[{"title":"High-Throughput Hypocotyl Grafting and Vascular Reconnection Assessment in Arabidopsis Seedlings","place":"New York, NY","_id":"23126","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1007/978-1-0716-5488-0_33","series_title":"MIMB","day":"03","page":"431-448","publication_identifier":{"eissn":["1940-6029"],"issn":["1064-3745"],"eisbn":["9781071654880"],"isbn":["9781071654873"]},"edition":"2","doi":"10.1007/978-1-0716-5488-0_33","alternative_title":["Methods in Molecular Biology"],"article_processing_charge":"No","external_id":{"pmid":["42681141"]},"abstract":[{"text":"Plant grafting is a powerful tool in research and agriculture, enabling the study of long-distance signaling and improving crop performance. Hypocotyl grafting in Arabidopsis thaliana has become a key method for investigating inter-tissue communication, root-to-shoot transport, and vascular regeneration. Here, we describe a high-throughput hypocotyl grafting protocol that consistently achieves success rates above 90% while minimizing complications, such as adventitious root formation, through an optimized hypocotyl cutting position. Our streamlined approach eliminates the need for silicone tubes and fine forceps, requiring only a standard scalpel for the cutting and joining procedure. With proper training, an experienced user can graft up to 1000 plants per day, facilitating large-scale experiments. Additionally, we present vascular connectivity assays using fluorescent dyes and the adjuvant Adigor to enable phloem and xylem transport analysis across the graft junction without the need for wounding. By simplifying the grafting process while maintaining high efficiency, our protocol makes Arabidopsis grafting more accessible and scalable, facilitating research on long-distance molecular transport, vascular development, and plant biotechnology applications.","lang":"eng"}],"language":[{"iso":"eng"}],"type":"book_chapter","status":"public","quality_controlled":"1","date_updated":"2026-10-14T08:58:03Z","OA_type":"closed access","scopus_import":"1","author":[{"full_name":"Bartusch, Kai","id":"0c51b9f5-90c8-11f1-b4ef-9ad5d3d9a34a","last_name":"Bartusch","first_name":"Kai","orcid":"0000-0003-2708-5545"},{"first_name":"Elisabeth","last_name":"Truernit","full_name":"Truernit, Elisabeth"}],"date_created":"2026-10-13T11:14:23Z","publication":"Phloem","year":"2026","publication_status":"published","citation":{"ista":"Bartusch K, Truernit E. 2026.High-Throughput Hypocotyl Grafting and Vascular Reconnection Assessment in Arabidopsis Seedlings. In: Phloem. Methods in Molecular Biology, , 431–448.","ieee":"K. Bartusch and E. Truernit, “High-Throughput Hypocotyl Grafting and Vascular Reconnection Assessment in Arabidopsis Seedlings,” in <i>Phloem</i>, 2nd ed., J. Liesche and S. Sevanto, Eds. New York, NY: Springer, 2026, pp. 431–448.","ama":"Bartusch K, Truernit E. High-Throughput Hypocotyl Grafting and Vascular Reconnection Assessment in Arabidopsis Seedlings. In: Liesche J, Sevanto S, eds. <i>Phloem</i>. 2nd ed. MIMB. New York, NY: Springer; 2026:431-448. doi:<a href=\"https://doi.org/10.1007/978-1-0716-5488-0_33\">10.1007/978-1-0716-5488-0_33</a>","chicago":"Bartusch, Kai, and Elisabeth Truernit. “High-Throughput Hypocotyl Grafting and Vascular Reconnection Assessment in Arabidopsis Seedlings.” In <i>Phloem</i>, edited by Johannes Liesche and Sanna Sevanto, 2nd ed., 431–48. MIMB. New York, NY: Springer, 2026. <a href=\"https://doi.org/10.1007/978-1-0716-5488-0_33\">https://doi.org/10.1007/978-1-0716-5488-0_33</a>.","mla":"Bartusch, Kai, and Elisabeth Truernit. “High-Throughput Hypocotyl Grafting and Vascular Reconnection Assessment in Arabidopsis Seedlings.” <i>Phloem</i>, edited by Johannes Liesche and Sanna Sevanto, 2nd ed., Springer, 2026, pp. 431–48, doi:<a href=\"https://doi.org/10.1007/978-1-0716-5488-0_33\">10.1007/978-1-0716-5488-0_33</a>.","apa":"Bartusch, K., &#38; Truernit, E. (2026). High-Throughput Hypocotyl Grafting and Vascular Reconnection Assessment in Arabidopsis Seedlings. In J. Liesche &#38; S. Sevanto (Eds.), <i>Phloem</i> (2nd ed., pp. 431–448). New York, NY: Springer. <a href=\"https://doi.org/10.1007/978-1-0716-5488-0_33\">https://doi.org/10.1007/978-1-0716-5488-0_33</a>","short":"K. Bartusch, E. Truernit, in:, J. Liesche, S. Sevanto (Eds.), Phloem, 2nd ed., Springer, New York, NY, 2026, pp. 431–448."},"oa_version":"None","editor":[{"full_name":"Liesche, Johannes","first_name":"Johannes","last_name":"Liesche"},{"full_name":"Sevanto, Sanna","first_name":"Sanna","last_name":"Sevanto"}],"pmid":1,"date_published":"2026-09-03T00:00:00Z","extern":"1","month":"09","publisher":"Springer"},{"place":"New York, NY","_id":"18765","title":"Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM)","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"SiHi"}],"fulldoi":"https://doi.org/10.1007/978-1-0716-4310-5_7","acknowledged_ssus":[{"_id":"Bio"}],"series_title":"MIMB","page":"139-151","day":"03","publication_identifier":{"eisbn":["9781071643105"],"isbn":["9781071643099"],"eissn":["1940-6029"],"issn":["1064-3745"]},"corr_author":"1","doi":"10.1007/978-1-0716-4310-5_7","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"volume":2886,"external_id":{"pmid":["39745639"]},"article_processing_charge":"No","alternative_title":["Methods in Molecular Biology"],"type":"book_chapter","abstract":[{"text":"Mosaic Analysis with Double Markers (MADM) represents a mouse genetic approach coupling differential fluorescent labeling to genetic manipulations in dividing cells and their lineages. MADM uniquely enables the generation and visualization of individual control or homozygous mutant cells in a heterozygous genetic environment. Among its diverse applications, MADM has been used to dissect cell-autonomous gene functions important for cortical development and neural development in general. The high cellular resolution offered by MADM also permits the analysis of transcriptomic changes of individual cells upon genetic manipulations. In this chapter, we describe an experimental protocol combining the generation and isolation of MADM-labeled cells with downstream single-cell RNA-sequencing technologies to probe cell-type specific phenotypes due to genetic mutations at single-cell resolution.","lang":"eng"}],"language":[{"iso":"eng"}],"quality_controlled":"1","status":"public","date_updated":"2025-04-14T07:43:46Z","OA_type":"closed access","scopus_import":"1","author":[{"orcid":"0000-0001-8457-2572","id":"471195F6-F248-11E8-B48F-1D18A9856A87","full_name":"Cheung, Giselle T","first_name":"Giselle T","last_name":"Cheung"},{"full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","first_name":"Florian","orcid":"0000-0002-7462-0048"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon"}],"acknowledgement":"We thank all Hippenmeyer lab members for support and discussions. Experimental steps described were optimized with support provided by the Imaging & Optics Facility (IOF) and Preclinical Facility (PCF) at ISTA, Vienna BioCenter Core Facilities (VBCF), and Christoph Bock lab at Center for Molecular Medicine (CeMM). G.C. received funding from European Commission (IST plus postdoctoral fellowship). This work was supported by ISTA institutional funds: The Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H.","intvolume":"      2886","date_created":"2025-01-07T08:36:47Z","year":"2025","publication":"Lineage Tracing","publication_status":"published","editor":[{"last_name":"Garcia-Marques","first_name":"Jorge","full_name":"Garcia-Marques, Jorge"},{"first_name":"Tzumin","last_name":"Lee","full_name":"Lee, Tzumin"}],"citation":{"ista":"Cheung GT, Pauler F, Hippenmeyer S. 2025.Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In: Lineage Tracing. Methods in Molecular Biology, vol. 2886, 139–151.","ieee":"G. T. Cheung, F. Pauler, and S. Hippenmeyer, “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM),” in <i>Lineage Tracing</i>, vol. 2886, J. Garcia-Marques and T. Lee, Eds. New York, NY: Springer Nature, 2025, pp. 139–151.","ama":"Cheung GT, Pauler F, Hippenmeyer S. Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In: Garcia-Marques J, Lee T, eds. <i>Lineage Tracing</i>. Vol 2886. MIMB. New York, NY: Springer Nature; 2025:139-151. doi:<a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">10.1007/978-1-0716-4310-5_7</a>","mla":"Cheung, Giselle T., et al. “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).” <i>Lineage Tracing</i>, edited by Jorge Garcia-Marques and Tzumin Lee, vol. 2886, Springer Nature, 2025, pp. 139–51, doi:<a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">10.1007/978-1-0716-4310-5_7</a>.","chicago":"Cheung, Giselle T, Florian Pauler, and Simon Hippenmeyer. “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).” In <i>Lineage Tracing</i>, edited by Jorge Garcia-Marques and Tzumin Lee, 2886:139–51. MIMB. New York, NY: Springer Nature, 2025. <a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">https://doi.org/10.1007/978-1-0716-4310-5_7</a>.","apa":"Cheung, G. T., Pauler, F., &#38; Hippenmeyer, S. (2025). Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In J. Garcia-Marques &#38; T. Lee (Eds.), <i>Lineage Tracing</i> (Vol. 2886, pp. 139–151). New York, NY: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">https://doi.org/10.1007/978-1-0716-4310-5_7</a>","short":"G.T. Cheung, F. Pauler, S. Hippenmeyer, in:, J. Garcia-Marques, T. Lee (Eds.), Lineage Tracing, Springer Nature, New York, NY, 2025, pp. 139–151."},"oa_version":"None","month":"01","publisher":"Springer Nature","pmid":1,"date_published":"2025-01-03T00:00:00Z"},{"acknowledgement":"We thank all Hippenmeyer lab members for support and discussions. This work was supported by the Scientific Service Units (SSU) at ISTA through resources provided by the Imaging & Optics Facility (IOF). O.A.M was a recipient of a DOC Fellowship (26253) of the Austrian Academy of Sciences. This work was supported by ISTA institutional funds, and The Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H.","intvolume":"      2831","publication":"Neuronal Morphogenesis","year":"2024","date_created":"2024-08-13T12:16:41Z","publication_status":"published","editor":[{"full_name":"Toyooka, Kazuhito","last_name":"Toyooka","first_name":"Kazuhito"}],"citation":{"ama":"Miranda O, Cheung GT, Hippenmeyer S. Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Toyooka K, ed. <i>Neuronal Morphogenesis</i>. Vol 2831. 1st ed. MIMB. New York, NY: Springer Nature; 2024:283-299. doi:<a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">10.1007/978-1-0716-3969-6_19</a>","ieee":"O. Miranda, G. T. Cheung, and S. Hippenmeyer, “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers,” in <i>Neuronal Morphogenesis</i>, 1st ed., vol. 2831, K. Toyooka, Ed. New York, NY: Springer Nature, 2024, pp. 283–299.","ista":"Miranda O, Cheung GT, Hippenmeyer S. 2024.Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Neuronal Morphogenesis. Methods in Molecular Biology, vol. 2831, 283–299.","apa":"Miranda, O., Cheung, G. T., &#38; Hippenmeyer, S. (2024). Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In K. Toyooka (Ed.), <i>Neuronal Morphogenesis</i> (1st ed., Vol. 2831, pp. 283–299). New York, NY: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">https://doi.org/10.1007/978-1-0716-3969-6_19</a>","chicago":"Miranda, Osvaldo, Giselle T Cheung, and Simon Hippenmeyer. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” In <i>Neuronal Morphogenesis</i>, edited by Kazuhito Toyooka, 1st ed., 2831:283–99. MIMB. New York, NY: Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">https://doi.org/10.1007/978-1-0716-3969-6_19</a>.","mla":"Miranda, Osvaldo, et al. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” <i>Neuronal Morphogenesis</i>, edited by Kazuhito Toyooka, 1st ed., vol. 2831, Springer Nature, 2024, pp. 283–99, doi:<a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">10.1007/978-1-0716-3969-6_19</a>.","short":"O. Miranda, G.T. Cheung, S. Hippenmeyer, in:, K. Toyooka (Ed.), Neuronal Morphogenesis, 1st ed., Springer Nature, New York, NY, 2024, pp. 283–299."},"oa_version":"None","month":"08","publisher":"Springer Nature","pmid":1,"date_published":"2024-08-13T00:00:00Z","type":"book_chapter","abstract":[{"text":"Mosaic Analysis with Double Markers (MADM) is a powerful genetic method typically used for lineage tracing and to disentangle cell autonomous and tissue-wide roles of candidate genes with single cell resolution. Given the relatively sparse labeling, depending on which of the 19 MADM chromosomes one chooses, the MADM approach represents the perfect opportunity for cell morphology analysis. Various MADM studies include reports of morphological anomalies and phenotypes in the central nervous system (CNS). MADM for any candidate gene can easily incorporate morphological analysis within the experimental workflow. Here, we describe the methods of morphological cell analysis which we developed in the course of diverse recent MADM studies. This chapter will specifically focus on methods to quantify aspects of the morphology of neurons and astrocytes within the CNS, but these methods can broadly be applied to any MADM-labeled cells throughout the entire organism. We will cover two analyses—soma volume and dendrite characterization—of physical characteristics of pyramidal neurons in the somatosensory cortex, and two analyses—volume and Sholl analysis—of astrocyte morphology.","lang":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"20212","status":"public"}]},"language":[{"iso":"eng"}],"status":"public","quality_controlled":"1","date_updated":"2026-11-09T23:31:11Z","scopus_import":"1","author":[{"full_name":"Miranda, Osvaldo","id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","last_name":"Miranda","first_name":"Osvaldo","orcid":"0000-0001-6618-6889"},{"orcid":"0000-0001-8457-2572","id":"471195F6-F248-11E8-B48F-1D18A9856A87","full_name":"Cheung, Giselle T","first_name":"Giselle T","last_name":"Cheung"},{"first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061"}],"corr_author":"1","researchdata_availability":"no","edition":"1","project":[{"_id":"34c9fbcb-11ca-11ed-8bc3-98fa5658610d","name":"Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development","grant_number":"26253"},{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression"}],"doi":"10.1007/978-1-0716-3969-6_19","volume":2831,"external_id":{"pmid":["39134857"]},"das_tickbox":"0","alternative_title":["Methods in Molecular Biology"],"article_processing_charge":"No","place":"New York, NY","_id":"17425","title":"Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"supplementarymaterial":"yes","fulldoi":"https://doi.org/10.1007/978-1-0716-3969-6_19","series_title":"MIMB","acknowledged_ssus":[{"_id":"Bio"}],"publication_identifier":{"eisbn":["9781071639696"],"isbn":["9781071639689"],"eissn":["1940-6029"],"issn":["1064-3745"]},"page":"283-299","day":"13"},{"pmid":1,"date_published":"2023-03-01T00:00:00Z","month":"03","publisher":"Springer Nature","oa_version":"Submitted Version","citation":{"ieee":"S. Arroyo-Urea, J. Watson, and J. García-Nafría, “Molecular Cloning Using In Vivo DNA Assembly,” in <i>DNA Manipulation and Analysis</i>, vol. 2633, G. Scarlett, Ed. New York, NY, United States: Springer Nature, 2023, pp. 33–44.","ista":"Arroyo-Urea S, Watson J, García-Nafría J. 2023.Molecular Cloning Using In Vivo DNA Assembly. In: DNA Manipulation and Analysis. Methods in Molecular Biology, vol. 2633, 33–44.","ama":"Arroyo-Urea S, Watson J, García-Nafría J. Molecular Cloning Using In Vivo DNA Assembly. In: Scarlett G, ed. <i>DNA Manipulation and Analysis</i>. Vol 2633. MIMB. New York, NY, United States: Springer Nature; 2023:33-44. doi:<a href=\"https://doi.org/10.1007/978-1-0716-3004-4_3\">10.1007/978-1-0716-3004-4_3</a>","short":"S. Arroyo-Urea, J. Watson, J. García-Nafría, in:, G. Scarlett (Ed.), DNA Manipulation and Analysis, Springer Nature, New York, NY, United States, 2023, pp. 33–44.","chicago":"Arroyo-Urea, Sandra, Jake Watson, and Javier García-Nafría. “Molecular Cloning Using In Vivo DNA Assembly.” In <i>DNA Manipulation and Analysis</i>, edited by Garry Scarlett, 2633:33–44. MIMB. New York, NY, United States: Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-1-0716-3004-4_3\">https://doi.org/10.1007/978-1-0716-3004-4_3</a>.","mla":"Arroyo-Urea, Sandra, et al. “Molecular Cloning Using In Vivo DNA Assembly.” <i>DNA Manipulation and Analysis</i>, edited by Garry Scarlett, vol. 2633, Springer Nature, 2023, pp. 33–44, doi:<a href=\"https://doi.org/10.1007/978-1-0716-3004-4_3\">10.1007/978-1-0716-3004-4_3</a>.","apa":"Arroyo-Urea, S., Watson, J., &#38; García-Nafría, J. (2023). Molecular Cloning Using In Vivo DNA Assembly. In G. Scarlett (Ed.), <i>DNA Manipulation and Analysis</i> (Vol. 2633, pp. 33–44). New York, NY, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-3004-4_3\">https://doi.org/10.1007/978-1-0716-3004-4_3</a>"},"editor":[{"first_name":"Garry","last_name":"Scarlett","full_name":"Scarlett, Garry"}],"publication":"DNA Manipulation and Analysis","date_created":"2023-03-12T23:01:02Z","year":"2023","publication_status":"published","intvolume":"      2633","author":[{"last_name":"Arroyo-Urea","first_name":"Sandra","full_name":"Arroyo-Urea, Sandra"},{"first_name":"Jake","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E","full_name":"Watson, Jake","orcid":"0000-0002-8698-3823"},{"full_name":"García-Nafría, Javier","first_name":"Javier","last_name":"García-Nafría"}],"date_updated":"2025-06-25T05:56:45Z","scopus_import":"1","OA_type":"green","quality_controlled":"1","status":"public","abstract":[{"text":"Here we describe the in vivo DNA assembly approach, where molecular cloning procedures are performed using an E. coli recA-independent recombination pathway, which assembles linear fragments of DNA with short homologous termini. This pathway is present in all standard laboratory E. coli strains and, by bypassing the need for in vitro DNA assembly, allows simplified molecular cloning to be performed without the plasmid instability issues associated with specialized recombination-cloning bacterial strains. The methodology requires specific primer design and can perform all standard plasmid modifications (insertions, deletions, mutagenesis, and sub-cloning) in a rapid, simple, and cost-efficient manner, as it does not require commercial kits or specialized bacterial strains. Additionally, this approach can be used to perform complex procedures such as multiple modifications to a plasmid, as up to 6 linear fragments can be assembled in vivo by this recombination pathway. Procedures generally require less than 3 h, involving PCR amplification, DpnI digestion of template DNA, and transformation, upon which circular plasmids are assembled. In this chapter we describe the requirements, procedure, and potential pitfalls when using this technique, as well as protocol variations to overcome the most common issues.","lang":"eng"}],"language":[{"iso":"eng"}],"type":"book_chapter","OA_place":"repository","article_processing_charge":"No","alternative_title":["Methods in Molecular Biology"],"external_id":{"pmid":["36853454"]},"main_file_link":[{"url":"https://zaguan.unizar.es/record/125930/files/texto_completo.pdf","open_access":"1"}],"volume":2633,"doi":"10.1007/978-1-0716-3004-4_3","oa":1,"page":"33-44","publication_identifier":{"eisbn":["978-1-0716-3004-4"],"isbn":["978-1-0716-3003-7"],"eissn":["1940-6029"],"issn":["1064-3745"]},"day":"01","series_title":"MIMB","fulldoi":"https://doi.org/10.1007/978-1-0716-3004-4_3","department":[{"_id":"PeJo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Molecular Cloning Using In Vivo DNA Assembly","place":"New York, NY, United States","_id":"12720"},{"volume":2654,"external_id":{"pmid":["37106180"]},"alternative_title":["Methods in Molecular Biology"],"article_processing_charge":"No","project":[{"name":"Cellular Navigation Along Spatial Gradients","grant_number":"724373","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425"}],"doi":"10.1007/978-1-0716-3135-5_9","department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"fulldoi":"https://doi.org/10.1007/978-1-0716-3135-5_9","series_title":"MIMB","publication_identifier":{"eisbn":["9781071631355"],"isbn":["9781071631348"],"eissn":["1940-6029"],"issn":["1064-3745"]},"day":"28","page":"137-147","place":"New York, NY","_id":"13052","title":"En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"editor":[{"full_name":"Baldari, Cosima","first_name":"Cosima","last_name":"Baldari"},{"full_name":"Dustin, Michael","last_name":"Dustin","first_name":"Michael"}],"citation":{"apa":"Leithner, A. F., Merrin, J., &#38; Sixt, M. K. (2023). En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses. In C. Baldari &#38; M. Dustin (Eds.), <i>The Immune Synapse</i> (Vol. 2654, pp. 137–147). New York, NY: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-3135-5_9\">https://doi.org/10.1007/978-1-0716-3135-5_9</a>","mla":"Leithner, Alexander F., et al. “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses.” <i>The Immune Synapse</i>, edited by Cosima Baldari and Michael Dustin, vol. 2654, Springer Nature, 2023, pp. 137–47, doi:<a href=\"https://doi.org/10.1007/978-1-0716-3135-5_9\">10.1007/978-1-0716-3135-5_9</a>.","chicago":"Leithner, Alexander F, Jack Merrin, and Michael K Sixt. “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses.” In <i>The Immune Synapse</i>, edited by Cosima Baldari and Michael Dustin, 2654:137–47. MIMB. New York, NY: Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-1-0716-3135-5_9\">https://doi.org/10.1007/978-1-0716-3135-5_9</a>.","short":"A.F. Leithner, J. Merrin, M.K. Sixt, in:, C. Baldari, M. Dustin (Eds.), The Immune Synapse, Springer Nature, New York, NY, 2023, pp. 137–147.","ama":"Leithner AF, Merrin J, Sixt MK. En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses. In: Baldari C, Dustin M, eds. <i>The Immune Synapse</i>. Vol 2654. MIMB. New York, NY: Springer Nature; 2023:137-147. doi:<a href=\"https://doi.org/10.1007/978-1-0716-3135-5_9\">10.1007/978-1-0716-3135-5_9</a>","ista":"Leithner AF, Merrin J, Sixt MK. 2023.En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses. In: The Immune Synapse. Methods in Molecular Biology, vol. 2654, 137–147.","ieee":"A. F. Leithner, J. Merrin, and M. K. Sixt, “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses,” in <i>The Immune Synapse</i>, vol. 2654, C. Baldari and M. Dustin, Eds. New York, NY: Springer Nature, 2023, pp. 137–147."},"oa_version":"None","month":"04","publisher":"Springer Nature","pmid":1,"date_published":"2023-04-28T00:00:00Z","acknowledgement":"A.L. was funded by an Erwin Schrödinger postdoctoral fellowship of the Austrian Science Fund (FWF, project number: J4542-B) and is an EMBO non-stipendiary postdoctoral fellow. This work was supported by a European Research Council grant ERC-CoG-72437 to M.S. We thank the Imaging & Optics facility, the Nanofabrication facility, and the Miba Machine Shop of ISTA for their excellent support.","intvolume":"      2654","publication":"The Immune Synapse","year":"2023","date_created":"2023-05-22T08:41:48Z","publication_status":"published","date_updated":"2025-04-14T07:42:07Z","scopus_import":"1","author":[{"orcid":"0000-0002-1073-744X","last_name":"Leithner","first_name":"Alexander F","full_name":"Leithner, Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5145-4609","first_name":"Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack"},{"orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"}],"type":"book_chapter","abstract":[{"text":"Imaging of the immunological synapse (IS) between dendritic cells (DCs) and T cells in suspension is hampered by suboptimal alignment of cell-cell contacts along the vertical imaging plane. This requires optical sectioning that often results in unsatisfactory resolution in time and space. Here, we present a workflow where DCs and T cells are confined between a layer of glass and polydimethylsiloxane (PDMS) that orients the cells along one, horizontal imaging plane, allowing for fast en-face-imaging of the DC-T cell IS.","lang":"eng"}],"language":[{"iso":"eng"}],"status":"public","quality_controlled":"1"},{"OA_type":"closed access","scopus_import":"1","date_updated":"2026-10-14T10:33:41Z","author":[{"orcid":"0000-0003-2708-5545","first_name":"Kai","last_name":"Bartusch","id":"0c51b9f5-90c8-11f1-b4ef-9ad5d3d9a34a","full_name":"Bartusch, Kai"},{"first_name":"Noel","last_name":"Blanco-Touriñán","full_name":"Blanco-Touriñán, Noel"},{"first_name":"Antia","last_name":"Rodriguez-Villalón","full_name":"Rodriguez-Villalón, Antia"},{"full_name":"Truernit, Elisabeth","last_name":"Truernit","first_name":"Elisabeth"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Fluorescent dyes are often used to observe transport mechanisms in plant vascular tissues. However, it has been technically challenging to apply fluorescent dyes on roots to monitor xylem transport in vivo. Here, we present a fast, noninvasive, and high-throughput protocol to monitor xylem transport in seedlings. Using the fluorescent dyes 5(6)-carboxyfluorescein diacetate (CFDA) and Rhodamine WT, we were able to observe xylem transport on a cellular level in Arabidopsis thaliana roots. We describe how to apply these dyes on primary roots of young seedlings, how to monitor root-to-shoot xylem transport, and how to measure xylem transport velocity in roots. Moreover, we show that our protocol can also be applied to lateral roots and grafted seedlings to assess xylem (re)connection. Altogether, these techniques are useful for investigating xylem functionality in diverse experimental setups."}],"type":"book_chapter","quality_controlled":"1","status":"public","oa_version":"None","citation":{"short":"K. Bartusch, N. Blanco-Touriñán, A. Rodriguez-Villalón, E. Truernit, in:, Xylem, 2nd ed., Springer, New York, NY, 2023, pp. 3–15.","mla":"Bartusch, Kai, et al. “Monitoring Xylem Transport in Arabidopsis Thaliana Seedlings Using Fluorescent Dyes.” <i>Xylem</i>, 2nd ed., vol. 2722, Springer, 2023, pp. 3–15, doi:<a href=\"https://doi.org/10.1007/978-1-0716-3477-6_1\">10.1007/978-1-0716-3477-6_1</a>.","chicago":"Bartusch, Kai, Noel Blanco-Touriñán, Antia Rodriguez-Villalón, and Elisabeth Truernit. “Monitoring Xylem Transport in Arabidopsis Thaliana Seedlings Using Fluorescent Dyes.” In <i>Xylem</i>, 2nd ed., 2722:3–15. MIMB. New York, NY: Springer, 2023. <a href=\"https://doi.org/10.1007/978-1-0716-3477-6_1\">https://doi.org/10.1007/978-1-0716-3477-6_1</a>.","apa":"Bartusch, K., Blanco-Touriñán, N., Rodriguez-Villalón, A., &#38; Truernit, E. (2023). Monitoring Xylem Transport in Arabidopsis thaliana Seedlings Using Fluorescent Dyes. In <i>Xylem</i> (2nd ed., Vol. 2722, pp. 3–15). New York, NY: Springer. <a href=\"https://doi.org/10.1007/978-1-0716-3477-6_1\">https://doi.org/10.1007/978-1-0716-3477-6_1</a>","ista":"Bartusch K, Blanco-Touriñán N, Rodriguez-Villalón A, Truernit E. 2023.Monitoring Xylem Transport in Arabidopsis thaliana Seedlings Using Fluorescent Dyes. In: Xylem. Methods in Molecular Biology, vol. 2722, 3–15.","ieee":"K. Bartusch, N. Blanco-Touriñán, A. Rodriguez-Villalón, and E. Truernit, “Monitoring Xylem Transport in Arabidopsis thaliana Seedlings Using Fluorescent Dyes,” in <i>Xylem</i>, 2nd ed., vol. 2722, New York, NY: Springer, 2023, pp. 3–15.","ama":"Bartusch K, Blanco-Touriñán N, Rodriguez-Villalón A, Truernit E. Monitoring Xylem Transport in Arabidopsis thaliana Seedlings Using Fluorescent Dyes. In: <i>Xylem</i>. Vol 2722. 2nd ed. MIMB. New York, NY: Springer; 2023:3-15. doi:<a href=\"https://doi.org/10.1007/978-1-0716-3477-6_1\">10.1007/978-1-0716-3477-6_1</a>"},"date_published":"2023-10-29T00:00:00Z","pmid":1,"publisher":"Springer","extern":"1","month":"10","intvolume":"      2722","publication_status":"published","publication":"Xylem","year":"2023","date_created":"2026-10-13T11:15:03Z","fulldoi":"https://doi.org/10.1007/978-1-0716-3477-6_1","series_title":"MIMB","page":"3-15","publication_identifier":{"eissn":["1940-6029"],"issn":["1064-3745"],"eisbn":["9781071634776"],"isbn":["9781071634769"]},"day":"29","title":"Monitoring Xylem Transport in Arabidopsis thaliana Seedlings Using Fluorescent Dyes","_id":"23130","place":"New York, NY","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":2722,"article_processing_charge":"No","alternative_title":["Methods in Molecular Biology"],"external_id":{"pmid":["37897596"]},"doi":"10.1007/978-1-0716-3477-6_1","edition":"2"},{"oa_version":"None","citation":{"ieee":"L. Hörmayer, J. Friml, and M. Glanc, “Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy,” in <i>Plant Cell Division</i>, vol. 2382, Humana Press, 2021, pp. 105–114.","ista":"Hörmayer L, Friml J, Glanc M. 2021.Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy. In: Plant Cell Division. Methods in Molecular Biology, vol. 2382, 105–114.","ama":"Hörmayer L, Friml J, Glanc M. Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy. In: <i>Plant Cell Division</i>. Vol 2382. MIMB. Humana Press; 2021:105-114. doi:<a href=\"https://doi.org/10.1007/978-1-0716-1744-1_6\">10.1007/978-1-0716-1744-1_6</a>","short":"L. Hörmayer, J. Friml, M. Glanc, in:, Plant Cell Division, Humana Press, 2021, pp. 105–114.","mla":"Hörmayer, Lukas, et al. “Automated Time-Lapse Imaging and Manipulation of Cell Divisions in Arabidopsis Roots by Vertical-Stage Confocal Microscopy.” <i>Plant Cell Division</i>, vol. 2382, Humana Press, 2021, pp. 105–14, doi:<a href=\"https://doi.org/10.1007/978-1-0716-1744-1_6\">10.1007/978-1-0716-1744-1_6</a>.","chicago":"Hörmayer, Lukas, Jiří Friml, and Matous Glanc. “Automated Time-Lapse Imaging and Manipulation of Cell Divisions in Arabidopsis Roots by Vertical-Stage Confocal Microscopy.” In <i>Plant Cell Division</i>, 2382:105–14. MIMB. Humana Press, 2021. <a href=\"https://doi.org/10.1007/978-1-0716-1744-1_6\">https://doi.org/10.1007/978-1-0716-1744-1_6</a>.","apa":"Hörmayer, L., Friml, J., &#38; Glanc, M. (2021). Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy. In <i>Plant Cell Division</i> (Vol. 2382, pp. 105–114). Humana Press. <a href=\"https://doi.org/10.1007/978-1-0716-1744-1_6\">https://doi.org/10.1007/978-1-0716-1744-1_6</a>"},"month":"10","publisher":"Humana Press","pmid":1,"date_published":"2021-10-28T00:00:00Z","acknowledgement":"We thank B. De Rybel for allowing M.G. to work on this manuscript during a postdoc in his laboratory, and EMBO for supporting M.G. with a Long-Term fellowship (ALTF 1005-2019) during this time. We acknowledge the service and support by the Bioimaging Facility at IST Austria, and finally, we thank A. Mally for proofreading and correcting the manuscript.","intvolume":"      2382","year":"2021","publication":"Plant Cell Division","date_created":"2021-11-11T10:03:30Z","publication_status":"published","date_updated":"2022-06-03T06:47:06Z","scopus_import":"1","author":[{"last_name":"Hörmayer","first_name":"Lukas","full_name":"Hörmayer, Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","first_name":"Matous","orcid":"0000-0003-0619-7783"}],"type":"book_chapter","abstract":[{"text":"The analysis of dynamic cellular processes such as plant cytokinesis stands and falls with live-cell time-lapse confocal imaging. Conventional approaches to time-lapse imaging of cell division in Arabidopsis root tips are tedious and have low throughput. Here, we describe a protocol for long-term time-lapse simultaneous imaging of multiple root tips on a vertical-stage confocal microscope with automated root tracking. We also provide modifications of the basic protocol to implement this imaging method in the analysis of genetic, pharmacological or laser ablation wounding-mediated experimental manipulations. Our method dramatically improves the efficiency of cell division time-lapse imaging by increasing the throughput, while reducing the person-hour requirements of such experiments.","lang":"eng"}],"language":[{"iso":"eng"}],"quality_controlled":"1","status":"public","volume":2382,"external_id":{"pmid":["34705235"]},"alternative_title":["Methods in Molecular Biology"],"article_processing_charge":"No","doi":"10.1007/978-1-0716-1744-1_6","department":[{"_id":"JiFr"}],"fulldoi":"https://doi.org/10.1007/978-1-0716-1744-1_6","acknowledged_ssus":[{"_id":"Bio"}],"series_title":"MIMB","page":"105-114","publication_identifier":{"eissn":["1940-6029"],"issn":["1064-3745"],"eisbn":["978-1-0716-1744-1"],"isbn":["978-1-0716-1743-4"]},"day":"28","_id":"10268","title":"Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_updated":"2026-07-06T13:11:10Z","scopus_import":"1","author":[{"orcid":"0000-0002-5419-7756","first_name":"Peng","last_name":"Xia","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","full_name":"Xia, Peng"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"abstract":[{"lang":"eng","text":"Tissue morphogenesis is driven by mechanical forces triggering cell movements and shape changes. Quantitatively measuring tension within tissues is of great importance for understanding the role of mechanical signals acting on the cell and tissue level during morphogenesis. Here we introduce laser ablation as a useful tool to probe tissue tension within the granulosa layer, an epithelial monolayer of somatic cells that surround the zebrafish female gamete during folliculogenesis. We describe in detail how to isolate follicles, mount samples, perform laser surgery, and analyze the data."}],"language":[{"iso":"eng"}],"type":"book_chapter","quality_controlled":"1","status":"public","oa_version":"None","citation":{"chicago":"Xia, Peng, and Carl-Philipp J Heisenberg. “Quantifying Tissue Tension in the Granulosa Layer after Laser Surgery.” In <i>Germline Development in the Zebrafish</i>, edited by Roland Dosch, 2218:117–28. Humana Press, 2021. <a href=\"https://doi.org/10.1007/978-1-0716-0970-5_10\">https://doi.org/10.1007/978-1-0716-0970-5_10</a>.","mla":"Xia, Peng, and Carl-Philipp J. Heisenberg. “Quantifying Tissue Tension in the Granulosa Layer after Laser Surgery.” <i>Germline Development in the Zebrafish</i>, edited by Roland Dosch, vol. 2218, Humana Press, 2021, pp. 117–28, doi:<a href=\"https://doi.org/10.1007/978-1-0716-0970-5_10\">10.1007/978-1-0716-0970-5_10</a>.","apa":"Xia, P., &#38; Heisenberg, C.-P. J. (2021). Quantifying tissue tension in the granulosa layer after laser surgery. In R. Dosch (Ed.), <i>Germline Development in the Zebrafish</i> (Vol. 2218, pp. 117–128). Humana Press. <a href=\"https://doi.org/10.1007/978-1-0716-0970-5_10\">https://doi.org/10.1007/978-1-0716-0970-5_10</a>","short":"P. Xia, C.-P.J. Heisenberg, in:, R. Dosch (Ed.), Germline Development in the Zebrafish, Humana Press, 2021, pp. 117–128.","ista":"Xia P, Heisenberg C-PJ. 2021.Quantifying tissue tension in the granulosa layer after laser surgery. In: Germline Development in the Zebrafish. Methods in Molecular Biology, vol. 2218, 117–128.","ieee":"P. Xia and C.-P. J. Heisenberg, “Quantifying tissue tension in the granulosa layer after laser surgery,” in <i>Germline Development in the Zebrafish</i>, vol. 2218, R. Dosch, Ed. Humana Press, 2021, pp. 117–128.","ama":"Xia P, Heisenberg C-PJ. Quantifying tissue tension in the granulosa layer after laser surgery. In: Dosch R, ed. <i>Germline Development in the Zebrafish</i>. Vol 2218. Humana Press; 2021:117-128. doi:<a href=\"https://doi.org/10.1007/978-1-0716-0970-5_10\">10.1007/978-1-0716-0970-5_10</a>"},"editor":[{"full_name":"Dosch, Roland","first_name":"Roland","last_name":"Dosch"}],"pmid":1,"date_published":"2021-02-20T00:00:00Z","month":"02","publisher":"Humana Press","acknowledgement":"We thank Prof. Masazumi Tada and Roland Dosch for providing transgenic zebrafish lines, the Heisenberg lab for technical assistance and feedback on the manuscript, and the Bioimaging and Fish facilities of IST Austria for continuous support. This work was funded by an ERC advanced grant (MECSPEC to C.-P.H.).","intvolume":"      2218","date_created":"2021-03-14T23:01:34Z","publication":"Germline Development in the Zebrafish","year":"2021","publication_status":"published","fulldoi":"https://doi.org/10.1007/978-1-0716-0970-5_10","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"department":[{"_id":"CaHe"}],"publication_identifier":{"issn":["1064-3745"],"eissn":["1940-6029"],"isbn":["978-1-0716-0969-9"],"eisbn":["978-1-0716-0970-5"]},"day":"20","page":"117-128","title":"Quantifying tissue tension in the granulosa layer after laser surgery","_id":"9245","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":2218,"article_processing_charge":"No","alternative_title":["Methods in Molecular Biology"],"external_id":{"pmid":["33606227"]},"das_tickbox":"1","corr_author":"1","keyword":["Tissue tension","Morphogenesis","Laser ablation","Zebrafish folliculogenesis","Granulosa cells"],"doi":"10.1007/978-1-0716-0970-5_10","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}]},{"doi":"10.1007/978-1-0716-0755-8_16","alternative_title":["Methods in Molecular Biology"],"article_processing_charge":"No","external_id":{"pmid":["32651922"]},"volume":2173,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Design and application of light-regulated receptor tyrosine kinases","_id":"8173","publication_identifier":{"isbn":["9781071607541"],"eisbn":["9781071607558"],"issn":["1064-3745"],"eissn":["1940-6029"]},"page":"233-246","day":"11","series_title":"MIMB","fulldoi":"https://doi.org/10.1007/978-1-0716-0755-8_16","department":[{"_id":"CaGu"}],"publication_status":"published","date_created":"2020-07-26T22:01:03Z","year":"2020","publication":"Photoswitching Proteins","intvolume":"      2173","date_published":"2020-07-11T00:00:00Z","pmid":1,"publisher":"Springer Nature","month":"07","citation":{"ama":"Kainrath S, Janovjak HL. Design and application of light-regulated receptor tyrosine kinases. In: Niopek D, ed. <i>Photoswitching Proteins</i>. Vol 2173. MIMB. Springer Nature; 2020:233-246. doi:<a href=\"https://doi.org/10.1007/978-1-0716-0755-8_16\">10.1007/978-1-0716-0755-8_16</a>","ieee":"S. Kainrath and H. L. Janovjak, “Design and application of light-regulated receptor tyrosine kinases,” in <i>Photoswitching Proteins</i>, vol. 2173, D. Niopek, Ed. Springer Nature, 2020, pp. 233–246.","ista":"Kainrath S, Janovjak HL. 2020.Design and application of light-regulated receptor tyrosine kinases. In: Photoswitching Proteins. Methods in Molecular Biology, vol. 2173, 233–246.","short":"S. Kainrath, H.L. Janovjak, in:, D. Niopek (Ed.), Photoswitching Proteins, Springer Nature, 2020, pp. 233–246.","apa":"Kainrath, S., &#38; Janovjak, H. L. (2020). Design and application of light-regulated receptor tyrosine kinases. In D. Niopek (Ed.), <i>Photoswitching Proteins</i> (Vol. 2173, pp. 233–246). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-0755-8_16\">https://doi.org/10.1007/978-1-0716-0755-8_16</a>","chicago":"Kainrath, Stephanie, and Harald L Janovjak. “Design and Application of Light-Regulated Receptor Tyrosine Kinases.” In <i>Photoswitching Proteins</i>, edited by Dominik Niopek, 2173:233–46. MIMB. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-1-0716-0755-8_16\">https://doi.org/10.1007/978-1-0716-0755-8_16</a>.","mla":"Kainrath, Stephanie, and Harald L. Janovjak. “Design and Application of Light-Regulated Receptor Tyrosine Kinases.” <i>Photoswitching Proteins</i>, edited by Dominik Niopek, vol. 2173, Springer Nature, 2020, pp. 233–46, doi:<a href=\"https://doi.org/10.1007/978-1-0716-0755-8_16\">10.1007/978-1-0716-0755-8_16</a>."},"oa_version":"None","editor":[{"last_name":"Niopek","first_name":"Dominik","full_name":"Niopek, Dominik"}],"status":"public","language":[{"iso":"eng"}],"abstract":[{"text":"Understanding how the activity of membrane receptors and cellular signaling pathways shapes cell behavior is of fundamental interest in basic and applied research. Reengineering receptors to react to light instead of their cognate ligands allows for generating defined signaling inputs with high spatial and temporal precision and facilitates the dissection of complex signaling networks. Here, we describe fundamental considerations in the design of light-regulated receptor tyrosine kinases (Opto-RTKs) and appropriate control experiments. We also introduce methods for transient receptor expression in HEK293 cells, quantitative assessment of signaling activity in reporter gene assays, semiquantitative assessment of (in)activation time courses through Western blot (WB) analysis, and easy to implement light stimulation hardware.","lang":"eng"}],"type":"book_chapter","author":[{"orcid":"0000-0002-6709-2195","last_name":"Kainrath","first_name":"Stephanie","full_name":"Kainrath, Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8023-9315","first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L"}],"scopus_import":"1","date_updated":"2026-04-16T09:22:45Z"},{"intvolume":"      2074","publication_status":"published","date_created":"2022-08-16T06:54:48Z","publication":"Protein-Protein Interaction Networks","year":"2019","editor":[{"last_name":"Canzar","first_name":"Stefan","full_name":"Canzar, Stefan"},{"last_name":"Rojas Ringeling","first_name":"Francisca","full_name":"Rojas Ringeling, Francisca"}],"oa_version":"None","citation":{"ieee":"S. Biedermann, M. Henzinger, C. Schulz, and B. Schuster, “Vienna Graph Clustering,” in <i>Protein-Protein Interaction Networks</i>, vol. 2074, S. Canzar and F. Rojas Ringeling, Eds. Springer Nature, 2019, pp. 215–231.","ista":"Biedermann S, Henzinger M, Schulz C, Schuster B. 2019.Vienna Graph Clustering. In: Protein-Protein Interaction Networks. Methods in Molecular Biology, vol. 2074, 215–231.","ama":"Biedermann S, Henzinger M, Schulz C, Schuster B. Vienna Graph Clustering. In: Canzar S, Rojas Ringeling F, eds. <i>Protein-Protein Interaction Networks</i>. Vol 2074. MIMB. Springer Nature; 2019:215–231. doi:<a href=\"https://doi.org/10.1007/978-1-4939-9873-9_16\">10.1007/978-1-4939-9873-9_16</a>","mla":"Biedermann, Sonja, et al. “Vienna Graph Clustering.” <i>Protein-Protein Interaction Networks</i>, edited by Stefan Canzar and Francisca Rojas Ringeling, vol. 2074, Springer Nature, 2019, pp. 215–231, doi:<a href=\"https://doi.org/10.1007/978-1-4939-9873-9_16\">10.1007/978-1-4939-9873-9_16</a>.","chicago":"Biedermann, Sonja, Monika Henzinger, Christian Schulz, and Bernhard Schuster. “Vienna Graph Clustering.” In <i>Protein-Protein Interaction Networks</i>, edited by Stefan Canzar and Francisca Rojas Ringeling, 2074:215–231. MIMB. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-1-4939-9873-9_16\">https://doi.org/10.1007/978-1-4939-9873-9_16</a>.","apa":"Biedermann, S., Henzinger, M., Schulz, C., &#38; Schuster, B. (2019). Vienna Graph Clustering. In S. Canzar &#38; F. Rojas Ringeling (Eds.), <i>Protein-Protein Interaction Networks</i> (Vol. 2074, pp. 215–231). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-4939-9873-9_16\">https://doi.org/10.1007/978-1-4939-9873-9_16</a>","short":"S. Biedermann, M. Henzinger, C. Schulz, B. Schuster, in:, S. Canzar, F. Rojas Ringeling (Eds.), Protein-Protein Interaction Networks, Springer Nature, 2019, pp. 215–231."},"publisher":"Springer Nature","month":"10","extern":"1","date_published":"2019-10-04T00:00:00Z","pmid":1,"type":"book_chapter","language":[{"iso":"eng"}],"abstract":[{"text":"This paper serves as a user guide to the Vienna graph clustering framework. We review our general memetic algorithm, VieClus, to tackle the graph clustering problem. A key component of our contribution are natural recombine operators that employ ensemble clusterings as well as multi-level techniques. Lastly, we combine these techniques with a scalable communication protocol, producing a system that is able to compute high-quality solutions in a short amount of time. After giving a description of the algorithms employed, we establish the connection of the graph clustering problem to protein–protein interaction networks and moreover give a description on how the software can be used, what file formats are expected, and how this can be used to find functional groups in protein–protein interaction networks.","lang":"eng"}],"status":"public","quality_controlled":"1","scopus_import":"1","date_updated":"2024-11-06T12:17:08Z","author":[{"first_name":"Sonja","last_name":"Biedermann","full_name":"Biedermann, Sonja"},{"orcid":"0000-0002-5008-6530","last_name":"Henzinger","first_name":"Monika H","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Schulz, Christian","first_name":"Christian","last_name":"Schulz"},{"last_name":"Schuster","first_name":"Bernhard","full_name":"Schuster, Bernhard"}],"doi":"10.1007/978-1-4939-9873-9_16","volume":2074,"external_id":{"pmid":["31583641"]},"article_processing_charge":"No","alternative_title":["Methods in Molecular Biology"],"_id":"11847","title":"Vienna Graph Clustering","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1007/978-1-4939-9873-9_16","series_title":"MIMB","page":"215–231","publication_identifier":{"eissn":["1940-6029"],"issn":["1064-3745"],"eisbn":["9781493998739"],"isbn":["9781493998722"]},"day":"04"},{"article_processing_charge":"No","alternative_title":["Methods in Molecular Biology"],"volume":1863,"has_accepted_license":"1","file":[{"content_type":"application/pdf","file_id":"8656","date_created":"2020-10-13T14:20:37Z","file_size":4906815,"file_name":"2018_MIMB_Zagorski.pdf","creator":"dernst","checksum":"2a97d0649fdcfcf1bdca7c8ad1dce71b","access_level":"open_access","success":1,"relation":"main_file","date_updated":"2020-10-13T14:20:37Z"}],"oa":1,"project":[{"_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037","call_identifier":"H2020"}],"doi":"10.1007/978-1-4939-8772-6_4","day":"16","publication_identifier":{"issn":["1064-3745"],"isbn":["978-1-4939-8771-9"]},"page":"47 - 63","department":[{"_id":"AnKi"}],"series_title":"MIMB","fulldoi":"https://doi.org/10.1007/978-1-4939-8772-6_4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"_id":"37","title":"Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube","publisher":"Springer Nature","month":"10","ddc":["570"],"date_published":"2018-10-16T00:00:00Z","oa_version":"Submitted Version","citation":{"ista":"Zagórski MP, Kicheva A. 2018.Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: Morphogen Gradients . Methods in Molecular Biology, vol. 1863, 47–63.","ieee":"M. P. Zagórski and A. Kicheva, “Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube,” in <i>Morphogen Gradients </i>, vol. 1863, Springer Nature, 2018, pp. 47–63.","ama":"Zagórski MP, Kicheva A. Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: <i>Morphogen Gradients </i>. Vol 1863. MIMB. Springer Nature; 2018:47-63. doi:<a href=\"https://doi.org/10.1007/978-1-4939-8772-6_4\">10.1007/978-1-4939-8772-6_4</a>","mla":"Zagórski, Marcin P., and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” <i>Morphogen Gradients </i>, vol. 1863, Springer Nature, 2018, pp. 47–63, doi:<a href=\"https://doi.org/10.1007/978-1-4939-8772-6_4\">10.1007/978-1-4939-8772-6_4</a>.","chicago":"Zagórski, Marcin P, and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” In <i>Morphogen Gradients </i>, 1863:47–63. MIMB. Springer Nature, 2018. <a href=\"https://doi.org/10.1007/978-1-4939-8772-6_4\">https://doi.org/10.1007/978-1-4939-8772-6_4</a>.","apa":"Zagórski, M. P., &#38; Kicheva, A. (2018). Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In <i>Morphogen Gradients </i> (Vol. 1863, pp. 47–63). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-4939-8772-6_4\">https://doi.org/10.1007/978-1-4939-8772-6_4</a>","short":"M.P. Zagórski, A. Kicheva, in:, Morphogen Gradients , Springer Nature, 2018, pp. 47–63."},"publication_status":"published","date_created":"2018-12-11T11:44:17Z","publication":"Morphogen Gradients ","year":"2018","intvolume":"      1863","file_date_updated":"2020-10-13T14:20:37Z","author":[{"orcid":"0000-0001-7896-7762","full_name":"Zagórski, Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","last_name":"Zagórski","first_name":"Marcin P"},{"last_name":"Kicheva","first_name":"Anna","full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998"}],"scopus_import":"1","publist_id":"8018","date_updated":"2025-04-14T07:27:29Z","status":"public","quality_controlled":"1","type":"book_chapter","language":[{"iso":"eng"}],"abstract":[{"text":"Developmental processes are inherently dynamic and understanding them requires quantitative measurements of gene and protein expression levels in space and time. While live imaging is a powerful approach for obtaining such data, it is still a challenge to apply it over long periods of time to large tissues, such as the embryonic spinal cord in mouse and chick. Nevertheless, dynamics of gene expression and signaling activity patterns in this organ can be studied by collecting tissue sections at different developmental stages. In combination with immunohistochemistry, this allows for measuring the levels of multiple developmental regulators in a quantitative manner with high spatiotemporal resolution. The mean protein expression levels over time, as well as embryo-to-embryo variability can be analyzed. A key aspect of the approach is the ability to compare protein levels across different samples. This requires a number of considerations in sample preparation, imaging and data analysis. Here we present a protocol for obtaining time course data of dorsoventral expression patterns from mouse and chick neural tube in the first 3 days of neural tube development. The described workflow starts from embryo dissection and ends with a processed dataset. Software scripts for data analysis are included. The protocol is adaptable and instructions that allow the user to modify different steps are provided. Thus, the procedure can be altered for analysis of time-lapse images and applied to systems other than the neural tube.","lang":"eng"}]},{"intvolume":"      1761","date_created":"2018-12-11T11:46:18Z","year":"2018","publication":"Root Development ","publication_status":"published","citation":{"short":"H. Trinh, I. Verstraeten, D. Geelen, in:, Root Development , Springer Nature, 2018, pp. 95–102.","apa":"Trinh, H., Verstraeten, I., &#38; Geelen, D. (2018). In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In <i>Root Development </i> (Vol. 1761, pp. 95–102). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-4939-7747-5_7\">https://doi.org/10.1007/978-1-4939-7747-5_7</a>","chicago":"Trinh, Hoang, Inge Verstraeten, and Danny Geelen. “In Vitro Assay for Induction of Adventitious Rooting on Intact Arabidopsis Hypocotyls.” In <i>Root Development </i>, 1761:95–102. Springer Nature, 2018. <a href=\"https://doi.org/10.1007/978-1-4939-7747-5_7\">https://doi.org/10.1007/978-1-4939-7747-5_7</a>.","mla":"Trinh, Hoang, et al. “In Vitro Assay for Induction of Adventitious Rooting on Intact Arabidopsis Hypocotyls.” <i>Root Development </i>, vol. 1761, Springer Nature, 2018, pp. 95–102, doi:<a href=\"https://doi.org/10.1007/978-1-4939-7747-5_7\">10.1007/978-1-4939-7747-5_7</a>.","ama":"Trinh H, Verstraeten I, Geelen D. In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In: <i>Root Development </i>. Vol 1761. Springer Nature; 2018:95-102. doi:<a href=\"https://doi.org/10.1007/978-1-4939-7747-5_7\">10.1007/978-1-4939-7747-5_7</a>","ista":"Trinh H, Verstraeten I, Geelen D. 2018.In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In: Root Development . MIMB, vol. 1761, 95–102.","ieee":"H. Trinh, I. Verstraeten, and D. Geelen, “In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls,” in <i>Root Development </i>, vol. 1761, Springer Nature, 2018, pp. 95–102."},"oa_version":"None","month":"03","publisher":"Springer Nature","pmid":1,"date_published":"2018-03-01T00:00:00Z","type":"book_chapter","abstract":[{"text":"Adventitious roots (AR) are de novo formed roots that emerge from any part of the plant or from callus in tissue culture, except root tissue. The plant tissue origin and the method by which they are induced determine the physiological properties of emerged ARs. Hence, a standard method encompassing all types of AR does not exist. Here we describe a method for the induction and analysis of AR that emerge from the etiolated hypocotyl of dicot plants. The hypocotyl is formed during embryogenesis and shows a determined developmental pattern which usually does not involve AR formation. However, the hypocotyl shows propensity to form de novo roots under specific circumstances such as removal of the root system, high humidity or flooding, or during de-etiolation. The hypocotyl AR emerge from a pericycle-like cell layer surrounding the vascular tissue of the central cylinder, which is reminiscent to the developmental program of lateral roots. Here we propose an easy protocol for in vitro hypocotyl AR induction from etiolated Arabidopsis seedlings.","lang":"eng"}],"language":[{"iso":"eng"}],"quality_controlled":"1","status":"public","date_updated":"2021-01-12T07:54:21Z","publist_id":"7421","scopus_import":"1","author":[{"first_name":"Hoang","last_name":"Trinh","full_name":"Trinh, Hoang"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge","first_name":"Inge","last_name":"Verstraeten","orcid":"0000-0001-7241-2328"},{"last_name":"Geelen","first_name":"Danny","full_name":"Geelen, Danny"}],"doi":"10.1007/978-1-4939-7747-5_7","volume":1761,"external_id":{"pmid":["29525951"]},"alternative_title":["MIMB"],"article_processing_charge":"No","_id":"408","title":"In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"}],"fulldoi":"https://doi.org/10.1007/978-1-4939-7747-5_7","day":"01","page":"95 - 102","publication_identifier":{"issn":["1064-3745"]}},{"abstract":[{"lang":"eng","text":"Methyl groups are very useful probes of structure, dynamics, and interactions in protein NMR spectroscopy. In particular, methyl-directed experiments provide high sensitivity even in very large proteins, such as membrane proteins in a membrane-mimicking environment. In this chapter, we discuss the approach for labeling methyl groups in E. coli-based protein expression, as exemplified with the mitochondrial carrier GGC."}],"title":"Methyl-specific isotope labeling strategies for NMR studies of membrane proteins","language":[{"iso":"eng"}],"type":"book_chapter","_id":"8450","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","status":"public","date_updated":"2022-08-26T09:14:20Z","fulldoi":"https://doi.org/10.1007/978-1-4939-7151-0_6","page":"109-123","author":[{"full_name":"Kurauskas, Vilius","last_name":"Kurauskas","first_name":"Vilius"},{"orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul"},{"last_name":"Sounier","first_name":"Remy","full_name":"Sounier, Remy"}],"publication_identifier":{"issn":["1064-3745","1940-6029"],"isbn":["9781493971497","9781493971510"]},"day":"29","intvolume":"      1635","publication":"Membrane protein structure and function characterization","year":"2017","date_created":"2020-09-18T10:06:44Z","doi":"10.1007/978-1-4939-7151-0_6","publication_status":"published","oa_version":"None","citation":{"mla":"Kurauskas, Vilius, et al. “Methyl-Specific Isotope Labeling Strategies for NMR Studies of Membrane Proteins.” <i>Membrane Protein Structure and Function Characterization</i>, vol. 1635, Springer Nature, 2017, pp. 109–23, doi:<a href=\"https://doi.org/10.1007/978-1-4939-7151-0_6\">10.1007/978-1-4939-7151-0_6</a>.","chicago":"Kurauskas, Vilius, Paul Schanda, and Remy Sounier. “Methyl-Specific Isotope Labeling Strategies for NMR Studies of Membrane Proteins.” In <i>Membrane Protein Structure and Function Characterization</i>, 1635:109–23. Springer Nature, 2017. <a href=\"https://doi.org/10.1007/978-1-4939-7151-0_6\">https://doi.org/10.1007/978-1-4939-7151-0_6</a>.","apa":"Kurauskas, V., Schanda, P., &#38; Sounier, R. (2017). Methyl-specific isotope labeling strategies for NMR studies of membrane proteins. In <i>Membrane protein structure and function characterization</i> (Vol. 1635, pp. 109–123). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-4939-7151-0_6\">https://doi.org/10.1007/978-1-4939-7151-0_6</a>","short":"V. Kurauskas, P. Schanda, R. Sounier, in:, Membrane Protein Structure and Function Characterization, Springer Nature, 2017, pp. 109–123.","ieee":"V. Kurauskas, P. Schanda, and R. Sounier, “Methyl-specific isotope labeling strategies for NMR studies of membrane proteins,” in <i>Membrane protein structure and function characterization</i>, vol. 1635, Springer Nature, 2017, pp. 109–123.","ista":"Kurauskas V, Schanda P, Sounier R. 2017.Methyl-specific isotope labeling strategies for NMR studies of membrane proteins. In: Membrane protein structure and function characterization. Methods in Molecular Biology, vol. 1635, 109–123.","ama":"Kurauskas V, Schanda P, Sounier R. Methyl-specific isotope labeling strategies for NMR studies of membrane proteins. In: <i>Membrane Protein Structure and Function Characterization</i>. Vol 1635. Springer Nature; 2017:109-123. doi:<a href=\"https://doi.org/10.1007/978-1-4939-7151-0_6\">10.1007/978-1-4939-7151-0_6</a>"},"volume":1635,"date_published":"2017-07-29T00:00:00Z","alternative_title":["Methods in Molecular Biology"],"article_processing_charge":"No","month":"07","extern":"1","publisher":"Springer Nature"},{"scopus_import":"1","date_updated":"2025-07-10T12:01:52Z","publist_id":"6451","author":[{"first_name":"Ben","last_name":"Clifton","full_name":"Clifton, Ben"},{"full_name":"Whitfield, Jason","last_name":"Whitfield","first_name":"Jason"},{"first_name":"Inmaculada","last_name":"Sanchez Romero","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","full_name":"Sanchez Romero, Inmaculada"},{"full_name":"Herde, Michel","last_name":"Herde","first_name":"Michel"},{"last_name":"Henneberger","first_name":"Christian","full_name":"Henneberger, Christian"},{"orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L"},{"full_name":"Jackson, Colin","first_name":"Colin","last_name":"Jackson"}],"language":[{"iso":"eng"}],"abstract":[{"text":"Small molecule biosensors based on Forster resonance energy transfer (FRET) enable small molecule signaling to be monitored with high spatial and temporal resolution in complex cellular environments. FRET sensors can be constructed by fusing a pair of fluorescent proteins to a suitable recognition domain, such as a member of the solute-binding protein (SBP) superfamily. However, naturally occurring SBPs may be unsuitable for incorporation into FRET sensors due to their low thermostability, which may preclude imaging under physiological conditions, or because the positions of their N- and C-termini may be suboptimal for fusion of fluorescent proteins, which may limit the dynamic range of the resulting sensors. Here, we show how these problems can be overcome using ancestral protein reconstruction and circular permutation. Ancestral protein reconstruction, used as a protein engineering strategy, leverages phylogenetic information to improve the thermostability of proteins, while circular permutation enables the termini of an SBP to be repositioned to maximize the dynamic range of the resulting FRET sensor. We also provide a protocol for cloning the engineered SBPs into FRET sensor constructs using Golden Gate assembly and discuss considerations for in situ characterization of the FRET sensors.","lang":"eng"}],"type":"book_chapter","quality_controlled":"1","status":"public","oa_version":"None","citation":{"ista":"Clifton B, Whitfield J, Sanchez-Romero I, Herde M, Henneberger C, Janovjak HL, Jackson C. 2017.Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Synthetic Protein Switches. Methods in Molecular Biology, vol. 1596, 71–87.","ieee":"B. Clifton <i>et al.</i>, “Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors,” in <i>Synthetic Protein Switches</i>, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 71–87.","ama":"Clifton B, Whitfield J, Sanchez-Romero I, et al. Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Stein V, ed. <i>Synthetic Protein Switches</i>. Vol 1596. Synthetic Protein Switches. Springer; 2017:71-87. doi:<a href=\"https://doi.org/10.1007/978-1-4939-6940-1_5\">10.1007/978-1-4939-6940-1_5</a>","short":"B. Clifton, J. Whitfield, I. Sanchez-Romero, M. Herde, C. Henneberger, H.L. Janovjak, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 71–87.","mla":"Clifton, Ben, et al. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” <i>Synthetic Protein Switches</i>, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 71–87, doi:<a href=\"https://doi.org/10.1007/978-1-4939-6940-1_5\">10.1007/978-1-4939-6940-1_5</a>.","chicago":"Clifton, Ben, Jason Whitfield, Inmaculada Sanchez-Romero, Michel Herde, Christian Henneberger, Harald L Janovjak, and Colin Jackson. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” In <i>Synthetic Protein Switches</i>, edited by Viktor Stein, 1596:71–87. Synthetic Protein Switches. Springer, 2017. <a href=\"https://doi.org/10.1007/978-1-4939-6940-1_5\">https://doi.org/10.1007/978-1-4939-6940-1_5</a>.","apa":"Clifton, B., Whitfield, J., Sanchez-Romero, I., Herde, M., Henneberger, C., Janovjak, H. L., &#38; Jackson, C. (2017). Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In V. Stein (Ed.), <i>Synthetic Protein Switches</i> (Vol. 1596, pp. 71–87). Springer. <a href=\"https://doi.org/10.1007/978-1-4939-6940-1_5\">https://doi.org/10.1007/978-1-4939-6940-1_5</a>"},"editor":[{"first_name":"Viktor","last_name":"Stein","full_name":"Stein, Viktor"}],"date_published":"2017-03-15T00:00:00Z","publisher":"Springer","month":"03","intvolume":"      1596","publication_status":"published","date_created":"2018-12-11T11:49:24Z","publication":"Synthetic Protein Switches","year":"2017","fulldoi":"https://doi.org/10.1007/978-1-4939-6940-1_5","series_title":"Synthetic Protein Switches","department":[{"_id":"HaJa"}],"page":"71 - 87","publication_identifier":{"issn":["1064-3745"]},"day":"15","title":"Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors","_id":"957","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":1596,"alternative_title":["Methods in Molecular Biology"],"article_processing_charge":"No","project":[{"grant_number":"RGY0084/2012","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors","_id":"255BFFFA-B435-11E9-9278-68D0E5697425"}],"doi":"10.1007/978-1-4939-6940-1_5"},{"author":[{"full_name":"Mitchell, Joshua","last_name":"Mitchell","first_name":"Joshua"},{"first_name":"William","last_name":"Zhang","full_name":"Zhang, William"},{"full_name":"Herde, Michel","last_name":"Herde","first_name":"Michel"},{"full_name":"Henneberger, Christian","last_name":"Henneberger","first_name":"Christian"},{"last_name":"Janovjak","first_name":"Harald L","full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315"},{"first_name":"Megan","last_name":"O'Mara","full_name":"O'Mara, Megan"},{"last_name":"Jackson","first_name":"Colin","full_name":"Jackson, Colin"}],"scopus_import":"1","date_updated":"2025-07-10T12:01:54Z","publist_id":"6450","status":"public","quality_controlled":"1","type":"book_chapter","language":[{"iso":"eng"}],"abstract":[{"text":"Biosensors that exploit Forster resonance energy transfer (FRET) can be used to visualize biological and physiological processes and are capable of providing detailed information in both spatial and temporal dimensions. In a FRET-based biosensor, substrate binding is associated with a change in the relative positions of two fluorophores, leading to a change in FRET efficiency that may be observed in the fluorescence spectrum. As a result, their design requires a ligand-binding protein that exhibits a conformational change upon binding. However, not all ligand-binding proteins produce responsive sensors upon conjugation to fluorescent proteins or dyes, and identifying the optimum locations for the fluorophores often involves labor-intensive iterative design or high-throughput screening. Combining the genetic fusion of a fluorescent protein to the ligand-binding protein with site-specific covalent attachment of a fluorescent dye can allow fine control over the positions of the two fluorophores, allowing the construction of very sensitive sensors. This relies upon the accurate prediction of the locations of the two fluorophores in bound and unbound states. In this chapter, we describe a method for computational identification of dye-attachment sites that allows the use of cysteine modification to attach synthetic dyes that can be paired with a fluorescent protein for the purposes of creating FRET sensors.","lang":"eng"}],"publisher":"Springer","month":"05","date_published":"2017-05-15T00:00:00Z","editor":[{"first_name":"Viktor","last_name":"Stein","full_name":"Stein, Viktor"}],"citation":{"short":"J. Mitchell, W. Zhang, M. Herde, C. Henneberger, H.L. Janovjak, M. O’Mara, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 89–99.","apa":"Mitchell, J., Zhang, W., Herde, M., Henneberger, C., Janovjak, H. L., O’Mara, M., &#38; Jackson, C. (2017). Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In V. Stein (Ed.), <i>Synthetic Protein Switches</i> (Vol. 1596, pp. 89–99). Springer. <a href=\"https://doi.org/10.1007/978-1-4939-6940-1_6\">https://doi.org/10.1007/978-1-4939-6940-1_6</a>","chicago":"Mitchell, Joshua, William Zhang, Michel Herde, Christian Henneberger, Harald L Janovjak, Megan O’Mara, and Colin Jackson. “Method for Developing Optical Sensors Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.” In <i>Synthetic Protein Switches</i>, edited by Viktor Stein, 1596:89–99. Synthetic Protein Switches. Springer, 2017. <a href=\"https://doi.org/10.1007/978-1-4939-6940-1_6\">https://doi.org/10.1007/978-1-4939-6940-1_6</a>.","mla":"Mitchell, Joshua, et al. “Method for Developing Optical Sensors Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.” <i>Synthetic Protein Switches</i>, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 89–99, doi:<a href=\"https://doi.org/10.1007/978-1-4939-6940-1_6\">10.1007/978-1-4939-6940-1_6</a>.","ama":"Mitchell J, Zhang W, Herde M, et al. Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In: Stein V, ed. <i>Synthetic Protein Switches</i>. Vol 1596. Synthetic Protein Switches. Springer; 2017:89-99. doi:<a href=\"https://doi.org/10.1007/978-1-4939-6940-1_6\">10.1007/978-1-4939-6940-1_6</a>","ista":"Mitchell J, Zhang W, Herde M, Henneberger C, Janovjak HL, O’Mara M, Jackson C. 2017.Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In: Synthetic Protein Switches. Methods in Molecular Biology, vol. 1596, 89–99.","ieee":"J. Mitchell <i>et al.</i>, “Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment,” in <i>Synthetic Protein Switches</i>, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 89–99."},"oa_version":"None","publication_status":"published","publication":"Synthetic Protein Switches","date_created":"2018-12-11T11:49:24Z","year":"2017","intvolume":"      1596","page":"89 - 99","publication_identifier":{"issn":["1064-3745"]},"day":"15","department":[{"_id":"HaJa"}],"fulldoi":"https://doi.org/10.1007/978-1-4939-6940-1_6","series_title":"Synthetic Protein Switches","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"958","title":"Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment","article_processing_charge":"No","alternative_title":["Methods in Molecular Biology"],"volume":1596,"doi":"10.1007/978-1-4939-6940-1_6"},{"month":"03","ddc":["575"],"publisher":"Springer","date_published":"2017-03-17T00:00:00Z","oa_version":"Submitted Version","citation":{"chicago":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” <i>Auxins and Cytokinins in Plant Biology</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/978-1-4939-6831-2_1\">https://doi.org/10.1007/978-1-4939-6831-2_1</a>.","mla":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” <i>Auxins and Cytokinins in Plant Biology</i>, vol. 1569, Springer, 2017, pp. 1–29, doi:<a href=\"https://doi.org/10.1007/978-1-4939-6831-2_1\">10.1007/978-1-4939-6831-2_1</a>.","apa":"Hurny, A., &#38; Benková, E. (2017). Methodological advances in auxin and cytokinin biology. <i>Auxins and Cytokinins in Plant Biology</i>. Springer. <a href=\"https://doi.org/10.1007/978-1-4939-6831-2_1\">https://doi.org/10.1007/978-1-4939-6831-2_1</a>","short":"A. Hurny, E. Benková, Auxins and Cytokinins in Plant Biology 1569 (2017) 1–29.","ieee":"A. Hurny and E. Benková, “Methodological advances in auxin and cytokinin biology,” <i>Auxins and Cytokinins in Plant Biology</i>, vol. 1569. Springer, pp. 1–29, 2017.","ista":"Hurny A, Benková E. 2017. Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. 1569, 1–29.","ama":"Hurny A, Benková E. Methodological advances in auxin and cytokinin biology. <i>Auxins and Cytokinins in Plant Biology</i>. 2017;1569:1-29. doi:<a href=\"https://doi.org/10.1007/978-1-4939-6831-2_1\">10.1007/978-1-4939-6831-2_1</a>"},"year":"2017","publication":"Auxins and Cytokinins in Plant Biology","date_created":"2018-12-11T11:49:45Z","publication_status":"published","intvolume":"      1569","file_date_updated":"2019-10-15T07:47:05Z","author":[{"orcid":"0000-0003-3638-1426","full_name":"Hurny, Andrej","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","last_name":"Hurny","first_name":"Andrej"},{"first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"}],"date_updated":"2026-11-09T23:30:54Z","publist_id":"6369","scopus_import":"1","pubrep_id":"1019","quality_controlled":"1","status":"public","type":"journal_article","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"539"}]},"abstract":[{"text":"The history of auxin and cytokinin biology including the initial discoveries by father–son duo Charles Darwin and Francis Darwin (1880), and Gottlieb Haberlandt (1919) is a beautiful demonstration of unceasing continuity of research. Novel findings are integrated into existing hypotheses and models and deepen our understanding of biological principles. At the same time new questions are triggered and hand to hand with this new methodologies are developed to address these new challenges.","lang":"eng"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","alternative_title":["Methods in Molecular Biology"],"has_accepted_license":"1","volume":1569,"file":[{"date_updated":"2019-10-15T07:47:05Z","relation":"main_file","access_level":"open_access","file_size":840646,"file_name":"IST-2018-1019-v1+1_Hurny_MethodsMolBiol_2017.pdf","creator":"system","content_type":"application/pdf","file_id":"5068","date_created":"2018-12-12T10:14:18Z"}],"oa":1,"project":[{"_id":"2542D156-B435-11E9-9278-68D0E5697425","grant_number":"I 1774-B16","name":"Hormone cross-talk drives nutrient dependent plant development","call_identifier":"FWF"}],"doi":"10.1007/978-1-4939-6831-2_1","corr_author":"1","day":"17","publication_identifier":{"issn":["1064-3745"]},"page":"1 - 29","department":[{"_id":"EvBe"}],"fulldoi":"https://doi.org/10.1007/978-1-4939-6831-2_1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1024","title":"Methodological advances in auxin and cytokinin biology"},{"alternative_title":["Methods in Molecular Biology"],"article_processing_charge":"No","volume":1056,"doi":"10.1007/978-1-62703-592-7_23","publication_identifier":{"issn":["1064-3745"]},"page":"255 - 264","day":"01","department":[{"_id":"JiFr"}],"series_title":"Methods in Molecular Biology","fulldoi":"https://doi.org/10.1007/978-1-62703-592-7_23","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2245","title":"Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters","publisher":"Springer","month":"01","date_published":"2014-01-01T00:00:00Z","editor":[{"first_name":"Glenn","last_name":"Hicks","full_name":"Hicks, Glenn"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"}],"citation":{"mla":"Simon, Sibu, et al. “Analyzing the in Vivo Status of Exogenously Applied Auxins: A HPLC-Based Method to Characterize the Intracellularly Localized Auxin Transporters.” <i>Plant Chemical Genomics</i>, edited by Glenn Hicks and Stéphanie Robert, vol. 1056, Springer, 2014, pp. 255–64, doi:<a href=\"https://doi.org/10.1007/978-1-62703-592-7_23\">10.1007/978-1-62703-592-7_23</a>.","chicago":"Simon, Sibu, Petr Skůpa, Petre Dobrev, Jan Petrášek, Eva Zažímalová, and Jiří Friml. “Analyzing the in Vivo Status of Exogenously Applied Auxins: A HPLC-Based Method to Characterize the Intracellularly Localized Auxin Transporters.” In <i>Plant Chemical Genomics</i>, edited by Glenn Hicks and Stéphanie Robert, 1056:255–64. Methods in Molecular Biology. Springer, 2014. <a href=\"https://doi.org/10.1007/978-1-62703-592-7_23\">https://doi.org/10.1007/978-1-62703-592-7_23</a>.","apa":"Simon, S., Skůpa, P., Dobrev, P., Petrášek, J., Zažímalová, E., &#38; Friml, J. (2014). Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters. In G. Hicks &#38; S. Robert (Eds.), <i>Plant Chemical Genomics</i> (Vol. 1056, pp. 255–264). Springer. <a href=\"https://doi.org/10.1007/978-1-62703-592-7_23\">https://doi.org/10.1007/978-1-62703-592-7_23</a>","short":"S. Simon, P. Skůpa, P. Dobrev, J. Petrášek, E. Zažímalová, J. Friml, in:, G. Hicks, S. Robert (Eds.), Plant Chemical Genomics, Springer, 2014, pp. 255–264.","ista":"Simon S, Skůpa P, Dobrev P, Petrášek J, Zažímalová E, Friml J. 2014.Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters. In: Plant Chemical Genomics. Methods in Molecular Biology, vol. 1056, 255–264.","ieee":"S. Simon, P. Skůpa, P. Dobrev, J. Petrášek, E. Zažímalová, and J. Friml, “Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters,” in <i>Plant Chemical Genomics</i>, vol. 1056, G. Hicks and S. Robert, Eds. Springer, 2014, pp. 255–264.","ama":"Simon S, Skůpa P, Dobrev P, Petrášek J, Zažímalová E, Friml J. Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters. In: Hicks G, Robert S, eds. <i>Plant Chemical Genomics</i>. Vol 1056. Methods in Molecular Biology. Springer; 2014:255-264. doi:<a href=\"https://doi.org/10.1007/978-1-62703-592-7_23\">10.1007/978-1-62703-592-7_23</a>"},"oa_version":"None","publication_status":"published","date_created":"2018-12-11T11:56:32Z","publication":"Plant Chemical Genomics","year":"2014","intvolume":"      1056","author":[{"full_name":"Simon, Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","last_name":"Simon","first_name":"Sibu","orcid":"0000-0002-1998-6741"},{"first_name":"Petr","last_name":"Skůpa","full_name":"Skůpa, Petr"},{"last_name":"Dobrev","first_name":"Petre","full_name":"Dobrev, Petre"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"first_name":"Eva","last_name":"Zažímalová","full_name":"Zažímalová, Eva"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"}],"scopus_import":"1","date_updated":"2025-07-10T11:52:16Z","publist_id":"4704","status":"public","quality_controlled":"1","type":"book_chapter","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Exogenous application of biologically important molecules for plant growth promotion and/or regulation is very common both in plant research and horticulture. Plant hormones such as auxins and cytokinins are classes of compounds which are often applied exogenously. Nevertheless, plants possess a well-established machinery to regulate the active pool of exogenously applied compounds by converting them to metabolites and conjugates. Consequently, it is often very useful to know the in vivo status of applied compounds to connect them with some of the regulatory events in plant developmental processes. The in vivo status of applied compounds can be measured by incubating plants with radiolabeled compounds, followed by extraction, purification, and HPLC metabolic profiling of plant extracts. Recently we have used this method to characterize the intracellularly localized PIN protein, PIN5. Here we explain the method in detail, with a focus on general application. "}]},{"date_updated":"2026-04-16T10:31:19Z","author":[{"orcid":"0000-0002-5920-9090","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","full_name":"Smutny, Michael","first_name":"Michael","last_name":"Smutny"},{"full_name":"Behrndt, Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","last_name":"Behrndt","first_name":"Martin"},{"orcid":"0000-0002-8526-5416","last_name":"Campinho","first_name":"Pedro","full_name":"Campinho, Pedro","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4088-8633","full_name":"Ruprecht, Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","last_name":"Ruprecht","first_name":"Verena"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"language":[{"iso":"eng"}],"abstract":[{"text":"Mechanically coupled cells can generate forces driving cell and tissue morphogenesis during development. Visualization and measuring of these forces is of major importance to better understand the complexity of the biomechanic processes that shape cells and tissues. Here, we describe how UV laser ablation can be utilized to quantitatively assess mechanical tension in different tissues of the developing zebrafish and in cultures of primary germ layer progenitor cells ex vivo.","lang":"eng"}],"type":"book_chapter","quality_controlled":"1","status":"public","oa_version":"None","citation":{"apa":"Smutny, M., Behrndt, M., Campinho, P., Ruprecht, V., &#38; Heisenberg, C.-P. J. (2014). UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In C. Nelson (Ed.), <i>Tissue Morphogenesis</i> (Vol. 1189, pp. 219–235). New York: Springer. <a href=\"https://doi.org/10.1007/978-1-4939-1164-6_15\">https://doi.org/10.1007/978-1-4939-1164-6_15</a>","chicago":"Smutny, Michael, Martin Behrndt, Pedro Campinho, Verena Ruprecht, and Carl-Philipp J Heisenberg. “UV Laser Ablation to Measure Cell and Tissue-Generated Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” In <i>Tissue Morphogenesis</i>, edited by Celeste Nelson, 1189:219–35. MIMB. New York: Springer, 2014. <a href=\"https://doi.org/10.1007/978-1-4939-1164-6_15\">https://doi.org/10.1007/978-1-4939-1164-6_15</a>.","mla":"Smutny, Michael, et al. “UV Laser Ablation to Measure Cell and Tissue-Generated Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” <i>Tissue Morphogenesis</i>, edited by Celeste Nelson, vol. 1189, Springer, 2014, pp. 219–35, doi:<a href=\"https://doi.org/10.1007/978-1-4939-1164-6_15\">10.1007/978-1-4939-1164-6_15</a>.","short":"M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, C.-P.J. Heisenberg, in:, C. Nelson (Ed.), Tissue Morphogenesis, Springer, New York, 2014, pp. 219–235.","ama":"Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In: Nelson C, ed. <i>Tissue Morphogenesis</i>. Vol 1189. MIMB. New York: Springer; 2014:219-235. doi:<a href=\"https://doi.org/10.1007/978-1-4939-1164-6_15\">10.1007/978-1-4939-1164-6_15</a>","ista":"Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. 2014.UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In: Tissue Morphogenesis. Methods in Molecular Biology, vol. 1189, 219–235.","ieee":"M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, and C.-P. J. Heisenberg, “UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo,” in <i>Tissue Morphogenesis</i>, vol. 1189, C. Nelson, Ed. New York: Springer, 2014, pp. 219–235."},"editor":[{"first_name":"Celeste","last_name":"Nelson","full_name":"Nelson, Celeste"}],"date_published":"2014-08-22T00:00:00Z","pmid":1,"publisher":"Springer","month":"08","intvolume":"      1189","publication_status":"published","date_created":"2019-03-26T08:55:59Z","year":"2014","publication":"Tissue Morphogenesis","series_title":"MIMB","fulldoi":"https://doi.org/10.1007/978-1-4939-1164-6_15","department":[{"_id":"CaHe"}],"day":"22","page":"219-235","publication_identifier":{"isbn":["9781493911639"],"eisbn":["9781493911646"],"issn":["1064-3745"],"eissn":["1940-6029"]},"title":"UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo","_id":"6178","place":"New York","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","volume":1189,"article_processing_charge":"No","alternative_title":["Methods in Molecular Biology"],"external_id":{"pmid":["25245697"]},"corr_author":"1","doi":"10.1007/978-1-4939-1164-6_15"},{"publication_status":"published","year":"2013","publication":"Chemokines","date_created":"2022-03-21T07:47:41Z","intvolume":"      1013","acknowledgement":"We would like to thank Alexander Eichner and Ingrid de Vries for discussion and critical reading of the manuscript, and Mary Frank for assistance with the recording of videos and images in Fig. 1. M.S. is supported through funding from the German Research Foundation (DFG). M.W. acknowledges the Alexander von Humboldt Foundation for funding.","publisher":"Humana Press","month":"04","date_published":"2013-04-03T00:00:00Z","pmid":1,"editor":[{"full_name":"Cardona, Astrid","first_name":"Astrid","last_name":"Cardona"},{"first_name":"Eroboghene","last_name":"Ubogu","full_name":"Ubogu, Eroboghene"}],"citation":{"ama":"Weber M, Sixt MK. Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In: Cardona A, Ubogu E, eds. <i>Chemokines</i>. Vol 1013. MIMB. Totowa, NJ: Humana Press; 2013:215-226. doi:<a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">10.1007/978-1-62703-426-5_14</a>","ista":"Weber M, Sixt MK. 2013.Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In: Chemokines. Methods in Molecular Biology, vol. 1013, 215–226.","ieee":"M. Weber and M. K. Sixt, “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations,” in <i>Chemokines</i>, vol. 1013, A. Cardona and E. Ubogu, Eds. Totowa, NJ: Humana Press, 2013, pp. 215–226.","apa":"Weber, M., &#38; Sixt, M. K. (2013). Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In A. Cardona &#38; E. Ubogu (Eds.), <i>Chemokines</i> (Vol. 1013, pp. 215–226). Totowa, NJ: Humana Press. <a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">https://doi.org/10.1007/978-1-62703-426-5_14</a>","chicago":"Weber, Michele, and Michael K Sixt. “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations.” In <i>Chemokines</i>, edited by Astrid Cardona and Eroboghene Ubogu, 1013:215–26. MIMB. Totowa, NJ: Humana Press, 2013. <a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">https://doi.org/10.1007/978-1-62703-426-5_14</a>.","mla":"Weber, Michele, and Michael K. Sixt. “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations.” <i>Chemokines</i>, edited by Astrid Cardona and Eroboghene Ubogu, vol. 1013, Humana Press, 2013, pp. 215–26, doi:<a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">10.1007/978-1-62703-426-5_14</a>.","short":"M. Weber, M.K. Sixt, in:, A. Cardona, E. Ubogu (Eds.), Chemokines, Humana Press, Totowa, NJ, 2013, pp. 215–226."},"oa_version":"None","status":"public","quality_controlled":"1","type":"book_chapter","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Leukocyte migration through the interstitial space is crucial for the maintenance of tolerance and immunity. The main cues for leukocyte trafficking are chemokines thought to directionally guide these cells towards their targets. However, model systems that facilitate quantification of chemokine-guided leukocyte migration in vivo are uncommon. Here we describe an ex vivo crawl-in assay using explanted mouse ears that allows the visualization of chemokine-dependent dendritic cell (DC) motility in the dermal interstitium in real time. We present methods for the preparation of mouse ear sheets and their use in multidimensional confocal imaging experiments to monitor and analyze the directional migration of fluorescently labelled DCs through the dermis and into afferent lymphatic vessels. The assay provides a more physiological approach to study leukocyte migration than in vitro three-dimensional (3D) or 2-dimensional (2D) migration assays such as collagen gels and transwell assays."}],"author":[{"first_name":"Michele","last_name":"Weber","id":"3A3FC708-F248-11E8-B48F-1D18A9856A87","full_name":"Weber, Michele"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179"}],"scopus_import":"1","date_updated":"2024-10-09T21:02:37Z","doi":"10.1007/978-1-62703-426-5_14","corr_author":"1","external_id":{"pmid":["23625502"]},"article_processing_charge":"No","alternative_title":["Methods in Molecular Biology"],"volume":1013,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10900","place":"Totowa, NJ","title":"Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations","publication_identifier":{"isbn":["9781627034258"],"eisbn":["9781627034265"],"issn":["1064-3745"],"eissn":["1940-6029"]},"page":"215-226","day":"03","department":[{"_id":"MiSi"}],"fulldoi":"https://doi.org/10.1007/978-1-62703-426-5_14","series_title":"MIMB"}]