present in almost equimolar amounts and each of them appears as a series of isoelectric variants, including some labeled by [32P]phosphate in tissue slices. The two desmoplakin polypeptides are closely related as shown by tryptic peptide map analysis and are different from keratin-like proteins and other major polypeptides of desmosome-rich fractions. Guinea pig antibodies raised against desmoplakins and specific for these proteins do not cross-react with other desmosomal antigen(s) or constituents of other types of junctions. Using desmoplakin antibodies we have identified desmoplakins as the major constituents of the desmosomal plaques present in epithelial and myocardiac cells of diverse species. The significance of this group of cell type-specific membrane-associated cytoskeletal proteins and their possible cytoskeletal functions are discussed.},
  file = {/Users/snaik/Zotero/storage/ED6BW37E/Mueller and Franke - 1983 - Biochemical and immunological characterization of desmoplakins I and II, the major polypeptides of t.pdf;/Users/snaik/Zotero/storage/BS99URTU/002228368390116X.html}
}
@article{gallicano2001Rescuingdesmoplakinfunction,
  title = {Rescuing Desmoplakin Function in Extra-Embryonic Ectoderm Reveals the Importance of This Protein in Embryonic Heart, Neuroepithelium, Skin and Vasculature},
  author = {Gallicano, G. Ian and Bauer, Christoph and Fuchs, Elaine},
  year = {2001},
  month = mar,
  journal = {Development},
  volume = {128},
  number = {6},
  pages = {929--941},
  issn = {0950-1991},
  doi = {10.1242/dev.128.6.929},
  urldate = {2025-04-15},
  abstract = {Desmosomes mediate intercellular adhesion through desmosomal cadherins, which interface with plakoglobin (PG) and desmoplakin (DP) to associate with the intermediate filament (IF) cytoskeleton. Desmosomes first assemble in the E3.5 mouse trophectoderm, concomitant with establishment of epithelial polarity and appearance of a blastocoel cavity. Increasing in size and number, desmosomes continue their prominence in extra-embryonic tissues, but as development proceeds, they also become abundant in a number of embryonic tissues, including heart muscle, epidermis and neuroepithelium. Previously, we explored the functional importance of desmosomes by ablating the Dsp gene. Homozygous Dsp mutant embryos progressed through implantation, but did not survive beyond E6.5, owing to a loss or instability of desmosomes and tissue integrity. We have now rescued the extra-embryonic tissues by aggregation of tetraploid (wild-type) and diploid (Dsp mutant) morulae. These animals survive several days longer, but die shortly after gastrulation, with major defects in the heart muscle, neuroepithelium and skin epithelium, all of which possess desmosomes, as well as the microvasculature, which does not. Interestingly, although wild-type endothelial cells of capillaries do not form desmosomes, they possess unusual intercellular junctions composed of DP, PG and VE-cadherin. The severity in phenotype and the breadth of defects in the Dsp mutant embryo is greater than PG mutant embryos, substantiating redundancy between PG and other armadillo proteins (e.g. {$\beta$}-catenin). The timing of lethality is similar to that of the VE-cadherin null embryo, suggesting that a participating cause of death may be a defect in vasculature, not reported for PG null embryos.},
  file = {/Users/snaik/Zotero/storage/4IZ8EG6M/Gallicano et al. - 2001 - Rescuing desmoplakin function in extra-embryonic ectoderm reveals the importance of this protein in.pdf}
}
@article{vasioukhin2001Desmoplakinessentialepidermal,
  title = {Desmoplakin Is Essential in Epidermal Sheet Formation},
  author = {Vasioukhin, Valeri and Bowers, Ethan and Bauer, Christoph and Degenstein, Linda and Fuchs, Elaine},
  year = {2001},
  month = dec,
  journal = {Nature Cell Biology},
  volume = {3},
  number = {12},
  pages = {1076--1085},
  publisher = {Nature Publishing Group},
  issn = {1476-4679},
  doi = {10.1038/ncb1201-1076},
  urldate = {2025-04-15},
  abstract = {We have generated an epidermis-specific desmoplakin (DP) mouse knockout, and show that epidermal integrity requires DP; mechanical stresses to DP-null skin cause intercellular separations. The number of epidermal desmosomes in DP-null skin is similar to wild type (WT), but they lack keratin filaments, which compromise their function. DP-null keratinocytes have few desmosomes in vitro, and are unable to undergo actin reorganization and membrane sealing during epithelial sheet formation. Adherens junctions are also reduced. In vitro, DP transgene expression rescues these defects. DP is therefore required for assembly of functional desmosomes, maintaining cytoskeletal architecture and reinforcing membrane attachments essential for stable intercellular adhesion.},
  copyright = {2001 Springer Nature Limited},
  langid = {english},
  keywords = {Cancer Research,Cell Biology,Developmental Biology,general,Life Sciences,Stem Cells},
  file = {/Users/snaik/Zotero/storage/IILFCUYC/Vasioukhin et al. - 2001 - Desmoplakin is essential in epidermal sheet formation.pdf}
}
@article{nolting2014MechanicsIndividualKeratin,
  title = {Mechanics of {{Individual Keratin Bundles}} in {{Living Cells}}},
  author = {Nolting, Jens-Friedrich and M{\"o}bius, Wiebke and K{\"o}ster, Sarah},
  year = {2014},
  month = dec,
  journal = {Biophysical Journal},
  volume = {107},
  number = {11},
  pages = {2693--2699},
  publisher = {Elsevier},
  issn = {0006-3495, 1542-0086},
  doi = {10.1016/j.bpj.2014.10.039},
  urldate = {2025-04-12},
  langid = {english},
  pmid = {25468348},
  file = {/Users/snaik/Zotero/storage/8T9GU3H6/Nolting et al. - 2014 - Mechanics of Individual Keratin Bundles in Living Cells.pdf}
}
@article{el-brolosyGeneticCompensationTriggered2019,
  title = {Genetic Compensation Triggered by Mutant {{mRNA}} Degradation},
  author = {{El-Brolosy}, Mohamed A. and Kontarakis, Zacharias and Rossi, Andrea and Kuenne, Carsten and G{\"u}nther, Stefan and Fukuda, Nana and Kikhi, Khrievono and Boezio, Giulia L. M. and Takacs, Carter M. and Lai, Shih-Lei and Fukuda, Ryuichi and Gerri, Claudia and Giraldez, Antonio J. and Stainier, Didier Y. R.},
  year = {2019},
  month = apr,
  journal = {Nature},
  volume = {568},
  number = {7751},
  pages = {193--197},
  publisher = {Nature Publishing Group},
  issn = {1476-4687},
  doi = {10.1038/s41586-019-1064-z},
  urldate = {2021-08-16},
  abstract = {Genetic robustness, or the ability of an organism to maintain fitness in the presence of harmful mutations, can be achieved via protein feedback loops. Previous work has suggested that organisms may also respond to mutations by transcriptional adaptation, a process by which related gene(s) are upregulated independently of protein feedback loops. However, the prevalence of transcriptional adaptation and its underlying molecular mechanisms are unknown. Here, by analysing several models of transcriptional adaptation in zebrafish and mouse, we uncover a requirement for mutant mRNA degradation. Alleles that fail to transcribe the mutated gene do not exhibit transcriptional adaptation, and these alleles give rise to more severe phenotypes than alleles displaying mutant mRNA decay. Transcriptome analysis in alleles displaying mutant mRNA decay reveals the upregulation of a substantial proportion of the genes that exhibit sequence similarity with the mutated gene's mRNA, suggesting a sequence-dependent mechanism. These findings have implications for our understanding of disease-causing mutations, and will help in the design of mutant alleles with minimal transcriptional adaptation-derived compensation.},
  copyright = {2019 The Author(s), under exclusive licence to Springer Nature Limited},
  langid = {english},
  annotation = {Bandiera\_abtest: a\\
Cg\_type: Nature Research Journals\\
Primary\_atype: Research\\
Subject\_term: Development;Developmental biology;Gene regulation;Non-coding RNAs;Transcription\\
Subject\_term\_id: development;developmental-biology;gene-regulation;non-coding-rnas;transcription},
  file = {/Users/snaik/Zotero/storage/CP4STATR/El-Brolosy et al_2019_Genetic compensation triggered by mutant mRNA degradation.pdf;/Users/snaik/Zotero/storage/8EJ2D8UX/s41586-019-1064-z.html}
}
@incollection{vijayaraj2007KeratinTransgenicKnockout,
  title = {Keratin {{Transgenic}} and {{Knockout Mice}}},
  booktitle = {Target {{Discovery}} and {{Validation Reviews}} and {{Protocols}}: {{Volume}} 1, {{Emerging Strategies}} for {{Targets}} and {{Biomarker Discovery}}},
  author = {Vijayaraj, Preethi and S{\"o}hl, Goran and Magin, Thomas M.},
  editor = {Sioud, Mouldy},
  year = {2007},
  pages = {203--251},
  publisher = {Humana Press},
  address = {Totowa, NJ},
  doi = {10.1385/1-59745-165-7:203},
  urldate = {2025-04-17},
  abstract = {Summary The intermediate filament (IF) cytoskeleton of mammalian epithelia is generated from pairs of type I and type II keratins that are encoded by two large gene families, made up of 54 genes in humans and the mouse. These genes are expressed in a spatiotemporal and tissue-specific manner from the blastocyst stage onward. Since the discovery of keratin mutations leading to epidermolysis bullosa simplex, mutations in at least 18 keratin genes have been identified that result in keratinopathies of the epidermis and its appendages. Recently, noncanonical mutations in simple epithelial keratins were associated with pancreatic, liver, and intestinal disorders, demonstrating that keratins protect epithelia against mechanical and other forms of stress. In recent years, animal models provided novel insight and significantly improved understanding of IF function in tissue homeostasis and its role in disease. Pathological phenotypes detected in mutant mice generated so far range from embryonic lethality to tissue fragility to subtlety, which often depends on their genetic background. This range implies at least a partial influence of yet unidentified modifier genes on the phenotype after the ablation of the respective keratin. To date, nearly all available keratin mouse models were generated by taking advantage of conventional gene-targeting strategies. To reveal their cell type-specific functions and the mechanisms by which mutations lead to disease, it will be necessary to use conditional gene-targeting strategies and the introduction of point-mutated gene copies. Furthermore, conditional strategies offer the possibility to overcome embryonic or neonatal lethality in some of the keratin-deficient mice.},
  isbn = {978-1-59745-165-9},
  langid = {english},
  keywords = {Blastocysts injection,Cre/LoxP system,embryonic stem (ES) cell culture,epidermolysis bullosa simplex (EBS),epidermolytic hyperkeratosis (EHK),Flp/FRT system,genomic cluster knockout,intermediate filaments,knockout mice,pachyonychia congenita,tetraploids,transgenic mice},
  file = {/Users/snaik/Zotero/storage/YA9ACIRR/Vijayaraj et al. - 2007 - Keratin Transgenic and Knockout Mice.pdf}
}
@article{tamai2000Cytokeratins819,
  title = {Cytokeratins 8 and 19 in the {{Mouse Placental Development}}},
  author = {Tamai, Yoshitaka and Ishikawa, Tomo-o and B{\"o}sl, Michael R. and Mori, Masahiko and Nozaki, Masami and Baribault, Hel{\'e}ne and Oshima, Robert G. and Taketo, Makoto M.},
  year = {2000},
  month = oct,
  journal = {Journal of Cell Biology},
  volume = {151},
  number = {3},
  pages = {563--572},
  issn = {0021-9525},
  doi = {10.1083/jcb.151.3.563},
  urldate = {2025-04-17},
  abstract = {To investigate the expression and biological roles of cytokeratin 19 (K19) in development and in adult tissues, we inactivated the mouse K19 gene (Krt1-19) by inserting a bacterial {$\beta$}-galactosidase gene (lacZ) by homologous recombination in embryonic stem cells, and established germ line mutant mice. Both heterozygous and homozygous mutant mice were viable, fertile, and appeared normal. By 7.5--8.0 days post coitum (dpc), heterozygous mutant embryos expressed lacZ in the notochordal plate and hindgut diverticulum, reflecting the fact that the notochord and the gut endoderm are derived from the axial mesoderm-originated cells. In the adult mutant, lacZ was expressed mainly in epithelial tissues. To investigate the possible functional cooperation and synergy between K19 and K8, we then constructed compound homozygous mutants, whose embryos died {$\sim$}10 dpc. The lethality resulted from defects in the placenta where both K19 and K8 are normally expressed. As early as 9.5 dpc, the compound mutant placenta had an excessive number of giant trophoblasts, but lacked proper labyrinthine trophoblast or spongiotrophoblast development, which apparently caused flooding of the maternal blood into the embryonic placenta. These results indicate that K19 and K8 cooperate in ensuring the normal development of placental tissues.},
  file = {/Users/snaik/Zotero/storage/658I4R4H/Tamai et al. - 2000 - Cytokeratins 8 and 19 in the Mouse Placental Development.pdf;/Users/snaik/Zotero/storage/PUJDGU69/tamai2000.pdf;/Users/snaik/Zotero/storage/SSG5QQT7/Cytokeratins-8-and-19-in-the-Mouse-Placental.html}
}
@article{sivaramakrishnanShearStressInduced2009,
  title = {Shear Stress Induced Reorganization of the Keratin Intermediate Filament Network Requires Phosphorylation by Protein Kinase {{C}} Zeta},
  author = {Sivaramakrishnan, Sivaraj and Schneider, Jaime L. and Sitikov, Albert and Goldman, Robert D. and Ridge, Karen M.},
  year = {2009},
  month = jun,
  journal = {Molecular Biology of the Cell},
  volume = {20},
  number = {11},
  pages = {2755--2765},
  issn = {1939-4586},
  doi = {10.1091/mbc.e08-10-1028},
  abstract = {Keratin intermediate filaments (KIFs) form a fibrous polymer network that helps epithelial cells withstand external mechanical forces. Recently, we established a correlation between the structure of the KIF network and its local mechanical properties in alveolar epithelial cells. Shear stress applied across the cell surface resulted in the structural remodeling of KIF and a substantial increase in the elastic modulus of the network. This study examines the mechanosignaling that regulates the structural remodeling of the KIF network. We report that the shear stress-mediated remodeling of the KIF network is facilitated by a twofold increase in the dynamic exchange rate of KIF subunits, which is regulated in a PKC zeta and 14-3-3-dependent manner. PKC zeta phosphorylates K18pSer33, and this is required for the structural reorganization because the KIF network in A549 cells transfected with a dominant negative PKC zeta, or expressing the K18Ser33Ala mutation, is unchanged. Blocking the shear stress-mediated reorganization results in reduced cellular viability and increased apoptotic levels. These data suggest that shear stress mediates the phosphorylation of K18pSer33, which is required for the reorganization of the KIF network, resulting in changes in mechanical properties of the cell that help maintain the integrity of alveolar epithelial cells.},
  langid = {english},
  pmcid = {PMC2688554},
  pmid = {19357195},
  keywords = {14-3-3 Proteins,Amino Acid Substitution,Cell Cycle,Cell Line Tumor,Fluorescent Antibody Technique,Green Fluorescent Proteins,Humans,Immunoblotting,Immunoprecipitation,Intermediate Filaments,Keratin-18,Keratins,Microscopy Confocal,Mutation,Phosphorylation,Protein Binding,Protein Kinase C,Serine,Stress Mechanical},
  file = {/Users/snaik/Zotero/storage/TNCGCHAG/Sivaramakrishnan et al_2009_Shear stress induced reorganization of the keratin intermediate filament.pdf}
}
@article{duqueRuptureStrengthLiving2024,
  title = {Rupture Strength of Living Cell Monolayers},
  author = {Duque, Julia and Bonfanti, Alessandra and Fouchard, Jonathan and Baldauf, Lucia and Azenha, Sara R. and Ferber, Emma and Harris, Andrew and Barriga, Elias H. and Kabla, Alexandre J. and Charras, Guillaume},
  year = {2024},
  month = nov,
  journal = {Nature Materials},
  volume = {23},
  number = {11},
  pages = {1563--1574},
  publisher = {Nature Publishing Group},
  issn = {1476-4660},
  doi = {10.1038/s41563-024-02027-3},
  urldate = {2025-02-05},
  abstract = {To fulfil their function, epithelial tissues need to sustain mechanical stresses and avoid rupture. Although rupture is usually undesired, it is central to some developmental processes, for example, blastocoel formation. Nonetheless, little is known about tissue rupture because it is a multiscale phenomenon that necessitates comprehension of the interplay between mechanical forces and biological processes at the molecular and cellular scales. Here we characterize rupture in epithelial monolayers using mechanical measurements, live imaging and computational modelling. We show that despite consisting of only a single layer of cells, monolayers can withstand surprisingly large deformations, often accommodating several-fold increases in their length before rupture. At large deformation, epithelia increase their stiffness multiple fold in a process controlled by a supracellular network of keratin filaments. Perturbing the keratin network organization fragilized the monolayers and prevented strain-stiffening. Although the kinetics of adhesive bond rupture ultimately control tissue strength, tissue rheology and the history of deformation set the strain and stress at the onset of fracture.},
  copyright = {2024 The Author(s)},
  langid = {english},
  keywords = {Biopolymers in vivo,Rheology},
  file = {/Users/snaik/Zotero/storage/ZYTKGSY2/Duque et al. - 2024 - Rupture strength of living cell monolayers.pdf}
}
@article{mayerAnisotropiesCorticalTension2010,
  title = {Anisotropies in Cortical Tension Reveal the Physical Basis of Polarizing Cortical Flows},
  author = {Mayer, Mirjam and Depken, Martin and Bois, Justin S. and J{\"u}licher, Frank and Grill, Stephan W.},
  year = {2010},
  month = sep,
  journal = {Nature},
  volume = {467},
  number = {7315},
  pages = {617--621},
  publisher = {Nature Publishing Group},
  issn = {1476-4687},
  doi = {10.1038/nature09376},
  urldate = {2021-01-28},
  abstract = {Cortical flows of actomyosin are central to many processes in cellular and developmental biology. In the one-cell Caenorhabditis elegans embryo, anteroposterior polarity, a prerequisite for asymmetric cell division, is established by large-scale flow of the actomyosin cortex that segregates cortical polarity proteins between the anterior and posterior domains. The underlying forces and physical principles behind long-range flow remain unclear. Mayer et al. have devised a novel method to measure cortical tension (total mechanical tension) and find that cortical flows are driven by contractility of the actomyosin network. The direction of flow depends on anisotropies in the cortical tension, and long-range cortical flow occurs only if the cortex is sufficiently viscous.},
  langid = {english},
  keywords = {Actomyosincortex,Lasercuts},
  file = {/Users/snaik/Zotero/storage/GFLGYHFT/Mayer et al. - 2010 - Anisotropies in cortical tension reveal the physic.pdf;/Users/snaik/Zotero/storage/HZ6JIT9B/Mayer et al. - 2010 - Anisotropies in cortical tension reveal the physic.pdf;/Users/snaik/Zotero/storage/9H59AX5K/nature09376.html}
}
@article{clarke2021Actinbasedforcegenerationa,
  title = {Actin-Based Force Generation and Cell Adhesion in Tissue Morphogenesis},
  author = {Clarke, D. Nathaniel and Martin, Adam C.},
  year = {2021},
  month = may,
  journal = {Current Biology},
  volume = {31},
  number = {10},
  pages = {R667-R680},
  issn = {09609822},
  doi = {10.1016/j.cub.2021.03.031},
  urldate = {2025-06-20},
  abstract = {The generation of organismal form (i.e., morphogenesis) arises from forces produced at the cellular level. In animal cells, much of this force is produced by the actin cytoskeleton. Here, we review how mechanisms of actin-based force generation are deployed during animal morphogenesis to sculpt organs and organisms. Furthermore, we discuss how cytoskeletal forces are coupled through cell adhesions to propagate across tissues, and cases where cytoskeletal force or adhesion is patterned across a tissue to direct shape changes. Together, our review highlights a conceptual framework to reflect our current understanding of animal morphogenesis and provides perspectives on future opportunities of study.},
  langid = {english},
  file = {/Users/snaik/Zotero/storage/D4NQIJBX/Clarke and Martin - 2021 - Actin-based force generation and cell adhesion in tissue morphogenesis.pdf}
}

@article{park2017Tissuescalecoordinationcellular,
  title = {Tissue-Scale Coordination of Cellular Behaviour Promotes Epidermal Wound Repair in Live Mice},
  author = {Park, Sangbum and Gonzalez, David G. and Guirao, Boris and Boucher, Jonathan D. and Cockburn, Katie and Marsh, Edward D. and Mesa, Kailin R. and Brown, Samara and Rompolas, Panteleimon and Haberman, Ann M. and Bella{\"i}che, Yohanns and Greco, Valentina},
  year = {2017},
  month = mar,
  journal = {Nature Cell Biology},
  volume = {19},
  number = {3},
  pages = {155--163},
  publisher = {Nature Publishing Group},
  issn = {1476-4679},
  doi = {10.1038/ncb3472},
  urldate = {2025-04-17},
  abstract = {Tissue repair is fundamental to our survival as tissues are challenged by recurrent damage. During mammalian skin repair, cells respond by migrating and proliferating to close the wound. However, the coordination of cellular repair behaviours and their effects on homeostatic functions in a live mammal remains unclear. Here we capture the spatiotemporal dynamics of individual epithelial behaviours by imaging wound re-epithelialization in live mice. Differentiated cells migrate while the rate of differentiation changes depending on local rate of migration and tissue architecture. Cells depart from a highly proliferative zone by directionally dividing towards the wound while collectively migrating. This regional coexistence of proliferation and migration leads to local expansion and elongation of the repairing epithelium. Finally, proliferation functions to pattern and restrict the recruitment of undamaged cells. This study elucidates the interplay of cellular repair behaviours and consequent changes in homeostatic behaviours that support tissue-scale organization of wound re-epithelialization.},
  copyright = {2017 Springer Nature Limited},
  langid = {english},
  keywords = {Microscopy,Mouse,Regeneration},
  file = {/Users/snaik/Zotero/storage/KKAZ75SQ/Park et al. - 2017 - Tissue-scale coordination of cellular behaviour promotes epidermal wound repair in live mice.pdf}
}
@article{campinhoTensionorientedCellDivisions2013,
  title = {Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading during Zebrafish Epiboly},
  author = {Campinho, Pedro and Behrndt, Martin and Ranft, Jonas and Risler, Thomas and Minc, Nicolas and Heisenberg, Carl-Philipp},
  year = {2013},
  month = dec,
  journal = {Nature Cell Biology},
  volume = {15},
  number = {12},
  pages = {1405--1414},
  publisher = {Nature Publishing Group},
  issn = {1476-4679},
  doi = {10.1038/ncb2869},
  urldate = {2020-12-14},
  abstract = {Epithelial spreading is a common and fundamental aspect of various developmental and disease-related processes such as epithelial closure and wound healing. A key challenge for epithelial tissues undergoing spreading is to increase their surface area without disrupting epithelial integrity. Here we show that orienting cell divisions by tension constitutes an efficient mechanism by which the enveloping cell layer (EVL) releases anisotropic tension while undergoing spreading during zebrafish epiboly. The control of EVL cell-division orientation by tension involves cell elongation and requires myosin II activity to align the mitotic spindle with the main tension axis. We also found that in the absence of tension-oriented cell divisions and in the presence of increased tissue tension, EVL cells undergo ectopic fusions, suggesting that the reduction of tension anisotropy by oriented cell divisions is required to prevent EVL cells from fusing. We conclude that cell-division orientation by tension constitutes a key mechanism for limiting tension anisotropy and thus promoting tissue spreading during EVL epiboly.},
  copyright = {2013 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  langid = {english},
  keywords = {Actomyosincortex,cell fate specification,CellDivision,CParticles,Epithelia,Lasercuts},
  file = {/Users/snaik/Zotero/storage/YUAQWYYG/Campinho et al_2013_Tension-oriented cell divisions limit anisotropic tissue tension in epithelial.pdf;/Users/snaik/Zotero/storage/ZP8JXKSM/ncb2869.html}
}

@article{goldner2023Evidencethattissue,
  title = {Evidence That Tissue Recoil in the Early {{Drosophila}} Embryo Is a Passive Not Active Process},
  author = {Goldner, Amanda Nicole and Fessehaye, Salena M. and Rodriguez, Nataly and Mapes, Kelly Ann and Osterfield, Miriam and Doubrovinski, Konstantin},
  year = {2023},
  month = sep,
  journal = {Molecular Biology of the Cell},
  volume = {34},
  number = {10},
  pages = {br16},
  publisher = {American Society for Cell Biology (mboc)},
  issn = {1059-1524},
  doi = {10.1091/mbc.E22-09-0409},
  urldate = {2025-04-17},
  abstract = {Understanding tissue morphogenesis is impossible without knowing the mechanical properties of the tissue being shaped. Although techniques for measuring tissue material properties are continually being developed, methods for determining how individual proteins contribute to mechanical properties are very limited. Here, we developed two complementary techniques for the acute inactivation of spaghetti squash (the Drosophila myosin regulatory light chain), one based on the recently introduced (auxin-inducible degron 2 (AID2) system, and the other based on a novel method for conditional protein aggregation that results in nearly instantaneous protein inactivation. Combining these techniques with rheological measurements, we show that passive material properties of the cellularization-stage Drosophila embryo are essentially unaffected by myosin activity. These results suggest that this tissue is elastic, not predominantly viscous, on the developmentally relevant timescale.},
  file = {/Users/snaik/Zotero/storage/GFPS6ED8/Goldner et al. - 2023 - Evidence that tissue recoil in the early Drosophila embryo is a passive not active process.pdf}
}

@article{bouameurPlakinsVersatileFamily2014,
  title = {Plakins, a {{Versatile Family}} of {{Cytolinkers}}: {{Roles}} in {{Skin Integrity}} and in {{Human Diseases}}},
  shorttitle = {Plakins, a {{Versatile Family}} of {{Cytolinkers}}},
  author = {Bouameur, Jamal-Eddine and Favre, Bertrand and Borradori, Luca},
  year = {2014},
  month = apr,
  journal = {Journal of Investigative Dermatology},
  volume = {134},
  number = {4},
  pages = {885--894},
  issn = {0022-202X},
  doi = {10.1038/jid.2013.498},
  urldate = {2021-07-12},
  abstract = {The plakin family consists of giant proteins involved in the cross-linking and organization of the cytoskeleton and adhesion complexes. They further modulate several fundamental biological processes, such as cell adhesion, migration, and polarization or signaling pathways. Inherited and acquired defects of plakins in humans and in animal models potentially lead to dramatic manifestations in the skin, striated muscles, and/or nervous system. These observations unequivocally demonstrate the key role of plakins in the maintenance of tissue integrity. Here we review the characteristics of the mammalian plakin members BPAG1 (bullous pemphigoid antigen 1), desmoplakin, plectin, envoplakin, epiplakin, MACF1 (microtubule-actin cross-linking factor 1), and periplakin, highlighting their role in skin homeostasis and diseases.},
  langid = {english},
  file = {/Users/snaik/Zotero/storage/8QAAJLFW/Bouameur et al_2014_Plakins, a Versatile Family of Cytolinkers.pdf;/Users/snaik/Zotero/storage/D98SBAIP/S0022202X15367506.html}
}
@article{snider2014Posttranslationalmodificationsintermediate,
  title = {Post-Translational Modifications of Intermediate Filament Proteins: Mechanisms and Functions},
  shorttitle = {Post-Translational Modifications of Intermediate Filament Proteins},
  author = {Snider, Natasha T. and Omary, M. Bishr},
  year = {2014},
  month = mar,
  journal = {Nature Reviews Molecular Cell Biology},
  volume = {15},
  number = {3},
  pages = {163--177},
  publisher = {Nature Publishing Group},
  issn = {1471-0080},
  doi = {10.1038/nrm3753},
  urldate = {2025-06-04},
  abstract = {Intermediate filament (IF) proteins comprise a large family of tissue-specific cytoskeletal proteins that include the nuclear IFs (lamins) and cytoplasmic IFs (keratins, vimentin, desmin, peripherin, glial fibrillary acidic protein, neurofilaments (NFs), nestin, filensin, phakinin, synemin and syncoilin). Mutations in genes encoding IF proteins cause or predispose to more than 80 human diseases.IF proteins undergo several post-translational modifications (PTMs), including phosphorylation, glycosylation, sumoylation, acetylation, prenylation, ubiquitylation and transamidation, which regulate each other through crosstalk and binding of IFs to other proteins. Prenylation is found exclusively in lamins, whereas most of the remaining modifications involve both cytoplasmic and nuclear IFs.IF phosphorylation is a multifunctional PTM that regulates axonal transport (NFs), cell growth and stress responses (keratins), nuclear viral egress and nucleocytoplasmic transport of ribonucleoproteins (lamins), neuromuscular development (nestin), epithelial-to-mesenchymal transition and cell migration (vimentin and keratins).IF sumoylation has been identified in lamins, keratins and vimentin, but is likely to involve most, if not all, IFs. Low-level sumoylation promotes IF solubility, whereas hypersumoylation inhibits it. Hypersumoylation is found in stress and disease contexts.Other functional roles for IF PTMs include sensing of the metabolic environment (acetylation), regulation of IF turnover (ubiquitylation), regulation of cell survival mechanisms and protein--protein interactions (glycosylation and phosphorylation), association with the nuclear membrane (farnesylation) and formation of the cornified envelope in the skin (transamidation).IFs undergo considerable disease-associated PTM changes that may manifest as site-specific decreases or increases. An increase in a site-specific PTM is exemplified by IF hyperphosphorylation (a stress marker in many diseases), IF hyperubiquitylation (due to proteasome inhibition) and IF transamidation (found in hepatocyte Mallory--Denk body inclusions). IF PTMs are attractive candidates as biomarkers of human disease and potential therapeutic targets.},
  copyright = {2014 Springer Nature Limited},
  langid = {english},
  keywords = {Cytoskeleton,Intermediate filaments,Nucleoskeleton,Post-translational modifications},
  file = {/Users/snaik/Zotero/storage/CUWF3DGB/Snider and Omary - 2014 - Post-translational modifications of intermediate filament proteins mechanisms and functions.pdf}
}

@article{schwayer2019MechanosensationTightJunctions,
  title = {Mechanosensation of {{Tight Junctions Depends}} on {{ZO-1 Phase Separation}} and {{Flow}}},
  author = {Schwayer, Cornelia and Shamipour, Shayan and {Pranjic-Ferscha}, Kornelija and Schauer, Alexandra and Balda, Maria and Tada, Masazumi and Matter, Karl and Heisenberg, Carl-Philipp},
  year = {2019},
  month = oct,
  journal = {Cell},
  volume = {179},
  number = {4},
  pages = {937-952.e18},
  publisher = {Elsevier},
  issn = {0092-8674, 1097-4172},
  doi = {10.1016/j.cell.2019.10.006},
  urldate = {2025-06-06},
  langid = {english},
  pmid = {31675500},
  keywords = {actomyosin flow,mechanosensation,phase separation,tight junction,zebrafish,ZO-1},
  file = {/Users/snaik/Zotero/storage/MXKGL2TZ/Schwayer et al. - 2019 - Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.pdf}
}
@article{hannezo2014Theoryepithelialsheet,
  title = {Theory of Epithelial Sheet Morphology in Three Dimensions},
  author = {Hannezo, Edouard and Prost, Jacques and Joanny, Jean-Francois},
  year = {2014},
  month = jan,
  journal = {Proceedings of the National Academy of Sciences},
  volume = {111},
  number = {1},
  pages = {27--32},
  publisher = {Proceedings of the National Academy of Sciences},
  doi = {10.1073/pnas.1312076111},
  urldate = {2025-06-11},
  abstract = {Morphogenesis during embryo development requires the coordination of mechanical forces to generate the macroscopic shapes of organs. We propose a minimal theoretical model, based on cell adhesion and actomyosin contractility, which describes the various shapes of epithelial cells and the bending and buckling of epithelial sheets, as well as the relative stability of cellular tubes and spheres. We show that, to understand these processes, a full 3D description of the cells is needed, but that simple scaling laws can still be derived. The morphologies observed in vivo can be understood as stable points of mechanical equations and the transitions between them are either continuous or discontinuous. We then focus on epithelial sheet bending, a ubiquitous morphogenetic process. We calculate the curvature of an epithelium as a function of actin belt tension as well as of cell--cell and and cell--substrate tension. The model allows for a comparison of the relative stabilities of spherical or cylindrical cellular structures (acini or tubes). Finally, we propose a unique type of buckling instability of epithelia, driven by a flattening of individual cell shapes, and discuss experimental tests to verify our predictions.},
  file = {/Users/snaik/Zotero/storage/P8E5BF39/Hannezo et al. - 2014 - Theory of epithelial sheet morphology in three dimensions.pdf}
}
@article{sumigray2012Desmoplakincontrolsmicrovilli,
  title = {Desmoplakin Controls Microvilli Length but Not Cell Adhesion or Keratin Organization in the Intestinal Epithelium},
  author = {Sumigray, Kaelyn D. and Lechler, Terry},
  year = {2012},
  month = mar,
  journal = {Molecular Biology of the Cell},
  volume = {23},
  number = {5},
  pages = {792--799},
  publisher = {American Society for Cell Biology (mboc)},
  issn = {1059-1524},
  doi = {10.1091/mbc.e11-11-0923},
  urldate = {2025-06-13},
  abstract = {Maintaining proper cell--cell adhesion in the intestine is essential for tissue homeostasis and barrier function. This adhesion is thought to be mediated by cell adhesion structures, including tight junctions, adherens junctions, and desmosomes, which concentrate in the apical junctional region. While clear roles for adherens and tight junctions have been established in simple epithelia, the function of desmosomes has not been addressed. In stratified epithelia, desmosomes impart mechanical strength to tissues by organizing and anchoring the keratin filament network. In this paper, we report that the desmosomal protein desmoplakin (DP) is not essential for cell adhesion in the intestinal epithelium. Surprisingly, when DP is lacking, keratin filament localization is also unperturbed, although keratin filaments no longer anchor at desmosomes. Unexpectedly, DP is important for proper microvillus structure. Our study highlights the tissue-specific functions of desmosomes and reveals that the canonical functions for these structures are not conserved in simple epithelium.},
  file = {/Users/snaik/Zotero/storage/VMFFW5K5/Sumigray and Lechler - 2012 - Desmoplakin controls microvilli length but not cell adhesion or keratin organization in the intestin.pdf}
}

@article{luciano2022Appreciatingrolecell,
  title = {Appreciating the Role of Cell Shape Changes in the Mechanobiology of Epithelial Tissues},
  author = {Luciano, Marine and Versaevel, Marie and Vercruysse, El{\'e}onore and Proc{\`e}s, Anthony and Kalukula, Yohalie and Remson, Alexandre and Deridoux, Amandine and Gabriele, Sylvain},
  year = {2022},
  month = mar,
  journal = {Biophysics Reviews},
  volume = {3},
  number = {1},
  pages = {011305},
  issn = {2688-4089},
  doi = {10.1063/5.0074317},
  urldate = {2025-06-12},
  abstract = {The wide range of epithelial cell shapes reveals the complexity and diversity of the intracellular mechanisms that serve to construct their morphology and regulate their functions. Using mechanosensitive steps, epithelial cells can sense a variety of different mechanochemical stimuli and adapt their behavior by reshaping their morphology. These changes of cell shape rely on a structural reorganization in space and time that generates modifications of the tensional state and activates biochemical cascades. Recent studies have started to unveil how the cell shape maintenance is involved in mechanical homeostatic tasks to sustain epithelial tissue folding, identity, and self-renewal. Here, we review relevant works that integrated mechanobiology to elucidate some of the core principles of how cell shape may be conveyed into spatial information to guide collective processes such as epithelial morphogenesis. Among many other parameters, we show that the regulation of the cell shape can be understood as the result of the interplay between two counteracting mechanisms: actomyosin contractility and intercellular adhesions, and that both do not act independently but are functionally integrated to operate on molecular, cellular, and tissue scales. We highlight the role of cadherin-based adhesions in force-sensing and mechanotransduction, and we report recent developments that exploit physics of liquid crystals to connect cell shape changes to orientational order in cell aggregates. Finally, we emphasize that the further intermingling of different disciplines to develop new mechanobiology assays will lead the way toward a unified picture of the contribution of cell shape to the pathophysiological behavior of epithelial tissues.},
  file = {/Users/snaik/Zotero/storage/TGWPVQBY/Luciano et al. - 2022 - Appreciating the role of cell shape changes in the mechanobiology of epithelial tissues.pdf}
}
@article{maitreAdhesionFunctionsCell2012,
  title = {Adhesion {{Functions}} in {{Cell Sorting}} by {{Mechanically Coupling}} the {{Cortices}} of {{Adhering Cells}}},
  author = {Ma{\^i}tre, Jean-L{\'e}on and Berthoumieux, H{\'e}l{\`e}ne and Krens, Simon Frederik Gabriel and Salbreux, Guillaume and J{\"u}licher, Frank and Paluch, Ewa and Heisenberg, Carl-Philipp},
  year = {2012},
  month = oct,
  journal = {Science},
  volume = {338},
  number = {6104},
  pages = {253--256},
  publisher = {American Association for the Advancement of Science},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1225399},
  urldate = {2020-12-14},
  abstract = {Embryonic Cell Sorting and Movement Differential cell adhesion has long been thought to drive cell sorting. Ma{\^i}tre et al. (p. 253, published online 23 August) show that cell sorting in zebrafish gastrulation is triggered by differences in the ability of cells to modulate cortex tension at cell-cell contacts, thereby controlling contact expansion. Cell adhesion functions in this process by mechanically coupling the cortices of adhering cells at their contacts, allowing cortex tension to control contact expansion. In zebrafish epiboly the enveloping cell layer (EVL)---a surface epithelium formed at the animal pole of the gastrula---gradually spreads over the entire yolk cell to engulf it at the end of gastrulation. Behrndt et al. (p. 257) show that an actomyosin ring connected to the epithelial margin triggers EVL spreading both by contracting around its circumference and by generating a pulling force through resistance against retrograde actomyosin flow. Differential cell adhesion and cortex tension are thought to drive cell sorting by controlling cell-cell contact formation. Here, we show that cell adhesion and cortex tension have different mechanical functions in controlling progenitor cell-cell contact formation and sorting during zebrafish gastrulation. Cortex tension controls cell-cell contact expansion by modulating interfacial tension at the contact. By contrast, adhesion has little direct function in contact expansion, but instead is needed to mechanically couple the cortices of adhering cells at their contacts, allowing cortex tension to control contact expansion. The coupling function of adhesion is mediated by E-cadherin and limited by the mechanical anchoring of E-cadherin to the cortex. Thus, cell adhesion provides the mechanical scaffold for cell cortex tension to drive cell sorting during gastrulation. Cell adhesion provides a mechanical scaffold for cell cortex tension to drive cell sorting during zebrafish gastrulation. Cell adhesion provides a mechanical scaffold for cell cortex tension to drive cell sorting during zebrafish gastrulation.},
  chapter = {Report},
  copyright = {Copyright {\copyright} 2012, American Association for the Advancement of Science},
  langid = {english},
  pmid = {22923438},
  keywords = {Actomyosincortex,Adhesion,CParticles,DualPipette,NParticle},
  file = {/Users/snaik/Zotero/storage/29WYVNH3/Maître et al_2012_Adhesion Functions in Cell Sorting by Mechanically Coupling the Cortices of.pdf;/Users/snaik/Zotero/storage/AQB9K5R8/253.html;/Users/snaik/Zotero/storage/U6B9WHB9/253.html}
}
@article{tsaiAdhesionCodeEnsures2020,
  title = {An Adhesion Code Ensures Robust Pattern Formation during Tissue Morphogenesis},
  author = {Tsai, Tony Y.-C. and Sikora, Mateusz and Xia, Peng and {Colak-Champollion}, Tugba and Knaut, Holger and Heisenberg, Carl-Philipp and Megason, Sean G.},
  year = {2020},
  month = oct,
  journal = {Science},
  volume = {370},
  number = {6512},
  pages = {113--116},
  publisher = {American Association for the Advancement of Science},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.aba6637},
  urldate = {2021-03-29},
  abstract = {Convergence of paradigms yields patterns In embryo development, spatial patterns of distinct cell types arise reproducibly. In the zebrafish spinal cord, neural progenitors form stereotypic stripe patterns despite the noisy instructive signals and large-scale cellular rearrangement required during morphogenesis. Tsai et al. show that a cell type--specific adhesion code, regulated by a Shh morphogen gradient composed of three adhesion molecules, provides adhesion specificity for three neural progenitor types and mediates patterning robustness in the zebrafish spinal cord. Although insufficient on their own, the integration of the morphogen gradient and differential adhesion mechanisms enables robust pattern formation during tissue morphogenesis. Science, this issue p. 113 Animal development entails the organization of specific cell types in space and time, and spatial patterns must form in a robust manner. In the zebrafish spinal cord, neural progenitors form stereotypic patterns despite noisy morphogen signaling and large-scale cellular rearrangements during morphogenesis and growth. By directly measuring adhesion forces and preferences for three types of endogenous neural progenitors, we provide evidence for the differential adhesion model in which differences in intercellular adhesion mediate cell sorting. Cell type--specific combinatorial expression of different classes of cadherins (N-cadherin, cadherin 11, and protocadherin 19) results in homotypic preference ex vivo and patterning robustness in vivo. Furthermore, the differential adhesion code is regulated by the sonic hedgehog morphogen gradient. We propose that robust patterning during tissue morphogenesis results from interplay between adhesion-based self-organization and morphogen-directed patterning. Pattern formation in the neural tube results from cellular self-organization based on an adhesion code instructed by the morphogen sonic hedgehog. Pattern formation in the neural tube results from cellular self-organization based on an adhesion code instructed by the morphogen sonic hedgehog.},
  chapter = {Report},
  copyright = {Copyright {\copyright} 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. https://www-sciencemag-org.libraryproxy.ist.ac.at/about/science-licenses-journal-article-reuseThis is an article distributed under the terms of the Science Journals Default License.},
  langid = {english},
  pmid = {33004519},
  file = {/Users/snaik/Zotero/storage/FEB7FGXF/Tsai et al_2020_An adhesion code ensures robust pattern formation during tissue morphogenesis.pdf;/Users/snaik/Zotero/storage/BZBJ2HEG/113.html}
}
@article{hitt1994Membraneinteractionsactin,
  title = {Membrane Interactions with the Actin Cytoskeleton},
  author = {Hitt, Anne L. and Luna, Elizabeth J.},
  year = {1994},
  month = feb,
  journal = {Current Opinion in Cell Biology},
  series = {Cytoskeleton},
  volume = {6},
  number = {1},
  pages = {120--130},
  issn = {0955-0674},
  doi = {10.1016/0955-0674(94)90125-2},
  urldate = {2025-06-17},
  abstract = {Recent advances have been made in our understanding of the direct binding of actin to integral membrane proteins. New information has been obtained about indirect actin-membrane associations through spectrin superfamily members and through proteins at the cytoplasmic surfaces of focal contacts and adherens junctions.},
  file = {/Users/snaik/Zotero/storage/JQEKJDGA/Hitt and Luna - 1994 - Membrane interactions with the actin cytoskeleton.pdf}
}
@article{theodoropoulos1992Hepatocyteswellingleads,
  title = {Hepatocyte Swelling Leads to Rapid Decrease of the {{G-}}/Total Actin Ratio and Increases Actin {{mRNA}} Levels},
  author = {Theodoropoulos, Panayotis A. and Stournaras, Christos and Stoll, Barbara and Markogiannakis, Emmanuel and Lang, Florian and Gravanis, Achilles and H{\"a}ussinger, Dieter},
  year = {1992},
  journal = {FEBS Letters},
  volume = {311},
  number = {3},
  pages = {241--245},
  issn = {1873-3468},
  doi = {10.1016/0014-5793(92)81111-X},
  urldate = {2025-06-17},
  abstract = {Exposure of isolated rat hepatocytes to hypotonic (190 mosinol/1) incubation media lowered the cellular G-actin level without affecting the total actin content: here the G-/total actin ratio decreased by 15.5 {\textpm} 1.4\% (n=7). Similar effects were observed following isotonic cell swelling by either addition of glutamine (10 mM) or insulin (100 nM), resulting in a decrease of the G-/total actin ratios by 13.5 {\textpm} 2.1 \% (n = 5) and 14.1 {\textpm} 1.1\% (n = 11), respectively. The effects of hypotonic exposure, glutamine and insulin on the G-/total actin ratio largely occurred within 1 min and persisted for at least 2 h in presence of the respective effectors. After a 120 min exposure to hypotonic media, glutamine or insulin the actin mRNA levels were increased 2.4-, 2.0- and 3.6-fold, respectively. Hypertonic exposure lowered the G-/total actin ratio by only 4.9 {\textpm} 2.5\% (n = 4) and increased actin mRNA levels only 1.2-fold. There was a close relationship between glutamine- and hypotonicity-induced cell swelling and the decrease of G-/total actin ratios. The data suggest that cell swelling exerts rapid and marked effects on the state of actin polymerization and increases actin mRNA levels. Thus, cytoskeletal alterations in response to cell swelling may be involved in the regulation of hepatic metabolism by cell volume.},
  langid = {english},
  keywords = {Actin,Anisotonicity,Cell swelling,Cell volume,Cytoskeleton,Gene expression,Glutamine,Hypertonic,Hypotonic,Insulin,Isolated hepatocyte},
  file = {/Users/snaik/Zotero/storage/XELHFS2M/Theodoropoulos et al. - 1992 - Hepatocyte swelling leads to rapid decrease of the G-total actin ratio and increases actin mRNA lev.pdf;/Users/snaik/Zotero/storage/J9724UTJ/0014-5793(92)81111-X.html}
}


@article{papakonstanti2000Actincytoskeletonsignalinga,
  title = {Actin Cytoskeleton: A Signaling Sensor in Cell Volume Regulation},
  shorttitle = {Actin Cytoskeleton},
  author = {Papakonstanti, E. A. and Vardaki, E. A. and Stournaras, C.},
  year = {2000},
  journal = {Cellular Physiology and Biochemistry: International Journal of Experimental Cellular Physiology, Biochemistry, and Pharmacology},
  volume = {10},
  number = {5-6},
  pages = {257--264},
  issn = {1015-8987},
  doi = {10.1159/000016366},
  abstract = {The actin microfilaments are well known dynamic structures that support and organize the cell membrane and functions associated with the membrane such as ion channels and transporters. In addition, many aspects of cellular physiology seem to be actively modulated by changes in actin cytoskeleton dynamics, which involve reorganization and restructuring of the filaments. For both of these reasons, the actin cytoskeleton has attracted special attention since the early days of cell volume regulation research. Mechanisms controlling the actin equilibrium in response to external stimuli were studied and the signaling cascades leading to the regulation of actin cytoskeleton dynamics have been partially elucidated. They include: a) activation of specific actin binding proteins that regulate actin polymerization dynamics, b) activation of protein kinases or phosphatases regulating phosphorylation of specific cytoskeletal proteins and c) activation of signal transduction pathways leading from membrane receptor activation to actin reorganization involving small GTPases of the Rho and Rac families. These intracellular signal transducers are activated by extracellular stimuli that include hormones, growth factors, cytokines, or ions, many of them in turn are partially known to participate in cell volume regulation. These findings provide strong evidence that the actin cytoskeleton is involved in cell volume regulation by sensing and mediating extracellular signals.},
  langid = {english},
  pmid = {11125204},
  keywords = {Actins,Cell Size,Cytoskeleton,Signal Transduction}
}

@article{luna1992CytoskeletonPlasmaMembraneInteractions,
  title = {Cytoskeleton-{{Plasma Membrane Interactions}}},
  author = {Luna, Elizabeth J. and Hitt, Anne L.},
  year = {1992},
  journal = {Science},
  volume = {258},
  number = {5084},
  eprint = {2881669},
  eprinttype = {jstor},
  pages = {955--964},
  publisher = {American Association for the Advancement of Science},
  issn = {0036-8075},
  urldate = {2025-06-17},
  abstract = {Proteins at the boundary between the cytoskeleton and the plasma membrane control cell shape, delimit specialized membrane domains, and stabilize attachments to other cells and to the substrate. These proteins also regulate cell locomotion and cytoplasmic responses to growth factors and other external stimuli. This diversity of cellular functions is matched by the large number of biochemical mechanisms that mediate the connections between membrane proteins and the underlying cytoskeleton, the so-called membrane skeleton. General organizational themes are beginning to emerge from examination of this biochemical diversity.}
}

@article{bonnet2012Mechanicalstatematerial,
  title = {Mechanical State, Material Properties and Continuous Description of an Epithelial Tissue},
  author = {Bonnet, Isabelle and Marcq, Philippe and Bosveld, Floris and Fetler, Luc and Bella{\"i}che, Yohanns and Graner, Fran{\c c}ois},
  year = {2012},
  month = may,
  journal = {Journal of The Royal Society Interface},
  volume = {9},
  number = {75},
  pages = {2614--2623},
  publisher = {Royal Society},
  doi = {10.1098/rsif.2012.0263},
  urldate = {2025-06-11},
  abstract = {During development, epithelial tissues undergo extensive morphogenesis based on coordinated changes of cell shape and position over time. Continuum mechanics describes tissue mechanical state and shape changes in terms of strain and stress. It accounts for individual cell properties using only a few spatially averaged material parameters. To determine the mechanical state and parameters in the Drosophila pupa dorsal thorax epithelium, we severed in vivo the adherens junctions around a disc-shaped domain comprising typically a hundred cells. This enabled a direct measurement of the strain along different orientations at once. The amplitude and the anisotropy of the strain increased during development. We also measured the stress-to-viscosity ratio and similarly found an increase in amplitude and anisotropy. The relaxation time was of the order of 10 s. We propose a space--time, continuous model of the relaxation. Good agreement with experimental data validates the description of the epithelial domain as a continuous, linear, visco-elastic material. We discuss the relevant time and length scales. Another material parameter, the ratio of external friction to internal viscosity, is estimated by fitting the initial velocity profile. Together, our results contribute to quantify forces and displacements, and their time evolution, during morphogenesis.},
  keywords = {continuum mechanics,Drosophila development,epithelial tissue,laser severing,live imaging},
  file = {/Users/snaik/Zotero/storage/QENG6HDE/Bonnet et al. - 2012 - Mechanical state, material properties and continuous description of an epithelial tissue.pdf}
}

@article{koppen2006Coordinatedcellshapechanges,
  title = {Coordinated Cell-Shape Changes Control Epithelial Movement in Zebrafish and {{Drosophila}}},
  author = {K{\"o}ppen, Mathias and Fern{\'a}ndez, Beatriz Garc{\'i}a and Carvalho, Lara and Jacinto, Antonio and Heisenberg, Carl-Philipp},
  year = {2006},
  month = jul,
  journal = {Development},
  volume = {133},
  number = {14},
  pages = {2671--2681},
  issn = {0950-1991},
  doi = {10.1242/dev.02439},
  urldate = {2025-06-08},
  abstract = {Epithelial morphogenesis depends on coordinated changes in cell shape, a process that is still poorly understood. During zebrafish epiboly and Drosophila dorsal closure, cell-shape changes at the epithelial margin are of critical importance. Here evidence is provided for a conserved mechanism of local actin and myosin 2 recruitment during theses events. It was found that during epiboly of the zebrafish embryo, the movement of the outer epithelium (enveloping layer) over the yolk cell surface involves the constriction of marginal cells. This process depends on the recruitment of actin and myosin 2 within the yolk cytoplasm along the margin of the enveloping layer. Actin and myosin 2 recruitment within the yolk cytoplasm requires the Ste20-like kinase Msn1, an orthologue of DrosophilaMisshapen. Similarly, in Drosophila, actin and myosin 2 localization and cell constriction at the margin of the epidermis mediate dorsal closure and are controlled by Misshapen. Thus, this study has characterized a conserved mechanism underlying coordinated cell-shape changes during epithelial morphogenesis.},
  file = {/Users/snaik/Zotero/storage/DX5IC4AX/Köppen et al. - 2006 - Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila.pdf}
}
@article{karschIntactKeratinNetwork2020,
  title = {An Intact Keratin Network Is Crucial for Mechanical Integrity and Barrier Function in Keratinocyte Cell Sheets},
  author = {Karsch, Susanne and B{\"u}chau, Fanny and Magin, Thomas M. and Janshoff, Andreas},
  year = {2020},
  month = nov,
  journal = {Cellular and Molecular Life Sciences},
  volume = {77},
  number = {21},
  pages = {4397--4411},
  issn = {1420-9071},
  doi = {10.1007/s00018-019-03424-7},
  urldate = {2024-10-02},
  abstract = {The isotype-specific composition of the keratin cytoskeleton is important for strong adhesion, force resilience, and barrier function of the epidermis. However, the mechanisms by which keratins regulate these functions are still incompletely understood. In this study, the role and significance of the keratin network for mechanical integrity, force transmission, and barrier formation were analyzed in murine keratinocytes. Following the time-course of single-cell wound~closure, wild-type (WT) cells slowly closed the gap in a collective fashion involving tightly connected neighboring cells. In contrast, the mechanical response of neighboring cells was compromised in keratin-deficient cells, causing an increased wound area initially and an inefficient overall wound closure. Furthermore, the loss of the keratin network led to impaired, fragmented cell--cell junctions, and triggered a profound change in the overall cellular actomyosin architecture. Electric cell-substrate impedance sensing of cell junctions revealed a dysfunctional barrier in knockout (Kty-/-) cells compared to WT cells. These findings demonstrate that Kty-/- cells display a novel phenotype characterized by loss of mechanocoupling and failure to form a functional barrier. Re-expression of K5/K14 rescued the barrier defect to a significant extent and reestablished the mechanocoupling with remaining discrepancies likely due to the low abundance of keratins in that setting. Our study reveals the major role of the keratin network for mechanical homeostasis and barrier functionality in keratinocyte layers.},
  langid = {english},
  keywords = {Barrier functionality,Keratin cytoskeleton,Mechanical homeostasis,Wound closure},
  file = {/Users/snaik/Zotero/storage/UUPTYHVL/Karsch et al. - 2020 - An intact keratin network is crucial for mechanica.pdf}
}

@article{schaedel2021Vimentinintermediatefilaments,
  title = {Vimentin Intermediate Filaments Stabilize Dynamic Microtubules by Direct Interactions},
  author = {Schaedel, Laura and Lorenz, Charlotta and Schepers, Anna V. and Klumpp, Stefan and K{\"o}ster, Sarah},
  year = {2021},
  month = jun,
  journal = {Nature Communications},
  volume = {12},
  number = {1},
  pages = {3799},
  publisher = {Nature Publishing Group},
  issn = {2041-1723},
  doi = {10.1038/s41467-021-23523-z},
  urldate = {2025-04-08},
  abstract = {The cytoskeleton determines cell mechanics and lies at the heart of important cellular functions. Growing evidence suggests that the manifold tasks of the cytoskeleton rely on the interactions between its filamentous components---actin filaments, intermediate filaments, and microtubules. However, the nature of these interactions and their impact on cytoskeletal dynamics are largely unknown. Here, we show in a reconstituted in vitro system that vimentin intermediate filaments stabilize microtubules against depolymerization and support microtubule rescue. To understand these stabilizing effects, we directly measure the interaction forces between individual microtubules and vimentin filaments. Combined with numerical simulations, our observations provide detailed insight into the physical nature of the interactions and how they affect microtubule dynamics. Thus, we describe an additional, direct mechanism by which cells establish the fundamental cross talk of cytoskeletal components alongside linker proteins. Moreover, we suggest a strategy to estimate the binding energy of tubulin dimers within the microtubule lattice.},
  copyright = {2021 The Author(s)},
  langid = {english},
  keywords = {Biological physics,Biophysics},
  file = {/Users/snaik/Zotero/storage/R86YU8QG/Schaedel et al. - 2021 - Vimentin intermediate filaments stabilize dynamic microtubules by direct interactions.pdf}
}
@misc{windofferQuantitativeMappingKeratin2021,
  title = {Quantitative {{Mapping}} of {{Keratin Networks}} in {{3D}}},
  author = {Windoffer, Reinhard and Schwarz, Nicole and Yoon, Sungjun and Piskova, Teodora and Scholkemper, Michael and Stegmaier, Johannes and B{\"o}nsch, Andrea and Russo, Jacopo Di and Leube, Rudolf E.},
  year = {2021},
  month = dec,
  pages = {2021.12.06.470977},
  institution = {Cold Spring Harbor Laboratory},
  doi = {10.1101/2021.12.06.470977},
  urldate = {2021-12-13},
  abstract = {Mechanobiology requires precise quantitative information on processes taking place in specific 3D microenvironments. Connecting the abundance of microscopical, molecular, biochemical and cell mechanical data with defined topologies has turned out to be extremely difficult. Establishing such structural and functional 3D maps needed for biophysical modeling is a particular challenge for the cytoskeleton, which consists of long and interwoven filamentous polymers coordinating subcellular processes and interactions of cells with their environment. To date, useful tools are available for the segmentation and modeling of actin filaments and microtubules but comprehensive tools for the mapping of intermediate filament organization are still lacking. In this work, we describe a workflow to model and examine the complete 3D arrangement of the keratin intermediate filament cytoskeleton in epithelial cells both in vitro and in vivo. Numerical models are derived from super resolution 3D imaging of fluorescence-tagged keratin filaments. They are interrogated and annotated at different length scales using different modes of visualization including immersive virtual reality. In this way, information is provided on network organization at the subcellular level including mesh arrangement, density and isotropic configuration as well as details on filament morphology such as bundling, curvature and orientation. We show that the comparison of these parameters helps to identify, in quantitative terms, similarities and differences of keratin network organization in epithelial cell types defining subcellular domains, notably basal, apical, lateral and perinuclear systems. The described approach and the presented data are pivotal for generating mechanobiological models that can be experimentally tested.},
  chapter = {New Results},
  copyright = {{\copyright} 2021, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
  langid = {english},
  keywords = {Assembly,Keratin},
  file = {/Users/snaik/Zotero/storage/2KBVY5TE/Windoffer et al_2021_Quantitative Mapping of Keratin Networks in 3D.pdf}
}
@article{miravet2003TyrosinePhosphorylationPlakoglobin,
  title = {Tyrosine {{Phosphorylation}} of {{Plakoglobin Causes Contrary Effects}} on {{Its Association}} with {{Desmosomes}} and {{Adherens Junction Components}} and {{Modulates}} {$\beta$}-{{Catenin-Mediated Transcription}}},
  author = {Miravet, Susana and Piedra, Jos{\'e} and Casta{\~n}o, Julio and Raurell, Imma and Franc{\'i}, Clara and Du{\~n}ach, Mireia and de Herreros, Antonio Garc{\'i}a},
  year = {2003},
  month = oct,
  journal = {Molecular and Cellular Biology},
  publisher = {Taylor \& Francis},
  doi = {10.1128/MCB.23.20.7391-7402.2003},
  urldate = {2025-04-10},
  abstract = {Plakoglobin is a protein closely related to {$\beta$}-catenin that links desmosomal cadherins to intermediate filaments. Plakoglobin can also substitute for {$\beta$}-catenin in adherens junctions, providing a con...},
  copyright = {Copyright {\copyright} 2003, American Society for Microbiology},
  langid = {english},
  file = {/Users/snaik/Zotero/storage/6TV8CTXS/Miravet et al. - 2003 - Tyrosine Phosphorylation of Plakoglobin Causes Contrary Effects on Its Association with Desmosomes a.pdf;/Users/snaik/Zotero/storage/WNIUMUSU/MCB.23.20.7391-7402.html}
}
@article{acehan2008PlakoglobinRequiredEffective,
  title = {Plakoglobin {{Is Required}} for {{Effective Intermediate Filament Anchorage}} to {{Desmosomes}}},
  author = {Acehan, Devrim and Petzold, Christopher and Gumper, Iwona and Sabatini, David D. and M{\"u}ller, Eliane J. and Cowin, Pamela and Stokes, David L.},
  year = {2008},
  month = nov,
  journal = {Journal of Investigative Dermatology},
  volume = {128},
  number = {11},
  pages = {2665--2675},
  issn = {0022-202X},
  doi = {10.1038/jid.2008.141},
  urldate = {2021-03-18},
  abstract = {Desmosomes are adhesive junctions that provide mechanical coupling between cells. Plakoglobin (PG) is a major component of the intracellular plaque that serves to connect transmembrane elements to the cytoskeleton. We have used electron tomography and immunolabeling to investigate the consequences of PG knockout on the molecular architecture of the intracellular plaque in cultured keratinocytes. Although knockout keratinocytes form substantial numbers of desmosome-like junctions and have a relatively normal intercellular distribution of desmosomal cadherins, their cytoplasmic plaques are sparse and anchoring of intermediate filaments is defective. In the knockout, {$\beta$}-catenin appears to substitute for PG in the clustering of cadherins, but is unable to recruit normal levels of plakophilin-1 and desmoplakin to the plaque. By comparing tomograms of wild type and knockout desmosomes, we have assigned particular densities to desmoplakin and described their interaction with intermediate filaments. Desmoplakin molecules are more extended in wild type than knockout desmosomes, as if intermediate filament connections produced tension within the plaque. On the basis of our observations, we propose a particular assembly sequence, beginning with cadherin clustering within the plasma membrane, followed by recruitment of plakophilin and desmoplakin to the plaque, and ending with anchoring of intermediate filaments, which represents the key to adhesive strength.},
  langid = {english},
  file = {/Users/snaik/Zotero/storage/6QAJAIPM/Acehan et al_2008_Plakoglobin Is Required for Effective Intermediate Filament Anchorage to.pdf;/Users/snaik/Zotero/storage/C4W9G9EG/1-s2.0-S0022202X15336691-main.pdf;/Users/snaik/Zotero/storage/YQX4KPQ8/S0022202X15336691.html}
}
@article{hoUpdateKeratinGene2022,
  title = {Update of the Keratin Gene Family: Evolution, Tissue-Specific Expression Patterns, and Relevance to Clinical Disorders},
  shorttitle = {Update of the Keratin Gene Family},
  author = {Ho, Minh and Thompson, Brian and Fisk, Jeffrey Nicholas and Nebert, Daniel W. and Bruford, Elspeth A. and Vasiliou, Vasilis and Bunick, Christopher G.},
  year = {2022},
  month = jan,
  journal = {Human Genomics},
  volume = {16},
  number = {1},
  pages = {1},
  issn = {1479-7364},
  doi = {10.1186/s40246-021-00374-9},
  urldate = {2022-11-19},
  abstract = {Intermediate filament (IntFil) genes arose during early metazoan evolution, to provide mechanical support for plasma~membranes contacting/interacting with other cells and the extracellular matrix. Keratin genes comprise the largest subset of IntFil genes. Whereas the first keratin gene appeared in sponge, and three genes in arthropods, more rapid increases in keratin genes occurred in lungfish and amphibian genomes, concomitant with land animal-sea animal divergence ({\textasciitilde}\,440 to 410 million years ago). Human, mouse and zebrafish genomes contain 18, 17 and 24 non-keratin IntFil genes, respectively. Human has 27 of 28 type I ``acidic'' keratin genes clustered at chromosome (Chr) 17q21.2, and all 26 type II ``basic'' keratin genes clustered at Chr 12q13.13. Mouse has 27 of 28 type I keratin genes clustered on Chr 11, and all 26 type II clustered on Chr 15. Zebrafish has 18 type I keratin genes scattered on five chromosomes, and 3 type II keratin genes on two chromosomes. Types I and II keratin clusters---reflecting evolutionary blooms of keratin genes along one chromosomal segment---are found in all land animal genomes examined, but not fishes; such rapid gene expansions likely reflect sudden requirements for many novel paralogous proteins having divergent functions to enhance species survival following sea-to-land transition. Using data from the Genotype-Tissue Expression (GTEx) project, tissue-specific keratin expression throughout the human body was reconstructed. Clustering of gene expression patterns revealed similarities in tissue-specific expression patterns for previously described ``keratin pairs'' (i.e., KRT1/KRT10, KRT8/KRT18, KRT5/KRT14, KRT6/KRT16 and KRT6/KRT17 proteins). The ClinVar database currently lists 26 human disease-causing variants within the various domains of keratin proteins.},
  keywords = {Evolutionary blooms,Gene duplications,Gene expression,Intermediate filament,Keratin,Markov-chain Monte Carlo (MCMC),MrBayes program to estimate phylogeny,Synteny},
  file = {/Users/snaik/Zotero/storage/T2L7Q5DY/Ho et al_2022_Update of the keratin gene family.pdf}
}
@article{zimek2005Terrestrialvertebrateshave,
  title = {Terrestrial Vertebrates Have Two Keratin Gene Clusters; Striking Differences in Teleost Fish},
  author = {Zimek, Alexander and Weber, Klaus},
  year = {2005},
  month = jul,
  journal = {European Journal of Cell Biology},
  volume = {84},
  number = {6},
  pages = {623--635},
  issn = {0171-9335},
  doi = {10.1016/j.ejcb.2005.01.007},
  urldate = {2025-04-10},
  abstract = {Keratins I and II form the largest subgroups of mammalian intermediate filament (IF) proteins and account as obligatory heteropolymers for the keratin filaments of epithelia. All human type I genes except for the K18 gene are clustered on chromosome 17q21, while all type II genes form a cluster on chromosome 12q13, that ends with the type I gene K18. Highly related keratin gene clusters are found in rat and mouse. Since fish seem to lack a keratin II cluster we screened the recently established draft genomes of a bird (chicken) and an amphibian (Xenopus). The results show that keratin I and II gene clusters are a feature of all terrestrial vertebrates. Because hair with its multiple hair keratins and inner root sheath keratins is a mammalian acquisition, the keratin gene clusters of chicken and Xenopus tropicalis have only about half the number of genes found in mammals. Within the type I clusters all genes have the same orientation. In type II clusters there is a rare gene of opposite orientation. Finally we show that the genes for keratins 8 and 18, which are the first expression pair in embryology, are not only adjacent in mammals, but also in Xenopus and three different fish. Thus neighboring K8 and K18 genes seem a feature shared by all vertebrates. In contrast to the two well defined keratin gene clusters of terrestrial vertebrates, three teleost fish show an excess of type I over type II genes, the lack of a keratin type II gene cluster and a striking dispersal of type I genes, that are probably the result of the teleost-specific whole genome duplication followed by a massive gene loss. This raises the question whether keratin gene clusters extend beyond the ancestral bony vertebrate to cartilage fish and lamprey. We also analyzed the complement of non-keratin IF genes of the chicken. Surprisingly, an additional nuclear lamin gene, previously overlooked by cDNA cloning, is documented on chromosome 10. The two splice variants closely resemble the lamin LIII a+b of amphibia and fish. This lamin gene is lost on the mammalian lineage.},
  keywords = {Amphibia,Birds,Fish,Intermediate filaments,Keratin gene clusters,Lamin genes,Mammals,Teleosts,Vertebrate genomes,Zebrafish},
  file = {/Users/snaik/Zotero/storage/7VHTPFIR/S0171933505000257.html}
}
@article{krushnapadhi2006Independentexpansionkeratin,
  title = {Independent Expansion of the Keratin Gene Family in Teleostean Fish and Mammals: {{An}} Insight from Phylogenetic Analysis and Radiation Hybrid Mapping of Keratin Genes in Zebrafish},
  shorttitle = {Independent Expansion of the Keratin Gene Family in Teleostean Fish and Mammals},
  author = {Krushna Padhi, Bhaja and Akimenko, Marie-Andr{\'e}e and Ekker, Marc},
  year = {2006},
  month = mar,
  journal = {Gene},
  volume = {368},
  pages = {37--45},
  issn = {0378-1119},
  doi = {10.1016/j.gene.2005.09.016},
  urldate = {2025-04-10},
  abstract = {The sequence and chromosomal distribution of keratin genes of zebrafish were compared with that of other fishes and mammals to provide an insight into the evolution of this gene family in vertebrates. By comparative sequence analysis and radiation hybrid mapping, we identified 16 type I and 7 type II keratin genes in the zebrafish genome. This contrasts with mammals, where type I and type II keratin genes are similar in number. The keratin genes are scattered in the fish genome, contrasting with the two clusters of keratin genes in mammalian genomes. Compared to genes from two species of pufferfish, the zebrafish type I keratin genes underwent an expansion by independent tandem duplications. Expression profiles based on EST counts suggest that some of the tandemly duplicated type I keratin genes from zebrafish either underwent sub-functionalization or acquired new expression domains. The chromosomal arrangement of keratins 8, keratin18, and a second type II keratin, as a cluster of three genes, has remained conserved in vertebrate evolution, except for duplication of the three-gene cluster in some teleosts. This contrasts with other members of the keratin gene family, which diverged independently between fish and mammals.},
  file = {/Users/snaik/Zotero/storage/5GGIA2RA/Krushna Padhi et al. - 2006 - Independent expansion of the keratin gene family in teleostean fish and mammals An insight from phy.pdf;/Users/snaik/Zotero/storage/VM65MFF3/S0378111905005974.html}
}
@article{farrell2018Singlecellreconstructiondevelopmental,
  title = {Single-Cell Reconstruction of Developmental Trajectories during Zebrafish Embryogenesis},
  author = {Farrell, Jeffrey A. and Wang, Yiqun and Riesenfeld, Samantha J. and Shekhar, Karthik and Regev, Aviv and Schier, Alexander F.},
  year = {2018},
  month = jun,
  journal = {Science},
  volume = {360},
  number = {6392},
  pages = {eaar3131},
  publisher = {American Association for the Advancement of Science},
  doi = {10.1126/science.aar3131},
  urldate = {2024-09-30},
  abstract = {During embryogenesis, cells acquire distinct fates by transitioning through transcriptional states. To uncover these transcriptional trajectories during zebrafish embryogenesis, we sequenced 38,731 cells and developed URD, a simulated diffusion-based computational reconstruction method. URD identified the trajectories of 25 cell types through early somitogenesis, gene expression along them, and their spatial origin in the blastula. Analysis of Nodal signaling mutants revealed that their transcriptomes were canalized into a subset of wild-type transcriptional trajectories. Some wild-type developmental branch points contained cells that express genes characteristic of multiple fates. These cells appeared to trans-specify from one fate to another. These findings reconstruct the transcriptional trajectories of a vertebrate embryo, highlight the concurrent canalization and plasticity of embryonic specification, and provide a framework with which to reconstruct complex developmental trees from single-cell transcriptomes.},
  file = {/Users/snaik/Zotero/storage/I7EVJLR8/Farrell et al. - 2018 - Single-cell reconstruction of developmental trajec.pdf;/Users/snaik/Zotero/storage/TLX5E36X/science.html}
}
@article{ehrlich2019Comparativegenomicssuggests,
  title = {Comparative Genomics Suggests Loss of Keratin {{K24}} in Three Evolutionary Lineages of Mammals},
  author = {Ehrlich, Florian and Laggner, Maria and Langbein, Lutz and Burger, Pamela and Pollreisz, Andreas and Tschachler, Erwin and Eckhart, Leopold},
  year = {2019},
  month = jul,
  journal = {Scientific Reports},
  volume = {9},
  number = {1},
  pages = {10924},
  publisher = {Nature Publishing Group},
  issn = {2045-2322},
  doi = {10.1038/s41598-019-47422-y},
  urldate = {2025-04-10},
  abstract = {Keratins are the main cytoskeletal proteins of epithelial cells and changes in the expression of keratins have contributed to the evolutionary adaptation of epithelia to different environments. Keratin K24 was proposed to be a differentiation marker of epidermal keratinocytes but the significance of K24 expression in the epidermis versus other tissues has remained elusive. Here, we show by RT-PCR, western blot, and immunofluorescence analyses that K24 is highly expressed in the epithelium of the cornea whereas its expression levels are significantly lower in other stratified epithelia including in the epidermis. To investigate the evolutionary history of K24, we screened the genome sequences of vertebrates for orthologs of the human KRT24 gene. The results of this comparative genomics study suggested that KRT24 originated in a common ancestor of amniotes and that it was lost independently in three clades of mammals, i.e. camels, cetaceans, and a subclade of pinnipeds comprising eared seals and the walrus. Together, the results of this study identify K24 as component of the cytoskeleton in the human corneal epithelium and reveal previously unknown differences of keratin gene content among mammalian species.},
  copyright = {2019 The Author(s)},
  langid = {english},
  keywords = {Gene expression,Molecular evolution},
  file = {/Users/snaik/Zotero/storage/YNFRSBJK/Ehrlich et al. - 2019 - Comparative genomics suggests loss of keratin K24 in three evolutionary lineages of mammals.pdf}
}
@article{chung2013Networkinggaloreintermediate,
  title = {Networking Galore: Intermediate Filaments and Cell Migration},
  shorttitle = {Networking Galore},
  author = {Chung, Byung-Min and Rotty, Jeremy D and Coulombe, Pierre A},
  year = {2013},
  month = oct,
  journal = {Current Opinion in Cell Biology},
  series = {Cell Adhesion and Migration},
  volume = {25},
  number = {5},
  pages = {600--612},
  issn = {0955-0674},
  doi = {10.1016/j.ceb.2013.06.008},
  urldate = {2025-04-11},
  abstract = {Intermediate filaments (IFs) are assembled from a diverse group of evolutionarily conserved proteins and are specified in a tissue-dependent, cell type-dependent, and context-dependent fashion in the body. IFs are involved in multiple cellular processes that are crucial for the maintenance of cell and tissue integrity and the response and adaptation to various stresses, as conveyed by the broad array of crippling clinical disorders caused by inherited mutations in IF coding sequences. Accordingly, the expression, assembly, and organization of IFs are tightly regulated. Migration is a fitting example of a cell-based phenomenon in which IFs participate as both effectors and regulators. With a particular focus on vimentin and keratin, we here review how the contributions of IFs to the cell's mechanical properties, to cytoarchitecture and adhesion, and to regulatory pathways collectively exert a significant impact on cell migration.},
  file = {/Users/snaik/Zotero/storage/RXXW7DWN/Chung et al. - 2013 - Networking galore intermediate filaments and cell migration.pdf;/Users/snaik/Zotero/storage/9NJBL77D/S0955067413001117.html}
}

@article{mendezVimentinInducesChanges2010,
  title = {Vimentin Induces Changes in Cell Shape, Motility, and Adhesion during the Epithelial to Mesenchymal Transition},
  author = {Mendez, Melissa G. and Kojima, Shin-Ichiro and Goldman, Robert D.},
  year = {2010},
  journal = {The FASEB Journal},
  volume = {24},
  number = {6},
  pages = {1838--1851},
  issn = {1530-6860},
  doi = {10.1096/fj.09-151639},
  urldate = {2023-02-04},
  abstract = {Vimentin is used widely as a marker of the epithelial to mesenchymal transitions (EMTs) that take place during embryogenesis and metastasis, yet the functional implications of the expression of this type III intermediate filament (IF) protein are poorly understood. Using form factor analysis and quantitative Western blotting of normal, metastatic, and vimentin-null cell lines, we show that the level of expression of vimentin IFs (VIFs) correlates with mesenchymal cell shape and motile behavior. The reorganization of VIFs caused by expressing a dominant-negative mutant or by silencing vimentin with shRNA (neither of which alter microtubule or microfilament assembly) causes mesenchymal cells to adopt epithelial shapes. Following the microinjection of vimentin or transfection with vimentin cDNA, epithelial cells rapidly adopt mesenchymal shapes coincident with VIF assembly. These shape transitions are accompanied by a loss of desmosomal contacts, an increase in cell motility, and a significant increase in focal adhesion dynamics. Our results demonstrate that VIFs play a predominant role in the changes in shape, adhesion, and motility that occur during the EMT.---Mendez, M. G., Kojima, S.-I., Goldman, R. D. Vimentin induces changes in cell shape, motility, and adhesion during the epithelial to mesenchymal transition. FASEB J. 24, 1838--1851 (2010). www.fasebj.org},
  langid = {english},
  file = {/home/snaik/zotero-database/Mendez et al/mendez_et_al_2010_vimentin_induces_changes_in_cell_shape,_motility,_and_adhesion_during_the.pdf;/Users/snaik/Zotero/storage/956HJZFM/fj.html}
}
@article{gan2016Vimentinintermediatefilaments,
  title = {Vimentin Intermediate Filaments Template Microtubule Networks to Enhance Persistence in Cell Polarity and Directed Migration},
  author = {Gan, Zhuo and Ding, Liya and Burckhardt, Christoph J. and Lowery, Jason and Zaritsky, Assaf and Sitterley, Karlyndsay and Mota, Andressa and Costigliola, Nancy and Starker, Colby G. and Voytas, Daniel F. and Tytell, Jessica and Goldman, Robert D. and Danuser, Gaudenz},
  year = {2016},
  month = sep,
  journal = {Cell systems},
  volume = {3},
  number = {3},
  pages = {252-263.e8},
  issn = {2405-4712},
  doi = {10.1016/j.cels.2016.08.007},
  urldate = {2025-04-08},
  abstract = {Increased expression of vimentin intermediate filaments (VIF) enhances directed cell migration, but the mechanism behind VIF's effect on motility is not understood. VIF interact with microtubules, whose organization contributes to polarity maintenance in migrating cells. Here we characterize the dynamic coordination of VIF and microtubule networks in wounded monolayers of Retinal Pigment Epithelial cells. By genome editing we fluorescently labelled endogenous vimentin and {$\alpha$}-tubulin and we developed computational image analysis to delineate architecture and interactions of the two networks. Our results show that VIF assemble an ultrastructural copy of the previously polarized microtubule network. Because the VIF network is long-lived compared to the microtubule network, VIF template future microtubule growth along previous microtubule tracks, thus providing a feedback mechanism that maintains cell polarity. VIF knockdown prevents cells from polarizing and migrating properly during wound healing. We suggest that VIF's templating function establishes a memory in microtubule organization that enhances persistence in cell polarization in general and migration in particular.,},
  pmcid = {PMC5055390},
  pmid = {27667364},
  file = {/Users/snaik/Zotero/storage/ME23FFR8/Gan et al. - 2016 - Vimentin intermediate filaments template microtubule networks to enhance persistence in cell polarit.pdf}
}
@article{eldirany2019human,
  title={Human keratin 1/10-1B tetramer structures reveal a knob-pocket mechanism in intermediate filament assembly},
  author={Eldirany, Sherif A and Ho, Minh and Hinbest, Alexander J and Lomakin, Ivan B and Bunick, Christopher G},
  journal={The EMBO journal},
  volume={38},
  number={11},
  pages={e100741},
  year={2019}
}
@article{mochKeratinDesmosomeScaffold2020,
  title = {The Keratin--Desmosome Scaffold: Pivotal Role of Desmosomes for Keratin Network Morphogenesis},
  shorttitle = {The Keratin--Desmosome Scaffold},
  author = {Moch, Marcin and Schwarz, Nicole and Windoffer, Reinhard and Leube, Rudolf E.},
  year = {2020},
  month = feb,
  journal = {Cellular and Molecular Life Sciences},
  volume = {77},
  number = {3},
  pages = {543--558},
  issn = {1420-9071},
  doi = {10.1007/s00018-019-03198-y},
  urldate = {2021-07-13},
  abstract = {Desmosome-anchored keratin intermediate filaments (KFs) are essential for epithelial coherence. Yet, desmosomal KF attachment and network organization are still unexplored in vivo. We, therefore, monitored KF network morphogenesis in fluorescent keratin 8 knock-in murine embryos revealing keratin enrichment at newly formed desmosomes followed by KF formation, KF elongation and KF fusion. To examine details of this process and its coupling to desmosome formation, we studied fluorescent keratin and desmosomal protein reporter dynamics in the periphery of expanding HaCaT keratinocyte colonies. Less than 3~min after the start of desmosomal proteins clustering non-filamentous keratin enriched at these sites followed by KF formation and elongation. Subsequently, desmosome-anchored KFs merged into stable bundles generating a rim-and-spokes system consisting of subcortical KFs connecting desmosomes to each other and radial KFs connecting desmosomes to the cytoplasmic KF network. We conclude that desmosomes are organizing centers for the KF cytoskeleton with a hitherto unknown nucleation capacity.},
  langid = {english},
  file = {/Users/snaik/Zotero/storage/6B64KRQ3/Moch et al_2020_The keratin–desmosome scaffold.pdf}
}
@article{quinlan2017rimandspokehypothesisexplain,
  title = {A Rim-and-Spoke Hypothesis to Explain the Biomechanical Roles for Cytoplasmic Intermediate Filament Networks},
  author = {Quinlan, Roy A. and Schwarz, Nicole and Windoffer, Reinhard and Richardson, Christine and Hawkins, Tim and Broussard, Joshua A. and Green, Kathleen J. and Leube, Rudolf E.},
  year = {2017},
  month = oct,
  journal = {Journal of Cell Science},
  volume = {130},
  number = {20},
  pages = {3437--3445},
  issn = {0021-9533},
  doi = {10.1242/jcs.202168},
  urldate = {2025-04-09},
  abstract = {Textbook images of keratin intermediate filament (IF) networks in epithelial cells and the functional compromization of the epidermis by keratin mutations promulgate a mechanical role for this important cytoskeletal component. In stratified epithelia, keratin filaments form prominent radial spokes that are focused onto cell-cell contact sites, i.e. the desmosomes. In this Hypothesis, we draw attention to a subset of keratin filaments that are apposed to the plasma membrane. They form a rim of filaments interconnecting the desmosomes in a circumferential network. We hypothesize that they are part of a rim-and-spoke arrangement of IFs in epithelia. From our review of the literature, we extend this functional role for the subplasmalemmal rim of IFs to any cell, in which plasma membrane support is required, provided these filaments connect directly or indirectly to the plasma membrane. Furthermore, cytoplasmic IF networks physically link the outer nuclear and plasma membranes, but their participation in mechanotransduction processes remain largely unconsidered. Therefore, we also discuss the potential biomechanical and mechanosensory role(s) of the cytoplasmic IF network in terms of such a rim (i.e. subplasmalemmal)-and-spoke arrangement for cytoplasmic IF networks.},
  file = {/Users/snaik/Zotero/storage/ZFBBSBXE/Quinlan et al. - 2017 - A rim-and-spoke hypothesis to explain the biomechanical roles for cytoplasmic intermediate filament.pdf;/Users/snaik/Zotero/storage/BAAFKJF4/A-rim-and-spoke-hypothesis-to-explain-the.html}
}
@article{latorreActiveSuperelasticityThreedimensional2018,
  title = {Active Superelasticity in Three-Dimensional Epithelia of Controlled Shape},
  author = {Latorre, Ernest and Kale, Sohan and Casares, Laura and {G{\'o}mez-Gonz{\'a}lez}, Manuel and Uroz, Marina and Valon, L{\'e}o and Nair, Roshna V. and Garreta, Elena and Montserrat, Nuria and {del Campo}, Ar{\'a}nzazu and Ladoux, Benoit and Arroyo, Marino and Trepat, Xavier},
  year = {2018},
  month = nov,
  journal = {Nature},
  volume = {563},
  number = {7730},
  pages = {203--208},
  publisher = {Nature Publishing Group},
  issn = {1476-4687},
  doi = {10.1038/s41586-018-0671-4},
  urldate = {2023-02-04},
  abstract = {Fundamental biological processes are carried out by curved epithelial sheets that enclose a pressurized lumen. How these sheets develop and withstand three-dimensional deformations has remained unclear. Here we combine measurements of epithelial tension and shape with theoretical modelling to show that epithelial sheets are active superelastic materials. We produce arrays of epithelial domes with controlled geometry. Quantification of luminal pressure and epithelial tension reveals a tensional plateau over several-fold areal strains. These extreme strains in the~tissue are accommodated by highly heterogeneous strains at a cellular level, in seeming contradiction to the measured tensional uniformity. This phenomenon is reminiscent of superelasticity, a behaviour that is generally attributed to microscopic material instabilities in metal alloys. We show that in epithelial cells this instability is triggered by a stretch-induced dilution of the actin cortex, and is rescued by the intermediate filament network. Our study reveals a type of mechanical behaviour---which we term active superelasticity---that enables epithelial sheets to sustain extreme stretching under constant tension.},
  copyright = {2018 Springer Nature Limited},
  langid = {english},
  keywords = {Biological physics,Biomaterials - cells,Biophysics,Cytoskeleton,Mechanical engineering},
  file = {/home/snaik/zotero-database/Latorre et al/latorre_et_al_2018_active_superelasticity_in_three-dimensional_epithelia_of_controlled_shape.pdf}
}
@article{schepersMultiscaleMechanicsTemporal2021,
  title = {Multiscale Mechanics and Temporal Evolution of Vimentin Intermediate Filament Networks},
  author = {Schepers, Anna V. and Lorenz, Charlotta and Nietmann, Peter and Janshoff, Andreas and Klumpp, Stefan and K{\"o}ster, Sarah},
  year = {2021},
  month = jan,
  journal = {bioRxiv},
  pages = {2021.01.30.428887},
  publisher = {Cold Spring Harbor Laboratory},
  doi = {10.1101/2021.01.30.428887},
  urldate = {2021-06-01},
  abstract = {{$<$}h3{$>$}Abstract{$<$}/h3{$>$} {$<$}p{$>$}The cytoskeleton, an intricate network of protein filaments, motor proteins, and crosslinkers, largely determines the mechanical properties of cells. Among the three filamentous components, F-actin, microtubules, and intermediate filaments (IFs), the IF network is by far the most extensible and resilient to stress. We present a multiscale approach to disentangle the three main contributions to vimentin IF network mechanics -- single filament mechanics, filament length, and interactions between filaments -- including their temporal evolution. Combining particle tracking, quadruple optical trapping and computational modeling, we derive quantitative information on the strength and kinetics of filament interactions. Specifically, we find that hydrophobic contributions to network mechanics enter mostly via filament elongation kinetics, whereas electrostatics have a direct influence on filament--filament interactions. These results indicate that cells might need to explicitly suppress attractive interactions to re-organize the extremely stable cellular vimentin network.{$<$}/p{$>$}},
  chapter = {New Results},
  copyright = {{\copyright} 2021, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
  langid = {english},
  file = {/Users/snaik/Zotero/storage/72G4I7ZA/Schepers et al_2021_Multiscale mechanics and temporal evolution of vimentin intermediate filament.pdf;/Users/snaik/Zotero/storage/PFKRA7QT/Schepers et al_2021_Multiscale mechanics and temporal evolution of vimentin intermediate filament.pdf;/Users/snaik/Zotero/storage/7REVMS3M/2021.01.30.428887v1.html;/Users/snaik/Zotero/storage/X6W8C66N/2021.01.30.428887v1.html}
}
@article{lorenz2023Keratinfilamentmechanics,
  title = {Keratin Filament Mechanics and Energy Dissipation Are Determined by Metal-like Plasticity},
  author = {Lorenz, Charlotta and Forsting, Johanna and Style, Robert W. and Klumpp, Stefan and K{\"o}ster, Sarah},
  year = {2023},
  month = jun,
  journal = {Matter},
  volume = {6},
  number = {6},
  pages = {2019--2033},
  publisher = {Elsevier},
  issn = {2590-2393, 2590-2385},
  doi = {10.1016/j.matt.2023.04.014},
  urldate = {2025-04-08},
  langid = {english},
  keywords = {biomaterials,cancer metastasis,cytoskeleton,double-network gel,EMT,epithelial-to-mesenchymal transition,force,MAP3: Understanding,material properties,strain,wound healing},
  file = {/Users/snaik/Zotero/storage/QFPTYF5Z/Lorenz et al. - 2023 - Keratin filament mechanics and energy dissipation are determined by metal-like plasticity.pdf}
}
@article{colakoglu2009Intermediatefilamentsexchange,
  title = {Intermediate Filaments Exchange Subunits along Their Length and Elongate by End-to-End Annealing},
  author = {{\c C}olako{\u g}lu, G{\"u}lsen and Brown, Anthony},
  year = {2009},
  month = may,
  journal = {Journal of Cell Biology},
  volume = {185},
  number = {5},
  pages = {769--777},
  issn = {0021-9525},
  doi = {10.1083/jcb.200809166},
  urldate = {2025-04-09},
  abstract = {Actin filaments and microtubules lengthen and shorten by addition and loss of subunits at their ends, but it is not known whether this is also true for intermediate filaments. In fact, several studies suggest that in vivo, intermediate filaments may lengthen by end-to-end annealing and that addition and loss of subunits is not confined to the filament ends. To test these hypotheses, we investigated the assembly dynamics of neurofilament and vimentin intermediate filament proteins in cultured cells using cell fusion, photobleaching, and photoactivation strategies in combination with conventional and photoactivatable fluorescent fusion proteins. We show that neurofilaments and vimentin filaments lengthen by end-to-end annealing of assembled filaments. We also show that neurofilaments and vimentin filaments incorporate subunits along their length by intercalation into the filament wall with no preferential addition of subunits to the filament ends, a process which we term intercalary subunit exchange.},
  file = {/Users/snaik/Zotero/storage/BUU3QHSJ/Çolakoğlu and Brown - 2009 - Intermediate filaments exchange subunits along their length and elongate by end-to-end annealing.pdf;/Users/snaik/Zotero/storage/QXBAJC8D/Intermediate-filaments-exchange-subunits-along.html}
}
@article{sonavane2017Mechanicalsignalingroles,
  title = {Mechanical and Signaling Roles for Keratin Intermediate Filaments in the Assembly and Morphogenesis of {{Xenopus}} Mesendoderm Tissue at Gastrulation},
  author = {Sonavane, Pooja R. and Wang, Chong and Dzamba, Bette and Weber, Gregory F. and Periasamy, Ammasi and DeSimone, Douglas W.},
  year = {2017},
  month = dec,
  journal = {Development},
  volume = {144},
  number = {23},
  pages = {4363--4376},
  issn = {0950-1991},
  doi = {10.1242/dev.155200},
  urldate = {2025-04-09},
  abstract = {The coordination of individual cell behaviors is a crucial step in the assembly and morphogenesis of tissues. Xenopus mesendoderm cells migrate collectively along a fibronectin (FN) substrate at gastrulation, but how the adhesive and mechanical forces required for these movements are generated and transmitted is unclear. Traction force microscopy (TFM) was used to establish that traction stresses are limited primarily to leading edge cells in mesendoderm explants, and that these forces are balanced by intercellular stresses in follower rows. This is further reflected in the morphology of these cells, with broad lamellipodial protrusions, mature focal adhesions and a gradient of activated Rac1 evident at the leading edge, while small protrusions, rapid turnover of immature focal adhesions and lack of a Rac1 activity gradient characterize cells in following rows. Depletion of keratin (krt8) with antisense morpholinos results in high traction stresses in follower row cells, misdirected protrusions and the formation of actin stress fibers anchored in streak-like focal adhesions. We propose that maintenance of mechanical integrity in the mesendoderm by keratin intermediate filaments is required to balance stresses within the tissue to regulate collective cell movements.},
  file = {/Users/snaik/Zotero/storage/ZHEIX2CL/Sonavane et al. - 2017 - Mechanical and signaling roles for keratin intermediate filaments in the assembly and morphogenesis.pdf;/Users/snaik/Zotero/storage/6U2WTXC3/Mechanical-and-signaling-roles-for-keratin.html}
}
@article{lorenzLateralSubunitCoupling2019,
  title = {Lateral {{Subunit Coupling Determines Intermediate Filament Mechanics}}},
  author = {Lorenz, Charlotta and Forsting, Johanna and Schepers, Anna V. and Kraxner, Julia and Bauch, Susanne and Witt, Hannes and Klumpp, Stefan and K{\"o}ster, Sarah},
  year = {2019},
  month = nov,
  journal = {Physical Review Letters},
  volume = {123},
  number = {18},
  pages = {188102},
  issn = {1079-7114},
  doi = {10.1103/PhysRevLett.123.188102},
  abstract = {The cytoskeleton is a composite network of three types of protein filaments, among which intermediate filaments (IFs) are the most extensible ones. Two very important IFs are keratin and vimentin, which have similar molecular architectures but different mechanical behaviors. Here we compare the mechanical response of single keratin and vimentin filaments using optical tweezers. We show that the mechanics of vimentin strongly depends on the ionic strength of the buffer and that its force-strain curve suggests a high degree of cooperativity between subunits. Indeed, a computational model indicates that in contrast to keratin, vimentin is characterized by strong lateral subunit coupling of its charged monomers during unfolding of {$\alpha$} helices. We conclude that cells can tune their mechanics by differential use of keratin versus vimentin.},
  langid = {english},
  pmid = {31763918},
  keywords = {Biomechanical Phenomena,Buffers,Cytoskeleton,Keratins,Microscopy Atomic Force,Models Biological,Optical Tweezers,Osmolar Concentration,Protein Conformation alpha-Helical,Vimentin},
  file = {/Users/snaik/Zotero/storage/WZFTW7EY/Lorenz et al_2019_Lateral Subunit Coupling Determines Intermediate Filament Mechanics.pdf;/Users/snaik/Zotero/storage/X7YTQRBH/Lorenz et al_2019_Lateral Subunit Coupling Determines Intermediate Filament Mechanics.pdf;/Users/snaik/Zotero/storage/5PY7ECXW/PhysRevLett.123.html}
}

@article{tyler2003epithelium,
  title={Epithelium—the primary building block for metazoan complexity},
  author={Tyler, Seth},
  journal={Integrative and comparative biology},
  volume={43},
  number={1},
  pages={55--63},
  year={2003},
  publisher={Oxford University Press}
}
@article{adler2023tissue,
  title={Tissue biology: in search of a new paradigm},
  author={Adler, Miri and Chavan, Arun R and Medzhitov, Ruslan},
  journal={Annual Review of Cell and Developmental Biology},
  volume={39},
  number={1},
  pages={67--89},
  year={2023},
  publisher={Annual Reviews}
}

@article{wu2018rapid,
  title={A rapid method for directed gene knockout for screening in G0 zebrafish},
  author={Wu, Roland S and Lam, Ian I and Clay, Hilary and Duong, Daniel N and Deo, Rahul C and Coughlin, Shaun R},
  journal={Developmental cell},
  volume={46},
  number={1},
  pages={112--125},
  year={2018},
  publisher={Elsevier}
}
@inproceedings{kojima2014timing,
  title={Timing of developmental events in the early mouse embryo},
  author={Kojima, Yoji and Tam, Oliver H and Tam, Patrick PL},
  booktitle={Seminars in cell \& developmental biology},
  volume={34},
  pages={65--75},
  year={2014},
  organization={Elsevier}
}
@article{farrell2018single,
  title={Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis},
  author={Farrell, Jeffrey A and Wang, Yiqun and Riesenfeld, Samantha J and Shekhar, Karthik and Regev, Aviv and Schier, Alexander F},
  journal={Science},
  volume={360},
  number={6392},
  pages={eaar3131},
  year={2018},
  publisher={American Association for the Advancement of Science}
}