[{"title":"The persistent Morse complex segmentation of a 3-manifold","publist_id":"2160","volume":5903,"ddc":["000"],"day":"17","publisher":"Springer","_id":"3968","oa":1,"alternative_title":["LNCS"],"year":"2009","date_published":"2009-11-17T00:00:00Z","quality_controlled":"1","abstract":[{"lang":"eng","text":"We describe an algorithm for segmenting three-dimensional medical imaging data modeled as a continuous function on a 3-manifold. It is related to watershed algorithms developed in image processing but is closer to its mathematical roots, which are Morse theory and homological algebra. It allows for the implicit treatment of an underlying mesh, thus combining the structural integrity of its mathematical foundations with the computational efficiency of image processing."}],"date_created":"2018-12-11T12:06:10Z","intvolume":"      5903","conference":{"end_date":"2009-12-02","location":"Zermatt, Switzerland","start_date":"2009-11-29","name":"3DPH: Modelling the Physiological Human"},"month":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"11fc85bcc19bab1f020e706a4b8a4660","relation":"main_file","file_size":165090,"date_updated":"2020-07-14T12:46:21Z","file_name":"IST-2016-535-v1+1_2009-P-04-3ManifoldSegmentation.pdf","creator":"system","content_type":"application/pdf","file_id":"4694","date_created":"2018-12-12T10:08:33Z","access_level":"open_access"}],"acknowledgement":"This research was partially supported by Geomagic, Inc., and by the Defense Advanced Research Projects Agency (DARPA) under grants HR0011-05-1-0007 and HR0011-05-1-0057.","page":"36 - 50","pubrep_id":"535","language":[{"iso":"eng"}],"has_accepted_license":"1","citation":{"ista":"Edelsbrunner H, Harer J. 2009. The persistent Morse complex segmentation of a 3-manifold. 3DPH: Modelling the Physiological Human, LNCS, vol. 5903, 36–50.","ieee":"H. Edelsbrunner and J. Harer, “The persistent Morse complex segmentation of a 3-manifold,” presented at the 3DPH: Modelling the Physiological Human, Zermatt, Switzerland, 2009, vol. 5903, pp. 36–50.","short":"H. Edelsbrunner, J. Harer, in:, Springer, 2009, pp. 36–50.","mla":"Edelsbrunner, Herbert, and John Harer. <i>The Persistent Morse Complex Segmentation of a 3-Manifold</i>. Vol. 5903, Springer, 2009, pp. 36–50, doi:<a href=\"https://doi.org/10.1007/978-3-642-10470-1_4\">10.1007/978-3-642-10470-1_4</a>.","apa":"Edelsbrunner, H., &#38; Harer, J. (2009). The persistent Morse complex segmentation of a 3-manifold (Vol. 5903, pp. 36–50). Presented at the 3DPH: Modelling the Physiological Human, Zermatt, Switzerland: Springer. <a href=\"https://doi.org/10.1007/978-3-642-10470-1_4\">https://doi.org/10.1007/978-3-642-10470-1_4</a>","chicago":"Edelsbrunner, Herbert, and John Harer. “The Persistent Morse Complex Segmentation of a 3-Manifold,” 5903:36–50. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-10470-1_4\">https://doi.org/10.1007/978-3-642-10470-1_4</a>.","ama":"Edelsbrunner H, Harer J. The persistent Morse complex segmentation of a 3-manifold. In: Vol 5903. Springer; 2009:36-50. doi:<a href=\"https://doi.org/10.1007/978-3-642-10470-1_4\">10.1007/978-3-642-10470-1_4</a>"},"file_date_updated":"2020-07-14T12:46:21Z","corr_author":"1","scopus_import":1,"author":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"full_name":"Harer, John","last_name":"Harer","first_name":"John"}],"department":[{"_id":"HeEd"}],"date_updated":"2024-10-09T20:53:56Z","status":"public","oa_version":"Submitted Version","type":"conference","doi":"10.1007/978-3-642-10470-1_4","publication_status":"published"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"11","page":"E186 - E204","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1086/659642"}]},"external_id":{"pmid":[" 19788353"],"isi":["000271021900002"]},"citation":{"ieee":"J. Polechova, N. H. Barton, and G. Marion, “Species’ range: Adaptation in space and time,” <i>American Naturalist</i>, vol. 174, no. 5. University of Chicago Press, pp. E186–E204, 2009.","short":"J. Polechova, N.H. Barton, G. Marion, American Naturalist 174 (2009) E186–E204.","ista":"Polechova J, Barton NH, Marion G. 2009. Species’ range: Adaptation in space and time. American Naturalist. 174(5), E186–E204.","mla":"Polechova, Jitka, et al. “Species’ Range: Adaptation in Space and Time.” <i>American Naturalist</i>, vol. 174, no. 5, University of Chicago Press, 2009, pp. E186–204, doi:<a href=\"https://doi.org/10.1086/605958\">10.1086/605958</a>.","ama":"Polechova J, Barton NH, Marion G. Species’ range: Adaptation in space and time. <i>American Naturalist</i>. 2009;174(5):E186-E204. doi:<a href=\"https://doi.org/10.1086/605958\">10.1086/605958</a>","apa":"Polechova, J., Barton, N. H., &#38; Marion, G. (2009). Species’ range: Adaptation in space and time. <i>American Naturalist</i>. University of Chicago Press. <a href=\"https://doi.org/10.1086/605958\">https://doi.org/10.1086/605958</a>","chicago":"Polechova, Jitka, Nicholas H Barton, and Glenn Marion. “Species’ Range: Adaptation in Space and Time.” <i>American Naturalist</i>. University of Chicago Press, 2009. <a href=\"https://doi.org/10.1086/605958\">https://doi.org/10.1086/605958</a>."},"language":[{"iso":"eng"}],"pubrep_id":"552","scopus_import":"1","corr_author":"1","article_processing_charge":"No","author":[{"orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","first_name":"Jitka","last_name":"Polechova","full_name":"Polechova, Jitka"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"},{"last_name":"Marion","full_name":"Marion, Glenn","first_name":"Glenn"}],"date_updated":"2025-09-30T09:53:09Z","department":[{"_id":"NiBa"}],"isi":1,"status":"public","publication_status":"published","doi":"10.1086/605958","type":"journal_article","oa_version":"Published Version","publist_id":"1986","volume":174,"article_type":"original","title":"Species' range: Adaptation in space and time","publication":"American Naturalist","ddc":["570"],"pmid":1,"_id":"4136","publisher":"University of Chicago Press","day":"05","oa":1,"date_published":"2009-11-05T00:00:00Z","year":"2009","issue":"5","intvolume":"       174","date_created":"2018-12-11T12:07:09Z","abstract":[{"lang":"eng","text":"Populations living in a spatially and temporally changing environment can adapt to the changing optimum and/or migrate toward favorable habitats. Here we extend previous analyses with a static optimum to allow the environment to vary in time as well as in space. The model follows both population dynamics and the trait mean under stabilizing selection, and the outcomes can be understood by comparing the loads due to genetic variance, dispersal, and temporal change. With fixed genetic variance, we obtain two regimes: (1) adaptation that is uniform along the environmental gradient and that responds to the moving optimum as expected for panmictic populations and when the spatial gradient is sufficiently steep, and (2) a population with limited range that adapts more slowly than the environmental optimum changes in both time and space; the population therefore becomes locally extinct and migrates toward suitable habitat. We also use a population‐genetic model with many loci to allow genetic variance to evolve, and we show that the only solution now has uniform adaptation."}],"main_file_link":[{"url":"https://www.doi.org/10.1086/605958","open_access":"1"}],"quality_controlled":"1"},{"date_updated":"2025-07-02T05:50:01Z","date_published":"2009-01-01T00:00:00Z","alternative_title":[" Ecological Reviews"],"year":"2009","author":[{"first_name":"Jon","last_name":"Bridle","full_name":"Bridle, Jon"},{"full_name":"Polechova, Jitka","last_name":"Polechova","orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","first_name":"Jitka"},{"full_name":"Vines, Timothy","last_name":"Vines","first_name":"Timothy"}],"article_processing_charge":"No","doi":"10.1017/CBO9780511815683.007","publication_status":"published","abstract":[{"text":"Why do species have finite ranges in space and time?\r\n\r\nAll species have limited ecological distributions, and all species eventually become extinct. At the heart of these distributional limits is the idea of trade-offs: a single population or species cannot maximize its fitness in all environments (Woodward and Kelly 2003). Each species therefore occupies a limited range of ecological conditions, or a particular period in history, and interacts in complex ways in ecosystems consisting of many co-existing species. These interactions may in turn generate more specialization (Nosil & Harmon, this volume; Schemske, this volume). However, from an evolutionary biology perspective this explanation is incomplete. Populations clearly adapt to novel environments in some circumstances, otherwise there would be no life on land, no mammals in the ocean, and only a few species on oceanic islands such as Hawaii (Wagner & Funk 1995). What processes, therefore, act to constrain adaptation to changing environments and continually prevent the expansion of species into new habitats at the edge of their range?\r\n\r\nUnderstanding the factors that limit the temporal or spatial persistence of species is of key practical importance, given ongoing changes in global climate (Root et al. 2003), coupled with rapid habitat loss and alteration by the introduction of exotic species of parasites, predators and competitors.","lang":"eng"}],"date_created":"2018-12-11T12:07:09Z","oa_version":"None","quality_controlled":"1","type":"book_chapter","status":"public","OA_type":"closed access","publication":"Speciation and Patterns of Diversity","page":"77 - 101","publication_identifier":{"eissn":["9780511815683"]},"publist_id":"1984","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","title":"Limits to adaptation and patterns of biodiversity","scopus_import":"1","_id":"4137","extern":"1","day":"01","publisher":"Cambridge University Press","citation":{"ama":"Bridle J, Polechova J, Vines T. Limits to adaptation and patterns of biodiversity. In: R. K. Butlin JR, Bridle J, Schluter D, eds. <i>Speciation and Patterns of Diversity</i>. Cambridge University Press; 2009:77-101. doi:<a href=\"https://doi.org/10.1017/CBO9780511815683.007\">10.1017/CBO9780511815683.007</a>","chicago":"Bridle, Jon, Jitka Polechova, and Timothy Vines. “Limits to Adaptation and Patterns of Biodiversity.” In <i>Speciation and Patterns of Diversity</i>, edited by J.R. R. K. Butlin, Jon Bridle, and D. Schluter, 77–101. Cambridge University Press, 2009. <a href=\"https://doi.org/10.1017/CBO9780511815683.007\">https://doi.org/10.1017/CBO9780511815683.007</a>.","apa":"Bridle, J., Polechova, J., &#38; Vines, T. (2009). Limits to adaptation and patterns of biodiversity. In J. R. R. K. Butlin, J. Bridle, &#38; D. Schluter (Eds.), <i>Speciation and Patterns of Diversity</i> (pp. 77–101). Cambridge University Press. <a href=\"https://doi.org/10.1017/CBO9780511815683.007\">https://doi.org/10.1017/CBO9780511815683.007</a>","mla":"Bridle, Jon, et al. “Limits to Adaptation and Patterns of Biodiversity.” <i>Speciation and Patterns of Diversity</i>, edited by J.R. R. K. Butlin et al., Cambridge University Press, 2009, pp. 77–101, doi:<a href=\"https://doi.org/10.1017/CBO9780511815683.007\">10.1017/CBO9780511815683.007</a>.","ieee":"J. Bridle, J. Polechova, and T. Vines, “Limits to adaptation and patterns of biodiversity,” in <i>Speciation and Patterns of Diversity</i>, J. R. R. K. Butlin, J. Bridle, and D. Schluter, Eds. Cambridge University Press, 2009, pp. 77–101.","short":"J. Bridle, J. Polechova, T. Vines, in:, J.R. R. K. Butlin, J. Bridle, D. Schluter (Eds.), Speciation and Patterns of Diversity, Cambridge University Press, 2009, pp. 77–101.","ista":"Bridle J, Polechova J, Vines T. 2009.Limits to adaptation and patterns of biodiversity. In: Speciation and Patterns of Diversity.  Ecological Reviews, , 77–101."},"language":[{"iso":"eng"}],"editor":[{"first_name":"J.R.","last_name":"R. K. Butlin","full_name":"R. K. Butlin, J.R."},{"last_name":"Bridle","full_name":"Bridle, Jon","first_name":"Jon"},{"first_name":"D.","full_name":"Schluter, D.","last_name":"Schluter"}]},{"status":"public","type":"journal_article","oa_version":"None","publication_status":"published","intvolume":"        10","date_created":"2018-12-11T12:07:12Z","abstract":[{"lang":"eng","text":"The migration of single cells and epithelial sheets is of great importance for gastrulation and organ formation in developing embryos and, if misregulated, can have dire consequences e.g. during cancer metastasis. A keystone of cell migration is the regulation of adhesive contacts, which are dynamically assembled and disassembled via endocytosis. Here, we discuss some of the basic concepts about the function of endocytic trafficking during cell migration: transport of integrins from the cell rear to the leading edge in fibroblasts; confinement of signalling to the front of single cells by endocytic transport of growth factors; regulation of movement coherence in multicellular sheets by cadherin turnover; and shaping of extracellular chemokine gradients. Taken together, endocytosis enables migrating cells and tissues to dynamically modulate their adhesion and signalling, allowing them to efficiently migrate through their extracellular environment."}],"doi":"10.1111/j.1600-0854.2009.00929.x","author":[{"full_name":"Ulrich, Florian","last_name":"Ulrich","first_name":"Florian"},{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"article_processing_charge":"No","year":"2009","issue":"7","date_published":"2009-05-20T00:00:00Z","date_updated":"2021-01-12T07:54:49Z","language":[{"iso":"eng"}],"citation":{"chicago":"Ulrich, Florian, and Carl-Philipp J Heisenberg. “Trafficking and Cell Migration.” <i>Traffic</i>. Wiley-Blackwell, 2009. <a href=\"https://doi.org/10.1111/j.1600-0854.2009.00929.x\">https://doi.org/10.1111/j.1600-0854.2009.00929.x</a>.","apa":"Ulrich, F., &#38; Heisenberg, C.-P. J. (2009). Trafficking and cell migration. <i>Traffic</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1600-0854.2009.00929.x\">https://doi.org/10.1111/j.1600-0854.2009.00929.x</a>","ama":"Ulrich F, Heisenberg C-PJ. Trafficking and cell migration. <i>Traffic</i>. 2009;10(7):811-818. doi:<a href=\"https://doi.org/10.1111/j.1600-0854.2009.00929.x\">10.1111/j.1600-0854.2009.00929.x</a>","mla":"Ulrich, Florian, and Carl-Philipp J. Heisenberg. “Trafficking and Cell Migration.” <i>Traffic</i>, vol. 10, no. 7, Wiley-Blackwell, 2009, pp. 811–18, doi:<a href=\"https://doi.org/10.1111/j.1600-0854.2009.00929.x\">10.1111/j.1600-0854.2009.00929.x</a>.","ieee":"F. Ulrich and C.-P. J. Heisenberg, “Trafficking and cell migration,” <i>Traffic</i>, vol. 10, no. 7. Wiley-Blackwell, pp. 811–818, 2009.","ista":"Ulrich F, Heisenberg C-PJ. 2009. Trafficking and cell migration. Traffic. 10(7), 811–818.","short":"F. Ulrich, C.-P.J. Heisenberg, Traffic 10 (2009) 811–818."},"publisher":"Wiley-Blackwell","day":"20","extern":"1","_id":"4143","title":"Trafficking and cell migration","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","publist_id":"1976","volume":10,"page":"811 - 818","publication":"Traffic"},{"page":"S168 - S168","publication":"Mechanisms of Development","title":"The role of the extracellular matrix in Kupffer's vesicle formation in zebrafish","month":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"1970","volume":126,"publisher":"Elsevier","day":"01","_id":"4149","extern":"1","language":[{"iso":"eng"}],"citation":{"ista":"Soete G, Heisenberg C-PJ. 2009. The role of the extracellular matrix in Kupffer’s vesicle formation in zebrafish. Mechanisms of Development. 126, S168–S168.","short":"G. Soete, C.-P.J. Heisenberg, Mechanisms of Development 126 (2009) S168–S168.","ieee":"G. Soete and C.-P. J. Heisenberg, “The role of the extracellular matrix in Kupffer’s vesicle formation in zebrafish,” <i>Mechanisms of Development</i>, vol. 126. Elsevier, pp. S168–S168, 2009.","mla":"Soete, Gwen, and Carl-Philipp J. Heisenberg. “The Role of the Extracellular Matrix in Kupffer’s Vesicle Formation in Zebrafish.” <i>Mechanisms of Development</i>, vol. 126, Elsevier, 2009, pp. S168–S168, doi:<a href=\"https://doi.org/10.1016/j.mod.2009.06.391\">10.1016/j.mod.2009.06.391</a>.","apa":"Soete, G., &#38; Heisenberg, C.-P. J. (2009). The role of the extracellular matrix in Kupffer’s vesicle formation in zebrafish. <i>Mechanisms of Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mod.2009.06.391\">https://doi.org/10.1016/j.mod.2009.06.391</a>","chicago":"Soete, Gwen, and Carl-Philipp J Heisenberg. “The Role of the Extracellular Matrix in Kupffer’s Vesicle Formation in Zebrafish.” <i>Mechanisms of Development</i>. Elsevier, 2009. <a href=\"https://doi.org/10.1016/j.mod.2009.06.391\">https://doi.org/10.1016/j.mod.2009.06.391</a>.","ama":"Soete G, Heisenberg C-PJ. The role of the extracellular matrix in Kupffer’s vesicle formation in zebrafish. <i>Mechanisms of Development</i>. 2009;126:S168-S168. doi:<a href=\"https://doi.org/10.1016/j.mod.2009.06.391\">10.1016/j.mod.2009.06.391</a>"},"year":"2009","date_published":"2009-08-01T00:00:00Z","date_updated":"2021-01-12T07:54:52Z","article_processing_charge":"No","author":[{"first_name":"Gwen","full_name":"Soete, Gwen","last_name":"Soete"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"type":"journal_article","oa_version":"None","date_created":"2018-12-11T12:07:14Z","publication_status":"published","intvolume":"       126","abstract":[{"lang":"eng","text":"An important step in the formation of all epithelial organs is the coordinated polarisation of their constituent cells. One of the factors thought to be crucial for this process is the extracellular matrix (ECM), which provides positional information for cells and directs polarity specification and epithelial cyst formation in 3D culture. However, in vivo evidence for the role of the ECM in epithelial tissue polarisation is scarce.\r\n\r\nTo gain insight in the factors involved in establishing cell polarity during organogenesis, we are studying a group of epithelial cells called the Dorsal Forerunner Cells (DFCs) in zebrafish embryos. These cells migrate as a cluster towards the vegetal pole of the developing embryo, where they involute. During this process they polarise, and make foci that open up to form a ciliated lumen called Kupffer’s vesicle.\r\n\r\nWe find that interfering with the deposition of components of the extracellular matrix, or with the intracellular anchors of the cells to the matrix, impairs the polarisation of the DFC’s and leads to subsequent defects in lumen formation. In addition, we have developed a method to culture the DFCs ex vivo, allowing us to precisely manipulate the extracellular environment. The possibility of combining the genetic study of Kupffer’s vesicle formation in the live embryo with cell biological techniques in organ culture make this system uniquely relevant for studying the role of the ECM in polarisation during organogenesis.\r\n"}],"doi":"10.1016/j.mod.2009.06.391","status":"public"},{"author":[{"full_name":"Paluch, Ewa","last_name":"Paluch","first_name":"Ewa"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"article_processing_charge":"No","date_published":"2009-09-15T00:00:00Z","date_updated":"2021-01-12T07:54:56Z","year":"2009","issue":"17","status":"public","publication_status":"published","intvolume":"        19","date_created":"2018-12-11T12:07:17Z","abstract":[{"lang":"eng","text":"Together with cell growth, division and death, changes in cell shape are of central importance for tissue morphogenesis during development. Cell shape is the product of a cell's material and active properties balanced by external forces. Control of cell shape, therefore, relies on both tight regulation of intracellular mechanics and the cell's physical interaction with its environment. In this review, we first discuss the biological and physical mechanisms of cell shape control. We next examine a number of develop mental processes in which cell shape change - either individually or in a coordinated manner - drives embryonic morphogenesis and discuss how cell shape is controlled in these processes. Finally, we emphasize that cell shape control during tissue morphogenesis can only be fully understood by using a combination of cellular, molecular, developmental and biophysical approaches."}],"doi":"10.1016/j.cub.2009.07.029","type":"journal_article","oa_version":"None","month":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"1960","volume":19,"title":"Biology and physics of cell shape changes in development","publication":"Current Biology","page":"R790 - R799","citation":{"apa":"Paluch, E., &#38; Heisenberg, C.-P. J. (2009). Biology and physics of cell shape changes in development. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2009.07.029\">https://doi.org/10.1016/j.cub.2009.07.029</a>","chicago":"Paluch, Ewa, and Carl-Philipp J Heisenberg. “Biology and Physics of Cell Shape Changes in Development.” <i>Current Biology</i>. Cell Press, 2009. <a href=\"https://doi.org/10.1016/j.cub.2009.07.029\">https://doi.org/10.1016/j.cub.2009.07.029</a>.","ama":"Paluch E, Heisenberg C-PJ. Biology and physics of cell shape changes in development. <i>Current Biology</i>. 2009;19(17):R790-R799. doi:<a href=\"https://doi.org/10.1016/j.cub.2009.07.029\">10.1016/j.cub.2009.07.029</a>","ieee":"E. Paluch and C.-P. J. Heisenberg, “Biology and physics of cell shape changes in development,” <i>Current Biology</i>, vol. 19, no. 17. Cell Press, pp. R790–R799, 2009.","ista":"Paluch E, Heisenberg C-PJ. 2009. Biology and physics of cell shape changes in development. Current Biology. 19(17), R790–R799.","short":"E. Paluch, C.-P.J. Heisenberg, Current Biology 19 (2009) R790–R799.","mla":"Paluch, Ewa, and Carl-Philipp J. Heisenberg. “Biology and Physics of Cell Shape Changes in Development.” <i>Current Biology</i>, vol. 19, no. 17, Cell Press, 2009, pp. R790–99, doi:<a href=\"https://doi.org/10.1016/j.cub.2009.07.029\">10.1016/j.cub.2009.07.029</a>."},"language":[{"iso":"eng"}],"extern":"1","_id":"4158","publisher":"Cell Press","day":"15"},{"language":[{"iso":"eng"}],"citation":{"ama":"Paluch E, Heisenberg C-PJ. Chaos begets order: Asynchronous cell contractions drive epithelial morphogenesis. <i>Developmental Cell</i>. 2009;16(1):4-6. doi:<a href=\"https://doi.org/10.1016/j.devcel.2008.12.011\">10.1016/j.devcel.2008.12.011</a>","chicago":"Paluch, Ewa, and Carl-Philipp J Heisenberg. “Chaos Begets Order: Asynchronous Cell Contractions Drive Epithelial Morphogenesis.” <i>Developmental Cell</i>. Cell Press, 2009. <a href=\"https://doi.org/10.1016/j.devcel.2008.12.011\">https://doi.org/10.1016/j.devcel.2008.12.011</a>.","apa":"Paluch, E., &#38; Heisenberg, C.-P. J. (2009). Chaos begets order: Asynchronous cell contractions drive epithelial morphogenesis. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2008.12.011\">https://doi.org/10.1016/j.devcel.2008.12.011</a>","mla":"Paluch, Ewa, and Carl-Philipp J. Heisenberg. “Chaos Begets Order: Asynchronous Cell Contractions Drive Epithelial Morphogenesis.” <i>Developmental Cell</i>, vol. 16, no. 1, Cell Press, 2009, pp. 4–6, doi:<a href=\"https://doi.org/10.1016/j.devcel.2008.12.011\">10.1016/j.devcel.2008.12.011</a>.","ista":"Paluch E, Heisenberg C-PJ. 2009. Chaos begets order: Asynchronous cell contractions drive epithelial morphogenesis. Developmental Cell. 16(1), 4–6.","short":"E. Paluch, C.-P.J. Heisenberg, Developmental Cell 16 (2009) 4–6.","ieee":"E. Paluch and C.-P. J. Heisenberg, “Chaos begets order: Asynchronous cell contractions drive epithelial morphogenesis,” <i>Developmental Cell</i>, vol. 16, no. 1. Cell Press, pp. 4–6, 2009."},"day":"20","publisher":"Cell Press","_id":"4159","extern":"1","title":"Chaos begets order: Asynchronous cell contractions drive epithelial morphogenesis","publist_id":"1961","volume":16,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","publication":"Developmental Cell","page":"4 - 6","status":"public","oa_version":"None","type":"journal_article","doi":"10.1016/j.devcel.2008.12.011","abstract":[{"lang":"eng","text":"Apical cell contraction triggers tissue folding and invagination in epithelia. During Drosophila gastrulation, ventral furrow formation was thought to be driven by smooth, purse-string-like constriction of an actomyosin belt underlying adherens junctions. Now Martin et al. report in Nature that ventral furrow formation is triggered by asynchronous pulsed contractions of the apical acto-myosin cortex in individual cells."}],"publication_status":"published","date_created":"2018-12-11T12:07:18Z","intvolume":"        16","author":[{"full_name":"Paluch, Ewa","last_name":"Paluch","first_name":"Ewa"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"article_processing_charge":"No","issue":"1","year":"2009","date_updated":"2021-01-12T07:54:56Z","date_published":"2009-01-20T00:00:00Z"},{"publication":"Mechanisms of Development","acknowledgement":"Grant sponsors: HHMI, CONICYT (PBCT ACT47, PBCT Red6), ICM P04-048-F, EU FP6-2004-NEST-PATH EDCBNL, DAAD.","page":"S11 - S11","title":"Linking organ formation to left-right patterning in the embryonic zebrafish","volume":126,"publist_id":"1959","month":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"05","publisher":"Elsevier","_id":"4160","extern":"1","language":[{"iso":"eng"}],"citation":{"mla":"Oteíza, Pablo, et al. “Linking Organ Formation to Left-Right Patterning in the Embryonic Zebrafish.” <i>Mechanisms of Development</i>, vol. 126, no. Supplement 1, Elsevier, 2009, pp. S11–S11, doi:<a href=\"https://doi.org/10.1016/j.mod.2009.06.970\">10.1016/j.mod.2009.06.970</a>.","ieee":"P. Oteíza <i>et al.</i>, “Linking organ formation to left-right patterning in the embryonic zebrafish,” <i>Mechanisms of Development</i>, vol. 126, no. Supplement 1. Elsevier, pp. S11–S11, 2009.","ista":"Oteíza P, Lemus C, Köppen M, Palma K, Krieg M, Melo C, Farias C, Pulgar E, Preibisch S, Hartel S, Heisenberg C-PJ, Concha M. 2009. Linking organ formation to left-right patterning in the embryonic zebrafish. Mechanisms of Development. 126(Supplement 1), S11–S11.","short":"P. Oteíza, C. Lemus, M. Köppen, K. Palma, M. Krieg, C. Melo, C. Farias, E. Pulgar, S. Preibisch, S. Hartel, C.-P.J. Heisenberg, M. Concha, Mechanisms of Development 126 (2009) S11–S11.","ama":"Oteíza P, Lemus C, Köppen M, et al. Linking organ formation to left-right patterning in the embryonic zebrafish. <i>Mechanisms of Development</i>. 2009;126(Supplement 1):S11-S11. doi:<a href=\"https://doi.org/10.1016/j.mod.2009.06.970\">10.1016/j.mod.2009.06.970</a>","chicago":"Oteíza, Pablo, Carmen Lemus, Mathias Köppen, Karina Palma, Michael Krieg, Cristina Melo, Cecilia Farias, et al. “Linking Organ Formation to Left-Right Patterning in the Embryonic Zebrafish.” <i>Mechanisms of Development</i>. Elsevier, 2009. <a href=\"https://doi.org/10.1016/j.mod.2009.06.970\">https://doi.org/10.1016/j.mod.2009.06.970</a>.","apa":"Oteíza, P., Lemus, C., Köppen, M., Palma, K., Krieg, M., Melo, C., … Concha, M. (2009). Linking organ formation to left-right patterning in the embryonic zebrafish. <i>Mechanisms of Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mod.2009.06.970\">https://doi.org/10.1016/j.mod.2009.06.970</a>"},"issue":"Supplement 1","year":"2009","date_updated":"2021-01-12T07:54:57Z","date_published":"2009-08-05T00:00:00Z","article_processing_charge":"No","author":[{"full_name":"Oteíza, Pablo","last_name":"Oteíza","first_name":"Pablo"},{"first_name":"Carmen","last_name":"Lemus","full_name":"Lemus, Carmen"},{"first_name":"Mathias","last_name":"Köppen","full_name":"Köppen, Mathias"},{"last_name":"Palma","full_name":"Palma, Karina","first_name":"Karina"},{"first_name":"Michael","full_name":"Krieg, Michael","last_name":"Krieg"},{"full_name":"Melo, Cristina","last_name":"Melo","first_name":"Cristina"},{"first_name":"Cecilia","last_name":"Farias","full_name":"Farias, Cecilia"},{"last_name":"Pulgar","full_name":"Pulgar, Eduardo","first_name":"Eduardo"},{"first_name":"Steffen","last_name":"Preibisch","full_name":"Preibisch, Steffen"},{"full_name":"Hartel, Steffen","last_name":"Hartel","first_name":"Steffen"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Miguel","last_name":"Concha","full_name":"Concha, Miguel"}],"oa_version":"None","type":"journal_article","doi":"10.1016/j.mod.2009.06.970","publication_status":"published","intvolume":"       126","date_created":"2018-12-11T12:07:18Z","abstract":[{"lang":"eng","text":"While the function of patterning in organogenesis is being extensively studied, considerably less is known of reverse effects that organ formation imposes on patterning. In zebrafish, the Kupffer’s vesicle (KV) and parapineal (PP) are embryonic struc- tures that share mechanisms of organogenesis and whose func- tion is essential for normal patterning along the left–right axis. Early morphogenesis of KV and PP organs involve the compaction of progenitor cells into a tight cluster within which three-dimen- sional cellular rosettes are formed. Organisation into rosettes pre- cedes the detachment of progenitor cells from neighbouring tissue and thus represents a key step towards organ formation. Such morphogenetic event is essential for organ function and its disruption has profound effects on left–right patterning."}],"status":"public"},{"article_processing_charge":"No","author":[{"full_name":"Oteíza, Pablo","last_name":"Oteíza","first_name":"Pablo"},{"last_name":"Köppen","full_name":"Köppen, Mathias","first_name":"Mathias"},{"first_name":"Michael","last_name":"Krieg","full_name":"Krieg, Michael"},{"last_name":"Preibisch","full_name":"Preibisch, Steffen","first_name":"Steffen"},{"last_name":"Haertel","full_name":"Haertel, Steffen","first_name":"Steffen"},{"full_name":"Müller, Daniel","last_name":"Müller","first_name":"Daniel"},{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Concha, Miguel","last_name":"Concha","first_name":"Miguel"}],"year":"2009","issue":"Supplement 1","date_published":"2009-08-05T00:00:00Z","date_updated":"2021-01-12T07:54:58Z","status":"public","type":"journal_article","oa_version":"None","date_created":"2018-12-11T12:07:19Z","intvolume":"       126","publication_status":"published","abstract":[{"text":"Organ formation requires the precise assembly of progenitor cells into a functional unit. Mechanical forces are likely to play a critical role in this process, but it is unclear how these are molecularly controlled during development. Here, we show that Wnt11/ Pk1a-mediated planar cell polarity (PCP) signalling coordinates formation of the zebrafish laterality organ (Kupffer’s vesicle, KV) by regulating adhesion forces between organ progenitor cells (the dorsal forerunner cells, DFCs).","lang":"eng"}],"doi":"10.1016/j.mod.2009.06.098","title":"Wnt11/Pk1a-mediated planar cell polarity signalling orchestrates epithelial organ morphogenesis by regulating N-cadherin dependent cell adhesion forces","month":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":126,"publist_id":"1957","page":"S80 - S80","publication":"Mechanisms of Development","language":[{"iso":"eng"}],"citation":{"chicago":"Oteíza, Pablo, Mathias Köppen, Michael Krieg, Steffen Preibisch, Steffen Haertel, Daniel Müller, Carl-Philipp J Heisenberg, and Miguel Concha. “Wnt11/Pk1a-Mediated Planar Cell Polarity Signalling Orchestrates Epithelial Organ Morphogenesis by Regulating N-Cadherin Dependent Cell Adhesion Forces.” <i>Mechanisms of Development</i>. Elsevier, 2009. <a href=\"https://doi.org/10.1016/j.mod.2009.06.098\">https://doi.org/10.1016/j.mod.2009.06.098</a>.","apa":"Oteíza, P., Köppen, M., Krieg, M., Preibisch, S., Haertel, S., Müller, D., … Concha, M. (2009). Wnt11/Pk1a-mediated planar cell polarity signalling orchestrates epithelial organ morphogenesis by regulating N-cadherin dependent cell adhesion forces. <i>Mechanisms of Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mod.2009.06.098\">https://doi.org/10.1016/j.mod.2009.06.098</a>","ama":"Oteíza P, Köppen M, Krieg M, et al. Wnt11/Pk1a-mediated planar cell polarity signalling orchestrates epithelial organ morphogenesis by regulating N-cadherin dependent cell adhesion forces. <i>Mechanisms of Development</i>. 2009;126(Supplement 1):S80-S80. doi:<a href=\"https://doi.org/10.1016/j.mod.2009.06.098\">10.1016/j.mod.2009.06.098</a>","mla":"Oteíza, Pablo, et al. “Wnt11/Pk1a-Mediated Planar Cell Polarity Signalling Orchestrates Epithelial Organ Morphogenesis by Regulating N-Cadherin Dependent Cell Adhesion Forces.” <i>Mechanisms of Development</i>, vol. 126, no. Supplement 1, Elsevier, 2009, pp. S80–S80, doi:<a href=\"https://doi.org/10.1016/j.mod.2009.06.098\">10.1016/j.mod.2009.06.098</a>.","ieee":"P. Oteíza <i>et al.</i>, “Wnt11/Pk1a-mediated planar cell polarity signalling orchestrates epithelial organ morphogenesis by regulating N-cadherin dependent cell adhesion forces,” <i>Mechanisms of Development</i>, vol. 126, no. Supplement 1. Elsevier, pp. S80–S80, 2009.","short":"P. Oteíza, M. Köppen, M. Krieg, S. Preibisch, S. Haertel, D. Müller, C.-P.J. Heisenberg, M. Concha, Mechanisms of Development 126 (2009) S80–S80.","ista":"Oteíza P, Köppen M, Krieg M, Preibisch S, Haertel S, Müller D, Heisenberg C-PJ, Concha M. 2009. Wnt11/Pk1a-mediated planar cell polarity signalling orchestrates epithelial organ morphogenesis by regulating N-cadherin dependent cell adhesion forces. Mechanisms of Development. 126(Supplement 1), S80–S80."},"publisher":"Elsevier","day":"05","extern":"1","_id":"4162"},{"title":"Quantitative approaches in developmental biology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"08","publist_id":"1953","volume":10,"page":"517 - 530","publication":"Nature Reviews Genetics","language":[{"iso":"eng"}],"citation":{"ama":"Oates A, Gorfinkiel N, Gonzalez Gaitan M, Heisenberg C-PJ. Quantitative approaches in developmental biology. <i>Nature Reviews Genetics</i>. 2009;10(8):517-530. doi:<a href=\"https://doi.org/10.1038/nrg2548\">10.1038/nrg2548</a>","chicago":"Oates, Andrew, Nicole Gorfinkiel, Marcos Gonzalez Gaitan, and Carl-Philipp J Heisenberg. “Quantitative Approaches in Developmental Biology.” <i>Nature Reviews Genetics</i>. Nature Publishing Group, 2009. <a href=\"https://doi.org/10.1038/nrg2548\">https://doi.org/10.1038/nrg2548</a>.","apa":"Oates, A., Gorfinkiel, N., Gonzalez Gaitan, M., &#38; Heisenberg, C.-P. J. (2009). Quantitative approaches in developmental biology. <i>Nature Reviews Genetics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nrg2548\">https://doi.org/10.1038/nrg2548</a>","mla":"Oates, Andrew, et al. “Quantitative Approaches in Developmental Biology.” <i>Nature Reviews Genetics</i>, vol. 10, no. 8, Nature Publishing Group, 2009, pp. 517–30, doi:<a href=\"https://doi.org/10.1038/nrg2548\">10.1038/nrg2548</a>.","short":"A. Oates, N. Gorfinkiel, M. Gonzalez Gaitan, C.-P.J. Heisenberg, Nature Reviews Genetics 10 (2009) 517–530.","ista":"Oates A, Gorfinkiel N, Gonzalez Gaitan M, Heisenberg C-PJ. 2009. Quantitative approaches in developmental biology. Nature Reviews Genetics. 10(8), 517–530.","ieee":"A. Oates, N. Gorfinkiel, M. Gonzalez Gaitan, and C.-P. J. Heisenberg, “Quantitative approaches in developmental biology,” <i>Nature Reviews Genetics</i>, vol. 10, no. 8. Nature Publishing Group, pp. 517–530, 2009."},"publisher":"Nature Publishing Group","day":"01","extern":"1","_id":"4165","author":[{"first_name":"Andrew","full_name":"Oates, Andrew","last_name":"Oates"},{"last_name":"Gorfinkiel","full_name":"Gorfinkiel, Nicole","first_name":"Nicole"},{"full_name":"Gonzalez Gaitan, Marcos","last_name":"Gonzalez Gaitan","first_name":"Marcos"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","year":"2009","issue":"8","date_published":"2009-08-01T00:00:00Z","date_updated":"2021-01-12T07:54:59Z","status":"public","type":"journal_article","oa_version":"None","intvolume":"        10","abstract":[{"lang":"eng","text":"The tissues of a developing embryo are simultaneously patterned, moved and differentiated according to an exchange of information between their constituent cells. We argue that these complex self-organizing phenomena can only be fully understood with quantitative mathematical frameworks that allow specific hypotheses to be formulated and tested. The quantitative and dynamic imaging of growing embryos at the molecular, cellular and tissue level is the key experimental advance required to achieve this interaction between theory and experiment. Here we describe how mathematical modelling has become an invaluable method to integrate quantitative biological information across temporal and spatial scales, serving to connect the activity of regulatory molecules with the morphological development of organisms."}],"date_created":"2018-12-11T12:07:20Z","publication_status":"published","doi":"10.1038/nrg2548"},{"page":"S132 - S132","publication":"Mechanisms of Development","title":"Regulation of planar cell polarity signalling by the prenylation pathway","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"08","volume":126,"publist_id":"1927","publisher":"Elsevier","day":"05","_id":"4192","extern":"1","language":[{"iso":"eng"}],"citation":{"mla":"Kai, Masatake, et al. “Regulation of Planar Cell Polarity Signalling by the Prenylation Pathway.” <i>Mechanisms of Development</i>, vol. 126, no. Supplement 1, Elsevier, 2009, pp. S132–S132, doi:<a href=\"https://doi.org/10.1016/j.mod.2009.06.269\">10.1016/j.mod.2009.06.269</a>.","short":"M. Kai, N. Buchan, C.-P.J. Heisenberg, M. Tada, Mechanisms of Development 126 (2009) S132–S132.","ista":"Kai M, Buchan N, Heisenberg C-PJ, Tada M. 2009. Regulation of planar cell polarity signalling by the prenylation pathway. Mechanisms of Development. 126(Supplement 1), S132–S132.","ieee":"M. Kai, N. Buchan, C.-P. J. Heisenberg, and M. Tada, “Regulation of planar cell polarity signalling by the prenylation pathway,” <i>Mechanisms of Development</i>, vol. 126, no. Supplement 1. Elsevier, pp. S132–S132, 2009.","ama":"Kai M, Buchan N, Heisenberg C-PJ, Tada M. Regulation of planar cell polarity signalling by the prenylation pathway. <i>Mechanisms of Development</i>. 2009;126(Supplement 1):S132-S132. doi:<a href=\"https://doi.org/10.1016/j.mod.2009.06.269\">10.1016/j.mod.2009.06.269</a>","chicago":"Kai, Masatake, Nina Buchan, Carl-Philipp J Heisenberg, and Masazumi Tada. “Regulation of Planar Cell Polarity Signalling by the Prenylation Pathway.” <i>Mechanisms of Development</i>. Elsevier, 2009. <a href=\"https://doi.org/10.1016/j.mod.2009.06.269\">https://doi.org/10.1016/j.mod.2009.06.269</a>.","apa":"Kai, M., Buchan, N., Heisenberg, C.-P. J., &#38; Tada, M. (2009). Regulation of planar cell polarity signalling by the prenylation pathway. <i>Mechanisms of Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mod.2009.06.269\">https://doi.org/10.1016/j.mod.2009.06.269</a>"},"year":"2009","issue":"Supplement 1","date_published":"2009-08-05T00:00:00Z","date_updated":"2021-01-12T07:55:11Z","author":[{"full_name":"Kai, Masatake","last_name":"Kai","first_name":"Masatake"},{"first_name":"Nina","last_name":"Buchan","full_name":"Buchan, Nina"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"},{"full_name":"Tada, Masazumi","last_name":"Tada","first_name":"Masazumi"}],"article_processing_charge":"No","type":"journal_article","oa_version":"None","abstract":[{"lang":"eng","text":"During vertebrate gastrulation, the body axis is established by a variety of co-ordinated and directed movements of cells. One of these movements is convergence and extension (CE), which is regulated by a non-canonical Wnt/planar cell polarity (PCP) pathway. From our forward genetic screen, we have identified 3-hydroxy-3-methyglutaryl-coenzyme A reductase 1b (hmgcr1b) gene as a dominant enhancer of the silberblick (slb)/wnt11 CE phenotype. hmgcr1b mutant embryos exhibit only very mild CE phenotype during gastrulation while showing a thicker yolk extension at pharyngula stages. Notably, abrogation of hmgcr1b also enhances the CE defects of other core PCP mutants/morphants. The prenylation pathway is one of branches downstream of HMGCR, and has been implicated for lipid modification at the C-terminus of proteins. To test the possibility that the prenylation pathway regulates activities of the PCP pathway, we abrogated farnesyl transferase (FT) or geranylgeranyl transferase (GGT) function using morpholinos on PCP mutant/morphant backgrounds. Consistent with the notion that FT preferentially performs lipid modification on to proteins with the CAAX motif including the core PCP protein Prickle (Pk), abrogation of FT, but not GGT, enhances the pk1a or pk1b morphant CE phenotype, suggesting the specif icity for targets of the prenylation enzymes.\r\n"}],"intvolume":"       126","publication_status":"published","date_created":"2018-12-11T12:07:30Z","doi":"10.1016/j.mod.2009.06.269","status":"public"},{"date_updated":"2021-01-12T07:55:17Z","date_published":"2009-12-01T00:00:00Z","issue":"12","year":"2009","author":[{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"article_processing_charge":"No","doi":"10.1002/bies.200900109","abstract":[{"text":"Dorsal closure (DC), the closure of a hole in the dorsal epidermis of Drosophila embryos by the joining of opposing epithelial cell sheets, has been used as a model process to study the molecular and cellular mechanisms underlying epithelial spreading and wound healing. Recent studies have provided novel insights into how different tissues function cooperatively in this process. Specifically, they demonstrate a critical function of the epidermis surrounding the hole in modulating the behavior of the amnioserosa cells inside. These findings shed light not only on the mechanisms by which the behavior of different tissues is coordinated during DC, but also on the general mechanisms by which tissues interact to trigger global morphogenesis, an essential but yet poorly explored aspect of embryogenesis.","lang":"eng"}],"date_created":"2018-12-11T12:07:35Z","intvolume":"        31","publication_status":"published","oa_version":"None","type":"journal_article","status":"public","publication":"Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology","page":"1284 - 1287","volume":31,"publist_id":"1911","month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Dorsal closure in Drosophila: cells cannot get out of the tight spot","_id":"4206","extern":"1","day":"01","publisher":"Wiley-Blackwell","citation":{"mla":"Heisenberg, Carl-Philipp J. “Dorsal Closure in Drosophila: Cells Cannot Get out of the Tight Spot.” <i>Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology</i>, vol. 31, no. 12, Wiley-Blackwell, 2009, pp. 1284–87, doi:<a href=\"https://doi.org/10.1002/bies.200900109\">10.1002/bies.200900109</a>.","ieee":"C.-P. J. Heisenberg, “Dorsal closure in Drosophila: cells cannot get out of the tight spot,” <i>Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology</i>, vol. 31, no. 12. Wiley-Blackwell, pp. 1284–1287, 2009.","short":"C.-P.J. Heisenberg, Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology 31 (2009) 1284–1287.","ista":"Heisenberg C-PJ. 2009. Dorsal closure in Drosophila: cells cannot get out of the tight spot. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 31(12), 1284–1287.","chicago":"Heisenberg, Carl-Philipp J. “Dorsal Closure in Drosophila: Cells Cannot Get out of the Tight Spot.” <i>Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology</i>. Wiley-Blackwell, 2009. <a href=\"https://doi.org/10.1002/bies.200900109\">https://doi.org/10.1002/bies.200900109</a>.","apa":"Heisenberg, C.-P. J. (2009). Dorsal closure in Drosophila: cells cannot get out of the tight spot. <i>Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/bies.200900109\">https://doi.org/10.1002/bies.200900109</a>","ama":"Heisenberg C-PJ. Dorsal closure in Drosophila: cells cannot get out of the tight spot. <i>Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology</i>. 2009;31(12):1284-1287. doi:<a href=\"https://doi.org/10.1002/bies.200900109\">10.1002/bies.200900109</a>"},"language":[{"iso":"eng"}]},{"status":"public","type":"journal_article","oa_version":"None","date_created":"2018-12-11T12:07:39Z","intvolume":"       136","publication_status":"published","abstract":[{"text":"Nuclear movements play an essential role in metazoan development. Although the intracellular transport mechanisms underlying nuclear movements have been studied in detail, relatively little is known about signals from surrounding cells and tissues controlling these movements. Here, we show that, in gastrulating zebrafish embryos, convergence movements of nuclei within the yolk syncytial layer (YSL) are guided by mesoderm and endoderm progenitors migrating along the surface of the yolk towards the dorsal side of the developing gastrula. Progenitor cells direct the convergence movements of internal yolk syncytial nuclei (iYSN) by modulating cortical flow within the YSL in which the iYSN are entrained. The effect of mesoderm and endoderm progenitors on the convergence movement of iYSN depends on the expression of E-cadherin, indicating that adhesive contact between the cells and the YSL is required for the mesendoderm-modulated YSL cortical flow mediating nuclear convergence. In summary, our data reveal a crucial function for cortical flow in the coordination of syncytial nuclear movements with surrounding cells and tissues during zebrafish gastrulation.","lang":"eng"}],"doi":"10.1242/dev.026922","author":[{"last_name":"Carvalho","full_name":"Carvalho, Lara","first_name":"Lara"},{"first_name":"Jan","last_name":"Stuehmer","full_name":"Stuehmer, Jan"},{"first_name":"Justin","full_name":"Bois, Justin","last_name":"Bois"},{"first_name":"Yannis","full_name":"Kalaidzidis, Yannis","last_name":"Kalaidzidis"},{"first_name":"Virginie","last_name":"Lecaudey","full_name":"Lecaudey, Virginie"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"article_processing_charge":"No","year":"2009","issue":"8","date_published":"2009-04-15T00:00:00Z","date_updated":"2021-01-12T07:55:22Z","language":[{"iso":"eng"}],"citation":{"ama":"Carvalho L, Stuehmer J, Bois J, Kalaidzidis Y, Lecaudey V, Heisenberg C-PJ. Control of convergent yolk syncytial layer nuclear movement in zebrafish. <i>Development</i>. 2009;136(8):1305-1315. doi:<a href=\"https://doi.org/10.1242/dev.026922\">10.1242/dev.026922</a>","apa":"Carvalho, L., Stuehmer, J., Bois, J., Kalaidzidis, Y., Lecaudey, V., &#38; Heisenberg, C.-P. J. (2009). Control of convergent yolk syncytial layer nuclear movement in zebrafish. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.026922\">https://doi.org/10.1242/dev.026922</a>","chicago":"Carvalho, Lara, Jan Stuehmer, Justin Bois, Yannis Kalaidzidis, Virginie Lecaudey, and Carl-Philipp J Heisenberg. “Control of Convergent Yolk Syncytial Layer Nuclear Movement in Zebrafish.” <i>Development</i>. Company of Biologists, 2009. <a href=\"https://doi.org/10.1242/dev.026922\">https://doi.org/10.1242/dev.026922</a>.","ieee":"L. Carvalho, J. Stuehmer, J. Bois, Y. Kalaidzidis, V. Lecaudey, and C.-P. J. Heisenberg, “Control of convergent yolk syncytial layer nuclear movement in zebrafish,” <i>Development</i>, vol. 136, no. 8. Company of Biologists, pp. 1305–1315, 2009.","ista":"Carvalho L, Stuehmer J, Bois J, Kalaidzidis Y, Lecaudey V, Heisenberg C-PJ. 2009. Control of convergent yolk syncytial layer nuclear movement in zebrafish. Development. 136(8), 1305–1315.","short":"L. Carvalho, J. Stuehmer, J. Bois, Y. Kalaidzidis, V. Lecaudey, C.-P.J. Heisenberg, Development 136 (2009) 1305–1315.","mla":"Carvalho, Lara, et al. “Control of Convergent Yolk Syncytial Layer Nuclear Movement in Zebrafish.” <i>Development</i>, vol. 136, no. 8, Company of Biologists, 2009, pp. 1305–15, doi:<a href=\"https://doi.org/10.1242/dev.026922\">10.1242/dev.026922</a>."},"publisher":"Company of Biologists","day":"15","_id":"4217","extern":"1","title":"Control of convergent yolk syncytial layer nuclear movement in zebrafish","month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":136,"publist_id":"1901","publication":"Development","page":"1305 - 1315"},{"author":[{"last_name":"Swoboda","full_name":"Swoboda, Jonathan","first_name":"Jonathan"},{"first_name":"Timothy","full_name":"Meredith, Timothy","last_name":"Meredith"},{"full_name":"Campbell, Jennifer","last_name":"Campbell","first_name":"Jennifer"},{"first_name":"Stephanie","last_name":"Brown","full_name":"Brown, Stephanie"},{"first_name":"Takashi","full_name":"Suzuki, Takashi","last_name":"Suzuki"},{"last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias"},{"full_name":"Malhowski, Amy","last_name":"Malhowski","first_name":"Amy"},{"first_name":"Roy","last_name":"Kishony","full_name":"Kishony, Roy"},{"full_name":"Gilmore, Michael","last_name":"Gilmore","first_name":"Michael"},{"first_name":"Suzanne","full_name":"Walker, Suzanne","last_name":"Walker"}],"article_processing_charge":"No","date_published":"2009-08-18T00:00:00Z","date_updated":"2021-01-12T07:55:25Z","year":"2009","issue":"10","status":"public","publication_status":"published","date_created":"2018-12-11T12:07:41Z","intvolume":"         4","abstract":[{"text":"Both Gram-positive and Gram-negative bacteria contain bactoprenol-dependent biosynthetic pathways expressing non-essential cell surface polysaccharides that function as virulence factors. Although these polymers are not required for bacterial viability in vitro, genes in many of the biosynthetic pathways are conditionally essential: they cannot be deleted except in strains incapable of initiating polymer synthesis. We report a cell-based, pathway-specific strategy to screen for small molecule inhibitors of conditionally essential enzymes. The screen identifies molecules that prevent the growth of a wildtype bacterial strain but do not affect the growth of a mutant strain incapable of initiating polymer synthesis. We have applied this approach to discover inhibitors of wall teichoic acid (WTA) biosynthesis in Staphylococcus aureus. WTAs are anionic cell surface polysaccharides required for host colonization that have been suggested as targets for new antimicrobials. We have identified a small molecule, 7-chloro-N,N-diethyl-3-(phenylsulfonyl)-[1,2,3]triazolo[1,5-a]quinolin-5-amine (1835F03), that inhibits the growth of a panel of S. aureus strains (MIC = 1−3 μg mL−1), including clinical methicillin-resistant S. aureus (MRSA) isolates. Using a combination of biochemistry and genetics, we have identified the molecular target as TarG, the transmembrane component of the ABC transporter that exports WTAs to the cell surface. We also show that preventing the completion of WTA biosynthesis once it has been initiated triggers growth arrest. The discovery of 1835F03 validates our chemical genetics strategy for identifying inhibitors of conditionally essential enzymes, and the strategy should be applicable to many other bactoprenol-dependent biosynthetic pathways in the pursuit of novel antibacterials and probes of bacterial stress responses.","lang":"eng"}],"main_file_link":[{"url":"10.1021/cb900151k [doi]"}],"doi":"10.1021/cb900151k","type":"journal_article","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"08","volume":4,"publist_id":"1894","title":"Discovery of a Small Molecule that Blocks Wall Teichoic Acid Biosynthesis in Staphylococcus aureus","page":"875 - 883","publication":"ACS Chemical Biology","citation":{"ama":"Swoboda J, Meredith T, Campbell J, et al. Discovery of a Small Molecule that Blocks Wall Teichoic Acid Biosynthesis in Staphylococcus aureus. <i>ACS Chemical Biology</i>. 2009;4(10):875-883. doi:<a href=\"https://doi.org/10.1021/cb900151k\">10.1021/cb900151k</a>","chicago":"Swoboda, Jonathan, Timothy Meredith, Jennifer Campbell, Stephanie Brown, Takashi Suzuki, Mark Tobias Bollenbach, Amy Malhowski, Roy Kishony, Michael Gilmore, and Suzanne Walker. “Discovery of a Small Molecule That Blocks Wall Teichoic Acid Biosynthesis in Staphylococcus Aureus.” <i>ACS Chemical Biology</i>. American Chemical Society, 2009. <a href=\"https://doi.org/10.1021/cb900151k\">https://doi.org/10.1021/cb900151k</a>.","apa":"Swoboda, J., Meredith, T., Campbell, J., Brown, S., Suzuki, T., Bollenbach, M. T., … Walker, S. (2009). Discovery of a Small Molecule that Blocks Wall Teichoic Acid Biosynthesis in Staphylococcus aureus. <i>ACS Chemical Biology</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/cb900151k\">https://doi.org/10.1021/cb900151k</a>","mla":"Swoboda, Jonathan, et al. “Discovery of a Small Molecule That Blocks Wall Teichoic Acid Biosynthesis in Staphylococcus Aureus.” <i>ACS Chemical Biology</i>, vol. 4, no. 10, American Chemical Society, 2009, pp. 875–83, doi:<a href=\"https://doi.org/10.1021/cb900151k\">10.1021/cb900151k</a>.","short":"J. Swoboda, T. Meredith, J. Campbell, S. Brown, T. Suzuki, M.T. Bollenbach, A. Malhowski, R. Kishony, M. Gilmore, S. Walker, ACS Chemical Biology 4 (2009) 875–883.","ieee":"J. Swoboda <i>et al.</i>, “Discovery of a Small Molecule that Blocks Wall Teichoic Acid Biosynthesis in Staphylococcus aureus,” <i>ACS Chemical Biology</i>, vol. 4, no. 10. American Chemical Society, pp. 875–883, 2009.","ista":"Swoboda J, Meredith T, Campbell J, Brown S, Suzuki T, Bollenbach MT, Malhowski A, Kishony R, Gilmore M, Walker S. 2009. Discovery of a Small Molecule that Blocks Wall Teichoic Acid Biosynthesis in Staphylococcus aureus. ACS Chemical Biology. 4(10), 875–883."},"language":[{"iso":"eng"}],"extern":"1","_id":"4223","publisher":"American Chemical Society","day":"18"},{"title":"Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions","publist_id":"1890","volume":139,"month":"01","page":"707 - 718","publication":"Cell","citation":{"ista":"Bollenbach T, Quan S, Chait RP, Kishony R. 2009. Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions. Cell. 139(4), 707–718.","ieee":"T. Bollenbach, S. Quan, R. P. Chait, and R. Kishony, “Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions,” <i>Cell</i>, vol. 139, no. 4. Cell Press, pp. 707–718, 2009.","short":"T. Bollenbach, S. Quan, R.P. Chait, R. Kishony, Cell 139 (2009) 707–718.","mla":"Bollenbach, Tobias, et al. “Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions.” <i>Cell</i>, vol. 139, no. 4, Cell Press, 2009, pp. 707–18, doi:<a href=\"https://doi.org/10.1016/j.cell.2009.10.025\">10.1016/j.cell.2009.10.025</a>.","apa":"Bollenbach, T., Quan, S., Chait, R. P., &#38; Kishony, R. (2009). Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2009.10.025\">https://doi.org/10.1016/j.cell.2009.10.025</a>","chicago":"Bollenbach, Tobias, Selwyn Quan, Remy P Chait, and Roy Kishony. “Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions.” <i>Cell</i>. Cell Press, 2009. <a href=\"https://doi.org/10.1016/j.cell.2009.10.025\">https://doi.org/10.1016/j.cell.2009.10.025</a>.","ama":"Bollenbach T, Quan S, Chait RP, Kishony R. Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions. <i>Cell</i>. 2009;139(4):707-718. doi:<a href=\"https://doi.org/10.1016/j.cell.2009.10.025\">10.1016/j.cell.2009.10.025</a>"},"day":"01","publisher":"Cell Press","extern":1,"_id":"4228","author":[{"full_name":"Bollenbach, Tobias","last_name":"Bollenbach","first_name":"Tobias"},{"first_name":"Selwyn","last_name":"Quan","full_name":"Quan, Selwyn"},{"id":"3464AE84-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0876-3187","first_name":"Remy P","full_name":"Remy Chait","last_name":"Chait"},{"full_name":"Kishony, Roy","last_name":"Kishony","first_name":"Roy"}],"issue":"4","year":"2009","date_updated":"2021-01-12T07:55:27Z","date_published":"2009-01-01T00:00:00Z","status":"public","quality_controlled":0,"type":"journal_article","doi":"10.1016/j.cell.2009.10.025","intvolume":"       139","publication_status":"published","date_created":"2018-12-11T12:07:43Z","abstract":[{"text":"Suppressive drug interactions, in which one antibiotic can actually help bacterial cells to grow faster in the presence of another, occur between protein and DNA synthesis inhibitors. Here, we show that this suppression results from nonoptimal regulation of ribosomal genes in the presence of DNA stress. Using GFP-tagged transcription reporters in Escherichia coli, we find that ribosomal genes are not directly regulated by DNA stress, leading to an imbalance between cellular DNA and protein content. To test whether ribosomal gene expression under DNA stress is nonoptimal for growth rate, we sequentially deleted up to six of the seven ribosomal RNA operons. These synthetic manipulations of ribosomal gene expression correct the protein-DNA imbalance, lead to improved survival and growth, and completely remove the suppressive drug interaction. A simple mathematical model explains the nonoptimal regulation in different nutrient environments. These results reveal the genetic mechanism underlying an important class of suppressive drug interactions.","lang":"eng"}]},{"page":"997 - 1011","acknowledgement":"N.B. was supported by the Engineering and Physical Sciences Research Council (GR/T11753 and GR/T19537) and by the Royal Society.\r\nWe are grateful to Ellen Baake for helping to initiate this project and for her comments on this manuscript. We also thank Michael Turelli for his comments on the manuscript and I. Pen for discussions and support in this project. This project was a result of a collaboration supported by the European Science Foundation grant “Integrating population genetics and conservation biology.” ","external_id":{"isi":["000270213500018"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"03","scopus_import":"1","corr_author":"1","citation":{"ama":"Barton NH, De Vladar H. Statistical mechanics and the evolution of polygenic quantitative traits. <i>Genetics</i>. 2009;181(3):997-1011. doi:<a href=\"https://doi.org/10.1534/genetics.108.099309\">10.1534/genetics.108.099309</a>","apa":"Barton, N. H., &#38; De Vladar, H. (2009). Statistical mechanics and the evolution of polygenic quantitative traits. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.108.099309\">https://doi.org/10.1534/genetics.108.099309</a>","chicago":"Barton, Nicholas H, and Harold De Vladar. “Statistical Mechanics and the Evolution of Polygenic Quantitative Traits.” <i>Genetics</i>. Genetics Society of America, 2009. <a href=\"https://doi.org/10.1534/genetics.108.099309\">https://doi.org/10.1534/genetics.108.099309</a>.","short":"N.H. Barton, H. De Vladar, Genetics 181 (2009) 997–1011.","ieee":"N. H. Barton and H. De Vladar, “Statistical mechanics and the evolution of polygenic quantitative traits,” <i>Genetics</i>, vol. 181, no. 3. Genetics Society of America, pp. 997–1011, 2009.","ista":"Barton NH, De Vladar H. 2009. Statistical mechanics and the evolution of polygenic quantitative traits. Genetics. 181(3), 997–1011.","mla":"Barton, Nicholas H., and Harold De Vladar. “Statistical Mechanics and the Evolution of Polygenic Quantitative Traits.” <i>Genetics</i>, vol. 181, no. 3, Genetics Society of America, 2009, pp. 997–1011, doi:<a href=\"https://doi.org/10.1534/genetics.108.099309\">10.1534/genetics.108.099309</a>."},"language":[{"iso":"eng"}],"date_updated":"2025-09-30T09:52:35Z","department":[{"_id":"NiBa"}],"article_processing_charge":"No","author":[{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"first_name":"Harold","full_name":"De Vladar, Harold","last_name":"De Vladar"}],"publication_status":"published","doi":"10.1534/genetics.108.099309","type":"journal_article","oa_version":"None","isi":1,"status":"public","publication":"Genetics","publist_id":"1882","volume":181,"title":"Statistical mechanics and the evolution of polygenic quantitative traits","_id":"4231","publisher":"Genetics Society of America","day":"01","date_published":"2009-03-01T00:00:00Z","year":"2009","issue":"3","intvolume":"       181","date_created":"2018-12-11T12:07:44Z","abstract":[{"text":"The evolution of quantitative characters depends on the frequencies of the alleles involved, yet these frequencies cannot usually be measured. Previous groups have proposed an approximation to the dynamics of quantitative traits, based on an analogy with statistical mechanics. We present a modified version of that approach, which makes the analogy more precise and applies quite generally to describe the evolution of allele frequencies. We calculate explicitly how the macroscopic quantities (i.e., quantities that depend on the quantitative trait) depend on evolutionary forces, in a way that is independent of the microscopic details. We first show that the stationary distribution of allele frequencies under drift, selection, and mutation maximizes a certain measure of entropy, subject to constraints on the expectation of observable quantities. We then approximate the dynamical changes in these expectations, assuming that the distribution of allele frequencies always maximizes entropy, conditional on the expected values. When applied to directional selection on an additive trait, this gives a very good approximation to the evolution of the trait mean and the genetic variance, when the number of mutations per generation is sufficiently high (4Nμ &gt; 1). We show how the method can be modified for small mutation rates (4Nμ → 0). We outline how this method describes epistatic interactions as, for example, with stabilizing selection.","lang":"eng"}],"quality_controlled":"1"},{"title":"Stochasticity and Variability in the dynamics and genetics of populations","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","publist_id":"1883","language":[{"iso":"eng"}],"citation":{"ieee":"H. de Vladar, “Stochasticity and Variability in the dynamics and genetics of populations,” Faculty of mathematical and natural sciences, University of Groningen, 2009.","short":"H. de Vladar, Stochasticity and Variability in the Dynamics and Genetics of Populations, Faculty of mathematical and natural sciences, University of Groningen, 2009.","ista":"de Vladar H. 2009. Stochasticity and Variability in the dynamics and genetics of populations. Faculty of mathematical and natural sciences, University of Groningen.","mla":"de Vladar, Harold. <i>Stochasticity and Variability in the Dynamics and Genetics of Populations</i>. Faculty of mathematical and natural sciences, University of Groningen, 2009.","ama":"de Vladar H. Stochasticity and Variability in the dynamics and genetics of populations. 2009.","apa":"de Vladar, H. (2009). <i>Stochasticity and Variability in the dynamics and genetics of populations</i>. Faculty of mathematical and natural sciences, University of Groningen.","chicago":"Vladar, Harold de. “Stochasticity and Variability in the Dynamics and Genetics of Populations.” Faculty of mathematical and natural sciences, University of Groningen, 2009."},"publisher":"Faculty of mathematical and natural sciences, University of Groningen","day":"01","extern":"1","_id":"4232","author":[{"last_name":"Vladar","full_name":"Vladar, Harold","orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87","first_name":"Harold"}],"article_processing_charge":"No","year":"2009","date_published":"2009-01-01T00:00:00Z","date_updated":"2025-07-02T06:46:07Z","status":"public","type":"dissertation","oa_version":"None","publication_status":"published","date_created":"2018-12-11T12:07:44Z"},{"day":"01","publisher":"Wiley","_id":"4242","ddc":["570"],"publication":"Evolution; International Journal of Organic Evolution","title":"The evolution of strong reproductive isolation","publist_id":"1866","volume":63,"quality_controlled":"1","intvolume":"        63","date_created":"2018-12-11T12:07:48Z","abstract":[{"text":"Felsenstein distinguished two ways by which selection can directly strengthen isolation. First, a modifier that strengthens prezygotic isolation can be favored everywhere. This fits with the traditional view of reinforcement as an adaptation to reduce deleterious hybridization by strengthening assortative mating. Second, selection can favor association between different incompatibilities, despite recombination. We generalize this “two allele” model to follow associations among any number of incompatibilities, which may include both assortment and hybrid inviability. Our key argument is that this process, of coupling between incompatibilities, may be quite different from the usual view of reinforcement: strong isolation can evolve through the coupling of any kind of incompatibility, whether prezygotic or postzygotic. Single locus incompatibilities become coupled because associations between them increase the variance in compatibility, which in turn increases mean fitness if there is positive epistasis. Multiple incompatibilities, each maintained by epistasis, can become coupled in the same way. In contrast, a single-locus incompatibility can become coupled with loci that reduce the viability of haploid hybrids because this reduces harmful recombination. We obtain simple approximations for the limits of tight linkage, and strong assortment, and show how assortment alleles can invade through associations with other components of reproductive isolation.","lang":"eng"}],"issue":"5","year":"2009","date_published":"2009-05-01T00:00:00Z","oa":1,"file_date_updated":"2020-07-14T12:46:25Z","corr_author":"1","scopus_import":"1","pubrep_id":"551","language":[{"iso":"eng"}],"has_accepted_license":"1","citation":{"mla":"Barton, Nicholas H., and Maria De Cara. “The Evolution of Strong Reproductive Isolation.” <i>Evolution; International Journal of Organic Evolution</i>, vol. 63, no. 5, Wiley, 2009, pp. 1171–90, doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2009.00622.x\">10.1111/j.1558-5646.2009.00622.x</a>.","ista":"Barton NH, De Cara M. 2009. The evolution of strong reproductive isolation. Evolution; International Journal of Organic Evolution. 63(5), 1171–1190.","ieee":"N. H. Barton and M. De Cara, “The evolution of strong reproductive isolation,” <i>Evolution; International Journal of Organic Evolution</i>, vol. 63, no. 5. Wiley, pp. 1171–1190, 2009.","short":"N.H. Barton, M. De Cara, Evolution; International Journal of Organic Evolution 63 (2009) 1171–1190.","chicago":"Barton, Nicholas H, and Maria De Cara. “The Evolution of Strong Reproductive Isolation.” <i>Evolution; International Journal of Organic Evolution</i>. Wiley, 2009. <a href=\"https://doi.org/10.1111/j.1558-5646.2009.00622.x\">https://doi.org/10.1111/j.1558-5646.2009.00622.x</a>.","apa":"Barton, N. H., &#38; De Cara, M. (2009). The evolution of strong reproductive isolation. <i>Evolution; International Journal of Organic Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/j.1558-5646.2009.00622.x\">https://doi.org/10.1111/j.1558-5646.2009.00622.x</a>","ama":"Barton NH, De Cara M. The evolution of strong reproductive isolation. <i>Evolution; International Journal of Organic Evolution</i>. 2009;63(5):1171-1190. doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2009.00622.x\">10.1111/j.1558-5646.2009.00622.x</a>"},"external_id":{"isi":["000265145800006"]},"page":"1171 - 1190","acknowledgement":"This work was supported by a Royal Society/Wolfson Research Merit award, and by a grant from the Natural Environment Research Council.\r\nWe are very grateful for insightful comments from S. P. Otto, and for helpful suggestions from the referees and the Associate Editor, Maria Servedio.","file":[{"content_type":"application/pdf","creator":"system","access_level":"open_access","date_created":"2018-12-12T10:11:46Z","file_id":"4903","file_size":720913,"relation":"main_file","checksum":"1920d2e25ef335833764256c1a47bbfb","date_updated":"2020-07-14T12:46:25Z","file_name":"IST-2016-551-v1+1_BartonDeCaraRevNew.pdf"},{"checksum":"c1c51bbc10d4f328fc96fc5b0e5dc25d","relation":"main_file","file_size":290160,"date_updated":"2020-07-14T12:46:25Z","file_name":"IST-2016-551-v1+2_BartonDeCaraRevNewSI.pdf","content_type":"application/pdf","creator":"system","file_id":"4904","date_created":"2018-12-12T10:11:47Z","access_level":"open_access"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"05","oa_version":"Submitted Version","type":"journal_article","doi":"10.1111/j.1558-5646.2009.00622.x","publication_status":"published","status":"public","isi":1,"department":[{"_id":"NiBa"}],"date_updated":"2025-09-30T09:52:11Z","article_processing_charge":"No","author":[{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"first_name":"Maria","full_name":"De Cara, Maria","last_name":"De Cara"}]},{"author":[{"last_name":"Bollback","full_name":"Jonathan Bollback","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P"},{"first_name":"John","last_name":"Huelsenbeck","full_name":"Huelsenbeck, John P"}],"year":"2009","issue":"1","date_published":"2009-01-01T00:00:00Z","date_updated":"2021-01-12T07:56:22Z","status":"public","type":"journal_article","quality_controlled":0,"abstract":[{"text":"Parallel evolution is the acquisition of identical adaptive traits in independently evolving populations. Understanding whether the genetic changes underlying adaptation to a common selective environment are parallel within and between species is interesting because it sheds light on the degree of evolutionary constraints. If parallel evolution is perfect, then the implication is that forces such as functional constraints, epistasis, and pleiotropy play an important role in shaping the outcomes of adaptive evolution. In addition, population genetic theory predicts that the probability of parallel evolution will decline with an increase in the number of adaptive solutions-if a single adaptive solution exists, then parallel evolution will be observed among highly divergent species. For this reason, it is predicted that close relatives-which likely overlap more in the details of their adaptive solutions-will show more parallel evolution. By adapting three related bacteriophage species to a novel environment we find (1) a high rate of parallel genetic evolution at orthologous nucleotide and amino acid residues within species, (2) parallel beneficial mutations do not occur in a common order in which they fix or appear in an evolving population, (3) low rates of parallel evolution and convergent evolution between species, and (4) the probability of parallel and convergent evolution between species is strongly effected by divergence.","lang":"eng"}],"intvolume":"       181","publication_status":"published","date_created":"2018-12-11T12:08:26Z","doi":"10.1534/genetics.107.085225","title":"Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence","month":"01","publist_id":"1101","volume":181,"publication":"Genetics","page":"225 - 234","citation":{"ista":"Bollback JP, Huelsenbeck J. 2009. Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence. Genetics. 181(1), 225–234.","ieee":"J. P. Bollback and J. Huelsenbeck, “Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence,” <i>Genetics</i>, vol. 181, no. 1. Genetics Society of America, pp. 225–234, 2009.","short":"J.P. Bollback, J. Huelsenbeck, Genetics 181 (2009) 225–234.","mla":"Bollback, Jonathan P., and John Huelsenbeck. “Parallel Genetic Evolution within and between Bacteriophage Species of Varying Degrees of Divergence.” <i>Genetics</i>, vol. 181, no. 1, Genetics Society of America, 2009, pp. 225–34, doi:<a href=\"https://doi.org/10.1534/genetics.107.085225\">10.1534/genetics.107.085225</a>.","apa":"Bollback, J. P., &#38; Huelsenbeck, J. (2009). Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.107.085225\">https://doi.org/10.1534/genetics.107.085225</a>","chicago":"Bollback, Jonathan P, and John Huelsenbeck. “Parallel Genetic Evolution within and between Bacteriophage Species of Varying Degrees of Divergence.” <i>Genetics</i>. Genetics Society of America, 2009. <a href=\"https://doi.org/10.1534/genetics.107.085225\">https://doi.org/10.1534/genetics.107.085225</a>.","ama":"Bollback JP, Huelsenbeck J. Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence. <i>Genetics</i>. 2009;181(1):225-234. doi:<a href=\"https://doi.org/10.1534/genetics.107.085225\">10.1534/genetics.107.085225</a>"},"publisher":"Genetics Society of America","day":"01","extern":1,"_id":"4357"},{"publisher":"Springer","day":"01","_id":"4360","extern":"1","scopus_import":"1","language":[{"iso":"eng"}],"citation":{"mla":"Wies, Thomas, et al. “Combining Theories with Shared Set Operations.” <i>7th International Symposium on Frontiers of Combining Systems</i>, vol. 5749, Springer, 2009, pp. 366–82, doi:<a href=\"https://doi.org/10.1007/978-3-642-04222-5_23\">10.1007/978-3-642-04222-5_23</a>.","short":"T. Wies, R. Piskac, V. Kuncak, in:, 7th International Symposium on Frontiers of Combining Systems, Springer, 2009, pp. 366–382.","ista":"Wies T, Piskac R, Kuncak V. 2009. Combining theories with shared set operations. 7th International Symposium on Frontiers of Combining Systems. FroCoS: Frontiers of Combining Systems, LNCS, vol. 5749, 366–382.","ieee":"T. Wies, R. Piskac, and V. Kuncak, “Combining theories with shared set operations,” in <i>7th International Symposium on Frontiers of Combining Systems</i>, Trento, Italy, 2009, vol. 5749, pp. 366–382.","ama":"Wies T, Piskac R, Kuncak V. Combining theories with shared set operations. In: <i>7th International Symposium on Frontiers of Combining Systems</i>. Vol 5749. Springer; 2009:366-382. doi:<a href=\"https://doi.org/10.1007/978-3-642-04222-5_23\">10.1007/978-3-642-04222-5_23</a>","chicago":"Wies, Thomas, Ruzica Piskac, and Viktor Kuncak. “Combining Theories with Shared Set Operations.” In <i>7th International Symposium on Frontiers of Combining Systems</i>, 5749:366–82. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-04222-5_23\">https://doi.org/10.1007/978-3-642-04222-5_23</a>.","apa":"Wies, T., Piskac, R., &#38; Kuncak, V. (2009). Combining theories with shared set operations. In <i>7th International Symposium on Frontiers of Combining Systems</i> (Vol. 5749, pp. 366–382). Trento, Italy: Springer. <a href=\"https://doi.org/10.1007/978-3-642-04222-5_23\">https://doi.org/10.1007/978-3-642-04222-5_23</a>"},"page":"366 - 382","publication":"7th International Symposium on Frontiers of Combining Systems","title":"Combining theories with shared set operations","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","conference":{"end_date":"2009-09-18","name":"FroCoS: Frontiers of Combining Systems","start_date":"2009-09-16","location":"Trento, Italy"},"volume":5749,"publist_id":"1098","quality_controlled":"1","type":"conference","oa_version":"None","date_created":"2018-12-11T12:08:27Z","intvolume":"      5749","abstract":[{"text":"Motivated by applications in software verification, we explore automated reasoning about the non-disjoint combination of theories of infinitely many finite structures, where the theories share set variables and set operations. We prove a combination theorem and apply it to show the decidability of the satisfiability problem for a class of formulas obtained by applying propositional connectives to formulas belonging to: 1) Boolean Algebra with Presburger Arithmetic (with quantifiers over sets and integers), 2) weak monadic second-order logic over trees (with monadic second-order quantifiers), 3) two-variable logic with counting quantifiers (ranging over elements), 4) the Bernays-Schönfinkel-Ramsey class of first-order logic with equality (with ∃ * ∀ * quantifier prefix), and 5) the quantifier-free logic of multisets with cardinality constraints.","lang":"eng"}],"publication_status":"published","doi":"10.1007/978-3-642-04222-5_23","status":"public","year":"2009","alternative_title":["LNCS"],"date_published":"2009-01-01T00:00:00Z","date_updated":"2025-07-02T06:21:09Z","author":[{"last_name":"Wies","full_name":"Wies, Thomas","first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ruzica","last_name":"Piskac","full_name":"Piskac, Ruzica"},{"last_name":"Kuncak","full_name":"Kuncak, Viktor","first_name":"Viktor"}],"article_processing_charge":"No"}]