[{"has_accepted_license":"1","doi":"10.15479/AT:ISTA:6392","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"publication_identifier":{"isbn":["978-3-99078-001-5"],"issn":["2663-337X"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2021-02-11T11:17:16Z","citation":{"short":"M. Lukacisin, Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory, IST Austria, 2019.","ama":"Lukacisin M. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6392\">10.15479/AT:ISTA:6392</a>","apa":"Lukacisin, M. (2019). <i>Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6392\">https://doi.org/10.15479/AT:ISTA:6392</a>","ista":"Lukacisin M. 2019. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. IST Austria.","mla":"Lukacisin, Martin. <i>Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory</i>. IST Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6392\">10.15479/AT:ISTA:6392</a>.","chicago":"Lukacisin, Martin. “Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory.” IST Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6392\">https://doi.org/10.15479/AT:ISTA:6392</a>.","ieee":"M. Lukacisin, “Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory,” IST Austria, 2019."},"month":"05","file":[{"creator":"mlukacisin","checksum":"829bda074444857c7935171237bb7c0c","file_id":"6409","file_size":43740796,"date_created":"2019-05-10T13:51:49Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"hidden","embargo_to":"open_access","access_level":"closed","date_updated":"2020-07-14T12:47:29Z","file_name":"Thesis_Draft_v3.4Final.docx"},{"embargo":"2020-04-17","file_name":"Thesis_Draft_v3.4FinalA.pdf","relation":"main_file","access_level":"open_access","date_updated":"2021-02-11T11:17:16Z","file_id":"6410","content_type":"application/pdf","file_size":35228388,"date_created":"2019-05-10T14:13:42Z","creator":"mlukacisin","checksum":"56cb5e97f5f8fc41692401b53832d8e0"}],"_id":"6392","abstract":[{"text":"The regulation of gene expression is one of the most fundamental processes in living systems. In recent years, thanks to advances in sequencing technology and automation, it has become possible to study gene expression quantitatively, genome-wide and in high-throughput. This leads to the possibility of exploring changes in gene expression in the context of many external perturbations and their combinations, and thus of characterising the basic principles governing gene regulation. In this thesis, I present quantitative experimental approaches to studying transcriptional and protein level changes in response to combinatorial drug treatment, as well as a theoretical data-driven approach to analysing thermodynamic principles guiding transcription of protein coding genes.  \r\nIn the first part of this work, I present a novel methodological framework for quantifying gene expression changes in drug combinations, termed isogrowth profiling. External perturbations through small molecule drugs influence the growth rate of the cell, leading to wide-ranging changes in cellular physiology and gene expression. This confounds the gene expression changes specifically elicited by the particular drug. Combinatorial perturbations, owing to the increased stress they exert, influence the growth rate even more strongly and hence suffer the convolution problem to a greater extent when measuring gene expression changes. Isogrowth profiling is a way to experimentally abstract non-specific, growth rate related changes, by performing the measurement using varying ratios of two drugs at such concentrations that the overall inhibition rate is constant. Using a robotic setup for automated high-throughput re-dilution culture of Saccharomyces cerevisiae, the budding yeast, I investigate all pairwise interactions of four small molecule drugs through sequencing RNA along a growth isobole. Through principal component analysis, I demonstrate here that isogrowth profiling can uncover drug-specific as well as drug-interaction-specific gene expression changes. I show that drug-interaction-specific gene expression changes can be used for prediction of higher-order drug interactions. I propose a simplified generalised framework of isogrowth profiling, with few measurements needed for each drug pair, enabling the broad application of isogrowth profiling to high-throughput screening of inhibitors of cellular growth and beyond. Such high-throughput screenings of gene expression changes specific to pairwise drug interactions will be instrumental for predicting the higher-order interactions of the drugs.\r\n\r\nIn the second part of this work, I extend isogrowth profiling to single-cell measurements of gene expression, characterising population heterogeneity in the budding yeast in response to combinatorial drug perturbation while controlling for non-specific growth rate effects. Through flow cytometry of strains with protein products fused to green fluorescent protein, I discover multiple proteins with bi-modally distributed expression levels in the population in response to drug treatment. I characterize more closely the effect of an ionic stressor, lithium chloride, and find that it inhibits the splicing of mRNA, most strongly affecting ribosomal protein transcripts and leading to a bi-stable behaviour of a small ribosomal subunit protein Rps22B. Time-lapse microscopy of a microfluidic culture system revealed that the induced Rps22B heterogeneity leads to preferential survival of Rps22B-low cells after long starvation, but to preferential proliferation of Rps22B-high cells after short starvation. Overall, this suggests that yeast cells might use splicing of ribosomal genes for bet-hedging in fluctuating environments. I give specific examples of how further exploration of cellular heterogeneity in yeast in response to external perturbation has the potential to reveal yet-undiscovered gene regulation circuitry.\r\n\r\nIn the last part of this thesis, a re-analysis of a published sequencing dataset of nascent elongating transcripts is used to characterise the thermodynamic constraints for RNA polymerase II (RNAP) elongation. Population-level data on RNAP position throughout the transcribed genome with single nucleotide resolution are used to infer the sequence specific thermodynamic determinants of RNAP pausing and backtracking. This analysis reveals that the basepairing strength of the eight nucleotide-long RNA:DNA duplex relative to the basepairing strength of the same sequence when in DNA:DNA duplex, and the change in this quantity during RNA polymerase movement, is the key determinant of RNAP pausing. This is true for RNAP pausing while elongating, but also of RNAP pausing while backtracking and of the backtracking length. The quantitative dependence of RNAP pausing on basepairing energetics is used to infer the increase in pausing due to transcriptional mismatches, leading to a hypothesis that pervasive RNA polymerase II pausing is due to basepairing energetics, as an evolutionary cost for increased RNA polymerase II fidelity.\r\n\r\nThis work advances our understanding of the general principles governing gene expression, with the goal of making computational predictions of single-cell gene expression responses to combinatorial perturbations based on the individual perturbations possible. This ability would substantially facilitate the design of drug combination treatments and, in the long term, lead to our increased ability to more generally design targeted manipulations to any biological system. ","lang":"eng"}],"department":[{"_id":"ToBo"}],"supervisor":[{"orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"1029","relation":"part_of_dissertation","status":"public"}]},"alternative_title":["IST Austria Thesis"],"date_updated":"2025-07-10T11:49:51Z","extern":"1","oa":1,"publisher":"IST Austria","publication_status":"published","status":"public","date_created":"2019-05-09T19:53:00Z","author":[{"orcid":"0000-0001-6549-4177","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisin","first_name":"Martin","full_name":"Lukacisin, Martin"}],"year":"2019","title":"Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory","oa_version":"Published Version","page":"103","day":"09","ddc":["570"],"type":"dissertation","language":[{"iso":"eng"}],"date_published":"2019-05-09T00:00:00Z"},{"issue":"6","date_published":"2019-05-30T00:00:00Z","scopus_import":"1","isi":1,"language":[{"iso":"eng"}],"page":"1463-1479.e18","ddc":["570"],"day":"30","type":"journal_article","article_processing_charge":"No","title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes","oa_version":"Published Version","ec_funded":1,"pmid":1,"author":[{"full_name":"Shamipour, Shayan","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Shamipour"},{"last_name":"Kardos","id":"4039350E-F248-11E8-B48F-1D18A9856A87","full_name":"Kardos, Roland","first_name":"Roland"},{"last_name":"Xue","id":"31D2C804-F248-11E8-B48F-1D18A9856A87","first_name":"Shi-lei","full_name":"Xue, Shi-lei"},{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B"},{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"year":"2019","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"},{"name":"Active mechano-chemical description of the cell cytoskeleton","grant_number":"P31639","_id":"268294B6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"acknowledgement":"We would like to thank Pierre Recho, Guillaume Salbreux, and Silvia Grigolon for advice on the theory, Lila Solnica-Krezel for kindly providing us with zebrafish dachsous mutants, members of the Heisenberg and Hannezo groups for fruitful discussions, and the Bioimaging and zebrafish facilities at IST Austria for their continuous support. This project has received funding from the European Union (European Research Council Advanced Grant 742573 to C.P.H.) and from the Austrian Science Fund (FWF) (P 31639 to E.H.).","date_created":"2019-06-02T21:59:12Z","status":"public","publisher":"Elsevier","publication_status":"published","oa":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8350"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-the-cytoplasm-separates-from-the-yolk/","relation":"press_release"}]},"date_updated":"2026-05-20T22:30:09Z","external_id":{"isi":["000469415100013"],"pmid":["31080065"]},"publication":"Cell","department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"BjHo"}],"volume":177,"article_type":"original","month":"05","file":[{"file_name":"2019_Cell_Shamipour_accepted.pdf","relation":"main_file","access_level":"open_access","date_updated":"2020-10-21T07:22:34Z","file_id":"8686","content_type":"application/pdf","file_size":3356292,"date_created":"2020-10-21T07:22:34Z","success":1,"creator":"dernst","checksum":"aea43726d80e35ce3885073a5f05c3e3"}],"abstract":[{"text":"Segregation of maternal determinants within the oocyte constitutes the first step in embryo patterning. In zebrafish oocytes, extensive ooplasmic streaming leads to the segregation of ooplasm from yolk granules along the animal-vegetal axis of the oocyte. Here, we show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the oocyte. This wave functions in segregation by both pulling ooplasm animally and pushing yolk granules vegetally. Using biophysical experimentation and theory, we show that ooplasm pulling is mediated by bulk actin network flows exerting friction forces on the ooplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. Our study defines a novel role of cell-cycle-controlled bulk actin polymerization waves in oocyte polarization via ooplasmic segregation.","lang":"eng"}],"_id":"6508","intvolume":"       177","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2019.04.030","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-10-21T07:22:34Z","citation":{"short":"S. Shamipour, R. Kardos, S. Xue, B. Hof, E.B. Hannezo, C.-P.J. Heisenberg, Cell 177 (2019) 1463–1479.e18.","ama":"Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. Bulk actin dynamics drive phase segregation in zebrafish oocytes. <i>Cell</i>. 2019;177(6):1463-1479.e18. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.030\">10.1016/j.cell.2019.04.030</a>","mla":"Shamipour, Shayan, et al. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” <i>Cell</i>, vol. 177, no. 6, Elsevier, 2019, p. 1463–1479.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.030\">10.1016/j.cell.2019.04.030</a>.","ista":"Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. 2019. Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. 177(6), 1463–1479.e18.","apa":"Shamipour, S., Kardos, R., Xue, S., Hof, B., Hannezo, E. B., &#38; Heisenberg, C.-P. J. (2019). Bulk actin dynamics drive phase segregation in zebrafish oocytes. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2019.04.030\">https://doi.org/10.1016/j.cell.2019.04.030</a>","chicago":"Shamipour, Shayan, Roland Kardos, Shi-lei Xue, Björn Hof, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” <i>Cell</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.04.030\">https://doi.org/10.1016/j.cell.2019.04.030</a>.","ieee":"S. Shamipour, R. Kardos, S. Xue, B. Hof, E. B. Hannezo, and C.-P. J. Heisenberg, “Bulk actin dynamics drive phase segregation in zebrafish oocytes,” <i>Cell</i>, vol. 177, no. 6. Elsevier, p. 1463–1479.e18, 2019."},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"has_accepted_license":"1","doi":"10.1016/j.cell.2019.04.030"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2020-10-21T07:09:45Z","citation":{"ista":"Schwayer C, Shamipour S, Pranjic-Ferscha K, Schauer A, Balda M, Tada M, Matter K, Heisenberg C-PJ. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. 179(4), 937–952.e18.","mla":"Schwayer, Cornelia, et al. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” <i>Cell</i>, vol. 179, no. 4, Cell Press, 2019, p. 937–952.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">10.1016/j.cell.2019.10.006</a>.","apa":"Schwayer, C., Shamipour, S., Pranjic-Ferscha, K., Schauer, A., Balda, M., Tada, M., … Heisenberg, C.-P. J. (2019). Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">https://doi.org/10.1016/j.cell.2019.10.006</a>","chicago":"Schwayer, Cornelia, Shayan Shamipour, Kornelija Pranjic-Ferscha, Alexandra Schauer, M Balda, M Tada, K Matter, and Carl-Philipp J Heisenberg. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” <i>Cell</i>. Cell Press, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">https://doi.org/10.1016/j.cell.2019.10.006</a>.","ieee":"C. Schwayer <i>et al.</i>, “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” <i>Cell</i>, vol. 179, no. 4. Cell Press, p. 937–952.e18, 2019.","short":"C. Schwayer, S. Shamipour, K. Pranjic-Ferscha, A. Schauer, M. Balda, M. Tada, K. Matter, C.-P.J. Heisenberg, Cell 179 (2019) 937–952.e18.","ama":"Schwayer C, Shamipour S, Pranjic-Ferscha K, et al. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. <i>Cell</i>. 2019;179(4):937-952.e18. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">10.1016/j.cell.2019.10.006</a>"},"quality_controlled":"1","doi":"10.1016/j.cell.2019.10.006","has_accepted_license":"1","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"external_id":{"isi":["000493898000012"],"pmid":["31675500"]},"date_updated":"2026-05-20T22:30:09Z","related_material":{"record":[{"status":"public","id":"7186","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"8350","status":"public"}],"link":[{"description":"News auf IST Website","url":"https://ist.ac.at/en/news/biochemistry-meets-mechanics-the-sensitive-nature-of-cell-cell-contact-formation-in-embryo-development/","relation":"press_release"}]},"oa":1,"month":"10","article_type":"original","_id":"7001","intvolume":"       179","file":[{"creator":"dernst","checksum":"33dac4bb77ee630e2666e936b4d57980","file_id":"8684","content_type":"application/pdf","file_size":8805878,"success":1,"date_created":"2020-10-21T07:09:45Z","relation":"main_file","date_updated":"2020-10-21T07:09:45Z","access_level":"open_access","file_name":"2019_Cell_Schwayer_accepted.pdf"}],"department":[{"_id":"CaHe"},{"_id":"BjHo"}],"publication":"Cell","volume":179,"year":"2019","author":[{"orcid":"0000-0001-5130-2226","last_name":"Schwayer","id":"3436488C-F248-11E8-B48F-1D18A9856A87","first_name":"Cornelia","full_name":"Schwayer, Cornelia"},{"id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Shamipour","first_name":"Shayan","full_name":"Shamipour, Shayan"},{"id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","last_name":"Pranjic-Ferscha","full_name":"Pranjic-Ferscha, Kornelija","first_name":"Kornelija"},{"last_name":"Schauer","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandra","full_name":"Schauer, Alexandra","orcid":"0000-0001-7659-9142"},{"first_name":"M","full_name":"Balda, M","last_name":"Balda"},{"last_name":"Tada","full_name":"Tada, M","first_name":"M"},{"first_name":"K","full_name":"Matter, K","last_name":"Matter"},{"first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"oa_version":"Submitted Version","ec_funded":1,"title":"Mechanosensation of tight junctions depends on ZO-1 phase separation and flow","article_processing_charge":"No","pmid":1,"publisher":"Cell Press","publication_status":"published","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"}],"status":"public","date_created":"2019-11-12T12:51:06Z","date_published":"2019-10-31T00:00:00Z","issue":"4","type":"journal_article","page":"937-952.e18","ddc":["570"],"day":"31","scopus_import":"1","language":[{"iso":"eng"}],"isi":1},{"publication_status":"published","publisher":"Elsevier","date_created":"2019-04-28T21:59:14Z","status":"public","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Marhavá","id":"44E59624-F248-11E8-B48F-1D18A9856A87","first_name":"Petra","full_name":"Marhavá, Petra"},{"orcid":"0000-0001-8295-2926","last_name":"Hörmayer","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Hörmayer, Lukas","first_name":"Lukas"},{"id":"2E46069C-F248-11E8-B48F-1D18A9856A87","last_name":"Yoshida","first_name":"Saiko","full_name":"Yoshida, Saiko","orcid":"0000-0001-6111-9353"},{"orcid":"0000-0001-5227-5741","first_name":"Peter","full_name":"Marhavy, Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavy"},{"orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva"},{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"year":"2019","pmid":1,"article_processing_charge":"No","title":"Re-activation of stem cell pathways for pattern restoration in plant wound healing","ec_funded":1,"oa_version":"Published Version","page":"957-969.e13","ddc":["570"],"day":"02","type":"journal_article","isi":1,"language":[{"iso":"eng"}],"scopus_import":"1","date_published":"2019-05-02T00:00:00Z","issue":"4","has_accepted_license":"1","doi":"10.1016/j.cell.2019.04.015","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"acknowledged_ssus":[{"_id":"Bio"}],"file_date_updated":"2020-07-14T12:47:28Z","citation":{"short":"P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, J. Friml, Cell 177 (2019) 957–969.e13.","ama":"Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. Re-activation of stem cell pathways for pattern restoration in plant wound healing. <i>Cell</i>. 2019;177(4):957-969.e13. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">10.1016/j.cell.2019.04.015</a>","chicago":"Marhavá, Petra, Lukas Hörmayer, Saiko Yoshida, Peter Marhavý, Eva Benková, and Jiří Friml. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” <i>Cell</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">https://doi.org/10.1016/j.cell.2019.04.015</a>.","apa":"Marhavá, P., Hörmayer, L., Yoshida, S., Marhavý, P., Benková, E., &#38; Friml, J. (2019). Re-activation of stem cell pathways for pattern restoration in plant wound healing. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">https://doi.org/10.1016/j.cell.2019.04.015</a>","mla":"Marhavá, Petra, et al. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” <i>Cell</i>, vol. 177, no. 4, Elsevier, 2019, p. 957–969.e13, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">10.1016/j.cell.2019.04.015</a>.","ista":"Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. 2019. Re-activation of stem cell pathways for pattern restoration in plant wound healing. Cell. 177(4), 957–969.e13.","ieee":"P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, and J. Friml, “Re-activation of stem cell pathways for pattern restoration in plant wound healing,” <i>Cell</i>, vol. 177, no. 4. Elsevier, p. 957–969.e13, 2019."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","file":[{"access_level":"open_access","date_updated":"2020-07-14T12:47:28Z","relation":"main_file","file_name":"2019_Cell_Marhava.pdf","checksum":"4ceba04a96a74f5092ec3ce2c579a0c7","creator":"dernst","content_type":"application/pdf","date_created":"2019-05-13T06:12:45Z","file_size":10272032,"file_id":"6411"}],"intvolume":"       177","_id":"6351","abstract":[{"lang":"eng","text":"A process of restorative patterning in plant roots correctly replaces eliminated cells to heal local injuries despite the absence of cell migration, which underpins wound healing in animals. \r\n\r\nPatterning in plants relies on oriented cell divisions and acquisition of specific cell identities. Plants regularly endure wounds caused by abiotic or biotic environmental stimuli and have developed extraordinary abilities to restore their tissues after injuries. Here, we provide insight into a mechanism of restorative patterning that repairs tissues after wounding. Laser-assisted elimination of different cells in Arabidopsis root combined with live-imaging tracking during vertical growth allowed analysis of the regeneration processes in vivo. Specifically, the cells adjacent to the inner side of the injury re-activated their stem cell transcriptional programs. They accelerated their progression through cell cycle, coordinately changed the cell division orientation, and ultimately acquired de novo the correct cell fates to replace missing cells. These observations highlight existence of unknown intercellular positional signaling and demonstrate the capability of specified cells to re-acquire stem cell programs as a crucial part of the plant-specific mechanism of wound healing."}],"month":"05","volume":177,"publication":"Cell","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"date_updated":"2026-05-20T22:30:47Z","related_material":{"record":[{"relation":"dissertation_contains","id":"9992","status":"public"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/specialized-plant-cells-regain-stem-cell-features-to-heal-wounds/","relation":"press_release"}]},"external_id":{"pmid":["31051107"],"isi":["000466843000015"]},"corr_author":"1","oa":1},{"publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"LifeSc"}],"doi":"10.15479/AT:ISTA:6435","has_accepted_license":"1","file_date_updated":"2021-02-11T11:17:15Z","citation":{"ama":"Casillas Perez BE. Collective defenses of garden ants against a fungal pathogen. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6435\">10.15479/AT:ISTA:6435</a>","short":"B.E. Casillas Perez, Collective Defenses of Garden Ants against a Fungal Pathogen, Institute of Science and Technology Austria, 2019.","ieee":"B. E. Casillas Perez, “Collective defenses of garden ants against a fungal pathogen,” Institute of Science and Technology Austria, 2019.","mla":"Casillas Perez, Barbara E. <i>Collective Defenses of Garden Ants against a Fungal Pathogen</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6435\">10.15479/AT:ISTA:6435</a>.","ista":"Casillas Perez BE. 2019. Collective defenses of garden ants against a fungal pathogen. Institute of Science and Technology Austria.","apa":"Casillas Perez, B. E. (2019). <i>Collective defenses of garden ants against a fungal pathogen</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6435\">https://doi.org/10.15479/AT:ISTA:6435</a>","chicago":"Casillas Perez, Barbara E. “Collective Defenses of Garden Ants against a Fungal Pathogen.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6435\">https://doi.org/10.15479/AT:ISTA:6435</a>."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","keyword":["Social Immunity","Sanitary care","Social Insects","Organisational Immunity","Colony development","Multi-target tracking"],"supervisor":[{"first_name":"Sylvia M","full_name":"Cremer, Sylvia M","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"}],"department":[{"_id":"SyCr"}],"abstract":[{"lang":"eng","text":"Social insect colonies tend to have numerous members which function together like a single organism in such harmony that the term ``super-organism'' is often used. In this analogy the reproductive caste is analogous to the primordial germ\r\ncells of a metazoan, while the sterile worker caste corresponds to somatic cells. The worker castes, like tissues, are\r\nin charge of all functions of a living being, besides reproduction. The establishment of new super-organismal units\r\n(i.e. new colonies) is accomplished by the co-dependent castes. The term oftentimes goes beyond a metaphor. We invoke it when we speak about the metabolic rate, thermoregulation, nutrient regulation and gas exchange of a social insect colony. Furthermore, we assert that the super-organism has an immune system, and benefits from ``social immunity''.\r\n\r\nSocial immunity was first summoned by evolutionary biologists to resolve the apparent discrepancy between the expected high frequency of disease outbreak amongst numerous, closely related tightly-interacting hosts, living in stable and microbially-rich environments, against the exceptionally scarce epidemic accounts in natural populations. Social\r\nimmunity comprises a multi-layer assembly of behaviours which have evolved to effectively keep the pathogenic enemies of a colony at bay. The field of social immunity has drawn interest, as it becomes increasingly urgent to stop\r\nthe collapse of pollinator species and curb the growth of invasive pests. In the past decade, several mechanisms of\r\nsocial immune responses have been dissected, but many more questions remain open.\r\n\r\nI present my work in two experimental chapters. In the first, I use invasive garden ants (*Lasius neglectus*) to study how pathogen load and its distribution among nestmates affect the grooming response of the group. Any given group of ants will carry out the same total grooming work, but will direct their grooming effort towards individuals\r\ncarrying a relatively higher spore load. Contrary to expectation, the highest risk of transmission does not stem from grooming highly contaminated ants, but instead, we suggest that the grooming response likely minimizes spore loss to the environment, reducing contamination from inadvertent pickup from the substrate.\r\n\r\nThe second is a comparative developmental approach. I follow black garden ant queens (*Lasius niger*) and their colonies from mating flight, through hibernation for a year. Colonies which grow fast from the start, have a lower chance of survival through hibernation, and those which survive grow at a lower pace later. This is true for colonies of naive\r\nand challenged queens. Early pathogen exposure of the queens changes colony dynamics in an unexpected way: colonies from exposed queens are more likely to grow slowly and recover in numbers only after they survive hibernation.\r\n\r\nIn addition to the two experimental chapters, this thesis includes a co-authored published review on organisational\r\nimmunity, where we enlist the experimental evidence and theoretical framework on which this hypothesis is built,\r\nidentify the caveats and underline how the field is ripe to overcome them. In a final chapter, I describe my part in\r\ntwo collaborative efforts, one to develop an image-based tracker, and the second to develop a classifier for ant\r\nbehaviour."}],"_id":"6435","file":[{"file_id":"6438","file_size":3895187,"date_created":"2019-05-13T09:16:20Z","content_type":"application/pdf","creator":"casillas","checksum":"6daf2d2086111aa8fd3fbc919a3e2833","embargo":"2020-05-08","file_name":"tesisDoctoradoBC.pdf","relation":"main_file","access_level":"open_access","date_updated":"2021-02-11T11:17:15Z"},{"file_name":"tesisDoctoradoBC.zip","access_level":"closed","date_updated":"2020-07-14T12:47:30Z","relation":"source_file","embargo_to":"open_access","date_created":"2019-05-13T09:16:20Z","file_size":7365118,"content_type":"application/zip","file_id":"6439","checksum":"3d221aaff7559a7060230a1ff610594f","creator":"casillas"}],"month":"05","corr_author":"1","oa":1,"date_updated":"2026-04-08T14:02:12Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1999"}]},"alternative_title":["ISTA Thesis"],"date_created":"2019-05-13T08:58:35Z","status":"public","project":[{"_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Epidemics in ant societies on a chip","grant_number":"771402"}],"publication_status":"published","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","ec_funded":1,"title":"Collective defenses of garden ants against a fungal pathogen","article_processing_charge":"No","year":"2019","author":[{"first_name":"Barbara E","full_name":"Casillas Perez, Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","last_name":"Casillas Perez"}],"OA_place":"publisher","language":[{"iso":"eng"}],"type":"dissertation","ddc":["570","006","578","592"],"day":"07","page":"183","date_published":"2019-05-07T00:00:00Z"},{"file_date_updated":"2021-02-10T23:30:09Z","citation":{"short":"D.K. Rangel Guerrero, The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics, Institute of Science and Technology Austria, 2019.","ama":"Rangel Guerrero DK. The role of CCK-interneurons in regulating hippocampal network dynamics. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6849\">10.15479/AT:ISTA:6849</a>","ista":"Rangel Guerrero DK. 2019. The role of CCK-interneurons in regulating hippocampal network dynamics. Institute of Science and Technology Austria.","apa":"Rangel Guerrero, D. K. (2019). <i>The role of CCK-interneurons in regulating hippocampal network dynamics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6849\">https://doi.org/10.15479/AT:ISTA:6849</a>","mla":"Rangel Guerrero, Dámaris K. <i>The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6849\">10.15479/AT:ISTA:6849</a>.","chicago":"Rangel Guerrero, Dámaris K. “The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6849\">https://doi.org/10.15479/AT:ISTA:6849</a>.","ieee":"D. K. Rangel Guerrero, “The role of CCK-interneurons in regulating hippocampal network dynamics,” Institute of Science and Technology Austria, 2019."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","has_accepted_license":"1","doi":"10.15479/AT:ISTA:6849","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-003-9"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"M-Shop"}],"date_updated":"2026-04-08T13:56:53Z","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"id":"5914","relation":"part_of_dissertation","status":"public"}]},"corr_author":"1","oa":1,"file":[{"relation":"source_file","embargo_to":"open_access","access_level":"closed","date_updated":"2021-02-10T23:30:09Z","file_name":"Thesis_Damaris_Rangel_source.docx","creator":"drangel","checksum":"244dc4f74dbfc94f414156092298831f","file_id":"6865","file_size":18253100,"date_created":"2019-09-09T13:09:45Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"relation":"main_file","access_level":"open_access","date_updated":"2020-09-11T22:30:04Z","file_name":"Thesis_Damaris_Rangel_pdfa.pdf","embargo":"2020-09-10","creator":"drangel","checksum":"59c73be40eeaa1c4db24067270151555","request_a_copy":0,"file_id":"6866","file_size":2160109,"date_created":"2019-09-09T13:09:52Z","content_type":"application/pdf"}],"abstract":[{"lang":"eng","text":"Brain function is mediated by complex dynamical interactions between excitatory and inhibitory cell types. The Cholecystokinin-expressing inhibitory cells (CCK-interneurons) are one of the least studied types, despite being suspected to play important roles in cognitive processes. We studied the network effects of optogenetic silencing of CCK-interneurons in the CA1 hippocampal area during exploration and sleep states. The cell firing pattern in response to light pulses allowed us to classify the recorded neurons in 5 classes, including disinhibited and non-responsive pyramidal cell and interneurons, and the inhibited interneurons corresponding to the CCK group. The light application, which inhibited the activity of CCK interneurons triggered wider changes in the firing dynamics of cells. We observed rate changes (i.e. remapping) of pyramidal cells during the exploration session in which the light was applied relative to the previous control session that was not restricted neither in time nor space to the light delivery. Also, the disinhibited pyramidal cells had higher increase in bursting than in single spike firing rate as a result of CCK silencing. In addition, the firing activity patterns during exploratory periods were more weakly reactivated in sleep for those periods in which CCK-interneuron were silenced than in the unaffected periods. Furthermore, light pulses during sleep disrupted the reactivation of recent waking patterns. Hence, silencing CCK neurons during exploration suppressed the reactivation of waking firing patterns in sleep and CCK interneuron activity was also required during sleep for the normal reactivation of waking patterns. These findings demonstrate the involvement of CCK cells in reactivation-related memory consolidation. An important part of our analysis was to test the relationship of the identified CCKinterneurons to brain oscillations. Our findings showed that these cells exhibited different oscillatory behaviour during anaesthesia and natural waking and sleep conditions. We showed that: 1) Contrary to the past studies performed under anaesthesia, the identified CCKinterneurons fired on the descending portion of the theta phase in waking exploration. 2) CCKinterneuron preferred phases around the trough of gamma oscillations. 3) Contrary to anaesthesia conditions, the average firing rate of the CCK-interneurons increased around the peak activity of the sharp-wave ripple (SWR) events in natural sleep, which is congruent with new reports about their functional connectivity. We also found that light driven CCK-interneuron silencing altered the dynamics on the CA1 network oscillatory activity: 1) Pyramidal cells negatively shifted their preferred theta phases when the light was applied, while interneurons responses were less consistent. 2) As a population, pyramidal cells negatively shifted their preferred activity during gamma oscillations, albeit we did not find gamma modulation differences related to the light application when pyramidal cells were subdivided into the disinhibited and unaffected groups. 3) During the peak of SWR events, all but the CCK-interneurons had a reduction in their relative firing rate change during the light application as compared to the change observed at SWR initiation. Finally, regarding to the place field activity of the recorded pyramidal neurons, we showed that the disinhibited pyramidal cells had reduced place field similarity, coherence and spatial information, but only during the light application. The mechanisms behind such observed behaviours might involve eCB signalling and plastic changes in CCK-interneuron synapses. In conclusion, the observed changes related to the light-mediated silencing of CCKinterneurons have unravelled characteristics of this interneuron subpopulation that might change the understanding not only of their particular network interactions, but also of the current theories about the emergence of certain cognitive processes such as place coding needed for navigation or hippocampus-dependent memory consolidation. "}],"_id":"6849","month":"09","supervisor":[{"orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L"}],"department":[{"_id":"JoCs"}],"author":[{"full_name":"Rangel Guerrero, Dámaris K","first_name":"Dámaris K","last_name":"Rangel Guerrero","id":"4871BCE6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8602-4374"}],"year":"2019","OA_place":"publisher","article_processing_charge":"No","title":"The role of CCK-interneurons in regulating hippocampal network dynamics","oa_version":"Published Version","publication_status":"published","publisher":"Institute of Science and Technology Austria","status":"public","date_created":"2019-09-06T06:54:16Z","date_published":"2019-09-09T00:00:00Z","ddc":["570"],"day":"09","page":"97","type":"dissertation","language":[{"iso":"eng"}]},{"date_published":"2019-02-04T00:00:00Z","type":"dissertation","page":"138","ddc":["575"],"day":"04","language":[{"iso":"eng"}],"OA_place":"publisher","year":"2019","author":[{"orcid":"0000-0002-8600-0671","last_name":"Narasimhan","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","full_name":"Narasimhan, Madhumitha","first_name":"Madhumitha"}],"oa_version":"Published Version","article_processing_charge":"No","title":"Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants ","publisher":"Institute of Science and Technology Austria","publication_status":"published","status":"public","date_created":"2019-04-09T14:37:06Z","alternative_title":["ISTA Thesis"],"date_updated":"2026-04-08T14:00:24Z","related_material":{"record":[{"status":"public","id":"412","relation":"part_of_dissertation"}]},"oa":1,"corr_author":"1","month":"02","abstract":[{"text":"Clathrin-Mediated Endocytosis (CME) is an aspect of cellular trafficking that is constantly regulated for mediating developmental and physiological responses. The main aim of my thesis is to decipher the basic mechanisms of CME and post-endocytic trafficking in the whole multicellular organ systems of Arabidopsis. The first chapter of my thesis describes the search for new components involved in CME. Tandem affinity purification was conducted using CLC and its interacting partners were identified. Amongst the identified proteins were the Auxilin-likes1 and 2 (Axl1/2), putative uncoating factors, for which we made a full functional analysis. Over-expression of Axl1/2 causes extreme modifications in the dynamics of the machinery proteins and inhibition of endocytosis altogether. However the loss of function of the axl1/2 did not present any cellular or physiological phenotype, meaning Auxilin-likes do not form the major uncoating machinery. The second chapter of my thesis describes the establishment/utilisation of techniques to capture the dynamicity and the complexity of CME and post-endocytic trafficking. We have studied the development of endocytic pits at the PM – specifically, the mode of membrane remodeling during pit development and the role of actin in it, given plant cells possess high turgor pressure. Utilizing the improved z-resolution of TIRF and VAEM techniques, we captured the time-lapse of the endocytic events at the plasma membrane; and using particle detection software, we quantitatively analysed all the endocytic trajectories in an unbiased way to obtain the endocytic rate of the system. This together with the direct analysis of cargo internalisation from the PM provided an estimate on the endocytic potential of the cell. We also developed a methodology for ultrastructural analysis of different populations of Clathrin-Coated Structures (CCSs) in both PM and endomembranes in unroofed protoplasts. Structural analysis, together with the intensity profile of CCSs at the PM show that the mode of CCP development at the PM follows ‘Constant curvature model’; meaning that clathrin polymerisation energy is a major contributing factor of membrane remodeling. In addition, other analyses clearly show that actin is not required for membrane remodeling during invagination or any other step of CCP development, despite the prevalent high turgor pressure. However, actin is essential in orchestrating the post-endocytic trafficking of CCVs facilitating the EE formation. We also observed that the uncoating process post-endocytosis is not immediate; an alternative mechanism of uncoating – Sequential multi-step process – functions in the cell. Finally we also looked at one of the important physiological stimuli modulating the process – hormone, auxin. auxin has been known to influence CME before. We have made a detailed study on the concentration-time based effect of auxin on the machinery proteins, CCP development, and the specificity of cargoes endocytosed. To this end, we saw no general effect of auxin on CME at earlier time points. However, very low concentration of IAA, such as 50nM, accelerates endocytosis of specifically PIN2 through CME. Such a tight regulatory control with high specificity to PIN2 could be essential in modulating its polarity. 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Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596"}],"department":[{"_id":"JiFr"}],"degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file_date_updated":"2021-02-11T23:30:15Z","citation":{"ieee":"M. Narasimhan, “Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants ,” Institute of Science and Technology Austria, 2019.","ista":"Narasimhan M. 2019. Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . Institute of Science and Technology Austria.","mla":"Narasimhan, Madhumitha. <i>Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants </i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/at:ista:th1075\">10.15479/at:ista:th1075</a>.","apa":"Narasimhan, M. (2019). <i>Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:th1075\">https://doi.org/10.15479/at:ista:th1075</a>","chicago":"Narasimhan, Madhumitha. “Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants .” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/at:ista:th1075\">https://doi.org/10.15479/at:ista:th1075</a>.","ama":"Narasimhan M. Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . 2019. doi:<a href=\"https://doi.org/10.15479/at:ista:th1075\">10.15479/at:ista:th1075</a>","short":"M. Narasimhan, Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants , Institute of Science and Technology Austria, 2019."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.15479/at:ista:th1075","has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"}],"publication_identifier":{"issn":["2663-337X"]}},{"supervisor":[{"orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","first_name":"Michael K"}],"department":[{"_id":"MiSi"}],"month":"10","_id":"6947","abstract":[{"lang":"eng","text":"Lymph nodes  are es s ential organs  of the immune  s ys tem where adaptive immune responses originate, and consist of various leukocyte populations and a stromal backbone. Fibroblastic reticular  cells (FRCs) are  the  main  stromal  cells and  form  a sponge-like extracellular matrix network,   called  conduits ,  which  they   thems elves   enwrap   and  contract.  Lymph,  containing  s oluble  antigens ,  arrive in  lymph  nodes  via afferent lymphatic  vessels that  connect  to  the  s ubcaps ular  s inus   and  conduit  network.  According  to  the  current  paradigm,  the  conduit  network   dis tributes   afferent  lymph  through   lymph  nodes   and  thus   provides   acces s   for  immune  cells to lymph-borne  antigens. An  elas tic  caps ule  s urrounds   the  organ  and  confines   the immune  cells and  FRC  network.   Lymph   nodes   are  completely  packed  with  lymphocytes   and  lymphocyte  numbers  directly  dictates  the size  of  the  organ.  Although  lymphocytes   cons tantly  enter  and  leave  the  lymph  node,  its   s ize  remains   remarkedly   s table  under  homeostatic conditions. It is only partly known  how the cellularity and s ize of the lymph node is regulated and  how  the  lymph  node  is able to swell in inflammation.  The role of the FRC network   in  lymph  node   s welling  and  trans fer  of  fluids   are  inves tigated in  this   thes is.  Furthermore,   we  s tudied  what  trafficking  routes   are  us ed  by  cancer  cells   in  lymph  nodes   to  form  distal metastases.We examined the role of a mechanical feedback in regulation of lymph  node swelling. Using parallel plate compression  and UV-las er  cutting  experiments   we  dis s ected  the  mechanical  force dynamics  of the whole lymph  node, and individually for FRCs  and the  caps ule. Physical forces   generated  by  packed  lymphocytes   directly  affect  the  tens ion  on  the  FRC  network  and  capsule,  which  increases  its  resistance  to   swelling.  This  implies  a  feedback  mechanism  between   tis s ue   pres s ure   and   ability   of   lymphocytes    to   enter   the   organ.   Following   inflammation,  the  lymph  node  swells ∼10 fold in two weeks . Yet, what  is  the role  for tens ion on  the  FRC  network   and  caps ule,  and  how  are  lymphocytes   able  to  enter  in  conditions  that resist swelling remain open ques tions . We s how that tens ion on the FRC network is  important to  limit  the  swelling  rate  of  the  organ  so  that  the  FRC  network  can  grow  in  a  coordinated  fashion. This is illustrated by interfering with FRC contractility, which leads to faster swelling rates  and a dis organized FRC network  in the inflamed lymph  node. Growth  of the FRC network  in  turn  is   expected  to  releas e  tens ion  on  thes e  s tructures   and  lowers   the  res is tance  to  swelling, thereby allowing more lymphocytes to enter the organ and drive more swelling. Halt of  swelling coincides   with  a  thickening  of  the  caps ule,  which  forms   a  thick  res is tant  band  around  the organ and lowers  tens ion on the FRC network  to form a new force equilibrium.The  FRC  and  conduit   network   are  further   believed  to  be  a  privileged  s ite  of  s oluble  information  within  the  lymph  node,  although  many  details   remain  uns olved.  We  s how  by  3D  ultra-recons truction   that  FRCs   and  antigen  pres enting  cells   cover  the  s urface  of  conduit  s ys tem for more  than 99% and we dis cus s  the implications  for s oluble information  exchangeat the conduit level.Finally, there  is an ongoing debate in the cancer field whether and how cancer cells  in lymph nodes   s eed  dis tal  metas tas es .  We  s how  that  cancer  cells   infus ed  into  the  lymph  node  can  utilize trafficking routes of immune  cells and  rapidly  migrate  to  blood  vessels. Once  in  the  blood circulation,  these cells are able to form  metastases in distal tissues."}],"file":[{"creator":"fassen","checksum":"53a739752a500f84d0f8ec953cbbd0b6","file_id":"6990","file_size":214172667,"date_created":"2019-11-06T12:30:02Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","embargo_to":"open_access","date_updated":"2020-11-07T23:30:03Z","access_level":"closed","file_name":"PhDthesis_FrankAssen_revised2.docx"},{"file_name":"PhDthesis_FrankAssen_revised2.pdf","embargo":"2020-11-06","relation":"main_file","access_level":"open_access","date_updated":"2020-11-07T23:30:03Z","file_id":"6991","content_type":"application/pdf","date_created":"2019-11-06T12:30:57Z","file_size":83637532,"creator":"fassen","checksum":"8c156b65d9347bb599623a4b09f15d15"}],"oa":1,"corr_author":"1","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"402"},{"status":"public","relation":"part_of_dissertation","id":"664"}]},"alternative_title":["ISTA Thesis"],"date_updated":"2026-04-08T14:01:50Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:6947","has_accepted_license":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","citation":{"short":"F.P. Assen, Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking, Institute of Science and Technology Austria, 2019.","ama":"Assen FP. Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6947\">10.15479/AT:ISTA:6947</a>","chicago":"Assen, Frank P. “Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6947\">https://doi.org/10.15479/AT:ISTA:6947</a>.","apa":"Assen, F. P. (2019). <i>Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6947\">https://doi.org/10.15479/AT:ISTA:6947</a>","ista":"Assen FP. 2019. Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. Institute of Science and Technology Austria.","mla":"Assen, Frank P. <i>Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6947\">10.15479/AT:ISTA:6947</a>.","ieee":"F. P. Assen, “Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking,” Institute of Science and Technology Austria, 2019."},"file_date_updated":"2020-11-07T23:30:03Z","language":[{"iso":"eng"}],"type":"dissertation","page":"142","day":"09","ddc":["570"],"date_published":"2019-10-09T00:00:00Z","status":"public","date_created":"2019-10-14T16:54:52Z","publisher":"Institute of Science and Technology Austria","publication_status":"published","oa_version":"Published Version","title":"Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking","article_processing_charge":"No","OA_place":"publisher","year":"2019","author":[{"orcid":"0000-0003-3470-6119","first_name":"Frank P","full_name":"Assen, Frank P","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","last_name":"Assen"}]},{"language":[{"iso":"eng"}],"type":"dissertation","ddc":["570"],"day":"07","page":"141","date_published":"2019-06-07T00:00:00Z","project":[{"_id":"253CDE40-B435-11E9-9278-68D0E5697425","grant_number":"24283","name":"Examination of the role of a MFS transporter in the migration of Drosophila immune cells"}],"date_created":"2019-06-07T12:49:19Z","status":"public","publisher":"Institute of Science and Technology Austria","publication_status":"published","oa_version":"Published Version","article_processing_charge":"No","title":"The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration","OA_place":"publisher","year":"2019","author":[{"orcid":"0000-0002-7926-0221","id":"46F146FC-F248-11E8-B48F-1D18A9856A87","last_name":"Valosková","full_name":"Valosková, Katarina","first_name":"Katarina"}],"department":[{"_id":"DaSi"}],"supervisor":[{"first_name":"Daria E","full_name":"Siekhaus, Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353"}],"month":"06","_id":"6546","abstract":[{"text":"Invasive migration plays a crucial role not only during development and homeostasis but also in pathological states, such as tumor metastasis. Drosophila macrophage migration into the extended germband is an interesting system to study invasive migration. It carries similarities to immune cell transmigration and cancer cell invasion, therefore studying this process could also bring new understanding of invasion in higher organisms. In our work, we uncover a highly conserved member of the major facilitator family that plays a role in tissue invasion through regulation of glycosylation on a subgroup of proteins and/or by aiding the precise timing of DN-Cadherin downregulation. \r\n\r\nAberrant display of the truncated core1 O-glycan T-antigen is a common feature of human cancer cells that correlates with metastasis. Here we show that T-antigen in Drosophila melanogaster macrophages is involved in their developmentally programmed tissue invasion. Higher macrophage T-antigen levels require an atypical major facilitator superfamily (MFS) member that we named Minerva which enables macrophage dissemination and invasion. We characterize for the first time the T and Tn glycoform O-glycoproteome of the Drosophila melanogaster embryo, and determine that Minerva increases the presence of T-antigen on proteins in pathways previously linked to cancer, most strongly on the sulfhydryl oxidase Qsox1 which we show is required for macrophage tissue entry. Minerva’s vertebrate ortholog, MFSD1, rescues the minerva mutant’s migration and T-antigen glycosylation defects. We thus identify \r\na key conserved regulator that orchestrates O-glycosylation on a protein subset to activate \r\na program governing migration steps important for both development and cancer metastasis. \r\n","lang":"eng"}],"file":[{"checksum":"68949c2d96210b45b981a23e9c9cd93c","creator":"khribikova","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2019-06-07T13:00:04Z","file_size":14110626,"file_id":"6549","access_level":"closed","date_updated":"2020-07-14T12:47:33Z","embargo_to":"open_access","relation":"source_file","file_name":"Katarina Valoskova_PhD thesis_final version.docx"},{"file_name":"Katarina Valoskova_PhD thesis_final version.pdf","embargo":"2020-06-07","relation":"main_file","date_updated":"2021-02-11T11:17:14Z","access_level":"open_access","file_id":"6550","content_type":"application/pdf","date_created":"2019-06-07T13:00:08Z","file_size":10054156,"creator":"khribikova","checksum":"555329cd76e196c96f5278c480ee2e6e"}],"corr_author":"1","oa":1,"alternative_title":["ISTA Thesis"],"date_updated":"2026-04-08T13:58:36Z","related_material":{"record":[{"status":"public","id":"544","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6187","status":"public"}]},"acknowledged_ssus":[{"_id":"Bio"}],"publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:6546","has_accepted_license":"1","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file_date_updated":"2021-02-11T11:17:14Z","citation":{"ama":"Valosková K. The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6546\">10.15479/AT:ISTA:6546</a>","short":"K. Valosková, The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration, Institute of Science and Technology Austria, 2019.","ieee":"K. Valosková, “The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration,” Institute of Science and Technology Austria, 2019.","chicago":"Valosková, Katarina. “The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6546\">https://doi.org/10.15479/AT:ISTA:6546</a>.","apa":"Valosková, K. (2019). <i>The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6546\">https://doi.org/10.15479/AT:ISTA:6546</a>","mla":"Valosková, Katarina. <i>The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6546\">10.15479/AT:ISTA:6546</a>.","ista":"Valosková K. 2019. The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration. Institute of Science and Technology Austria."}},{"publisher":"Elsevier","publication_status":"published","acknowledgement":"We thank R Chait and M Lagator for sharing Bacillus subtilis CR_Y1 and pZS*_2R-cIPtet-Venus-Prm, respectively. We are grateful to T Pilizota and all members of the Guet lab for critically reading the manuscript. We also thank the Bioimaging facility at IST Austria for assistance using the FACSAria III system.\r\n\r\n","status":"public","date_created":"2018-12-11T11:46:50Z","author":[{"orcid":"0000-0003-3768-877X","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","last_name":"Tomasek","first_name":"Kathrin","full_name":"Tomasek, Kathrin"},{"orcid":"0000-0001-5396-4346","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias","first_name":"Tobias"},{"last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"}],"year":"2018","article_processing_charge":"No","title":"Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains","oa_version":"None","page":"40 - 52","day":"20","type":"journal_article","scopus_import":"1","isi":1,"language":[{"iso":"eng"}],"date_published":"2018-02-20T00:00:00Z","doi":"10.1016/j.jbiotec.2018.01.008","acknowledged_ssus":[{"_id":"Bio"}],"publist_id":"7317","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"K. Tomasek, T. Bergmiller, and C. C. Guet, “Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains,” <i>Journal of Biotechnology</i>, vol. 268. Elsevier, pp. 40–52, 2018.","chicago":"Tomasek, Kathrin, Tobias Bergmiller, and Calin C Guet. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” <i>Journal of Biotechnology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.jbiotec.2018.01.008\">https://doi.org/10.1016/j.jbiotec.2018.01.008</a>.","mla":"Tomasek, Kathrin, et al. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” <i>Journal of Biotechnology</i>, vol. 268, Elsevier, 2018, pp. 40–52, doi:<a href=\"https://doi.org/10.1016/j.jbiotec.2018.01.008\">10.1016/j.jbiotec.2018.01.008</a>.","ista":"Tomasek K, Bergmiller T, Guet CC. 2018. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. 268, 40–52.","apa":"Tomasek, K., Bergmiller, T., &#38; Guet, C. C. (2018). Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. <i>Journal of Biotechnology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jbiotec.2018.01.008\">https://doi.org/10.1016/j.jbiotec.2018.01.008</a>","ama":"Tomasek K, Bergmiller T, Guet CC. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. <i>Journal of Biotechnology</i>. 2018;268:40-52. doi:<a href=\"https://doi.org/10.1016/j.jbiotec.2018.01.008\">10.1016/j.jbiotec.2018.01.008</a>","short":"K. Tomasek, T. Bergmiller, C.C. Guet, Journal of Biotechnology 268 (2018) 40–52."},"quality_controlled":"1","month":"02","_id":"503","abstract":[{"lang":"eng","text":"Buffers are essential for diluting bacterial cultures for flow cytometry analysis in order to study bacterial physiology and gene expression parameters based on fluorescence signals. Using a variety of constitutively expressed fluorescent proteins in Escherichia coli K-12 strain MG1655, we found strong artifactual changes in fluorescence levels after dilution into the commonly used flow cytometry buffer phosphate-buffered saline (PBS) and two other buffer solutions, Tris-HCl and M9 salts. These changes appeared very rapidly after dilution, and were linked to increased membrane permeability and loss in cell viability. We observed buffer-related effects in several different E. coli strains, K-12, C and W, but not E. coli B, which can be partially explained by differences in lipopolysaccharide (LPS) and outer membrane composition. Supplementing the buffers with divalent cations responsible for outer membrane stability, Mg2+ and Ca2+, preserved fluorescence signals, membrane integrity and viability of E. coli. Thus, stabilizing the bacterial outer membrane is essential for precise and unbiased measurements of fluorescence parameters using flow cytometry."}],"intvolume":"       268","publication":"Journal of Biotechnology","department":[{"_id":"CaGu"}],"volume":268,"date_updated":"2024-10-09T20:58:29Z","external_id":{"isi":["000425715100006"]},"corr_author":"1"},{"date_published":"2018-04-12T00:00:00Z","pubrep_id":"998","language":[{"iso":"eng"}],"type":"dissertation","page":"99","day":"12","ddc":["571","599","610"],"oa_version":"Published Version","article_processing_charge":"No","title":"Branched actin networks in dendritic cell biology","year":"2018","author":[{"last_name":"Leithner","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander F","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X"}],"date_created":"2018-12-11T11:45:49Z","status":"public","acknowledgement":"First of all I would like to thank Michael Sixt for giving me the opportunity to work in \r\nhis group and for his support throughout the years. He is a truly inspiring person and \r\nthe  best  boss  one  can  imagine.  I  would  also  like  to  thank  all  current  and  past \r\nmembers of the Sixt group for their help and the great working atmosphere in the lab. \r\nIt is a true privilege to work with such a bright, funny and friendly group of people and \r\nI’m  proud  that  I  could  be  part  of  it.  Furthermore,  I  would  like  to  say  ‘thank  you’  to Daria Siekhaus for all the meetings and discussion we had throughout the years \r\nand to  Federica  Benvenuti  for  being  part  of  my  committee.  I  am  also  grateful  to  Jack \r\nMerrin  in  the  nanofabrication  facility  and  all  the  people  working  in  the  bioimaging-\r\n, the electron microscopy- and the preclinical facilities.","publication_status":"published","publisher":"Institute of Science and Technology Austria","oa":1,"corr_author":"1","related_material":{"record":[{"status":"public","id":"1321","relation":"part_of_dissertation"}]},"date_updated":"2025-09-22T08:27:34Z","alternative_title":["ISTA Thesis"],"supervisor":[{"orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt"}],"department":[{"_id":"MiSi"}],"abstract":[{"text":"In the here presented thesis, we explore the role of branched actin networks in cell migration and antigen presentation, the two most relevant processes in dendritic cell biology. Branched actin networks construct lamellipodial protrusions at the leading edge of migrating cells. These are typically seen as adhesive structures, which mediate force transduction to the extracellular matrix that leads to forward locomotion. We ablated Arp2/3 nucleation promoting factor WAVE in DCs and found that the resulting cells lack lamellipodial protrusions. Instead, depending on the maturation state, one or multiple filopodia were formed. By challenging these cells in a variety of migration assays we found that lamellipodial protrusions are dispensable for the locomotion of leukocytes and actually dampen the speed of migration. However, lamellipodia are critically required to negotiate complex environments that DCs experience while they travel to the next draining lymph node. Taken together our results suggest that leukocyte lamellipodia have rather a sensory- than a force transducing function. Furthermore, we show for the first time structure and dynamics of dendritic cell F-actin at the immunological synapse with naïve T cells. Dendritic cell F-actin appears as dynamic foci that are nucleated by the Arp2/3 complex. WAVE ablated dendritic cells show increased membrane tension, leading to an altered ultrastructure of the immunological synapse and severe T cell priming defects. These results point towards a previously unappreciated role of the cellular mechanics of dendritic cells in T cell activation. Additionally, we present a novel cell culture based system for the differentiation of dendritic cells from conditionally immortalized hematopoietic precursors. These precursor cells are genetically tractable via the CRISPR/Cas9 system while they retain their ability to differentiate into highly migratory dendritic cells and other immune cells. This will foster the study of all aspects of dendritic cell biology and beyond. ","lang":"eng"}],"_id":"323","file":[{"file_name":"PhD_thesis_AlexLeithner_final_version.docx","access_level":"closed","date_updated":"2021-02-11T23:30:17Z","embargo_to":"open_access","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2019-04-05T09:23:11Z","file_size":29027671,"file_id":"6219","checksum":"d5e3edbac548c26c1fa43a4b37a54a4c","creator":"dernst"},{"creator":"dernst","checksum":"071f7476db29e41146824ebd0697cb10","file_id":"6220","file_size":66045341,"date_created":"2019-04-05T09:23:11Z","content_type":"application/pdf","relation":"main_file","date_updated":"2021-02-11T11:17:16Z","access_level":"open_access","file_name":"PhD_thesis_AlexLeithner.pdf","embargo":"2019-04-15"}],"month":"04","citation":{"ama":"Leithner AF. Branched actin networks in dendritic cell biology. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_998\">10.15479/AT:ISTA:th_998</a>","short":"A.F. Leithner, Branched Actin Networks in Dendritic Cell Biology, Institute of Science and Technology Austria, 2018.","ieee":"A. F. Leithner, “Branched actin networks in dendritic cell biology,” Institute of Science and Technology Austria, 2018.","chicago":"Leithner, Alexander F. “Branched Actin Networks in Dendritic Cell Biology.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_998\">https://doi.org/10.15479/AT:ISTA:th_998</a>.","apa":"Leithner, A. F. (2018). <i>Branched actin networks in dendritic cell biology</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_998\">https://doi.org/10.15479/AT:ISTA:th_998</a>","ista":"Leithner AF. 2018. Branched actin networks in dendritic cell biology. Institute of Science and Technology Austria.","mla":"Leithner, Alexander F. <i>Branched Actin Networks in Dendritic Cell Biology</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_998\">10.15479/AT:ISTA:th_998</a>."},"file_date_updated":"2021-02-11T23:30:17Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","degree_awarded":"PhD","publist_id":"7542","publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"doi":"10.15479/AT:ISTA:th_998","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"doi":"10.1126/science.aal3662","publist_id":"7428","acknowledged_ssus":[{"_id":"Bio"}],"citation":{"ama":"Brown M, Assen FP, Leithner AF, et al. Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. <i>Science</i>. 2018;359(6382):1408-1411. doi:<a href=\"https://doi.org/10.1126/science.aal3662\">10.1126/science.aal3662</a>","short":"M. Brown, F.P. Assen, A.F. Leithner, J. Abe, H. Schachner, G. Asfour, Z. Bagó Horváth, J. Stein, P. Uhrin, M.K. Sixt, D. Kerjaschki, Science 359 (2018) 1408–1411.","ieee":"M. Brown <i>et al.</i>, “Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice,” <i>Science</i>, vol. 359, no. 6382. American Association for the Advancement of Science, pp. 1408–1411, 2018.","chicago":"Brown, Markus, Frank P Assen, Alexander F Leithner, Jun Abe, Helga Schachner, Gabriele Asfour, Zsuzsanna Bagó Horváth, et al. “Lymph Node Blood Vessels Provide Exit Routes for Metastatic Tumor Cell Dissemination in Mice.” <i>Science</i>. American Association for the Advancement of Science, 2018. <a href=\"https://doi.org/10.1126/science.aal3662\">https://doi.org/10.1126/science.aal3662</a>.","ista":"Brown M, Assen FP, Leithner AF, Abe J, Schachner H, Asfour G, Bagó Horváth Z, Stein J, Uhrin P, Sixt MK, Kerjaschki D. 2018. Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. 359(6382), 1408–1411.","mla":"Brown, Markus, et al. “Lymph Node Blood Vessels Provide Exit Routes for Metastatic Tumor Cell Dissemination in Mice.” <i>Science</i>, vol. 359, no. 6382, American Association for the Advancement of Science, 2018, pp. 1408–11, doi:<a href=\"https://doi.org/10.1126/science.aal3662\">10.1126/science.aal3662</a>.","apa":"Brown, M., Assen, F. P., Leithner, A. F., Abe, J., Schachner, H., Asfour, G., … Kerjaschki, D. (2018). Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aal3662\">https://doi.org/10.1126/science.aal3662</a>"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"url":"https://doi.org/10.1126/science.aal3662","open_access":"1"}],"quality_controlled":"1","intvolume":"       359","_id":"402","abstract":[{"lang":"eng","text":"During metastasis, malignant cells escape the primary tumor, intravasate lymphatic vessels, and reach draining sentinel lymph nodes before they colonize distant organs via the blood circulation. Although lymph node metastasis in cancer patients correlates with poor prognosis, evidence is lacking as to whether and how tumor cells enter the bloodstream via lymph nodes. To investigate this question, we delivered carcinoma cells into the lymph nodes of mice by microinfusing the cells into afferent lymphatic vessels. We found that tumor cells rapidly infiltrated the lymph node parenchyma, invaded blood vessels, and seeded lung metastases without involvement of the thoracic duct. These results suggest that the lymph node blood vessels can serve as an exit route for systemic dissemination of cancer cells in experimental mouse models. Whether this form of tumor cell spreading occurs in cancer patients remains to be determined."}],"article_type":"original","month":"03","volume":359,"department":[{"_id":"MiSi"}],"publication":"Science","external_id":{"pmid":["29567714"],"isi":["000428043600047"]},"related_material":{"record":[{"status":"public","id":"6947","relation":"dissertation_contains"}]},"date_updated":"2026-05-20T22:31:02Z","corr_author":"1","oa":1,"publication_status":"published","publisher":"American Association for the Advancement of Science","status":"public","date_created":"2018-12-11T11:46:16Z","acknowledgement":"M.B. was supported by the Cell Communication in Health and Disease graduate study program of the Austrian Science Fund (FWF) and the Medical University of Vienna. M.S. was supported by the European Research Council (grant ERC GA 281556) and an FWF START award.\r\nWe thank C. Moussion for establishing the intralymphatic injection at IST Austria and for providing anti-PNAd hybridoma supernatant, R. Förster and A. Braun for sharing the intralymphatic injection technology, K. Vaahtomeri for the lentiviral constructs, M. Hons for establishing in vivo multiphoton imaging, the Sixt lab for intellectual input, M. Schunn for help with the design of the in vivo experiments, F. Langer for technical assistance with the in vivo experiments, the bioimaging facility of IST Austria for support, and R. Efferl for providing the CT26 cell line.","project":[{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes","grant_number":"Y 564-B12","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425"}],"year":"2018","author":[{"first_name":"Markus","full_name":"Brown, Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","last_name":"Brown"},{"id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","last_name":"Assen","full_name":"Assen, Frank P","first_name":"Frank P","orcid":"0000-0003-3470-6119"},{"last_name":"Leithner","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander F","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X"},{"last_name":"Abe","full_name":"Abe, Jun","first_name":"Jun"},{"last_name":"Schachner","full_name":"Schachner, Helga","first_name":"Helga"},{"last_name":"Asfour","first_name":"Gabriele","full_name":"Asfour, Gabriele"},{"first_name":"Zsuzsanna","full_name":"Bagó Horváth, Zsuzsanna","last_name":"Bagó Horváth"},{"last_name":"Stein","full_name":"Stein, Jens","first_name":"Jens"},{"full_name":"Uhrin, Pavel","first_name":"Pavel","last_name":"Uhrin"},{"orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt"},{"last_name":"Kerjaschki","first_name":"Dontscho","full_name":"Kerjaschki, Dontscho"}],"pmid":1,"oa_version":"Published Version","ec_funded":1,"article_processing_charge":"No","title":"Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice","type":"journal_article","day":"23","page":"1408 - 1411","language":[{"iso":"eng"}],"isi":1,"scopus_import":"1","date_published":"2018-03-23T00:00:00Z","issue":"6382"},{"month":"03","_id":"395","abstract":[{"lang":"eng","text":"Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. Despite the remarkable number of scientific breakthroughs of the last 100 years, the treatment of neurodevelopmental disorders (e.g. autism spectrum disorder, intellectual disability, epilepsy) remains a great challenge. Recent advancements in geno mics, like whole-exome or whole-genome sequencing, have enabled scientists to identify numerous mutations underlying neurodevelopmental disorders. Given the few hundred risk genes that were discovered, the etiological variability and the heterogeneous phenotypic outcomes, the need for genotype -along with phenotype- based diagnosis of individual patients becomes a requisite. Driven by this rationale, in a previous study our group described mutations, identified via whole - exome sequencing, in the gene BCKDK – encoding for a key regulator of branched chain amin o acid (BCAA) catabolism - as a cause of ASD. Following up on the role of BCAAs, in the study described here we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized mainly at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation and severe neurolo gical abnormalities. Additionally, deletion of Slc7a5 from the neural progenitor cell population leads to microcephaly. Interestingly, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Furthermore, whole - exome sequencing of patients diagnosed with neurological dis o r ders helped us identify several patients with autistic traits, microcephaly and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. In conclusion, our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for t he BCAA s in human bra in function. Together with r ecent studies (described in chapter two) that have successfully made the transition into clinical practice, our findings on the role of B CAAs might have a crucial impact on the development of novel individualized therapeutic strategies for ASD. "}],"file":[{"file_id":"6217","file_size":43684035,"date_created":"2019-04-05T09:19:17Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"dernst","checksum":"9f5231c96e0ad945040841a8630232da","file_name":"2018_Thesis_Tarlungeanu_source.docx","relation":"source_file","embargo_to":"open_access","date_updated":"2021-02-11T23:30:15Z","access_level":"closed"},{"creator":"dernst","checksum":"0c33c370aa2010df5c552db57a6d01e9","file_id":"6218","content_type":"application/pdf","date_created":"2019-04-05T09:19:17Z","file_size":30511532,"relation":"main_file","access_level":"open_access","date_updated":"2021-02-11T11:17:16Z","file_name":"2018_Thesis_Tarlungeanu.pdf","embargo":"2018-03-15"}],"department":[{"_id":"GaNo"}],"supervisor":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1183"}]},"date_updated":"2026-04-08T14:15:20Z","alternative_title":["ISTA Thesis"],"oa":1,"corr_author":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.15479/AT:ISTA:th_992","has_accepted_license":"1","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"}],"publist_id":"7434","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"chicago":"Tarlungeanu, Dora-Clara. “The Branched Chain Amino Acids in Autism Spectrum Disorders .” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_992\">https://doi.org/10.15479/AT:ISTA:th_992</a>.","mla":"Tarlungeanu, Dora-Clara. <i>The Branched Chain Amino Acids in Autism Spectrum Disorders </i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_992\">10.15479/AT:ISTA:th_992</a>.","ista":"Tarlungeanu D-C. 2018. The branched chain amino acids in autism spectrum disorders . Institute of Science and Technology Austria.","apa":"Tarlungeanu, D.-C. (2018). <i>The branched chain amino acids in autism spectrum disorders </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_992\">https://doi.org/10.15479/AT:ISTA:th_992</a>","ieee":"D.-C. Tarlungeanu, “The branched chain amino acids in autism spectrum disorders ,” Institute of Science and Technology Austria, 2018.","short":"D.-C. Tarlungeanu, The Branched Chain Amino Acids in Autism Spectrum Disorders , Institute of Science and Technology Austria, 2018.","ama":"Tarlungeanu D-C. The branched chain amino acids in autism spectrum disorders . 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_992\">10.15479/AT:ISTA:th_992</a>"},"file_date_updated":"2021-02-11T23:30:15Z","type":"dissertation","page":"88","day":"01","ddc":["570","616"],"language":[{"iso":"eng"}],"pubrep_id":"992","date_published":"2018-03-01T00:00:00Z","publisher":"Institute of Science and Technology Austria","publication_status":"published","project":[{"name":"Transmembrane Transporters in Health and Disease","grant_number":"F03523","call_identifier":"FWF","_id":"25473368-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:46:14Z","status":"public","OA_place":"publisher","year":"2018","author":[{"id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","last_name":"Tarlungeanu","first_name":"Dora-Clara","full_name":"Tarlungeanu, Dora-Clara"}],"oa_version":"Published Version","title":"The branched chain amino acids in autism spectrum disorders ","article_processing_charge":"No"},{"quality_controlled":"1","citation":{"ama":"Baranova NS, Loose M. Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers. In: Echard A, ed. <i>Cytokinesis</i>. Vol 137. Academic Press; 2017:355-370. doi:<a href=\"https://doi.org/10.1016/bs.mcb.2016.03.036\">10.1016/bs.mcb.2016.03.036</a>","short":"N.S. Baranova, M. Loose, in:, A. Echard (Ed.), Cytokinesis, Academic Press, 2017, pp. 355–370.","ieee":"N. S. Baranova and M. Loose, “Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers,” in <i>Cytokinesis</i>, vol. 137, A. Echard, Ed. Academic Press, 2017, pp. 355–370.","chicago":"Baranova, Natalia S., and Martin Loose. “Single-Molecule Measurements to Study Polymerization Dynamics of FtsZ-FtsA Copolymers.” In <i>Cytokinesis</i>, edited by Arnaud  Echard, 137:355–70. Academic Press, 2017. <a href=\"https://doi.org/10.1016/bs.mcb.2016.03.036\">https://doi.org/10.1016/bs.mcb.2016.03.036</a>.","apa":"Baranova, N. S., &#38; Loose, M. (2017). Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers. In A. Echard (Ed.), <i>Cytokinesis</i> (Vol. 137, pp. 355–370). Academic Press. <a href=\"https://doi.org/10.1016/bs.mcb.2016.03.036\">https://doi.org/10.1016/bs.mcb.2016.03.036</a>","ista":"Baranova NS, Loose M. 2017.Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers. In: Cytokinesis. Methods in Cell Biology, vol. 137, 355–370.","mla":"Baranova, Natalia S., and Martin Loose. “Single-Molecule Measurements to Study Polymerization Dynamics of FtsZ-FtsA Copolymers.” <i>Cytokinesis</i>, edited by Arnaud  Echard, vol. 137, Academic Press, 2017, pp. 355–70, doi:<a href=\"https://doi.org/10.1016/bs.mcb.2016.03.036\">10.1016/bs.mcb.2016.03.036</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0091-679X"]},"publist_id":"6134","acknowledged_ssus":[{"_id":"Bio"}],"doi":"10.1016/bs.mcb.2016.03.036","alternative_title":["Methods in Cell Biology"],"date_updated":"2025-07-10T11:50:24Z","external_id":{"isi":["000403542900022"]},"volume":137,"publication":"Cytokinesis","department":[{"_id":"MaLo"}],"_id":"1213","intvolume":"       137","abstract":[{"text":"Bacterial cytokinesis is commonly initiated by the Z-ring, a dynamic cytoskeletal structure that assembles at the site of division. Its primary component is FtsZ, a tubulin-like GTPase, that like its eukaryotic relative forms protein filaments in the presence of GTP. Since the discovery of the Z-ring 25 years ago, various models for the role of FtsZ have been suggested. However, important information about the architecture and dynamics of FtsZ filaments during cytokinesis is still missing. One reason for this lack of knowledge has been the small size of bacteria, which has made it difficult to resolve the orientation and dynamics of individual FtsZ filaments in the Z-ring. While superresolution microscopy experiments have helped to gain more information about the organization of the Z-ring in the dividing cell, they were not yet able to elucidate a mechanism of how FtsZ filaments reorganize during assembly and disassembly of the Z-ring. In this chapter, we explain how to use an in vitro reconstitution approach to investigate the self-organization of FtsZ filaments recruited to a biomimetic lipid bilayer by its membrane anchor FtsA. We show how to perform single-molecule experiments to study the behavior of individual FtsZ monomers during the constant reorganization of the FtsZ-FtsA filament network. We describe how to analyze the dynamics of single molecules and explain why this information can help to shed light onto possible mechanism of Z-ring constriction. We believe that similar experimental approaches will be useful to study the mechanism of membrane-based polymerization of other cytoskeletal systems, not only from prokaryotic but also eukaryotic origin.","lang":"eng"}],"month":"12","title":"Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers","article_processing_charge":"No","oa_version":"None","ec_funded":1,"author":[{"last_name":"Baranova","id":"38661662-F248-11E8-B48F-1D18A9856A87","full_name":"Baranova, Natalia","first_name":"Natalia","orcid":"0000-0002-3086-9124"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724"}],"year":"2017","acknowledgement":"Natalia Baranova is supported by an EMBO Long-Term Fellowship (EMBO ALTF 1163-2015) and Martin Loose by an ERC Starting Grant (ERCStG-2015-SelfOrganiCell).","date_created":"2018-12-11T11:50:45Z","status":"public","project":[{"grant_number":"ALTF 2015-1163","name":"Synthesis of bacterial cell wall","_id":"2596EAB6-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","publisher":"Academic Press","editor":[{"first_name":"Arnaud ","full_name":"Echard, Arnaud ","last_name":"Echard"}],"date_published":"2017-12-01T00:00:00Z","isi":1,"language":[{"iso":"eng"}],"scopus_import":"1","page":"355 - 370","day":"01","type":"book_chapter"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"e55044","citation":{"short":"D. von Wangenheim, R. Hauschild, J. Friml, Journal of Visualized Experiments JoVE 2017 (2017).","ama":"von Wangenheim D, Hauschild R, Friml J. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. <i>Journal of visualized experiments JoVE</i>. 2017;2017(119). doi:<a href=\"https://doi.org/10.3791/55044\">10.3791/55044</a>","mla":"von Wangenheim, Daniel, et al. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” <i>Journal of Visualized Experiments JoVE</i>, vol. 2017, no. 119, e55044, Journal of Visualized Experiments, 2017, doi:<a href=\"https://doi.org/10.3791/55044\">10.3791/55044</a>.","apa":"von Wangenheim, D., Hauschild, R., &#38; Friml, J. (2017). Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. <i>Journal of Visualized Experiments JoVE</i>. Journal of Visualized Experiments. <a href=\"https://doi.org/10.3791/55044\">https://doi.org/10.3791/55044</a>","ista":"von Wangenheim D, Hauschild R, Friml J. 2017. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. Journal of visualized experiments JoVE. 2017(119), e55044.","chicago":"Wangenheim, Daniel von, Robert Hauschild, and Jiří Friml. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” <i>Journal of Visualized Experiments JoVE</i>. Journal of Visualized Experiments, 2017. <a href=\"https://doi.org/10.3791/55044\">https://doi.org/10.3791/55044</a>.","ieee":"D. von Wangenheim, R. Hauschild, and J. Friml, “Light sheet fluorescence microscopy of plant roots growing on the surface of a gel,” <i>Journal of visualized experiments JoVE</i>, vol. 2017, no. 119. Journal of Visualized Experiments, 2017."},"file_date_updated":"2018-12-12T10:16:32Z","has_accepted_license":"1","doi":"10.3791/55044","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"publist_id":"6302","related_material":{"record":[{"status":"public","id":"5565","relation":"popular_science"}]},"date_updated":"2025-04-15T06:50:23Z","external_id":{"isi":["000397847200041"]},"oa":1,"month":"01","file":[{"file_name":"IST-2017-808-v1+1_2017_VWangenheim_list.pdf","relation":"main_file","access_level":"open_access","date_updated":"2018-12-12T10:16:31Z","file_id":"5219","content_type":"application/pdf","file_size":57678,"date_created":"2018-12-12T10:16:31Z","creator":"system"},{"file_name":"IST-2017-808-v1+2_2017_VWangenheim_article.pdf","date_updated":"2018-12-12T10:16:32Z","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:16:32Z","file_size":1317820,"content_type":"application/pdf","file_id":"5220","creator":"system"}],"abstract":[{"text":"One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. ","lang":"eng"}],"_id":"1078","intvolume":"      2017","publication":"Journal of visualized experiments JoVE","department":[{"_id":"JiFr"},{"_id":"Bio"}],"volume":2017,"author":[{"orcid":"0000-0002-6862-1247","last_name":"Von Wangenheim","id":"49E91952-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","full_name":"Von Wangenheim, Daniel"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","full_name":"Hauschild, Robert","first_name":"Robert","orcid":"0000-0001-9843-3522"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"year":"2017","title":"Light sheet fluorescence microscopy of plant roots growing on the surface of a gel","article_processing_charge":"No","oa_version":"Published Version","ec_funded":1,"publisher":"Journal of Visualized Experiments","publication_status":"published","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"status":"public","date_created":"2018-12-11T11:50:01Z","date_published":"2017-01-18T00:00:00Z","pubrep_id":"808","issue":"119","ddc":["580"],"day":"18","type":"journal_article","scopus_import":"1","isi":1,"language":[{"iso":"eng"}]},{"oa":1,"date_updated":"2025-07-10T11:55:00Z","external_id":{"isi":["000408372400014"]},"publication":"Cell","department":[{"_id":"CaHe"}],"volume":170,"month":"08","file":[{"date_created":"2019-01-18T13:45:40Z","file_size":17666637,"content_type":"application/pdf","file_id":"5852","checksum":"64897b0c5373f22273f598e4672c60ff","creator":"dernst","file_name":"2017_Cell_Samwer.pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:08Z","relation":"main_file"}],"intvolume":"       170","_id":"803","abstract":[{"lang":"eng","text":"Eukaryotic cells store their chromosomes in a single nucleus. This is important to maintain genomic integrity, as chromosomes packaged into separate nuclei (micronuclei) are prone to massive DNA damage. During mitosis, higher eukaryotes disassemble their nucleus and release individualized chromosomes for segregation. How numerous chromosomes subsequently reform a single nucleus has remained unclear. Using image-based screening of human cells, we identified barrier-to-autointegration factor (BAF) as a key factor guiding membranes to form a single nucleus. Unexpectedly, nuclear assembly does not require BAF?s association with inner nuclear membrane proteins but instead relies on BAF?s ability to bridge distant DNA sites. Live-cell imaging and in vitro reconstitution showed that BAF enriches around the mitotic chromosome ensemble to induce a densely cross-bridged chromatin layer that is mechanically stiff and limits membranes to the surface. Our study reveals that BAF-mediated changes in chromosome mechanics underlie nuclear assembly with broad implications for proper genome function."}],"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"M. Samwer, M. Schneider, R. Hoefler, P.S. Schmalhorst, J. Jude, J. Zuber, D. Gerlic, Cell 170 (2017) 956–972.","ama":"Samwer M, Schneider M, Hoefler R, et al. DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes. <i>Cell</i>. 2017;170(5):956-972. doi:<a href=\"https://doi.org/10.1016/j.cell.2017.07.038\">10.1016/j.cell.2017.07.038</a>","apa":"Samwer, M., Schneider, M., Hoefler, R., Schmalhorst, P. S., Jude, J., Zuber, J., &#38; Gerlic, D. (2017). DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2017.07.038\">https://doi.org/10.1016/j.cell.2017.07.038</a>","ista":"Samwer M, Schneider M, Hoefler R, Schmalhorst PS, Jude J, Zuber J, Gerlic D. 2017. DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes. Cell. 170(5), 956–972.","mla":"Samwer, Matthias, et al. “DNA Cross-Bridging Shapes a Single Nucleus from a Set of Mitotic Chromosomes.” <i>Cell</i>, vol. 170, no. 5, Cell Press, 2017, pp. 956–72, doi:<a href=\"https://doi.org/10.1016/j.cell.2017.07.038\">10.1016/j.cell.2017.07.038</a>.","chicago":"Samwer, Matthias, Maximilian Schneider, Rudolf Hoefler, Philipp S Schmalhorst, Julian Jude, Johannes Zuber, and Daniel Gerlic. “DNA Cross-Bridging Shapes a Single Nucleus from a Set of Mitotic Chromosomes.” <i>Cell</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cell.2017.07.038\">https://doi.org/10.1016/j.cell.2017.07.038</a>.","ieee":"M. Samwer <i>et al.</i>, “DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes,” <i>Cell</i>, vol. 170, no. 5. Cell Press, pp. 956–972, 2017."},"file_date_updated":"2020-07-14T12:48:08Z","acknowledged_ssus":[{"_id":"Bio"}],"publication_identifier":{"issn":["0092-8674"]},"publist_id":"6848","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"has_accepted_license":"1","doi":"10.1016/j.cell.2017.07.038","issue":"5","date_published":"2017-08-24T00:00:00Z","scopus_import":"1","isi":1,"language":[{"iso":"eng"}],"ddc":["570"],"page":"956 - 972","day":"24","type":"journal_article","title":"DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes","article_processing_charge":"No","oa_version":"Published Version","author":[{"last_name":"Samwer","first_name":"Matthias","full_name":"Samwer, Matthias"},{"first_name":"Maximilian","full_name":"Schneider, Maximilian","last_name":"Schneider"},{"full_name":"Hoefler, Rudolf","first_name":"Rudolf","last_name":"Hoefler"},{"last_name":"Schmalhorst","id":"309D50DA-F248-11E8-B48F-1D18A9856A87","full_name":"Schmalhorst, Philipp S","first_name":"Philipp S","orcid":"0000-0002-5795-0133"},{"full_name":"Jude, Julian","first_name":"Julian","last_name":"Jude"},{"first_name":"Johannes","full_name":"Zuber, Johannes","last_name":"Zuber"},{"first_name":"Daniel","full_name":"Gerlic, Daniel","last_name":"Gerlic"}],"year":"2017","status":"public","date_created":"2018-12-11T11:48:35Z","publisher":"Cell Press","publication_status":"published"},{"volume":6,"department":[{"_id":"JiFr"},{"_id":"Bio"},{"_id":"CaHe"},{"_id":"EvBe"}],"publication":"eLife","abstract":[{"lang":"eng","text":"Roots navigate through soil integrating environmental signals to orient their growth. The Arabidopsis root is a widely used model for developmental, physiological and cell biological studies. Live imaging greatly aids these efforts, but the horizontal sample position and continuous root tip displacement present significant difficulties. Here, we develop a confocal microscope setup for vertical sample mounting and integrated directional illumination. We present TipTracker – a custom software for automatic tracking of diverse moving objects usable on various microscope setups. Combined, this enables observation of root tips growing along the natural gravity vector over prolonged periods of time, as well as the ability to induce rapid gravity or light stimulation. We also track migrating cells in the developing zebrafish embryo, demonstrating the utility of this system in the acquisition of high-resolution data sets of dynamic samples. We provide detailed descriptions of the tools enabling the easy implementation on other microscopes."}],"_id":"946","intvolume":"         6","file":[{"file_name":"IST-2017-847-v1+1_elife-26792-v2.pdf","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:48:15Z","file_id":"5315","content_type":"application/pdf","file_size":19581847,"date_created":"2018-12-12T10:17:57Z","creator":"system","checksum":"9af3398cb0d81f99d79016a616df22e9"}],"month":"06","oa":1,"external_id":{"isi":["000404728300001"]},"date_updated":"2025-04-15T06:37:26Z","related_material":{"record":[{"status":"public","id":"5566","relation":"popular_science"}]},"publist_id":"6471","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"doi":"10.7554/eLife.26792","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","file_date_updated":"2020-07-14T12:48:15Z","citation":{"short":"D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, J. Friml, ELife 6 (2017).","ama":"von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. Live tracking of moving samples in confocal microscopy for vertically grown roots. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/eLife.26792\">10.7554/eLife.26792</a>","apa":"von Wangenheim, D., Hauschild, R., Fendrych, M., Barone, V., Benková, E., &#38; Friml, J. (2017). Live tracking of moving samples in confocal microscopy for vertically grown roots. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.26792\">https://doi.org/10.7554/eLife.26792</a>","ista":"von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. 2017. Live tracking of moving samples in confocal microscopy for vertically grown roots. eLife. 6, e26792.","mla":"von Wangenheim, Daniel, et al. “Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots.” <i>ELife</i>, vol. 6, e26792, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/eLife.26792\">10.7554/eLife.26792</a>.","chicago":"Wangenheim, Daniel von, Robert Hauschild, Matyas Fendrych, Vanessa Barone, Eva Benková, and Jiří Friml. “Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/eLife.26792\">https://doi.org/10.7554/eLife.26792</a>.","ieee":"D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, and J. Friml, “Live tracking of moving samples in confocal microscopy for vertically grown roots,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017."},"article_number":"e26792","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"isi":1,"scopus_import":"1","type":"journal_article","ddc":["570"],"day":"19","date_published":"2017-06-19T00:00:00Z","pubrep_id":"847","status":"public","date_created":"2018-12-11T11:49:21Z","acknowledgement":"Funding: Marie Curie Actions (FP7/2007-2013 no 291734) to Daniel von Wangenheim; Austrian Science Fund (M 2128-B21) to Matyáš Fendrych; Austrian Science Fund (FWF01_I1774S) to Eva Benková; European Research Council (FP7/2007-2013 no 282300) to Jiří Friml. \r\nThe authors are grateful to the Miba Machine Shop at IST Austria for their contribution to the microscope setup and to Yvonne Kemper for reading, understanding and correcting the manuscript.\r\n#BioimagingFacility","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2572ED28-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular basis of root growth inhibition by auxin","grant_number":"M02128"},{"name":"Hormone cross-talk drives nutrient dependent plant development","grant_number":"I 1774-B16","_id":"2542D156-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"publication_status":"published","publisher":"eLife Sciences Publications","oa_version":"Published Version","ec_funded":1,"title":"Live tracking of moving samples in confocal microscopy for vertically grown roots","article_processing_charge":"Yes","year":"2017","author":[{"orcid":"0000-0002-6862-1247","last_name":"Von Wangenheim","id":"49E91952-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","full_name":"Von Wangenheim, Daniel"},{"full_name":"Hauschild, Robert","first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522"},{"orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","full_name":"Fendrych, Matyas","first_name":"Matyas"},{"first_name":"Vanessa","full_name":"Barone, Vanessa","last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367"},{"orcid":"0000-0002-8510-9739","first_name":"Eva","full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí"}]},{"year":"2017","author":[{"id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","full_name":"Chen, Chong","first_name":"Chong"},{"first_name":"Itaru","full_name":"Arai, Itaru","last_name":"Arai","id":"32A73F6C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Satterield, Rachel","first_name":"Rachel","last_name":"Satterield"},{"first_name":"Samuel","full_name":"Young, Samuel","last_name":"Young"},{"orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas"}],"ec_funded":1,"oa_version":"Published Version","article_processing_charge":"No","title":"Synaptotagmin 2 is the fast Ca2+ sensor at a central inhibitory synapse","publisher":"Cell Press","publication_status":"published","project":[{"_id":"25C26B1E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Mechanisms of transmitter release at GABAergic synapses","grant_number":"P24909-B24"},{"_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"268548","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons"}],"date_created":"2018-12-11T11:50:14Z","status":"public","date_published":"2017-01-17T00:00:00Z","pubrep_id":"751","issue":"3","type":"journal_article","ddc":["571"],"day":"17","page":"723 - 736","scopus_import":"1","language":[{"iso":"eng"}],"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chen, Chong, et al. “Synaptotagmin 2 Is the Fast Ca2+ Sensor at a Central Inhibitory Synapse.” <i>Cell Reports</i>, vol. 18, no. 3, Cell Press, 2017, pp. 723–36, doi:<a href=\"https://doi.org/10.1016/j.celrep.2016.12.067\">10.1016/j.celrep.2016.12.067</a>.","apa":"Chen, C., Arai,  itaru, Satterield, R., Young, S., &#38; Jonas, P. M. (2017). Synaptotagmin 2 is the fast Ca2+ sensor at a central inhibitory synapse. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2016.12.067\">https://doi.org/10.1016/j.celrep.2016.12.067</a>","ista":"Chen C, Arai  itaru, Satterield R, Young S, Jonas PM. 2017. Synaptotagmin 2 is the fast Ca2+ sensor at a central inhibitory synapse. Cell Reports. 18(3), 723–736.","chicago":"Chen, Chong, itaru Arai, Rachel Satterield, Samuel Young, and Peter M Jonas. “Synaptotagmin 2 Is the Fast Ca2+ Sensor at a Central Inhibitory Synapse.” <i>Cell Reports</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.celrep.2016.12.067\">https://doi.org/10.1016/j.celrep.2016.12.067</a>.","ieee":"C. Chen,  itaru Arai, R. Satterield, S. Young, and P. M. Jonas, “Synaptotagmin 2 is the fast Ca2+ sensor at a central inhibitory synapse,” <i>Cell Reports</i>, vol. 18, no. 3. Cell Press, pp. 723–736, 2017.","short":"C. Chen,  itaru Arai, R. Satterield, S. Young, P.M. Jonas, Cell Reports 18 (2017) 723–736.","ama":"Chen C, Arai  itaru, Satterield R, Young S, Jonas PM. Synaptotagmin 2 is the fast Ca2+ sensor at a central inhibitory synapse. <i>Cell Reports</i>. 2017;18(3):723-736. doi:<a href=\"https://doi.org/10.1016/j.celrep.2016.12.067\">10.1016/j.celrep.2016.12.067</a>"},"file_date_updated":"2018-12-12T10:16:09Z","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1016/j.celrep.2016.12.067","has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"publist_id":"6245","publication_identifier":{"issn":["2211-1247"]},"external_id":{"isi":["000396470600013"]},"date_updated":"2026-04-08T14:09:28Z","related_material":{"record":[{"relation":"dissertation_contains","id":"324","status":"public"}]},"oa":1,"month":"01","_id":"1117","abstract":[{"lang":"eng","text":"GABAergic synapses in brain circuits generate inhibitory output signals with submillisecond latency and temporal precision. Whether the molecular identity of the release sensor contributes to these signaling properties remains unclear. Here, we examined the Ca^2+ sensor of exocytosis at GABAergic basket cell (BC) to Purkinje cell (PC) synapses in cerebellum. Immunolabeling suggested that BC terminals selectively expressed synaptotagmin 2 (Syt2), whereas synaptotagmin 1 (Syt1) was enriched in excitatory terminals. Genetic elimination of Syt2 reduced action potential-evoked release to ∼10%, identifying Syt2 as the major Ca^2+ sensor at BC-PC synapses. Differential adenovirus-mediated rescue revealed that Syt2 triggered release with shorter latency and higher temporal precision and mediated faster vesicle pool replenishment than Syt1. Furthermore, deletion of Syt2 severely reduced and delayed disynaptic inhibition following parallel fiber stimulation. Thus, the selective use of Syt2 as release sensor at BC-PC synapses ensures fast and efficient feedforward inhibition in cerebellar microcircuits. #bioimagingfacility-author"}],"intvolume":"        18","file":[{"creator":"system","file_size":4427591,"date_created":"2018-12-12T10:16:09Z","content_type":"application/pdf","file_id":"5195","date_updated":"2018-12-12T10:16:09Z","access_level":"open_access","relation":"main_file","file_name":"IST-2017-751-v1+1_1-s2.0-S2211124716317740-main.pdf"}],"department":[{"_id":"PeJo"}],"publication":"Cell Reports","volume":18},{"project":[{"grant_number":"618444","name":"Molecular Mechanisms of Cerebral Cortex Development","_id":"25D61E48-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25D7962E-B435-11E9-9278-68D0E5697425","grant_number":"RGP0053/2014","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level"}],"date_created":"2018-12-11T11:49:20Z","status":"public","publisher":"Cell Press","publication_status":"published","title":"Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells","article_processing_charge":"No","ec_funded":1,"oa_version":"None","author":[{"orcid":"0000-0002-8483-8753","first_name":"Robert J","full_name":"Beattie, Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","last_name":"Beattie"},{"id":"2C67902A-F248-11E8-B48F-1D18A9856A87","last_name":"Postiglione","full_name":"Postiglione, Maria P","first_name":"Maria P"},{"last_name":"Burnett","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","full_name":"Burnett, Laura","orcid":"0000-0002-8937-410X"},{"last_name":"Laukoter","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","full_name":"Laukoter, Susanne","first_name":"Susanne","orcid":"0000-0002-7903-3010"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher","first_name":"Carmen","full_name":"Streicher, Carmen"},{"full_name":"Pauler, Florian","first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048"},{"last_name":"Xiao","full_name":"Xiao, Guanxi","first_name":"Guanxi"},{"last_name":"Klezovitch","full_name":"Klezovitch, Olga","first_name":"Olga"},{"full_name":"Vasioukhin, Valeri","first_name":"Valeri","last_name":"Vasioukhin"},{"full_name":"Ghashghaei, Troy","first_name":"Troy","last_name":"Ghashghaei"},{"first_name":"Simon","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061"}],"year":"2017","scopus_import":"1","isi":1,"language":[{"iso":"eng"}],"page":"517 - 533.e3","day":"03","type":"journal_article","issue":"3","date_published":"2017-05-03T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"publication_identifier":{"issn":["0896-6273"]},"publist_id":"6473","doi":"10.1016/j.neuron.2017.04.012","quality_controlled":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"short":"R.J. Beattie, M.P. Postiglione, L. Burnett, S. Laukoter, C. Streicher, F. Pauler, G. Xiao, O. Klezovitch, V. Vasioukhin, T. Ghashghaei, S. Hippenmeyer, Neuron 94 (2017) 517–533.e3.","ama":"Beattie RJ, Postiglione MP, Burnett L, et al. Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. <i>Neuron</i>. 2017;94(3):517-533.e3. doi:<a href=\"https://doi.org/10.1016/j.neuron.2017.04.012\">10.1016/j.neuron.2017.04.012</a>","mla":"Beattie, Robert J., et al. “Mosaic Analysis with Double Markers Reveals Distinct Sequential Functions of Lgl1 in Neural Stem Cells.” <i>Neuron</i>, vol. 94, no. 3, Cell Press, 2017, p. 517–533.e3, doi:<a href=\"https://doi.org/10.1016/j.neuron.2017.04.012\">10.1016/j.neuron.2017.04.012</a>.","apa":"Beattie, R. J., Postiglione, M. P., Burnett, L., Laukoter, S., Streicher, C., Pauler, F., … Hippenmeyer, S. (2017). Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. <i>Neuron</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.neuron.2017.04.012\">https://doi.org/10.1016/j.neuron.2017.04.012</a>","ista":"Beattie RJ, Postiglione MP, Burnett L, Laukoter S, Streicher C, Pauler F, Xiao G, Klezovitch O, Vasioukhin V, Ghashghaei T, Hippenmeyer S. 2017. Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. Neuron. 94(3), 517–533.e3.","chicago":"Beattie, Robert J, Maria P Postiglione, Laura Burnett, Susanne Laukoter, Carmen Streicher, Florian Pauler, Guanxi Xiao, et al. “Mosaic Analysis with Double Markers Reveals Distinct Sequential Functions of Lgl1 in Neural Stem Cells.” <i>Neuron</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.neuron.2017.04.012\">https://doi.org/10.1016/j.neuron.2017.04.012</a>.","ieee":"R. J. Beattie <i>et al.</i>, “Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells,” <i>Neuron</i>, vol. 94, no. 3. Cell Press, p. 517–533.e3, 2017."},"publication":"Neuron","department":[{"_id":"SiHi"},{"_id":"MaJö"}],"volume":94,"month":"05","intvolume":"        94","_id":"944","abstract":[{"text":"The concerted production of neurons and glia by neural stem cells (NSCs) is essential for neural circuit assembly. In the developing cerebral cortex, radial glia progenitors (RGPs) generate nearly all neocortical neurons and certain glia lineages. RGP proliferation behavior shows a high degree of non-stochasticity, thus a deterministic characteristic of neuron and glia production. However, the cellular and molecular mechanisms controlling RGP behavior and proliferation dynamics in neurogenesis and glia generation remain unknown. By using mosaic analysis with double markers (MADM)-based genetic paradigms enabling the sparse and global knockout with unprecedented single-cell resolution, we identified Lgl1 as a critical regulatory component. We uncover Lgl1-dependent tissue-wide community effects required for embryonic cortical neurogenesis and novel cell-autonomous Lgl1 functions controlling RGP-mediated glia genesis and postnatal NSC behavior. These results suggest that NSC-mediated neuron and glia production is tightly regulated through the concerted interplay of sequential Lgl1-dependent global and cell intrinsic mechanisms.","lang":"eng"}],"corr_author":"1","date_updated":"2026-04-16T09:57:27Z","external_id":{"isi":["000400466700011"]}},{"quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ama":"Schwarz J, Sixt MK. Quantitative analysis of dendritic cell haptotaxis. <i>Methods in Enzymology</i>. 2016;570:567-581. doi:<a href=\"https://doi.org/10.1016/bs.mie.2015.11.004\">10.1016/bs.mie.2015.11.004</a>","short":"J. Schwarz, M.K. Sixt, Methods in Enzymology 570 (2016) 567–581.","ieee":"J. Schwarz and M. K. Sixt, “Quantitative analysis of dendritic cell haptotaxis,” <i>Methods in Enzymology</i>, vol. 570. Elsevier, pp. 567–581, 2016.","chicago":"Schwarz, Jan, and Michael K Sixt. “Quantitative Analysis of Dendritic Cell Haptotaxis.” <i>Methods in Enzymology</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/bs.mie.2015.11.004\">https://doi.org/10.1016/bs.mie.2015.11.004</a>.","ista":"Schwarz J, Sixt MK. 2016. Quantitative analysis of dendritic cell haptotaxis. Methods in Enzymology. 570, 567–581.","apa":"Schwarz, J., &#38; Sixt, M. K. (2016). Quantitative analysis of dendritic cell haptotaxis. <i>Methods in Enzymology</i>. Elsevier. <a href=\"https://doi.org/10.1016/bs.mie.2015.11.004\">https://doi.org/10.1016/bs.mie.2015.11.004</a>","mla":"Schwarz, Jan, and Michael K. Sixt. “Quantitative Analysis of Dendritic Cell Haptotaxis.” <i>Methods in Enzymology</i>, vol. 570, Elsevier, 2016, pp. 567–81, doi:<a href=\"https://doi.org/10.1016/bs.mie.2015.11.004\">10.1016/bs.mie.2015.11.004</a>."},"acknowledged_ssus":[{"_id":"Bio"}],"publist_id":"5573","doi":"10.1016/bs.mie.2015.11.004","corr_author":"1","date_updated":"2025-09-18T11:02:13Z","external_id":{"isi":["000375648700025"],"pmid":["26921962"]},"publication":"Methods in Enzymology","department":[{"_id":"MiSi"}],"volume":570,"article_type":"original","month":"01","_id":"1597","abstract":[{"text":"Chemokines are the main guidance cues directing leukocyte migration. Opposed to early assumptions, chemokines do not necessarily act as soluble cues but are often immobilized within tissues, e.g., dendritic cell migration toward lymphatic vessels is guided by a haptotactic gradient of the chemokine CCL21. Controlled assay systems to quantitatively study haptotaxis in vitro are still missing. In this chapter, we describe an in vitro haptotaxis assay optimized for the unique properties of dendritic cells. The chemokine CCL21 is immobilized in a bioactive state, using laser-assisted protein adsorption by photobleaching. The cells follow this immobilized CCL21 gradient in a haptotaxis chamber, which provides three dimensionally confined migration conditions.","lang":"eng"}],"intvolume":"       570","title":"Quantitative analysis of dendritic cell haptotaxis","article_processing_charge":"No","ec_funded":1,"oa_version":"None","pmid":1,"author":[{"full_name":"Schwarz, Jan","first_name":"Jan","last_name":"Schwarz","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"}],"year":"2016","project":[{"grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","grant_number":"Y 564-B12"}],"acknowledgement":"This work was supported by the Boehringer Ingelheim Fonds, the European Research Council (ERC StG 281556), and a START Award of the Austrian Science Foundation (FWF). We thank Robert Hauschild, Anne Reversat, and Jack Merrin for valuable input and the Imaging Facility of IST Austria for excellent support.","status":"public","date_created":"2018-12-11T11:52:56Z","publisher":"Elsevier","publication_status":"published","date_published":"2016-01-01T00:00:00Z","scopus_import":"1","isi":1,"language":[{"iso":"eng"}],"day":"01","page":"567 - 581","type":"journal_article"}]