--- _id: '12875' abstract: - lang: eng text: The superior colliculus (SC) in the mammalian midbrain is essential for multisensory integration and is composed of a rich diversity of excitatory and inhibitory neurons and glia. However, the developmental principles directing the generation of SC cell-type diversity are not understood. Here, we pursued systematic cell lineage tracing in silico and in vivo, preserving full spatial information, using genetic mosaic analysis with double markers (MADM)-based clonal analysis with single-cell sequencing (MADM-CloneSeq). The analysis of clonally related cell lineages revealed that radial glial progenitors (RGPs) in SC are exceptionally multipotent. Individual resident RGPs have the capacity to produce all excitatory and inhibitory SC neuron types, even at the stage of terminal division. While individual clonal units show no pre-defined cellular composition, the establishment of appropriate relative proportions of distinct neuronal types occurs in a PTEN-dependent manner. Collectively, our findings provide an inaugural framework at the single-RGP/-cell level of the mammalian SC ontogeny. acknowledged_ssus: - _id: Bio - _id: M-Shop - _id: LifeSc - _id: PreCl acknowledgement: "We thank Liqun Luo for his continued support, for providing essential resources for generating Fzd10-CreER mice which were generated in his laboratory, and for comments on the manuscript; W. Zhong for providing Nestin-Cre transgenic mouse line for this study; A. Heger for mouse colony management; R. Beattie and T. Asenov for designing and producing components of acute slice recovery chamber for MADM-CloneSeq experiments; and K. Leopold, J. Rodarte and N. Amberg for initial experiments, technical support and/or assistance. This study was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging & Optics Facility (IOF), Laboratory Support Facility (LSF), Miba Machine Shop, and Pre-clinical Facility (PCF). G.C. received funding from European Commission (IST plus postdoctoral fellowship). This work was supported by ISTA institutional\r\nfunds; the Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H. " article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Peter full_name: Koppensteiner, Peter id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87 last_name: Koppensteiner orcid: 0000-0002-3509-1948 - first_name: Thomas full_name: Krausgruber, Thomas last_name: Krausgruber - first_name: Carmen full_name: Streicher, Carmen id: 36BCB99C-F248-11E8-B48F-1D18A9856A87 last_name: Streicher - first_name: Martin full_name: Schrammel, Martin id: f13e7cae-e8bd-11ed-841a-96dedf69f46d last_name: Schrammel - first_name: Natalie Y full_name: Özgen, Natalie Y id: e68ece33-f6e0-11ea-865d-ae1031dcc090 last_name: Özgen - first_name: Alexis full_name: Ivec, Alexis id: 1d144691-e8be-11ed-9b33-bdd3077fad4c last_name: Ivec - first_name: Christoph full_name: Bock, Christoph last_name: Bock - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Cheung GT, Pauler F, Koppensteiner P, et al. Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. 2024;112(2):230-246.e11. doi:10.1016/j.neuron.2023.11.009 apa: Cheung, G. T., Pauler, F., Koppensteiner, P., Krausgruber, T., Streicher, C., Schrammel, M., … Hippenmeyer, S. (2024). Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.11.009 chicago: Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, Thomas Krausgruber, Carmen Streicher, Martin Schrammel, Natalie Y Özgen, et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” Neuron. Elsevier, 2024. https://doi.org/10.1016/j.neuron.2023.11.009. ieee: G. T. Cheung et al., “Multipotent progenitors instruct ontogeny of the superior colliculus,” Neuron, vol. 112, no. 2. Elsevier, p. 230–246.e11, 2024. ista: Cheung GT, Pauler F, Koppensteiner P, Krausgruber T, Streicher C, Schrammel M, Özgen NY, Ivec A, Bock C, Shigemoto R, Hippenmeyer S. 2024. Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. 112(2), 230–246.e11. mla: Cheung, Giselle T., et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” Neuron, vol. 112, no. 2, Elsevier, 2024, p. 230–246.e11, doi:10.1016/j.neuron.2023.11.009. short: G.T. Cheung, F. Pauler, P. Koppensteiner, T. Krausgruber, C. Streicher, M. Schrammel, N.Y. Özgen, A. Ivec, C. Bock, R. Shigemoto, S. Hippenmeyer, Neuron 112 (2024) 230–246.e11. corr_author: '1' date_created: 2023-04-27T09:41:48Z date_published: 2024-01-17T00:00:00Z date_updated: 2025-12-30T10:54:12Z day: '17' ddc: - '570' department: - _id: SiHi - _id: RySh doi: 10.1016/j.neuron.2023.11.009 external_id: isi: - '001163937900001' pmid: - '38096816' file: - access_level: open_access checksum: 32b3788f7085cf44a84108d8faaff3ce content_type: application/pdf creator: dernst date_created: 2024-02-06T13:56:15Z date_updated: 2024-02-06T13:56:15Z file_id: '14944' file_name: 2024_Neuron_Cheung.pdf file_size: 5942467 relation: main_file success: 1 file_date_updated: 2024-02-06T13:56:15Z has_accepted_license: '1' intvolume: ' 112' isi: 1 issue: '2' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 230-246.e11 pmid: 1 project: - _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E grant_number: F7805 name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression publication: Neuron publication_identifier: issn: - 0896-6273 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on ISTA Website relation: press_release url: https://ista.ac.at/en/news/the-pedigree-of-brain-cells/ scopus_import: '1' status: public title: Multipotent progenitors instruct ontogeny of the superior colliculus tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2024' ... --- _id: '14683' abstract: - lang: eng text: "Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice and high-resolution phenotyping at the individual cell level. Here, we present a protocol for isolating MADM-labeled cells with high yield for downstream molecular analyses using fluorescence-activated cell sorting (FACS). We describe steps for generating MADM-labeled mice, perfusion, single-cell suspension, and debris removal. We then detail procedures for cell sorting by FACS and downstream analysis. This protocol is suitable for embryonic to adult mice.\r\nFor complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).1" acknowledged_ssus: - _id: Bio - _id: PreCl acknowledgement: This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Imaging & Optics Facility (IOF) and Preclinical Facilities (PCF). N.A. received support from FWF Firnberg-Programme (T 1031). G.C. received support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411 as an ISTplus postdoctoral fellow. This work was also supported by IST Austria institutional funds, FWF SFB F78 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H. article_number: '102771' article_processing_charge: Yes (in subscription journal) article_type: review author: - first_name: Nicole full_name: Amberg, Nicole id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87 last_name: Amberg orcid: 0000-0002-3183-8207 - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Amberg N, Cheung GT, Hippenmeyer S. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. 2024;5(1). doi:10.1016/j.xpro.2023.102771 apa: Amberg, N., Cheung, G. T., & Hippenmeyer, S. (2024). Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2023.102771 chicago: Amberg, Nicole, Giselle T Cheung, and Simon Hippenmeyer. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2023.102771. ieee: N. Amberg, G. T. Cheung, and S. Hippenmeyer, “Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry,” STAR Protocols, vol. 5, no. 1. Elsevier, 2024. ista: Amberg N, Cheung GT, Hippenmeyer S. 2024. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. 5(1), 102771. mla: Amberg, Nicole, et al. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” STAR Protocols, vol. 5, no. 1, 102771, Elsevier, 2024, doi:10.1016/j.xpro.2023.102771. short: N. Amberg, G.T. Cheung, S. Hippenmeyer, STAR Protocols 5 (2024). corr_author: '1' date_created: 2023-12-13T11:48:05Z date_published: 2024-03-15T00:00:00Z date_updated: 2025-04-15T08:23:06Z day: '15' ddc: - '570' department: - _id: SiHi doi: 10.1016/j.xpro.2023.102771 ec_funded: 1 external_id: pmid: - '38070137' file: - access_level: open_access checksum: 3f0ee62e04bf5a44b45b035662826e95 content_type: application/pdf creator: dernst date_created: 2024-07-16T11:50:03Z date_updated: 2024-07-16T11:50:03Z file_id: '17260' file_name: 2024_STARProtoc_Amberg.pdf file_size: 8871807 relation: main_file success: 1 file_date_updated: 2024-07-16T11:50:03Z has_accepted_license: '1' intvolume: ' 5' issue: '1' keyword: - General Immunology and Microbiology - General Biochemistry - Genetics and Molecular Biology - General Neuroscience language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 268F8446-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: T01031 name: Role of Eed in neural stem cell lineage progression - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E grant_number: F7805 name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression - _id: 260018B0-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '725780' name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development publication: STAR Protocols publication_identifier: issn: - 2666-1667 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2024' ... --- APC_amount: 804 EUR OA_place: publisher OA_type: gold _id: '17187' abstract: - lang: eng text: "The generation of diverse cell types during development is fundamental to brain\r\nfunctions. We outline a protocol to quantitatively assess the clonal output of individual neural progenitors using mosaic analysis with double markers (MADM) in\r\nmice. We first describe steps to acquire and reconstruct adult MADM clones in\r\nthe superior colliculus. Then we detail analysis pipelines to determine clonal\r\ncomposition and architecture. This protocol enables the buildup of quantitative\r\nframeworks of lineage progression with precise spatial resolution in the brain.\r\nFor complete details on the use and execution of this protocol, please refer to\r\nCheung et al.1" acknowledged_ssus: - _id: Bio - _id: PreCl acknowledgement: We thank A. Heger for mouse breeding support. This work was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging & Optics and Preclinical facilities. G.C. received funding from the European Commission (IST plus postdoctoral fellowship); S.H. was funded by ISTA institutional funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro Stem Modulation). article_number: '103157' article_processing_charge: Yes article_type: original author: - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Carmen full_name: Streicher, Carmen id: 36BCB99C-F248-11E8-B48F-1D18A9856A87 last_name: Streicher - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Cheung GT, Streicher C, Hippenmeyer S. Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. STAR Protocols. 2024;5(3). doi:10.1016/j.xpro.2024.103157 apa: Cheung, G. T., Streicher, C., & Hippenmeyer, S. (2024). Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2024.103157 chicago: Cheung, Giselle T, Carmen Streicher, and Simon Hippenmeyer. “Protocol for Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double Markers in Mice.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2024.103157. ieee: G. T. Cheung, C. Streicher, and S. Hippenmeyer, “Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice,” STAR Protocols, vol. 5, no. 3. Elsevier, 2024. ista: Cheung GT, Streicher C, Hippenmeyer S. 2024. Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. STAR Protocols. 5(3), 103157. mla: Cheung, Giselle T., et al. “Protocol for Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double Markers in Mice.” STAR Protocols, vol. 5, no. 3, 103157, Elsevier, 2024, doi:10.1016/j.xpro.2024.103157. short: G.T. Cheung, C. Streicher, S. Hippenmeyer, STAR Protocols 5 (2024). corr_author: '1' date_created: 2024-06-30T22:01:04Z date_published: 2024-09-20T00:00:00Z date_updated: 2025-12-30T10:54:11Z day: '20' ddc: - '570' department: - _id: SiHi doi: 10.1016/j.xpro.2024.103157 ec_funded: 1 external_id: pmid: - '38935508' file: - access_level: open_access checksum: d8a8cdba82a394e731aa699ace1ae433 content_type: application/pdf creator: dernst date_created: 2025-01-09T12:12:40Z date_updated: 2025-01-09T12:12:40Z file_id: '18809' file_name: 2024_STARProtoc_Cheung.pdf file_size: 5186071 relation: main_file success: 1 file_date_updated: 2025-01-09T12:12:40Z has_accepted_license: '1' intvolume: ' 5' issue: '3' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E grant_number: F7805 name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression publication: STAR Protocols publication_identifier: eissn: - 2666-1667 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2024' ... --- APC_amount: 804 EUR OA_place: publisher OA_type: gold _id: '17232' abstract: - lang: eng text: "The lineage relationship of clonally-related cells offers important insights into the ontogeny and cytoarchitecture of the brain in health and disease. Here, we provide a protocol to concurrently assess cell lineage relationship and cell-type identity among clonally-related cells in situ. We first describe the preparation and screening of acute brain slices containing clonally-related cells labeled using mosaic analysis with double markers (MADM). We then outline steps to collect RNA from individual cells for downstream applications and cell-type identification using RNA sequencing.\r\nFor complete details on the use and execution of this protocol, please refer to Cheung et al.\r\n1" acknowledged_ssus: - _id: Bio - _id: M-Shop - _id: PreCl acknowledgement: We thank R. Beattie and T. Asenov for designing and producing components of the multi-well slice recover chamber. We thank R. Shigemoto for providing equipment access. We thank C. Streicher and A. Heger for mouse breeding support. This work was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging & Optics, Miba Machine Shop, and Preclinical facilities. G.C. received funding from the European Commission (IST plus postdoctoral fellowship) and S.H. was funded by ISTA institutional funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro Stem Modulation). article_number: '103168' article_processing_charge: Yes article_type: original author: - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Peter full_name: Koppensteiner, Peter id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87 last_name: Koppensteiner orcid: 0000-0002-3509-1948 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. STAR Protocols. 2024;5(3). doi:10.1016/j.xpro.2024.103168 apa: Cheung, G. T., Pauler, F., Koppensteiner, P., & Hippenmeyer, S. (2024). Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2024.103168 chicago: Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, and Simon Hippenmeyer. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2024.103168. ieee: G. T. Cheung, F. Pauler, P. Koppensteiner, and S. Hippenmeyer, “Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq,” STAR Protocols, vol. 5, no. 3. Elsevier, 2024. ista: Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. 2024. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. STAR Protocols. 5(3), 103168. mla: Cheung, Giselle T., et al. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” STAR Protocols, vol. 5, no. 3, 103168, Elsevier, 2024, doi:10.1016/j.xpro.2024.103168. short: G.T. Cheung, F. Pauler, P. Koppensteiner, S. Hippenmeyer, STAR Protocols 5 (2024). corr_author: '1' date_created: 2024-07-14T22:01:10Z date_published: 2024-09-20T00:00:00Z date_updated: 2025-12-30T10:54:12Z day: '20' ddc: - '570' department: - _id: SiHi - _id: PreCl doi: 10.1016/j.xpro.2024.103168 external_id: pmid: - '38968076' file: - access_level: open_access checksum: 464f52ecc6ec92f509552823bb82bf79 content_type: application/pdf creator: dernst date_created: 2025-01-09T12:16:53Z date_updated: 2025-01-09T12:16:53Z file_id: '18810' file_name: 2024_STARProtoc_Cheung2.pdf file_size: 6445556 relation: main_file success: 1 file_date_updated: 2025-01-09T12:16:53Z has_accepted_license: '1' intvolume: ' 5' issue: '3' language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E grant_number: F7805 name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression publication: STAR Protocols publication_identifier: eissn: - 2666-1667 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2024' ... --- _id: '17425' abstract: - lang: eng text: Mosaic Analysis with Double Markers (MADM) is a powerful genetic method typically used for lineage tracing and to disentangle cell autonomous and tissue-wide roles of candidate genes with single cell resolution. Given the relatively sparse labeling, depending on which of the 19 MADM chromosomes one chooses, the MADM approach represents the perfect opportunity for cell morphology analysis. Various MADM studies include reports of morphological anomalies and phenotypes in the central nervous system (CNS). MADM for any candidate gene can easily incorporate morphological analysis within the experimental workflow. Here, we describe the methods of morphological cell analysis which we developed in the course of diverse recent MADM studies. This chapter will specifically focus on methods to quantify aspects of the morphology of neurons and astrocytes within the CNS, but these methods can broadly be applied to any MADM-labeled cells throughout the entire organism. We will cover two analyses—soma volume and dendrite characterization—of physical characteristics of pyramidal neurons in the somatosensory cortex, and two analyses—volume and Sholl analysis—of astrocyte morphology. acknowledged_ssus: - _id: Bio acknowledgement: We thank all Hippenmeyer lab members for support and discussions. This work was supported by the Scientific Service Units (SSU) at ISTA through resources provided by the Imaging & Optics Facility (IOF). O.A.M was a recipient of a DOC Fellowship (26253) of the Austrian Academy of Sciences. This work was supported by ISTA institutional funds, and The Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H. alternative_title: - Methods in Molecular Biology article_processing_charge: No author: - first_name: Osvaldo full_name: Miranda, Osvaldo id: 862A3C56-A8BF-11E9-B4FA-D9E3E5697425 last_name: Miranda orcid: 0000-0001-6618-6889 - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: 'Miranda O, Cheung GT, Hippenmeyer S. Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Toyooka K, ed. Neuronal Morphogenesis. Vol 2831. 1st ed. MIMB. New York, NY: Springer Nature; 2024:283-299. doi:10.1007/978-1-0716-3969-6_19' apa: 'Miranda, O., Cheung, G. T., & Hippenmeyer, S. (2024). Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In K. Toyooka (Ed.), Neuronal Morphogenesis (1st ed., Vol. 2831, pp. 283–299). New York, NY: Springer Nature. https://doi.org/10.1007/978-1-0716-3969-6_19' chicago: 'Miranda, Osvaldo, Giselle T Cheung, and Simon Hippenmeyer. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” In Neuronal Morphogenesis, edited by Kazuhito Toyooka, 1st ed., 2831:283–99. MIMB. New York, NY: Springer Nature, 2024. https://doi.org/10.1007/978-1-0716-3969-6_19.' ieee: 'O. Miranda, G. T. Cheung, and S. Hippenmeyer, “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers,” in Neuronal Morphogenesis, 1st ed., vol. 2831, K. Toyooka, Ed. New York, NY: Springer Nature, 2024, pp. 283–299.' ista: 'Miranda O, Cheung GT, Hippenmeyer S. 2024.Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Neuronal Morphogenesis. Methods in Molecular Biology, vol. 2831, 283–299.' mla: Miranda, Osvaldo, et al. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” Neuronal Morphogenesis, edited by Kazuhito Toyooka, 1st ed., vol. 2831, Springer Nature, 2024, pp. 283–99, doi:10.1007/978-1-0716-3969-6_19. short: O. Miranda, G.T. Cheung, S. Hippenmeyer, in:, K. Toyooka (Ed.), Neuronal Morphogenesis, 1st ed., Springer Nature, New York, NY, 2024, pp. 283–299. corr_author: '1' date_created: 2024-08-13T12:16:41Z date_published: 2024-08-13T00:00:00Z date_updated: 2026-04-07T12:32:35Z day: '13' department: - _id: GradSch - _id: SiHi doi: 10.1007/978-1-0716-3969-6_19 edition: '1' editor: - first_name: Kazuhito full_name: Toyooka, Kazuhito last_name: Toyooka external_id: pmid: - '39134857' intvolume: ' 2831' language: - iso: eng month: '08' oa_version: None page: 283-299 place: New York, NY pmid: 1 project: - _id: 34c9fbcb-11ca-11ed-8bc3-98fa5658610d grant_number: '26253' name: Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development - _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E grant_number: F7805 name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression publication: Neuronal Morphogenesis publication_identifier: eisbn: - '9781071639696' eissn: - 1940-6029 isbn: - '9781071639689' issn: - 1064-3745 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '20212' relation: dissertation_contains status: public scopus_import: '1' series_title: MIMB status: public title: Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2831 year: '2024' ... --- OA_place: repository _id: '18688' abstract: - lang: eng text: The human brain has remarkable computational power. It generates sophisticated behavioral sequences, stores engrams over an individual’s lifetime, and produces higher cognitive functions up to the level of consciousness. However, so little of our neuroscience knowledge covers the human brain, and it remains unknown whether this organ is truly unique, or is a scaled version of the extensively studied rodent brain. To address this fundamental question, we determined the cellular, synaptic, and connectivity rules of the hippocampal CA3 recurrent circuit using multicellular patch clamp-recording. This circuit is the largest autoassociative network in the brain, and plays a key role in memory and higher-order computations such as pattern separation and pattern completion. We demonstrate that human hippocampal CA3 employs sparse connectivity, in stark contrast to neocortical recurrent networks. Connectivity sparsifies from rodents to humans, providing a circuit architecture that maximizes associational power. Unitary synaptic events at human CA3–CA3 synapses showed both distinct species-specific and circuit-dependent properties, with high reliability, unique amplitude precision, and long integration times. We also identify differential scaling rules between hippocampal pathways from rodents to humans, with a moderate increase in the convergence of CA3 inputs per cell, but a marked increase in human mossy fiber innervation. Anatomically guided full-scale modeling suggests that the human brain’s sparse connectivity, expanded neuronal number, and reliable synaptic signaling combine to enhance the associative memory storage capacity of CA3. Together, our results reveal unique rules of connectivity and synaptic signaling in the human hippocampus, demonstrating the absolute necessity of human brain research and beginning to unravel the remarkable performance of our autoassociative memory circuits. acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: M-Shop - _id: PreCl - _id: ScienComp acknowledgement: We thank Florian Marr for excellent technical assistance, Christina Altmutter and Julia Flor for technical support, Alois Schlögl for programming, Todor Asenov for development of the transportation box for human brain tissue, Tim Vogels for guidance on simulations, Marcus Huber for mathematical advice, and Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA, and we are particularly grateful for assistance from Christoph Sommer and the Imaging and Optics Facility, Preclinical Facility, Life Science Facility, Miba Machine Shop, and Scientific Computing. We also acknowledge the excellent support of the Medical University of Vienna Department of Neurosurgery staff, Romana Hoeftberger and the Division of Neuropathology and Neurochemistry, and Gregor Kasprian and the Division of Neuroradiology and Musculoskeletal Radiology. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 to J.F.W.), the Austrian Science Fund (FWF; grant PAT 4178023 to P.J.; grant DK W1232 to M.R.T. and J.G.D.) and the Austrian Academy of Sciences (DOC fellowship 26137 to M.R.T.). article_processing_charge: No author: - first_name: Jake F. full_name: Watson, Jake F. last_name: Watson - first_name: Victor full_name: Vargas-Barroso, Victor last_name: Vargas-Barroso - first_name: Rebecca J. full_name: Morse-Mora, Rebecca J. last_name: Morse-Mora - first_name: Andrea full_name: Navas-Olive, Andrea last_name: Navas-Olive - first_name: Mojtaba full_name: Tavakoli, Mojtaba id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87 last_name: Tavakoli orcid: 0000-0002-7667-6854 - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Matthias full_name: Tomschik, Matthias last_name: Tomschik - first_name: Karl full_name: Rössler, Karl last_name: Rössler - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Watson JF, Vargas-Barroso V, Morse-Mora RJ, et al. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. bioRxiv. doi:10.1101/2024.05.02.592169 apa: Watson, J. F., Vargas-Barroso, V., Morse-Mora, R. J., Navas-Olive, A., Tavakoli, M., Danzl, J. G., … Jonas, P. M. (n.d.). Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. bioRxiv. https://doi.org/10.1101/2024.05.02.592169 chicago: Watson, Jake F., Victor Vargas-Barroso, Rebecca J. Morse-Mora, Andrea Navas-Olive, Mojtaba Tavakoli, Johann G Danzl, Matthias Tomschik, Karl Rössler, and Peter M Jonas. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” BioRxiv, n.d. https://doi.org/10.1101/2024.05.02.592169. ieee: J. F. Watson et al., “Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory,” bioRxiv. . ista: Watson JF, Vargas-Barroso V, Morse-Mora RJ, Navas-Olive A, Tavakoli M, Danzl JG, Tomschik M, Rössler K, Jonas PM. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. bioRxiv, 10.1101/2024.05.02.592169. mla: Watson, Jake F., et al. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” BioRxiv, doi:10.1101/2024.05.02.592169. short: J.F. Watson, V. Vargas-Barroso, R.J. Morse-Mora, A. Navas-Olive, M. Tavakoli, J.G. Danzl, M. Tomschik, K. Rössler, P.M. Jonas, BioRxiv (n.d.). corr_author: '1' date_created: 2024-12-19T11:35:08Z date_published: 2024-05-02T00:00:00Z date_updated: 2026-04-14T08:34:32Z day: '02' department: - _id: JoDa - _id: PeJo doi: 10.1101/2024.05.02.592169 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2024.05.02.592169 month: '05' oa: 1 oa_version: Preprint project: - _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9 call_identifier: H2020 grant_number: '101026635' name: Synaptic computations of the hippocampal CA3 circuitry - _id: 26AA4EF2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets - _id: 6285a163-2b32-11ec-9570-8e204ca2dba5 grant_number: '26137' name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy publication: bioRxiv publication_status: draft related_material: record: - id: '18681' relation: dissertation_contains status: public - id: '18879' relation: later_version status: public status: public title: Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '14257' abstract: - lang: eng text: Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease. acknowledged_ssus: - _id: ScienComp - _id: Bio - _id: PreCl - _id: LifeSc - _id: M-Shop - _id: E-Lib acknowledgement: 'We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I. Erber for technical assistance; and M. Tomschik for support with obtaining human samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata for computational support and hardware control. We are grateful to R. Shigemoto and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University) for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly provided by S. Grant (University of Edinburgh). We acknowledge expert support by Institute of Science and Technology Austria’s scientific computing, imaging and optics, preclinical and lab support facilities and by the Miba machine shop and library. We gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Julia M full_name: Michalska, Julia M id: 443DB6DE-F248-11E8-B48F-1D18A9856A87 last_name: Michalska orcid: 0000-0003-3862-1235 - first_name: Julia full_name: Lyudchik, Julia id: 46E28B80-F248-11E8-B48F-1D18A9856A87 last_name: Lyudchik - first_name: Philipp full_name: Velicky, Philipp id: 39BDC62C-F248-11E8-B48F-1D18A9856A87 last_name: Velicky orcid: 0000-0002-2340-7431 - first_name: Hana full_name: Korinkova, Hana id: ee3cb6ca-ec98-11ea-ae11-ff703e2254ed last_name: Korinkova - first_name: Jake full_name: Watson, Jake id: 63836096-4690-11EA-BD4E-32803DDC885E last_name: Watson orcid: 0000-0002-8698-3823 - first_name: Alban full_name: Cenameri, Alban id: 9ac8f577-2357-11eb-997a-e566c5550886 last_name: Cenameri - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Nicole full_name: Amberg, Nicole id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87 last_name: Amberg orcid: 0000-0002-3183-8207 - first_name: Alessandro full_name: Venturino, Alessandro id: 41CB84B2-F248-11E8-B48F-1D18A9856A87 last_name: Venturino orcid: 0000-0003-2356-9403 - first_name: Karl full_name: Roessler, Karl last_name: Roessler - first_name: Thomas full_name: Czech, Thomas last_name: Czech - first_name: Romana full_name: Höftberger, Romana last_name: Höftberger - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 citation: ama: Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. 2024;42:1051-1064. doi:10.1038/s41587-023-01911-8 apa: Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri, A., … Danzl, J. G. (2024). Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-023-01911-8 chicago: Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake Watson, Alban Cenameri, Christoph M Sommer, et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” Nature Biotechnology. Springer Nature, 2024. https://doi.org/10.1038/s41587-023-01911-8. ieee: J. M. Michalska et al., “Imaging brain tissue architecture across millimeter to nanometer scales,” Nature Biotechnology, vol. 42. Springer Nature, pp. 1051–1064, 2024. ista: Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer CM, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino G, Jonas PM, Danzl JG. 2024. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. 42, 1051–1064. mla: Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” Nature Biotechnology, vol. 42, Springer Nature, 2024, pp. 1051–64, doi:10.1038/s41587-023-01911-8. short: J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri, C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S. Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology 42 (2024) 1051–1064. corr_author: '1' date_created: 2023-09-03T22:01:15Z date_published: 2024-07-01T00:00:00Z date_updated: 2026-04-14T08:34:35Z day: '01' ddc: - '570' department: - _id: SaSi - _id: GaNo - _id: PeJo - _id: JoDa - _id: Bio - _id: RySh doi: 10.1038/s41587-023-01911-8 ec_funded: 1 external_id: isi: - '001065254200001' pmid: - '37653226' file: - access_level: open_access checksum: 57d5fafb16f02dcb9f7dddb1bd7e2a71 content_type: application/pdf creator: dernst date_created: 2025-01-09T07:48:01Z date_updated: 2025-01-09T07:48:01Z file_id: '18784' file_name: 2024_NatureBiotech_Michalska.pdf file_size: 26065165 relation: main_file success: 1 file_date_updated: 2025-01-09T07:48:01Z has_accepted_license: '1' intvolume: ' 42' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 1051-1064 pmid: 1 project: - _id: 265CB4D0-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03600 name: Optical control of synaptic function via adhesion molecules - _id: 2548AE96-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232 name: Molecular Drug Targets - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: Synaptic communication in neuronal microcircuits - _id: 23889792-32DE-11EA-91FC-C7463DDC885E grant_number: LS18-022 name: High content imaging to decode human immune cell interactions in health and allergic disease - _id: 25444568-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715508' name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glutamatergic synapse - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9 call_identifier: H2020 grant_number: '101026635' name: Synaptic computations of the hippocampal CA3 circuitry publication: Nature Biotechnology publication_identifier: eissn: - 1546-1696 issn: - 1087-0156 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: software url: https://github.com/danzllab/CATS record: - id: '18660' relation: dissertation_contains status: deleted - id: '13126' relation: research_data status: public - id: '18674' relation: dissertation_contains status: public scopus_import: '1' status: public title: Imaging brain tissue architecture across millimeter to nanometer scales tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 42 year: '2024' ... --- OA_place: publisher _id: '18674' abstract: - lang: eng text: Mapping the complex and dense arrangement of cells and their connectivity in brain tissue requires volumetric imaging at nanoscale spatial resolution. While light microscopy excels at visualizing specific molecules and individual cells, achieving dense, synapse-level circuit reconstruction has not been possible with any light microscopy technique. Thus, the goal of my work was to develop image and data analysis pipelines for brain tissue visualization and reconstruction with light microscopy. To achieve dense circuit reconstruction with single-synapse resolution, I developed both conventional and deep-learning-based synapse detection algorithms, as well as connectivity analysis pipelines that integrate synapse detection with volumetric segmentation of brain tissue. acknowledged_ssus: - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Julia full_name: Lyudchik, Julia id: 46E28B80-F248-11E8-B48F-1D18A9856A87 last_name: Lyudchik citation: ama: Lyudchik J. Image analysis for brain tissue reconstruction with super-resolution light microscopy. 2024. doi:10.15479/at:ista:18674 apa: Lyudchik, J. (2024). Image analysis for brain tissue reconstruction with super-resolution light microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18674 chicago: Lyudchik, Julia. “Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18674. ieee: J. Lyudchik, “Image analysis for brain tissue reconstruction with super-resolution light microscopy,” Institute of Science and Technology Austria, 2024. ista: Lyudchik J. 2024. Image analysis for brain tissue reconstruction with super-resolution light microscopy. Institute of Science and Technology Austria. mla: Lyudchik, Julia. Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18674. short: J. Lyudchik, Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-12-18T14:24:43Z date_published: 2024-12-18T00:00:00Z date_updated: 2026-04-14T08:34:35Z day: '18' ddc: - '004' degree_awarded: PhD department: - _id: GradSch - _id: JoDa doi: 10.15479/at:ista:18674 ec_funded: 1 file: - access_level: open_access checksum: 1b42b8073e2bc09fc504da52372248c1 content_type: application/pdf creator: jlyudchi date_created: 2024-12-18T14:17:34Z date_updated: 2024-12-18T14:17:34Z file_id: '18675' file_name: 18122024_PhDthesis_corrected_final_pdfa.pdf file_size: 160536833 relation: main_file success: 1 - access_level: closed checksum: b4da84624060745519723698f7ddf54b content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: jlyudchi date_created: 2024-12-18T14:21:06Z date_updated: 2024-12-18T14:41:53Z file_id: '18676' file_name: 18122024_PhDthesis_corrected_final_JL_markup.docx file_size: 99172203 relation: source_file file_date_updated: 2024-12-18T14:41:53Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '217' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - ' 978-3-99078-051-0' issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11160' relation: part_of_dissertation status: public - id: '18677' relation: part_of_dissertation status: public - id: '13267' relation: part_of_dissertation status: public - id: '14257' relation: part_of_dissertation status: public status: public supervisor: - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 title: Image analysis for brain tissue reconstruction with super-resolution light microscopy tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- APC_amount: 3197,23 EUR DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18481' abstract: - lang: eng text: A tight regulation of morphogen production is key for morphogen gradient formation and thereby for reproducible and organised organ development. Although many genetic interactions involved in the establishment of morphogen production domains are known, the biophysical mechanisms of morphogen source formation are poorly understood. Here we addressed this by focusing on the morphogen Sonic hedgehog (Shh) in the vertebrate neural tube. Shh is produced by the adjacently located notochord and by the floor plate of the neural tube. Using a data-constrained computational screen, we identified different possible mechanisms by which floor plate formation can occur, only one of which is consistent with experimental data. In this mechanism, the floor plate is established rapidly in response to Shh from the notochord and the dynamics of regulatory interactions within the neural tube. In this process, uniform activators and Shh-dependent repressors are key for establishing the floor plate size. Subsequently, the floor plate becomes insensitive to Shh and increases in size due to tissue growth, leading to scaling of the floor plate with neural tube size. In turn, this results in scaling of the Shh amplitude with tissue growth. Thus, this mechanism ensures a separation of time scales in floor plate formation, so that the floor plate domain becomes growth-dependent after an initial rapid establishment phase. Our study raises the possibility that the time scale separation between specification and growth might be a common strategy for scaling the morphogen gradient amplitude in growing organs. The model that we developed provides a new opportunity for quantitative studies of morphogen source formation in growing tissues. acknowledgement: "We thank Martina Greunz-Schindler for technical support, and Thomas Minchington and James Briscoe for comments on the manuscript.\r\nRDJGH, MM and MZ were supported by a grant from the Priority Research Area DigiWorld\r\nunder the Strategic Programme Excellence Initiative at Jagiellonian University. The research\r\nwas supported by the Polish National Agency for Academic Exchange, PN/PPO/2018/1/00011/U/00001 which paid the salary of MM and MZ up to Feb 2023. The research received support from National Science Center, Poland, 2021/42/E/NZ2/00188 which paid salary of MZ. Work in the AK labis supported by ISTA to KK and AK, the European\r\nResearch Council under Horizon Europe: grant 101044579 to AK, and Austrian Science Fund\r\n(FWF): Grant DOI 10.55776/F78 to AK. The salaries of AK and KK were paid by ISTA. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." article_number: e1012508 article_processing_charge: No article_type: original author: - first_name: Richard D.J.G. full_name: Ho, Richard D.J.G. last_name: Ho - first_name: Kasumi full_name: Kishi, Kasumi id: 3065DFC4-F248-11E8-B48F-1D18A9856A87 last_name: Kishi orcid: 0000-0001-6060-4795 - first_name: Maciej full_name: Majka, Maciej last_name: Majka - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: Marcin P full_name: Zagórski, Marcin P id: 343DA0DC-F248-11E8-B48F-1D18A9856A87 last_name: Zagórski orcid: 0000-0001-7896-7762 citation: ama: Ho RDJG, Kishi K, Majka M, Kicheva A, Zagórski MP. Dynamics of morphogen source formation in a growing tissue. PLoS Computational Biology. 2024;20. doi:10.1371/journal.pcbi.1012508 apa: Ho, R. D. J. G., Kishi, K., Majka, M., Kicheva, A., & Zagórski, M. P. (2024). Dynamics of morphogen source formation in a growing tissue. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1012508 chicago: Ho, Richard D.J.G., Kasumi Kishi, Maciej Majka, Anna Kicheva, and Marcin P Zagórski. “Dynamics of Morphogen Source Formation in a Growing Tissue.” PLoS Computational Biology. Public Library of Science, 2024. https://doi.org/10.1371/journal.pcbi.1012508. ieee: R. D. J. G. Ho, K. Kishi, M. Majka, A. Kicheva, and M. P. Zagórski, “Dynamics of morphogen source formation in a growing tissue,” PLoS Computational Biology, vol. 20. Public Library of Science, 2024. ista: Ho RDJG, Kishi K, Majka M, Kicheva A, Zagórski MP. 2024. Dynamics of morphogen source formation in a growing tissue. PLoS Computational Biology. 20, e1012508. mla: Ho, Richard D. J. G., et al. “Dynamics of Morphogen Source Formation in a Growing Tissue.” PLoS Computational Biology, vol. 20, e1012508, Public Library of Science, 2024, doi:10.1371/journal.pcbi.1012508. short: R.D.J.G. Ho, K. Kishi, M. Majka, A. Kicheva, M.P. Zagórski, PLoS Computational Biology 20 (2024). corr_author: '1' date_created: 2024-10-27T23:01:45Z date_published: 2024-10-14T00:00:00Z date_updated: 2026-04-07T12:31:58Z day: '14' ddc: - '570' department: - _id: AnKi doi: 10.1371/journal.pcbi.1012508 external_id: isi: - '001331700300003' pmid: - '39401260' file: - access_level: open_access checksum: 42fa714459943cb3961b40fab8fd82c8 content_type: application/pdf creator: dernst date_created: 2024-10-29T11:59:09Z date_updated: 2024-10-29T11:59:09Z file_id: '18487' file_name: 2024_PloSComBio_Ho.pdf file_size: 3732443 relation: main_file success: 1 file_date_updated: 2024-10-29T11:59:09Z has_accepted_license: '1' intvolume: ' 20' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 project: - _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa grant_number: '101044579' name: Mechanisms of tissue size regulation in spinal cord development - _id: 059DF620-7A3F-11EA-A408-12923DDC885E grant_number: F7802 name: Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord publication: PLoS Computational Biology publication_identifier: eissn: - 1553-7358 issn: - 1553-734X publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: record: - id: '20393' relation: dissertation_contains status: public scopus_import: '1' status: public title: Dynamics of morphogen source formation in a growing tissue tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 20 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18902' acknowledgement: 'MZ is supported by National Science Center, Poland, 2021/42/E/NZ2/00188, the Polish National Agency for Academic Exchange, and by a grant from the Priority Research Area DigiWorld under the Strategic Programme Excellence Initiative at Jagiellonian University. Work in JB’s lab is supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK, the UK Medical Research Council and Wellcome Trust (all under CC001051). Work in the AK lab is supported by ISTA, the European Research Council under Horizon Europe: grant 101044579, and Austrian Science Fund (FWF): F78 (Neural Stem Cell Modulation).' article_number: '929' article_processing_charge: Yes article_type: letter_note author: - first_name: Marcin full_name: Zagorski, Marcin last_name: Zagorski - first_name: Nathalie full_name: Brandenberg, Nathalie last_name: Brandenberg - first_name: Matthias full_name: Lutolf, Matthias last_name: Lutolf - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X - first_name: James full_name: Briscoe, James last_name: Briscoe - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 citation: ama: Zagorski M, Brandenberg N, Lutolf M, et al. Assessing the precision of morphogen gradients in neural tube development. Nature Communications. 2024;15. doi:10.1038/s41467-024-45148-8 apa: Zagorski, M., Brandenberg, N., Lutolf, M., Tkačik, G., Bollenbach, M. T., Briscoe, J., & Kicheva, A. (2024). Assessing the precision of morphogen gradients in neural tube development. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-45148-8 chicago: Zagorski, Marcin, Nathalie Brandenberg, Matthias Lutolf, Gašper Tkačik, Mark Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Assessing the Precision of Morphogen Gradients in Neural Tube Development.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-45148-8. ieee: M. Zagorski et al., “Assessing the precision of morphogen gradients in neural tube development,” Nature Communications, vol. 15. Springer Nature, 2024. ista: Zagorski M, Brandenberg N, Lutolf M, Tkačik G, Bollenbach MT, Briscoe J, Kicheva A. 2024. Assessing the precision of morphogen gradients in neural tube development. Nature Communications. 15, 929. mla: Zagorski, Marcin, et al. “Assessing the Precision of Morphogen Gradients in Neural Tube Development.” Nature Communications, vol. 15, 929, Springer Nature, 2024, doi:10.1038/s41467-024-45148-8. short: M. Zagorski, N. Brandenberg, M. Lutolf, G. Tkačik, M.T. Bollenbach, J. Briscoe, A. Kicheva, Nature Communications 15 (2024). corr_author: '1' date_created: 2025-01-27T13:01:01Z date_published: 2024-02-01T00:00:00Z date_updated: 2025-12-30T10:57:08Z day: '01' ddc: - '570' department: - _id: GaTk - _id: AnKi doi: 10.1038/s41467-024-45148-8 external_id: isi: - '001156218500022' pmid: - '38302459' file: - access_level: open_access checksum: acf75f2b6fa84a64d1f590dd4a53cbf7 content_type: application/pdf creator: dernst date_created: 2025-01-27T13:04:03Z date_updated: 2025-01-27T13:04:03Z file_id: '18903' file_name: 2024_NatureComm_Zagorski.pdf file_size: 4723831 relation: main_file success: 1 file_date_updated: 2025-01-27T13:04:03Z has_accepted_license: '1' intvolume: ' 15' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 project: - _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa grant_number: '101044579' name: Mechanisms of tissue size regulation in spinal cord development - _id: 059DF620-7A3F-11EA-A408-12923DDC885E grant_number: F7802 name: Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Assessing the precision of morphogen gradients in neural tube development tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 15 year: '2024' ... --- OA_place: publisher _id: '17133' abstract: - lang: eng text: "An ideal quantum computer relies on qubits capable of performing fast gate operations and\r\nmaintaining strong interconnections while preserving their quantum coherence. Since the\r\ninception of experimental eforts toward building a quantum computer, the community has\r\nfaced challenges in engineering such a system. Among the various methods of implementing a\r\nquantum computer, superconducting qubits have shown fast gates close to tens of nanoseconds,\r\nwith the state-of-the-art reaching a coherence of a few milliseconds. However, achieving\r\nsimultaneously long lifetimes with fast qubit operations poses an inherent paradox. Qubits\r\nwith high coherence require isolation from the environment, while fast operation necessitates\r\nstrong coupling of the qubit. This thesis approaches this issue by proposing the idea of\r\nengineering superconducting qubits capable of transitioning between operating in a protected\r\nregime, where the qubit is completely isolated from the environment, and coupling to the\r\ncommunication channels as needed. In this direction, we use the geometric superinductor to\r\nscan the parameter space of rf-SQUID devices, searching for a regime where we can take the\r\nqubit protection to its extreme.\r\n\r\nThis leads us to the inductively shunted transmon (IST) regime, characterized by EJ /EC ≫ 1\r\nand EJ /EL ≫ 1, where the circuit potential exhibits a double well with a large barrier\r\nseparating the local ground states of each quantum well. In this regime, although it is\r\nanticipated that the two quantum wells would be isolated from each other, we observe single\r\nfuxon tunneling between them. The interplay of the cavity photons and the fuxon transition\r\nforms a rich physical system, containing resonance conditions that allow the preparation of the\r\nfuxon ground or excited states. This enables us to study the relaxation rate of such transition\r\nand show that it can be as large as 3.6 hours. Dynamically controlling the barrier height\r\nbetween the two quantum wells allows for controllable coupling, which scales exponentially,\r\nfor a qubit encoded in two fuxon states.\r\nThe 0-π qubit is one of the very few known superconducting circuit types that ofers exponential\r\nprotection from both relaxation and dephasing simultaneously. However, this qubit is not\r\nexempt from the fact that such protection comes at the expense of complex readout and\r\ncontrol. In this thesis, we propose a way to controllably break the circuit symmetry, the\r\nkey reason for the protection, to momentarily restore the ability to control and manipulate\r\nthe qubit. An asymmetry in capacitances and inductances in the 0-π circuit is detrimental\r\nsince they lead to coupling of the protected state to the thermally occupied parasitic mode\r\nof the circuit. However, here we try to exploit a controlled asymmetry in Josephson energies\r\nand show that this can be used as a tunable coupler between the protected states. In the\r\nfuture, this should allow to perform gate operations by dynamically controlling the asymmetry\r\ninstead of driving the protected transition with microwave pulses. Therefore, we believe that\r\nthe proposed method can make the use of protected qubits more practical in experimental\r\nrealizations of quantum computing." acknowledged_ssus: - _id: NanoFab - _id: M-Shop alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Farid full_name: Hassani, Farid id: 2AED110C-F248-11E8-B48F-1D18A9856A87 last_name: Hassani orcid: 0000-0001-6937-5773 citation: ama: Hassani F. Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. 2024. doi:10.15479/at:ista:17133 apa: Hassani, F. (2024). Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17133 chicago: Hassani, Farid. “Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17133. ieee: F. Hassani, “Superconducting qubits capable of dynamic switching between protected and high-speed control regimes,” Institute of Science and Technology Austria, 2024. ista: Hassani F. 2024. Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. Institute of Science and Technology Austria. mla: Hassani, Farid. Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17133. short: F. Hassani, Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-06-11T18:20:05Z date_published: 2024-06-11T00:00:00Z date_updated: 2026-04-15T06:43:02Z day: '11' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: JoFi doi: 10.15479/at:ista:17133 file: - access_level: open_access checksum: 258c353d47fa37ea63ea43b1e10a34a0 content_type: application/pdf creator: fhassani date_created: 2024-06-12T07:53:19Z date_updated: 2024-06-20T11:52:22Z file_id: '17137' file_name: Thesis_main_final.pdf file_size: 28370759 relation: main_file - access_level: closed checksum: deffa5d0db88093f74812fa71520d5e1 content_type: text/x-tex creator: fhassani date_created: 2024-06-12T07:54:27Z date_updated: 2024-06-12T07:54:27Z file_id: '17138' file_name: Thesis_main.tex file_size: 445735 relation: source_file file_date_updated: 2024-06-20T11:52:22Z has_accepted_license: '1' keyword: - Quantum information - Qubits - Superconducting devices language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '06' oa: 1 oa_version: Published Version page: '161' project: - _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A name: NOMIS Fellowship Program - _id: bdb108fd-d553-11ed-ba76-83dc74a9864f grant_number: F07105 name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits publication_identifier: isbn: - 978-3-99078-040-4 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '13227' relation: part_of_dissertation status: public - id: '9928' relation: part_of_dissertation status: public - id: '8755' relation: part_of_dissertation status: public status: public supervisor: - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X title: Superconducting qubits capable of dynamic switching between protected and high-speed control regimes tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '15362' abstract: - lang: eng text: Constitutional heterozygous pathogenic variants in the exonuclease domain of POLE and POLD1, which affect the proofreading activity of the corresponding polymerases, cause a cancer predisposition syndrome characterized by increased risk of gastrointestinal polyposis, colorectal cancer, endometrial cancer and other tumor types. The generally accepted explanation for the connection between the disruption of the proofreading activity of polymerases epsilon and delta and cancer development is through an increase in the somatic mutation rate. Here we studied an extended family with multiple members heterozygous for the pathogenic POLD1 variant c.1421T>C p.(Leu474Pro), which segregates with the polyposis and cancer phenotypes. Through the analysis of mutational patterns of patient-derived fibroblasts colonies and de novo mutations obtained by parent-offspring comparisons, we concluded that heterozygous POLD1 L474P just subtly increases the somatic and germline mutation burden. In contrast, tumors developed in individuals with a heterozygous mutation in the exonuclease domain of POLD1, including L474P, have an extremely high mutation rate (>100 mut/Mb) associated with signature SBS10d. We solved this contradiction through the observation that tumorigenesis involves somatic inactivation of the wildtype POLD1 allele. These results imply that exonuclease deficiency of polymerase delta has a recessive effect on mutation rate. acknowledgement: 'This study was funded by the Spanish Ministry of Science and Innovation (Agencia Estatal de Investigación), co-funded by FEDER funds a way to build Europe [PID2020-112595RB-I00 (LV)], Instituto de Salud Carlos III [CIBERONC CB16/12/00234 (LV); ISCIII-AES-2017 PI17/01082 (JLS), PMP22/00064], Government of Catalonia [AGAUR 2021SGR01112, CERCA Program for institutional support (LV)], Scientific Foundation Asociación Española Contra el Cáncer [AECC Investigador (MT)], Austrian Science Fund FWF [Grant Agreement # I5127-B (FK)], German Research Foundation DFG [Grant Agreement # 429960716 (FK)], and ERC Consolidator [Grant Agreement # 771209 ChrFL (FK)].' article_processing_charge: No article_type: original author: - first_name: Maria A. full_name: Andrianova, Maria A. last_name: Andrianova - first_name: Vladimir B. full_name: Seplyarskiy, Vladimir B. last_name: Seplyarskiy - first_name: Mariona full_name: Terradas, Mariona last_name: Terradas - first_name: Ana Beatriz full_name: Sánchez-Heras, Ana Beatriz last_name: Sánchez-Heras - first_name: Pilar full_name: Mur, Pilar last_name: Mur - first_name: José Luis full_name: Soto, José Luis last_name: Soto - first_name: Gemma full_name: Aiza, Gemma last_name: Aiza - first_name: Emma full_name: Borràs, Emma last_name: Borràs - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Alexey S. full_name: Kondrashov, Alexey S. last_name: Kondrashov - first_name: Georgii A. full_name: Bazykin, Georgii A. last_name: Bazykin - first_name: Laura full_name: Valle, Laura last_name: Valle citation: ama: Andrianova MA, Seplyarskiy VB, Terradas M, et al. Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells. European Journal of Human Genetics. 2024;32:837-845. doi:10.1038/s41431-024-01598-8 apa: Andrianova, M. A., Seplyarskiy, V. B., Terradas, M., Sánchez-Heras, A. B., Mur, P., Soto, J. L., … Valle, L. (2024). Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells. European Journal of Human Genetics. Springer Nature. https://doi.org/10.1038/s41431-024-01598-8 chicago: Andrianova, Maria A., Vladimir B. Seplyarskiy, Mariona Terradas, Ana Beatriz Sánchez-Heras, Pilar Mur, José Luis Soto, Gemma Aiza, et al. “Discovery of Recessive Effect of Human Polymerase δ Proofreading Deficiency through Mutational Analysis of POLD1-Mutated Normal and Cancer Cells.” European Journal of Human Genetics. Springer Nature, 2024. https://doi.org/10.1038/s41431-024-01598-8. ieee: M. A. Andrianova et al., “Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells,” European Journal of Human Genetics, vol. 32. Springer Nature, pp. 837–845, 2024. ista: Andrianova MA, Seplyarskiy VB, Terradas M, Sánchez-Heras AB, Mur P, Soto JL, Aiza G, Borràs E, Kondrashov F, Kondrashov AS, Bazykin GA, Valle L. 2024. Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells. European Journal of Human Genetics. 32, 837–845. mla: Andrianova, Maria A., et al. “Discovery of Recessive Effect of Human Polymerase δ Proofreading Deficiency through Mutational Analysis of POLD1-Mutated Normal and Cancer Cells.” European Journal of Human Genetics, vol. 32, Springer Nature, 2024, pp. 837–45, doi:10.1038/s41431-024-01598-8. short: M.A. Andrianova, V.B. Seplyarskiy, M. Terradas, A.B. Sánchez-Heras, P. Mur, J.L. Soto, G. Aiza, E. Borràs, F. Kondrashov, A.S. Kondrashov, G.A. Bazykin, L. Valle, European Journal of Human Genetics 32 (2024) 837–845. date_created: 2024-05-05T22:01:04Z date_published: 2024-07-01T00:00:00Z date_updated: 2026-04-15T08:51:09Z day: '01' ddc: - '570' department: - _id: FyKo doi: 10.1038/s41431-024-01598-8 ec_funded: 1 external_id: isi: - '001207703200001' pmid: - '38658779' file: - access_level: open_access checksum: e45fc987f4e9ebafdd0ec4f0e9027de4 content_type: application/pdf creator: dernst date_created: 2025-01-09T09:21:25Z date_updated: 2025-01-09T09:21:25Z file_id: '18799' file_name: 2024_EJHG_Andrianova.pdf file_size: 3060724 relation: main_file success: 1 file_date_updated: 2025-01-09T09:21:25Z has_accepted_license: '1' intvolume: ' 32' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 837-845 pmid: 1 project: - _id: 9B767A34-BA93-11EA-9121-9846C619BF3A grant_number: '429960716' name: Evolution of Sensorimotor Transformation Across Diptera - _id: 26580278-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771209' name: Characterizing the fitness landscape on population and global scales - _id: 34e076d6-11ca-11ed-8bc3-aec76c41a181 grant_number: I05127 name: Evolutionary analysis of gene regulation publication: European Journal of Human Genetics publication_identifier: eissn: - 1476-5438 issn: - 1018-4813 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2024' ... --- OA_place: publisher _id: '18135' abstract: - lang: eng text: "This thesis consists of two separate parts. In the first part we consider a dilute Fermi gas interacting through a repulsive interaction in dimensions $d=1,2,3$. Our focus is mostly on the physically most relevant dimension $d=3$ \r\nand the setting of a spin-polarized (equivalently spinless) gas, where the Pauli exclusion principle plays a key role. We show that, at zero temperature, the ground state energy density of the interacting spin-polarized gas differs (to leading order) from that of the free (i.e. non-interacting) gas by a term of order $a_p^d\\rho^{2+2/d}$ \ with $a_p$ the $p$-wave scattering length of the repulsive interaction and $\\rho$ the density. Further, we extend this to positive temperature and show that the pressure of an interacting spin-polarized gas differs from that of the free gas by a now temperature dependent term, again of order $a_p^d\\rho^{2+2/d}$. Lastly, we consider the setting of a spin-$\\frac{1}{2}$ Fermi gas in $d=3$ dimensions and show that here, as an upper bound, the ground state energy density differs from that of the free system by a term of order $a_s \\rho^2$ with an error smaller than $a_s \\rho^2 (a_s\\rho^{1/3})^{1-\\eps}$ for any $\\eps > 0$, where $a_s$ is the $s$-wave scattering length of the repulsive interaction. \r\n\r\nThese asymptotic formulas complement the similar formulas in the literature for the dilute Bose and spin-$\\frac{1}{2}$ Fermi gas, where the ground state energies or pressures differ from that of the corresponding free systems by a term of order $a_s \\rho^2$ in dimension $d=3$. In the spin-polarized setting, the corrections, of order $a_p^3\\rho^{8/3}$ in dimension $d=3$, are thus much smaller and requires a more delicate analysis.\r\n\r\nIn the second part of the thesis we consider the Bardeen--Cooper--Schrieffer (BCS) theory of superconductivity and in particular its associated critical temperature and energy gap. We prove that the ratio of the zero-temperature energy gap and critical temperature $\\Xi(T=0)/T_c$ approaches a universal constant $\\pi e^{-\\gamma}\\approx 1.76$ in both the limit of high density in dimension $d=3$ and in the limit of weak coupling in dimensions $d=1,2$. This complements the proofs in the literature of this universal behaviour in the limit of weak coupling or low density in dimension $d=3$. Secondly, we prove that the ratio of the energy gap at positive temperature and critical temperature $\\Xi(T)/T_c$ approaches a universal function of the relative temperature $T/T_c$ in the limit of weak coupling in dimensions $d=1,2,3$." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Asbjørn Bækgaard full_name: Lauritsen, Asbjørn Bækgaard id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1 last_name: Lauritsen orcid: 0000-0003-4476-2288 citation: ama: Lauritsen AB. Energies of dilute Fermi gases and universalities in BCS theory. 2024. doi:10.15479/at:ista:18135 apa: Lauritsen, A. B. (2024). Energies of dilute Fermi gases and universalities in BCS theory. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18135 chicago: Lauritsen, Asbjørn Bækgaard. “Energies of Dilute Fermi Gases and Universalities in BCS Theory.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18135. ieee: A. B. Lauritsen, “Energies of dilute Fermi gases and universalities in BCS theory,” Institute of Science and Technology Austria, 2024. ista: Lauritsen AB. 2024. Energies of dilute Fermi gases and universalities in BCS theory. Institute of Science and Technology Austria. mla: Lauritsen, Asbjørn Bækgaard. Energies of Dilute Fermi Gases and Universalities in BCS Theory. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18135. short: A.B. Lauritsen, Energies of Dilute Fermi Gases and Universalities in BCS Theory, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-09-24T10:56:25Z date_published: 2024-09-23T00:00:00Z date_updated: 2026-04-16T08:17:55Z day: '23' ddc: - '515' - '539' degree_awarded: PhD department: - _id: GradSch - _id: RoSe doi: 10.15479/at:ista:18135 ec_funded: 1 file: - access_level: open_access checksum: c7bc3b31e430d57c65393051ca439575 content_type: application/pdf creator: alaurits date_created: 2024-09-26T13:11:24Z date_updated: 2024-09-26T13:11:24Z file_id: '18147' file_name: Lauritsen-thesis-final.pdf file_size: 3648831 relation: main_file success: 1 - access_level: closed checksum: 39f6b1b7f83e25a3bf9f933f1ea0bc06 content_type: application/x-zip-compressed creator: alaurits date_created: 2024-09-26T13:12:55Z date_updated: 2024-09-26T13:12:55Z file_id: '18148' file_name: Lauritsen-thesis-source.zip file_size: 1625888 relation: source_file file_date_updated: 2024-09-26T13:12:55Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '353' project: - _id: bda63fe5-d553-11ed-ba76-a16e3d2f256b grant_number: I06427 name: Mathematical Challenges in BCS Theory of Superconductivity - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication_identifier: isbn: - 978-3-99078-042-8 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11732' relation: part_of_dissertation status: public - id: '14542' relation: part_of_dissertation status: public - id: '18107' relation: part_of_dissertation status: public - id: '17240' relation: part_of_dissertation status: public - id: '14931' relation: part_of_dissertation status: public status: public supervisor: - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 title: Energies of dilute Fermi gases and universalities in BCS theory tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- _id: '14931' abstract: - lang: eng text: We prove an upper bound on the ground state energy of the dilute spin-polarized Fermi gas capturing the leading correction to the kinetic energy resulting from repulsive interactions. One of the main ingredients in the proof is a rigorous implementation of the fermionic cluster expansion of Gaudin et al. (1971) [15]. acknowledgement: A.B.L. would like to thank Johannes Agerskov and Jan Philip Solovej for valuable discussions. We thank Alessandro Giuliani for helpful discussions and for pointing out the reference [18]. Funding from the European Union's Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is acknowledged. Financial support by the Austrian Science Fund (FWF) through project number I 6427-N (as part of the SFB/TRR 352) is gratefully acknowledged. article_number: '110320' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Asbjørn Bækgaard full_name: Lauritsen, Asbjørn Bækgaard id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1 last_name: Lauritsen orcid: 0000-0003-4476-2288 - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: 'Lauritsen AB, Seiringer R. Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis. 2024;286(7). doi:10.1016/j.jfa.2024.110320' apa: 'Lauritsen, A. B., & Seiringer, R. (2024). Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2024.110320' chicago: 'Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” Journal of Functional Analysis. Elsevier, 2024. https://doi.org/10.1016/j.jfa.2024.110320.' ieee: 'A. B. Lauritsen and R. Seiringer, “Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion,” Journal of Functional Analysis, vol. 286, no. 7. Elsevier, 2024.' ista: 'Lauritsen AB, Seiringer R. 2024. Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis. 286(7), 110320.' mla: 'Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” Journal of Functional Analysis, vol. 286, no. 7, 110320, Elsevier, 2024, doi:10.1016/j.jfa.2024.110320.' short: A.B. Lauritsen, R. Seiringer, Journal of Functional Analysis 286 (2024). corr_author: '1' date_created: 2024-02-04T23:00:53Z date_published: 2024-04-01T00:00:00Z date_updated: 2026-04-16T08:17:56Z day: '01' ddc: - '510' department: - _id: RoSe doi: 10.1016/j.jfa.2024.110320 ec_funded: 1 external_id: arxiv: - '2301.04894' isi: - '001170294000001' file: - access_level: open_access checksum: ee203cf2dc4420ad90d3c9970d246a78 content_type: application/pdf creator: dernst date_created: 2024-07-22T11:11:56Z date_updated: 2024-07-22T11:11:56Z file_id: '17305' file_name: 2024_JourFunctAnalysis_Lauritsen.pdf file_size: 1381063 relation: main_file success: 1 file_date_updated: 2024-07-22T11:11:56Z has_accepted_license: '1' intvolume: ' 286' isi: 1 issue: '7' language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems - _id: bda63fe5-d553-11ed-ba76-a16e3d2f256b grant_number: I06427 name: Mathematical Challenges in BCS Theory of Superconductivity publication: Journal of Functional Analysis publication_identifier: eissn: - 1096-0783 issn: - 0022-1236 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '18135' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 286 year: '2024' ... --- _id: '15012' abstract: - lang: eng text: We solve a problem of Dujmović and Wood (2007) by showing that a complete convex geometric graph on n vertices cannot be decomposed into fewer than n-1 star-forests, each consisting of noncrossing edges. This bound is clearly tight. We also discuss similar questions for abstract graphs. acknowledgement: János Pach’s Research partially supported by European Research Council (ERC), grant “GeoScape” No. 882971 and by the Hungarian Science Foundation (NKFIH), grant K-131529. Work by Morteza Saghafian is partially supported by the European Research Council (ERC), grant No. 788183, and by the Wittgenstein Prize, Austrian Science Fund (FWF), grant No. Z 342-N31. alternative_title: - LNCS article_processing_charge: No arxiv: 1 author: - first_name: János full_name: Pach, János id: E62E3130-B088-11EA-B919-BF823C25FEA4 last_name: Pach - first_name: Morteza full_name: Saghafian, Morteza id: f86f7148-b140-11ec-9577-95435b8df824 last_name: Saghafian - first_name: Patrick full_name: Schnider, Patrick last_name: Schnider citation: ama: 'Pach J, Saghafian M, Schnider P. Decomposition of geometric graphs into star-forests. In: 31st International Symposium on Graph Drawing and Network Visualization. Vol 14465. Springer Nature; 2024:339-346. doi:10.1007/978-3-031-49272-3_23' apa: 'Pach, J., Saghafian, M., & Schnider, P. (2024). Decomposition of geometric graphs into star-forests. In 31st International Symposium on Graph Drawing and Network Visualization (Vol. 14465, pp. 339–346). Isola delle Femmine, Palermo, Italy: Springer Nature. https://doi.org/10.1007/978-3-031-49272-3_23' chicago: Pach, János, Morteza Saghafian, and Patrick Schnider. “Decomposition of Geometric Graphs into Star-Forests.” In 31st International Symposium on Graph Drawing and Network Visualization, 14465:339–46. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-49272-3_23. ieee: J. Pach, M. Saghafian, and P. Schnider, “Decomposition of geometric graphs into star-forests,” in 31st International Symposium on Graph Drawing and Network Visualization, Isola delle Femmine, Palermo, Italy, 2024, vol. 14465, pp. 339–346. ista: 'Pach J, Saghafian M, Schnider P. 2024. Decomposition of geometric graphs into star-forests. 31st International Symposium on Graph Drawing and Network Visualization. GD: Graph Drawing and Network Visualization, LNCS, vol. 14465, 339–346.' mla: Pach, János, et al. “Decomposition of Geometric Graphs into Star-Forests.” 31st International Symposium on Graph Drawing and Network Visualization, vol. 14465, Springer Nature, 2024, pp. 339–46, doi:10.1007/978-3-031-49272-3_23. short: J. Pach, M. Saghafian, P. Schnider, in:, 31st International Symposium on Graph Drawing and Network Visualization, Springer Nature, 2024, pp. 339–346. conference: end_date: 2023-09-22 location: Isola delle Femmine, Palermo, Italy name: 'GD: Graph Drawing and Network Visualization' start_date: 2023-09-20 date_created: 2024-02-18T23:01:03Z date_published: 2024-01-01T00:00:00Z date_updated: 2026-04-16T09:12:37Z day: '01' department: - _id: HeEd doi: 10.1007/978-3-031-49272-3_23 ec_funded: 1 external_id: arxiv: - '2306.13201' isi: - '001207939600023' intvolume: ' 14465' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2306.13201 month: '01' oa: 1 oa_version: Preprint page: 339-346 project: - _id: 266A2E9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '788183' name: Alpha Shape Theory Extended - _id: 268116B8-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00342 name: Mathematics, Computer Science publication: 31st International Symposium on Graph Drawing and Network Visualization publication_identifier: eisbn: - '9783031492723' eissn: - 1611-3349 isbn: - '9783031492716' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '21253' relation: later_version status: public scopus_import: '1' status: public title: Decomposition of geometric graphs into star-forests type: conference user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 14465 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '12738' abstract: - lang: eng text: We study turn-based stochastic zero-sum games with lexicographic preferences over objectives. Stochastic games are standard models in control, verification, and synthesis of stochastic reactive systems that exhibit both randomness as well as controllable and adversarial non-determinism. Lexicographic order allows one to consider multiple objectives with a strict preference order. To the best of our knowledge, stochastic games with lexicographic objectives have not been studied before. For a mixture of reachability and safety objectives, we show that deterministic lexicographically optimal strategies exist and memory is only required to remember the already satisfied and violated objectives. For a constant number of objectives, we show that the relevant decision problem is in NP∩coNP, matching the current known bound for single objectives; and in general the decision problem is PSPACE-hard and can be solved in NEXPTIME∩coNEXPTIME. We present an algorithm that computes the lexicographically optimal strategies via a reduction to the computation of optimal strategies in a sequence of single-objectives games. For omega-regular objectives, we restrict our analysis to one-player games, also known as Markov decision processes. We show that lexicographically optimal strategies exist and need either randomization or finite memory. We present an algorithm that solves the relevant decision problem in polynomial time. We have implemented our algorithms and report experimental results on various case studies. acknowledgement: Tobias Winkler and Joost-Pieter Katoen are supported by the DFG RTG 2236 UnRAVeL and the innovation programme under the Marie Skłodowska-Curie grant agreement No. 101008233 (Mission). Krishnendu Chatterjee is supported by the ERC CoG 863818 (ForM-SMArt) and the Vienna Science and Technology Fund (WWTF) Project ICT15-003. Maximilian Weininger is supported by the DFG projects 383882557 Statistical Unbounded Verification (SUV) and 427755713 Group-By Objectives in Probabilistic Verification (GOPro). Stefanie Mohr is supported by the DFG RTG 2428 CONVEY. Open Access funding enabled and organized by Projekt DEAL. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Joost P full_name: Katoen, Joost P id: 4524F760-F248-11E8-B48F-1D18A9856A87 last_name: Katoen orcid: 0000-0002-6143-1926 - first_name: Stefanie full_name: Mohr, Stefanie last_name: Mohr - first_name: Maximilian full_name: Weininger, Maximilian last_name: Weininger - first_name: Tobias full_name: Winkler, Tobias last_name: Winkler citation: ama: Chatterjee K, Katoen JP, Mohr S, Weininger M, Winkler T. Stochastic games with lexicographic objectives. Formal Methods in System Design. 2024;63:40-80. doi:10.1007/s10703-023-00411-4 apa: Chatterjee, K., Katoen, J. P., Mohr, S., Weininger, M., & Winkler, T. (2024). Stochastic games with lexicographic objectives. Formal Methods in System Design. Springer Nature. https://doi.org/10.1007/s10703-023-00411-4 chicago: Chatterjee, Krishnendu, Joost P Katoen, Stefanie Mohr, Maximilian Weininger, and Tobias Winkler. “Stochastic Games with Lexicographic Objectives.” Formal Methods in System Design. Springer Nature, 2024. https://doi.org/10.1007/s10703-023-00411-4. ieee: K. Chatterjee, J. P. Katoen, S. Mohr, M. Weininger, and T. Winkler, “Stochastic games with lexicographic objectives,” Formal Methods in System Design, vol. 63. Springer Nature, pp. 40–80, 2024. ista: Chatterjee K, Katoen JP, Mohr S, Weininger M, Winkler T. 2024. Stochastic games with lexicographic objectives. Formal Methods in System Design. 63, 40–80. mla: Chatterjee, Krishnendu, et al. “Stochastic Games with Lexicographic Objectives.” Formal Methods in System Design, vol. 63, Springer Nature, 2024, pp. 40–80, doi:10.1007/s10703-023-00411-4. short: K. Chatterjee, J.P. Katoen, S. Mohr, M. Weininger, T. Winkler, Formal Methods in System Design 63 (2024) 40–80. date_created: 2023-03-19T23:00:59Z date_published: 2024-10-01T00:00:00Z date_updated: 2026-04-16T09:31:13Z day: '01' ddc: - '000' department: - _id: KrCh doi: 10.1007/s10703-023-00411-4 ec_funded: 1 external_id: isi: - '000946174300001' file: - access_level: open_access checksum: 111e76b76163640a2c89237642af586f content_type: application/pdf creator: dernst date_created: 2025-01-09T07:31:31Z date_updated: 2025-01-09T07:31:31Z file_id: '18781' file_name: 2024_FromMethodsSys_Chatterjee.pdf file_size: 2614190 relation: main_file success: 1 file_date_updated: 2025-01-09T07:31:31Z has_accepted_license: '1' intvolume: ' 63' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 40-80 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification publication: Formal Methods in System Design publication_identifier: eissn: - 1572-8102 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '8272' relation: earlier_version status: public scopus_import: '1' status: public title: Stochastic games with lexicographic objectives tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 63 year: '2024' ... --- APC_amount: 6468 EUR DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '14793' abstract: - lang: eng text: Superconductor/semiconductor hybrid devices have attracted increasing interest in the past years. Superconducting electronics aims to complement semiconductor technology, while hybrid architectures are at the forefront of new ideas such as topological superconductivity and protected qubits. In this work, we engineer the induced superconductivity in two-dimensional germanium hole gas by varying the distance between the quantum well and the aluminum. We demonstrate a hard superconducting gap and realize an electrically and flux tunable superconducting diode using a superconducting quantum interference device (SQUID). This allows to tune the current phase relation (CPR), to a regime where single Cooper pair tunneling is suppressed, creating a sin(2y) CPR. Shapiro experiments complement this interpretation and the microwave drive allows to create a diode with ≈ 100% efficiency. The reported results open up the path towards integration of spin qubit devices, microwave resonators and (protected) superconducting qubits on the same silicon technology compatible platform. acknowledged_ssus: - _id: M-Shop - _id: NanoFab acknowledgement: "We acknowledge Alexander Brinkmann, Alessandro Crippa, Francesco Giazotto, Andrew Higginbotham, Andrea Iorio, Giordano Scappucci, Christian Schonenberger, and Lukas Splitthoff for helpful discussions. We thank Marcel Verheijen for the support in the TEM analysis. This research and related results were made possible with the support of the NOMIS\r\nFoundation. It was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the nanofabrication facility, the European Union’s Horizon 2020 research andinnovation programme under Grant Agreement No 862046, the HORIZONRIA\r\n101069515 project, the European Innovation Council Pathfinder grant no. 101115315 (QuKiT), and the FWF Projects #P-32235, #P-36507 and #F-8606. For the purpose of open access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. R.S.S. acknowledges Spanish CM “Talento Program\"\r\nProject No. 2022-T1/IND-24070. J.J. acknowledges European Research Council TOCINA 834290." article_number: '169' article_processing_charge: Yes article_type: original author: - first_name: Marco full_name: Valentini, Marco id: C0BB2FAC-D767-11E9-B658-BC13E6697425 last_name: Valentini - first_name: Oliver full_name: Sagi, Oliver id: 71616374-A8E9-11E9-A7CA-09ECE5697425 last_name: Sagi - first_name: Levon full_name: Baghumyan, Levon id: 7aa1f788-b527-11ee-aa9e-e6111a79e0c7 last_name: Baghumyan - first_name: Thijs full_name: de Gijsel, Thijs id: a0ece13c-b527-11ee-929d-bad130106eee last_name: de Gijsel - first_name: Jason full_name: Jung, Jason id: 4C9ACE7A-F248-11E8-B48F-1D18A9856A87 last_name: Jung - first_name: Stefano full_name: Calcaterra, Stefano last_name: Calcaterra - first_name: Andrea full_name: Ballabio, Andrea last_name: Ballabio - first_name: Juan L full_name: Aguilera Servin, Juan L id: 2A67C376-F248-11E8-B48F-1D18A9856A87 last_name: Aguilera Servin orcid: 0000-0002-2862-8372 - first_name: Kushagra full_name: Aggarwal, Kushagra id: b22ab905-3539-11eb-84c3-fc159dcd79cb last_name: Aggarwal orcid: 0000-0001-9985-9293 - first_name: Marian full_name: Janik, Marian id: 396A1950-F248-11E8-B48F-1D18A9856A87 last_name: Janik orcid: 0009-0003-9037-8831 - first_name: Thomas full_name: Adletzberger, Thomas id: 38756BB2-F248-11E8-B48F-1D18A9856A87 last_name: Adletzberger - first_name: Rubén full_name: Seoane Souto, Rubén last_name: Seoane Souto - first_name: Martin full_name: Leijnse, Martin last_name: Leijnse - first_name: Jeroen full_name: Danon, Jeroen last_name: Danon - first_name: Constantin full_name: Schrade, Constantin last_name: Schrade - first_name: Erik full_name: Bakkers, Erik last_name: Bakkers - first_name: Daniel full_name: Chrastina, Daniel last_name: Chrastina - first_name: Giovanni full_name: Isella, Giovanni last_name: Isella - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X citation: ama: Valentini M, Sagi O, Baghumyan L, et al. Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium. Nature Communications. 2024;15. doi:10.1038/s41467-023-44114-0 apa: Valentini, M., Sagi, O., Baghumyan, L., de Gijsel, T., Jung, J., Calcaterra, S., … Katsaros, G. (2024). Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-44114-0 chicago: Valentini, Marco, Oliver Sagi, Levon Baghumyan, Thijs de Gijsel, Jason Jung, Stefano Calcaterra, Andrea Ballabio, et al. “Parity-Conserving Cooper-Pair Transport and Ideal Superconducting Diode in Planar Germanium.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-023-44114-0. ieee: M. Valentini et al., “Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium,” Nature Communications, vol. 15. Springer Nature, 2024. ista: Valentini M, Sagi O, Baghumyan L, de Gijsel T, Jung J, Calcaterra S, Ballabio A, Aguilera Servin JL, Aggarwal K, Janik M, Adletzberger T, Seoane Souto R, Leijnse M, Danon J, Schrade C, Bakkers E, Chrastina D, Isella G, Katsaros G. 2024. Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium. Nature Communications. 15, 169. mla: Valentini, Marco, et al. “Parity-Conserving Cooper-Pair Transport and Ideal Superconducting Diode in Planar Germanium.” Nature Communications, vol. 15, 169, Springer Nature, 2024, doi:10.1038/s41467-023-44114-0. short: M. Valentini, O. Sagi, L. Baghumyan, T. de Gijsel, J. Jung, S. Calcaterra, A. Ballabio, J.L. Aguilera Servin, K. Aggarwal, M. Janik, T. Adletzberger, R. Seoane Souto, M. Leijnse, J. Danon, C. Schrade, E. Bakkers, D. Chrastina, G. Isella, G. Katsaros, Nature Communications 15 (2024). corr_author: '1' date_created: 2024-01-14T23:00:56Z date_published: 2024-01-02T00:00:00Z date_updated: 2025-10-15T06:31:47Z day: '02' ddc: - '530' department: - _id: GeKa doi: 10.1038/s41467-023-44114-0 ec_funded: 1 external_id: isi: - '001142794000839' pmid: - '38167818' file: - access_level: open_access checksum: ef79173b45eeaf984ffa61ef2f8a52ab content_type: application/pdf creator: dernst date_created: 2024-01-17T11:03:00Z date_updated: 2024-01-17T11:03:00Z file_id: '14825' file_name: 2024_NatureComm_Valentini.pdf file_size: 2336595 relation: main_file success: 1 file_date_updated: 2024-01-17T11:03:00Z has_accepted_license: '1' intvolume: ' 15' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 237E5020-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '862046' name: TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS - _id: 34c0acea-11ca-11ed-8bc3-8775e10fd452 grant_number: '101069515' name: Integrated Germanium Quantum Technology - _id: bdc2ca30-d553-11ed-ba76-cf164a5bb811 grant_number: '101115315' name: Quantum bits with Kitaev Transmons - _id: 237B3DA4-32DE-11EA-91FC-C7463DDC885E call_identifier: FWF grant_number: P32235 name: Towards scalable hut wire quantum devices - _id: bd8bd29e-d553-11ed-ba76-f0070d4b237a grant_number: P36507 name: Merging spin and superconducting qubits in planar Ge - _id: 34a66131-11ca-11ed-8bc3-a31681c6b03e grant_number: F8606 name: 'Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional and unconventional topological superconductors' - _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1 call_identifier: FWF name: FWF Open Access Fund publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 15 year: '2024' ... --- APC_amount: 6248,82 EUR DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18603' abstract: - lang: eng text: It is widely believed that information storage in neuronal circuits involves nanoscopic structural changes at synapses, resulting in the formation of synaptic engrams. However, direct evidence for this hypothesis is lacking. To test this conjecture, we combined chemical potentiation, functional analysis by paired pre-postsynaptic recordings, and structural analysis by electron microscopy (EM) and freeze-fracture replica labeling (FRL) at the rodent hippocampal mossy fiber synapse, a key synapse in the trisynaptic circuit of the hippocampus. Biophysical analysis of synaptic transmission revealed that forskolin-induced chemical potentiation increased the readily releasable vesicle pool size and vesicular release probability by 146% and 49%, respectively. Structural analysis of mossy fiber synapses by EM and FRL demonstrated an increase in the number of vesicles close to the plasma membrane and the number of clusters of the priming protein Munc13-1, indicating an increase in the number of both docked and primed vesicles. Furthermore, FRL analysis revealed a significant reduction of the distance between Munc13-1 and CaV2.1 Ca2+ channels, suggesting reconfiguration of the channel-vesicle coupling nanotopography. Our results indicate that presynaptic plasticity is associated with structural reorganization of active zones. We propose that changes in potential nanoscopic organization at synaptic vesicle release sites may be correlates of learning and memory at a plastic central synapse. acknowledged_ssus: - _id: EM-Fac - _id: PreCl acknowledgement: "We thank Carolina Borges-Merjane, Jing-Jing Chen, Katharina Lichter, and Samuel Young for critically reading the manuscript; the Electron Microscopy Facility of ISTA, in particular Vanessa Zheden, for extensive support, advice, and experimental assistance; the Preclinical Facility of ISTA, in particular Victoria Wimmer and Michael Schunn, for experimental assistance; Florian Marr and Christina Altmutter for technical support; Alois Schlögl for help with analysis; and Eleftheria Kralli-Beller for manuscript editing. We also thank Cordelia Imig for providing Munc13-1cKO-Munc13-2/3(−/−) mutant mice. Part of the work has been published in O.K.’s thesis in partial fulfillment of the requirements for the degree of Doctor of Philosophy.\r\nThis project received funding from the European Research Council and European Union’s Horizon 2020 research and innovation programme (ERC 692692 to P.J.; https://cordis.europa.eu/project/id/692692/de) and from the Fond zur Förderung der Wissenschaftlichen Forschung (Z312-B27 Wittgenstein award to P.J., https://www.fwf.ac.at/en/funding/portfolio/projects/fwf-wittgenstein-award; W1205-B09 and P36232-B to P.J., https://www.fwf.ac.at/en/funding; I6166-B to R.S.; https://www.fwf.ac.at/en/funding). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." article_number: e3002879 article_processing_charge: Yes article_type: original author: - first_name: Olena full_name: Kim, Olena id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87 last_name: Kim orcid: 0000-0003-2344-1039 - first_name: Yuji full_name: Okamoto, Yuji id: 3337E116-F248-11E8-B48F-1D18A9856A87 last_name: Okamoto orcid: 0000-0003-0408-6094 - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Nils full_name: Brose, Nils last_name: Brose - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Kim O, Okamoto Y, Kaufmann W, Brose N, Shigemoto R, Jonas PM. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. PLoS Biology. 2024;22(11). doi:10.1371/journal.pbio.3002879 apa: Kim, O., Okamoto, Y., Kaufmann, W., Brose, N., Shigemoto, R., & Jonas, P. M. (2024). Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.3002879 chicago: Kim, Olena, Yuji Okamoto, Walter Kaufmann, Nils Brose, Ryuichi Shigemoto, and Peter M Jonas. “Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber Boutons.” PLoS Biology. Public Library of Science, 2024. https://doi.org/10.1371/journal.pbio.3002879. ieee: O. Kim, Y. Okamoto, W. Kaufmann, N. Brose, R. Shigemoto, and P. M. Jonas, “Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons,” PLoS Biology, vol. 22, no. 11. Public Library of Science, 2024. ista: Kim O, Okamoto Y, Kaufmann W, Brose N, Shigemoto R, Jonas PM. 2024. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. PLoS Biology. 22(11), e3002879. mla: Kim, Olena, et al. “Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber Boutons.” PLoS Biology, vol. 22, no. 11, e3002879, Public Library of Science, 2024, doi:10.1371/journal.pbio.3002879. short: O. Kim, Y. Okamoto, W. Kaufmann, N. Brose, R. Shigemoto, P.M. Jonas, PLoS Biology 22 (2024). corr_author: '1' date_created: 2024-12-01T23:01:54Z date_published: 2024-11-18T00:00:00Z date_updated: 2026-04-16T12:20:34Z day: '18' ddc: - '570' department: - _id: PeJo - _id: EM-Fac - _id: RySh doi: 10.1371/journal.pbio.3002879 ec_funded: 1 external_id: isi: - '001358568700003' pmid: - '39556620' file: - access_level: open_access checksum: 7de2dcb50deb65dde05c80082bb85a82 content_type: application/pdf creator: dernst date_created: 2024-12-03T08:56:53Z date_updated: 2024-12-03T08:56:53Z file_id: '18608' file_name: 2024_PloSBio_Kim.pdf file_size: 3057631 relation: main_file success: 1 file_date_updated: 2024-12-03T08:56:53Z has_accepted_license: '1' intvolume: ' 22' isi: 1 issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glutamatergic synapse - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: Synaptic communication in neuronal microcircuits - _id: bd88be38-d553-11ed-ba76-81d5a70a6ef5 grant_number: P36232 name: Mechanisms of GABA release in hippocampal circuits - _id: b1b85715-d554-11ed-a5ad-84a07fc9f18e grant_number: I06166 name: Structural & functional basis of presynaptic plasticity - _id: 25C3DBB6-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W01205 name: Zellkommunikation in Gesundheit und Krankheit - _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1 call_identifier: FWF name: FWF Open Access Fund publication: PLoS Biology publication_identifier: eissn: - 1545-7885 issn: - 1544-9173 publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: record: - id: '18296' relation: research_data status: public scopus_import: '1' status: public title: Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 22 year: '2024' ... --- _id: '18296' abstract: - lang: eng text: It is widely believed that information storage in neuronal circuits involves nanoscopic structural changes at synapses, resulting in the formation of synaptic engrams. However, direct evidence for this hypothesis is lacking. To test this conjecture, we combined chemical potentiation, functional analysis by paired pre-postsynaptic recordings, and structural analysis by electron microscopy (EM) and freeze-fracture replica labeling (FRL) at the murine hippocampal mossy fiber synapse, a key synapse in the trisynaptic circuit of the hippocampus. Biophysical analysis of synaptic transmission revealed that forskolin-induced chemical potentiation increased the readily releasable vesicle pool size and vesicular release probability by 146% and 49%, respectively. Structural analysis of mossy fiber synapses by EM and FRL demonstrated an increase in the number of vesicles close to the plasma membrane and the number of clusters of the priming protein Munc13-1, indicating an increase in the number of both docked and primed vesicles. Furthermore, FRL analysis revealed a significant reduction of the distance between Munc13-1 and CaV2.1 Ca2+ channels, suggesting reconfiguration of the channel-vesicle coupling nanotopography. Our results indicate that presynaptic plasticity is associated with structural reorganization of active zones. We propose that changes in potential nanoscopic organization at synaptic vesicle release sites may be correlates of learning and memory at a plastic central synapse. article_processing_charge: No author: - first_name: Olena full_name: Kim, Olena id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87 last_name: Kim orcid: 0000-0003-2344-1039 citation: ama: Kim O. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. 2024. doi:10.15479/AT:ISTA:18296 apa: Kim, O. (2024). Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:18296 chicago: Kim, Olena. “Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber Boutons.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:18296. ieee: O. Kim, “Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons.” Institute of Science and Technology Austria, 2024. ista: Kim O. 2024. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons, Institute of Science and Technology Austria, 10.15479/AT:ISTA:18296. mla: Kim, Olena. Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber Boutons. Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:18296. short: O. Kim, (2024). contributor: - contributor_type: researcher first_name: Olena id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87 last_name: Kim - contributor_type: researcher first_name: Yuji id: 3337E116-F248-11E8-B48F-1D18A9856A87 last_name: Okamoto orcid: 0000-0003-0408-6094 - contributor_type: researcher first_name: Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - contributor_type: researcher first_name: 'Nils ' last_name: Brose - contributor_type: researcher first_name: Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - contributor_type: supervisor first_name: Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 corr_author: '1' date_created: 2024-10-11T10:12:17Z date_published: 2024-10-11T00:00:00Z date_updated: 2026-04-16T12:20:33Z day: '11' ddc: - '570' department: - _id: PeJo - _id: RySh - _id: EM-Fac doi: 10.15479/AT:ISTA:18296 ec_funded: 1 file: - access_level: open_access checksum: 0a977e7df54c418251b10dfd3f8a015c content_type: application/zip creator: okim date_created: 2024-10-11T10:04:19Z date_updated: 2024-10-11T10:04:19Z file_id: '18297' file_name: Kim_et_al_2024_PlosBio_Source_data.zip file_size: 164382 relation: main_file success: 1 - access_level: open_access checksum: 5b9343d6b2035ac3185e390fad4d3830 content_type: text/plain creator: okim date_created: 2024-10-11T10:04:23Z date_updated: 2024-10-11T10:04:23Z file_id: '18298' file_name: info.txt file_size: 654 relation: main_file success: 1 file_date_updated: 2024-10-11T10:04:23Z has_accepted_license: '1' keyword: - Hippocampal mossy fiber synapses - short-term potentiation - long-term potentiation - presynaptic plasticity - electron microscopy - freeze-fracture replica labeling - paired recordings - forskolin - cyclic adenosine monophosphate (cAMP) - protein kinase A (PKA) - neuromodulation - synaptic vesicle pools - presynaptic Ca2+ channels - Munc13 - docking - priming - active zone month: '10' oa: 1 oa_version: Submitted Version project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glutamatergic synapse publisher: Institute of Science and Technology Austria related_material: record: - id: '18603' relation: used_in_publication status: public status: public title: Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2024' ... --- APC_amount: 1530 EUR OA_place: publisher OA_type: gold _id: '15401' abstract: - lang: eng text: Amide-proton-detected magic-angle-spinning NMR of deuterated proteins has become a main technique in NMR-based structural biology. In standard deuteration protocols that rely on D2O-based culture media, non-exchangeable amide sites remain deuterated, making these sites unobservable. Here we demonstrate that proteins produced with a H2O-based culture medium doped with deuterated cell lysate allow scientists to overcome this “reprotonation bottleneck” while retaining a high level of deuteration (ca. 80 %) and narrow linewidths. We quantified coherence lifetimes of several proteins prepared with this labeling pattern over a range of magic-angle-spinning (MAS) frequencies (40–100 kHz). We demonstrate that under commonly used conditions (50–60 kHz MAS), the amide 1H linewidths with our labeling approach are comparable to those of perdeuterated proteins and better than those of protonated samples at 100 kHz. For three proteins in the 33–50 kDa size range, many previously unobserved amides become visible. We report how to prepare the deuterated cell lysate for our approach from fractions of perdeuterated cultures which are usually discarded, and we show that such media can be used identically to commercial media. The residual protonation of Hα sites allows for well-resolved Hα-detected spectra and Hα resonance assignment, exemplified by the de novo assignment of 168 Hα sites in a 39 kDa protein. The approach based on this H2O/cell-lysate deuteration and MAS frequencies compatible with 1.3 or 1.9 mm rotors presents a strong sensitivity benefit over 0.7 mm 100 kHz MAS experiments. acknowledged_ssus: - _id: NMR acknowledgement: "We thank Dominique Madern (IBS Grenoble) for providing the plasmid for MalDH and feedback on the article, Alicia Vallet for excellent support at the Grenoble NMR facility, and Petra Rovo and Margarita Valhondo at the IST Austria NMR Service Unit. We thank Dorothea Anrather in the mass spectrometry facility of Max Perutz Labs for the mass spectrometry analysis using the instruments of the Vienna BioCenter Core Facilities (VBCF). We are grateful to Jean-Pierre Andrieu (Plateforme Seq3A, IBS Grenoble) for the analysis of the amino acid composition of the in-house-prepared lysates. We are grateful to Rasmus Linser (Technical University Dortmund) for sharing a paper draft describing a similar study. This work was supported by the Austrian Science Fund (FWF; project number I5812-B). We thank Tobias Schubeis (Lyon) and the reviewers for constructive input.\r\nThis research has been supported by the Austrian Science Fund (grant no. I5812-B). Part of this work used the platforms of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for 40 Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003). IBS acknowledges integration into the Interdisciplinary Research Institute of Grenoble (IRIG, 45 CEA). Charles-Adrien Arnaud was funded by GRAL." article_processing_charge: Yes article_type: original author: - first_name: Federico full_name: Napoli, Federico id: d42e08e7-f4fc-11eb-af0a-d71e26138f1b last_name: Napoli orcid: 0000-0002-9043-136X - first_name: Jia-Ying full_name: Guan, Jia-Ying last_name: Guan - first_name: Charles-Adrien full_name: Arnaud, Charles-Adrien last_name: Arnaud - first_name: Pavel full_name: Macek, Pavel last_name: Macek - first_name: Hugo full_name: Fraga, Hugo last_name: Fraga - first_name: Cécile full_name: Breyton, Cécile last_name: Breyton - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: 'Napoli F, Guan J-Y, Arnaud C-A, et al. Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck. Magnetic Resonance. 2024;5(1):33-49. doi:10.5194/mr-5-33-2024' apa: 'Napoli, F., Guan, J.-Y., Arnaud, C.-A., Macek, P., Fraga, H., Breyton, C., & Schanda, P. (2024). Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck. Magnetic Resonance. Copernicus Publications. https://doi.org/10.5194/mr-5-33-2024' chicago: 'Napoli, Federico, Jia-Ying Guan, Charles-Adrien Arnaud, Pavel Macek, Hugo Fraga, Cécile Breyton, and Paul Schanda. “Deuteration of Proteins Boosted by Cell Lysates: High-Resolution Amide and Ha Magic-Angle-Spinning (MAS) NMR without the Reprotonation Bottleneck.” Magnetic Resonance. Copernicus Publications, 2024. https://doi.org/10.5194/mr-5-33-2024.' ieee: 'F. Napoli et al., “Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck,” Magnetic Resonance, vol. 5, no. 1. Copernicus Publications, pp. 33–49, 2024.' ista: 'Napoli F, Guan J-Y, Arnaud C-A, Macek P, Fraga H, Breyton C, Schanda P. 2024. Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck. Magnetic Resonance. 5(1), 33–49.' mla: 'Napoli, Federico, et al. “Deuteration of Proteins Boosted by Cell Lysates: High-Resolution Amide and Ha Magic-Angle-Spinning (MAS) NMR without the Reprotonation Bottleneck.” Magnetic Resonance, vol. 5, no. 1, Copernicus Publications, 2024, pp. 33–49, doi:10.5194/mr-5-33-2024.' short: F. Napoli, J.-Y. Guan, C.-A. Arnaud, P. Macek, H. Fraga, C. Breyton, P. Schanda, Magnetic Resonance 5 (2024) 33–49. corr_author: '1' date_created: 2024-05-16T15:02:43Z date_published: 2024-04-19T00:00:00Z date_updated: 2025-07-17T08:12:23Z day: '19' ddc: - '530' department: - _id: PaSc doi: 10.5194/mr-5-33-2024 external_id: pmid: - '40384771' file: - access_level: open_access checksum: 80ea50114e428461ca9530d3bd5d89e4 content_type: application/pdf creator: dernst date_created: 2024-05-22T07:01:15Z date_updated: 2024-05-22T07:01:15Z file_id: '15413' file_name: 2024_MagneticResonance_Napoli.pdf file_size: 6657865 relation: main_file success: 1 file_date_updated: 2024-05-22T07:01:15Z has_accepted_license: '1' intvolume: ' 5' issue: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 33-49 pmid: 1 project: - _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf grant_number: I05812 name: AlloSpace. The emergence and mechanisms of allostery - _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1 call_identifier: FWF name: FWF Open Access Fund publication: Magnetic Resonance publication_identifier: issn: - 2699-0016 publication_status: published publisher: Copernicus Publications quality_controlled: '1' scopus_import: '1' status: public title: 'Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2024' ...