[{"volume":453,"author":[{"last_name":"Lämmermann","first_name":"Tim","full_name":"Lämmermann, Tim"},{"full_name":"Bader, Bernhard L","first_name":"Bernhard","last_name":"Bader"},{"first_name":"Susan","last_name":"Monkley","full_name":"Monkley, Susan J"},{"full_name":"Worbs, Tim","last_name":"Worbs","first_name":"Tim"},{"full_name":"Wedlich-Söldner, Roland","last_name":"Wedlich Söldner","first_name":"Roland"},{"full_name":"Hirsch, Karin","last_name":"Hirsch","first_name":"Karin"},{"full_name":"Keller, Markus","last_name":"Keller","first_name":"Markus"},{"last_name":"Förster","first_name":"Reinhold","full_name":"Förster, Reinhold"},{"first_name":"David","last_name":"Critchley","full_name":"Critchley, David R"},{"last_name":"Fässler","first_name":"Reinhard","full_name":"Fässler, Reinhard"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Michael Sixt"}],"citation":{"short":"T. Lämmermann, B. Bader, S. Monkley, T. Worbs, R. Wedlich Söldner, K. Hirsch, M. Keller, R. Förster, D. Critchley, R. Fässler, M.K. Sixt, Nature 453 (2008) 51–55.","chicago":"Lämmermann, Tim, Bernhard Bader, Susan Monkley, Tim Worbs, Roland Wedlich Söldner, Karin Hirsch, Markus Keller, et al. “Rapid Leukocyte Migration by Integrin-Independent Flowing and Squeezing.” Nature. Nature Publishing Group, 2008. https://doi.org/10.1038/nature06887.","ista":"Lämmermann T, Bader B, Monkley S, Worbs T, Wedlich Söldner R, Hirsch K, Keller M, Förster R, Critchley D, Fässler R, Sixt MK. 2008. Rapid leukocyte migration by integrin-independent flowing and squeezing. Nature. 453(7191), 51–55.","ama":"Lämmermann T, Bader B, Monkley S, et al. Rapid leukocyte migration by integrin-independent flowing and squeezing. Nature. 2008;453(7191):51-55. doi:10.1038/nature06887","apa":"Lämmermann, T., Bader, B., Monkley, S., Worbs, T., Wedlich Söldner, R., Hirsch, K., … Sixt, M. K. (2008). Rapid leukocyte migration by integrin-independent flowing and squeezing. Nature. Nature Publishing Group. https://doi.org/10.1038/nature06887","ieee":"T. Lämmermann et al., “Rapid leukocyte migration by integrin-independent flowing and squeezing,” Nature, vol. 453, no. 7191. Nature Publishing Group, pp. 51–55, 2008.","mla":"Lämmermann, Tim, et al. “Rapid Leukocyte Migration by Integrin-Independent Flowing and Squeezing.” Nature, vol. 453, no. 7191, Nature Publishing Group, 2008, pp. 51–55, doi:10.1038/nature06887."},"issue":"7191","month":"05","doi":"10.1038/nature06887","date_published":"2008-05-01T00:00:00Z","abstract":[{"lang":"eng","text":"All metazoan cells carry transmembrane receptors of the integrin family, which couple the contractile force of the actomyosin cytoskeleton to the extracellular environment. In agreement with this principle, rapidly migrating leukocytes use integrin-mediated adhesion when moving over two-dimensional surfaces. As migration on two-dimensional substrates naturally overemphasizes the role of adhesion, the contribution of integrins during three-dimensional movement of leukocytes within tissues has remained controversial. We studied the interplay between adhesive, contractile and protrusive forces during interstitial leukocyte chemotaxis in vivo and in vitro. We ablated all integrin heterodimers from murine leukocytes, and show here that functional integrins do not contribute to migration in three-dimensional environments. Instead, these cells migrate by the sole force of actin-network expansion, which promotes protrusive flowing of the leading edge. Myosin II-dependent contraction is only required on passage through narrow gaps, where a squeezing contraction of the trailing edge propels the rigid nucleus."}],"publication_status":"published","year":"2008","status":"public","date_created":"2018-12-11T12:06:00Z","intvolume":" 453","quality_controlled":0,"_id":"3941","date_updated":"2021-01-12T07:53:21Z","title":"Rapid leukocyte migration by integrin-independent flowing and squeezing","day":"01","type":"journal_article","publication":"Nature","publisher":"Nature Publishing Group","extern":1,"page":"51 - 55","publist_id":"2186"},{"author":[{"full_name":"Frommhold, David","last_name":"Frommhold","first_name":"David"},{"full_name":"Ludwig, Andreas","last_name":"Ludwig","first_name":"Andreas"},{"full_name":"Bixel, M Gabriele","first_name":"M Gabriele","last_name":"Bixel"},{"last_name":"Zarbock","first_name":"Alexander","full_name":"Zarbock, Alexander"},{"full_name":"Babushkina, Inna","last_name":"Babushkina","first_name":"Inna"},{"first_name":"Melitta","last_name":"Weissinger","full_name":"Weissinger, Melitta"},{"full_name":"Cauwenberghs, Sandra","first_name":"Sandra","last_name":"Cauwenberghs"},{"first_name":"Lesley","last_name":"Ellies","full_name":"Ellies, Lesley G"},{"full_name":"Marth, Jamey D","last_name":"Marth","first_name":"Jamey"},{"full_name":"Beck-Sickinger, Annette G","last_name":"Beck Sickinger","first_name":"Annette"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Michael Sixt"},{"full_name":"Lange-Sperandio, Bärbel","last_name":"Lange Sperandio","first_name":"Bärbel"},{"full_name":"Zernecke, Alma","last_name":"Zernecke","first_name":"Alma"},{"last_name":"Brandt","first_name":"Ernst","full_name":"Brandt, Ernst"},{"last_name":"Weber","first_name":"Christian","full_name":"Weber, Christian"},{"full_name":"Vestweber, Dietmar","first_name":"Dietmar","last_name":"Vestweber"},{"full_name":"Ley, Klaus","last_name":"Ley","first_name":"Klaus"},{"last_name":"Sperandio","first_name":"Markus","full_name":"Sperandio, Markus"}],"volume":205,"doi":"10.1084/jem.20070846","month":"06","citation":{"ieee":"D. Frommhold et al., “Sialyltransferase ST3Gal-IV controls CXCR2-mediated firm leukocyte arrest during inflammation,” The Journal of Experimental Medicine, vol. 205, no. 6. Rockefeller University Press, pp. 1435–1446, 2008.","apa":"Frommhold, D., Ludwig, A., Bixel, M. G., Zarbock, A., Babushkina, I., Weissinger, M., … Sperandio, M. (2008). Sialyltransferase ST3Gal-IV controls CXCR2-mediated firm leukocyte arrest during inflammation. The Journal of Experimental Medicine. Rockefeller University Press. https://doi.org/10.1084/jem.20070846","mla":"Frommhold, David, et al. “Sialyltransferase ST3Gal-IV Controls CXCR2-Mediated Firm Leukocyte Arrest during Inflammation.” The Journal of Experimental Medicine, vol. 205, no. 6, Rockefeller University Press, 2008, pp. 1435–46, doi:10.1084/jem.20070846.","ama":"Frommhold D, Ludwig A, Bixel MG, et al. Sialyltransferase ST3Gal-IV controls CXCR2-mediated firm leukocyte arrest during inflammation. The Journal of Experimental Medicine. 2008;205(6):1435-1446. doi:10.1084/jem.20070846","short":"D. Frommhold, A. Ludwig, M.G. Bixel, A. Zarbock, I. Babushkina, M. Weissinger, S. Cauwenberghs, L. Ellies, J. Marth, A. Beck Sickinger, M.K. Sixt, B. Lange Sperandio, A. Zernecke, E. Brandt, C. Weber, D. Vestweber, K. Ley, M. Sperandio, The Journal of Experimental Medicine 205 (2008) 1435–1446.","chicago":"Frommhold, David, Andreas Ludwig, M Gabriele Bixel, Alexander Zarbock, Inna Babushkina, Melitta Weissinger, Sandra Cauwenberghs, et al. “Sialyltransferase ST3Gal-IV Controls CXCR2-Mediated Firm Leukocyte Arrest during Inflammation.” The Journal of Experimental Medicine. Rockefeller University Press, 2008. https://doi.org/10.1084/jem.20070846.","ista":"Frommhold D, Ludwig A, Bixel MG, Zarbock A, Babushkina I, Weissinger M, Cauwenberghs S, Ellies L, Marth J, Beck Sickinger A, Sixt MK, Lange Sperandio B, Zernecke A, Brandt E, Weber C, Vestweber D, Ley K, Sperandio M. 2008. Sialyltransferase ST3Gal-IV controls CXCR2-mediated firm leukocyte arrest during inflammation. The Journal of Experimental Medicine. 205(6), 1435–1446."},"issue":"6","year":"2008","publication_status":"published","abstract":[{"text":"Recent in vitro studies have suggested a role for sialylation in chemokine receptor binding to its ligand (Bannert, N., S. Craig, M. Farzan, D. Sogah, N.V. Santo, H. Choe, and J. Sodroski. 2001. J. Exp. Med. 194:1661-1673). This prompted us to investigate chemokine-induced leukocyte adhesion in inflamed cremaster muscle venules of alpha2,3 sialyltransferase (ST3Gal-IV)-deficient mice. We found a marked reduction in leukocyte adhesion to inflamed microvessels upon injection of the CXCR2 ligands CXCL1 (keratinocyte-derived chemokine) or CXCL8 (interleukin 8). In addition, extravasation of ST3Gal-IV(-/-) neutrophils into thioglycollate-pretreated peritoneal cavities was significantly decreased. In vitro assays revealed that CXCL8 binding to isolated ST3Gal-IV(-/-) neutrophils was markedly impaired. Furthermore, CXCL1-mediated adhesion of ST3Gal-IV(-/-) leukocytes at physiological flow conditions, as well as transendothelial migration of ST3Gal-IV(-/-) leukocytes in response to CXCL1, was significantly reduced. In human neutrophils, enzymatic desialylation decreased binding of CXCR2 ligands to the neutrophil surface and diminished neutrophil degranulation in response to these chemokines. In addition, binding of alpha2,3-linked sialic acid-specific Maackia amurensis lectin II to purified CXCR2 from neuraminidase-treated CXCR2-transfected HEK293 cells was markedly impaired. Collectively, we provide substantial evidence that sialylation by ST3Gal-IV significantly contributes to CXCR2-mediated leukocyte adhesion during inflammation in vivo.","lang":"eng"}],"date_published":"2008-06-02T00:00:00Z","quality_controlled":0,"status":"public","intvolume":" 205","date_created":"2018-12-11T12:06:01Z","type":"journal_article","day":"02","date_updated":"2021-01-12T07:53:21Z","title":"Sialyltransferase ST3Gal-IV controls CXCR2-mediated firm leukocyte arrest during inflammation","_id":"3942","publisher":"Rockefeller University Press","publication":"The Journal of Experimental Medicine","publist_id":"2185","page":"1435 - 1446","extern":1},{"volume":118,"author":[{"full_name":"Kessenbrock, Kai","first_name":"Kai","last_name":"Kessenbrock"},{"first_name":"Leopold","last_name":"Fröhlich","full_name":"Fröhlich, Leopold"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K","full_name":"Michael Sixt"},{"last_name":"Lämmermann","first_name":"Tim","full_name":"Lämmermann, Tim"},{"last_name":"Pfister","first_name":"Heiko","full_name":"Pfister, Heiko"},{"full_name":"Bateman, Andrew","last_name":"Bateman","first_name":"Andrew"},{"full_name":"Belaaouaj, Azzaq","first_name":"Azzaq","last_name":"Belaaouaj"},{"full_name":"Ring, Johannes","last_name":"Ring","first_name":"Johannes"},{"last_name":"Ollert","first_name":"Markus","full_name":"Ollert, Markus"},{"full_name":"Fässler, Reinhard","last_name":"Fässler","first_name":"Reinhard"},{"full_name":"Jenne, Dieter E","first_name":"Dieter","last_name":"Jenne"}],"doi":"10.1172/JCI34694","citation":{"ista":"Kessenbrock K, Fröhlich L, Sixt MK, Lämmermann T, Pfister H, Bateman A, Belaaouaj A, Ring J, Ollert M, Fässler R, Jenne D. 2008. Proteinase 3 and neutrophil elastase enhance inflammation in mice by inactivating antiinflammatory progranulin. The Journal of Clinical Investigation. 118(7), 2438–2447.","chicago":"Kessenbrock, Kai, Leopold Fröhlich, Michael K Sixt, Tim Lämmermann, Heiko Pfister, Andrew Bateman, Azzaq Belaaouaj, et al. “Proteinase 3 and Neutrophil Elastase Enhance Inflammation in Mice by Inactivating Antiinflammatory Progranulin.” The Journal of Clinical Investigation. American Society for Clinical Investigation, 2008. https://doi.org/10.1172/JCI34694.","short":"K. Kessenbrock, L. Fröhlich, M.K. Sixt, T. Lämmermann, H. Pfister, A. Bateman, A. Belaaouaj, J. Ring, M. Ollert, R. Fässler, D. Jenne, The Journal of Clinical Investigation 118 (2008) 2438–2447.","ama":"Kessenbrock K, Fröhlich L, Sixt MK, et al. Proteinase 3 and neutrophil elastase enhance inflammation in mice by inactivating antiinflammatory progranulin. The Journal of Clinical Investigation. 2008;118(7):2438-2447. doi:10.1172/JCI34694","mla":"Kessenbrock, Kai, et al. “Proteinase 3 and Neutrophil Elastase Enhance Inflammation in Mice by Inactivating Antiinflammatory Progranulin.” The Journal of Clinical Investigation, vol. 118, no. 7, American Society for Clinical Investigation, 2008, pp. 2438–47, doi:10.1172/JCI34694.","apa":"Kessenbrock, K., Fröhlich, L., Sixt, M. K., Lämmermann, T., Pfister, H., Bateman, A., … Jenne, D. (2008). Proteinase 3 and neutrophil elastase enhance inflammation in mice by inactivating antiinflammatory progranulin. The Journal of Clinical Investigation. American Society for Clinical Investigation. https://doi.org/10.1172/JCI34694","ieee":"K. Kessenbrock et al., “Proteinase 3 and neutrophil elastase enhance inflammation in mice by inactivating antiinflammatory progranulin,” The Journal of Clinical Investigation, vol. 118, no. 7. American Society for Clinical Investigation, pp. 2438–2447, 2008."},"issue":"7","month":"07","publication_status":"published","year":"2008","date_published":"2008-07-01T00:00:00Z","abstract":[{"lang":"eng","text":"Neutrophil granulocytes form the body's first line of antibacterial defense, but they also contribute to tissue injury and noninfectious, chronic inflammation. Proteinase 3 (PR3) and neutrophil elastase (NE) are 2 abundant neutrophil serine proteases implicated in antimicrobial defense with overlapping and potentially redundant substrate specificity. Here, we unraveled a cooperative role for PR3 and NE in neutrophil activation and noninfectious inflammation in vivo, which we believe to be novel. Mice lacking both PR3 and NE demonstrated strongly diminished immune complex-mediated (IC-mediated) neutrophil infiltration in vivo as well as reduced activation of isolated neutrophils by ICs in vitro. In contrast, in mice lacking just NE, neutrophil recruitment to ICs was only marginally impaired. The defects in mice lacking both PR3 and NE were directly linked to the accumulation of antiinflammatory progranulin (PGRN). Both PR3 and NE cleaved PGRN in vitro and during neutrophil activation and inflammation in vivo. Local administration of recombinant PGRN potently inhibited neutrophilic inflammation in vivo, demonstrating that PGRN represents a crucial inflammation-suppressing mediator. We conclude that PR3 and NE enhance neutrophil-dependent inflammation by eliminating the local antiinflammatory activity of PGRN. Our results support the use of serine protease inhibitors as antiinflammatory agents."}],"quality_controlled":0,"date_created":"2018-12-11T12:06:01Z","status":"public","intvolume":" 118","day":"01","type":"journal_article","_id":"3943","title":"Proteinase 3 and neutrophil elastase enhance inflammation in mice by inactivating antiinflammatory progranulin","date_updated":"2021-01-12T07:53:22Z","publication":"The Journal of Clinical Investigation","publisher":"American Society for Clinical Investigation","page":"2438 - 2447","publist_id":"2183","extern":1},{"volume":5,"author":[{"full_name":"Riedl, Julia","first_name":"Julia","last_name":"Riedl"},{"last_name":"Crevenna","first_name":"Alvaro","full_name":"Crevenna, Alvaro H"},{"first_name":"Kai","last_name":"Kessenbrock","full_name":"Kessenbrock, Kai"},{"first_name":"Jerry","last_name":"Yu","full_name":"Yu, Jerry Haochen"},{"full_name":"Neukirchen, Dorothee","last_name":"Neukirchen","first_name":"Dorothee"},{"full_name":"Bista, Michal","last_name":"Bista","first_name":"Michal"},{"full_name":"Bradke, Frank","last_name":"Bradke","first_name":"Frank"},{"first_name":"Dieter","last_name":"Jenne","full_name":"Jenne, Dieter"},{"full_name":"Holak, Tad A","last_name":"Holak","first_name":"Tad"},{"last_name":"Werb","first_name":"Zena","full_name":"Werb, Zena"},{"last_name":"Sixt","first_name":"Michael K","full_name":"Michael Sixt","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wedlich Soldner","first_name":"Roland","full_name":"Wedlich-Soldner, Roland"}],"doi":"10.1038/nmeth.1220","issue":"7","citation":{"ista":"Riedl J, Crevenna A, Kessenbrock K, Yu J, Neukirchen D, Bista M, Bradke F, Jenne D, Holak T, Werb Z, Sixt MK, Wedlich Soldner R. 2008. Lifeact: a versatile marker to visualize F-actin. Nature Methods. 5(7), 605–607.","chicago":"Riedl, Julia, Alvaro Crevenna, Kai Kessenbrock, Jerry Yu, Dorothee Neukirchen, Michal Bista, Frank Bradke, et al. “Lifeact: A Versatile Marker to Visualize F-Actin.” Nature Methods. Nature Publishing Group, 2008. https://doi.org/10.1038/nmeth.1220.","short":"J. Riedl, A. Crevenna, K. Kessenbrock, J. Yu, D. Neukirchen, M. Bista, F. Bradke, D. Jenne, T. Holak, Z. Werb, M.K. Sixt, R. Wedlich Soldner, Nature Methods 5 (2008) 605–607.","mla":"Riedl, Julia, et al. “Lifeact: A Versatile Marker to Visualize F-Actin.” Nature Methods, vol. 5, no. 7, Nature Publishing Group, 2008, pp. 605–07, doi:10.1038/nmeth.1220.","apa":"Riedl, J., Crevenna, A., Kessenbrock, K., Yu, J., Neukirchen, D., Bista, M., … Wedlich Soldner, R. (2008). Lifeact: a versatile marker to visualize F-actin. Nature Methods. Nature Publishing Group. https://doi.org/10.1038/nmeth.1220","ieee":"J. Riedl et al., “Lifeact: a versatile marker to visualize F-actin,” Nature Methods, vol. 5, no. 7. Nature Publishing Group, pp. 605–607, 2008.","ama":"Riedl J, Crevenna A, Kessenbrock K, et al. Lifeact: a versatile marker to visualize F-actin. Nature Methods. 2008;5(7):605-607. doi:10.1038/nmeth.1220"},"month":"06","publication_status":"published","year":"2008","date_published":"2008-06-08T00:00:00Z","abstract":[{"lang":"eng","text":"Live imaging of the actin cytoskeleton is crucial for the study of many fundamental biological processes, but current approaches to visualize actin have several limitations. Here we describe Lifeact, a 17-amino-acid peptide, which stained filamentous actin (F-actin) structures in eukaryotic cells and tissues. Lifeact did not interfere with actin dynamics in vitro and in vivo and in its chemically modified peptide form allowed visualization of actin dynamics in nontransfectable cells."}],"quality_controlled":0,"intvolume":" 5","status":"public","date_created":"2018-12-11T12:06:02Z","day":"08","type":"journal_article","_id":"3944","title":"Lifeact: a versatile marker to visualize F-actin","date_updated":"2021-01-12T07:53:22Z","publication":"Nature Methods","publisher":"Nature Publishing Group","page":"605 - 607","publist_id":"2184","extern":1},{"publisher":"Elsevier","publication":"Immunobiology","publist_id":"2182","page":"715 - 28","extern":1,"quality_controlled":0,"date_created":"2018-12-11T12:06:02Z","intvolume":" 213","status":"public","type":"journal_article","day":"30","date_updated":"2021-01-12T07:53:23Z","title":"The lymph vessel network in mouse skin visualised with antibodies against the hyaluronan receptor LYVE-1","_id":"3945","year":"2008","publication_status":"published","date_published":"2008-08-30T00:00:00Z","abstract":[{"text":"Langerhans cells and dermal dendritic cells migrate to the draining lymph nodes through dermal lymphatic vessels. They do so in the steady-state and under inflammatory conditions. Peripheral T cell tolerance or T cell priming, respectively, are the consequences of migration. The nature of dendritic cell-containing vessels was mostly defined by electron microscopy or by their lack of blood endothelial markers. Selective markers for murine lymph endothelium were hitherto rare or not available. Here, we utilised recently developed antibodies against the murine hyaluronan receptor, LYVE-1, to study the lymph vessel network in mouse skin in more detail. In hairless skin from the ears, lymph vessels were spread out in a horizontal plane. They formed anastomoses, and they possessed frequent blind endings that were occasionally open. Lymph vessels were wider than blood vessels, which were identified by their strong CD31 expression. In body wall skin LYVE-1 reactive vessels did not extend laterally but they dived straight down into the deeper dermis. There, they are connected to each other and formed a network similar to ear skin. The number and width of lymph vessels did not grossly change upon inflammatory stimuli such as skin explant culture or tape stripping. There were also no marked changes in caliber in response to the TLR 7/8 ligand Imiquimod. Double-labelling experiments of cultured skin showed that most of the strongly cell surface MHC II-expressing (i.e. activated) dendritic cells were confined to the lymph vessels. Langerin/CD207(+) cells within this population appeared later than dermal dendritic cells, i.e. langerin-negative cells. Comparable results were obtained after stimulating the skin in vivo with the TLR 7/8 ligand Imiquimod or by tape stripping. In untreated skin (i.e. steady state) a few MHC II(+) and Langerin/CD207(+) cells, presumably migrating skin dendritic cells including epidermal Langerhans cells, were consistently observed within the lymph vessels. The novel antibody reagents may serve as important tools to further study the dendritic cell traffic in the skin under physiological conditions as well as in conditions of adoptive dendritic cell transfer in immunotherapy.","lang":"eng"}],"author":[{"first_name":"Christoph","last_name":"Tripp","full_name":"Tripp, Christoph H"},{"full_name":"Haid, Bernhard","last_name":"Haid","first_name":"Bernhard"},{"first_name":"Vincent","last_name":"Flacher","full_name":"Flacher, Vincent"},{"last_name":"Sixt","first_name":"Michael K","full_name":"Michael Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"},{"last_name":"Peter","first_name":"Hannes","full_name":"Peter, Hannes"},{"full_name":"Farkas, Julia","last_name":"Farkas","first_name":"Julia"},{"full_name":"Gschwentner, Robert","first_name":"Robert","last_name":"Gschwentner"},{"full_name":"Sorokin, Lydia","first_name":"Lydia","last_name":"Sorokin"},{"last_name":"Romani","first_name":"Nikolaus","full_name":"Romani, Nikolaus"},{"full_name":"Stoitzner, Patrizia","last_name":"Stoitzner","first_name":"Patrizia"}],"volume":213,"doi":"10.1016/j.imbio.2008.07.025","month":"08","citation":{"ista":"Tripp C, Haid B, Flacher V, Sixt MK, Peter H, Farkas J, Gschwentner R, Sorokin L, Romani N, Stoitzner P. 2008. The lymph vessel network in mouse skin visualised with antibodies against the hyaluronan receptor LYVE-1. Immunobiology. 213(9–10), 715–28.","chicago":"Tripp, Christoph, Bernhard Haid, Vincent Flacher, Michael K Sixt, Hannes Peter, Julia Farkas, Robert Gschwentner, Lydia Sorokin, Nikolaus Romani, and Patrizia Stoitzner. “The Lymph Vessel Network in Mouse Skin Visualised with Antibodies against the Hyaluronan Receptor LYVE-1.” Immunobiology. Elsevier, 2008. https://doi.org/10.1016/j.imbio.2008.07.025.","short":"C. Tripp, B. Haid, V. Flacher, M.K. Sixt, H. Peter, J. Farkas, R. Gschwentner, L. Sorokin, N. Romani, P. Stoitzner, Immunobiology 213 (2008) 715–28.","ama":"Tripp C, Haid B, Flacher V, et al. The lymph vessel network in mouse skin visualised with antibodies against the hyaluronan receptor LYVE-1. Immunobiology. 2008;213(9-10):715-728. doi:10.1016/j.imbio.2008.07.025","mla":"Tripp, Christoph, et al. “The Lymph Vessel Network in Mouse Skin Visualised with Antibodies against the Hyaluronan Receptor LYVE-1.” Immunobiology, vol. 213, no. 9–10, Elsevier, 2008, pp. 715–28, doi:10.1016/j.imbio.2008.07.025.","apa":"Tripp, C., Haid, B., Flacher, V., Sixt, M. K., Peter, H., Farkas, J., … Stoitzner, P. (2008). The lymph vessel network in mouse skin visualised with antibodies against the hyaluronan receptor LYVE-1. Immunobiology. Elsevier. https://doi.org/10.1016/j.imbio.2008.07.025","ieee":"C. Tripp et al., “The lymph vessel network in mouse skin visualised with antibodies against the hyaluronan receptor LYVE-1,” Immunobiology, vol. 213, no. 9–10. Elsevier, pp. 715–28, 2008."},"issue":"9-10"},{"status":"public","date_created":"2018-12-11T12:06:11Z","alternative_title":["Contemporary Mathematics"],"quality_controlled":0,"title":"Persistent homology - a survey","date_updated":"2021-01-12T07:53:33Z","_id":"3969","type":"book_chapter","day":"28","publisher":"American Mathematical Society","publication":"Surveys on Discrete and Computational Geometry: Twenty Years Later","extern":1,"acknowledgement":"Supported in part by DARPA under grants HR0011-05-1-0007 and HR0011-05-0057 and by the NSF under grant DBI-06-06873.","publist_id":"2156","page":"257 - 282","author":[{"full_name":"Herbert Edelsbrunner","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Harer","first_name":"John","full_name":"Harer, John"}],"month":"03","citation":{"ista":"Edelsbrunner H, Harer J. 2008.Persistent homology - a survey. In: Surveys on Discrete and Computational Geometry: Twenty Years Later. Contemporary Mathematics, , 257–282.","short":"H. Edelsbrunner, J. Harer, in:, Surveys on Discrete and Computational Geometry: Twenty Years Later, American Mathematical Society, 2008, pp. 257–282.","chicago":"Edelsbrunner, Herbert, and John Harer. “Persistent Homology - a Survey.” In Surveys on Discrete and Computational Geometry: Twenty Years Later, 257–82. American Mathematical Society, 2008.","ama":"Edelsbrunner H, Harer J. Persistent homology - a survey. In: Surveys on Discrete and Computational Geometry: Twenty Years Later. American Mathematical Society; 2008:257-282.","mla":"Edelsbrunner, Herbert, and John Harer. “Persistent Homology - a Survey.” Surveys on Discrete and Computational Geometry: Twenty Years Later, American Mathematical Society, 2008, pp. 257–82.","apa":"Edelsbrunner, H., & Harer, J. (2008). Persistent homology - a survey. In Surveys on Discrete and Computational Geometry: Twenty Years Later (pp. 257–282). American Mathematical Society.","ieee":"H. Edelsbrunner and J. Harer, “Persistent homology - a survey,” in Surveys on Discrete and Computational Geometry: Twenty Years Later, American Mathematical Society, 2008, pp. 257–282."},"abstract":[{"text":"Persistent homology is an algebraic tool for measuring topological features of shapes and functions. It casts the multi-scale organization we frequently observe in nature into a mathematical formalism. Here we give a record of the short history of persistent homology and present its basic concepts. Besides the mathematics we focus on algorithms and mention the various connections to applications, including to biomolecules, biological networks, data analysis, and geometric modeling.","lang":"eng"}],"date_published":"2008-03-28T00:00:00Z","year":"2008","publication_status":"published"},{"acknowledgement":"This research was partially supported by DARPA grant HR 0011-05-1-0057. HE and YM mathematical work was supported by DARPA grant HR0011-05-1-0007. AS research was supported by a Lucent Technologies Bell Labs Graduate Research. Fellowship; AK and MR research was supported by NIH grant GM U54 GM74942; and SA research was supported by Association pour la Recherche sur le Cancer (ARC), France. OP, AM, MLD, EG and GH research was supported by the Stowers Institute for Medical Research. OP is a Howard Hughes Medical Institute Investigator.","extern":1,"publist_id":"2157","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Public Library of Science","publication":"PLoS One","title":"Comparison of pattern detection methods in microarray time series of the segmentation clock","date_updated":"2021-01-12T07:53:33Z","_id":"3970","type":"journal_article","day":"06","status":"public","date_created":"2018-12-11T12:06:11Z","intvolume":" 3","quality_controlled":0,"date_published":"2008-08-06T00:00:00Z","abstract":[{"lang":"eng","text":"While genome-wide gene expression data are generated at an increasing rate, the repertoire of approaches for pattern discovery in these data is still limited. Identifying subtle patterns of interest in large amounts of data (tens of thousands of profiles) associated with a certain level of noise remains a challenge. A microarray time series was recently generated to study the transcriptional program of the mouse segmentation clock, a biological oscillator associated with the periodic formation of the segments of the body axis. A method related to Fourier analysis, the Lomb-Scargle periodogram, was used to detect periodic profiles in the dataset, leading to the identification of a novel set of cyclic genes associated with the segmentation clock. Here, we applied to the same microarray time series dataset four distinct mathematical methods to identify significant patterns in gene expression profiles. These methods are called: Phase consistency, Address reduction, Cyclohedron test and Stable persistence, and are based on different conceptual frameworks that are either hypothesis- or data-driven. Some of the methods, unlike Fourier transforms, are not dependent on the assumption of periodicity of the pattern of interest. Remarkably, these methods identified blindly the expression profiles of known cyclic genes as the most significant patterns in the dataset. Many candidate genes predicted by more than one approach appeared to be true positive cyclic genes and will be of particular interest for future research. In addition, these methods predicted novel candidate cyclic genes that were consistent with previous biological knowledge and experimental validation in mouse embryos. Our results demonstrate the utility of these novel pattern detection strategies, notably for detection of periodic profiles, and suggest that combining several distinct mathematical approaches to analyze microarray datasets is a valuable strategy for identifying genes that exhibit novel, interesting transcriptional patterns."}],"year":"2008","publication_status":"published","license":"https://creativecommons.org/licenses/by/4.0/","month":"08","issue":"8","citation":{"short":"M. Dequéant, S. Ahnert, H. Edelsbrunner, T. Fink, E. Glynn, G. Hattem, A. Kudlicki, Y. Mileyko, J. Morton, A. Mushegian, L. Pachter, M. Rowicka, A. Shiu, B. Sturmfels, O. Pourquie, PLoS One 3 (2008).","chicago":"Dequéant, Mary, Sebastian Ahnert, Herbert Edelsbrunner, Thomas Fink, Earl Glynn, Gaye Hattem, Andrzej Kudlicki, et al. “Comparison of Pattern Detection Methods in Microarray Time Series of the Segmentation Clock.” PLoS One. Public Library of Science, 2008. https://doi.org/10.1371/journal.pone.0002856.","ista":"Dequéant M, Ahnert S, Edelsbrunner H, Fink T, Glynn E, Hattem G, Kudlicki A, Mileyko Y, Morton J, Mushegian A, Pachter L, Rowicka M, Shiu A, Sturmfels B, Pourquie O. 2008. Comparison of pattern detection methods in microarray time series of the segmentation clock. PLoS One. 3(8).","ama":"Dequéant M, Ahnert S, Edelsbrunner H, et al. Comparison of pattern detection methods in microarray time series of the segmentation clock. PLoS One. 2008;3(8). doi:10.1371/journal.pone.0002856","ieee":"M. Dequéant et al., “Comparison of pattern detection methods in microarray time series of the segmentation clock,” PLoS One, vol. 3, no. 8. Public Library of Science, 2008.","apa":"Dequéant, M., Ahnert, S., Edelsbrunner, H., Fink, T., Glynn, E., Hattem, G., … Pourquie, O. (2008). Comparison of pattern detection methods in microarray time series of the segmentation clock. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0002856","mla":"Dequéant, Mary, et al. “Comparison of Pattern Detection Methods in Microarray Time Series of the Segmentation Clock.” PLoS One, vol. 3, no. 8, Public Library of Science, 2008, doi:10.1371/journal.pone.0002856."},"doi":"10.1371/journal.pone.0002856","author":[{"first_name":"Mary","last_name":"Dequéant","full_name":"Dequéant, Mary-Lee"},{"full_name":"Ahnert, Sebastian","last_name":"Ahnert","first_name":"Sebastian"},{"full_name":"Herbert Edelsbrunner","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"last_name":"Fink","first_name":"Thomas","full_name":"Fink, Thomas M"},{"full_name":"Glynn, Earl F","last_name":"Glynn","first_name":"Earl"},{"last_name":"Hattem","first_name":"Gaye","full_name":"Hattem, Gaye"},{"full_name":"Kudlicki, Andrzej","first_name":"Andrzej","last_name":"Kudlicki"},{"full_name":"Mileyko, Yuriy","first_name":"Yuriy","last_name":"Mileyko"},{"full_name":"Morton, Jason","first_name":"Jason","last_name":"Morton"},{"last_name":"Mushegian","first_name":"Arcady","full_name":"Mushegian, Arcady R"},{"first_name":"Lior","last_name":"Pachter","full_name":"Pachter, Lior"},{"full_name":"Rowicka, Maga","last_name":"Rowicka","first_name":"Maga"},{"full_name":"Shiu, Anne","first_name":"Anne","last_name":"Shiu"},{"first_name":"Bernd","last_name":"Sturmfels","full_name":"Sturmfels, Bernd"},{"last_name":"Pourquie","first_name":"Olivier","full_name":"Pourquie, Olivier"}],"volume":3},{"status":"public","intvolume":" 41","date_created":"2018-12-11T12:06:12Z","quality_controlled":0,"_id":"3971","title":"Time-varying Reeb graphs for continuous space-time data","date_updated":"2021-01-12T07:53:34Z","day":"01","type":"journal_article","publication":"Computational Geometry: Theory and Applications","publisher":"Elsevier","extern":1,"page":"149 - 166","publist_id":"2158","volume":41,"author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Herbert Edelsbrunner"},{"full_name":"Harer, John","last_name":"Harer","first_name":"John"},{"full_name":"Mascarenhas, Ajith","first_name":"Ajith","last_name":"Mascarenhas"},{"full_name":"Pascucci, Valerio","last_name":"Pascucci","first_name":"Valerio"},{"last_name":"Snoeyink","first_name":"Jack","full_name":"Snoeyink, Jack"}],"citation":{"ista":"Edelsbrunner H, Harer J, Mascarenhas A, Pascucci V, Snoeyink J. 2008. Time-varying Reeb graphs for continuous space-time data. Computational Geometry: Theory and Applications. 41(3), 149–166.","short":"H. Edelsbrunner, J. Harer, A. Mascarenhas, V. Pascucci, J. Snoeyink, Computational Geometry: Theory and Applications 41 (2008) 149–166.","chicago":"Edelsbrunner, Herbert, John Harer, Ajith Mascarenhas, Valerio Pascucci, and Jack Snoeyink. “Time-Varying Reeb Graphs for Continuous Space-Time Data.” Computational Geometry: Theory and Applications. Elsevier, 2008. https://doi.org/10.1016/j.comgeo.2007.11.001.","ama":"Edelsbrunner H, Harer J, Mascarenhas A, Pascucci V, Snoeyink J. Time-varying Reeb graphs for continuous space-time data. Computational Geometry: Theory and Applications. 2008;41(3):149-166. doi:10.1016/j.comgeo.2007.11.001","mla":"Edelsbrunner, Herbert, et al. “Time-Varying Reeb Graphs for Continuous Space-Time Data.” Computational Geometry: Theory and Applications, vol. 41, no. 3, Elsevier, 2008, pp. 149–66, doi:10.1016/j.comgeo.2007.11.001.","apa":"Edelsbrunner, H., Harer, J., Mascarenhas, A., Pascucci, V., & Snoeyink, J. (2008). Time-varying Reeb graphs for continuous space-time data. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2007.11.001","ieee":"H. Edelsbrunner, J. Harer, A. Mascarenhas, V. Pascucci, and J. Snoeyink, “Time-varying Reeb graphs for continuous space-time data,” Computational Geometry: Theory and Applications, vol. 41, no. 3. Elsevier, pp. 149–166, 2008."},"issue":"3","month":"11","doi":"10.1016/j.comgeo.2007.11.001","date_published":"2008-11-01T00:00:00Z","abstract":[{"lang":"eng","text":"The Reeb graph is a useful tool in visualizing real-valued data obtained from computational simulations of physical processes. We characterize the evolution of the Reeb graph of a time-varying continuous function defined in three-dimensional space. We show how to maintain the Reeb graph over time and compress the entire sequence of Reeb graphs into a single, partially persistent data structure, and augment this data structure with Betti numbers to describe the topology of level sets and with path seeds to assist in the fast extraction of level sets for visualization."}],"publication_status":"published","year":"2008"},{"extern":1,"conference":{"name":"SCG: Symposium on Computational Geometry"},"publist_id":"2155","page":"242 - 250","publisher":"ACM","date_updated":"2021-01-12T07:53:35Z","title":"Reeb spaces of piecewise linear mappings","_id":"3974","type":"conference","day":"01","status":"public","date_created":"2018-12-11T12:06:13Z","quality_controlled":0,"abstract":[{"text":"Generalizing the concept of a Reeb graph, the Reeb space of a multivariate continuous mapping identifies points of the domain that belong to a common component of the preimage of a point in the range. We study the local and global structure of this space for generic, piecewise linear mappings on a combinatorial manifold.","lang":"eng"}],"date_published":"2008-01-01T00:00:00Z","year":"2008","publication_status":"published","month":"01","citation":{"ama":"Edelsbrunner H, Harer J, Patel A. Reeb spaces of piecewise linear mappings. In: ACM; 2008:242-250. doi:10.1145/1377676.1377720","mla":"Edelsbrunner, Herbert, et al. Reeb Spaces of Piecewise Linear Mappings. ACM, 2008, pp. 242–50, doi:10.1145/1377676.1377720.","apa":"Edelsbrunner, H., Harer, J., & Patel, A. (2008). Reeb spaces of piecewise linear mappings (pp. 242–250). Presented at the SCG: Symposium on Computational Geometry, ACM. https://doi.org/10.1145/1377676.1377720","ieee":"H. Edelsbrunner, J. Harer, and A. Patel, “Reeb spaces of piecewise linear mappings,” presented at the SCG: Symposium on Computational Geometry, 2008, pp. 242–250.","ista":"Edelsbrunner H, Harer J, Patel A. 2008. Reeb spaces of piecewise linear mappings. SCG: Symposium on Computational Geometry, 242–250.","chicago":"Edelsbrunner, Herbert, John Harer, and Amit Patel. “Reeb Spaces of Piecewise Linear Mappings,” 242–50. ACM, 2008. https://doi.org/10.1145/1377676.1377720.","short":"H. Edelsbrunner, J. Harer, A. Patel, in:, ACM, 2008, pp. 242–250."},"doi":"10.1145/1377676.1377720","author":[{"last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Herbert Edelsbrunner","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Harer, John","first_name":"John","last_name":"Harer"},{"id":"34A254A0-F248-11E8-B48F-1D18A9856A87","full_name":"Amit Patel","first_name":"Amit","last_name":"Patel"}]},{"doi":"10.1111/j.1461-0248.2008.01206.x","issue":"8","citation":{"ama":"Storch D, Šizling A, Reif J, Polechova J, Šizlingová E, Gaston K. The quest for a null model for macroecological patterns: Geometry of species distributions at multiple spatial scales. Ecology Letters. 2008;11(8):771-784. doi:10.1111/j.1461-0248.2008.01206.x","apa":"Storch, D., Šizling, A., Reif, J., Polechova, J., Šizlingová, E., & Gaston, K. (2008). The quest for a null model for macroecological patterns: Geometry of species distributions at multiple spatial scales. Ecology Letters. Wiley. https://doi.org/10.1111/j.1461-0248.2008.01206.x","ieee":"D. Storch, A. Šizling, J. Reif, J. Polechova, E. Šizlingová, and K. Gaston, “The quest for a null model for macroecological patterns: Geometry of species distributions at multiple spatial scales,” Ecology Letters, vol. 11, no. 8. Wiley, pp. 771–784, 2008.","mla":"Storch, D., et al. “The Quest for a Null Model for Macroecological Patterns: Geometry of Species Distributions at Multiple Spatial Scales.” Ecology Letters, vol. 11, no. 8, Wiley, 2008, pp. 771–84, doi:10.1111/j.1461-0248.2008.01206.x.","chicago":"Storch, D., A. Šizling, J. Reif, Jitka Polechova, E. Šizlingová, and K. Gaston. “The Quest for a Null Model for Macroecological Patterns: Geometry of Species Distributions at Multiple Spatial Scales.” Ecology Letters. Wiley, 2008. https://doi.org/10.1111/j.1461-0248.2008.01206.x.","short":"D. Storch, A. Šizling, J. Reif, J. Polechova, E. Šizlingová, K. Gaston, Ecology Letters 11 (2008) 771–784.","ista":"Storch D, Šizling A, Reif J, Polechova J, Šizlingová E, Gaston K. 2008. The quest for a null model for macroecological patterns: Geometry of species distributions at multiple spatial scales. Ecology Letters. 11(8), 771–784."},"month":"08","volume":11,"author":[{"first_name":"D.","last_name":"Storch","full_name":"Storch, D."},{"first_name":"A.","last_name":"Šizling","full_name":"Šizling, A."},{"last_name":"Reif","first_name":"J.","full_name":"Reif, J."},{"id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0951-3112","first_name":"Jitka","last_name":"Polechova","full_name":"Polechova, Jitka"},{"full_name":"Šizlingová, E.","last_name":"Šizlingová","first_name":"E."},{"full_name":"Gaston, K.","first_name":"K.","last_name":"Gaston"}],"scopus_import":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","publication_status":"published","year":"2008","abstract":[{"lang":"eng","text":"There have been several attempts to build a unified framework for macroecological patterns. However, these have mostly been based either on questionable assumptions or have had to be parameterized to obtain realistic predictions. Here, we propose a new model explicitly considering patterns of aggregated species distributions on multiple spatial scales, the property which lies behind all spatial macroecological patterns, using the idea we term ‘generalized fractals’. Species’ spatial distributions were modelled by a random hierarchical process in which the original ‘habitat’ patches were randomly replaced by sets of smaller patches nested within them, and the statistical properties of modelled species assemblages were compared with macroecological patterns in observed bird data. Without parameterization based on observed patterns, this simple model predicts realistic patterns of species abundance, distribution and diversity, including fractal-like spatial distributions, the frequency distribution of species occupancies/abundances and the species–area relationship. Although observed macroecological patterns may differ in some quantitative properties, our concept of random hierarchical aggregation can be considered as an appropriate null model of fundamental macroecological patterns which can potentially be modified to accommodate ecologically important variables."}],"date_published":"2008-08-01T00:00:00Z","article_processing_charge":"No","day":"01","type":"journal_article","_id":"4135","date_updated":"2025-07-02T05:52:43Z","title":"The quest for a null model for macroecological patterns: Geometry of species distributions at multiple spatial scales","quality_controlled":"1","date_created":"2018-12-11T12:07:09Z","status":"public","intvolume":" 11","page":"771 - 784","publist_id":"1985","extern":"1","publication":"Ecology Letters","publisher":"Wiley"},{"doi":"10.1016/j.ydbio.2008.05.529","citation":{"ama":"Vervenne H, Crombez K, Lambaerts K, et al. Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation. Developmental Biology. 2008;320(1):267-277. doi:10.1016/j.ydbio.2008.05.529","ieee":"H. Vervenne et al., “Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation,” Developmental Biology, vol. 320, no. 1. Elsevier, pp. 267–277, 2008.","apa":"Vervenne, H., Crombez, K., Lambaerts, K., Carvalho, L., Köppen, M., Heisenberg, C.-P. J., … Petit, M. (2008). Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation. Developmental Biology. Elsevier. https://doi.org/10.1016/j.ydbio.2008.05.529","mla":"Vervenne, Hilke, et al. “Lpp Is Involved in Wnt/PCP Signaling and Acts Together with Scrib to Mediate Convergence and Extension Movements during Zebrafish Gastrulation.” Developmental Biology, vol. 320, no. 1, Elsevier, 2008, pp. 267–77, doi:10.1016/j.ydbio.2008.05.529.","chicago":"Vervenne, Hilke, Koen Crombez, Kathleen Lambaerts, Lara Carvalho, Mathias Köppen, Carl-Philipp J Heisenberg, Wim Van De Ven, and Marleen Petit. “Lpp Is Involved in Wnt/PCP Signaling and Acts Together with Scrib to Mediate Convergence and Extension Movements during Zebrafish Gastrulation.” Developmental Biology. Elsevier, 2008. https://doi.org/10.1016/j.ydbio.2008.05.529.","short":"H. Vervenne, K. Crombez, K. Lambaerts, L. Carvalho, M. Köppen, C.-P.J. Heisenberg, W. Van De Ven, M. Petit, Developmental Biology 320 (2008) 267–277.","ista":"Vervenne H, Crombez K, Lambaerts K, Carvalho L, Köppen M, Heisenberg C-PJ, Van De Ven W, Petit M. 2008. Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation. Developmental Biology. 320(1), 267–277."},"issue":"1","month":"08","volume":320,"author":[{"last_name":"Vervenne","first_name":"Hilke","full_name":"Vervenne, Hilke"},{"full_name":"Crombez, Koen","first_name":"Koen","last_name":"Crombez"},{"first_name":"Kathleen","last_name":"Lambaerts","full_name":"Lambaerts, Kathleen"},{"full_name":"Carvalho, Lara","last_name":"Carvalho","first_name":"Lara"},{"full_name":"Köppen, Mathias","first_name":"Mathias","last_name":"Köppen"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"},{"last_name":"Van De Ven","first_name":"Wim","full_name":"Van De Ven, Wim"},{"first_name":"Marleen","last_name":"Petit","full_name":"Petit, Marleen"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","publication_status":"published","year":"2008","date_published":"2008-08-01T00:00:00Z","abstract":[{"text":"The zyxin-related LPP protein is localized at focal adhesions and cell-cell contacts and is involved in the regulation of smooth muscle cell migration. A known interaction partner of LPP in human is the tumor suppressor protein SCRIB. Knocking down scrib expression c uring zebrafish embryonic development results in defects of convergence and extension (C&E) movements, which occur during gastrulation and mediate elongation of the anterior-posterior body axis. Mediolateral cell polarization underlying C&E is regulated by a noncanonical Writ signaling pathway constituting the vertebrate planar cell polarity (PCP) pathway. Here, we investigated the role of Lpp during early zebrafish development. We show that morpholino knockdown of Ipp results in defects of C&E, phenocopying noncanonical Wnt signaling mutants. Time-lapse analysis associates the defective dorsal convergence movements with a reduced ability to migrate along straight paths. In addition, expression of Lpp is significantly reduced in Wnt11 morphants and in embryos overexpressing Wnt11 or a dominant-negative form of Rho kinase 2, which is a downstream effector of Wnt11, Suggesting that Lpp expression is dependent on noncanonical Wnt signaling. Finally, we demonstrate that Lpp interacts with the PCP protein Scrib in zebrafish, and that Lpp and Scrib cooperate for the mediation of C&E. (C) 2008 Elsevier Inc. All rights reserved.","lang":"eng"}],"article_processing_charge":"No","day":"01","type":"journal_article","_id":"4141","title":"Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation","date_updated":"2021-01-12T07:54:48Z","date_created":"2018-12-11T12:07:11Z","status":"public","intvolume":" 320","page":"267 - 277","publist_id":"1978","extern":"1","publication":"Developmental Biology","publisher":"Elsevier"},{"doi":"10.2976/1.2834817","issue":"1","citation":{"ama":"Schötz E, Burdine R, Julicher F, Steinberg M, Heisenberg C-PJ, Foty R. Quantitative differences in tissue surface tension influence zebrafish germ layer positioning. HFSP Journal. 2008;2(1):42-56. doi:10.2976/1.2834817","mla":"Schötz, Eva, et al. “Quantitative Differences in Tissue Surface Tension Influence Zebrafish Germ Layer Positioning.” HFSP Journal, vol. 2, no. 1, HFSP Publishing, 2008, pp. 42–56, doi:10.2976/1.2834817.","apa":"Schötz, E., Burdine, R., Julicher, F., Steinberg, M., Heisenberg, C.-P. J., & Foty, R. (2008). Quantitative differences in tissue surface tension influence zebrafish germ layer positioning. HFSP Journal. HFSP Publishing. https://doi.org/10.2976/1.2834817","ieee":"E. Schötz, R. Burdine, F. Julicher, M. Steinberg, C.-P. J. Heisenberg, and R. Foty, “Quantitative differences in tissue surface tension influence zebrafish germ layer positioning,” HFSP Journal, vol. 2, no. 1. HFSP Publishing, pp. 42–56, 2008.","ista":"Schötz E, Burdine R, Julicher F, Steinberg M, Heisenberg C-PJ, Foty R. 2008. Quantitative differences in tissue surface tension influence zebrafish germ layer positioning. HFSP Journal. 2(1), 42–56.","short":"E. Schötz, R. Burdine, F. Julicher, M. Steinberg, C.-P.J. Heisenberg, R. Foty, HFSP Journal 2 (2008) 42–56.","chicago":"Schötz, Eva, Rebecca Burdine, Frank Julicher, Malcolm Steinberg, Carl-Philipp J Heisenberg, and Ramsey Foty. “Quantitative Differences in Tissue Surface Tension Influence Zebrafish Germ Layer Positioning.” HFSP Journal. HFSP Publishing, 2008. https://doi.org/10.2976/1.2834817."},"month":"02","volume":2,"author":[{"full_name":"Schötz, Eva","first_name":"Eva","last_name":"Schötz"},{"full_name":"Burdine, Rebecca","last_name":"Burdine","first_name":"Rebecca"},{"full_name":"Julicher, Frank","last_name":"Julicher","first_name":"Frank"},{"first_name":"Malcolm","last_name":"Steinberg","full_name":"Steinberg, Malcolm"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J"},{"first_name":"Ramsey","last_name":"Foty","full_name":"Foty, Ramsey"}],"language":[{"iso":"eng"}],"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","year":"2008","abstract":[{"lang":"eng","text":"This study provides direct functional evidence that differential adhesion, measurable as quantitative differences in tissue surface tension, influences spatial positioning between zebrafish germ layer tissues. We show that embryonic ectodermal and mesendodermal tissues generated by mRNA-overexpression behave on long-time scales like immiscible fluids. When mixed in hanging drop culture, their cells segregate into discrete phases with ectoderm adopting an internal position relative to the mesendoderm. The position adopted directly correlates with differences in tissue surface tension. We also show that germ layer tissues from untreated embryos, when extirpated and placed in culture, adopt a configuration similar to those of their mRNA-overexpressing counterparts. Down-regulating E-cadherin expression in the ectoderm leads to reduced surface tension and results in phase reversal with E-cadherin-depleted ectoderm cells now adopting an external position relative to the mesendoderm. These results show that in vitro cell sorting of zebrafish mesendoderm and ectoderm tissues is specified by tissue interfacial tensions. We perform a mathematical analysis indicating that tissue interfacial tension between actively motile cells contributes to the spatial organization and dynamics of these zebrafish germ layers in vivo."}],"date_published":"2008-02-01T00:00:00Z","article_processing_charge":"No","day":"01","type":"journal_article","_id":"4150","title":"Quantitative differences in tissue surface tension influence zebrafish germ layer positioning","date_updated":"2021-01-12T07:54:52Z","status":"public","date_created":"2018-12-11T12:07:14Z","intvolume":" 2","page":"42 - 56","publist_id":"1969","extern":"1","publication":"HFSP Journal","publisher":"HFSP Publishing"},{"month":"08","citation":{"ama":"Oteíza P, Köppen M, Concha M, Heisenberg C-PJ. Origin and shaping of the laterality organ in zebrafish. Development. 2008;135(16):2807-2813. doi:10.1242/dev.022228","ieee":"P. Oteíza, M. Köppen, M. Concha, and C.-P. J. Heisenberg, “Origin and shaping of the laterality organ in zebrafish,” Development, vol. 135, no. 16. Company of Biologists, pp. 2807–2813, 2008.","apa":"Oteíza, P., Köppen, M., Concha, M., & Heisenberg, C.-P. J. (2008). Origin and shaping of the laterality organ in zebrafish. Development. Company of Biologists. https://doi.org/10.1242/dev.022228","mla":"Oteíza, Pablo, et al. “Origin and Shaping of the Laterality Organ in Zebrafish.” Development, vol. 135, no. 16, Company of Biologists, 2008, pp. 2807–13, doi:10.1242/dev.022228.","short":"P. Oteíza, M. Köppen, M. Concha, C.-P.J. Heisenberg, Development 135 (2008) 2807–2813.","chicago":"Oteíza, Pablo, Mathias Köppen, Miguel Concha, and Carl-Philipp J Heisenberg. “Origin and Shaping of the Laterality Organ in Zebrafish.” Development. Company of Biologists, 2008. https://doi.org/10.1242/dev.022228.","ista":"Oteíza P, Köppen M, Concha M, Heisenberg C-PJ. 2008. Origin and shaping of the laterality organ in zebrafish. Development. 135(16), 2807–2813."},"issue":"16","doi":"10.1242/dev.022228","author":[{"full_name":"Oteíza, Pablo","first_name":"Pablo","last_name":"Oteíza"},{"last_name":"Köppen","first_name":"Mathias","full_name":"Köppen, Mathias"},{"first_name":"Miguel","last_name":"Concha","full_name":"Concha, Miguel"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"volume":135,"language":[{"iso":"eng"}],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"Handedness of the vertebrate body plan critically depends on transient embryonic structures/ organs that generate cilia-dependent leftward fluid flow within constrained extracellular environments. Although the function of ciliated organs in laterality determination has been extensively studied, how they are formed during embryogenesis is still poorly understood. Here we show that Kupffer's vesicle (KV), the zebrafish organ of laterality, arises from a surface epithelium previously thought to adopt exclusively extra-embryonic fates. Live multi-photon confocal imaging reveals that surface epithelial cells undergo Nodal/TGF beta signalling-dependent ingression at the dorsal germ ring margin prior to gastrulation, to give rise to dorsal forerunner cells (DFCs), the precursors of KV. DFCs then migrate attached to the overlying surface epithelium and rearrange into rosette-like epithelial structures at the end of gastrulation. During early somitogenesis, these epithelial rosettes coalesce into a single rosette that differentiates into the KV with a ciliated lumen at its apical centre. Our results provide novel insights into the morphogenetic transformations that shape the laterality organ in zebrafish and suggest a conserved progenitor role of the surface epithelium during laterality organ formation in vertebrates."}],"date_published":"2008-08-15T00:00:00Z","year":"2008","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa_version":"None","date_updated":"2021-01-12T07:54:57Z","title":"Origin and shaping of the laterality organ in zebrafish","_id":"4161","type":"journal_article","day":"15","intvolume":" 135","status":"public","date_created":"2018-12-11T12:07:19Z","extern":"1","publist_id":"1956","page":"2807 - 2813","publisher":"Company of Biologists","publication":"Development"},{"status":"public","intvolume":" 47","date_created":"2018-12-11T12:07:26Z","_id":"4180","title":"A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics","date_updated":"2021-01-12T07:55:06Z","day":"01","type":"journal_article","publication":"Angewandte Chemie - International Edition","publisher":"Wiley-Blackwell","extern":"1","page":"9775 - 9777","publist_id":"1939","volume":47,"author":[{"last_name":"Krieg","first_name":"Michael","full_name":"Krieg, Michael"},{"first_name":"Jonne","last_name":"Helenius","full_name":"Helenius, Jonne"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg"},{"first_name":"Daniel","last_name":"Mueller","full_name":"Mueller, Daniel"}],"citation":{"ama":"Krieg M, Helenius J, Heisenberg C-PJ, Mueller D. A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics. Angewandte Chemie - International Edition. 2008;47(50):9775-9777. doi:10.1002/anie.200803552","mla":"Krieg, Michael, et al. “A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics.” Angewandte Chemie - International Edition, vol. 47, no. 50, Wiley-Blackwell, 2008, pp. 9775–77, doi:10.1002/anie.200803552.","ieee":"M. Krieg, J. Helenius, C.-P. J. Heisenberg, and D. Mueller, “A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics,” Angewandte Chemie - International Edition, vol. 47, no. 50. Wiley-Blackwell, pp. 9775–9777, 2008.","apa":"Krieg, M., Helenius, J., Heisenberg, C.-P. J., & Mueller, D. (2008). A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics. Angewandte Chemie - International Edition. Wiley-Blackwell. https://doi.org/10.1002/anie.200803552","ista":"Krieg M, Helenius J, Heisenberg C-PJ, Mueller D. 2008. A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics. Angewandte Chemie - International Edition. 47(50), 9775–9777.","short":"M. Krieg, J. Helenius, C.-P.J. Heisenberg, D. Mueller, Angewandte Chemie - International Edition 47 (2008) 9775–9777.","chicago":"Krieg, Michael, Jonne Helenius, Carl-Philipp J Heisenberg, and Daniel Mueller. “A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics.” Angewandte Chemie - International Edition. Wiley-Blackwell, 2008. https://doi.org/10.1002/anie.200803552."},"issue":"50","month":"12","doi":"10.1002/anie.200803552","date_published":"2008-12-01T00:00:00Z","abstract":[{"lang":"eng","text":"(Figure Presented) The name's Bond: Separated cells form membranous nanotubes whose tips are tethered by adhesive bonds (see picture). The lifetime of receptor-ligand interactions can be measured by using membrane nanotubes of living cells as constant force actuators. Because the nanotubes are extruded from living cells at conditions approaching the physiological, cellular processes can be both studied and utilized. "}],"article_processing_charge":"No","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","year":"2008","language":[{"iso":"eng"}]},{"date_created":"2018-12-11T12:07:26Z","intvolume":" 10","status":"public","day":"23","type":"journal_article","_id":"4181","date_updated":"2021-01-12T07:55:07Z","title":"Tensile forces govern germ-layer organization in zebrafish","publication":"Nature Cell Biology","publisher":"Nature Publishing Group","page":"429 - 436","publist_id":"1938","extern":"1","volume":10,"author":[{"full_name":"Krieg, Michael","last_name":"Krieg","first_name":"Michael"},{"full_name":"Arboleda Estudillo, Yohanna","first_name":"Yohanna","last_name":"Arboleda Estudillo"},{"full_name":"Puech, Pierre","first_name":"Pierre","last_name":"Puech"},{"last_name":"Käfer","first_name":"Jos","full_name":"Käfer, Jos"},{"first_name":"François","last_name":"Graner","full_name":"Graner, François"},{"first_name":"Daniel","last_name":"Mueller","full_name":"Mueller, Daniel"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"doi":"10.1038/ncb1705","issue":"4","citation":{"ama":"Krieg M, Arboleda Estudillo Y, Puech P, et al. Tensile forces govern germ-layer organization in zebrafish. Nature Cell Biology. 2008;10(4):429-436. doi:10.1038/ncb1705","apa":"Krieg, M., Arboleda Estudillo, Y., Puech, P., Käfer, J., Graner, F., Mueller, D., & Heisenberg, C.-P. J. (2008). Tensile forces govern germ-layer organization in zebrafish. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb1705","ieee":"M. Krieg et al., “Tensile forces govern germ-layer organization in zebrafish,” Nature Cell Biology, vol. 10, no. 4. Nature Publishing Group, pp. 429–436, 2008.","mla":"Krieg, Michael, et al. “Tensile Forces Govern Germ-Layer Organization in Zebrafish.” Nature Cell Biology, vol. 10, no. 4, Nature Publishing Group, 2008, pp. 429–36, doi:10.1038/ncb1705.","short":"M. Krieg, Y. Arboleda Estudillo, P. Puech, J. Käfer, F. Graner, D. Mueller, C.-P.J. Heisenberg, Nature Cell Biology 10 (2008) 429–436.","chicago":"Krieg, Michael, Yohanna Arboleda Estudillo, Pierre Puech, Jos Käfer, François Graner, Daniel Mueller, and Carl-Philipp J Heisenberg. “Tensile Forces Govern Germ-Layer Organization in Zebrafish.” Nature Cell Biology. Nature Publishing Group, 2008. https://doi.org/10.1038/ncb1705.","ista":"Krieg M, Arboleda Estudillo Y, Puech P, Käfer J, Graner F, Mueller D, Heisenberg C-PJ. 2008. Tensile forces govern germ-layer organization in zebrafish. Nature Cell Biology. 10(4), 429–436."},"month":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa_version":"None","year":"2008","date_published":"2008-03-23T00:00:00Z","abstract":[{"text":"Understanding the factors that direct tissue organization during development is one of the most fundamental goals in developmental biology. Various hypotheses explain cell sorting and tissue organization on the basis of the adhesive and mechanical properties of the constituent cells(1). However, validating these hypotheses has been difficult due to the lack of appropriate tools to measure these parameters. Here we use atomic force microscopy ( AFM) to quantify the adhesive and mechanical properties of individual ectoderm, mesoderm and endoderm progenitor cells from gastrulating zebrafish embryos. Combining these data with tissue self-assembly in vitro and the sorting behaviour of progenitors in vivo, we have shown that differential actomyosin-dependent cell-cortex tension, regulated by Nodal/ TGF beta-signalling ( transforming growth factor beta), constitutes a key factor that directs progenitor-cell sorting. These results demonstrate a previously unrecognized role for Nodal-controlled cell-cortex tension in germ-layer organization during gastrulation.","lang":"eng"}],"article_processing_charge":"No","language":[{"iso":"eng"}]},{"doi":"10.1242/dev.020396","month":"09","issue":"18","citation":{"ieee":"M. Kai, C.-P. J. Heisenberg, and M. Tada, “Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation,” Development, vol. 135, no. 18. Company of Biologists, pp. 3043–3051, 2008.","apa":"Kai, M., Heisenberg, C.-P. J., & Tada, M. (2008). Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation. Development. Company of Biologists. https://doi.org/10.1242/dev.020396","mla":"Kai, Masatake, et al. “Sphingosine-1-Phosphate Receptors Regulate Individual Cell Behaviours Underlying the Directed Migration of Prechordal Plate Progenitor Cells during Zebrafish Gastrulation.” Development, vol. 135, no. 18, Company of Biologists, 2008, pp. 3043–51, doi:10.1242/dev.020396.","ama":"Kai M, Heisenberg C-PJ, Tada M. Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation. Development. 2008;135(18):3043-3051. doi:10.1242/dev.020396","short":"M. Kai, C.-P.J. Heisenberg, M. Tada, Development 135 (2008) 3043–3051.","chicago":"Kai, Masatake, Carl-Philipp J Heisenberg, and Masazumi Tada. “Sphingosine-1-Phosphate Receptors Regulate Individual Cell Behaviours Underlying the Directed Migration of Prechordal Plate Progenitor Cells during Zebrafish Gastrulation.” Development. Company of Biologists, 2008. https://doi.org/10.1242/dev.020396.","ista":"Kai M, Heisenberg C-PJ, Tada M. 2008. Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation. Development. 135(18), 3043–3051."},"author":[{"first_name":"Masatake","last_name":"Kai","full_name":"Kai, Masatake"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg"},{"full_name":"Tada, Masazumi","last_name":"Tada","first_name":"Masazumi"}],"volume":135,"language":[{"iso":"eng"}],"year":"2008","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa_version":"None","article_processing_charge":"No","abstract":[{"lang":"eng","text":"During vertebrate gastrulation, cells forming the prechordal plate undergo directed migration as a cohesive cluster. Recent studies revealed that E-cadherin-mediated coherence between these cells plays an important role in effective anterior migration, and that platelet-derived growth factor (Pdgf) appears to act as a guidance cue in this process. However, the mechanisms underlying this process at the individual cell level remain poorly understood. We have identified miles apart (mil) as a suppressor of defective anterior migration of the prospective prechordal plate in silberblick (slb)/wnt11 mutant embryos, in which E-cadherin-mediated coherence of cell movement is reduced. mil encodes Edg5, a sphingosine-1-phosphate (S1P) receptor belonging to a family of five G-protein-coupled receptors (S1PRs). S1P is a lipid signalling molecule that has been implicated in regulating cytoskeletal rearrangements, cell motility and cell adhesion in a variety of cell types. We examined the roles of Mil in anterior migration of prechordal plate progenitor cells and found that, in slb embryos injected with mil-MO, cells migrate with increased motility but decreased directionality, without restoring the coherence of cell migration. This indicates that prechordal plate progenitor cells can migrate effectively as individuals, as well as in a coherent cluster of cells. Moreover, we demonstrate that Mil regulates cell motility and polarisation through Pdgf and its intracellular effecter PI3K, but modulates cell coherence independently of the Pdgf/PI3K pathway, thus co-ordinating cell motility and coherence. These results suggest that the net migration of prechordal plate progenitors is determined by different parameters, including motility, persistence and coherence."}],"date_published":"2008-09-15T00:00:00Z","type":"journal_article","day":"15","title":"Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation","date_updated":"2021-01-12T07:55:11Z","_id":"4190","status":"public","date_created":"2018-12-11T12:07:29Z","intvolume":" 135","publist_id":"1928","page":"3043 - 3051","extern":"1","publisher":"Company of Biologists","publication":"Development"},{"date_created":"2018-12-11T12:07:30Z","status":"public","intvolume":" 121","_id":"4193","date_updated":"2021-01-12T07:55:12Z","title":"Single-cell force spectroscopy","day":"01","type":"journal_article","publication":"Journal of Cell Science","publisher":"Company of Biologists","extern":"1","page":"1785 - 1791","publist_id":"1924","volume":121,"author":[{"last_name":"Helenius","first_name":"Jonne","full_name":"Helenius, Jonne"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"},{"full_name":"Gaub, Hermann","first_name":"Hermann","last_name":"Gaub"},{"full_name":"Mueller, Daniel","first_name":"Daniel","last_name":"Mueller"}],"issue":"11","citation":{"ista":"Helenius J, Heisenberg C-PJ, Gaub H, Mueller D. 2008. Single-cell force spectroscopy. Journal of Cell Science. 121(11), 1785–1791.","chicago":"Helenius, Jonne, Carl-Philipp J Heisenberg, Hermann Gaub, and Daniel Mueller. “Single-Cell Force Spectroscopy.” Journal of Cell Science. Company of Biologists, 2008. https://doi.org/10.1242/jcs.030999.","short":"J. Helenius, C.-P.J. Heisenberg, H. Gaub, D. Mueller, Journal of Cell Science 121 (2008) 1785–1791.","mla":"Helenius, Jonne, et al. “Single-Cell Force Spectroscopy.” Journal of Cell Science, vol. 121, no. 11, Company of Biologists, 2008, pp. 1785–91, doi:10.1242/jcs.030999.","apa":"Helenius, J., Heisenberg, C.-P. J., Gaub, H., & Mueller, D. (2008). Single-cell force spectroscopy. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.030999","ieee":"J. Helenius, C.-P. J. Heisenberg, H. Gaub, and D. Mueller, “Single-cell force spectroscopy,” Journal of Cell Science, vol. 121, no. 11. Company of Biologists, pp. 1785–1791, 2008.","ama":"Helenius J, Heisenberg C-PJ, Gaub H, Mueller D. Single-cell force spectroscopy. Journal of Cell Science. 2008;121(11):1785-1791. doi:10.1242/jcs.030999"},"month":"06","doi":"10.1242/jcs.030999","date_published":"2008-06-01T00:00:00Z","abstract":[{"text":"The controlled adhesion of cells to each other and to the extracellular matrix is crucial for tissue development and maintenance. Numerous assays have been developed to quantify cell adhesion. Among these, the use of atomic force microscopy (AFM) for single-cell force spectroscopy (SCFS) has recently been established. This assay permits the adhesion of living cells to be studied in near-physiological conditions. This implementation of AFM allows unrivaled spatial and temporal control of cells, as well as highly quantitative force actuation and force measurement that is sufficiently sensitive to characterize the interaction of single molecules. Therefore, not only overall cell adhesion but also the properties of single adhesion-receptor-ligand interactions can be studied. Here we describe current implementations and applications of SCFS, as well as potential pitfalls, and outline how developments will provide insight into the forces, energetics and kinetics of cell-adhesion processes.","lang":"eng"}],"article_processing_charge":"No","oa_version":"None","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2008","language":[{"iso":"eng"}]},{"extern":"1","page":"311 - 316","publist_id":"1918","publication":"Current Opinion in Genetics & Development","publisher":"Elsevier","_id":"4198","date_updated":"2021-01-12T07:55:14Z","title":"Back and forth between cell fate specification and movement during vertebrate gastrulation","day":"01","type":"journal_article","intvolume":" 18","status":"public","date_created":"2018-12-11T12:07:32Z","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Animal body plan arises during gastrulation and organogenesis by the coordination of inductive events and cell movements. Several signaling pathways, such as BMP, FGF, Hedgehog, Nodal, and Wnt have well-recognized instructive roles in cell fate specification during vertebrate embryogenesis. Growing evidence indicates that BMP, Nodal, and FGF signaling also regulate cell movements, and that they do so through mechanisms distinct from those that specify cell fates. Moreover, pathways controlling cell movements can also indirectly influence cell fate specification by regulating dimensions and relative positions of interacting tissues. The current challenge is to delineate the molecular mechanisms via which the major signaling pathways regulate cell fate specification and movements, and how these two processes are coordinated to ensure normal development."}],"date_published":"2008-01-01T00:00:00Z","article_processing_charge":"No","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","year":"2008","issue":"4","citation":{"ama":"Heisenberg C-PJ, Solnica Krezel L. Back and forth between cell fate specification and movement during vertebrate gastrulation. Current Opinion in Genetics & Development. 2008;18(4):311-316. doi:10.1016/j.gde.2008.07.011","mla":"Heisenberg, Carl-Philipp J., and Lilianna Solnica Krezel. “Back and Forth between Cell Fate Specification and Movement during Vertebrate Gastrulation.” Current Opinion in Genetics & Development, vol. 18, no. 4, Elsevier, 2008, pp. 311–16, doi:10.1016/j.gde.2008.07.011.","ieee":"C.-P. J. Heisenberg and L. Solnica Krezel, “Back and forth between cell fate specification and movement during vertebrate gastrulation,” Current Opinion in Genetics & Development, vol. 18, no. 4. Elsevier, pp. 311–316, 2008.","apa":"Heisenberg, C.-P. J., & Solnica Krezel, L. (2008). Back and forth between cell fate specification and movement during vertebrate gastrulation. Current Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2008.07.011","ista":"Heisenberg C-PJ, Solnica Krezel L. 2008. Back and forth between cell fate specification and movement during vertebrate gastrulation. Current Opinion in Genetics & Development. 18(4), 311–316.","short":"C.-P.J. Heisenberg, L. Solnica Krezel, Current Opinion in Genetics & Development 18 (2008) 311–316.","chicago":"Heisenberg, Carl-Philipp J, and Lilianna Solnica Krezel. “Back and Forth between Cell Fate Specification and Movement during Vertebrate Gastrulation.” Current Opinion in Genetics & Development. Elsevier, 2008. https://doi.org/10.1016/j.gde.2008.07.011."},"month":"01","doi":"10.1016/j.gde.2008.07.011","volume":18,"author":[{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"},{"full_name":"Solnica Krezel, Lilianna","last_name":"Solnica Krezel","first_name":"Lilianna"}]},{"publication":"Development","publisher":"Company of Biologists","extern":1,"page":"1137 - 1146","publist_id":"1889","status":"public","intvolume":" 135","date_created":"2018-12-11T12:07:42Z","quality_controlled":0,"_id":"4227","date_updated":"2021-01-12T07:55:27Z","title":"Precision of the Dpp gradient","day":"15","type":"journal_article","date_published":"2008-03-15T00:00:00Z","abstract":[{"lang":"eng","text":"Morphogen concentration gradients provide positional information by activating target genes in a concentration-dependent manner. Recent reports show that the gradient of the syncytial morphogen Bicoid seems to provide precise positional information to determine target gene domains. For secreted morphogenetic ligands, the precision of the gradients, the signal transduction and the reliability of target gene expression domains have not been studied. Here we investigate these issues for the TGF-beta-type morphogen Dpp. We first studied theoretically how cell-to-cell variability in the source, the target tissue, or both, contribute to the variations of the gradient. Fluctuations in the source and target generate a local maximum of precision at a finite distance to the source. We then determined experimentally in the wing epithelium: (1) the precision of the Dpp concentration gradient; (2) the precision of the Dpp signaling activity profile; and (3) the precision of activation of the Dpp target gene spalt. As captured by our theoretical description, the Dpp gradient provides positional information with a maximal precision a few cells away from the source. This maximal precision corresponds to a positional uncertainly of about a single cell diameter. The precision of the Dpp gradient accounts for the precision of the spalt expression range, implying that Dpp can act as a morphogen to coarsely determine the expression pattern of target genes."}],"publication_status":"published","year":"2008","volume":135,"author":[{"first_name":"Tobias","last_name":"Bollenbach","full_name":"Bollenbach, Tobias"},{"full_name":"Pantazis, Periklis","last_name":"Pantazis","first_name":"Periklis"},{"first_name":"Anna","last_name":"Kicheva","full_name":"Anna Kicheva","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bokel, Christian","first_name":"Christian","last_name":"Bokel"},{"full_name":"González-Gaitán, Marcos","first_name":"Marcos","last_name":"González Gaitán"},{"first_name":"Frank","last_name":"Julicher","full_name":"Julicher, Frank"}],"citation":{"chicago":"Bollenbach, Tobias, Periklis Pantazis, Anna Kicheva, Christian Bokel, Marcos González Gaitán, and Frank Julicher. “Precision of the Dpp Gradient.” Development. Company of Biologists, 2008. https://doi.org/10.1242/dev.012062.","short":"T. Bollenbach, P. Pantazis, A. Kicheva, C. Bokel, M. González Gaitán, F. Julicher, Development 135 (2008) 1137–1146.","ista":"Bollenbach T, Pantazis P, Kicheva A, Bokel C, González Gaitán M, Julicher F. 2008. Precision of the Dpp gradient. Development. 135(6), 1137–1146.","ama":"Bollenbach T, Pantazis P, Kicheva A, Bokel C, González Gaitán M, Julicher F. Precision of the Dpp gradient. Development. 2008;135(6):1137-1146. doi:10.1242/dev.012062","apa":"Bollenbach, T., Pantazis, P., Kicheva, A., Bokel, C., González Gaitán, M., & Julicher, F. (2008). Precision of the Dpp gradient. Development. Company of Biologists. https://doi.org/10.1242/dev.012062","ieee":"T. Bollenbach, P. Pantazis, A. Kicheva, C. Bokel, M. González Gaitán, and F. Julicher, “Precision of the Dpp gradient,” Development, vol. 135, no. 6. Company of Biologists, pp. 1137–1146, 2008.","mla":"Bollenbach, Tobias, et al. “Precision of the Dpp Gradient.” Development, vol. 135, no. 6, Company of Biologists, 2008, pp. 1137–46, doi:10.1242/dev.012062."},"issue":"6","month":"03","doi":"10.1242/dev.012062"},{"publication_status":"published","year":"2008","date_published":"2008-09-23T00:00:00Z","abstract":[{"lang":"eng","text":"This paper presents a new approach to optimization of an energy-constrained modulation scheme for wireless sensor networks by taking advantage of a novel bio-inspired optimization algorithm. The algorithm is inspired by Wrightpsilas shifting balance theory (SBT) of evolution in population genetics. The total energy consumption of an energy-constrained modulation scheme is minimized by using the new SBT-based optimization algorithm. The results obtained by this new algorithm are compared with other popular optimization algorithms. Numerical experiments are performed to demonstrate that the SBT-based algorithm could be used as an efficient optimizer for solving the optimization problems arising from currently emerging energy-efficient wireless sensor networks."}],"doi":"10.1109/CEC.2008.4631167","citation":{"short":"E. Yang, N.H. Barton, T. Arslan, A. Erdogan, in:, IEEE, 2008, pp. 2749–2756.","chicago":"Yang, Erfu, Nicholas H Barton, Tughrul Arslan, and Ahmet Erdogan. “A Novel Shifting Balance Theory-Based Approach to Optimization of an Energy-Constrained Modulation Scheme for Wireless Sensor Networks,” 2749–56. IEEE, 2008. https://doi.org/10.1109/CEC.2008.4631167.","ista":"Yang E, Barton NH, Arslan T, Erdogan A. 2008. A novel shifting balance theory-based approach to optimization of an energy-constrained modulation scheme for wireless sensor networks. WCCI: IEEE World Congress on Computational Intelligence, 2749–2756.","ama":"Yang E, Barton NH, Arslan T, Erdogan A. A novel shifting balance theory-based approach to optimization of an energy-constrained modulation scheme for wireless sensor networks. In: IEEE; 2008:2749-2756. doi:10.1109/CEC.2008.4631167","apa":"Yang, E., Barton, N. H., Arslan, T., & Erdogan, A. (2008). A novel shifting balance theory-based approach to optimization of an energy-constrained modulation scheme for wireless sensor networks (pp. 2749–2756). Presented at the WCCI: IEEE World Congress on Computational Intelligence, IEEE. https://doi.org/10.1109/CEC.2008.4631167","ieee":"E. Yang, N. H. Barton, T. Arslan, and A. Erdogan, “A novel shifting balance theory-based approach to optimization of an energy-constrained modulation scheme for wireless sensor networks,” presented at the WCCI: IEEE World Congress on Computational Intelligence, 2008, pp. 2749–2756.","mla":"Yang, Erfu, et al. A Novel Shifting Balance Theory-Based Approach to Optimization of an Energy-Constrained Modulation Scheme for Wireless Sensor Networks. IEEE, 2008, pp. 2749–56, doi:10.1109/CEC.2008.4631167."},"month":"09","author":[{"last_name":"Yang","first_name":"Erfu","full_name":"Yang, Erfu"},{"full_name":"Nicholas Barton","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Arslan, Tughrul","last_name":"Arslan","first_name":"Tughrul"},{"full_name":"Erdogan, Ahmet T","last_name":"Erdogan","first_name":"Ahmet"}],"page":"2749 - 2756","conference":{"name":"WCCI: IEEE World Congress on Computational Intelligence"},"publist_id":"1861","extern":1,"publisher":"IEEE","day":"23","type":"conference","_id":"4244","title":"A novel shifting balance theory-based approach to optimization of an energy-constrained modulation scheme for wireless sensor networks","date_updated":"2021-01-12T07:55:34Z","quality_controlled":0,"date_created":"2018-12-11T12:07:49Z","status":"public"}]