[{"author":[{"last_name":"Arroyo-Urea","full_name":"Arroyo-Urea, Sandra","first_name":"Sandra"},{"full_name":"Watson, Jake","orcid":"0000-0002-8698-3823","last_name":"Watson","first_name":"Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"first_name":"Javier","full_name":"García-Nafría, Javier","last_name":"García-Nafría"}],"external_id":{"pmid":["36853454"]},"article_processing_charge":"No","editor":[{"first_name":"Garry","full_name":"Scarlett, Garry","last_name":"Scarlett"}],"title":"Molecular Cloning Using In Vivo DNA Assembly","citation":{"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.","ieee":"S. Arroyo-Urea, J. Watson, and J. García-Nafría, “Molecular Cloning Using In Vivo DNA Assembly,” in DNA Manipulation and Analysis, vol. 2633, G. Scarlett, Ed. New York, NY, United States: Springer Nature, 2023, pp. 33–44.","apa":"Arroyo-Urea, S., Watson, J., & García-Nafría, J. (2023). Molecular Cloning Using In Vivo DNA Assembly. In G. Scarlett (Ed.), DNA Manipulation and Analysis (Vol. 2633, pp. 33–44). New York, NY, United States: Springer Nature. https://doi.org/10.1007/978-1-0716-3004-4_3","ama":"Arroyo-Urea S, Watson J, García-Nafría J. Molecular Cloning Using In Vivo DNA Assembly. In: Scarlett G, ed. DNA Manipulation and Analysis. Vol 2633. MIMB. New York, NY, United States: Springer Nature; 2023:33-44. doi:10.1007/978-1-0716-3004-4_3","mla":"Arroyo-Urea, Sandra, et al. “Molecular Cloning Using In Vivo DNA Assembly.” DNA Manipulation and Analysis, edited by Garry Scarlett, vol. 2633, Springer Nature, 2023, pp. 33–44, doi:10.1007/978-1-0716-3004-4_3.","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.","chicago":"Arroyo-Urea, Sandra, Jake Watson, and Javier García-Nafría. “Molecular Cloning Using In Vivo DNA Assembly.” In DNA Manipulation and Analysis, edited by Garry Scarlett, 2633:33–44. MIMB. New York, NY, United States: Springer Nature, 2023. https://doi.org/10.1007/978-1-0716-3004-4_3."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"33-44","date_published":"2023-03-01T00:00:00Z","doi":"10.1007/978-1-0716-3004-4_3","date_created":"2023-03-12T23:01:02Z","year":"2023","day":"01","publication":"DNA Manipulation and Analysis","quality_controlled":"1","publisher":"Springer Nature","department":[{"_id":"PeJo"}],"date_updated":"2023-03-16T08:34:24Z","type":"book_chapter","status":"public","_id":"12720","series_title":"MIMB","volume":2633,"publication_identifier":{"eisbn":["978-1-0716-3004-4"],"issn":["1064-3745"],"isbn":["978-1-0716-3003-7"],"eissn":["1940-6029"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","alternative_title":["Methods in Molecular Biology"],"place":"New York, NY, United States","month":"03","intvolume":" 2633","abstract":[{"lang":"eng","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."}],"pmid":1,"oa_version":"None"},{"date_updated":"2023-10-17T08:44:53Z","department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"series_title":"MIMB","_id":"13052","status":"public","type":"book_chapter","language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["9781071631355"],"issn":["1064-3745"],"eissn":["1940-6029"],"isbn":["9781071631348"]},"publication_status":"published","volume":2654,"ec_funded":1,"pmid":1,"oa_version":"None","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."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"place":"New York, NY","month":"04","intvolume":" 2654","alternative_title":["Methods in Molecular Biology"],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"A. F. Leithner, J. Merrin, and M. K. Sixt, “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses,” in The Immune Synapse, vol. 2654, C. Baldari and M. Dustin, Eds. New York, NY: Springer Nature, 2023, pp. 137–147.","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.","apa":"Leithner, A. F., Merrin, J., & Sixt, M. K. (2023). En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses. In C. Baldari & M. Dustin (Eds.), The Immune Synapse (Vol. 2654, pp. 137–147). New York, NY: Springer Nature. https://doi.org/10.1007/978-1-0716-3135-5_9","ama":"Leithner AF, Merrin J, Sixt MK. En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses. In: Baldari C, Dustin M, eds. The Immune Synapse. Vol 2654. MIMB. New York, NY: Springer Nature; 2023:137-147. doi:10.1007/978-1-0716-3135-5_9","mla":"Leithner, Alexander F., et al. “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses.” The Immune Synapse, edited by Cosima Baldari and Michael Dustin, vol. 2654, Springer Nature, 2023, pp. 137–47, doi:10.1007/978-1-0716-3135-5_9.","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.","chicago":"Leithner, Alexander F, Jack Merrin, and Michael K Sixt. “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses.” In The Immune Synapse, edited by Cosima Baldari and Michael Dustin, 2654:137–47. MIMB. New York, NY: Springer Nature, 2023. https://doi.org/10.1007/978-1-0716-3135-5_9."},"title":"En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses","editor":[{"first_name":"Cosima","full_name":"Baldari, Cosima","last_name":"Baldari"},{"last_name":"Dustin","full_name":"Dustin, Michael","first_name":"Michael"}],"author":[{"last_name":"Leithner","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X","first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"external_id":{"pmid":["37106180"]},"article_processing_charge":"No","project":[{"name":"Cellular navigation along spatial gradients","grant_number":"724373","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425"}],"day":"28","publication":"The Immune Synapse","year":"2023","date_published":"2023-04-28T00:00:00Z","doi":"10.1007/978-1-0716-3135-5_9","date_created":"2023-05-22T08:41:48Z","page":"137-147","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.","quality_controlled":"1","publisher":"Springer Nature"},{"article_processing_charge":"No","external_id":{"pmid":["34705235"]},"author":[{"last_name":"Hörmayer","full_name":"Hörmayer, Lukas","first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous","last_name":"Glanc","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783"}],"title":"Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy","citation":{"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.","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 Plant Cell Division, 2382:105–14. MIMB. Humana Press, 2021. https://doi.org/10.1007/978-1-0716-1744-1_6.","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: Plant Cell Division. Vol 2382. MIMB. Humana Press; 2021:105-114. doi:10.1007/978-1-0716-1744-1_6","apa":"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 (Vol. 2382, pp. 105–114). Humana Press. https://doi.org/10.1007/978-1-0716-1744-1_6","short":"L. Hörmayer, J. Friml, M. Glanc, in:, Plant Cell Division, Humana Press, 2021, pp. 105–114.","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 Plant Cell Division, vol. 2382, 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.” Plant Cell Division, vol. 2382, Humana Press, 2021, pp. 105–14, doi:10.1007/978-1-0716-1744-1_6."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Humana Press","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.","page":"105-114","date_created":"2021-11-11T10:03:30Z","date_published":"2021-10-28T00:00:00Z","doi":"10.1007/978-1-0716-1744-1_6","year":"2021","publication":"Plant Cell Division","day":"28","type":"book_chapter","status":"public","_id":"10268","series_title":"MIMB","department":[{"_id":"JiFr"}],"date_updated":"2022-06-03T06:47:06Z","scopus_import":"1","alternative_title":["Methods in Molecular Biology"],"intvolume":" 2382","month":"10","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."}],"acknowledged_ssus":[{"_id":"Bio"}],"oa_version":"None","pmid":1,"volume":2382,"publication_status":"published","publication_identifier":{"eissn":["1940-6029"],"isbn":["978-1-0716-1743-4"],"issn":["1064-3745"],"eisbn":["978-1-0716-1744-1"]},"language":[{"iso":"eng"}]},{"project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","external_id":{"pmid":["33606227"]},"author":[{"last_name":"Xia","full_name":"Xia, Peng","orcid":"0000-0002-5419-7756","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","first_name":"Peng"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"editor":[{"full_name":"Dosch, Roland","last_name":"Dosch","first_name":"Roland"}],"title":"Quantifying tissue tension in the granulosa layer after laser surgery","citation":{"chicago":"Xia, Peng, and Carl-Philipp J Heisenberg. “Quantifying Tissue Tension in the Granulosa Layer after Laser Surgery.” In Germline Development in the Zebrafish, edited by Roland Dosch, 2218:117–28. Humana, 2021. https://doi.org/10.1007/978-1-0716-0970-5_10.","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.","mla":"Xia, Peng, and Carl-Philipp J. Heisenberg. “Quantifying Tissue Tension in the Granulosa Layer after Laser Surgery.” Germline Development in the Zebrafish, edited by Roland Dosch, vol. 2218, Humana, 2021, pp. 117–28, doi:10.1007/978-1-0716-0970-5_10.","apa":"Xia, P., & Heisenberg, C.-P. J. (2021). Quantifying tissue tension in the granulosa layer after laser surgery. In R. Dosch (Ed.), Germline Development in the Zebrafish (Vol. 2218, pp. 117–128). Humana. https://doi.org/10.1007/978-1-0716-0970-5_10","ama":"Xia P, Heisenberg C-PJ. Quantifying tissue tension in the granulosa layer after laser surgery. In: Dosch R, ed. Germline Development in the Zebrafish. Vol 2218. Humana; 2021:117-128. doi:10.1007/978-1-0716-0970-5_10","ieee":"P. Xia and C.-P. J. Heisenberg, “Quantifying tissue tension in the granulosa layer after laser surgery,” in Germline Development in the Zebrafish, vol. 2218, R. Dosch, Ed. Humana, 2021, pp. 117–128.","short":"P. Xia, C.-P.J. Heisenberg, in:, R. Dosch (Ed.), Germline Development in the Zebrafish, Humana, 2021, pp. 117–128."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Humana","quality_controlled":"1","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.).","page":"117-128","date_created":"2021-03-14T23:01:34Z","doi":"10.1007/978-1-0716-0970-5_10","date_published":"2021-02-20T00:00:00Z","year":"2021","publication":"Germline Development in the Zebrafish","day":"20","type":"book_chapter","keyword":["Tissue tension","Morphogenesis","Laser ablation","Zebrafish folliculogenesis","Granulosa cells"],"status":"public","_id":"9245","department":[{"_id":"CaHe"}],"date_updated":"2022-06-03T10:57:55Z","alternative_title":["Methods in Molecular Biology"],"scopus_import":"1","intvolume":" 2218","month":"02","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"pmid":1,"oa_version":"None","ec_funded":1,"volume":2218,"publication_status":"published","publication_identifier":{"eisbn":["978-1-0716-0970-5"],"eissn":["1940-6029"],"isbn":["978-1-0716-0969-9"],"issn":["1064-3745"]},"language":[{"iso":"eng"}]},{"quality_controlled":"1","publisher":"Springer Nature","doi":"10.1007/978-1-4939-9873-9_16","date_published":"2019-10-04T00:00:00Z","date_created":"2022-08-16T06:54:48Z","page":"215–231","day":"04","publication":"Protein-Protein Interaction Networks","year":"2019","title":"Vienna Graph Clustering","editor":[{"full_name":"Canzar, Stefan","last_name":"Canzar","first_name":"Stefan"},{"first_name":"Francisca","last_name":"Rojas Ringeling","full_name":"Rojas Ringeling, Francisca"}],"author":[{"first_name":"Sonja","full_name":"Biedermann, Sonja","last_name":"Biedermann"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger"},{"full_name":"Schulz, Christian","last_name":"Schulz","first_name":"Christian"},{"first_name":"Bernhard","full_name":"Schuster, Bernhard","last_name":"Schuster"}],"external_id":{"pmid":["31583641"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Biedermann, S., Henzinger, M. H., Schulz, C., & Schuster, B. (2019). Vienna Graph Clustering. In S. Canzar & F. Rojas Ringeling (Eds.), Protein-Protein Interaction Networks (Vol. 2074, pp. 215–231). Springer Nature. https://doi.org/10.1007/978-1-4939-9873-9_16","ama":"Biedermann S, Henzinger MH, Schulz C, Schuster B. Vienna Graph Clustering. In: Canzar S, Rojas Ringeling F, eds. Protein-Protein Interaction Networks. Vol 2074. MIMB. Springer Nature; 2019:215–231. doi:10.1007/978-1-4939-9873-9_16","ieee":"S. Biedermann, M. H. Henzinger, C. Schulz, and B. Schuster, “Vienna Graph Clustering,” in Protein-Protein Interaction Networks, vol. 2074, S. Canzar and F. Rojas Ringeling, Eds. Springer Nature, 2019, pp. 215–231.","short":"S. Biedermann, M.H. Henzinger, C. Schulz, B. Schuster, in:, S. Canzar, F. Rojas Ringeling (Eds.), Protein-Protein Interaction Networks, Springer Nature, 2019, pp. 215–231.","mla":"Biedermann, Sonja, et al. “Vienna Graph Clustering.” Protein-Protein Interaction Networks, edited by Stefan Canzar and Francisca Rojas Ringeling, vol. 2074, Springer Nature, 2019, pp. 215–231, doi:10.1007/978-1-4939-9873-9_16.","ista":"Biedermann S, Henzinger MH, Schulz C, Schuster B. 2019.Vienna Graph Clustering. In: Protein-Protein Interaction Networks. Methods in Molecular Biology, vol. 2074, 215–231.","chicago":"Biedermann, Sonja, Monika H Henzinger, Christian Schulz, and Bernhard Schuster. “Vienna Graph Clustering.” In Protein-Protein Interaction Networks, edited by Stefan Canzar and Francisca Rojas Ringeling, 2074:215–231. MIMB. Springer Nature, 2019. https://doi.org/10.1007/978-1-4939-9873-9_16."},"month":"10","intvolume":" 2074","scopus_import":"1","alternative_title":["Methods in Molecular Biology"],"oa_version":"None","pmid":1,"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,"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781493998722"],"eissn":["1940-6029"],"issn":["1064-3745"],"eisbn":["9781493998739"]},"publication_status":"published","status":"public","type":"book_chapter","series_title":"MIMB","_id":"11847","extern":"1","date_updated":"2023-02-17T09:34:26Z"},{"day":"16","publication":"Morphogen Gradients ","has_accepted_license":"1","year":"2018","date_published":"2018-10-16T00:00:00Z","doi":"10.1007/978-1-4939-8772-6_4","date_created":"2018-12-11T11:44:17Z","page":"47 - 63","quality_controlled":"1","publisher":"Springer Nature","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"M.P. Zagórski, A. Kicheva, in:, Morphogen Gradients , Springer Nature, 2018, pp. 47–63.","ieee":"M. P. Zagórski and A. Kicheva, “Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube,” in Morphogen Gradients , 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: Morphogen Gradients . Vol 1863. MIMB. Springer Nature; 2018:47-63. doi:10.1007/978-1-4939-8772-6_4","apa":"Zagórski, M. P., & Kicheva, A. (2018). Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In Morphogen Gradients (Vol. 1863, pp. 47–63). Springer Nature. https://doi.org/10.1007/978-1-4939-8772-6_4","mla":"Zagórski, Marcin P., and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” Morphogen Gradients , vol. 1863, Springer Nature, 2018, pp. 47–63, doi:10.1007/978-1-4939-8772-6_4.","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.","chicago":"Zagórski, Marcin P, and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” In Morphogen Gradients , 1863:47–63. MIMB. Springer Nature, 2018. https://doi.org/10.1007/978-1-4939-8772-6_4."},"title":"Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube","publist_id":"8018","author":[{"last_name":"Zagórski","full_name":"Zagórski, Marcin P","orcid":"0000-0001-7896-7762","first_name":"Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"}],"article_processing_charge":"No","project":[{"_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020","name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037"}],"file":[{"creator":"dernst","date_updated":"2020-10-13T14:20:37Z","file_size":4906815,"date_created":"2020-10-13T14:20:37Z","file_name":"2018_MIMB_Zagorski.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"2a97d0649fdcfcf1bdca7c8ad1dce71b","file_id":"8656","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-1-4939-8771-9"],"issn":["1064-3745"]},"publication_status":"published","volume":1863,"ec_funded":1,"oa_version":"Submitted Version","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"}],"month":"10","intvolume":" 1863","alternative_title":["Methods in Molecular Biology"],"scopus_import":"1","ddc":["570"],"date_updated":"2021-01-12T07:49:03Z","department":[{"_id":"AnKi"}],"file_date_updated":"2020-10-13T14:20:37Z","series_title":"MIMB","_id":"37","status":"public","type":"book_chapter"},{"author":[{"first_name":"Hoang","full_name":"Trinh, Hoang","last_name":"Trinh"},{"last_name":"Verstraeten","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge"},{"last_name":"Geelen","full_name":"Geelen, Danny","first_name":"Danny"}],"publist_id":"7421","external_id":{"pmid":["29525951"]},"article_processing_charge":"No","title":"In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls","citation":{"apa":"Trinh, H., Verstraeten, I., & Geelen, D. (2018). In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In Root Development (Vol. 1761, pp. 95–102). Springer Nature. https://doi.org/10.1007/978-1-4939-7747-5_7","ama":"Trinh H, Verstraeten I, Geelen D. In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In: Root Development . Vol 1761. Springer Nature; 2018:95-102. doi:10.1007/978-1-4939-7747-5_7","ieee":"H. Trinh, I. Verstraeten, and D. Geelen, “In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls,” in Root Development , vol. 1761, Springer Nature, 2018, pp. 95–102.","short":"H. Trinh, I. Verstraeten, D. Geelen, in:, Root Development , Springer Nature, 2018, pp. 95–102.","mla":"Trinh, Hoang, et al. “In Vitro Assay for Induction of Adventitious Rooting on Intact Arabidopsis Hypocotyls.” Root Development , vol. 1761, Springer Nature, 2018, pp. 95–102, doi:10.1007/978-1-4939-7747-5_7.","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.","chicago":"Trinh, Hoang, Inge Verstraeten, and Danny Geelen. “In Vitro Assay for Induction of Adventitious Rooting on Intact Arabidopsis Hypocotyls.” In Root Development , 1761:95–102. Springer Nature, 2018. https://doi.org/10.1007/978-1-4939-7747-5_7."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"95 - 102","doi":"10.1007/978-1-4939-7747-5_7","date_published":"2018-03-01T00:00:00Z","date_created":"2018-12-11T11:46:18Z","year":"2018","day":"01","publication":"Root Development ","publisher":"Springer Nature","quality_controlled":"1","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T07:54:21Z","type":"book_chapter","status":"public","_id":"408","volume":1761,"publication_identifier":{"issn":["1064-3745"]},"publication_status":"published","language":[{"iso":"eng"}],"alternative_title":["MIMB"],"scopus_import":"1","month":"03","intvolume":" 1761","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"}],"oa_version":"None","pmid":1},{"month":"07","intvolume":" 1635","publisher":"Springer Nature","alternative_title":["Methods in Molecular Biology"],"quality_controlled":"1","oa_version":"None","abstract":[{"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.","lang":"eng"}],"doi":"10.1007/978-1-4939-7151-0_6","volume":1635,"date_published":"2017-07-29T00:00:00Z","date_created":"2020-09-18T10:06:44Z","page":"109-123","day":"29","publication":"Membrane protein structure and function characterization","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1064-3745","1940-6029"],"isbn":["9781493971497","9781493971510"]},"year":"2017","publication_status":"published","status":"public","type":"book_chapter","_id":"8450","title":"Methyl-specific isotope labeling strategies for NMR studies of membrane proteins","author":[{"full_name":"Kurauskas, Vilius","last_name":"Kurauskas","first_name":"Vilius"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda"},{"first_name":"Remy","last_name":"Sounier","full_name":"Sounier, Remy"}],"article_processing_charge":"No","extern":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Kurauskas, Vilius, et al. “Methyl-Specific Isotope Labeling Strategies for NMR Studies of Membrane Proteins.” Membrane Protein Structure and Function Characterization, vol. 1635, Springer Nature, 2017, pp. 109–23, doi:10.1007/978-1-4939-7151-0_6.","ieee":"V. Kurauskas, P. Schanda, and R. Sounier, “Methyl-specific isotope labeling strategies for NMR studies of membrane proteins,” in Membrane protein structure and function characterization, vol. 1635, Springer Nature, 2017, pp. 109–123.","short":"V. Kurauskas, P. Schanda, R. Sounier, in:, Membrane Protein Structure and Function Characterization, Springer Nature, 2017, pp. 109–123.","apa":"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 (Vol. 1635, pp. 109–123). Springer Nature. https://doi.org/10.1007/978-1-4939-7151-0_6","ama":"Kurauskas V, Schanda P, Sounier R. Methyl-specific isotope labeling strategies for NMR studies of membrane proteins. In: Membrane Protein Structure and Function Characterization. Vol 1635. Springer Nature; 2017:109-123. doi:10.1007/978-1-4939-7151-0_6","chicago":"Kurauskas, Vilius, Paul Schanda, and Remy Sounier. “Methyl-Specific Isotope Labeling Strategies for NMR Studies of Membrane Proteins.” In Membrane Protein Structure and Function Characterization, 1635:109–23. Springer Nature, 2017. https://doi.org/10.1007/978-1-4939-7151-0_6.","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."},"date_updated":"2022-08-26T09:14:20Z"},{"status":"public","type":"book_chapter","series_title":"Methods in Molecular Biology","_id":"6178","department":[{"_id":"CaHe"}],"date_updated":"2023-09-05T14:12:00Z","month":"08","place":"New York, NY","intvolume":" 1189","pmid":1,"oa_version":"None","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"}],"volume":1189,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1940-6029"],"isbn":["9781493911639","9781493911646"],"issn":["1064-3745"]},"publication_status":"published","editor":[{"first_name":"Celeste","last_name":"Nelson","full_name":"Nelson, Celeste"}],"title":"UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo","author":[{"id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","last_name":"Smutny","full_name":"Smutny, Michael","orcid":"0000-0002-5920-9090"},{"last_name":"Behrndt","full_name":"Behrndt, Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","first_name":"Pedro","orcid":"0000-0002-8526-5416","full_name":"Campinho, Pedro","last_name":"Campinho"},{"orcid":"0000-0003-4088-8633","full_name":"Ruprecht, Verena","last_name":"Ruprecht","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","first_name":"Verena"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"pmid":["25245697"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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 Tissue Morphogenesis, edited by Celeste Nelson, 1189:219–35. Methods in Molecular Biology. New York, NY: Springer, 2014. https://doi.org/10.1007/978-1-4939-1164-6_15.","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. 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.” Tissue Morphogenesis, edited by Celeste Nelson, vol. 1189, Springer, 2014, pp. 219–35, doi:10.1007/978-1-4939-1164-6_15.","short":"M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, C.-P.J. Heisenberg, in:, C. Nelson (Ed.), Tissue Morphogenesis, Springer, New York, NY, 2014, pp. 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 Tissue Morphogenesis, vol. 1189, C. Nelson, Ed. New York, NY: Springer, 2014, pp. 219–235.","apa":"Smutny, M., Behrndt, M., Campinho, P., Ruprecht, V., & 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.), Tissue Morphogenesis (Vol. 1189, pp. 219–235). New York, NY: Springer. https://doi.org/10.1007/978-1-4939-1164-6_15","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. Tissue Morphogenesis. Vol 1189. Methods in Molecular Biology. New York, NY: Springer; 2014:219-235. doi:10.1007/978-1-4939-1164-6_15"},"quality_controlled":"1","publisher":"Springer","date_published":"2014-08-22T00:00:00Z","doi":"10.1007/978-1-4939-1164-6_15","date_created":"2019-03-26T08:55:59Z","page":"219-235","day":"22","publication":"Tissue Morphogenesis","year":"2014"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"M. Weber and M. K. Sixt, “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations,” in Chemokines, vol. 1013, A. Cardona and E. Ubogu, Eds. Totowa, NJ: Humana Press, 2013, pp. 215–226.","short":"M. Weber, M.K. Sixt, in:, A. Cardona, E. Ubogu (Eds.), Chemokines, Humana Press, Totowa, NJ, 2013, pp. 215–226.","ama":"Weber M, Sixt MK. Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In: Cardona A, Ubogu E, eds. Chemokines. Vol 1013. MIMB. Totowa, NJ: Humana Press; 2013:215-226. doi:10.1007/978-1-62703-426-5_14","apa":"Weber, M., & Sixt, M. K. (2013). Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In A. Cardona & E. Ubogu (Eds.), Chemokines (Vol. 1013, pp. 215–226). Totowa, NJ: Humana Press. https://doi.org/10.1007/978-1-62703-426-5_14","mla":"Weber, Michele, and Michael K. Sixt. “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations.” Chemokines, edited by Astrid Cardona and Eroboghene Ubogu, vol. 1013, Humana Press, 2013, pp. 215–26, doi:10.1007/978-1-62703-426-5_14.","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.","chicago":"Weber, Michele, and Michael K Sixt. “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations.” In Chemokines, edited by Astrid Cardona and Eroboghene Ubogu, 1013:215–26. MIMB. Totowa, NJ: Humana Press, 2013. https://doi.org/10.1007/978-1-62703-426-5_14."},"editor":[{"full_name":"Cardona, Astrid","last_name":"Cardona","first_name":"Astrid"},{"first_name":"Eroboghene","full_name":"Ubogu, Eroboghene","last_name":"Ubogu"}],"title":"Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations","author":[{"last_name":"Weber","full_name":"Weber, Michele","id":"3A3FC708-F248-11E8-B48F-1D18A9856A87","first_name":"Michele"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt"}],"external_id":{"pmid":["23625502"]},"article_processing_charge":"No","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","quality_controlled":"1","day":"03","publication":"Chemokines","year":"2013","date_published":"2013-04-03T00:00:00Z","doi":"10.1007/978-1-62703-426-5_14","date_created":"2022-03-21T07:47:41Z","page":"215-226","series_title":"MIMB","_id":"10900","status":"public","type":"book_chapter","date_updated":"2023-09-05T13:15:33Z","department":[{"_id":"MiSi"}],"oa_version":"None","pmid":1,"abstract":[{"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.","lang":"eng"}],"month":"04","place":"Totowa, NJ","intvolume":" 1013","scopus_import":"1","alternative_title":["Methods in Molecular Biology"],"language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["9781627034265"],"eissn":["1940-6029"],"isbn":["9781627034258"],"issn":["1064-3745"]},"publication_status":"published","volume":1013}]