[{"intvolume":"      2886","external_id":{"pmid":["39745639"]},"scopus_import":"1","abstract":[{"lang":"eng","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."}],"volume":2886,"date_created":"2025-01-07T08:36:47Z","pmid":1,"oa_version":"None","OA_type":"closed access","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"day":"03","acknowledged_ssus":[{"_id":"Bio"}],"doi":"10.1007/978-1-0716-4310-5_7","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"SiHi"}],"status":"public","publication_status":"published","publication_identifier":{"eisbn":["9781071643105"],"issn":["1064-3745"],"isbn":["9781071643099"],"eissn":["1940-6029"]},"quality_controlled":"1","article_processing_charge":"No","publication":"Lineage Tracing","type":"book_chapter","place":"New York, NY","date_published":"2025-01-03T00:00:00Z","title":"Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM)","alternative_title":["Methods in Molecular Biology"],"author":[{"last_name":"Cheung","first_name":"Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87","full_name":"Cheung, Giselle T","orcid":"0000-0001-8457-2572"},{"last_name":"Pauler","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061"}],"series_title":"MIMB","ec_funded":1,"editor":[{"full_name":"Garcia-Marques, Jorge","last_name":"Garcia-Marques","first_name":"Jorge"},{"first_name":"Tzumin","last_name":"Lee","full_name":"Lee, Tzumin"}],"month":"01","_id":"18765","page":"139-151","date_updated":"2025-04-14T07:43:46Z","citation":{"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.","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.","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>.","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>","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.","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>."},"publisher":"Springer Nature","corr_author":"1","language":[{"iso":"eng"}],"year":"2025","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."},{"doi":"10.1007/978-1-0716-3778-4_21","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"}],"day":"25","publication_status":"published","status":"public","intvolume":"      2787","scopus_import":"1","external_id":{"pmid":["38656499"]},"volume":2787,"date_created":"2024-05-05T22:01:04Z","abstract":[{"text":"Bimolecular fluorescence complementation (BiFC) is a powerful tool for studying protein-protein interactions in living cells. By fusing interacting proteins to fluorescent protein fragments, BiFC allows visualization of spatial localization patterns of protein complexes. This method has been adapted to a variety of expression systems in different organisms and is widely used to study protein interactions in plant cells. The Agrobacterium-mediated transient expression protocol for BiFC assays in Nicotiana benthamiana (N. benthamiana) leaf cells is widely used, but in this chapter, a method for BiFC assay using Arabidopsis thaliana protoplasts is presented.","lang":"eng"}],"pmid":1,"oa_version":"None","editor":[{"last_name":"Maghuly","first_name":"Fatemeh","full_name":"Maghuly, Fatemeh"}],"publisher":"Springer Nature","language":[{"iso":"eng"}],"month":"04","_id":"15361","date_updated":"2024-05-06T06:39:10Z","page":"305-313","citation":{"mla":"Jayasree, Aswathy, et al. “Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis Thaliana Protoplasts from Leaf.” <i>Plant Functional Genomics</i>, edited by Fatemeh Maghuly, vol. 2787, Springer Nature, 2024, pp. 305–13, doi:<a href=\"https://doi.org/10.1007/978-1-0716-3778-4_21\">10.1007/978-1-0716-3778-4_21</a>.","ama":"Jayasree A, Salava H, Nodzynski T, Sravankumar T. Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf. In: Maghuly F, ed. <i>Plant Functional Genomics</i>. Vol 2787. MIMB. Springer Nature; 2024:305-313. doi:<a href=\"https://doi.org/10.1007/978-1-0716-3778-4_21\">10.1007/978-1-0716-3778-4_21</a>","ieee":"A. Jayasree, H. Salava, T. Nodzynski, and T. Sravankumar, “Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf,” in <i>Plant Functional Genomics</i>, vol. 2787, F. Maghuly, Ed. Springer Nature, 2024, pp. 305–313.","short":"A. Jayasree, H. Salava, T. Nodzynski, T. Sravankumar, in:, F. Maghuly (Ed.), Plant Functional Genomics, Springer Nature, 2024, pp. 305–313.","apa":"Jayasree, A., Salava, H., Nodzynski, T., &#38; Sravankumar, T. (2024). Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf. In F. Maghuly (Ed.), <i>Plant Functional Genomics</i> (Vol. 2787, pp. 305–313). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-3778-4_21\">https://doi.org/10.1007/978-1-0716-3778-4_21</a>","ista":"Jayasree A, Salava H, Nodzynski T, Sravankumar T. 2024.Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf. In: Plant Functional Genomics. Methods in Molecular Biology, vol. 2787, 305–313.","chicago":"Jayasree, Aswathy, Hymavathi Salava, Tomasz Nodzynski, and Thula Sravankumar. “Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis Thaliana Protoplasts from Leaf.” In <i>Plant Functional Genomics</i>, edited by Fatemeh Maghuly, 2787:305–13. MIMB. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-1-0716-3778-4_21\">https://doi.org/10.1007/978-1-0716-3778-4_21</a>."},"year":"2024","acknowledgement":"Special thanks to Dr. Marta Zwiewka for the support. Thanks to the Czech Science Foundation GA 20-20860Y for financial aid and support of A.S.S., respectively. Thanks go to Core Facility Cellular Imaging (CELLIM), and Plant Sciences Core Facility of CEITEC Masaryk University is acknowledged for the technical support.","article_processing_charge":"No","publication_identifier":{"isbn":["9781071637777"],"eissn":["1940-6029"]},"quality_controlled":"1","publication":"Plant Functional Genomics","date_published":"2024-04-25T00:00:00Z","type":"book_chapter","alternative_title":["Methods in Molecular Biology"],"title":"Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf","author":[{"full_name":"Jayasree, Aswathy","last_name":"Jayasree","first_name":"Aswathy"},{"full_name":"Salava, Hymavathi","last_name":"Salava","first_name":"Hymavathi"},{"full_name":"Nodzynski, Tomasz","last_name":"Nodzynski","first_name":"Tomasz"},{"full_name":"Sravankumar, Thula","first_name":"Thula","id":"055b7938-0b72-11ef-94eb-d14136011bb5","last_name":"Sravankumar","orcid":"0000-0001-6925-6950"}],"series_title":"MIMB"},{"publication_identifier":{"eissn":["1940-6029"],"issn":["1064-3745"],"eisbn":["9781071639696"],"isbn":["9781071639689"]},"quality_controlled":"1","article_processing_charge":"No","publication":"Neuronal Morphogenesis","type":"book_chapter","place":"New York, NY","date_published":"2024-08-13T00:00:00Z","alternative_title":["Methods in Molecular Biology"],"title":"Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers","series_title":"MIMB","author":[{"last_name":"Miranda","first_name":"Osvaldo","id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","full_name":"Miranda, Osvaldo","orcid":"0000-0001-6618-6889"},{"first_name":"Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87","last_name":"Cheung","full_name":"Cheung, Giselle T","orcid":"0000-0001-8457-2572"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"editor":[{"full_name":"Toyooka, Kazuhito","last_name":"Toyooka","first_name":"Kazuhito"}],"month":"08","citation":{"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>","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.","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.","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>.","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.","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>."},"_id":"17425","page":"283-299","date_updated":"2026-04-07T12:32:35Z","publisher":"Springer Nature","corr_author":"1","language":[{"iso":"eng"}],"year":"2024","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","external_id":{"pmid":["39134857"]},"scopus_import":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"20212"}]},"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"}],"date_created":"2024-08-13T12:16:41Z","volume":2831,"pmid":1,"oa_version":"None","project":[{"name":"Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development","grant_number":"26253","_id":"34c9fbcb-11ca-11ed-8bc3-98fa5658610d"},{"grant_number":"F7805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression"}],"day":"13","acknowledged_ssus":[{"_id":"Bio"}],"doi":"10.1007/978-1-0716-3969-6_19","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","edition":"1"},{"month":"01","_id":"12428","page":"183-205","date_updated":"2024-10-09T21:04:04Z","citation":{"chicago":"Hannezo, Edouard B, and Colinda L.G.J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” In <i>Cell Migration in Three Dimensions</i>, edited by Coert Margadant, 2608:183–205. MIMB. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-1-0716-2887-4_12\">https://doi.org/10.1007/978-1-0716-2887-4_12</a>.","ama":"Hannezo EB, Scheele CLGJ. A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Margadant C, ed. <i>Cell Migration in Three Dimensions</i>. Vol 2608. MIMB. Springer Nature; 2023:183-205. doi:<a href=\"https://doi.org/10.1007/978-1-0716-2887-4_12\">10.1007/978-1-0716-2887-4_12</a>","mla":"Hannezo, Edouard B., and Colinda L. G. J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” <i>Cell Migration in Three Dimensions</i>, edited by Coert Margadant, vol. 2608, Springer Nature, 2023, pp. 183–205, doi:<a href=\"https://doi.org/10.1007/978-1-0716-2887-4_12\">10.1007/978-1-0716-2887-4_12</a>.","ieee":"E. B. Hannezo and C. L. G. J. Scheele, “A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland,” in <i>Cell Migration in Three Dimensions</i>, vol. 2608, C. Margadant, Ed. Springer Nature, 2023, pp. 183–205.","short":"E.B. Hannezo, C.L.G.J. Scheele, in:, C. Margadant (Ed.), Cell Migration in Three Dimensions, Springer Nature, 2023, pp. 183–205.","apa":"Hannezo, E. B., &#38; Scheele, C. L. G. J. (2023). A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In C. Margadant (Ed.), <i>Cell Migration in Three Dimensions</i> (Vol. 2608, pp. 183–205). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-2887-4_12\">https://doi.org/10.1007/978-1-0716-2887-4_12</a>","ista":"Hannezo EB, Scheele CLGJ. 2023.A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Cell Migration in Three Dimensions. Methods in Molecular Biology, vol. 2608, 183–205."},"publisher":"Springer Nature","corr_author":"1","language":[{"iso":"eng"}],"editor":[{"last_name":"Margadant","first_name":"Coert","full_name":"Margadant, Coert"}],"file":[{"date_created":"2023-02-03T10:56:39Z","file_size":826598,"checksum":"aec1b8d3ba938ddf9d8fcb777f3c38ee","file_name":"2023_MIMB_Hannezo.pdf","creator":"dernst","file_id":"12500","relation":"main_file","content_type":"application/pdf","success":1,"access_level":"open_access","date_updated":"2023-02-03T10:56:39Z"}],"year":"2023","ddc":["570"],"publication":"Cell Migration in Three Dimensions","publication_identifier":{"eissn":["1940-6029"],"isbn":["9781071628867"],"eisbn":["9781071628874"]},"quality_controlled":"1","article_processing_charge":"No","alternative_title":["Methods in Molecular Biology"],"title":"A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland","series_title":"MIMB","author":[{"last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"first_name":"Colinda L.G.J.","last_name":"Scheele","full_name":"Scheele, Colinda L.G.J."}],"has_accepted_license":"1","type":"book_chapter","date_published":"2023-01-19T00:00:00Z","status":"public","publication_status":"published","day":"19","doi":"10.1007/978-1-0716-2887-4_12","department":[{"_id":"EdHa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"file_date_updated":"2023-02-03T10:56:39Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"pmid":["36653709"]},"scopus_import":"1","intvolume":"      2608","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The mammary gland consists of a bilayered epithelial structure with an extensively branched morphology. The majority of this epithelial tree is laid down during puberty, during which actively proliferating terminal end buds repeatedly elongate and bifurcate to form the basic structure of the ductal tree. Mammary ducts consist of a basal and luminal cell layer with a multitude of identified sub-lineages within both layers. The understanding of how these different cell lineages are cooperatively driving branching morphogenesis is a problem of crossing multiple scales, as this requires information on the macroscopic branched structure of the gland, as well as data on single-cell dynamics driving the morphogenic program. Here we describe a method to combine genetic lineage tracing with whole-gland branching analysis. Quantitative data on the global organ structure can be used to derive a model for mammary gland branching morphogenesis and provide a backbone on which the dynamics of individual cell lineages can be simulated and compared to lineage-tracing approaches. Eventually, these quantitative models and experiments allow to understand the couplings between the macroscopic shape of the mammary gland and the underlying single-cell dynamics driving branching morphogenesis."}],"volume":2608,"date_created":"2023-01-29T23:00:58Z"},{"date_published":"2023-03-01T00:00:00Z","place":"New York, NY, United States","type":"book_chapter","series_title":"MIMB","author":[{"full_name":"Arroyo-Urea, Sandra","first_name":"Sandra","last_name":"Arroyo-Urea"},{"orcid":"0000-0002-8698-3823","full_name":"Watson, Jake","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake"},{"last_name":"García-Nafría","first_name":"Javier","full_name":"García-Nafría, Javier"}],"title":"Molecular Cloning Using In Vivo DNA Assembly","alternative_title":["Methods in Molecular Biology"],"article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"eissn":["1940-6029"],"eisbn":["978-1-0716-3004-4"],"issn":["1064-3745"],"isbn":["978-1-0716-3003-7"]},"publication":"DNA Manipulation and Analysis","year":"2023","OA_place":"repository","editor":[{"first_name":"Garry","last_name":"Scarlett","full_name":"Scarlett, Garry"}],"language":[{"iso":"eng"}],"publisher":"Springer Nature","date_updated":"2025-06-25T05:56:45Z","_id":"12720","page":"33-44","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.","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>","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>.","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.","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.","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>","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>."},"month":"03","volume":2633,"date_created":"2023-03-12T23:01:02Z","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"}],"OA_type":"green","oa_version":"Submitted Version","pmid":1,"intvolume":"      2633","scopus_import":"1","external_id":{"pmid":["36853454"]},"main_file_link":[{"url":"https://zaguan.unizar.es/record/125930/files/texto_completo.pdf","open_access":"1"}],"oa":1,"department":[{"_id":"PeJo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-1-0716-3004-4_3","day":"01","publication_status":"published","status":"public"},{"abstract":[{"lang":"eng","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."}],"volume":2654,"date_created":"2023-05-22T08:41:48Z","pmid":1,"oa_version":"None","intvolume":"      2654","external_id":{"pmid":["37106180"]},"scopus_import":"1","day":"28","project":[{"call_identifier":"H2020","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular Navigation Along Spatial Gradients"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"doi":"10.1007/978-1-0716-3135-5_9","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"status":"public","publication_status":"published","type":"book_chapter","place":"New York, NY","date_published":"2023-04-28T00:00:00Z","title":"En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses","alternative_title":["Methods in Molecular Biology"],"author":[{"last_name":"Leithner","first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X"},{"last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"series_title":"MIMB","ec_funded":1,"publication_identifier":{"isbn":["9781071631348"],"eisbn":["9781071631355"],"issn":["1064-3745"],"eissn":["1940-6029"]},"quality_controlled":"1","article_processing_charge":"No","publication":"The Immune Synapse","year":"2023","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.","editor":[{"full_name":"Baldari, Cosima","first_name":"Cosima","last_name":"Baldari"},{"full_name":"Dustin, Michael","last_name":"Dustin","first_name":"Michael"}],"month":"04","date_updated":"2025-04-14T07:42:07Z","_id":"13052","page":"137-147","citation":{"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.","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>","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.","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.","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>.","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>","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>."},"publisher":"Springer Nature","language":[{"iso":"eng"}]},{"intvolume":"      2382","external_id":{"pmid":["34705235"]},"scopus_import":"1","abstract":[{"lang":"eng","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."}],"date_created":"2021-11-11T10:03:30Z","volume":2382,"pmid":1,"oa_version":"None","day":"28","acknowledged_ssus":[{"_id":"Bio"}],"doi":"10.1007/978-1-0716-1744-1_6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"}],"status":"public","publication_status":"published","publication_identifier":{"eissn":["1940-6029"],"eisbn":["978-1-0716-1744-1"],"issn":["1064-3745"],"isbn":["978-1-0716-1743-4"]},"quality_controlled":"1","article_processing_charge":"No","publication":"Plant Cell Division","type":"book_chapter","date_published":"2021-10-28T00:00:00Z","title":"Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy","alternative_title":["Methods in Molecular Biology"],"series_title":"MIMB","author":[{"full_name":"Hörmayer, Lukas","first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Hörmayer"},{"last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"orcid":"0000-0003-0619-7783","first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","full_name":"Glanc, Matous"}],"month":"10","_id":"10268","citation":{"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>.","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.","short":"L. Hörmayer, J. Friml, M. Glanc, in:, Plant Cell Division, Humana Press, 2021, pp. 105–114.","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>","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.","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>","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>."},"page":"105-114","date_updated":"2022-06-03T06:47:06Z","publisher":"Humana Press","language":[{"iso":"eng"}],"year":"2021","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."},{"editor":[{"first_name":"Roland","last_name":"Dosch","full_name":"Dosch, Roland"}],"month":"02","date_updated":"2025-04-14T07:46:58Z","_id":"9245","citation":{"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, 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>.","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; 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>","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, 2021, pp. 117–128.","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. <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, 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.","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, 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>."},"page":"117-128","publisher":"Humana","corr_author":"1","language":[{"iso":"eng"}],"year":"2021","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.).","publication_identifier":{"eissn":["1940-6029"],"eisbn":["978-1-0716-0970-5"],"issn":["1064-3745"],"isbn":["978-1-0716-0969-9"]},"quality_controlled":"1","article_processing_charge":"No","publication":"Germline Development in the Zebrafish","type":"book_chapter","date_published":"2021-02-20T00:00:00Z","title":"Quantifying tissue tension in the granulosa layer after laser surgery","alternative_title":["Methods in Molecular Biology"],"author":[{"full_name":"Xia, Peng","last_name":"Xia","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","first_name":"Peng","orcid":"0000-0002-5419-7756"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"ec_funded":1,"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"day":"20","doi":"10.1007/978-1-0716-0970-5_10","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"CaHe"}],"status":"public","publication_status":"published","keyword":["Tissue tension","Morphogenesis","Laser ablation","Zebrafish folliculogenesis","Granulosa cells"],"intvolume":"      2218","external_id":{"pmid":["33606227"]},"scopus_import":"1","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."}],"date_created":"2021-03-14T23:01:34Z","volume":2218,"pmid":1,"oa_version":"None"},{"publication_status":"published","status":"public","doi":"10.1007/978-1-0716-0755-8_16","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"CaGu"}],"day":"11","scopus_import":"1","external_id":{"pmid":["32651922"]},"intvolume":"      2173","pmid":1,"oa_version":"None","date_created":"2020-07-26T22:01:03Z","volume":2173,"abstract":[{"lang":"eng","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."}],"publisher":"Springer Nature","language":[{"iso":"eng"}],"month":"07","date_updated":"2026-04-16T09:22:45Z","_id":"8173","citation":{"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>.","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>","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.","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>","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>.","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."},"page":"233-246","editor":[{"last_name":"Niopek","first_name":"Dominik","full_name":"Niopek, Dominik"}],"year":"2020","publication":"Photoswitching Proteins","article_processing_charge":"No","publication_identifier":{"isbn":["9781071607541"],"issn":["1064-3745"],"eisbn":["9781071607558"],"eissn":["1940-6029"]},"alternative_title":["Methods in Molecular Biology"],"title":"Design and application of light-regulated receptor tyrosine kinases","series_title":"MIMB","author":[{"orcid":"0000-0002-6709-2195","full_name":"Kainrath, Stephanie","last_name":"Kainrath","first_name":"Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8023-9315","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","full_name":"Janovjak, Harald L"}],"date_published":"2020-07-11T00:00:00Z","type":"book_chapter"},{"publication":"Protein-Protein Interaction Networks","publication_identifier":{"eissn":["1940-6029"],"issn":["1064-3745"],"eisbn":["9781493998739"],"isbn":["9781493998722"]},"quality_controlled":"1","article_processing_charge":"No","alternative_title":["Methods in Molecular Biology"],"title":"Vienna Graph Clustering","series_title":"MIMB","author":[{"last_name":"Biedermann","first_name":"Sonja","full_name":"Biedermann, Sonja"},{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger"},{"first_name":"Christian","last_name":"Schulz","full_name":"Schulz, Christian"},{"first_name":"Bernhard","last_name":"Schuster","full_name":"Schuster, Bernhard"}],"type":"book_chapter","date_published":"2019-10-04T00:00:00Z","month":"10","date_updated":"2024-11-06T12:17:08Z","_id":"11847","page":"215–231","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.","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>.","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.","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.","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>","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>."},"publisher":"Springer Nature","language":[{"iso":"eng"}],"editor":[{"first_name":"Stefan","last_name":"Canzar","full_name":"Canzar, Stefan"},{"full_name":"Rojas Ringeling, Francisca","last_name":"Rojas Ringeling","first_name":"Francisca"}],"year":"2019","external_id":{"pmid":["31583641"]},"scopus_import":"1","intvolume":"      2074","pmid":1,"oa_version":"None","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"}],"volume":2074,"date_created":"2022-08-16T06:54:48Z","status":"public","publication_status":"published","day":"04","doi":"10.1007/978-1-4939-9873-9_16","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1"},{"author":[{"full_name":"Smutny, Michael","last_name":"Smutny","first_name":"Michael","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5920-9090"},{"full_name":"Behrndt, Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Behrndt"},{"full_name":"Campinho, Pedro","last_name":"Campinho","first_name":"Pedro","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8526-5416"},{"orcid":"0000-0003-4088-8633","full_name":"Ruprecht, Verena","last_name":"Ruprecht","first_name":"Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"series_title":"MIMB","alternative_title":["Methods in Molecular Biology"],"title":"UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo","place":"New York","type":"book_chapter","date_published":"2014-08-22T00:00:00Z","publication":"Tissue Morphogenesis","quality_controlled":"1","publication_identifier":{"isbn":["9781493911639"],"issn":["1064-3745"],"eisbn":["9781493911646"],"eissn":["1940-6029"]},"article_processing_charge":"No","year":"2014","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>","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.","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.","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>.","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>","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.","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>."},"_id":"6178","page":"219-235","date_updated":"2026-04-16T10:31:19Z","month":"08","language":[{"iso":"eng"}],"corr_author":"1","publisher":"Springer","editor":[{"first_name":"Celeste","last_name":"Nelson","full_name":"Nelson, Celeste"}],"oa_version":"None","pmid":1,"abstract":[{"lang":"eng","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."}],"volume":1189,"date_created":"2019-03-26T08:55:59Z","external_id":{"pmid":["25245697"]},"intvolume":"      1189","status":"public","publication_status":"published","day":"22","department":[{"_id":"CaHe"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.1007/978-1-4939-1164-6_15"},{"day":"03","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"MiSi"}],"doi":"10.1007/978-1-62703-426-5_14","status":"public","publication_status":"published","intvolume":"      1013","external_id":{"pmid":["23625502"]},"scopus_import":"1","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."}],"volume":1013,"date_created":"2022-03-21T07:47:41Z","oa_version":"None","pmid":1,"editor":[{"full_name":"Cardona, Astrid","last_name":"Cardona","first_name":"Astrid"},{"last_name":"Ubogu","first_name":"Eroboghene","full_name":"Ubogu, Eroboghene"}],"_id":"10900","page":"215-226","date_updated":"2024-10-09T21:02:37Z","citation":{"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>.","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.","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>.","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.","short":"M. Weber, M.K. Sixt, in:, A. Cardona, E. Ubogu (Eds.), Chemokines, Humana Press, Totowa, NJ, 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>"},"month":"04","language":[{"iso":"eng"}],"publisher":"Humana Press","corr_author":"1","year":"2013","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.","quality_controlled":"1","publication_identifier":{"isbn":["9781627034258"],"eisbn":["9781627034265"],"issn":["1064-3745"],"eissn":["1940-6029"]},"article_processing_charge":"No","publication":"Chemokines","place":"Totowa, NJ","type":"book_chapter","date_published":"2013-04-03T00:00:00Z","series_title":"MIMB","author":[{"full_name":"Weber, Michele","first_name":"Michele","id":"3A3FC708-F248-11E8-B48F-1D18A9856A87","last_name":"Weber"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt"}],"alternative_title":["Methods in Molecular Biology"],"title":"Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations"}]