--- _id: '8741' abstract: - lang: eng text: "In ecology, climate and other fields, (sub)systems have been identified that can transition into a qualitatively different state when a critical threshold or tipping point in a driving process is crossed. An understanding of those tipping elements is of great interest given the increasing influence of humans on the biophysical Earth system. Complex interactions exist between tipping elements, e.g. physical mechanisms connect subsystems of the climate system. Based on earlier work on such coupled nonlinear systems, we systematically assessed the qualitative long-term behaviour of interacting tipping elements. We developed an understanding of the consequences of interactions\r\non the tipping behaviour allowing for tipping cascades to emerge under certain conditions. The (narrative) application of\r\nthese qualitative results to real-world examples of interacting tipping elements indicates that tipping cascades with profound consequences may occur: the interacting Greenland ice sheet and thermohaline ocean circulation might tip before the tipping points of the isolated subsystems are crossed. The eutrophication of the first lake in a lake chain might propagate through the following lakes without a crossing of their individual critical nutrient input levels. The possibility of emerging cascading tipping dynamics calls for the development of a unified theory of interacting tipping elements and the quantitative analysis of interacting real-world tipping elements." acknowledgement: "V.K. thanks the German National Academic Foundation (Studienstiftung des deutschen Volkes) for financial\r\nsupport. J.F.D. is grateful for financial support by the Stordalen Foundation via the Planetary Boundary Research\r\nNetwork (PB.net), the Earth League’s EarthDoc program and the European Research Council Advanced Grant\r\nproject ERA (Earth Resilience in the Anthropocene). We are thankful for support by the Leibniz Association\r\n(project DominoES).\r\nAcknowledgements. This work has been performed in the context of the copan collaboration and the FutureLab on Earth\r\nResilience in the Anthropocene at the Potsdam Institute for Climate Impact Research. Furthermore, we acknowledge\r\ndiscussions with and helpful comments by N. Wunderling, J. Heitzig and M. Wiedermann." article_number: '200599' article_processing_charge: No article_type: original author: - first_name: Ann Kristin full_name: Klose, Ann Kristin last_name: Klose - first_name: Volker full_name: Karle, Volker id: D7C012AE-D7ED-11E9-95E8-1EC5E5697425 last_name: Karle orcid: 0000-0002-6963-0129 - first_name: Ricarda full_name: Winkelmann, Ricarda last_name: Winkelmann - first_name: Jonathan F. full_name: Donges, Jonathan F. last_name: Donges citation: ama: 'Klose AK, Karle V, Winkelmann R, Donges JF. Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements. Royal Society Open Science. 2020;7(6). doi:10.1098/rsos.200599' apa: 'Klose, A. K., Karle, V., Winkelmann, R., & Donges, J. F. (2020). Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements. Royal Society Open Science. The Royal Society. https://doi.org/10.1098/rsos.200599' chicago: 'Klose, Ann Kristin, Volker Karle, Ricarda Winkelmann, and Jonathan F. Donges. “Emergence of Cascading Dynamics in Interacting Tipping Elements of Ecology and Climate: Cascading Dynamics in Tipping Elements.” Royal Society Open Science. The Royal Society, 2020. https://doi.org/10.1098/rsos.200599.' ieee: 'A. K. Klose, V. Karle, R. Winkelmann, and J. F. Donges, “Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements,” Royal Society Open Science, vol. 7, no. 6. The Royal Society, 2020.' ista: 'Klose AK, Karle V, Winkelmann R, Donges JF. 2020. Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements. Royal Society Open Science. 7(6), 200599.' mla: 'Klose, Ann Kristin, et al. “Emergence of Cascading Dynamics in Interacting Tipping Elements of Ecology and Climate: Cascading Dynamics in Tipping Elements.” Royal Society Open Science, vol. 7, no. 6, 200599, The Royal Society, 2020, doi:10.1098/rsos.200599.' short: A.K. Klose, V. Karle, R. Winkelmann, J.F. Donges, Royal Society Open Science 7 (2020). date_created: 2020-11-08T23:01:25Z date_published: 2020-06-01T00:00:00Z date_updated: 2024-03-12T12:31:30Z day: '01' ddc: - '530' - '550' department: - _id: MiLe doi: 10.1098/rsos.200599 external_id: arxiv: - '1910.12042' isi: - '000545625200001' file: - access_level: open_access checksum: 5505c445de373bfd836eb4d3b48b1f37 content_type: application/pdf creator: dernst date_created: 2020-11-09T09:07:11Z date_updated: 2020-11-09T09:07:11Z file_id: '8748' file_name: 2020_RoyalSocOpenScience_Klose.pdf file_size: 1611485 relation: main_file success: 1 file_date_updated: 2020-11-09T09:07:11Z has_accepted_license: '1' intvolume: ' 7' isi: 1 issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Royal Society Open Science publication_identifier: eissn: - '20545703' publication_status: published publisher: The Royal Society quality_controlled: '1' scopus_import: '1' status: public title: 'Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements' 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: 7 year: '2020' ... --- _id: '7687' abstract: - lang: eng text: A working group, which was established within the Network of Repository Managers (RepManNet), has dealt with common certifications for repositories. In addition, current requirements of the research funding agencies FWF and EU were also taken into account. The Core Trust Seal was examined in more detail. For this purpose, a questionnaire was sent to those organizations that are already certified with CTS in Austria. The answers were summarized and evaluated anonymously. It is recommended to go for a repository certification. Moreover, the development of a DINI certificate in Austria is strongly suggested. - lang: ger text: ' Eine Arbeitsgruppe, die im Rahmen des Netzwerks für RepositorienmanagerInnen (RepManNet) entstanden ist, hat sich mit gängigen Zertifizierungen für Repositorien beschäftigt. Weiters wurden aktuelle Vorgaben der Forschungsförderer FWF und EU herangezogen. Das Core Trust Seal wurde genauer betrachtet. Hierfür wurden jenen Organisationen, die in Österreich bereits mit CTS zertifiziert sind, ein Fragebogen übermittelt. Die Antworten wurden anonymisiert zusammengefasst und ausgewertet. Plädiert wird für eine Zertifizierung von Repositorien und die Entwicklung einer DINI-Zertifizierung in Österreich.' article_processing_charge: No article_type: original author: - first_name: Doris full_name: Ernst, Doris id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 last_name: Ernst orcid: 0000-0002-2354-0195 - first_name: Gertraud full_name: Novotny, Gertraud last_name: Novotny - first_name: Eva Maria full_name: Schönher, Eva Maria last_name: Schönher citation: ama: Ernst D, Novotny G, Schönher EM. (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2020;73(1):46-59. doi:10.31263/voebm.v73i1.3491 apa: Ernst, D., Novotny, G., & Schönher, E. M. (2020). (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v73i1.3491 chicago: Ernst, Doris, Gertraud Novotny, and Eva Maria Schönher. “(Core Trust) Seal your repository!” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, 2020. https://doi.org/10.31263/voebm.v73i1.3491. ieee: D. Ernst, G. Novotny, and E. M. Schönher, “(Core Trust) Seal your repository!,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 73, no. 1. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, pp. 46–59, 2020. ista: Ernst D, Novotny G, Schönher EM. 2020. (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 73(1), 46–59. mla: Ernst, Doris, et al. “(Core Trust) Seal your repository!” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 73, no. 1, Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, 2020, pp. 46–59, doi:10.31263/voebm.v73i1.3491. short: D. Ernst, G. Novotny, E.M. Schönher, Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare 73 (2020) 46–59. date_created: 2020-04-28T08:37:38Z date_published: 2020-04-28T00:00:00Z date_updated: 2024-03-12T10:12:33Z day: '28' ddc: - '020' department: - _id: E-Lib doi: 10.31263/voebm.v73i1.3491 file: - access_level: open_access checksum: fee784f15a489deb7def6ccf8c5bf8c3 content_type: application/pdf creator: dernst date_created: 2020-06-17T10:50:13Z date_updated: 2024-03-12T10:12:33Z file_id: '7970' file_name: 2020_VOEB_Ernst.pdf file_size: 579291 relation: main_file file_date_updated: 2024-03-12T10:12:33Z has_accepted_license: '1' intvolume: ' 73' issue: '1' language: - iso: ger month: '04' oa: 1 oa_version: Published Version page: 46-59 popular_science: '1' publication: Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare publication_identifier: issn: - 1022-2588 publication_status: published publisher: Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare scopus_import: '1' status: public title: (Core Trust) Seal your repository! 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: 73 year: '2020' ... --- _id: '15071' abstract: - lang: eng text: "A mesophilic methanogenic culture, designated JL01, was isolated from Holocene permafrost in the Russian Arctic [1]. After long-term extensive cultivation at 15°C it turned out to be a tied binary culture of archaeal (JL01) and bacterial (Sphaerochaeta associata GLS2) strains.\r\nStrain JL01 was a strict anaerobe and grew on methanol, acetate and methylamines as energy and carbon sources. Cells were irregular coccoid, non-motile, non-spore-forming, and Gram-stainpositive. Optimum conditions for growth were 24-28 oC, pH 6.8–7.3 and 0.075-0.1 M NaCl.\r\nPhylogenetic tree reconstructions based on 16S rRNA and concatenated alignment of broadly\r\nconserved protein-coding genes revealed its close relation to Methanosarcina mazei S-6\r\nT (similarity 99.5%). The comparison of whole genomic sequences (ANI) of the isolate and the type strain of M.mazei was 98.5%, which is higher than the values recommended for new species. Thus strain JL01 (=VKM B-2370=JCM 31898) represents the first M. mazei isolated from permanently subzero Arcticsediments. The long-term co-cultivation of JL01 with S. associata GLS2T showed the methane production without any additional carbon and energy sources. Genome analysis of S. associata GLS2T revealed putative genes involved in methanochondroithin catabolism." acknowledgement: "The work was supported by of Russian Foundation of Basic Research: grant № 19-04-00831 for Viktoria Shcherbakova and Olga Troshina, grant № 18-34-00334 for Viktoriia Oshurkova and Vladimir Trubitsyn. \r\nWe thank Dr Natalia Suzina (IBPM RAS, Federal Research Center Pushchino Center for\r\nBiological Research RAS) for the help with the microscopic studies, respectively; Dr. Margarita Meyer (Division of Genetics, Department of Medicine, BWH and HMS, USA) and Dr Fedor Kondrashov (IST, Austria) for their help in obtaining the genomic sequence of strain JL01. " article_processing_charge: Yes author: - first_name: Viktoriia full_name: Oshurkova, Viktoriia last_name: Oshurkova - first_name: Olga full_name: Troshina, Olga last_name: Troshina - first_name: Vladimir full_name: Trubitsyn, Vladimir last_name: Trubitsyn - first_name: Yana full_name: Ryzhmanova, Yana last_name: Ryzhmanova - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Viktoria full_name: Shcherbakova, Viktoria last_name: Shcherbakova citation: ama: 'Oshurkova V, Troshina O, Trubitsyn V, Ryzhmanova Y, Bochkareva O, Shcherbakova V. Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T. In: Proceedings of 1st International Electronic Conference on Microbiology. MDPI; 2020. doi:10.3390/ecm2020-07116' apa: 'Oshurkova, V., Troshina, O., Trubitsyn, V., Ryzhmanova, Y., Bochkareva, O., & Shcherbakova, V. (2020). Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T. In Proceedings of 1st International Electronic Conference on Microbiology. Virtual: MDPI. https://doi.org/10.3390/ecm2020-07116' chicago: Oshurkova, Viktoriia, Olga Troshina, Vladimir Trubitsyn, Yana Ryzhmanova, Olga Bochkareva, and Viktoria Shcherbakova. “Characterization of Methanosarcina Mazei JL01 Isolated from Holocene Arctic Permafrost and Study of the Archaeon Cooperation with Bacterium Sphaerochaeta Associata GLS2T.” In Proceedings of 1st International Electronic Conference on Microbiology. MDPI, 2020. https://doi.org/10.3390/ecm2020-07116. ieee: V. Oshurkova, O. Troshina, V. Trubitsyn, Y. Ryzhmanova, O. Bochkareva, and V. Shcherbakova, “Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T,” in Proceedings of 1st International Electronic Conference on Microbiology, Virtual, 2020. ista: 'Oshurkova V, Troshina O, Trubitsyn V, Ryzhmanova Y, Bochkareva O, Shcherbakova V. 2020. Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T. Proceedings of 1st International Electronic Conference on Microbiology. ECM: Electronic Conference on Microbiology.' mla: Oshurkova, Viktoriia, et al. “Characterization of Methanosarcina Mazei JL01 Isolated from Holocene Arctic Permafrost and Study of the Archaeon Cooperation with Bacterium Sphaerochaeta Associata GLS2T.” Proceedings of 1st International Electronic Conference on Microbiology, MDPI, 2020, doi:10.3390/ecm2020-07116. short: V. Oshurkova, O. Troshina, V. Trubitsyn, Y. Ryzhmanova, O. Bochkareva, V. Shcherbakova, in:, Proceedings of 1st International Electronic Conference on Microbiology, MDPI, 2020. conference: end_date: 2020-11-30 location: Virtual name: 'ECM: Electronic Conference on Microbiology' start_date: 2020-11-02 date_created: 2024-03-04T11:41:31Z date_published: 2020-11-02T00:00:00Z date_updated: 2024-03-20T08:06:22Z day: '02' ddc: - '570' department: - _id: FyKo doi: 10.3390/ecm2020-07116 file: - access_level: open_access checksum: d1914af7811a21a4b2744eb51b5834e3 content_type: application/pdf creator: dernst date_created: 2024-03-20T08:05:46Z date_updated: 2024-03-20T08:05:46Z file_id: '15127' file_name: 2020_ECM_Oshurkova.pdf file_size: 595543 relation: main_file success: 1 file_date_updated: 2024-03-20T08:05:46Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Proceedings of 1st International Electronic Conference on Microbiology publication_status: published publisher: MDPI quality_controlled: '1' status: public title: Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T 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: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '15153' abstract: - lang: eng text: Mammalian circadian rhythms are generated by a transcription-based feedback loop in which CLOCK:BMAL1 drives transcription of its repressors (PER1/2, CRY1/2), which ultimately interact with CLOCK:BMAL1 to close the feedback loop with ~24 hr periodicity. Here we pinpoint a key difference between CRY1 and CRY2 that underlies their differential strengths as transcriptional repressors. Both cryptochromes bind the BMAL1 transactivation domain similarly to sequester it from coactivators and repress CLOCK:BMAL1 activity. However, we find that CRY1 is recruited with much higher affinity to the PAS domain core of CLOCK:BMAL1, allowing it to serve as a stronger repressor that lengthens circadian period. We discovered a dynamic serine-rich loop adjacent to the secondary pocket in the photolyase homology region (PHR) domain that regulates differential binding of cryptochromes to the PAS domain core of CLOCK:BMAL1. Notably, binding of the co-repressor PER2 remodels the serine loop of CRY2, making it more CRY1-like and enhancing its affinity for CLOCK:BMAL1. article_number: '55275' article_processing_charge: No article_type: original author: - first_name: Jennifer L full_name: Fribourgh, Jennifer L last_name: Fribourgh - first_name: Ashutosh full_name: Srivastava, Ashutosh last_name: Srivastava - first_name: Colby R full_name: Sandate, Colby R last_name: Sandate - first_name: Alicia Kathleen full_name: Michael, Alicia Kathleen id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael - first_name: Peter L full_name: Hsu, Peter L last_name: Hsu - first_name: Christin full_name: Rakers, Christin last_name: Rakers - first_name: Leslee T full_name: Nguyen, Leslee T last_name: Nguyen - first_name: Megan R full_name: Torgrimson, Megan R last_name: Torgrimson - first_name: Gian Carlo G full_name: Parico, Gian Carlo G last_name: Parico - first_name: Sarvind full_name: Tripathi, Sarvind last_name: Tripathi - first_name: Ning full_name: Zheng, Ning last_name: Zheng - first_name: Gabriel C full_name: Lander, Gabriel C last_name: Lander - first_name: Tsuyoshi full_name: Hirota, Tsuyoshi last_name: Hirota - first_name: Florence full_name: Tama, Florence last_name: Tama - first_name: Carrie L full_name: Partch, Carrie L last_name: Partch citation: ama: Fribourgh JL, Srivastava A, Sandate CR, et al. Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing. eLife. 2020;9. doi:10.7554/elife.55275 apa: Fribourgh, J. L., Srivastava, A., Sandate, C. R., Michael, A. K., Hsu, P. L., Rakers, C., … Partch, C. L. (2020). Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.55275 chicago: Fribourgh, Jennifer L, Ashutosh Srivastava, Colby R Sandate, Alicia K. Michael, Peter L Hsu, Christin Rakers, Leslee T Nguyen, et al. “Dynamics at the Serine Loop Underlie Differential Affinity of Cryptochromes for CLOCK:BMAL1 to Control Circadian Timing.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.55275. ieee: J. L. Fribourgh et al., “Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing,” eLife, vol. 9. eLife Sciences Publications, 2020. ista: Fribourgh JL, Srivastava A, Sandate CR, Michael AK, Hsu PL, Rakers C, Nguyen LT, Torgrimson MR, Parico GCG, Tripathi S, Zheng N, Lander GC, Hirota T, Tama F, Partch CL. 2020. Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing. eLife. 9, 55275. mla: Fribourgh, Jennifer L., et al. “Dynamics at the Serine Loop Underlie Differential Affinity of Cryptochromes for CLOCK:BMAL1 to Control Circadian Timing.” ELife, vol. 9, 55275, eLife Sciences Publications, 2020, doi:10.7554/elife.55275. short: J.L. Fribourgh, A. Srivastava, C.R. Sandate, A.K. Michael, P.L. Hsu, C. Rakers, L.T. Nguyen, M.R. Torgrimson, G.C.G. Parico, S. Tripathi, N. Zheng, G.C. Lander, T. Hirota, F. Tama, C.L. Partch, ELife 9 (2020). date_created: 2024-03-21T07:55:12Z date_published: 2020-02-26T00:00:00Z date_updated: 2024-03-25T12:25:02Z day: '26' doi: 10.7554/elife.55275 extern: '1' intvolume: ' 9' keyword: - General Immunology and Microbiology - General Biochemistry - Genetics and Molecular Biology - General Medicine - General Neuroscience language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.7554/eLife.55275 month: '02' oa: 1 oa_version: Published Version publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2020' ... --- _id: '7525' abstract: - lang: eng text: "The medial habenula (MHb) is an evolutionary conserved epithalamic structure important for the modulation of emotional memory. It is involved in regulation of anxiety, compulsive behavior, addiction (nicotinic and opioid), sexual and feeding behavior. MHb receives inputs from septal regions and projects exclusively to the interpeduncular nucleus (IPN). Distinct sub-regions of the septum project to different subnuclei of MHb: the bed nucleus of anterior commissure projects to dorsal MHb and the triangular septum projects to ventral MHb. Furthermore, the dorsal and ventral MHb project to the lateral and rostral/central IPN, respectively. Importantly, these projections have unique features of prominent co-release of different neurotransmitters and requirement of a peculiar type of calcium channel for release. In general, synaptic neurotransmission requires an activity-dependent influx of Ca2+ into the presynaptic terminal through voltage-gated calcium channels. The calcium channel family most commonly involved in neurotransmitter release comprises three members, P/Q-, N- and R-type with Cav2.1, Cav2.2 and Cav2.3 subunits, respectively. In contrast to most CNS synapses that mainly express Cav2.1 and/or Cav2.2, MHb terminals in the IPN exclusively express Cav2.3. In other parts of the brain, such as the hippocampus, Cav2.3 is mostly located to postsynaptic elements. This unusual presynaptic location of Cav2.3 in the MHb-IPN pathway implies unique mechanisms of glutamate release in this pathway. One potential example of such uniqueness is the facilitation of release by GABAB receptor (GBR) activation. Presynaptic GBRs usually inhibit the release of neurotransmitters by inhibiting presynaptic calcium channels. MHb shows the highest expression levels of GBR in the brain. GBRs comprise two subunits, GABAB1 (GB1) and GABAB2 (GB2), and are associated with auxiliary subunits, called potassium channel tetramerization domain containing proteins (KCTD) 8, 12, 12b and 16. Among these four subunits, KCTD12b is exclusively expressed in ventral MHb, and KCTD8 shows the strongest expression in the whole MHb among other brain regions, indicating that KCTD8 and KCTD12b may be involved in the unique mechanisms of neurotransmitter release mediated by Cav2.3 and regulated by GBRs in this pathway. \r\nIn the present study, we first verified that neurotransmission in both dorsal and ventral MHb-IPN pathways is mainly mediated by Cav2.3 using a selective blocker of R-type channels, SNX-482. We next found that baclofen, a GBR agonist, has facilitatory effects on release from ventral MHb terminal in rostral IPN, whereas it has inhibitory effects on release from dorsal MHb terminals in lateral IPN, indicating that KCTD12b expressed exclusively in ventral MHb may have a role in the facilitatory effects of GBR activation. In a heterologous expression system using HEK cells, we found that KCTD8 and KCTD12b but not KCTD12 directly bind with Cav2.3. Pre-embedding immunogold electron microscopy data show that Cav2.3 and KCTD12b are distributed most densely in presynaptic active zone in IPN with KCTD12b being present only in rostral/central but not lateral IPN, whereas GABAB, KCTD8 and KCTD12 are distributed most densely in perisynaptic sites with KCTD12 present more frequently in postsynaptic elements and only in rostral/central IPN. In freeze-fracture replica labelling, Cav2.3, KCTD8 and KCTD12b are co-localized with each other in the same active zone indicating that they may form complexes regulating vesicle release in rostral IPN. \r\nOn electrophysiological studies of wild type (WT) mice, we found that paired-pulse ratio in rostral IPN of KCTD12b knock-out (KO) mice is lower than those of WT and KCTD8 KO mice. Consistent with this finding, in mean variance analysis, release probability in rostral IPN of KCTD12b KO mice is higher than that of WT and KCTD8 KO mice. Although paired-pulse ratios are not different between WT and KCTD8 KO mice, the mean variance analysis revealed significantly lower release probability in rostral IPN of KCTD8 KO than WT mice. These results demonstrate bidirectional regulation of Cav2.3-mediated release by KCTD8 and KCTD12b without GBR activation in rostral IPN. Finally, we examined the baclofen effects in rostral IPN of KCTD8 and KCTD12b KO mice, and found the facilitation of release remained in both KO mice, indicating that the peculiar effects of the GBR activation in this pathway do not depend on the selective expression of these KCTD subunits in ventral MHb. However, we found that presynaptic potentiation of evoked EPSC amplitude by baclofen falls to baseline after washout faster in KCTD12b KO mice than WT, KCTD8 KO and KCTD8/12b double KO mice. This result indicates that KCTD12b is involved in sustained potentiation of vesicle release by GBR activation, whereas KCTD8 is involved in its termination in the absence of KCTD12b. Consistent with these functional findings, replica labelling revealed an increase in density of KCTD8, but not Cav2.3 or GBR at active zone in rostral IPN of KCTD12b KO mice compared with that of WT mice, suggesting that increased association of KCTD8 with Cav2.3 facilitates the release probability and termination of the GBR effect in the absence of KCTD12b.\r\nIn summary, our study provided new insights into the physiological roles of presynaptic Cav2.3, GBRs and their auxiliary subunits KCTDs at an evolutionary conserved neuronal circuit. Future studies will be required to identify the exact molecular mechanism underlying the GBR-mediated presynaptic potentiation on ventral MHb terminals. It remains to be determined whether the prominent presence of presynaptic KCTDs at active zone could exert similar neuromodulatory functions in different pathways of the brain.\r\n" acknowledged_ssus: - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Pradeep full_name: Bhandari, Pradeep id: 45EDD1BC-F248-11E8-B48F-1D18A9856A87 last_name: Bhandari orcid: 0000-0003-0863-4481 citation: ama: Bhandari P. Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. 2020. doi:10.15479/AT:ISTA:7525 apa: Bhandari, P. (2020). Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7525 chicago: Bhandari, Pradeep. “Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7525. ieee: P. Bhandari, “Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway,” Institute of Science and Technology Austria, 2020. ista: Bhandari P. 2020. Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. Institute of Science and Technology Austria. mla: Bhandari, Pradeep. Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7525. short: P. Bhandari, Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway, Institute of Science and Technology Austria, 2020. date_created: 2020-02-26T10:56:37Z date_published: 2020-02-28T00:00:00Z date_updated: 2023-09-07T13:20:03Z day: '28' ddc: - '570' degree_awarded: PhD department: - _id: RySh doi: 10.15479/AT:ISTA:7525 file: - access_level: open_access checksum: 4589234fdb12b4ad72273b311723a7b4 content_type: application/pdf creator: pbhandari date_created: 2020-02-28T08:37:53Z date_updated: 2021-03-01T23:30:04Z embargo: 2021-02-28 file_id: '7538' file_name: Pradeep Bhandari Thesis.pdf file_size: 9646346 relation: main_file title: Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway - access_level: closed checksum: aa79490553ca0a5c9b6fbcd152e93928 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: pbhandari date_created: 2020-02-28T08:47:14Z date_updated: 2021-03-01T23:30:04Z embargo_to: open_access file_id: '7539' file_name: Pradeep Bhandari Thesis.docx file_size: 35252164 relation: source_file title: Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway file_date_updated: 2021-03-01T23:30:04Z has_accepted_license: '1' keyword: - Cav2.3 - medial habenula (MHb) - interpeduncular nucleus (IPN) language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '79' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 title: Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '8586' abstract: - lang: eng text: Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications. acknowledged_ssus: - _id: ScienComp - _id: LifeSc - _id: Bio - _id: EM-Fac acknowledgement: This work was supported by the Austrian Science Fund (FWF, P33367) to FKMS. BZ acknowledges support by the Niederösterreich Fond. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF) and the Electron Microscopy Facility (EMF). We thank Georgi Dimchev (IST Austria) and Sonja Jacob (Vienna Biocenter Core Facilities) for testing our grid holders in different experimental setups and Daniel Gütl and the Kondrashov group (IST Austria) for granting us repeated access to their 3D printers. We also thank Jonna Alanko and the Sixt lab (IST Austria) for providing us HeLa cells, primary BL6 mouse tail fibroblasts, NIH 3T3 fibroblasts and human telomerase immortalised foreskin fibroblasts for our experiments. We are thankful to Ori Avinoam and William Wan for helpful comments on the manuscript and also thank Dorotea Fracchiolla (Art&Science) for illustrating the graphical abstract. article_number: '107633' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Florian full_name: Fäßler, Florian id: 404F5528-F248-11E8-B48F-1D18A9856A87 last_name: Fäßler orcid: 0000-0001-7149-769X - first_name: Bettina full_name: Zens, Bettina id: 45FD126C-F248-11E8-B48F-1D18A9856A87 last_name: Zens orcid: 0000-0002-9561-1239 - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 citation: ama: Fäßler F, Zens B, Hauschild R, Schur FK. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. 2020;212(3). doi:10.1016/j.jsb.2020.107633 apa: Fäßler, F., Zens, B., Hauschild, R., & Schur, F. K. (2020). 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2020.107633 chicago: Fäßler, Florian, Bettina Zens, Robert Hauschild, and Florian KM Schur. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Journal of Structural Biology. Elsevier, 2020. https://doi.org/10.1016/j.jsb.2020.107633. ieee: F. Fäßler, B. Zens, R. Hauschild, and F. K. Schur, “3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy,” Journal of Structural Biology, vol. 212, no. 3. Elsevier, 2020. ista: Fäßler F, Zens B, Hauschild R, Schur FK. 2020. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. 212(3), 107633. mla: Fäßler, Florian, et al. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Journal of Structural Biology, vol. 212, no. 3, 107633, Elsevier, 2020, doi:10.1016/j.jsb.2020.107633. short: F. Fäßler, B. Zens, R. Hauschild, F.K. Schur, Journal of Structural Biology 212 (2020). date_created: 2020-09-29T13:24:06Z date_published: 2020-12-01T00:00:00Z date_updated: 2024-03-27T23:30:05Z day: '01' ddc: - '570' department: - _id: FlSc doi: 10.1016/j.jsb.2020.107633 external_id: isi: - '000600997800008' file: - access_level: open_access checksum: c48cbf594e84fc2f91966ffaafc0918c content_type: application/pdf creator: dernst date_created: 2020-12-10T14:01:10Z date_updated: 2020-12-10T14:01:10Z file_id: '8937' file_name: 2020_JourStrucBiology_Faessler.pdf file_size: 7076870 relation: main_file success: 1 file_date_updated: 2020-12-10T14:01:10Z has_accepted_license: '1' intvolume: ' 212' isi: 1 issue: '3' keyword: - electron microscopy - cryo-EM - EM sample preparation - 3D printing - cell culture language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A grant_number: P33367 name: Structure and isoform diversity of the Arp2/3 complex - _id: 059B463C-7A3F-11EA-A408-12923DDC885E name: NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria publication: Journal of Structural Biology publication_identifier: issn: - 1047-8477 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '14592' relation: used_in_publication status: public - id: '12491' relation: dissertation_contains status: public scopus_import: '1' status: public title: 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 212 year: '2020' ... --- _id: '8657' abstract: - lang: eng text: "Synthesis of proteins – translation – is a fundamental process of life. Quantitative studies anchor translation into the context of bacterial physiology and reveal several mathematical relationships, called “growth laws,” which capture physiological feedbacks between protein synthesis and cell growth. Growth laws describe the dependency of the ribosome abundance as a function of growth rate, which can change depending on the growth conditions. Perturbations of translation reveal that bacteria employ a compensatory strategy in which the reduced translation capability results in increased expression of the translation machinery.\r\nPerturbations of translation are achieved in various ways; clinically interesting is the application of translation-targeting antibiotics – translation inhibitors. The antibiotic effects on bacterial physiology are often poorly understood. Bacterial responses to two or more simultaneously applied antibiotics are even more puzzling. The combined antibiotic effect determines the type of drug interaction, which ranges from synergy (the effect is stronger than expected) to antagonism (the effect is weaker) and suppression (one of the drugs loses its potency).\r\nIn the first part of this work, we systematically measure the pairwise interaction network for translation inhibitors that interfere with different steps in translation. We find that the interactions are surprisingly diverse and tend to be more antagonistic. To explore the underlying mechanisms, we begin with a minimal biophysical model of combined antibiotic action. We base this model on the kinetics of antibiotic uptake and binding together with the physiological response described by the growth laws. The biophysical model explains some drug interactions, but not all; it specifically fails to predict suppression.\r\nIn the second part of this work, we hypothesize that elusive suppressive drug interactions result from the interplay between ribosomes halted in different stages of translation. To elucidate this putative mechanism of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using in- ducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks partially causes these interactions.\r\nWe extend this approach by varying two translation bottlenecks simultaneously. This approach reveals the suppression of translocation inhibition by inhibited translation. We rationalize this effect by modeling dense traffic of ribosomes that move on transcripts in a translation factor-mediated manner. This model predicts a dissolution of traffic jams caused by inhibited translocation when the density of ribosome traffic is reduced by lowered initiation. We base this model on the growth laws and quantitative relationships between different translation and growth parameters.\r\nIn the final part of this work, we describe a set of tools aimed at quantification of physiological and translation parameters. We further develop a simple model that directly connects the abundance of a translation factor with the growth rate, which allows us to extract physiological parameters describing initiation. We demonstrate the development of tools for measuring translation rate.\r\nThis thesis showcases how a combination of high-throughput growth rate mea- surements, genetics, and modeling can reveal mechanisms of drug interactions. Furthermore, by a gradual transition from combinations of antibiotics to precise genetic interventions, we demonstrated the equivalency between genetic and chemi- cal perturbations of translation. These findings tile the path for quantitative studies of antibiotic combinations and illustrate future approaches towards the quantitative description of translation." acknowledged_ssus: - _id: LifeSc - _id: M-Shop acknowledgement: I thank Life Science Facilities for their continuous support with providing top-notch laboratory materials, keeping the devices humming, and coordinating the repairs and building of custom-designed laboratory equipment with the MIBA Machine shop. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Bor full_name: Kavcic, Bor id: 350F91D2-F248-11E8-B48F-1D18A9856A87 last_name: Kavcic orcid: 0000-0001-6041-254X citation: ama: 'Kavcic B. Perturbations of protein synthesis: from antibiotics to genetics and physiology. 2020. doi:10.15479/AT:ISTA:8657' apa: 'Kavcic, B. (2020). Perturbations of protein synthesis: from antibiotics to genetics and physiology. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8657' chicago: 'Kavcic, Bor. “Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8657.' ieee: 'B. Kavcic, “Perturbations of protein synthesis: from antibiotics to genetics and physiology,” Institute of Science and Technology Austria, 2020.' ista: 'Kavcic B. 2020. Perturbations of protein synthesis: from antibiotics to genetics and physiology. Institute of Science and Technology Austria.' mla: 'Kavcic, Bor. Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8657.' short: 'B. Kavcic, Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology, Institute of Science and Technology Austria, 2020.' date_created: 2020-10-13T16:46:14Z date_published: 2020-10-14T00:00:00Z date_updated: 2023-09-07T13:20:48Z day: '14' ddc: - '571' - '530' - '570' degree_awarded: PhD department: - _id: GaTk doi: 10.15479/AT:ISTA:8657 file: - access_level: open_access checksum: d708ecd62b6fcc3bc1feb483b8dbe9eb content_type: application/pdf creator: bkavcic date_created: 2020-10-15T06:41:20Z date_updated: 2021-10-07T22:30:03Z embargo: 2021-10-06 file_id: '8663' file_name: kavcicB_thesis202009.pdf file_size: 52636162 relation: main_file - access_level: closed checksum: bb35f2352a04db19164da609f00501f3 content_type: application/zip creator: bkavcic date_created: 2020-10-15T06:41:53Z date_updated: 2021-10-07T22:30:03Z embargo_to: open_access file_id: '8664' file_name: 2020b.zip file_size: 321681247 relation: source_file file_date_updated: 2021-10-07T22:30:03Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '271' publication_identifier: isbn: - 978-3-99078-011-4 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7673' relation: part_of_dissertation status: public - id: '8250' relation: part_of_dissertation status: public status: public supervisor: - 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 title: 'Perturbations of protein synthesis: from antibiotics to genetics and physiology' type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '7473' abstract: - lang: eng text: How structural and functional properties of synapses relate to each other is a fundamental question in neuroscience. Electrophysiology has elucidated mechanisms of synaptic transmission, and electron microscopy (EM) has provided insight into morphological properties of synapses. Here we describe an enhanced method for functional EM (“flash and freeze”), combining optogenetic stimulation with high-pressure freezing. We demonstrate that the improved method can be applied to intact networks in acute brain slices and organotypic slice cultures from mice. As a proof of concept, we probed vesicle pool changes during synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapse. Our findings show overlap of the docked vesicle pool and the functionally defined readily releasable pool and provide evidence of fast endocytosis at this synapse. Functional EM with acute slices and slice cultures has the potential to reveal the structural and functional mechanisms of transmission in intact, genetically perturbed, and disease-affected synapses. acknowledgement: This project has received funding from the European Research Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020 research and innovation programme (ERC grant agreement No. 692692 and Marie Sklodowska-Curie 708497) and from Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27 Wittgenstein award and DK W1205-B09). We thank Johann Danzl and Ryuichi Shigemoto for critically reading the manuscript; Walter Kaufmann, Daniel Gutl, and Vanessa Zheden for extensive EM training, advice, and experimental assistance; Benjamin Suter for substantial help with light stimulation, ImageJ plugins for analysis, and manuscript editing; Florian Marr and Christina Altmutter for technical support; Eleftheria Kralli-Beller for manuscript editing; Julia König and Paul Wurzinger (Leica Microsystems) for helpful technical discussions; and Taija Makinen for providing the Prox1-CreERT2 mouse line. article_processing_charge: No article_type: original author: - first_name: Carolina full_name: Borges Merjane, Carolina id: 4305C450-F248-11E8-B48F-1D18A9856A87 last_name: Borges Merjane orcid: 0000-0003-0005-401X - first_name: Olena full_name: Kim, Olena id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87 last_name: Kim - 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: Borges Merjane C, Kim O, Jonas PM. Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. Neuron. 2020;105:992-1006. doi:10.1016/j.neuron.2019.12.022 apa: Borges Merjane, C., Kim, O., & Jonas, P. M. (2020). Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.12.022 chicago: Borges Merjane, Carolina, Olena Kim, and Peter M Jonas. “Functional Electron Microscopy (‘Flash and Freeze’) of Identified Cortical Synapses in Acute Brain Slices.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2019.12.022. ieee: C. Borges Merjane, O. Kim, and P. M. Jonas, “Functional electron microscopy (‘Flash and Freeze’) of identified cortical synapses in acute brain slices,” Neuron, vol. 105. Elsevier, pp. 992–1006, 2020. ista: Borges Merjane C, Kim O, Jonas PM. 2020. Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. Neuron. 105, 992–1006. mla: Borges Merjane, Carolina, et al. “Functional Electron Microscopy (‘Flash and Freeze’) of Identified Cortical Synapses in Acute Brain Slices.” Neuron, vol. 105, Elsevier, 2020, pp. 992–1006, doi:10.1016/j.neuron.2019.12.022. short: C. Borges Merjane, O. Kim, P.M. Jonas, Neuron 105 (2020) 992–1006. date_created: 2020-02-10T15:59:45Z date_published: 2020-03-18T00:00:00Z date_updated: 2024-03-27T23:30:07Z day: '18' ddc: - '570' department: - _id: PeJo doi: 10.1016/j.neuron.2019.12.022 ec_funded: 1 external_id: isi: - '000520854700008' pmid: - '31928842' file: - access_level: open_access checksum: 3582664addf26859e86ac5bec3e01416 content_type: application/pdf creator: dernst date_created: 2020-11-20T08:58:53Z date_updated: 2020-11-20T08:58:53Z file_id: '8778' file_name: 2020_Neuron_BorgesMerjane.pdf file_size: 9712957 relation: main_file success: 1 file_date_updated: 2020-11-20T08:58:53Z has_accepted_license: '1' intvolume: ' 105' isi: 1 language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '03' oa: 1 oa_version: Published Version page: 992-1006 pmid: 1 project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glumatergic synapse - _id: 25BAF7B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '708497' name: Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: The Wittgenstein Prize - _id: 25C3DBB6-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W01205 name: Zellkommunikation in Gesundheit und Krankheit publication: Neuron publication_identifier: issn: - 0896-6273 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/flash-and-freeze-reveals-dynamics-of-nerve-connections/ record: - id: '11196' relation: dissertation_contains status: public scopus_import: '1' status: public title: Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 105 year: '2020' ... --- _id: '8250' abstract: - lang: eng text: 'Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by “translation bottlenecks”: points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of “continuous epistasis” in bacterial physiology.' acknowledgement: "We thank M. Hennessey-Wesen, I. Tomanek, K. Jain, A. Staron, K. Tomasek, M. Scott,\r\nK.C. Huang, and Z. Gitai for reading the manuscript and constructive comments. B.K. is\r\nindebted to C. Guet for additional guidance and generous support, which rendered this\r\nwork possible. B.K. thanks all members of Guet group for many helpful discussions and\r\nsharing of resources. B.K. additionally acknowledges the tremendous support from A.\r\nAngermayr and K. Mitosch with experimental work. We further thank E. Brown for\r\nhelpful comments regarding lamotrigine, and A. Buskirk for valuable suggestions\r\nregarding the ribosome footprint size. This work was supported in part by Austrian\r\nScience Fund (FWF) standalone grants P 27201-B22 (to T.B.) and P 28844 (to G.T.),\r\nHFSP program Grant RGP0042/2013 (to T.B.), German Research Foundation (DFG)\r\nstandalone grant BO 3502/2-1 (to T.B.), and German Research Foundation (DFG)\r\nCollaborative Research Centre (SFB) 1310 (to T.B.). Open access funding provided by\r\nProjekt DEAL." article_number: '4013' article_processing_charge: No article_type: original author: - first_name: Bor full_name: Kavcic, Bor id: 350F91D2-F248-11E8-B48F-1D18A9856A87 last_name: Kavcic orcid: 0000-0001-6041-254X - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 - first_name: Tobias full_name: Bollenbach, Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: ama: Kavcic B, Tkačik G, Bollenbach MT. Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. 2020;11. doi:10.1038/s41467-020-17734-z apa: Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2020). Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17734-z chicago: Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17734-z. ieee: B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Mechanisms of drug interactions between translation-inhibiting antibiotics,” Nature Communications, vol. 11. Springer Nature, 2020. ista: Kavcic B, Tkačik G, Bollenbach MT. 2020. Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. 11, 4013. mla: Kavcic, Bor, et al. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Nature Communications, vol. 11, 4013, Springer Nature, 2020, doi:10.1038/s41467-020-17734-z. short: B. Kavcic, G. Tkačik, M.T. Bollenbach, Nature Communications 11 (2020). date_created: 2020-08-12T09:13:50Z date_published: 2020-08-11T00:00:00Z date_updated: 2024-03-27T23:30:08Z day: '11' ddc: - '570' department: - _id: GaTk doi: 10.1038/s41467-020-17734-z external_id: isi: - '000562769300008' file: - access_level: open_access checksum: 986bebb308850a55850028d3d2b5b664 content_type: application/pdf creator: dernst date_created: 2020-08-17T07:36:57Z date_updated: 2020-08-17T07:36:57Z file_id: '8275' file_name: 2020_NatureComm_Kavcic.pdf file_size: 1965672 relation: main_file success: 1 file_date_updated: 2020-08-17T07:36:57Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 25E9AF9E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27201-B22 name: Revealing the mechanisms underlying drug interactions - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '8657' relation: dissertation_contains status: public status: public title: Mechanisms of drug interactions between translation-inhibiting antibiotics 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2020' ... --- _id: '7673' abstract: - lang: eng text: Combining drugs can improve the efficacy of treatments. However, predicting the effect of drug combinations is still challenging. The combined potency of drugs determines the drug interaction, which is classified as synergistic, additive, antagonistic, or suppressive. While probabilistic, non-mechanistic models exist, there is currently no biophysical model that can predict antibiotic interactions. Here, we present a physiologically relevant model of the combined action of antibiotics that inhibit protein synthesis by targeting the ribosome. This model captures the kinetics of antibiotic binding and transport, and uses bacterial growth laws to predict growth in the presence of antibiotic combinations. We find that this biophysical model can produce all drug interaction types except suppression. We show analytically that antibiotics which cannot bind to the ribosome simultaneously generally act as substitutes for one another, leading to additive drug interactions. Previously proposed null expectations for higher-order drug interactions follow as a limiting case of our model. We further extend the model to include the effects of direct physical or allosteric interactions between individual drugs on the ribosome. Notably, such direct interactions profoundly change the combined drug effect, depending on the kinetic parameters of the drugs used. The model makes additional predictions for the effects of resistance genes on drug interactions and for interactions between ribosome-targeting antibiotics and antibiotics with other targets. These findings enhance our understanding of the interplay between drug action and cell physiology and are a key step toward a general framework for predicting drug interactions. article_processing_charge: No author: - first_name: Bor full_name: Kavcic, Bor id: 350F91D2-F248-11E8-B48F-1D18A9856A87 last_name: Kavcic orcid: 0000-0001-6041-254X - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 - first_name: Tobias full_name: Bollenbach, Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: ama: Kavcic B, Tkačik G, Bollenbach MT. A minimal biophysical model of combined antibiotic action. bioRxiv. 2020. doi:10.1101/2020.04.18.047886 apa: Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2020). A minimal biophysical model of combined antibiotic action. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.04.18.047886 chicago: Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “A Minimal Biophysical Model of Combined Antibiotic Action.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.04.18.047886. ieee: B. Kavcic, G. Tkačik, and M. T. Bollenbach, “A minimal biophysical model of combined antibiotic action,” bioRxiv. Cold Spring Harbor Laboratory, 2020. ista: Kavcic B, Tkačik G, Bollenbach MT. 2020. A minimal biophysical model of combined antibiotic action. bioRxiv, 10.1101/2020.04.18.047886. mla: Kavcic, Bor, et al. “A Minimal Biophysical Model of Combined Antibiotic Action.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.18.047886. short: B. Kavcic, G. Tkačik, M.T. Bollenbach, BioRxiv (2020). date_created: 2020-04-22T08:27:56Z date_published: 2020-04-18T00:00:00Z date_updated: 2024-03-27T23:30:08Z day: '18' department: - _id: GaTk doi: 10.1101/2020.04.18.047886 language: - iso: eng main_file_link: - open_access: '1' url: 'https://doi.org/10.1101/2020.04.18.047886 ' month: '04' oa: 1 oa_version: Preprint project: - _id: 25E9AF9E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27201-B22 name: Revealing the mechanisms underlying drug interactions - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publication: bioRxiv publication_status: published publisher: Cold Spring Harbor Laboratory related_material: record: - id: '8997' relation: later_version status: public - id: '8657' relation: dissertation_contains status: public status: public title: A minimal biophysical model of combined antibiotic action type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8002' abstract: - lang: eng text: Wound healing in plant tissues, consisting of rigid cell wall-encapsulated cells, represents a considerable challenge and occurs through largely unknown mechanisms distinct from those in animals. Owing to their inability to migrate, plant cells rely on targeted cell division and expansion to regenerate wounds. Strict coordination of these wound-induced responses is essential to ensure efficient, spatially restricted wound healing. Single-cell tracking by live imaging allowed us to gain mechanistic insight into the wound perception and coordination of wound responses after laser-based wounding in Arabidopsis root. We revealed a crucial contribution of the collapse of damaged cells in wound perception and detected an auxin increase specific to cells immediately adjacent to the wound. This localized auxin increase balances wound-induced cell expansion and restorative division rates in a dose-dependent manner, leading to tumorous overproliferation when the canonical TIR1 auxin signaling is disrupted. Auxin and wound-induced turgor pressure changes together also spatially define the activation of key components of regeneration, such as the transcription regulator ERF115. Our observations suggest that the wound signaling involves the sensing of collapse of damaged cells and a local auxin signaling activation to coordinate the downstream transcriptional responses in the immediate wound vicinity. acknowledged_ssus: - _id: Bio - _id: LifeSc article_number: '202003346' article_processing_charge: No article_type: original author: - first_name: Lukas full_name: Hörmayer, Lukas id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87 last_name: Hörmayer orcid: 0000-0001-8295-2926 - first_name: Juan C full_name: Montesinos López, Juan C id: 310A8E3E-F248-11E8-B48F-1D18A9856A87 last_name: Montesinos López orcid: 0000-0001-9179-6099 - first_name: Petra full_name: Marhavá, Petra id: 44E59624-F248-11E8-B48F-1D18A9856A87 last_name: Marhavá - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Saiko full_name: Yoshida, Saiko id: 2E46069C-F248-11E8-B48F-1D18A9856A87 last_name: Yoshida - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Hörmayer L, Montesinos López JC, Marhavá P, Benková E, Yoshida S, Friml J. Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots. Proceedings of the National Academy of Sciences. 2020;117(26). doi:10.1073/pnas.2003346117 apa: Hörmayer, L., Montesinos López, J. C., Marhavá, P., Benková, E., Yoshida, S., & Friml, J. (2020). Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2003346117 chicago: Hörmayer, Lukas, Juan C Montesinos López, Petra Marhavá, Eva Benková, Saiko Yoshida, and Jiří Friml. “Wounding-Induced Changes in Cellular Pressure and Localized Auxin Signalling Spatially Coordinate Restorative Divisions in Roots.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2003346117. ieee: L. Hörmayer, J. C. Montesinos López, P. Marhavá, E. Benková, S. Yoshida, and J. Friml, “Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots,” Proceedings of the National Academy of Sciences, vol. 117, no. 26. Proceedings of the National Academy of Sciences, 2020. ista: Hörmayer L, Montesinos López JC, Marhavá P, Benková E, Yoshida S, Friml J. 2020. Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots. Proceedings of the National Academy of Sciences. 117(26), 202003346. mla: Hörmayer, Lukas, et al. “Wounding-Induced Changes in Cellular Pressure and Localized Auxin Signalling Spatially Coordinate Restorative Divisions in Roots.” Proceedings of the National Academy of Sciences, vol. 117, no. 26, 202003346, Proceedings of the National Academy of Sciences, 2020, doi:10.1073/pnas.2003346117. short: L. Hörmayer, J.C. Montesinos López, P. Marhavá, E. Benková, S. Yoshida, J. Friml, Proceedings of the National Academy of Sciences 117 (2020). date_created: 2020-06-22T13:33:52Z date_published: 2020-06-30T00:00:00Z date_updated: 2024-03-27T23:30:11Z day: '30' ddc: - '580' department: - _id: JiFr - _id: EvBe doi: 10.1073/pnas.2003346117 ec_funded: 1 external_id: isi: - '000565729700033' pmid: - '32541049' file: - access_level: open_access checksum: 908b09437680181de9990915f2113aca content_type: application/pdf creator: dernst date_created: 2020-06-23T11:30:53Z date_updated: 2020-07-14T12:48:07Z file_id: '8009' file_name: 2020_PNAS_Hoermayer.pdf file_size: 2407102 relation: main_file file_date_updated: 2020-07-14T12:48:07Z has_accepted_license: '1' intvolume: ' 117' isi: 1 issue: '26' language: - iso: eng month: '06' oa: 1 oa_version: None pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 262EF96E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29988 name: RNA-directed DNA methylation in plant development publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/how-wounded-plants-coordinate-their-healing/ record: - id: '9992' relation: dissertation_contains status: public scopus_import: '1' status: public title: Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 117 year: '2020' ... --- _id: '7680' abstract: - lang: eng text: "Proteins and their complex dynamic interactions regulate cellular mechanisms from sensing and transducing extracellular signals, to mediating genetic responses, and sustaining or changing cell morphology. To manipulate these protein-protein interactions (PPIs) that govern the behavior and fate of cells, synthetically constructed, genetically encoded tools provide the means to precisely target proteins of interest (POIs), and control their subcellular localization and activity in vitro and in vivo. Ideal synthetic tools react to an orthogonal cue, i.e. a trigger that does not activate any other endogenous process, thereby allowing manipulation of the POI alone.\r\nIn optogenetics, naturally occurring photosensory domain from plants, algae and bacteria are re-purposed and genetically fused to POIs. Illumination with light of a specific wavelength triggers a conformational change that can mediate PPIs, such as dimerization or oligomerization. By using light as a trigger, these tools can be activated with high spatial and temporal precision, on subcellular and millisecond scales. Chemogenetic tools consist of protein domains that recognize and bind small molecules. By genetic fusion to POIs, these domains can mediate PPIs upon addition of their specific ligands, which are often synthetically designed to provide highly specific interactions and exhibit good bioavailability.\r\nMost optogenetic tools to mediate PPIs are based on well-studied photoreceptors responding to red, blue or near-UV light, leaving a striking gap in the green band of the visible light spectrum. Among both optogenetic and chemogenetic tools, there is an abundance of methods to induce PPIs, but tools to disrupt them require UV illumination, rely on covalent linkage and subsequent enzymatic cleavage or initially result in protein clustering of unknown stoichiometry.\r\nThis work describes how the recently structurally and photochemically characterized green-light responsive cobalamin-binding domains (CBDs) from bacterial transcription factors were re-purposed to function as a green-light responsive optogenetic tool. In contrast to previously engineered optogenetic tools, CBDs do not induce PPI, but rather confer a PPI already upon expression, which can be rapidly disrupted by illumination. This was employed to mimic inhibition of constitutive activity of a growth factor receptor, and successfully implement for cell signalling in mammalian cells and in vivo to rescue development in zebrafish. This work further describes the development and application of a chemically induced de-dimerizer (CDD) based on a recently identified and structurally described bacterial oxyreductase. CDD forms a dimer upon expression in absence of its cofactor, the flavin derivative F420. Safety and of domain expression and ligand exposure are demonstrated in vitro and in vivo in zebrafish. The system is further applied to inhibit cell signalling output from a chimeric receptor upon F420 treatment.\r\nCBDs and CDD expand the repertoire of synthetic tools by providing novel mechanisms of mediating PPIs, and by recognizing previously not utilized cues. In the future, they can readily be combined with existing synthetic tools to functionally manipulate PPIs in vitro and in vivo." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Stephanie full_name: Kainrath, Stephanie id: 32CFBA64-F248-11E8-B48F-1D18A9856A87 last_name: Kainrath citation: ama: Kainrath S. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. 2020. doi:10.15479/AT:ISTA:7680 apa: Kainrath, S. (2020). Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7680 chicago: Kainrath, Stephanie. “Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7680. ieee: S. Kainrath, “Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals,” Institute of Science and Technology Austria, 2020. ista: Kainrath S. 2020. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. Institute of Science and Technology Austria. mla: Kainrath, Stephanie. Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7680. short: S. Kainrath, Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals, Institute of Science and Technology Austria, 2020. date_created: 2020-04-24T16:00:51Z date_published: 2020-04-24T00:00:00Z date_updated: 2023-09-22T09:20:10Z day: '24' ddc: - '570' degree_awarded: PhD department: - _id: CaGu doi: 10.15479/AT:ISTA:7680 file: - access_level: open_access checksum: fb9a4468eb27be92690728e35c823796 content_type: application/pdf creator: stgingl date_created: 2020-04-28T11:19:21Z date_updated: 2021-10-31T23:30:05Z embargo: 2021-10-30 file_id: '7692' file_name: Thesis_without-signatures_PDFA.pdf file_size: 3268017 relation: main_file - access_level: closed checksum: f6c80ca97104a631a328cb79a2c53493 content_type: application/octet-stream creator: stgingl date_created: 2020-04-28T11:19:24Z date_updated: 2021-10-31T23:30:05Z embargo_to: open_access file_id: '7693' file_name: Thesis_without signatures.docx file_size: 5167703 relation: source_file file_date_updated: 2021-10-31T23:30:05Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: None page: '98' publication_identifier: eissn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '1028' relation: dissertation_contains status: public status: public supervisor: - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 title: Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '8620' abstract: - lang: eng text: "The development of the human brain occurs through a tightly regulated series of dynamic and adaptive processes during prenatal and postnatal life. A disruption of this strictly orchestrated series of events can lead to a number of neurodevelopmental conditions, including Autism Spectrum Disorders (ASDs). ASDs are a very common, etiologically and phenotypically heterogeneous group of disorders sharing the core symptoms of social interaction and communication deficits and restrictive and repetitive interests and behaviors. They are estimated to affect one in 59 individuals in the U.S. and, over the last three decades, mutations in more than a hundred genetic loci have been convincingly linked to ASD pathogenesis. Yet, for the vast majority of these ASD-risk genes their role during brain development and precise molecular function still remain elusive.\r\nDe novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin 3 (CUL3) lead to ASD. In the study described here, we used Cul3 mouse models to evaluate the consequences of Cul3 mutations in vivo. Our results show that Cul3 heterozygous knockout mice exhibit deficits in motor coordination as well as ASD-relevant social and cognitive impairments. Cul3+/-, Cul3+/fl Emx1-Cre and Cul3fl/fl Emx1-Cre mutant brains display cortical lamination abnormalities due to defective migration of post-mitotic excitatory neurons, as well as reduced numbers of excitatory and inhibitory neurons. In line with the observed abnormal cortical organization, Cul3 heterozygous deletion is associated with decreased spontaneous excitatory and inhibitory activity in the cortex. At the molecular level we show that Cul3 regulates cytoskeletal and adhesion protein abundance in the mouse embryonic cortex. Abnormal regulation of cytoskeletal proteins in Cul3 mutant neural cells results in atypical organization of the actin mesh at the cell leading edge. Of note, heterozygous deletion of Cul3 in adult mice does not induce the majority of the behavioral defects observed in constitutive Cul3 haploinsufficient animals, pointing to a critical time-window for Cul3 deficiency.\r\nIn conclusion, our data indicate that Cul3 plays a critical role in the regulation of cytoskeletal proteins and neuronal migration. ASD-associated defects and behavioral abnormalities are primarily due to dosage sensitive Cul3 functions at early brain developmental stages." acknowledged_ssus: - _id: Bio - _id: PreCl acknowledgement: I would like to especially thank Armel Nicolas from the Proteomics and Christoph Sommer from the Bioimaging Facilities for the data analysis, and to thank the team of the Preclinical Facility, especially Sabina Deixler, Angela Schlerka, Anita Lepold, Mihalea Mihai and Michael Schun for taking care of the mouse line maintenance and their great support. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Jasmin full_name: Morandell, Jasmin id: 4739D480-F248-11E8-B48F-1D18A9856A87 last_name: Morandell citation: ama: Morandell J. Illuminating the role of Cul3 in autism spectrum disorder pathogenesis. 2020. doi:10.15479/AT:ISTA:8620 apa: Morandell, J. (2020). Illuminating the role of Cul3 in autism spectrum disorder pathogenesis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8620 chicago: Morandell, Jasmin. “Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8620. ieee: J. Morandell, “Illuminating the role of Cul3 in autism spectrum disorder pathogenesis,” Institute of Science and Technology Austria, 2020. ista: Morandell J. 2020. Illuminating the role of Cul3 in autism spectrum disorder pathogenesis. Institute of Science and Technology Austria. mla: Morandell, Jasmin. Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8620. short: J. Morandell, Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis, Institute of Science and Technology Austria, 2020. date_created: 2020-10-07T14:53:13Z date_published: 2020-10-12T00:00:00Z date_updated: 2023-09-07T13:22:14Z day: '12' ddc: - '610' degree_awarded: PhD department: - _id: GaNo doi: 10.15479/AT:ISTA:8620 file: - access_level: open_access checksum: 7ee83e42de3e5ce2fedb44dff472f75f content_type: application/pdf creator: jmorande date_created: 2020-10-07T14:41:49Z date_updated: 2021-10-16T22:30:04Z embargo: 2021-10-15 file_id: '8621' file_name: Jasmin_Morandell_Thesis-2020_final.pdf file_size: 16155786 relation: main_file - access_level: closed checksum: 5e0464af453734210ce7aab7b4a92e3a content_type: application/x-zip-compressed creator: jmorande date_created: 2020-10-07T14:45:07Z date_updated: 2021-10-16T22:30:04Z embargo_to: open_access file_id: '8622' file_name: Jasmin_Morandell_Thesis-2020_final.zip file_size: 24344152 relation: source_file file_date_updated: 2021-10-16T22:30:04Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '138' project: - _id: 2548AE96-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets - _id: 05A0D778-7A3F-11EA-A408-12923DDC885E grant_number: F07807 name: Neural stem cells in autism and epilepsy publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7800' relation: part_of_dissertation status: public - id: '8131' relation: part_of_dissertation status: public status: public supervisor: - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 title: Illuminating the role of Cul3 in autism spectrum disorder pathogenesis type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '8340' abstract: - lang: eng text: Mitochondria are sites of oxidative phosphorylation in eukaryotic cells. Oxidative phosphorylation operates by a chemiosmotic mechanism made possible by redox-driven proton pumping machines which establish a proton motive force across the inner mitochondrial membrane. This electrochemical proton gradient is used to drive ATP synthesis, which powers the majority of cellular processes such as protein synthesis, locomotion and signalling. In this thesis I investigate the structures and molecular mechanisms of two inner mitochondrial proton pumping enzymes, respiratory complex I and transhydrogenase. I present the first high-resolution structure of the full transhydrogenase from any species, and a significantly improved structure of complex I. Improving the resolution from 3.3 Å available previously to up to 2.3 Å in this thesis allowed us to model bound water molecules, crucial in the proton pumping mechanism. For both enzymes, up to five cryo-EM datasets with different substrates and inhibitors bound were solved to delineate the catalytic cycle and understand the proton pumping mechanism. In transhydrogenase, the proton channel is gated by reversible detachment of the NADP(H)-binding domain which opens the proton channel to the opposite sites of the membrane. In complex I, the proton channels are gated by reversible protonation of key glutamate and lysine residues and breaking of the water wire connecting the proton pumps with the quinone reduction site. The tight coupling between the redox and the proton pumping reactions in transhydrogenase is achieved by controlling the NADP(H) exchange which can only happen when the NADP(H)-binding domain interacts with the membrane domain. In complex I, coupling is achieved by cycling of the whole complex between the closed state, in which quinone can get reduced, and the open state, in which NADH can induce quinol ejection from the binding pocket. On the basis of these results I propose detailed mechanisms for catalytic cycles of transhydrogenase and complex I that are consistent with a large amount of previous work. In both enzymes, conformational and electrostatic mechanisms contribute to the overall catalytic process. Results presented here could be used for better understanding of the human pathologies arising from deficiencies of complex I or transhydrogenase and could be used to develop novel therapies. acknowledged_ssus: - _id: EM-Fac acknowledgement: 'I acknowledge the support of IST facilities, especially the Electron Miscroscopy facility for providing training and resources. Special thanks also go to cryo-EM specialists who helped me to collect the data present here: Dr Valentin Hodirnau (IST Austria), Dr Tom Heuser (IMBA, Vienna), Dr Rebecca Thompson (Uni. of Leeds) and Dr Jirka Nováček (CEITEC). This work has been supported by iNEXT, project number 653706, funded by the Horizon 2020 programme of the European Union. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Domen full_name: Kampjut, Domen id: 37233050-F248-11E8-B48F-1D18A9856A87 last_name: Kampjut citation: ama: Kampjut D. Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. 2020. doi:10.15479/AT:ISTA:8340 apa: Kampjut, D. (2020). Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8340 chicago: Kampjut, Domen. “Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8340. ieee: D. Kampjut, “Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes,” Institute of Science and Technology Austria, 2020. ista: Kampjut D. 2020. Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. Institute of Science and Technology Austria. mla: Kampjut, Domen. Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8340. short: D. Kampjut, Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes, Institute of Science and Technology Austria, 2020. date_created: 2020-09-07T18:42:23Z date_published: 2020-09-09T00:00:00Z date_updated: 2023-09-07T13:26:17Z day: '09' ddc: - '572' degree_awarded: PhD department: - _id: LeSa doi: 10.15479/AT:ISTA:8340 ec_funded: 1 file: - access_level: closed checksum: dd270baf82121eb4472ad19d77bf227c content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dkampjut date_created: 2020-09-08T13:32:06Z date_updated: 2021-09-11T22:30:04Z embargo_to: open_access file_id: '8345' file_name: ThesisFull20200908.docx file_size: 166146359 relation: source_file - access_level: open_access checksum: 82fce6f95ffa47ecc4ebca67ea2cc38c content_type: application/pdf creator: dernst date_created: 2020-09-14T15:02:20Z date_updated: 2021-09-11T22:30:04Z embargo: 2021-09-10 file_id: '8393' file_name: 2020_Thesis_Kampjut.pdf file_size: 13873769 relation: main_file file_date_updated: 2021-09-11T22:30:04Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: None page: '242' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-008-4 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6848' relation: part_of_dissertation status: public status: public supervisor: - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 title: Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '7800' abstract: - lang: eng text: De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 (CUL3) lead to autism spectrum disorder (ASD). Here, we used Cul3 mouse models to evaluate the consequences of Cul3 mutations in vivo. Our results show that Cul3 haploinsufficient mice exhibit deficits in motor coordination as well as ASD-relevant social and cognitive impairments. Cul3 mutant brain displays cortical lamination abnormalities due to defective neuronal migration and reduced numbers of excitatory and inhibitory neurons. In line with the observed abnormal columnar organization, Cul3 haploinsufficiency is associated with decreased spontaneous excitatory and inhibitory activity in the cortex. At the molecular level, employing a quantitative proteomic approach, we show that Cul3 regulates cytoskeletal and adhesion protein abundance in mouse embryos. Abnormal regulation of cytoskeletal proteins in Cul3 mutant neuronal cells results in atypical organization of the actin mesh at the cell leading edge, likely causing the observed migration deficits. In contrast to these important functions early in development, Cul3 deficiency appears less relevant at adult stages. In fact, induction of Cul3 haploinsufficiency in adult mice does not result in the behavioral defects observed in constitutive Cul3 haploinsufficient animals. Taken together, our data indicate that Cul3 has a critical role in the regulation of cytoskeletal proteins and neuronal migration and that ASD-associated defects and behavioral abnormalities are primarily due to Cul3 functions at early developmental stages. acknowledged_ssus: - _id: PreCl article_processing_charge: No author: - first_name: Jasmin full_name: Morandell, Jasmin id: 4739D480-F248-11E8-B48F-1D18A9856A87 last_name: Morandell - first_name: Lena A full_name: Schwarz, Lena A id: 29A8453C-F248-11E8-B48F-1D18A9856A87 last_name: Schwarz - first_name: Bernadette full_name: Basilico, Bernadette id: 36035796-5ACA-11E9-A75E-7AF2E5697425 last_name: Basilico orcid: 0000-0003-1843-3173 - first_name: Saren full_name: Tasciyan, Saren id: 4323B49C-F248-11E8-B48F-1D18A9856A87 last_name: Tasciyan orcid: 0000-0003-1671-393X - first_name: Armel full_name: Nicolas, Armel id: 2A103192-F248-11E8-B48F-1D18A9856A87 last_name: Nicolas - 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: Caroline full_name: Kreuzinger, Caroline id: 382077BA-F248-11E8-B48F-1D18A9856A87 last_name: Kreuzinger - first_name: Lisa full_name: Knaus, Lisa id: 3B2ABCF4-F248-11E8-B48F-1D18A9856A87 last_name: Knaus - first_name: Zoe full_name: Dobler, Zoe id: D23090A2-9057-11EA-883A-A8396FC7A38F last_name: Dobler - first_name: Emanuele full_name: Cacci, Emanuele last_name: Cacci - 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: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. bioRxiv. doi:10.1101/2020.01.10.902064 apa: Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Nicolas, A., Sommer, C. M., … Novarino, G. (n.d.). Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.01.10.902064 chicago: Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan, Armel Nicolas, Christoph M Sommer, Caroline Kreuzinger, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2020.01.10.902064 . ieee: J. Morandell et al., “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” bioRxiv. Cold Spring Harbor Laboratory. ista: Morandell J, Schwarz LA, Basilico B, Tasciyan S, Nicolas A, Sommer CM, Kreuzinger C, Knaus L, Dobler Z, Cacci E, Danzl JG, Novarino G. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. bioRxiv, 10.1101/2020.01.10.902064 . mla: Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2020.01.10.902064 . short: J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, A. Nicolas, C.M. Sommer, C. Kreuzinger, L. Knaus, Z. Dobler, E. Cacci, J.G. Danzl, G. Novarino, BioRxiv (n.d.). date_created: 2020-05-05T14:31:33Z date_published: 2020-01-11T00:00:00Z date_updated: 2024-03-27T23:30:14Z day: '11' ddc: - '570' department: - _id: JoDa - _id: GaNo - _id: LifeSc doi: '10.1101/2020.01.10.902064 ' file: - access_level: open_access checksum: c6799ab5daba80efe8e2ed63c15f8c81 content_type: application/pdf creator: rsix date_created: 2020-05-05T14:31:19Z date_updated: 2020-07-14T12:48:03Z file_id: '7801' file_name: 2020.01.10.902064v1.full.pdf file_size: 2931370 relation: main_file file_date_updated: 2020-07-14T12:48:03Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Preprint 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-B24 name: Molecular Drug Targets publication: bioRxiv publication_status: submitted publisher: Cold Spring Harbor Laboratory related_material: record: - id: '9429' relation: later_version status: public - id: '8620' relation: dissertation_contains status: public status: public title: Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development 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: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8131' abstract: - lang: eng text: The possibility to generate construct valid animal models enabled the development and testing of therapeutic strategies targeting the core features of autism spectrum disorders (ASDs). At the same time, these studies highlighted the necessity of identifying sensitive developmental time windows for successful therapeutic interventions. Animal and human studies also uncovered the possibility to stratify the variety of ASDs in molecularly distinct subgroups, potentially facilitating effective treatment design. Here, we focus on the molecular pathways emerging as commonly affected by mutations in diverse ASD-risk genes, on their role during critical windows of brain development and the potential treatments targeting these biological processes. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Bernadette full_name: Basilico, Bernadette id: 36035796-5ACA-11E9-A75E-7AF2E5697425 last_name: Basilico orcid: 0000-0003-1843-3173 - first_name: Jasmin full_name: Morandell, Jasmin id: 4739D480-F248-11E8-B48F-1D18A9856A87 last_name: Morandell - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Basilico B, Morandell J, Novarino G. Molecular mechanisms for targeted ASD treatments. Current Opinion in Genetics and Development. 2020;65(12):126-137. doi:10.1016/j.gde.2020.06.004 apa: Basilico, B., Morandell, J., & Novarino, G. (2020). Molecular mechanisms for targeted ASD treatments. Current Opinion in Genetics and Development. Elsevier. https://doi.org/10.1016/j.gde.2020.06.004 chicago: Basilico, Bernadette, Jasmin Morandell, and Gaia Novarino. “Molecular Mechanisms for Targeted ASD Treatments.” Current Opinion in Genetics and Development. Elsevier, 2020. https://doi.org/10.1016/j.gde.2020.06.004. ieee: B. Basilico, J. Morandell, and G. Novarino, “Molecular mechanisms for targeted ASD treatments,” Current Opinion in Genetics and Development, vol. 65, no. 12. Elsevier, pp. 126–137, 2020. ista: Basilico B, Morandell J, Novarino G. 2020. Molecular mechanisms for targeted ASD treatments. Current Opinion in Genetics and Development. 65(12), 126–137. mla: Basilico, Bernadette, et al. “Molecular Mechanisms for Targeted ASD Treatments.” Current Opinion in Genetics and Development, vol. 65, no. 12, Elsevier, 2020, pp. 126–37, doi:10.1016/j.gde.2020.06.004. short: B. Basilico, J. Morandell, G. Novarino, Current Opinion in Genetics and Development 65 (2020) 126–137. date_created: 2020-07-19T22:00:58Z date_published: 2020-12-01T00:00:00Z date_updated: 2024-03-27T23:30:14Z day: '01' ddc: - '570' department: - _id: GaNo doi: 10.1016/j.gde.2020.06.004 ec_funded: 1 external_id: isi: - '000598918900019' pmid: - '32659636' file: - access_level: open_access content_type: application/pdf creator: dernst date_created: 2020-07-22T06:47:45Z date_updated: 2020-07-22T06:47:45Z file_id: '8146' file_name: 2020_CurrentOpGenetics_Basilico.pdf file_size: 1381545 relation: main_file success: 1 file_date_updated: 2020-07-22T06:47:45Z has_accepted_license: '1' intvolume: ' 65' isi: 1 issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 126-137 pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 2548AE96-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets - _id: 05A0D778-7A3F-11EA-A408-12923DDC885E grant_number: F07807 name: Neural stem cells in autism and epilepsy publication: Current Opinion in Genetics and Development publication_identifier: eissn: - '18790380' issn: - 0959437X publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '8620' relation: dissertation_contains status: public scopus_import: '1' status: public title: Molecular mechanisms for targeted ASD treatments 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 65 year: '2020' ... --- _id: '8434' abstract: - lang: eng text: 'Efficient migration on adhesive surfaces involves the protrusion of lamellipodial actin networks and their subsequent stabilization by nascent adhesions. The actin-binding protein lamellipodin (Lpd) is thought to play a critical role in lamellipodium protrusion, by delivering Ena/VASP proteins onto the growing plus ends of actin filaments and by interacting with the WAVE regulatory complex, an activator of the Arp2/3 complex, at the leading edge. Using B16-F1 melanoma cell lines, we demonstrate that genetic ablation of Lpd compromises protrusion efficiency and coincident cell migration without altering essential parameters of lamellipodia, including their maximal rate of forward advancement and actin polymerization. We also confirmed lamellipodia and migration phenotypes with CRISPR/Cas9-mediated Lpd knockout Rat2 fibroblasts, excluding cell type-specific effects. Moreover, computer-aided analysis of cell-edge morphodynamics on B16-F1 cell lamellipodia revealed that loss of Lpd correlates with reduced temporal protrusion maintenance as a prerequisite of nascent adhesion formation. We conclude that Lpd optimizes protrusion and nascent adhesion formation by counteracting frequent, chaotic retraction and membrane ruffling.This article has an associated First Person interview with the first author of the paper. ' acknowledgement: This work was supported in part by Deutsche Forschungsgemeinschaft (DFG)[GRK2223/1, RO2414/5-1 (to K.R.), FA350/11-1 (to M.F.) and FA330/11-1 (to J.F.)],as well as by intramural funding from the Helmholtz Association (to T.E.B.S. andK.R.). G.D. was additionally funded by the Austrian Science Fund (FWF) LiseMeitner Program [M-2495]. A.C.H. and M.W. are supported by the Francis CrickInstitute, which receives its core funding from Cancer Research UK [FC001209], theMedical Research Council [FC001209] and the Wellcome Trust [FC001209]. M.K. issupported by the Biotechnology and Biological Sciences Research Council [BB/F011431/1, BB/J000590/1, BB/N000226/1]. Deposited in PMC for release after 6months. article_number: jcs239020 article_processing_charge: No article_type: original author: - first_name: Georgi A full_name: Dimchev, Georgi A id: 38C393BE-F248-11E8-B48F-1D18A9856A87 last_name: Dimchev orcid: 0000-0001-8370-6161 - first_name: Behnam full_name: Amiri, Behnam last_name: Amiri - first_name: Ashley C. full_name: Humphries, Ashley C. last_name: Humphries - first_name: Matthias full_name: Schaks, Matthias last_name: Schaks - first_name: Vanessa full_name: Dimchev, Vanessa last_name: Dimchev - first_name: Theresia E. B. full_name: Stradal, Theresia E. B. last_name: Stradal - first_name: Jan full_name: Faix, Jan last_name: Faix - first_name: Matthias full_name: Krause, Matthias last_name: Krause - first_name: Michael full_name: Way, Michael last_name: Way - first_name: Martin full_name: Falcke, Martin last_name: Falcke - first_name: Klemens full_name: Rottner, Klemens last_name: Rottner citation: ama: Dimchev GA, Amiri B, Humphries AC, et al. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science. 2020;133(7). doi:10.1242/jcs.239020 apa: Dimchev, G. A., Amiri, B., Humphries, A. C., Schaks, M., Dimchev, V., Stradal, T. E. B., … Rottner, K. (2020). Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.239020 chicago: Dimchev, Georgi A, Behnam Amiri, Ashley C. Humphries, Matthias Schaks, Vanessa Dimchev, Theresia E. B. Stradal, Jan Faix, et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” Journal of Cell Science. The Company of Biologists, 2020. https://doi.org/10.1242/jcs.239020. ieee: G. A. Dimchev et al., “Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation,” Journal of Cell Science, vol. 133, no. 7. The Company of Biologists, 2020. ista: Dimchev GA, Amiri B, Humphries AC, Schaks M, Dimchev V, Stradal TEB, Faix J, Krause M, Way M, Falcke M, Rottner K. 2020. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science. 133(7), jcs239020. mla: Dimchev, Georgi A., et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” Journal of Cell Science, vol. 133, no. 7, jcs239020, The Company of Biologists, 2020, doi:10.1242/jcs.239020. short: G.A. Dimchev, B. Amiri, A.C. Humphries, M. Schaks, V. Dimchev, T.E.B. Stradal, J. Faix, M. Krause, M. Way, M. Falcke, K. Rottner, Journal of Cell Science 133 (2020). date_created: 2020-09-17T14:00:33Z date_published: 2020-04-09T00:00:00Z date_updated: 2023-09-05T15:41:48Z day: '09' ddc: - '570' department: - _id: FlSc doi: 10.1242/jcs.239020 external_id: isi: - '000534387800005' pmid: - ' 32094266' file: - access_level: open_access checksum: ba917e551acc4ece2884b751434df9ae content_type: application/pdf creator: dernst date_created: 2020-09-17T14:07:51Z date_updated: 2020-10-11T22:30:02Z embargo: 2020-10-10 file_id: '8435' file_name: 2020_JournalCellScience_Dimchev.pdf file_size: 13493302 relation: main_file file_date_updated: 2020-10-11T22:30:02Z has_accepted_license: '1' intvolume: ' 133' isi: 1 issue: '7' keyword: - Cell Biology language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 2674F658-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02495 name: Protein structure and function in filopodia across scales publication: Journal of Cell Science publication_identifier: eissn: - 1477-9137 issn: - 0021-9533 publication_status: published publisher: The Company of Biologists quality_controlled: '1' status: public title: Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 133 year: '2020' ... --- _id: '7889' abstract: - lang: eng text: Autoluminescent plants engineered to express a bacterial bioluminescence gene cluster in plastids have not been widely adopted because of low light output. We engineered tobacco plants with a fungal bioluminescence system that converts caffeic acid (present in all plants) into luciferin and report self-sustained luminescence that is visible to the naked eye. Our findings could underpin development of a suite of imaging tools for plants. acknowledgement: "This study was designed, performed and funded by Planta LLC. We thank K. Wood for assisting in manuscript development. Planta acknowledges support from the Skolkovo Innovation Centre. We thank D. Bolotin and the Milaboratory (milaboratory.com) for access to computing and storage infrastructure. We thank S. Shakhov for providing\r\nphotography equipment. The Synthetic Biology Group is funded by the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0, K.S.S.). K.S.S. is supported by an Imperial College Research Fellowship. Experiments were partially carried out using equipment provided by the Institute of Bioorganic Chemistry of the Russian Academy\r\nof Sciences Сore Facility (CKP IBCH; supported by the Russian Ministry of Education and Science Grant RFMEFI62117X0018). The F.A.K. lab is supported by ERC grant agreement 771209—CharFL. This project received funding from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie\r\nGrant Agreement 665385. K.S.S. acknowledges support by President’s Grant 075-15-2019-411. Design and assembly of some of the plasmids was supported by Russian Science Foundation grant 19-74-10102. Imaging experiments were partially supported by Russian Science Foundation grant 17-14-01169p. LC-MS/MS analyses of extracts were\r\nsupported by Russian Science Foundation grant 16-14-00052p. Design and assembly of plasmids was partially supported by grant 075-15-2019-1789 from the Ministry of Science and Higher Education of the Russian Federation allocated to the Center for Precision Genome Editing and Genetic Technologies for Biomedicine. The authors\r\nwould like to acknowledge the work of Genomics Core Facility of the Skolkovo Institute of Science and Technology, which performed the sequencing and bioinformatic analysis." article_processing_charge: No article_type: original author: - first_name: Tatiana full_name: Mitiouchkina, Tatiana last_name: Mitiouchkina - first_name: Alexander S. full_name: Mishin, Alexander S. last_name: Mishin - first_name: Louisa full_name: Gonzalez Somermeyer, Louisa id: 4720D23C-F248-11E8-B48F-1D18A9856A87 last_name: Gonzalez Somermeyer orcid: 0000-0001-9139-5383 - first_name: Nadezhda M. full_name: Markina, Nadezhda M. last_name: Markina - first_name: Tatiana V. full_name: Chepurnyh, Tatiana V. last_name: Chepurnyh - first_name: Elena B. full_name: Guglya, Elena B. last_name: Guglya - first_name: Tatiana A. full_name: Karataeva, Tatiana A. last_name: Karataeva - first_name: Kseniia A. full_name: Palkina, Kseniia A. last_name: Palkina - first_name: Ekaterina S. full_name: Shakhova, Ekaterina S. last_name: Shakhova - first_name: Liliia I. full_name: Fakhranurova, Liliia I. last_name: Fakhranurova - first_name: Sofia V. full_name: Chekova, Sofia V. last_name: Chekova - first_name: Aleksandra S. full_name: Tsarkova, Aleksandra S. last_name: Tsarkova - first_name: Yaroslav V. full_name: Golubev, Yaroslav V. last_name: Golubev - first_name: Vadim V. full_name: Negrebetsky, Vadim V. last_name: Negrebetsky - first_name: Sergey A. full_name: Dolgushin, Sergey A. last_name: Dolgushin - first_name: Pavel V. full_name: Shalaev, Pavel V. last_name: Shalaev - first_name: Dmitry full_name: Shlykov, Dmitry last_name: Shlykov - first_name: Olesya A. full_name: Melnik, Olesya A. last_name: Melnik - first_name: Victoria O. full_name: Shipunova, Victoria O. last_name: Shipunova - first_name: Sergey M. full_name: Deyev, Sergey M. last_name: Deyev - first_name: Andrey I. full_name: Bubyrev, Andrey I. last_name: Bubyrev - first_name: Alexander S. full_name: Pushin, Alexander S. last_name: Pushin - first_name: Vladimir V. full_name: Choob, Vladimir V. last_name: Choob - first_name: Sergey V. full_name: Dolgov, Sergey V. last_name: Dolgov - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Ilia V. full_name: Yampolsky, Ilia V. last_name: Yampolsky - first_name: Karen S. full_name: Sarkisyan, Karen S. last_name: Sarkisyan citation: ama: Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, et al. Plants with genetically encoded autoluminescence. Nature Biotechnology. 2020;38:944-946. doi:10.1038/s41587-020-0500-9 apa: Mitiouchkina, T., Mishin, A. S., Gonzalez Somermeyer, L., Markina, N. M., Chepurnyh, T. V., Guglya, E. B., … Sarkisyan, K. S. (2020). Plants with genetically encoded autoluminescence. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-020-0500-9 chicago: Mitiouchkina, Tatiana, Alexander S. Mishin, Louisa Gonzalez Somermeyer, Nadezhda M. Markina, Tatiana V. Chepurnyh, Elena B. Guglya, Tatiana A. Karataeva, et al. “Plants with Genetically Encoded Autoluminescence.” Nature Biotechnology. Springer Nature, 2020. https://doi.org/10.1038/s41587-020-0500-9. ieee: T. Mitiouchkina et al., “Plants with genetically encoded autoluminescence,” Nature Biotechnology, vol. 38. Springer Nature, pp. 944–946, 2020. ista: Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, Markina NM, Chepurnyh TV, Guglya EB, Karataeva TA, Palkina KA, Shakhova ES, Fakhranurova LI, Chekova SV, Tsarkova AS, Golubev YV, Negrebetsky VV, Dolgushin SA, Shalaev PV, Shlykov D, Melnik OA, Shipunova VO, Deyev SM, Bubyrev AI, Pushin AS, Choob VV, Dolgov SV, Kondrashov F, Yampolsky IV, Sarkisyan KS. 2020. Plants with genetically encoded autoluminescence. Nature Biotechnology. 38, 944–946. mla: Mitiouchkina, Tatiana, et al. “Plants with Genetically Encoded Autoluminescence.” Nature Biotechnology, vol. 38, Springer Nature, 2020, pp. 944–46, doi:10.1038/s41587-020-0500-9. short: T. Mitiouchkina, A.S. Mishin, L. Gonzalez Somermeyer, N.M. Markina, T.V. Chepurnyh, E.B. Guglya, T.A. Karataeva, K.A. Palkina, E.S. Shakhova, L.I. Fakhranurova, S.V. Chekova, A.S. Tsarkova, Y.V. Golubev, V.V. Negrebetsky, S.A. Dolgushin, P.V. Shalaev, D. Shlykov, O.A. Melnik, V.O. Shipunova, S.M. Deyev, A.I. Bubyrev, A.S. Pushin, V.V. Choob, S.V. Dolgov, F. Kondrashov, I.V. Yampolsky, K.S. Sarkisyan, Nature Biotechnology 38 (2020) 944–946. date_created: 2020-05-25T15:02:00Z date_published: 2020-04-27T00:00:00Z date_updated: 2023-09-05T15:30:34Z day: '27' ddc: - '570' department: - _id: FyKo doi: 10.1038/s41587-020-0500-9 ec_funded: 1 external_id: isi: - '000529298800003' pmid: - '32341562' file: - access_level: open_access checksum: 1b30467500ec6277229a875b06e196d0 content_type: application/pdf creator: dernst date_created: 2020-08-28T08:57:07Z date_updated: 2021-03-02T23:30:03Z embargo: 2021-03-01 file_id: '8316' file_name: 2020_NatureBiotech_Mitiouchkina.pdf file_size: 1180086 relation: main_file file_date_updated: 2021-03-02T23:30:03Z has_accepted_license: '1' intvolume: ' 38' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 944-946 pmid: 1 project: - _id: 26580278-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771209' name: Characterizing the fitness landscape on population and global scales publication: Nature Biotechnology publication_identifier: eissn: - 1546-1696 issn: - 1087-0156 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41587-020-0578-0 scopus_import: '1' status: public title: Plants with genetically encoded autoluminescence type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 38 year: '2020' ... --- _id: '9750' abstract: - lang: eng text: Tension of the actomyosin cell cortex plays a key role in determining cell-cell contact growth and size. The level of cortical tension outside of the cell-cell contact, when pulling at the contact edge, scales with the total size to which a cell-cell contact can grow1,2. Here we show in zebrafish primary germ layer progenitor cells that this monotonic relationship only applies to a narrow range of cortical tension increase, and that above a critical threshold, contact size inversely scales with cortical tension. This switch from cortical tension increasing to decreasing progenitor cell-cell contact size is caused by cortical tension promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin at the contact. Once tension-mediated E-cadherin stabilization at the contact exceeds a critical threshold level, the rate by which the contact expands in response to pulling forces from the cortex sharply drops, leading to smaller contacts at physiologically relevant timescales of contact formation. Thus, the activity of cortical tension in expanding cell-cell contact size is limited by tension stabilizing E-cadherin-actin complexes at the contact. acknowledged_ssus: - _id: Bio - _id: EM-Fac - _id: SSU acknowledgement: We would like to thank Edouard Hannezo for discussions, Shayan Shami Pour and Daniel Capek for help with data analysis, Vanessa Barone and other members of the Heisenberg laboratory for thoughtful discussions and comments on the manuscript. We also thank Jack Merrin for preparing the microwells, and the Scientific Service Units at IST Austria, specifically Bioimaging and Electron Microscopy, and the Zebrafish Facility for continuous support. We acknowledge Hitoshi Morita for the kind gift of VinculinB-GFP plasmid. This research was supported by an ERC Advanced Grant (MECSPEC) to C.-P.H, EMBO Long Term grant (ALTF 187-2013) to M.S and IST Fellow Marie-Curie COFUND No. P_IST_EU01 to J.S. article_processing_charge: No author: - first_name: Jana full_name: Slovakova, Jana id: 30F3F2F0-F248-11E8-B48F-1D18A9856A87 last_name: Slovakova - first_name: Mateusz K full_name: Sikora, Mateusz K id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87 last_name: Sikora - first_name: Silvia full_name: Caballero Mancebo, Silvia id: 2F1E1758-F248-11E8-B48F-1D18A9856A87 last_name: Caballero Mancebo orcid: 0000-0002-5223-3346 - first_name: Gabriel full_name: Krens, Gabriel id: 2B819732-F248-11E8-B48F-1D18A9856A87 last_name: Krens orcid: 0000-0003-4761-5996 - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Karla full_name: Huljev, Karla id: 44C6F6A6-F248-11E8-B48F-1D18A9856A87 last_name: Huljev - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Slovakova J, Sikora MK, Caballero Mancebo S, et al. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. bioRxiv. 2020. doi:10.1101/2020.11.20.391284 apa: Slovakova, J., Sikora, M. K., Caballero Mancebo, S., Krens, G., Kaufmann, W., Huljev, K., & Heisenberg, C.-P. J. (2020). Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.11.20.391284 chicago: Slovakova, Jana, Mateusz K Sikora, Silvia Caballero Mancebo, Gabriel Krens, Walter Kaufmann, Karla Huljev, and Carl-Philipp J Heisenberg. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.11.20.391284. ieee: J. Slovakova et al., “Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion,” bioRxiv. Cold Spring Harbor Laboratory, 2020. ista: Slovakova J, Sikora MK, Caballero Mancebo S, Krens G, Kaufmann W, Huljev K, Heisenberg C-PJ. 2020. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. bioRxiv, 10.1101/2020.11.20.391284. mla: Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.11.20.391284. short: J. Slovakova, M.K. Sikora, S. Caballero Mancebo, G. Krens, W. Kaufmann, K. Huljev, C.-P.J. Heisenberg, BioRxiv (2020). date_created: 2021-07-29T11:29:50Z date_published: 2020-11-20T00:00:00Z date_updated: 2024-03-27T23:30:18Z day: '20' department: - _id: CaHe - _id: EM-Fac - _id: Bio doi: 10.1101/2020.11.20.391284 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2020.11.20.391284 month: '11' oa: 1 oa_version: Preprint page: '41' project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation - _id: 2521E28E-B435-11E9-9278-68D0E5697425 grant_number: 187-2013 name: Modulation of adhesion function in cell-cell contact formation by cortical tension publication: bioRxiv publication_status: published publisher: Cold Spring Harbor Laboratory related_material: record: - id: '10766' relation: later_version status: public - id: '9623' relation: dissertation_contains status: public status: public title: Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2020' ... --- _id: '7426' abstract: - lang: eng text: This paper presents a novel abstraction technique for analyzing Lyapunov and asymptotic stability of polyhedral switched systems. A polyhedral switched system is a hybrid system in which the continuous dynamics is specified by polyhedral differential inclusions, the invariants and guards are specified by polyhedral sets and the switching between the modes do not involve reset of variables. A finite state weighted graph abstracting the polyhedral switched system is constructed from a finite partition of the state–space, such that the satisfaction of certain graph conditions, such as the absence of cycles with product of weights on the edges greater than (or equal) to 1, implies the stability of the system. However, the graph is in general conservative and hence, the violation of the graph conditions does not imply instability. If the analysis fails to establish stability due to the conservativeness in the approximation, a counterexample (cycle with product of edge weights greater than or equal to 1) indicating a potential reason for the failure is returned. Further, a more precise approximation of the switched system can be constructed by considering a finer partition of the state–space in the construction of the finite weighted graph. We present experimental results on analyzing stability of switched systems using the above method. article_number: '100856' article_processing_charge: No article_type: original author: - first_name: Miriam full_name: Garcia Soto, Miriam id: 4B3207F6-F248-11E8-B48F-1D18A9856A87 last_name: Garcia Soto orcid: 0000−0003−2936−5719 - first_name: Pavithra full_name: Prabhakar, Pavithra last_name: Prabhakar citation: ama: 'Garcia Soto M, Prabhakar P. Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. 2020;36(5). doi:10.1016/j.nahs.2020.100856' apa: 'Garcia Soto, M., & Prabhakar, P. (2020). Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. Elsevier. https://doi.org/10.1016/j.nahs.2020.100856' chicago: 'Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification of Stability of Polyhedral Switched Systems.” Nonlinear Analysis: Hybrid Systems. Elsevier, 2020. https://doi.org/10.1016/j.nahs.2020.100856.' ieee: 'M. Garcia Soto and P. Prabhakar, “Abstraction based verification of stability of polyhedral switched systems,” Nonlinear Analysis: Hybrid Systems, vol. 36, no. 5. Elsevier, 2020.' ista: 'Garcia Soto M, Prabhakar P. 2020. Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. 36(5), 100856.' mla: 'Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification of Stability of Polyhedral Switched Systems.” Nonlinear Analysis: Hybrid Systems, vol. 36, no. 5, 100856, Elsevier, 2020, doi:10.1016/j.nahs.2020.100856.' short: 'M. Garcia Soto, P. Prabhakar, Nonlinear Analysis: Hybrid Systems 36 (2020).' date_created: 2020-02-02T23:00:59Z date_published: 2020-05-01T00:00:00Z date_updated: 2023-08-17T14:32:54Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1016/j.nahs.2020.100856 external_id: isi: - '000528828600003' file: - access_level: open_access checksum: 560abfddb53f9fe921b6744f59f2cfaa content_type: application/pdf creator: dernst date_created: 2020-10-21T13:16:45Z date_updated: 2022-05-16T22:30:04Z embargo: 2022-05-15 file_id: '8688' file_name: 2020_NAHS_GarciaSoto.pdf file_size: 818774 relation: main_file file_date_updated: 2022-05-16T22:30:04Z has_accepted_license: '1' intvolume: ' 36' isi: 1 issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version project: - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: 'Nonlinear Analysis: Hybrid Systems' publication_identifier: issn: - 1751-570X publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Abstraction based verification of stability of polyhedral switched systems 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 36 year: '2020' ... --- _id: '8983' abstract: - lang: eng text: Metabolic adaptation is a critical feature of migrating cells. It tunes the metabolic programs of migrating cells to allow them to efficiently exert their crucial roles in development, inflammatory responses and tumor metastasis. Cell migration through physically challenging contexts requires energy. However, how the metabolic reprogramming that underlies in vivo cell invasion is controlled is still unanswered. In my PhD project, I identify a novel conserved metabolic shift in Drosophila melanogaster immune cells that by modulating their bioenergetic potential controls developmentally programmed tissue invasion. We show that this regulation requires a novel conserved nuclear protein, named Atossa. Atossa enhances the transcription of a set of proteins, including an RNA helicase Porthos and two metabolic enzymes, each of which increases the tissue invasion of leading Drosophila macrophages and can rescue the atossa mutant phenotype. Porthos selectively regulates the translational efficiency of a subset of mRNAs containing a 5’-UTR cis-regulatory TOP-like sequence. These 5’TOPL mRNA targets encode mitochondrial-related proteins, including subunits of mitochondrial oxidative phosphorylation (OXPHOS) components III and V and other metabolic-related proteins. Porthos powers up mitochondrial OXPHOS to engender a sufficient ATP supply, which is required for tissue invasion of leading macrophages. Atossa’s two vertebrate orthologs rescue the invasion defect. In my PhD project, I elucidate that Atossa displays a conserved developmental metabolic control to modulate metabolic capacities and the cellular energy state, through altered transcription and translation, to aid the tissue infiltration of leading cells into energy demanding barriers. acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: E-Lib - _id: CampIT acknowledgement: Also, I would like to express my appreciation and thanks to the Bioimaging facility, LSF, GSO, library, and IT people at IST Austria. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Shamsi full_name: Emtenani, Shamsi id: 49D32318-F248-11E8-B48F-1D18A9856A87 last_name: Emtenani orcid: 0000-0001-6981-6938 citation: ama: Emtenani S. Metabolic regulation of Drosophila macrophage tissue invasion. 2020. doi:10.15479/AT:ISTA:8983 apa: Emtenani, S. (2020). Metabolic regulation of Drosophila macrophage tissue invasion. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8983 chicago: Emtenani, Shamsi. “Metabolic Regulation of Drosophila Macrophage Tissue Invasion.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8983. ieee: S. Emtenani, “Metabolic regulation of Drosophila macrophage tissue invasion,” Institute of Science and Technology Austria, 2020. ista: Emtenani S. 2020. Metabolic regulation of Drosophila macrophage tissue invasion. Institute of Science and Technology Austria. mla: Emtenani, Shamsi. Metabolic Regulation of Drosophila Macrophage Tissue Invasion. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8983. short: S. Emtenani, Metabolic Regulation of Drosophila Macrophage Tissue Invasion, Institute of Science and Technology Austria, 2020. date_created: 2020-12-30T15:41:26Z date_published: 2020-12-30T00:00:00Z date_updated: 2023-09-07T13:24:17Z day: '30' ddc: - '570' degree_awarded: PhD department: - _id: DaSi doi: 10.15479/AT:ISTA:8983 file: - access_level: open_access checksum: ec2797ab7a6f253b35df0572b36d1b43 content_type: application/pdf creator: semtenan date_created: 2020-12-30T15:34:01Z date_updated: 2021-12-31T23:30:04Z embargo: 2021-12-30 file_id: '8984' file_name: Thesis_Shamsi_Emtenani_pdfA.pdf file_size: 10848175 relation: main_file - access_level: closed checksum: cc30e6608a9815414024cf548dff3b3a content_type: application/pdf creator: semtenan date_created: 2020-12-30T15:37:36Z date_updated: 2021-12-31T23:30:04Z embargo_to: open_access file_id: '8985' file_name: Thesis_Shamsi_Emtenani_source file.pdf file_size: 10073648 relation: source_file file_date_updated: 2021-12-31T23:30:04Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '141' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8557' relation: part_of_dissertation status: public - id: '6187' relation: part_of_dissertation status: public status: public supervisor: - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 title: Metabolic regulation of Drosophila macrophage tissue invasion type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '8557' abstract: - lang: eng text: The infiltration of immune cells into tissues underlies the establishment of tissue resident macrophages, and responses to infections and tumors. Yet the mechanisms immune cells utilize to negotiate tissue barriers in living organisms are not well understood, and a role for cortical actin has not been examined. Here we find that the tissue invasion of Drosophila macrophages, also known as plasmatocytes or hemocytes, utilizes enhanced cortical F-actin levels stimulated by the Drosophila member of the fos proto oncogene transcription factor family (Dfos, Kayak). RNA sequencing analysis and live imaging show that Dfos enhances F-actin levels around the entire macrophage surface by increasing mRNA levels of the membrane spanning molecular scaffold tetraspanin TM4SF, and the actin cross-linking filamin Cheerio which are themselves required for invasion. Cortical F-actin levels are critical as expressing a dominant active form of Diaphanous, a actin polymerizing Formin, can rescue the Dfos Dominant Negative macrophage invasion defect. In vivo imaging shows that Dfos is required to enhance the efficiency of the initial phases of macrophage tissue entry. Genetic evidence argues that this Dfos-induced program in macrophages counteracts the constraint produced by the tension of surrounding tissues and buffers the mechanical properties of the macrophage nucleus from affecting tissue entry. We thus identify tuning the cortical actin cytoskeleton through Dfos as a key process allowing efficient forward movement of an immune cell into surrounding tissues. acknowledged_ssus: - _id: LifeSc acknowledgement: 'We thank the following for their contributions: The Drosophila Genomics Resource Center supported by NIH grant 2P40OD010949-10A1 for plasmids, K. Brueckner. B. Stramer, M. Uhlirova, O. Schuldiner, the Bloomington Drosophila Stock Center supported by NIH grant P40OD018537 and the Vienna Drosophila Resource Center for fly stocks, FlyBase (Thurmond et al., 2019) for essential genomic information, and the BDGP in situ database for data (Tomancak et al., 2002, 2007). For antibodies, we thank the Developmental Studies Hybridoma Bank, which was created by the Eunice Kennedy Shriver National Institute of Child Health and Human Development of the NIH, and is maintained at the University of Iowa, as well as J. Zeitlinger for her generous gift of Dfos antibody. We thank the Vienna BioCenter Core Facilities for RNA sequencing and analysis and the Life Scientific Service Units at IST Austria for technical support and assistance with microscopy and FACS analysis. We thank C.P. Heisenberg, P. Martin, M. Sixt and Siekhaus group members for discussions and T.Hurd, A. Ratheesh and P. Rangan for comments on the manuscript. A.G. was supported by the Austrian Science Fund (FWF) grant DASI_FWF01_P29638S, D.E.S. by Marie Curie CIG 334077/IRTIM. M.S. is supported by the FWF, PhD program W1212 915 and the European Research Council (ERC) Advanced grant (ERC-2015-AdG TNT-Tumors 694883). S.W. is supported by an OEAW, DOC fellowship.' article_processing_charge: No author: - first_name: Vera full_name: Belyaeva, Vera id: 47F080FE-F248-11E8-B48F-1D18A9856A87 last_name: Belyaeva - first_name: Stephanie full_name: Wachner, Stephanie id: 2A95E7B0-F248-11E8-B48F-1D18A9856A87 last_name: Wachner - first_name: Igor full_name: Gridchyn, Igor id: 4B60654C-F248-11E8-B48F-1D18A9856A87 last_name: Gridchyn orcid: 0000-0002-1807-1929 - first_name: Markus full_name: Linder, Markus last_name: Linder - first_name: Shamsi full_name: Emtenani, Shamsi id: 49D32318-F248-11E8-B48F-1D18A9856A87 last_name: Emtenani orcid: 0000-0001-6981-6938 - first_name: Attila full_name: György, Attila id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87 last_name: György orcid: 0000-0002-1819-198X - first_name: Maria full_name: Sibilia, Maria last_name: Sibilia - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 citation: ama: Belyaeva V, Wachner S, Gridchyn I, et al. Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. bioRxiv. doi:10.1101/2020.09.18.301481 apa: Belyaeva, V., Wachner, S., Gridchyn, I., Linder, M., Emtenani, S., György, A., … Siekhaus, D. E. (n.d.). Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. bioRxiv. https://doi.org/10.1101/2020.09.18.301481 chicago: Belyaeva, Vera, Stephanie Wachner, Igor Gridchyn, Markus Linder, Shamsi Emtenani, Attila György, Maria Sibilia, and Daria E Siekhaus. “Cortical Actin Properties Controlled by Drosophila Fos Aid Macrophage Infiltration against Surrounding Tissue Resistance.” BioRxiv, n.d. https://doi.org/10.1101/2020.09.18.301481. ieee: V. Belyaeva et al., “Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance,” bioRxiv. . ista: Belyaeva V, Wachner S, Gridchyn I, Linder M, Emtenani S, György A, Sibilia M, Siekhaus DE. Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. bioRxiv, 10.1101/2020.09.18.301481. mla: Belyaeva, Vera, et al. “Cortical Actin Properties Controlled by Drosophila Fos Aid Macrophage Infiltration against Surrounding Tissue Resistance.” BioRxiv, doi:10.1101/2020.09.18.301481. short: V. Belyaeva, S. Wachner, I. Gridchyn, M. Linder, S. Emtenani, A. György, M. Sibilia, D.E. Siekhaus, BioRxiv (n.d.). date_created: 2020-09-23T09:36:47Z date_published: 2020-09-18T00:00:00Z date_updated: 2024-03-27T23:30:24Z day: '18' department: - _id: DaSi - _id: JoCs doi: 10.1101/2020.09.18.301481 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2020.09.18.301481 month: '09' oa: 1 oa_version: Preprint project: - _id: 253B6E48-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29638 name: Drosophila TNFa´s Funktion in Immunzellen - _id: 2536F660-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '334077' name: Investigating the role of transporters in invasive migration through junctions - _id: 26199CA4-B435-11E9-9278-68D0E5697425 grant_number: '24800' name: Tissue barrier penetration is crucial for immunity and metastasis publication: bioRxiv publication_status: submitted related_material: record: - id: '10614' relation: later_version status: public - id: '8983' relation: dissertation_contains status: public status: public title: Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8831' abstract: - lang: eng text: Holes in planar Ge have high mobilities, strong spin-orbit interaction and electrically tunable g-factors, and are therefore emerging as a promising candidate for hybrid superconductorsemiconductor devices. This is further motivated by the observation of supercurrent transport in planar Ge Josephson Field effect transistors (JoFETs). A key challenge towards hybrid germanium quantum technology is the design of high quality interfaces and superconducting contacts that are robust against magnetic fields. By combining the assets of Al, which has a long superconducting coherence, and Nb, which has a significant superconducting gap, we form low-disordered JoFETs with large ICRN products that are capable of withstanding high magnetic fields. We furthermore demonstrate the ability of phase-biasing individual JoFETs opening up an avenue to explore topological superconductivity in planar Ge. The persistence of superconductivity in the reported hybrid devices beyond 1.8 T paves the way towards integrating spin qubits and proximity-induced superconductivity on the same chip. acknowledged_ssus: - _id: M-Shop - _id: NanoFab acknowledgement: "This research and related results were made possible with the support of the NOMIS Foundation. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility, the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement #844511 and the Grant Agreement #862046. ICN2 acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa\r\nprogram from Spanish MINECO (Grant No. SEV2017-0706) and is funded by the CERCA Programme / Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Aut`onoma de Barcelona Materials Science PhD program. The HAADF-STEM microscopy was conducted in the Laboratorio de Microscopias Avanzadas at Instituto de Nanociencia de Aragon-Universidad de Zaragoza. Authors acknowledge the LMA-INA for offering access to their instruments and expertise. We acknowledge support from CSIC Research Platform on Quantum Technologies PTI-001. This project has received funding from\r\nthe European Union’s Horizon 2020 research and innovation programme under grant agreement No 823717 – ESTEEM3. M.B. acknowledges support from SUR Generalitat de Catalunya and the EU Social Fund; project ref. 2020 FI 00103. GS and MV acknowledge support through a projectruimte grant associated with the Netherlands Organization of Scientific Research (NWO)." article_number: '2012.00322' article_processing_charge: No author: - first_name: Kushagra full_name: Aggarwal, Kushagra id: b22ab905-3539-11eb-84c3-fc159dcd79cb last_name: Aggarwal orcid: 0000-0001-9985-9293 - first_name: Andrea C full_name: Hofmann, Andrea C id: 340F461A-F248-11E8-B48F-1D18A9856A87 last_name: Hofmann - first_name: Daniel full_name: Jirovec, Daniel id: 4C473F58-F248-11E8-B48F-1D18A9856A87 last_name: Jirovec orcid: 0000-0002-7197-4801 - first_name: Ivan full_name: Prieto Gonzalez, Ivan id: 2A307FE2-F248-11E8-B48F-1D18A9856A87 last_name: Prieto Gonzalez orcid: 0000-0002-7370-5357 - first_name: Amir full_name: Sammak, Amir last_name: Sammak - first_name: Marc full_name: Botifoll, Marc last_name: Botifoll - first_name: Sara full_name: Marti-Sanchez, Sara last_name: Marti-Sanchez - first_name: Menno full_name: Veldhorst, Menno last_name: Veldhorst - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Giordano full_name: Scappucci, Giordano last_name: Scappucci - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X citation: ama: Aggarwal K, Hofmann AC, Jirovec D, et al. Enhancement of proximity induced superconductivity in planar Germanium. arXiv. apa: Aggarwal, K., Hofmann, A. C., Jirovec, D., Prieto Gonzalez, I., Sammak, A., Botifoll, M., … Katsaros, G. (n.d.). Enhancement of proximity induced superconductivity in planar Germanium. arXiv. chicago: Aggarwal, Kushagra, Andrea C Hofmann, Daniel Jirovec, Ivan Prieto Gonzalez, Amir Sammak, Marc Botifoll, Sara Marti-Sanchez, et al. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” ArXiv, n.d. ieee: K. Aggarwal et al., “Enhancement of proximity induced superconductivity in planar Germanium,” arXiv. . ista: Aggarwal K, Hofmann AC, Jirovec D, Prieto Gonzalez I, Sammak A, Botifoll M, Marti-Sanchez S, Veldhorst M, Arbiol J, Scappucci G, Katsaros G. Enhancement of proximity induced superconductivity in planar Germanium. arXiv, 2012.00322. mla: Aggarwal, Kushagra, et al. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” ArXiv, 2012.00322. short: K. Aggarwal, A.C. Hofmann, D. Jirovec, I. Prieto Gonzalez, A. Sammak, M. Botifoll, S. Marti-Sanchez, M. Veldhorst, J. Arbiol, G. Scappucci, G. Katsaros, ArXiv (n.d.). date_created: 2020-12-02T10:42:53Z date_published: 2020-12-02T00:00:00Z date_updated: 2024-03-27T23:30:26Z day: '02' ddc: - '530' department: - _id: GeKa ec_funded: 1 external_id: arxiv: - '2012.00322' file: - access_level: open_access checksum: 22a612e206232fa94b138b2c2f957582 content_type: application/pdf creator: gkatsaro date_created: 2020-12-02T10:42:31Z date_updated: 2020-12-02T10:42:31Z file_id: '8832' file_name: Superconducting_2D_Ge.pdf file_size: 1697939 relation: main_file file_date_updated: 2020-12-02T10:42:31Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Submitted Version project: - _id: 262116AA-B435-11E9-9278-68D0E5697425 name: Hybrid Semiconductor - Superconductor Quantum Devices - _id: 26A151DA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '844511' name: Majorana bound states in Ge/SiGe heterostructures - _id: 237E5020-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '862046' name: TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS publication: arXiv publication_status: submitted related_material: record: - id: '10559' relation: later_version status: public - id: '8834' relation: research_data status: public - id: '10058' relation: dissertation_contains status: public status: public title: Enhancement of proximity induced superconductivity in planar Germanium type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8532' abstract: - lang: eng text: The molecular anatomy of synapses defines their characteristics in transmission and plasticity. Precise measurements of the number and distribution of synaptic proteins are important for our understanding of synapse heterogeneity within and between brain regions. Freeze–fracture replica immunogold electron microscopy enables us to analyze them quantitatively on a two-dimensional membrane surface. Here, we introduce Darea software, which utilizes deep learning for analysis of replica images and demonstrate its usefulness for quick measurements of the pre- and postsynaptic areas, density and distribution of gold particles at synapses in a reproducible manner. We used Darea for comparing glutamate receptor and calcium channel distributions between hippocampal CA3-CA1 spine synapses on apical and basal dendrites, which differ in signaling pathways involved in synaptic plasticity. We found that apical synapses express a higher density of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors and a stronger increase of AMPA receptors with synaptic size, while basal synapses show a larger increase in N-methyl-D-aspartate (NMDA) receptors with size. Interestingly, AMPA and NMDA receptors are segregated within postsynaptic sites and negatively correlated in density among both apical and basal synapses. In the presynaptic sites, Cav2.1 voltage-gated calcium channels show similar densities in apical and basal synapses with distributions consistent with an exclusion zone model of calcium channel-release site topography. acknowledgement: "This research was funded by Austrian Academy of Sciences, DOC fellowship to D.K., European Research\r\nCouncil Advanced Grant 694539 and European Union Human Brain Project (HBP) SGA2 785907 to R.S.\r\nWe acknowledge Elena Hollergschwandtner for technical support." article_number: '6737' article_processing_charge: No article_type: original author: - first_name: David full_name: Kleindienst, David id: 42E121A4-F248-11E8-B48F-1D18A9856A87 last_name: Kleindienst - first_name: Jacqueline-Claire full_name: Montanaro-Punzengruber, Jacqueline-Claire id: 3786AB44-F248-11E8-B48F-1D18A9856A87 last_name: Montanaro-Punzengruber - first_name: Pradeep full_name: Bhandari, Pradeep id: 45EDD1BC-F248-11E8-B48F-1D18A9856A87 last_name: Bhandari orcid: 0000-0003-0863-4481 - first_name: Matthew J full_name: Case, Matthew J id: 44B7CA5A-F248-11E8-B48F-1D18A9856A87 last_name: Case - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 citation: ama: Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y, Shigemoto R. Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. International Journal of Molecular Sciences. 2020;21(18). doi:10.3390/ijms21186737 apa: Kleindienst, D., Montanaro-Punzengruber, J.-C., Bhandari, P., Case, M. J., Fukazawa, Y., & Shigemoto, R. (2020). Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms21186737 chicago: Kleindienst, David, Jacqueline-Claire Montanaro-Punzengruber, Pradeep Bhandari, Matthew J Case, Yugo Fukazawa, and Ryuichi Shigemoto. “Deep Learning-Assisted High-Throughput Analysis of Freeze-Fracture Replica Images Applied to Glutamate Receptors and Calcium Channels at Hippocampal Synapses.” International Journal of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21186737. ieee: D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M. J. Case, Y. Fukazawa, and R. Shigemoto, “Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses,” International Journal of Molecular Sciences, vol. 21, no. 18. MDPI, 2020. ista: Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y, Shigemoto R. 2020. Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. International Journal of Molecular Sciences. 21(18), 6737. mla: Kleindienst, David, et al. “Deep Learning-Assisted High-Throughput Analysis of Freeze-Fracture Replica Images Applied to Glutamate Receptors and Calcium Channels at Hippocampal Synapses.” International Journal of Molecular Sciences, vol. 21, no. 18, 6737, MDPI, 2020, doi:10.3390/ijms21186737. short: D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M.J. Case, Y. Fukazawa, R. Shigemoto, International Journal of Molecular Sciences 21 (2020). date_created: 2020-09-20T22:01:35Z date_published: 2020-09-14T00:00:00Z date_updated: 2024-03-27T23:30:30Z day: '14' ddc: - '570' department: - _id: RySh doi: 10.3390/ijms21186737 ec_funded: 1 external_id: isi: - '000579945300001' file: - access_level: open_access checksum: 2e4f62f3cfe945b7391fc3070e5a289f content_type: application/pdf creator: dernst date_created: 2020-09-21T14:08:58Z date_updated: 2020-09-21T14:08:58Z file_id: '8551' file_name: 2020_JournMolecSciences_Kleindienst.pdf file_size: 5748456 relation: main_file success: 1 file_date_updated: 2020-09-21T14:08:58Z has_accepted_license: '1' intvolume: ' 21' isi: 1 issue: '18' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 25CA28EA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694539' name: 'In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour' - _id: 25D32BC0-B435-11E9-9278-68D0E5697425 name: Mechanism of formation and maintenance of input side-dependent asymmetry in the hippocampus - _id: 26436750-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '785907' name: Human Brain Project Specific Grant Agreement 2 (HBP SGA 2) publication: International Journal of Molecular Sciences publication_identifier: eissn: - '14220067' issn: - '16616596' publication_status: published publisher: MDPI quality_controlled: '1' related_material: record: - id: '9562' relation: dissertation_contains status: public scopus_import: '1' status: public title: Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 21 year: '2020' ... --- _id: '7810' abstract: - lang: eng text: "Interprocedural data-flow analyses form an expressive and useful paradigm of numerous static analysis applications, such as live variables analysis, alias analysis and null pointers analysis. The most widely-used framework for interprocedural data-flow analysis is IFDS, which encompasses distributive data-flow functions over a finite domain. On-demand data-flow analyses restrict the focus of the analysis on specific program locations and data facts. This setting provides a natural split between (i) an offline (or preprocessing) phase, where the program is partially analyzed and analysis summaries are created, and (ii) an online (or query) phase, where analysis queries arrive on demand and the summaries are used to speed up answering queries.\r\nIn this work, we consider on-demand IFDS analyses where the queries concern program locations of the same procedure (aka same-context queries). We exploit the fact that flow graphs of programs have low treewidth to develop faster algorithms that are space and time optimal for many common data-flow analyses, in both the preprocessing and the query phase. We also use treewidth to develop query solutions that are embarrassingly parallelizable, i.e. the total work for answering each query is split to a number of threads such that each thread performs only a constant amount of work. Finally, we implement a static analyzer based on our algorithms, and perform a series of on-demand analysis experiments on standard benchmarks. Our experimental results show a drastic speed-up of the queries after only a lightweight preprocessing phase, which significantly outperforms existing techniques." alternative_title: - LNCS article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Amir Kafshdar full_name: Goharshady, Amir Kafshdar id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 citation: ama: 'Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. Optimal and perfectly parallel algorithms for on-demand data-flow analysis. In: European Symposium on Programming. Vol 12075. Springer Nature; 2020:112-140. doi:10.1007/978-3-030-44914-8_5' apa: 'Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., & Pavlogiannis, A. (2020). Optimal and perfectly parallel algorithms for on-demand data-flow analysis. In European Symposium on Programming (Vol. 12075, pp. 112–140). Dublin, Ireland: Springer Nature. https://doi.org/10.1007/978-3-030-44914-8_5' chicago: Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Optimal and Perfectly Parallel Algorithms for On-Demand Data-Flow Analysis.” In European Symposium on Programming, 12075:112–40. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-44914-8_5. ieee: K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and A. Pavlogiannis, “Optimal and perfectly parallel algorithms for on-demand data-flow analysis,” in European Symposium on Programming, Dublin, Ireland, 2020, vol. 12075, pp. 112–140. ista: 'Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. 2020. Optimal and perfectly parallel algorithms for on-demand data-flow analysis. European Symposium on Programming. ESOP: Programming Languages and Systems, LNCS, vol. 12075, 112–140.' mla: Chatterjee, Krishnendu, et al. “Optimal and Perfectly Parallel Algorithms for On-Demand Data-Flow Analysis.” European Symposium on Programming, vol. 12075, Springer Nature, 2020, pp. 112–40, doi:10.1007/978-3-030-44914-8_5. short: K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, A. Pavlogiannis, in:, European Symposium on Programming, Springer Nature, 2020, pp. 112–140. conference: end_date: 2020-04-30 location: Dublin, Ireland name: 'ESOP: Programming Languages and Systems' start_date: 2020-04-25 date_created: 2020-05-10T22:00:50Z date_published: 2020-04-18T00:00:00Z date_updated: 2024-03-27T23:30:33Z day: '18' ddc: - '000' department: - _id: KrCh doi: 10.1007/978-3-030-44914-8_5 external_id: isi: - '000681656800005' file: - access_level: open_access checksum: 8618b80f4cf7b39a60e61a6445ad9807 content_type: application/pdf creator: dernst date_created: 2020-05-26T13:34:48Z date_updated: 2020-07-14T12:48:03Z file_id: '7895' file_name: 2020_LNCS_Chatterjee.pdf file_size: 651250 relation: main_file file_date_updated: 2020-07-14T12:48:03Z has_accepted_license: '1' intvolume: ' 12075' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 112-140 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 266EEEC0-B435-11E9-9278-68D0E5697425 name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts - _id: 267066CE-B435-11E9-9278-68D0E5697425 name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies publication: European Symposium on Programming publication_identifier: eissn: - '16113349' isbn: - '9783030449131' issn: - '03029743' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '8934' relation: dissertation_contains status: public scopus_import: '1' status: public title: Optimal and perfectly parallel algorithms for on-demand data-flow analysis 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: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12075 year: '2020' ... --- _id: '8728' abstract: - lang: eng text: Discrete-time Markov Chains (MCs) and Markov Decision Processes (MDPs) are two standard formalisms in system analysis. Their main associated quantitative objectives are hitting probabilities, discounted sum, and mean payoff. Although there are many techniques for computing these objectives in general MCs/MDPs, they have not been thoroughly studied in terms of parameterized algorithms, particularly when treewidth is used as the parameter. This is in sharp contrast to qualitative objectives for MCs, MDPs and graph games, for which treewidth-based algorithms yield significant complexity improvements. In this work, we show that treewidth can also be used to obtain faster algorithms for the quantitative problems. For an MC with n states and m transitions, we show that each of the classical quantitative objectives can be computed in O((n+m)⋅t2) time, given a tree decomposition of the MC with width t. Our results also imply a bound of O(κ⋅(n+m)⋅t2) for each objective on MDPs, where κ is the number of strategy-iteration refinements required for the given input and objective. Finally, we make an experimental evaluation of our new algorithms on low-treewidth MCs and MDPs obtained from the DaCapo benchmark suite. Our experiments show that on low-treewidth MCs and MDPs, our algorithms outperform existing well-established methods by one or more orders of magnitude. alternative_title: - LNCS article_processing_charge: No author: - first_name: Ali full_name: Asadi, Ali last_name: Asadi - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Amir Kafshdar full_name: Goharshady, Amir Kafshdar id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 - first_name: Kiarash full_name: Mohammadi, Kiarash last_name: Mohammadi - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 citation: ama: 'Asadi A, Chatterjee K, Goharshady AK, Mohammadi K, Pavlogiannis A. Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth. In: Automated Technology for Verification and Analysis. Vol 12302. Springer Nature; 2020:253-270. doi:10.1007/978-3-030-59152-6_14' apa: 'Asadi, A., Chatterjee, K., Goharshady, A. K., Mohammadi, K., & Pavlogiannis, A. (2020). Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth. In Automated Technology for Verification and Analysis (Vol. 12302, pp. 253–270). Hanoi, Vietnam: Springer Nature. https://doi.org/10.1007/978-3-030-59152-6_14' chicago: Asadi, Ali, Krishnendu Chatterjee, Amir Kafshdar Goharshady, Kiarash Mohammadi, and Andreas Pavlogiannis. “Faster Algorithms for Quantitative Analysis of MCs and MDPs with Small Treewidth.” In Automated Technology for Verification and Analysis, 12302:253–70. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-59152-6_14. ieee: A. Asadi, K. Chatterjee, A. K. Goharshady, K. Mohammadi, and A. Pavlogiannis, “Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth,” in Automated Technology for Verification and Analysis, Hanoi, Vietnam, 2020, vol. 12302, pp. 253–270. ista: 'Asadi A, Chatterjee K, Goharshady AK, Mohammadi K, Pavlogiannis A. 2020. Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth. Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 12302, 253–270.' mla: Asadi, Ali, et al. “Faster Algorithms for Quantitative Analysis of MCs and MDPs with Small Treewidth.” Automated Technology for Verification and Analysis, vol. 12302, Springer Nature, 2020, pp. 253–70, doi:10.1007/978-3-030-59152-6_14. short: A. Asadi, K. Chatterjee, A.K. Goharshady, K. Mohammadi, A. Pavlogiannis, in:, Automated Technology for Verification and Analysis, Springer Nature, 2020, pp. 253–270. conference: end_date: 2020-10-23 location: Hanoi, Vietnam name: 'ATVA: Automated Technology for Verification and Analysis' start_date: 2020-10-19 date_created: 2020-11-06T07:30:05Z date_published: 2020-10-12T00:00:00Z date_updated: 2024-03-27T23:30:33Z day: '12' ddc: - '000' department: - _id: KrCh doi: 10.1007/978-3-030-59152-6_14 external_id: isi: - '000723555700014' file: - access_level: open_access checksum: ae83f27e5b189d5abc2e7514f1b7e1b5 content_type: application/pdf creator: dernst date_created: 2020-11-06T07:41:03Z date_updated: 2020-11-06T07:41:03Z file_id: '8729' file_name: 2020_LNCS_ATVA_Asadi_accepted.pdf file_size: 726648 relation: main_file success: 1 file_date_updated: 2020-11-06T07:41:03Z has_accepted_license: '1' intvolume: ' 12302' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 253-270 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 267066CE-B435-11E9-9278-68D0E5697425 name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies publication: Automated Technology for Verification and Analysis publication_identifier: eisbn: - '9783030591526' eissn: - 1611-3349 isbn: - '9783030591519' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '8934' relation: dissertation_contains status: public scopus_import: '1' status: public title: Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 12302 year: '2020' ... --- _id: '8089' abstract: - lang: eng text: "We consider the classical problem of invariant generation for programs with polynomial assignments and focus on synthesizing invariants that are a conjunction of strict polynomial inequalities. We present a sound and semi-complete method based on positivstellensaetze, i.e. theorems in semi-algebraic geometry that characterize positive polynomials over a semi-algebraic set.\r\n\r\nOn the theoretical side, the worst-case complexity of our approach is subexponential, whereas the worst-case complexity of the previous complete method (Kapur, ACA 2004) is doubly-exponential. Even when restricted to linear invariants, the best previous complexity for complete invariant generation is exponential (Colon et al, CAV 2003). On the practical side, we reduce the invariant generation problem to quadratic programming (QCLP), which is a classical optimization problem with many industrial solvers. We demonstrate the applicability of our approach by providing experimental results on several academic benchmarks. To the best of our knowledge, the only previous invariant generation method that provides completeness guarantees for invariants consisting of polynomial inequalities is (Kapur, ACA 2004), which relies on quantifier elimination and cannot even handle toy programs such as our running example." article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Hongfei full_name: Fu, Hongfei id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87 last_name: Fu - first_name: Amir Kafshdar full_name: Goharshady, Amir Kafshdar id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 - first_name: Ehsan Kafshdar full_name: Goharshady, Ehsan Kafshdar last_name: Goharshady citation: ama: 'Chatterjee K, Fu H, Goharshady AK, Goharshady EK. Polynomial invariant generation for non-deterministic recursive programs. In: Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2020:672-687. doi:10.1145/3385412.3385969' apa: 'Chatterjee, K., Fu, H., Goharshady, A. K., & Goharshady, E. K. (2020). Polynomial invariant generation for non-deterministic recursive programs. In Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation (pp. 672–687). London, United Kingdom: Association for Computing Machinery. https://doi.org/10.1145/3385412.3385969' chicago: Chatterjee, Krishnendu, Hongfei Fu, Amir Kafshdar Goharshady, and Ehsan Kafshdar Goharshady. “Polynomial Invariant Generation for Non-Deterministic Recursive Programs.” In Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, 672–87. Association for Computing Machinery, 2020. https://doi.org/10.1145/3385412.3385969. ieee: K. Chatterjee, H. Fu, A. K. Goharshady, and E. K. Goharshady, “Polynomial invariant generation for non-deterministic recursive programs,” in Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, London, United Kingdom, 2020, pp. 672–687. ista: 'Chatterjee K, Fu H, Goharshady AK, Goharshady EK. 2020. Polynomial invariant generation for non-deterministic recursive programs. Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 672–687.' mla: Chatterjee, Krishnendu, et al. “Polynomial Invariant Generation for Non-Deterministic Recursive Programs.” Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2020, pp. 672–87, doi:10.1145/3385412.3385969. short: K. Chatterjee, H. Fu, A.K. Goharshady, E.K. Goharshady, in:, Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2020, pp. 672–687. conference: end_date: 2020-06-20 location: London, United Kingdom name: 'PLDI: Programming Language Design and Implementation' start_date: 2020-06-15 date_created: 2020-07-05T22:00:45Z date_published: 2020-06-11T00:00:00Z date_updated: 2024-03-27T23:30:33Z day: '11' department: - _id: KrCh doi: 10.1145/3385412.3385969 external_id: arxiv: - '1902.04373' isi: - '000614622300045' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1902.04373 month: '06' oa: 1 oa_version: Preprint page: 672-687 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification publication: Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation publication_identifier: isbn: - '9781450376136' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' related_material: record: - id: '8934' relation: dissertation_contains status: public scopus_import: '1' status: public title: Polynomial invariant generation for non-deterministic recursive programs type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '6918' abstract: - lang: eng text: "We consider the classic problem of Network Reliability. A network is given together with a source vertex, one or more target vertices, and probabilities assigned to each of the edges. Each edge of the network is operable with its associated probability and the problem is to determine the probability of having at least one source-to-target path that is entirely composed of operable edges. This problem is known to be NP-hard.\r\n\r\nWe provide a novel scalable algorithm to solve the Network Reliability problem when the treewidth of the underlying network is small. We also show our algorithm’s applicability for real-world transit networks that have small treewidth, including the metro networks of major cities, such as London and Tokyo. Our algorithm leverages tree decompositions to shrink the original graph into much smaller graphs, for which reliability can be efficiently and exactly computed using a brute force method. To the best of our knowledge, this is the first exact algorithm for Network Reliability that can scale to handle real-world instances of the problem." acknowledgement: We are grateful to the anonymous reviewers for their comments, which significantly improved the present work. The research was partially supported by the EPSRC Early Career Fellowship EP/R023379/1, grant no. SC7-1718-01 of the London Mathematical Society, an IBM PhD Fellowship, and a DOC Fellowship of the Austrian Academy of Sciences (ÖAW). article_number: '106665' article_processing_charge: No article_type: original author: - first_name: Amir Kafshdar full_name: Goharshady, Amir Kafshdar id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 - first_name: Fatemeh full_name: Mohammadi, Fatemeh last_name: Mohammadi citation: ama: Goharshady AK, Mohammadi F. An efficient algorithm for computing network reliability in small treewidth. Reliability Engineering and System Safety. 2020;193. doi:10.1016/j.ress.2019.106665 apa: Goharshady, A. K., & Mohammadi, F. (2020). An efficient algorithm for computing network reliability in small treewidth. Reliability Engineering and System Safety. Elsevier. https://doi.org/10.1016/j.ress.2019.106665 chicago: Goharshady, Amir Kafshdar, and Fatemeh Mohammadi. “An Efficient Algorithm for Computing Network Reliability in Small Treewidth.” Reliability Engineering and System Safety. Elsevier, 2020. https://doi.org/10.1016/j.ress.2019.106665. ieee: A. K. Goharshady and F. Mohammadi, “An efficient algorithm for computing network reliability in small treewidth,” Reliability Engineering and System Safety, vol. 193. Elsevier, 2020. ista: Goharshady AK, Mohammadi F. 2020. An efficient algorithm for computing network reliability in small treewidth. Reliability Engineering and System Safety. 193, 106665. mla: Goharshady, Amir Kafshdar, and Fatemeh Mohammadi. “An Efficient Algorithm for Computing Network Reliability in Small Treewidth.” Reliability Engineering and System Safety, vol. 193, 106665, Elsevier, 2020, doi:10.1016/j.ress.2019.106665. short: A.K. Goharshady, F. Mohammadi, Reliability Engineering and System Safety 193 (2020). date_created: 2019-09-29T22:00:44Z date_published: 2020-01-01T00:00:00Z date_updated: 2024-03-27T23:30:33Z day: '01' department: - _id: KrCh doi: 10.1016/j.ress.2019.106665 external_id: arxiv: - '1712.09692' isi: - '000501641400050' intvolume: ' 193' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1712.09692 month: '01' oa: 1 oa_version: Preprint project: - _id: 266EEEC0-B435-11E9-9278-68D0E5697425 name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts publication: Reliability Engineering and System Safety publication_identifier: issn: - '09518320' publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '8934' relation: dissertation_contains status: public scopus_import: '1' status: public title: An efficient algorithm for computing network reliability in small treewidth type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 193 year: '2020' ... --- _id: '7161' abstract: - lang: eng text: In this paper, we introduce an inertial projection-type method with different updating strategies for solving quasi-variational inequalities with strongly monotone and Lipschitz continuous operators in real Hilbert spaces. Under standard assumptions, we establish different strong convergence results for the proposed algorithm. Primary numerical experiments demonstrate the potential applicability of our scheme compared with some related methods in the literature. acknowledgement: We are grateful to the anonymous referees and editor whose insightful comments helped to considerably improve an earlier version of this paper. The research of the first author is supported by an ERC Grant from the Institute of Science and Technology (IST). article_processing_charge: No article_type: original author: - first_name: Yekini full_name: Shehu, Yekini id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87 last_name: Shehu orcid: 0000-0001-9224-7139 - first_name: Aviv full_name: Gibali, Aviv last_name: Gibali - first_name: Simone full_name: Sagratella, Simone last_name: Sagratella citation: ama: Shehu Y, Gibali A, Sagratella S. Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization Theory and Applications. 2020;184:877–894. doi:10.1007/s10957-019-01616-6 apa: Shehu, Y., Gibali, A., & Sagratella, S. (2020). Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization Theory and Applications. Springer Nature. https://doi.org/10.1007/s10957-019-01616-6 chicago: Shehu, Yekini, Aviv Gibali, and Simone Sagratella. “Inertial Projection-Type Methods for Solving Quasi-Variational Inequalities in Real Hilbert Spaces.” Journal of Optimization Theory and Applications. Springer Nature, 2020. https://doi.org/10.1007/s10957-019-01616-6. ieee: Y. Shehu, A. Gibali, and S. Sagratella, “Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces,” Journal of Optimization Theory and Applications, vol. 184. Springer Nature, pp. 877–894, 2020. ista: Shehu Y, Gibali A, Sagratella S. 2020. Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization Theory and Applications. 184, 877–894. mla: Shehu, Yekini, et al. “Inertial Projection-Type Methods for Solving Quasi-Variational Inequalities in Real Hilbert Spaces.” Journal of Optimization Theory and Applications, vol. 184, Springer Nature, 2020, pp. 877–894, doi:10.1007/s10957-019-01616-6. short: Y. Shehu, A. Gibali, S. Sagratella, Journal of Optimization Theory and Applications 184 (2020) 877–894. date_created: 2019-12-09T21:33:44Z date_published: 2020-03-01T00:00:00Z date_updated: 2023-09-06T11:27:15Z day: '01' ddc: - '518' - '510' - '515' department: - _id: VlKo doi: 10.1007/s10957-019-01616-6 ec_funded: 1 external_id: isi: - '000511805200009' file: - access_level: open_access checksum: 9f6dc6c6bf2b48cb3a2091a9ed5feaf2 content_type: application/pdf creator: dernst date_created: 2020-10-12T10:40:27Z date_updated: 2021-03-16T23:30:04Z embargo: 2021-03-15 file_id: '8647' file_name: 2020_JourOptimizationTheoryApplic_Shehu.pdf file_size: 332641 relation: main_file file_date_updated: 2021-03-16T23:30:04Z has_accepted_license: '1' intvolume: ' 184' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 877–894 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: Journal of Optimization Theory and Applications publication_identifier: eissn: - 1573-2878 issn: - 0022-3239 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 184 year: '2020' ... --- _id: '7652' abstract: - lang: eng text: Organisms cope with change by taking advantage of transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. Here, we investigate whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using real-time monitoring of gene-copy-number mutations in Escherichia coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy-number and, therefore, expression-level polymorphisms. This amplification-mediated gene expression tuning (AMGET) occurs on timescales that are similar to canonical gene regulation and can respond to rapid environmental changes. Mathematical modelling shows that amplifications also tune gene expression in stochastic environments in which transcription-factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune the expression of any gene, without leaving any genomic signature. acknowledgement: We thank L. Hurst, N. Barton, M. Pleska, M. Steinrück, B. Kavcic and A. Staron for input on the manuscript, and To. Bergmiller and R. Chait for help with microfluidics experiments. I.T. is a recipient the OMV fellowship. R.G. is a recipient of a DOC (Doctoral Fellowship Programme of the Austrian Academy of Sciences) Fellowship of the Austrian Academy of Sciences. article_processing_charge: No article_type: original author: - first_name: Isabella full_name: Tomanek, Isabella id: 3981F020-F248-11E8-B48F-1D18A9856A87 last_name: Tomanek orcid: 0000-0001-6197-363X - first_name: Rok full_name: Grah, Rok id: 483E70DE-F248-11E8-B48F-1D18A9856A87 last_name: Grah orcid: 0000-0003-2539-3560 - first_name: M. full_name: Lagator, M. last_name: Lagator - first_name: A. M. C. full_name: Andersson, A. M. C. last_name: Andersson - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 citation: ama: Tomanek I, Grah R, Lagator M, et al. Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. 2020;4(4):612-625. doi:10.1038/s41559-020-1132-7 apa: Tomanek, I., Grah, R., Lagator, M., Andersson, A. M. C., Bollback, J. P., Tkačik, G., & Guet, C. C. (2020). Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. Springer Nature. https://doi.org/10.1038/s41559-020-1132-7 chicago: Tomanek, Isabella, Rok Grah, M. Lagator, A. M. C. Andersson, Jonathan P Bollback, Gašper Tkačik, and Calin C Guet. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Nature Ecology & Evolution. Springer Nature, 2020. https://doi.org/10.1038/s41559-020-1132-7. ieee: I. Tomanek et al., “Gene amplification as a form of population-level gene expression regulation,” Nature Ecology & Evolution, vol. 4, no. 4. Springer Nature, pp. 612–625, 2020. ista: Tomanek I, Grah R, Lagator M, Andersson AMC, Bollback JP, Tkačik G, Guet CC. 2020. Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. 4(4), 612–625. mla: Tomanek, Isabella, et al. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Nature Ecology & Evolution, vol. 4, no. 4, Springer Nature, 2020, pp. 612–25, doi:10.1038/s41559-020-1132-7. short: I. Tomanek, R. Grah, M. Lagator, A.M.C. Andersson, J.P. Bollback, G. Tkačik, C.C. Guet, Nature Ecology & Evolution 4 (2020) 612–625. date_created: 2020-04-08T15:20:53Z date_published: 2020-04-01T00:00:00Z date_updated: 2024-03-27T23:30:36Z day: '01' ddc: - '570' department: - _id: GaTk - _id: CaGu doi: 10.1038/s41559-020-1132-7 external_id: isi: - '000519008300005' file: - access_level: open_access checksum: ef3bbf42023e30b2c24a6278025d2040 content_type: application/pdf creator: dernst date_created: 2020-10-09T09:56:01Z date_updated: 2020-10-09T09:56:01Z file_id: '8640' file_name: 2020_NatureEcolEvo_Tomanek.pdf file_size: 745242 relation: main_file success: 1 file_date_updated: 2020-10-09T09:56:01Z has_accepted_license: '1' intvolume: ' 4' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 612-625 project: - _id: 267C84F4-B435-11E9-9278-68D0E5697425 name: Biophysically realistic genotype-phenotype maps for regulatory networks publication: Nature Ecology & Evolution publication_identifier: issn: - 2397-334X publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/how-to-thrive-without-gene-regulation/ record: - id: '8155' relation: dissertation_contains status: public - id: '7383' relation: research_data status: public - id: '7016' relation: research_data status: public - id: '8653' relation: used_in_publication status: public scopus_import: '1' status: public title: Gene amplification as a form of population-level gene expression regulation type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 4 year: '2020' ... --- _id: '7258' abstract: - lang: eng text: Many flows encountered in nature and applications are characterized by a chaotic motion known as turbulence. Turbulent flows generate intense friction with pipe walls and are responsible for considerable amounts of energy losses at world scale. The nature of turbulent friction and techniques aimed at reducing it have been subject of extensive research over the last century, but no definite answer has been found yet. In this thesis we show that in pipes at moderate turbulent Reynolds numbers friction is better described by the power law first introduced by Blasius and not by the Prandtl–von Kármán formula. At higher Reynolds numbers, large scale motions gradually become more important in the flow and can be related to the change in scaling of friction. Next, we present a series of new techniques that can relaminarize turbulence by suppressing a key mechanism that regenerates it at walls, the lift–up effect. In addition, we investigate the process of turbulence decay in several experiments and discuss the drag reduction potential. Finally, we examine the behavior of friction under pulsating conditions inspired by the human heart cycle and we show that under such circumstances turbulent friction can be reduced to produce energy savings. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Davide full_name: Scarselli, Davide id: 40315C30-F248-11E8-B48F-1D18A9856A87 last_name: Scarselli orcid: 0000-0001-5227-4271 citation: ama: Scarselli D. New approaches to reduce friction in turbulent pipe flow. 2020. doi:10.15479/AT:ISTA:7258 apa: Scarselli, D. (2020). New approaches to reduce friction in turbulent pipe flow. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7258 chicago: Scarselli, Davide. “New Approaches to Reduce Friction in Turbulent Pipe Flow.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7258. ieee: D. Scarselli, “New approaches to reduce friction in turbulent pipe flow,” Institute of Science and Technology Austria, 2020. ista: Scarselli D. 2020. New approaches to reduce friction in turbulent pipe flow. Institute of Science and Technology Austria. mla: Scarselli, Davide. New Approaches to Reduce Friction in Turbulent Pipe Flow. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7258. short: D. Scarselli, New Approaches to Reduce Friction in Turbulent Pipe Flow, Institute of Science and Technology Austria, 2020. date_created: 2020-01-12T16:07:26Z date_published: 2020-01-13T00:00:00Z date_updated: 2023-09-15T12:20:08Z day: '13' ddc: - '532' degree_awarded: PhD department: - _id: BjHo doi: 10.15479/AT:ISTA:7258 ec_funded: 1 file: - access_level: closed checksum: 4df1ab24e9896635106adde5a54615bf content_type: application/zip creator: dscarsel date_created: 2020-01-12T15:57:14Z date_updated: 2021-01-13T23:30:05Z embargo_to: open_access file_id: '7259' file_name: 2020_Scarselli_Thesis.zip file_size: 26640830 relation: source_file - access_level: open_access checksum: 48659ab98e3414293c7a721385c2fd1c content_type: application/pdf creator: dscarsel date_created: 2020-01-12T15:56:14Z date_updated: 2021-01-13T23:30:05Z embargo: 2021-01-12 file_id: '7260' file_name: 2020_Scarselli_Thesis.pdf file_size: 8515844 relation: main_file file_date_updated: 2021-01-13T23:30:05Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: None page: '174' project: - _id: 25152F3A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '306589' name: Decoding the complexity of turbulence at its origin - _id: 25104D44-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '737549' name: Eliminating turbulence in oil pipelines - _id: 25136C54-B435-11E9-9278-68D0E5697425 grant_number: HO 4393/1-2 name: Experimental studies of the turbulence transition and transport processes in turbulent Taylor-Couette currents publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6228' relation: part_of_dissertation status: public - id: '6486' relation: part_of_dissertation status: public - id: '461' relation: part_of_dissertation status: public - id: '422' relation: part_of_dissertation status: public status: public supervisor: - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 title: New approaches to reduce friction in turbulent pipe flow type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '8653' abstract: - lang: eng text: "Mutations are the raw material of evolution and come in many different flavors. Point mutations change a single letter in the DNA sequence, while copy number mutations like duplications or deletions add or remove many letters of the DNA sequence simultaneously. Each type of mutation exhibits specific properties like its rate of formation and reversal. \r\nGene expression is a fundamental phenotype that can be altered by both, point and copy number mutations. The following thesis is concerned with the dynamics of gene expression evolution and how it is affected by the properties exhibited by point and copy number mutations. Specifically, we are considering i) copy number mutations during adaptation to fluctuating environments and ii) the interaction of copy number and point mutations during adaptation to constant environments.  " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Isabella full_name: Tomanek, Isabella id: 3981F020-F248-11E8-B48F-1D18A9856A87 last_name: Tomanek orcid: 0000-0001-6197-363X citation: ama: Tomanek I. The evolution of gene expression by copy number and point mutations. 2020. doi:10.15479/AT:ISTA:8653 apa: Tomanek, I. (2020). The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8653 chicago: Tomanek, Isabella. “The Evolution of Gene Expression by Copy Number and Point Mutations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8653. ieee: I. Tomanek, “The evolution of gene expression by copy number and point mutations,” Institute of Science and Technology Austria, 2020. ista: Tomanek I. 2020. The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria. mla: Tomanek, Isabella. The Evolution of Gene Expression by Copy Number and Point Mutations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8653. short: I. Tomanek, The Evolution of Gene Expression by Copy Number and Point Mutations, Institute of Science and Technology Austria, 2020. date_created: 2020-10-13T13:02:33Z date_published: 2020-10-13T00:00:00Z date_updated: 2023-09-07T13:22:42Z day: '13' ddc: - '576' degree_awarded: PhD department: - _id: CaGu doi: 10.15479/AT:ISTA:8653 file: - access_level: closed checksum: c01d9f59794b4b70528f37637c17ad02 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: itomanek date_created: 2020-10-16T12:14:21Z date_updated: 2021-10-20T22:30:03Z embargo_to: open_access file_id: '8666' file_name: Thesis_ITomanek_final_201016.docx file_size: 25131884 relation: source_file - access_level: open_access checksum: f8edbc3b0f81a780e13ca1e561d42d8b content_type: application/pdf creator: itomanek date_created: 2020-10-16T12:14:21Z date_updated: 2021-10-20T22:30:03Z embargo: 2021-10-19 file_id: '8667' file_name: Thesis_ITomanek_final_201016.pdf file_size: 15405675 relation: main_file file_date_updated: 2021-10-20T22:30:03Z has_accepted_license: '1' keyword: - duplication - amplification - promoter - CNV - AMGET - experimental evolution - Escherichia coli language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '117' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7652' relation: research_data status: public status: public supervisor: - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 title: The evolution of gene expression by copy number and point mutations type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '7427' abstract: - lang: eng text: Plants, like other multicellular organisms, survive through a delicate balance between growth and defense against pathogens. Salicylic acid (SA) is a major defense signal in plants, and the perception mechanism as well as downstream signaling activating the immune response are known. Here, we identify a parallel SA signaling that mediates growth attenuation. SA directly binds to A subunits of protein phosphatase 2A (PP2A), inhibiting activity of this complex. Among PP2A targets, the PIN2 auxin transporter is hyperphosphorylated in response to SA, leading to changed activity of this important growth regulator. Accordingly, auxin transport and auxin-mediated root development, including growth, gravitropic response, and lateral root organogenesis, are inhibited. This study reveals how SA, besides activating immunity, concomitantly attenuates growth through crosstalk with the auxin distribution network. Further analysis of this dual role of SA and characterization of additional SA-regulated PP2A targets will provide further insights into mechanisms maintaining a balance between growth and defense. acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: "We thank Shigeyuki Betsuyaku (University of Tsukuba), Alison Delong (Brown University), Xinnian Dong (Duke University), Dolf Weijers (Wageningen University), Yuelin Zhang (UBC), and Martine Pastuglia (Institut Jean-Pierre Bourgin) for sharing published materials; Jana Riederer for help with cantharidin physiological analysis; David Domjan for help with cloning pET28a-PIN2HL; Qing Lu for help with DARTS; Hana Kozubı´kova´ for technical support on SA derivative synthesis; Zuzana Vondra´ kova´ for technical support with tobacco cells; Lucia Strader (Washington University), Bert De Rybel (Ghent University), Bartel Vanholme (Ghent University), and Lukas Mach (BOKU) for helpful discussions; and bioimaging and life science facilities of IST Austria for continuous support. We gratefully acknowledge the Nottingham Arabidopsis Stock Center (NASC) for providing T-DNA insertional mutants. The DSC and SPR instruments were provided by the EQ-BOKU VIBT GmbH and the BOKU Core Facility for Biomolecular and Cellular Analysis, with help of Irene Schaffner. The research leading to these results has received funding from the European Union’s Horizon 2020 program (ERC grant agreement no. 742985 to J.F.) and the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734. S.T. was supported by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). O.N. was supported by the Ministry of Education, Youth and Sports of the Czech Republic (European Regional Development Fund-Project ‘‘Centre for Experimental Plant Biology’’ no. CZ.02.1.01/0.0/0.0/16_019/0000738). J. Pospısil was supported by European Regional Development Fund Project ‘‘Centre for Experimental Plant Biology’’\r\n(no. CZ.02.1.01/0.0/0.0/16_019/0000738). J. Petrasek was supported by EU Operational Programme Prague-Competitiveness (no. CZ.2.16/3.1.00/21519). " article_processing_charge: No article_type: original author: - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Melinda F full_name: Abas, Melinda F id: 3CFB3B1C-F248-11E8-B48F-1D18A9856A87 last_name: Abas - first_name: Inge full_name: Verstraeten, Inge id: 362BF7FE-F248-11E8-B48F-1D18A9856A87 last_name: Verstraeten orcid: 0000-0001-7241-2328 - first_name: Matous full_name: Glanc, Matous id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2 last_name: Glanc orcid: 0000-0003-0619-7783 - first_name: Gergely full_name: Molnar, Gergely id: 34F1AF46-F248-11E8-B48F-1D18A9856A87 last_name: Molnar - first_name: Jakub full_name: Hajny, Jakub id: 4800CC20-F248-11E8-B48F-1D18A9856A87 last_name: Hajny orcid: 0000-0003-2140-7195 - first_name: Pavel full_name: Lasák, Pavel last_name: Lasák - first_name: Ivan full_name: Petřík, Ivan last_name: Petřík - first_name: Eugenia full_name: Russinova, Eugenia last_name: Russinova - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Ondřej full_name: Novák, Ondřej last_name: Novák - first_name: Jiří full_name: Pospíšil, Jiří last_name: Pospíšil - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Tan S, Abas MF, Verstraeten I, et al. Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. Current Biology. 2020;30(3):381-395.e8. doi:10.1016/j.cub.2019.11.058 apa: Tan, S., Abas, M. F., Verstraeten, I., Glanc, M., Molnar, G., Hajny, J., … Friml, J. (2020). Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2019.11.058 chicago: Tan, Shutang, Melinda F Abas, Inge Verstraeten, Matous Glanc, Gergely Molnar, Jakub Hajny, Pavel Lasák, et al. “Salicylic Acid Targets Protein Phosphatase 2A to Attenuate Growth in Plants.” Current Biology. Cell Press, 2020. https://doi.org/10.1016/j.cub.2019.11.058. ieee: S. Tan et al., “Salicylic acid targets protein phosphatase 2A to attenuate growth in plants,” Current Biology, vol. 30, no. 3. Cell Press, p. 381–395.e8, 2020. ista: Tan S, Abas MF, Verstraeten I, Glanc M, Molnar G, Hajny J, Lasák P, Petřík I, Russinova E, Petrášek J, Novák O, Pospíšil J, Friml J. 2020. Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. Current Biology. 30(3), 381–395.e8. mla: Tan, Shutang, et al. “Salicylic Acid Targets Protein Phosphatase 2A to Attenuate Growth in Plants.” Current Biology, vol. 30, no. 3, Cell Press, 2020, p. 381–395.e8, doi:10.1016/j.cub.2019.11.058. short: S. Tan, M.F. Abas, I. Verstraeten, M. Glanc, G. Molnar, J. Hajny, P. Lasák, I. Petřík, E. Russinova, J. Petrášek, O. Novák, J. Pospíšil, J. Friml, Current Biology 30 (2020) 381–395.e8. date_created: 2020-02-02T23:01:00Z date_published: 2020-02-03T00:00:00Z date_updated: 2024-03-27T23:30:37Z day: '03' ddc: - '580' department: - _id: JiFr - _id: EvBe doi: 10.1016/j.cub.2019.11.058 ec_funded: 1 external_id: isi: - '000511287900018' pmid: - '31956021' file: - access_level: open_access checksum: 16f7d51fe28f91c21e4896a2028df40b content_type: application/pdf creator: dernst date_created: 2020-09-22T09:51:28Z date_updated: 2020-09-22T09:51:28Z file_id: '8555' file_name: 2020_CurrentBiology_Tan.pdf file_size: 5360135 relation: main_file success: 1 file_date_updated: 2020-09-22T09:51:28Z has_accepted_license: '1' intvolume: ' 30' isi: 1 issue: '3' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 381-395.e8 pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 256FEF10-B435-11E9-9278-68D0E5697425 grant_number: 723-2015 name: Long Term Fellowship publication: Current Biology publication_identifier: issn: - '09609822' publication_status: published publisher: Cell Press quality_controlled: '1' related_material: record: - id: '8822' relation: dissertation_contains status: public scopus_import: '1' status: public title: Salicylic acid targets protein phosphatase 2A to attenuate growth in plants 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 30 year: '2020' ... --- _id: '7500' abstract: - lang: eng text: "Plant survival depends on vascular tissues, which originate in a self‐organizing manner as strands of cells co‐directionally transporting the plant hormone auxin. The latter phenomenon (also known as auxin canalization) is classically hypothesized to be regulated by auxin itself via the effect of this hormone on the polarity of its own intercellular transport. Correlative observations supported this concept, but molecular insights remain limited.\r\nIn the current study, we established an experimental system based on the model Arabidopsis thaliana, which exhibits auxin transport channels and formation of vasculature strands in response to local auxin application.\r\nOur methodology permits the genetic analysis of auxin canalization under controllable experimental conditions. By utilizing this opportunity, we confirmed the dependence of auxin canalization on a PIN‐dependent auxin transport and nuclear, TIR1/AFB‐mediated auxin signaling. We also show that leaf venation and auxin‐mediated PIN repolarization in the root require TIR1/AFB signaling.\r\nFurther studies based on this experimental system are likely to yield better understanding of the mechanisms underlying auxin transport polarization in other developmental contexts." acknowledgement: We thank Mark Estelle, José M. Alonso and the Arabidopsis Stock Centre for providing seeds. We acknowledge the core facility CELLIM of CEITEC supported by the MEYS CR (LM2015062 Czech‐BioImaging) and Plant Sciences Core Facility of CEITEC Masaryk University for help in generating essential data. This project received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement no. 742985) and the Czech Science Foundation GAČR (GA13‐40637S and GA18‐26981S) to JF. JH is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology. The authors declare no competing interests. article_processing_charge: No article_type: original author: - first_name: E full_name: Mazur, E last_name: Mazur - first_name: Ivan full_name: Kulik, Ivan id: F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB last_name: Kulik - first_name: Jakub full_name: Hajny, Jakub id: 4800CC20-F248-11E8-B48F-1D18A9856A87 last_name: Hajny orcid: 0000-0003-2140-7195 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Mazur E, Kulik I, Hajny J, Friml J. Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. New Phytologist. 2020;226(5):1375-1383. doi:10.1111/nph.16446 apa: Mazur, E., Kulik, I., Hajny, J., & Friml, J. (2020). Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. New Phytologist. Wiley. https://doi.org/10.1111/nph.16446 chicago: Mazur, E, Ivan Kulik, Jakub Hajny, and Jiří Friml. “Auxin Canalization and Vascular Tissue Formation by TIR1/AFB-Mediated Auxin Signaling in Arabidopsis.” New Phytologist. Wiley, 2020. https://doi.org/10.1111/nph.16446. ieee: E. Mazur, I. Kulik, J. Hajny, and J. Friml, “Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis,” New Phytologist, vol. 226, no. 5. Wiley, pp. 1375–1383, 2020. ista: Mazur E, Kulik I, Hajny J, Friml J. 2020. Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. New Phytologist. 226(5), 1375–1383. mla: Mazur, E., et al. “Auxin Canalization and Vascular Tissue Formation by TIR1/AFB-Mediated Auxin Signaling in Arabidopsis.” New Phytologist, vol. 226, no. 5, Wiley, 2020, pp. 1375–83, doi:10.1111/nph.16446. short: E. Mazur, I. Kulik, J. Hajny, J. Friml, New Phytologist 226 (2020) 1375–1383. date_created: 2020-02-18T10:03:47Z date_published: 2020-06-01T00:00:00Z date_updated: 2024-03-27T23:30:37Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1111/nph.16446 ec_funded: 1 external_id: isi: - '000514939700001' pmid: - '31971254' file: - access_level: open_access checksum: 17de728b0205979feb95ce663ba918c2 content_type: application/pdf creator: dernst date_created: 2020-11-20T09:32:10Z date_updated: 2020-11-20T09:32:10Z file_id: '8781' file_name: 2020_NewPhytologist_Mazur.pdf file_size: 2106888 relation: main_file success: 1 file_date_updated: 2020-11-20T09:32:10Z has_accepted_license: '1' intvolume: ' 226' isi: 1 issue: '5' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 1375-1383 pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 2699E3D2-B435-11E9-9278-68D0E5697425 grant_number: '25239' name: Cell surface receptor complexes for PIN polarity and auxin-mediated development publication: New Phytologist publication_identifier: eissn: - 1469-8137 issn: - 0028-646x publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '8822' relation: dissertation_contains status: public status: public title: Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 226 year: '2020' ... --- _id: '8822' abstract: - lang: eng text: "Self-organization is a hallmark of plant development manifested e.g. by intricate leaf vein patterns, flexible formation of vasculature during organogenesis or its regeneration following wounding. Spontaneously arising channels transporting the phytohormone auxin, created by coordinated polar localizations of PIN-FORMED 1 (PIN1) auxin exporter, provide positional cues for these as well as other plant patterning processes. To find regulators acting downstream of auxin and the TIR1/AFB auxin signaling pathway essential for PIN1 coordinated polarization during auxin canalization, we performed microarray experiments. Besides the known components of general PIN polarity maintenance, such as PID and PIP5K kinases, we identified and characterized a new regulator of auxin canalization, the transcription factor WRKY DNA-BINDING PROTEIN 23 (WRKY23).\r\nNext, we designed a subsequent microarray experiment to further uncover other molecular players, downstream of auxin-TIR1/AFB-WRKY23 involved in the regulation of auxin-mediated PIN repolarization. We identified a novel and crucial part of the molecular machinery underlying auxin canalization. The auxin-regulated malectin-type receptor-like kinase CAMEL and the associated leucine-rich repeat receptor-like kinase CANAR target and directly phosphorylate PIN auxin transporters. camel and canar mutants are impaired in PIN1 subcellular trafficking and auxin-mediated repolarization leading to defects in auxin transport, ultimately to leaf venation and vasculature regeneration defects. Our results describe the CAMEL-CANAR receptor complex, which is required for auxin feed-back on its own transport and thus for coordinated tissue polarization during auxin canalization." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Jakub full_name: Hajny, Jakub id: 4800CC20-F248-11E8-B48F-1D18A9856A87 last_name: Hajny orcid: 0000-0003-2140-7195 citation: ama: Hajny J. Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. 2020. doi:10.15479/AT:ISTA:8822 apa: Hajny, J. (2020). Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8822 chicago: Hajny, Jakub. “Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8822. ieee: J. Hajny, “Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration,” Institute of Science and Technology Austria, 2020. ista: Hajny J. 2020. Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. Institute of Science and Technology Austria. mla: Hajny, Jakub. Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8822. short: J. Hajny, Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration, Institute of Science and Technology Austria, 2020. date_created: 2020-12-01T12:38:18Z date_published: 2020-12-01T00:00:00Z date_updated: 2023-09-19T10:39:33Z day: '01' ddc: - '580' degree_awarded: PhD department: - _id: JiFr doi: 10.15479/AT:ISTA:8822 file: - access_level: closed checksum: 210a9675af5e4c78b0b56d920ac82866 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: jhajny date_created: 2020-12-04T07:27:52Z date_updated: 2021-07-16T22:30:03Z embargo_to: open_access file_id: '8919' file_name: Jakub Hajný IST Austria final_JH.docx file_size: 91279806 relation: source_file - access_level: open_access checksum: 1781385b4aa73eba89cc76c6172f71d2 content_type: application/pdf creator: jhajny date_created: 2020-12-09T15:04:41Z date_updated: 2021-12-08T23:30:03Z embargo: 2021-12-07 file_id: '8933' file_name: Jakub Hajný IST Austria final_JH-merged without Science.pdf file_size: 68707697 relation: main_file file_date_updated: 2021-12-08T23:30:03Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '249' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7427' relation: part_of_dissertation status: public - id: '6260' relation: part_of_dissertation status: public - id: '7500' relation: part_of_dissertation status: public - id: '191' relation: part_of_dissertation status: public - id: '449' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 title: Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '8350' abstract: - lang: eng text: "Cytoplasm is a gel-like crowded environment composed of tens of thousands of macromolecules, organelles, cytoskeletal networks and cytosol. The structure of the cytoplasm is thought to be highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules is very restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the jammed nature of the cytoplasm at the microscopic scale, large-scale reorganization of cytoplasm is essential for important cellular functions, such as nuclear positioning and cell division. How such mesoscale reorganization of the cytoplasm is achieved, especially for very large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, has only begun to be understood.\r\nIn this thesis, I focus on the recent advances in elucidating the molecular, cellular and biophysical principles underlying cytoplasmic organization across different scales, structures and species. First, I outline which of these principles have been identified by reductionist approaches, such as in vitro reconstitution assays, where boundary conditions and components can be modulated at ease. I then describe how the theoretical and experimental framework established in these reduced systems have been applied to their more complex in vivo counterparts, in particular oocytes and embryonic syncytial structures, and discuss how such complex biological systems can initiate symmetry breaking and establish patterning.\r\nSpecifically, I examine an example of large-scale reorganizations taking place in zebrafish embryos, where extensive cytoplasmic streaming leads to the segregation of cytoplasm from yolk granules along the animal-vegetal axis of the embryo. Using biophysical experimentation and theory, I investigate the forces underlying this process, to show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the embryo. This wave functions in segregation by both pulling cytoplasm animally and pushing yolk granules vegetally. Cytoplasm pulling is mediated by bulk actin network flows exerting friction forces on the cytoplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. This study defines a novel role of bulk actin polymerization waves in embryo polarization via cytoplasmic segregation. Lastly, I describe the cytoplasmic reorganizations taking place during zebrafish oocyte maturation, where the initial segregation of the cytoplasm and yolk granules occurs. Here, I demonstrate a previously uncharacterized wave of microtubule aster formation, traveling the oocyte along the animal-vegetal axis. Further research is required to determine the role of such microtubule structures in cytoplasmic reorganizations therein.\r\nCollectively, these studies provide further evidence for the coupling between cell cytoskeleton and cell cycle machinery, which can underlie a core self-organizing mechanism for orchestrating large-scale reorganizations in a cell-cycle-tunable manner, where the modulations of the force-generating machinery and cytoplasmic mechanics can be harbored to fulfill cellular functions." acknowledged_ssus: - _id: PreCl - _id: Bio - _id: EM-Fac acknowledgement: "I would have had no fish and hence no results without our wonderful fish facility crew, Verena Mayer, Eva Schlegl, Andreas Mlak and Matthias Nowak. Special thanks to Verena for being always happy to help and dealing with our chaotic schedules in the lab. Danke auch, Verena, für deine Geduld, mit mir auf Deutsch zu sprechen. Das hat mir sehr geholfen.\r\nSpecial thanks to the Bioimaging and EM facilities at IST Austria for supporting us every day. Very special thanks would go to Robert Hauschild for his continuous support on data analysis and also to Jack Merrin for designing and building microfabricated chambers for the project and for the various discussions on making zebrafish extracts." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Shayan full_name: Shamipour, Shayan id: 40B34FE2-F248-11E8-B48F-1D18A9856A87 last_name: Shamipour citation: ama: Shamipour S. Bulk actin dynamics drive phase segregation in zebrafish oocytes . 2020. doi:10.15479/AT:ISTA:8350 apa: Shamipour, S. (2020). Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8350 chicago: Shamipour, Shayan. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes .” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8350. ieee: S. Shamipour, “Bulk actin dynamics drive phase segregation in zebrafish oocytes ,” Institute of Science and Technology Austria, 2020. ista: Shamipour S. 2020. Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria. mla: Shamipour, Shayan. Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes . Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8350. short: S. Shamipour, Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes , Institute of Science and Technology Austria, 2020. date_created: 2020-09-09T11:12:10Z date_published: 2020-09-09T00:00:00Z date_updated: 2023-09-27T14:16:45Z day: '09' ddc: - '570' degree_awarded: PhD department: - _id: BjHo - _id: CaHe doi: 10.15479/AT:ISTA:8350 file: - access_level: closed checksum: 6e47871c74f85008b9876112eb3fcfa1 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: sshamip date_created: 2020-09-09T11:06:27Z date_updated: 2021-09-11T22:30:05Z embargo_to: open_access file_id: '8351' file_name: Shayan-Thesis-Final.docx file_size: 65194814 relation: source_file - access_level: open_access checksum: 1b44c57f04d7e8a6fe41b1c9c55a52a3 content_type: application/pdf creator: sshamip date_created: 2020-09-09T11:06:13Z date_updated: 2021-09-11T22:30:05Z embargo: 2021-09-10 file_id: '8352' file_name: Shayan-Thesis-Final.pdf file_size: 23729605 relation: main_file file_date_updated: 2021-09-11T22:30:05Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: None page: '107' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '661' relation: part_of_dissertation status: public - id: '6508' relation: part_of_dissertation status: public - id: '7001' relation: part_of_dissertation status: public - id: '735' relation: part_of_dissertation status: public status: public supervisor: - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 title: 'Bulk actin dynamics drive phase segregation in zebrafish oocytes ' type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '8569' abstract: - lang: eng text: Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final target lamina, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating the specific sequential steps of radial neuronal migration in vivo are however still unclear, let alone the effects and interactions with the extracellular environment. In any in vivo context, cells will always be exposed to a complex extracellular environment consisting of (1) secreted factors acting as potential signaling cues, (2) the extracellular matrix, and (3) other cells providing cell–cell interaction through receptors and/or direct physical stimuli. Most studies so far have described and focused mainly on intrinsic cell-autonomous gene functions in neuronal migration but there is accumulating evidence that non-cell-autonomous-, local-, systemic-, and/or whole tissue-wide effects substantially contribute to the regulation of radial neuronal migration. These non-cell-autonomous effects may differentially affect cortical neuron migration in distinct cellular environments. However, the cellular and molecular natures of such non-cell-autonomous mechanisms are mostly unknown. Furthermore, physical forces due to collective migration and/or community effects (i.e., interactions with surrounding cells) may play important roles in neocortical projection neuron migration. In this concise review, we first outline distinct models of non-cell-autonomous interactions of cortical projection neurons along their radial migration trajectory during development. We then summarize experimental assays and platforms that can be utilized to visualize and potentially probe non-cell-autonomous mechanisms. Lastly, we define key questions to address in the future. acknowledgement: AH was a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences. This work also received support from IST Austria institutional funds; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) under REA Grant Agreement No. 618444 to SH. article_number: '574382' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Andi H full_name: Hansen, Andi H id: 38853E16-F248-11E8-B48F-1D18A9856A87 last_name: Hansen - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Hansen AH, Hippenmeyer S. Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex. Frontiers in Cell and Developmental Biology. 2020;8(9). doi:10.3389/fcell.2020.574382 apa: Hansen, A. H., & Hippenmeyer, S. (2020). Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex. Frontiers in Cell and Developmental Biology. Frontiers. https://doi.org/10.3389/fcell.2020.574382 chicago: Hansen, Andi H, and Simon Hippenmeyer. “Non-Cell-Autonomous Mechanisms in Radial Projection Neuron Migration in the Developing Cerebral Cortex.” Frontiers in Cell and Developmental Biology. Frontiers, 2020. https://doi.org/10.3389/fcell.2020.574382. ieee: A. H. Hansen and S. Hippenmeyer, “Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex,” Frontiers in Cell and Developmental Biology, vol. 8, no. 9. Frontiers, 2020. ista: Hansen AH, Hippenmeyer S. 2020. Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex. Frontiers in Cell and Developmental Biology. 8(9), 574382. mla: Hansen, Andi H., and Simon Hippenmeyer. “Non-Cell-Autonomous Mechanisms in Radial Projection Neuron Migration in the Developing Cerebral Cortex.” Frontiers in Cell and Developmental Biology, vol. 8, no. 9, 574382, Frontiers, 2020, doi:10.3389/fcell.2020.574382. short: A.H. Hansen, S. Hippenmeyer, Frontiers in Cell and Developmental Biology 8 (2020). date_created: 2020-09-26T06:11:07Z date_published: 2020-09-25T00:00:00Z date_updated: 2024-03-27T23:30:40Z day: '25' ddc: - '570' department: - _id: SiHi doi: 10.3389/fcell.2020.574382 ec_funded: 1 external_id: isi: - '000577915900001' pmid: - '33102480' file: - access_level: open_access checksum: 01f731824194c94c81a5da360d997073 content_type: application/pdf creator: dernst date_created: 2020-09-28T13:11:17Z date_updated: 2020-09-28T13:11:17Z file_id: '8584' file_name: 2020_Frontiers_Hansen.pdf file_size: 5527139 relation: main_file success: 1 file_date_updated: 2020-09-28T13:11:17Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 2625A13E-B435-11E9-9278-68D0E5697425 grant_number: '24812' name: Molecular Mechanisms of Radial Neuronal Migration - _id: 25D61E48-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618444' name: Molecular Mechanisms of Cerebral Cortex Development publication: Frontiers in Cell and Developmental Biology publication_identifier: issn: - 2296-634X publication_status: published publisher: Frontiers quality_controlled: '1' related_material: record: - id: '9962' relation: dissertation_contains status: public scopus_import: '1' status: public title: Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 8 year: '2020' ... --- _id: '7815' abstract: - lang: eng text: Beginning from a limited pool of progenitors, the mammalian cerebral cortex forms highly organized functional neural circuits. However, the underlying cellular and molecular mechanisms regulating lineage transitions of neural stem cells (NSCs) and eventual production of neurons and glia in the developing neuroepithelium remains unclear. Methods to trace NSC division patterns and map the lineage of clonally related cells have advanced dramatically. However, many contemporary lineage tracing techniques suffer from the lack of cellular resolution of progeny cell fate, which is essential for deciphering progenitor cell division patterns. Presented is a protocol using mosaic analysis with double markers (MADM) to perform in vivo clonal analysis. MADM concomitantly manipulates individual progenitor cells and visualizes precise division patterns and lineage progression at unprecedented single cell resolution. MADM-based interchromosomal recombination events during the G2-X phase of mitosis, together with temporally inducible CreERT2, provide exact information on the birth dates of clones and their division patterns. Thus, MADM lineage tracing provides unprecedented qualitative and quantitative optical readouts of the proliferation mode of stem cell progenitors at the single cell level. MADM also allows for examination of the mechanisms and functional requirements of candidate genes in NSC lineage progression. This method is unique in that comparative analysis of control and mutant subclones can be performed in the same tissue environment in vivo. Here, the protocol is described in detail, and experimental paradigms to employ MADM for clonal analysis and lineage tracing in the developing cerebral cortex are demonstrated. Importantly, this protocol can be adapted to perform MADM clonal analysis in any murine stem cell niche, as long as the CreERT2 driver is present. acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: PreCl article_number: e61147 article_processing_charge: No article_type: original author: - first_name: Robert J full_name: Beattie, Robert J id: 2E26DF60-F248-11E8-B48F-1D18A9856A87 last_name: Beattie orcid: 0000-0002-8483-8753 - first_name: Carmen full_name: Streicher, Carmen id: 36BCB99C-F248-11E8-B48F-1D18A9856A87 last_name: Streicher - 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: Ximena full_name: Contreras, Ximena id: 475990FE-F248-11E8-B48F-1D18A9856A87 last_name: Contreras - first_name: Andi H full_name: Hansen, Andi H id: 38853E16-F248-11E8-B48F-1D18A9856A87 last_name: Hansen - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Beattie RJ, Streicher C, Amberg N, et al. Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). Journal of Visual Experiments. 2020;(159). doi:10.3791/61147 apa: Beattie, R. J., Streicher, C., Amberg, N., Cheung, G. T., Contreras, X., Hansen, A. H., & Hippenmeyer, S. (2020). Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). Journal of Visual Experiments. MyJove Corporation. https://doi.org/10.3791/61147 chicago: Beattie, Robert J, Carmen Streicher, Nicole Amberg, Giselle T Cheung, Ximena Contreras, Andi H Hansen, and Simon Hippenmeyer. “Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).” Journal of Visual Experiments. MyJove Corporation, 2020. https://doi.org/10.3791/61147. ieee: R. J. Beattie et al., “Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM),” Journal of Visual Experiments, no. 159. MyJove Corporation, 2020. ista: Beattie RJ, Streicher C, Amberg N, Cheung GT, Contreras X, Hansen AH, Hippenmeyer S. 2020. Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). Journal of Visual Experiments. (159), e61147. mla: Beattie, Robert J., et al. “Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).” Journal of Visual Experiments, no. 159, e61147, MyJove Corporation, 2020, doi:10.3791/61147. short: R.J. Beattie, C. Streicher, N. Amberg, G.T. Cheung, X. Contreras, A.H. Hansen, S. Hippenmeyer, Journal of Visual Experiments (2020). date_created: 2020-05-11T08:31:20Z date_published: 2020-05-08T00:00:00Z date_updated: 2024-03-27T23:30:41Z day: '08' ddc: - '570' department: - _id: SiHi doi: 10.3791/61147 ec_funded: 1 external_id: isi: - '000546406600043' file: - access_level: open_access checksum: 3154ea7f90b9fb45e084cd1c2770597d content_type: application/pdf creator: rbeattie date_created: 2020-05-11T08:28:38Z date_updated: 2020-07-14T12:48:03Z file_id: '7816' file_name: jove-protocol-61147-lineage-tracing-clonal-analysis-developing-cerebral-cortex-using.pdf file_size: 1352186 relation: main_file file_date_updated: 2020-07-14T12:48:03Z has_accepted_license: '1' isi: 1 issue: '159' language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 264E56E2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02416 name: Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex - _id: 268F8446-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: T0101031 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: 2625A13E-B435-11E9-9278-68D0E5697425 grant_number: '24812' name: Molecular Mechanisms of Radial Neuronal Migration - _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: Journal of Visual Experiments publication_identifier: issn: - 1940-087X publication_status: published publisher: MyJove Corporation quality_controlled: '1' related_material: record: - id: '7902' relation: part_of_dissertation status: public scopus_import: '1' status: public title: Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM) 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 year: '2020' ... --- _id: '7902' abstract: - lang: eng text: "Mosaic genetic analysis has been widely used in different model organisms such as the fruit fly to study gene-function in a cell-autonomous or tissue-specific fashion. More recently, and less easily conducted, mosaic genetic analysis in mice has also been enabled with the ambition to shed light on human gene function and disease. These genetic tools are of particular interest, but not restricted to, the study of the brain. Notably, the MADM technology offers a genetic approach in mice to visualize and concomitantly manipulate small subsets of genetically defined cells at a clonal level and single cell resolution. MADM-based analysis has already advanced the study of genetic mechanisms regulating brain development and is expected that further MADM-based analysis of genetic alterations will continue to reveal important insights on the fundamental principles of development and disease to potentially assist in the development of new therapies or treatments.\r\nIn summary, this work completed and characterized the necessary genome-wide genetic tools to perform MADM-based analysis at single cell level of the vast majority of mouse genes in virtually any cell type and provided a protocol to perform lineage tracing using the novel MADM resource. Importantly, this work also explored and revealed novel aspects of biologically relevant events in an in vivo context, such as the chromosome-specific bias of chromatid sister segregation pattern, the generation of cell-type diversity in the cerebral cortex and in the cerebellum and finally, the relevance of the interplay between the cell-autonomous gene function and cell-non-autonomous (community) effects in radial glial progenitor lineage progression.\r\nThis work provides a foundation and opens the door to further elucidating the molecular mechanisms underlying neuronal diversity and astrocyte generation." acknowledged_ssus: - _id: PreCl - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Ximena full_name: Contreras, Ximena id: 475990FE-F248-11E8-B48F-1D18A9856A87 last_name: Contreras citation: ama: Contreras X. Genetic dissection of neural development in health and disease at single cell resolution. 2020. doi:10.15479/AT:ISTA:7902 apa: Contreras, X. (2020). Genetic dissection of neural development in health and disease at single cell resolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7902 chicago: Contreras, Ximena. “Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7902. ieee: X. Contreras, “Genetic dissection of neural development in health and disease at single cell resolution,” Institute of Science and Technology Austria, 2020. ista: Contreras X. 2020. Genetic dissection of neural development in health and disease at single cell resolution. Institute of Science and Technology Austria. mla: Contreras, Ximena. Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7902. short: X. Contreras, Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution, Institute of Science and Technology Austria, 2020. date_created: 2020-05-29T08:27:32Z date_published: 2020-06-05T00:00:00Z date_updated: 2023-10-18T08:45:16Z day: '05' ddc: - '570' degree_awarded: PhD department: - _id: SiHi doi: 10.15479/AT:ISTA:7902 ec_funded: 1 file: - access_level: closed checksum: 43c172bf006c95b65992d473c7240d13 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: xcontreras date_created: 2020-06-05T08:18:08Z date_updated: 2021-06-07T22:30:03Z embargo_to: open_access file_id: '7927' file_name: PhDThesis_Contreras.docx file_size: 53134142 relation: source_file - access_level: open_access checksum: addfed9128271be05cae3608e03a6ec0 content_type: application/pdf creator: xcontreras date_created: 2020-06-05T08:18:07Z date_updated: 2021-06-07T22:30:03Z embargo: 2021-06-06 file_id: '7928' file_name: PhDThesis_Contreras.pdf file_size: 35117191 relation: main_file file_date_updated: 2021-06-07T22:30:03Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '214' project: - _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_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6830' relation: dissertation_contains status: public - id: '28' relation: dissertation_contains status: public - id: '7815' relation: dissertation_contains status: public status: public supervisor: - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 title: Genetic dissection of neural development in health and disease at single cell resolution type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8190' article_number: e202007029 article_processing_charge: No article_type: letter_note author: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Anna full_name: Huttenlocher, Anna last_name: Huttenlocher citation: ama: 'Sixt MK, Huttenlocher A. Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. 2020;219(8). doi:10.1083/jcb.202007029' apa: 'Sixt, M. K., & Huttenlocher, A. (2020). Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202007029' chicago: 'Sixt, Michael K, and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” The Journal of Cell Biology. Rockefeller University Press, 2020. https://doi.org/10.1083/jcb.202007029.' ieee: 'M. K. Sixt and A. Huttenlocher, “Zena Werb (1945-2020): Cell biology in context,” The Journal of Cell Biology, vol. 219, no. 8. Rockefeller University Press, 2020.' ista: 'Sixt MK, Huttenlocher A. 2020. Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. 219(8), e202007029.' mla: 'Sixt, Michael K., and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” The Journal of Cell Biology, vol. 219, no. 8, e202007029, Rockefeller University Press, 2020, doi:10.1083/jcb.202007029.' short: M.K. Sixt, A. Huttenlocher, The Journal of Cell Biology 219 (2020). date_created: 2020-08-02T22:00:57Z date_published: 2020-07-22T00:00:00Z date_updated: 2023-10-17T10:04:49Z day: '22' ddc: - '570' department: - _id: MiSi doi: 10.1083/jcb.202007029 external_id: isi: - '000573631000004' file: - access_level: open_access checksum: 30016d778d266b8e17d01094917873b8 content_type: application/pdf creator: dernst date_created: 2020-08-04T13:11:52Z date_updated: 2021-02-02T23:30:03Z embargo: 2021-02-01 file_id: '8200' file_name: 2020_JCB_Sixt.pdf file_size: 830725 relation: main_file file_date_updated: 2021-02-02T23:30:03Z has_accepted_license: '1' intvolume: ' 219' isi: 1 issue: '8' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '07' oa: 1 oa_version: Published Version publication: The Journal of Cell Biology publication_identifier: eissn: - 1540-8140 publication_status: published publisher: Rockefeller University Press scopus_import: '1' status: public title: 'Zena Werb (1945-2020): Cell biology in context' 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: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 219 year: '2020' ... --- _id: '8986' abstract: - lang: eng text: 'Flowering plants display the highest diversity among plant species and have notably shaped terrestrial landscapes. Nonetheless, the evolutionary origin of their unprecedented morphological complexity remains largely an enigma. Here, we show that the coevolution of cis-regulatory and coding regions of PIN-FORMED (PIN) auxin transporters confined their expression to certain cell types and directed their subcellular localization to particular cell sides, which together enabled dynamic auxin gradients across tissues critical to the complex architecture of flowering plants. Extensive intraspecies and interspecies genetic complementation experiments with PINs from green alga up to flowering plant lineages showed that PIN genes underwent three subsequent, critical evolutionary innovations and thus acquired a triple function to regulate the development of three essential components of the flowering plant Arabidopsis: shoot/root, inflorescence, and floral organ. Our work highlights the critical role of functional innovations within the PIN gene family as essential prerequisites for the origin of flowering plants.' acknowledgement: 'We thank C.Löhne (Botanic Gardens, University of Bonn) for providing us with A. trichopoda. We would like to thank T.Han, A.Mally (IST, Austria), and C.Hartinger (University of Oxford) for constructive comment and careful reading. Funding: The research leading to these results has received funding from the European Union’s Horizon 2020 Research and Innovation Programme (ERC grant agreement number 742985), Austrian Science Fund (FWF, grant number I 3630-B25), DOC Fellowship of the Austrian Academy of Sciences, and IST Fellow program. ' article_number: eabc8895 article_processing_charge: No article_type: original author: - first_name: Yuzhou full_name: Zhang, Yuzhou id: 3B6137F2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0003-2627-6956 - first_name: Lesia full_name: Rodriguez Solovey, Lesia id: 3922B506-F248-11E8-B48F-1D18A9856A87 last_name: Rodriguez Solovey orcid: 0000-0002-7244-7237 - first_name: Lanxin full_name: Li, Lanxin id: 367EF8FA-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0002-5607-272X - first_name: Xixi full_name: Zhang, Xixi id: 61A66458-47E9-11EA-85BA-8AEAAF14E49A last_name: Zhang orcid: 0000-0001-7048-4627 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Zhang Y, Rodriguez Solovey L, Li L, Zhang X, Friml J. Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. Science Advances. 2020;6(50). doi:10.1126/sciadv.abc8895 apa: Zhang, Y., Rodriguez Solovey, L., Li, L., Zhang, X., & Friml, J. (2020). Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. Science Advances. AAAS. https://doi.org/10.1126/sciadv.abc8895 chicago: Zhang, Yuzhou, Lesia Rodriguez Solovey, Lanxin Li, Xixi Zhang, and Jiří Friml. “Functional Innovations of PIN Auxin Transporters Mark Crucial Evolutionary Transitions during Rise of Flowering Plants.” Science Advances. AAAS, 2020. https://doi.org/10.1126/sciadv.abc8895. ieee: Y. Zhang, L. Rodriguez Solovey, L. Li, X. Zhang, and J. Friml, “Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants,” Science Advances, vol. 6, no. 50. AAAS, 2020. ista: Zhang Y, Rodriguez Solovey L, Li L, Zhang X, Friml J. 2020. Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. Science Advances. 6(50), eabc8895. mla: Zhang, Yuzhou, et al. “Functional Innovations of PIN Auxin Transporters Mark Crucial Evolutionary Transitions during Rise of Flowering Plants.” Science Advances, vol. 6, no. 50, eabc8895, AAAS, 2020, doi:10.1126/sciadv.abc8895. short: Y. Zhang, L. Rodriguez Solovey, L. Li, X. Zhang, J. Friml, Science Advances 6 (2020). date_created: 2021-01-03T23:01:23Z date_published: 2020-12-11T00:00:00Z date_updated: 2024-03-27T23:30:43Z day: '11' ddc: - '580' department: - _id: JiFr doi: 10.1126/sciadv.abc8895 ec_funded: 1 external_id: isi: - '000599903600014' pmid: - '33310852' file: - access_level: open_access checksum: 5ac2500b191c08ef6dab5327f40ff663 content_type: application/pdf creator: dernst date_created: 2021-01-07T12:44:33Z date_updated: 2021-01-07T12:44:33Z file_id: '8994' file_name: 2020_ScienceAdvances_Zhang.pdf file_size: 10578145 relation: main_file success: 1 file_date_updated: 2021-01-07T12:44:33Z has_accepted_license: '1' intvolume: ' 6' isi: 1 issue: '50' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants - _id: 26B4D67E-B435-11E9-9278-68D0E5697425 grant_number: '25351' name: 'A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root' publication: Science Advances publication_identifier: eissn: - 2375-2548 publication_status: published publisher: AAAS quality_controlled: '1' related_material: record: - id: '10083' relation: dissertation_contains status: public scopus_import: '1' status: public title: Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 6 year: '2020' ... --- _id: '8283' abstract: - lang: eng text: 'Drought and salt stress are the main environmental cues affecting the survival, development, distribution, and yield of crops worldwide. MYB transcription factors play a crucial role in plants’ biological processes, but the function of pineapple MYB genes is still obscure. In this study, one of the pineapple MYB transcription factors, AcoMYB4, was isolated and characterized. The results showed that AcoMYB4 is localized in the cell nucleus, and its expression is induced by low temperature, drought, salt stress, and hormonal stimulation, especially by abscisic acid (ABA). Overexpression of AcoMYB4 in rice and Arabidopsis enhanced plant sensitivity to osmotic stress; it led to an increase in the number stomata on leaf surfaces and lower germination rate under salt and drought stress. Furthermore, in AcoMYB4 OE lines, the membrane oxidation index, free proline, and soluble sugar contents were decreased. In contrast, electrolyte leakage and malondialdehyde (MDA) content increased significantly due to membrane injury, indicating higher sensitivity to drought and salinity stresses. Besides the above, both the expression level and activities of several antioxidant enzymes were decreased, indicating lower antioxidant activity in AcoMYB4 transgenic plants. Moreover, under osmotic stress, overexpression of AcoMYB4 inhibited ABA biosynthesis through a decrease in the transcription of genes responsible for ABA synthesis (ABA1 and ABA2) and ABA signal transduction factor ABI5. These results suggest that AcoMYB4 negatively regulates osmotic stress by attenuating cellular ABA biosynthesis and signal transduction pathways. ' acknowledgement: 'We would like to thank the reviewers for their helpful comments on the original manuscript. ' article_number: '5272' article_processing_charge: No article_type: original author: - first_name: Huihuang full_name: Chen, Huihuang last_name: Chen - first_name: Linyi full_name: Lai, Linyi last_name: Lai - first_name: Lanxin full_name: Li, Lanxin id: 367EF8FA-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0002-5607-272X - first_name: Liping full_name: Liu, Liping last_name: Liu - first_name: Bello Hassan full_name: Jakada, Bello Hassan last_name: Jakada - first_name: Youmei full_name: Huang, Youmei last_name: Huang - first_name: Qing full_name: He, Qing last_name: He - first_name: Mengnan full_name: Chai, Mengnan last_name: Chai - first_name: Xiaoping full_name: Niu, Xiaoping last_name: Niu - first_name: Yuan full_name: Qin, Yuan last_name: Qin citation: ama: Chen H, Lai L, Li L, et al. AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. 2020;21(16). doi:10.3390/ijms21165727 apa: Chen, H., Lai, L., Li, L., Liu, L., Jakada, B. H., Huang, Y., … Qin, Y. (2020). AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms21165727 chicago: Chen, Huihuang, Linyi Lai, Lanxin Li, Liping Liu, Bello Hassan Jakada, Youmei Huang, Qing He, Mengnan Chai, Xiaoping Niu, and Yuan Qin. “AcoMYB4, an Ananas Comosus L. MYB Transcription Factor, Functions in Osmotic Stress through Negative Regulation of ABA Signaling.” International Journal of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21165727. ieee: H. Chen et al., “AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling,” International Journal of Molecular Sciences, vol. 21, no. 16. MDPI, 2020. ista: Chen H, Lai L, Li L, Liu L, Jakada BH, Huang Y, He Q, Chai M, Niu X, Qin Y. 2020. AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. 21(16), 5272. mla: Chen, Huihuang, et al. “AcoMYB4, an Ananas Comosus L. MYB Transcription Factor, Functions in Osmotic Stress through Negative Regulation of ABA Signaling.” International Journal of Molecular Sciences, vol. 21, no. 16, 5272, MDPI, 2020, doi:10.3390/ijms21165727. short: H. Chen, L. Lai, L. Li, L. Liu, B.H. Jakada, Y. Huang, Q. He, M. Chai, X. Niu, Y. Qin, International Journal of Molecular Sciences 21 (2020). date_created: 2020-08-24T06:24:03Z date_published: 2020-08-10T00:00:00Z date_updated: 2024-03-27T23:30:43Z day: '10' ddc: - '570' department: - _id: JiFr doi: 10.3390/ijms21165727 external_id: isi: - '000565090300001' pmid: - '32785037' file: - access_level: open_access checksum: 03b039244e6ae80580385fd9f577e2b2 content_type: application/pdf creator: cziletti date_created: 2020-08-25T09:53:50Z date_updated: 2020-08-25T09:53:50Z file_id: '8292' file_name: 2020_IntMolecSciences_Chen.pdf file_size: 5718755 relation: main_file success: 1 file_date_updated: 2020-08-25T09:53:50Z has_accepted_license: '1' intvolume: ' 21' isi: 1 issue: '16' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: International Journal of Molecular Sciences publication_identifier: eissn: - '14220067' issn: - '16616596' publication_status: published publisher: MDPI quality_controlled: '1' related_material: record: - id: '10083' relation: dissertation_contains status: public scopus_import: '1' status: public title: AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 21 year: '2020' ... --- _id: '8139' abstract: - lang: eng text: 'Clathrin-mediated endocytosis (CME) is a crucial cellular process implicated in many aspects of plant growth, development, intra- and inter-cellular signaling, nutrient uptake and pathogen defense. Despite these significant roles, little is known about the precise molecular details of how it functions in planta. In order to facilitate the direct quantitative study of plant CME, here we review current routinely used methods and present refined, standardized quantitative imaging protocols which allow the detailed characterization of CME at multiple scales in plant tissues. These include: (i) an efficient electron microscopy protocol for the imaging of Arabidopsis CME vesicles in situ, thus providing a method for the detailed characterization of the ultra-structure of clathrin-coated vesicles; (ii) a detailed protocol and analysis for quantitative live-cell fluorescence microscopy to precisely examine the temporal interplay of endocytosis components during single CME events; (iii) a semi-automated analysis to allow the quantitative characterization of global internalization of cargos in whole plant tissues; and (iv) an overview and validation of useful genetic and pharmacological tools to interrogate the molecular mechanisms and function of CME in intact plant samples.' acknowledged_ssus: - _id: EM-Fac - _id: Bio acknowledgement: "This paper is dedicated to the memory of Christien Merrifield. He pioneered quantitative\r\nimaging approaches in mammalian CME and his mentorship inspired the development of all\r\nthe analysis methods presented here. His joy in research, pure scientific curiosity and\r\nmicroscopy excellence remain a constant inspiration. We thank Daniel Van Damme for gifting\r\nus the CLC2-GFP x TPLATE-TagRFP plants used in this manuscript. We further thank the\r\nScientific Service Units at IST Austria; specifically, the Electron Microscopy Facility for\r\ntechnical assistance (in particular Vanessa Zheden) and the BioImaging Facility BioImaging\r\nFacility for access to equipment. " article_number: jcs248062 article_processing_charge: No article_type: original author: - first_name: Alexander J full_name: Johnson, Alexander J id: 46A62C3A-F248-11E8-B48F-1D18A9856A87 last_name: Johnson orcid: 0000-0002-2739-8843 - first_name: Nataliia full_name: Gnyliukh, Nataliia id: 390C1120-F248-11E8-B48F-1D18A9856A87 last_name: Gnyliukh orcid: 0000-0002-2198-0509 - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Madhumitha full_name: Narasimhan, Madhumitha id: 44BF24D0-F248-11E8-B48F-1D18A9856A87 last_name: Narasimhan orcid: 0000-0002-8600-0671 - first_name: G full_name: Vert, G last_name: Vert - first_name: SY full_name: Bednarek, SY last_name: Bednarek - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Johnson AJ, Gnyliukh N, Kaufmann W, et al. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. 2020;133(15). doi:10.1242/jcs.248062 apa: Johnson, A. J., Gnyliukh, N., Kaufmann, W., Narasimhan, M., Vert, G., Bednarek, S., & Friml, J. (2020). Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.248062 chicago: Johnson, Alexander J, Nataliia Gnyliukh, Walter Kaufmann, Madhumitha Narasimhan, G Vert, SY Bednarek, and Jiří Friml. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of Cell Science. The Company of Biologists, 2020. https://doi.org/10.1242/jcs.248062. ieee: A. J. Johnson et al., “Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis,” Journal of Cell Science, vol. 133, no. 15. The Company of Biologists, 2020. ista: Johnson AJ, Gnyliukh N, Kaufmann W, Narasimhan M, Vert G, Bednarek S, Friml J. 2020. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. 133(15), jcs248062. mla: Johnson, Alexander J., et al. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of Cell Science, vol. 133, no. 15, jcs248062, The Company of Biologists, 2020, doi:10.1242/jcs.248062. short: A.J. Johnson, N. Gnyliukh, W. Kaufmann, M. Narasimhan, G. Vert, S. Bednarek, J. Friml, Journal of Cell Science 133 (2020). date_created: 2020-07-21T08:58:19Z date_published: 2020-08-06T00:00:00Z date_updated: 2023-12-01T13:51:07Z day: '06' ddc: - '575' department: - _id: JiFr - _id: EM-Fac doi: 10.1242/jcs.248062 ec_funded: 1 external_id: isi: - '000561047900021' pmid: - '32616560' file: - access_level: open_access checksum: 2d11f79a0b4e0a380fb002b933da331a content_type: application/pdf creator: ajohnson date_created: 2020-11-26T17:12:51Z date_updated: 2021-08-08T22:30:03Z embargo: 2021-08-07 file_id: '8815' file_name: 2020 - Johnson - JSC - plant CME toolbox.pdf file_size: 15150403 relation: main_file file_date_updated: 2021-08-08T22:30:03Z has_accepted_license: '1' intvolume: ' 133' isi: 1 issue: '15' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Journal of Cell Science publication_identifier: eissn: - 1477-9137 issn: - 0021-9533 publication_status: published publisher: The Company of Biologists quality_controlled: '1' related_material: record: - id: '14510' relation: dissertation_contains status: public scopus_import: '1' status: public title: Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 133 year: '2020' ... --- _id: '9160' abstract: - lang: eng text: Auxin is a key hormonal regulator, that governs plant growth and development in concert with other hormonal pathways. The unique feature of auxin is its polar, cell-to-cell transport that leads to the formation of local auxin maxima and gradients, which coordinate initiation and patterning of plant organs. The molecular machinery mediating polar auxin transport is one of the important points of interaction with other hormones. Multiple hormonal pathways converge at the regulation of auxin transport and form a regulatory network that integrates various developmental and environmental inputs to steer plant development. In this review, we discuss recent advances in understanding the mechanisms that underlie regulation of polar auxin transport by multiple hormonal pathways. Specifically, we focus on the post-translational mechanisms that contribute to fine-tuning of the abundance and polarity of auxin transporters at the plasma membrane and thereby enable rapid modification of the auxin flow to coordinate plant growth and development. acknowledgement: H.S. is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria. J.C.M. is the recipient of an EMBO Long-Term Fellowship (ALTF number 710-2016). We would like to thank Jiri Friml and Carina Baskett for critical reading of the manuscript and Shutang Tan and Maciek Adamowski for helpful discussions. No conflict of interest declared. article_number: '100048' article_processing_charge: No article_type: original author: - first_name: Hana full_name: Semeradova, Hana id: 42FE702E-F248-11E8-B48F-1D18A9856A87 last_name: Semeradova - first_name: Juan C full_name: Montesinos López, Juan C id: 310A8E3E-F248-11E8-B48F-1D18A9856A87 last_name: Montesinos López orcid: 0000-0001-9179-6099 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: 'Semerádová H, Montesinos López JC, Benková E. All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. 2020;1(3). doi:10.1016/j.xplc.2020.100048' apa: 'Semerádová, H., Montesinos López, J. C., & Benková, E. (2020). All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. Elsevier. https://doi.org/10.1016/j.xplc.2020.100048' chicago: 'Semerádová, Hana, Juan C Montesinos López, and Eva Benková. “All Roads Lead to Auxin: Post-Translational Regulation of Auxin Transport by Multiple Hormonal Pathways.” Plant Communications. Elsevier, 2020. https://doi.org/10.1016/j.xplc.2020.100048.' ieee: 'H. Semerádová, J. C. Montesinos López, and E. Benková, “All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways,” Plant Communications, vol. 1, no. 3. Elsevier, 2020.' ista: 'Semerádová H, Montesinos López JC, Benková E. 2020. All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. 1(3), 100048.' mla: 'Semerádová, Hana, et al. “All Roads Lead to Auxin: Post-Translational Regulation of Auxin Transport by Multiple Hormonal Pathways.” Plant Communications, vol. 1, no. 3, 100048, Elsevier, 2020, doi:10.1016/j.xplc.2020.100048.' short: H. Semerádová, J.C. Montesinos López, E. Benková, Plant Communications 1 (2020). date_created: 2021-02-18T10:18:43Z date_published: 2020-05-11T00:00:00Z date_updated: 2024-03-27T23:30:46Z day: '11' ddc: - '580' department: - _id: EvBe doi: 10.1016/j.xplc.2020.100048 external_id: isi: - '000654052800010' pmid: - '33367243' file: - access_level: open_access checksum: 785b266d82a94b007cf40dbbe7c4847e content_type: application/pdf creator: dernst date_created: 2021-02-18T10:23:59Z date_updated: 2021-02-18T10:23:59Z file_id: '9161' file_name: 2020_PlantComm_Semeradova.pdf file_size: 840289 relation: main_file success: 1 file_date_updated: 2021-02-18T10:23:59Z has_accepted_license: '1' intvolume: ' 1' isi: 1 issue: '3' language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 261821BC-B435-11E9-9278-68D0E5697425 grant_number: '24746' name: Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis. - _id: 253E54C8-B435-11E9-9278-68D0E5697425 grant_number: ALTF710-2016 name: Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants publication: Plant Communications publication_identifier: issn: - 2590-3462 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '10135' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways' 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 1 year: '2020' ... --- _id: '10354' abstract: - lang: eng text: "Background\r\nESCRT-III is a membrane remodelling filament with the unique ability to cut membranes from the inside of the membrane neck. It is essential for the final stage of cell division, the formation of vesicles, the release of viruses, and membrane repair. Distinct from other cytoskeletal filaments, ESCRT-III filaments do not consume energy themselves, but work in conjunction with another ATP-consuming complex. Despite rapid progress in describing the cell biology of ESCRT-III, we lack an understanding of the physical mechanisms behind its force production and membrane remodelling.\r\nResults\r\nHere we present a minimal coarse-grained model that captures all the experimentally reported cases of ESCRT-III driven membrane sculpting, including the formation of downward and upward cones and tubules. This model suggests that a change in the geometry of membrane bound ESCRT-III filaments—from a flat spiral to a 3D helix—drives membrane deformation. We then show that such repetitive filament geometry transitions can induce the fission of cargo-containing vesicles.\r\nConclusions\r\nOur model provides a general physical mechanism that explains the full range of ESCRT-III-dependent membrane remodelling and scission events observed in cells. This mechanism for filament force production is distinct from the mechanisms described for other cytoskeletal elements discovered so far. The mechanistic principles revealed here suggest new ways of manipulating ESCRT-III-driven processes in cells and could be used to guide the engineering of synthetic membrane-sculpting systems." acknowledgement: We thank Jeremy Carlton, Mike Staddon, Geraint Harker, and the Wellcome Trust Consortium “Archaeal Origins of Eukaryotic Cell Organisation” for fruitful conversations. We thank Peter Wirnsberger and Tine Curk for discussions about the membrane model implementation. article_number: '82' article_processing_charge: No article_type: original author: - first_name: Lena full_name: Harker-Kirschneck, Lena last_name: Harker-Kirschneck - first_name: Buzz full_name: Baum, Buzz last_name: Baum - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 citation: ama: Harker-Kirschneck L, Baum B, Šarić A. Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. BMC Biology. 2019;17(1). doi:10.1186/s12915-019-0700-2 apa: Harker-Kirschneck, L., Baum, B., & Šarić, A. (2019). Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. BMC Biology. Springer Nature. https://doi.org/10.1186/s12915-019-0700-2 chicago: Harker-Kirschneck, Lena, Buzz Baum, and Anđela Šarić. “Changes in ESCRT-III Filament Geometry Drive Membrane Remodelling and Fission in Silico.” BMC Biology. Springer Nature, 2019. https://doi.org/10.1186/s12915-019-0700-2. ieee: L. Harker-Kirschneck, B. Baum, and A. Šarić, “Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico,” BMC Biology, vol. 17, no. 1. Springer Nature, 2019. ista: Harker-Kirschneck L, Baum B, Šarić A. 2019. Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. BMC Biology. 17(1), 82. mla: Harker-Kirschneck, Lena, et al. “Changes in ESCRT-III Filament Geometry Drive Membrane Remodelling and Fission in Silico.” BMC Biology, vol. 17, no. 1, 82, Springer Nature, 2019, doi:10.1186/s12915-019-0700-2. short: L. Harker-Kirschneck, B. Baum, A. Šarić, BMC Biology 17 (2019). date_created: 2021-11-26T11:25:03Z date_published: 2019-10-22T00:00:00Z date_updated: 2021-11-26T11:54:29Z day: '22' ddc: - '570' doi: 10.1186/s12915-019-0700-2 extern: '1' external_id: pmid: - '31640700' file: - access_level: open_access checksum: 31d8bae55a376d30925f53f7e1a02396 content_type: application/pdf creator: cchlebak date_created: 2021-11-26T11:37:54Z date_updated: 2021-11-26T11:37:54Z file_id: '10356' file_name: 2019_BMCBio_Harker_Kirschneck.pdf file_size: 1648926 relation: main_file success: 1 file_date_updated: 2021-11-26T11:37:54Z has_accepted_license: '1' intvolume: ' 17' issue: '1' keyword: - cell biology language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/559898 month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: BMC Biology publication_identifier: issn: - 1741-7007 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico 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: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 17 year: '2019' ... --- _id: '10355' abstract: - lang: eng text: The molecular machinery of life is largely created via self-organisation of individual molecules into functional assemblies. Minimal coarse-grained models, in which a whole macromolecule is represented by a small number of particles, can be of great value in identifying the main driving forces behind self-organisation in cell biology. Such models can incorporate data from both molecular and continuum scales, and their results can be directly compared to experiments. Here we review the state of the art of models for studying the formation and biological function of macromolecular assemblies in living organisms. We outline the key ingredients of each model and their main findings. We illustrate the contribution of this class of simulations to identifying the physical mechanisms behind life and diseases, and discuss their future developments. acknowledgement: We acknowledge funding from EPSRC (A.E.H. and A.Š.), the Academy of Medical Sciences (J.K. and A.Š.), the Wellcome Trust (J.K. and A.Š.), and the Royal Society (A.Š.). We thank Shiladitya Banerjee and Nikola Ojkic for critically reading the manuscript, and Claudia Flandoli for helping us with figures and illustrations. article_processing_charge: No article_type: original author: - first_name: Anne E full_name: Hafner, Anne E last_name: Hafner - first_name: Johannes full_name: Krausser, Johannes last_name: Krausser - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 citation: ama: Hafner AE, Krausser J, Šarić A. Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. 2019;58:43-52. doi:10.1016/j.sbi.2019.05.018 apa: Hafner, A. E., Krausser, J., & Šarić, A. (2019). Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2019.05.018 chicago: Hafner, Anne E, Johannes Krausser, and Anđela Šarić. “Minimal Coarse-Grained Models for Molecular Self-Organisation in Biology.” Current Opinion in Structural Biology. Elsevier, 2019. https://doi.org/10.1016/j.sbi.2019.05.018. ieee: A. E. Hafner, J. Krausser, and A. Šarić, “Minimal coarse-grained models for molecular self-organisation in biology,” Current Opinion in Structural Biology, vol. 58. Elsevier, pp. 43–52, 2019. ista: Hafner AE, Krausser J, Šarić A. 2019. Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. 58, 43–52. mla: Hafner, Anne E., et al. “Minimal Coarse-Grained Models for Molecular Self-Organisation in Biology.” Current Opinion in Structural Biology, vol. 58, Elsevier, 2019, pp. 43–52, doi:10.1016/j.sbi.2019.05.018. short: A.E. Hafner, J. Krausser, A. Šarić, Current Opinion in Structural Biology 58 (2019) 43–52. date_created: 2021-11-26T11:33:21Z date_published: 2019-06-18T00:00:00Z date_updated: 2021-11-26T11:54:25Z day: '18' doi: 10.1016/j.sbi.2019.05.018 extern: '1' external_id: pmid: - '31226513' intvolume: ' 58' keyword: - molecular biology - structural biology language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1906.09349 month: '06' oa: 1 oa_version: Preprint page: 43-52 pmid: 1 publication: Current Opinion in Structural Biology publication_identifier: issn: - 0959-440X publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Minimal coarse-grained models for molecular self-organisation in biology type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 58 year: '2019' ... --- _id: '10621' abstract: - lang: eng text: Twisted bilayer graphene has recently emerged as a platform for hosting correlated phenomena. For twist angles near θ ≈ 1.1°, the low-energy electronic structure of twisted bilayer graphene features isolated bands with a flat dispersion1,2. Recent experiments have observed a variety of low-temperature phases that appear to be driven by electron interactions, including insulating states, superconductivity and magnetism3,4,5,6. Here we report electrical transport measurements up to room temperature for twist angles varying between 0.75° and 2°. We find that the resistivity, ρ, scales linearly with temperature, T, over a wide range of T before falling again owing to interband activation. The T-linear response is much larger than observed in monolayer graphene for all measured devices, and in particular increases by more than three orders of magnitude in the range where the flat band exists. Our results point to the dominant role of electron–phonon scattering in twisted bilayer graphene, with possible implications for the origin of the observed superconductivity. acknowledgement: The authors thank S. Das Sarma and F. Wu for sharing their unpublished theoretical results, and acknowledge further discussions with L. Balents and T. Senthil. Work at both Columbia and UCSB was funded by the Army Research Office under award W911NF-17-1-0323. Sample device design and fabrication was partially supported by DoE Pro-QM EFRC (DE-SC0019443). A.F.Y. and C.R.D. separately acknowledge the support of the David and Lucile Packard Foundation. K.W. and T.T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan and the CREST (JPMJCR15F3), JST. A portion of this work was carried out at the KITP, Santa Barbara, supported by the National Science Foundation under grant number NSF PHY-1748958. article_processing_charge: No article_type: original author: - first_name: Hryhoriy full_name: Polshyn, Hryhoriy id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48 last_name: Polshyn orcid: 0000-0001-8223-8896 - first_name: Matthew full_name: Yankowitz, Matthew last_name: Yankowitz - first_name: Shaowen full_name: Chen, Shaowen last_name: Chen - first_name: Yuxuan full_name: Zhang, Yuxuan last_name: Zhang - first_name: K. full_name: Watanabe, K. last_name: Watanabe - first_name: T. full_name: Taniguchi, T. last_name: Taniguchi - first_name: Cory R. full_name: Dean, Cory R. last_name: Dean - first_name: Andrea F. full_name: Young, Andrea F. last_name: Young citation: ama: Polshyn H, Yankowitz M, Chen S, et al. Large linear-in-temperature resistivity in twisted bilayer graphene. Nature Physics. 2019;15(10):1011-1016. doi:10.1038/s41567-019-0596-3 apa: Polshyn, H., Yankowitz, M., Chen, S., Zhang, Y., Watanabe, K., Taniguchi, T., … Young, A. F. (2019). Large linear-in-temperature resistivity in twisted bilayer graphene. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-019-0596-3 chicago: Polshyn, Hryhoriy, Matthew Yankowitz, Shaowen Chen, Yuxuan Zhang, K. Watanabe, T. Taniguchi, Cory R. Dean, and Andrea F. Young. “Large Linear-in-Temperature Resistivity in Twisted Bilayer Graphene.” Nature Physics. Springer Nature, 2019. https://doi.org/10.1038/s41567-019-0596-3. ieee: H. Polshyn et al., “Large linear-in-temperature resistivity in twisted bilayer graphene,” Nature Physics, vol. 15, no. 10. Springer Nature, pp. 1011–1016, 2019. ista: Polshyn H, Yankowitz M, Chen S, Zhang Y, Watanabe K, Taniguchi T, Dean CR, Young AF. 2019. Large linear-in-temperature resistivity in twisted bilayer graphene. Nature Physics. 15(10), 1011–1016. mla: Polshyn, Hryhoriy, et al. “Large Linear-in-Temperature Resistivity in Twisted Bilayer Graphene.” Nature Physics, vol. 15, no. 10, Springer Nature, 2019, pp. 1011–16, doi:10.1038/s41567-019-0596-3. short: H. Polshyn, M. Yankowitz, S. Chen, Y. Zhang, K. Watanabe, T. Taniguchi, C.R. Dean, A.F. Young, Nature Physics 15 (2019) 1011–1016. date_created: 2022-01-13T15:00:58Z date_published: 2019-08-05T00:00:00Z date_updated: 2022-01-20T09:33:38Z day: '05' doi: 10.1038/s41567-019-0596-3 extern: '1' external_id: arxiv: - '1902.00763' intvolume: ' 15' issue: '10' keyword: - general physics and astronomy language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1902.00763 month: '08' oa: 1 oa_version: Preprint page: 1011-1016 publication: Nature Physics publication_identifier: eissn: - 1745-2481 issn: - 1745-2473 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Large linear-in-temperature resistivity in twisted bilayer graphene type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 15 year: '2019' ... --- _id: '10622' abstract: - lang: eng text: We demonstrate a method for manipulating small ensembles of vortices in multiply connected superconducting structures. A micron-size magnetic particle attached to the tip of a silicon cantilever is used to locally apply magnetic flux through the superconducting structure. By scanning the tip over the surface of the device and by utilizing the dynamical coupling between the vortices and the cantilever, a high-resolution spatial map of the different vortex configurations is obtained. Moving the tip to a particular location in the map stabilizes a distinct multivortex configuration. Thus, the scanning of the tip over a particular trajectory in space permits nontrivial operations to be performed, such as braiding of individual vortices within a larger vortex ensemble—a key capability required by many proposals for topological quantum computing. acknowledgement: We are grateful to Nadya Mason, Taylor Hughes, and Alexey Bezryadin for useful discussions. This work was supported by the DOE Basic Energy Sciences under DE-SC0012649 and the Department of Physics and the Frederick Seitz Materials Research Laboratory Central Facilities at the University of Illinois. article_processing_charge: No article_type: original author: - first_name: Hryhoriy full_name: Polshyn, Hryhoriy id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48 last_name: Polshyn orcid: 0000-0001-8223-8896 - first_name: Tyler full_name: Naibert, Tyler last_name: Naibert - first_name: Raffi full_name: Budakian, Raffi last_name: Budakian citation: ama: Polshyn H, Naibert T, Budakian R. Manipulating multivortex states in superconducting structures. Nano Letters. 2019;19(8):5476-5482. doi:10.1021/acs.nanolett.9b01983 apa: Polshyn, H., Naibert, T., & Budakian, R. (2019). Manipulating multivortex states in superconducting structures. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.9b01983 chicago: Polshyn, Hryhoriy, Tyler Naibert, and Raffi Budakian. “Manipulating Multivortex States in Superconducting Structures.” Nano Letters. American Chemical Society, 2019. https://doi.org/10.1021/acs.nanolett.9b01983. ieee: H. Polshyn, T. Naibert, and R. Budakian, “Manipulating multivortex states in superconducting structures,” Nano Letters, vol. 19, no. 8. American Chemical Society, pp. 5476–5482, 2019. ista: Polshyn H, Naibert T, Budakian R. 2019. Manipulating multivortex states in superconducting structures. Nano Letters. 19(8), 5476–5482. mla: Polshyn, Hryhoriy, et al. “Manipulating Multivortex States in Superconducting Structures.” Nano Letters, vol. 19, no. 8, American Chemical Society, 2019, pp. 5476–82, doi:10.1021/acs.nanolett.9b01983. short: H. Polshyn, T. Naibert, R. Budakian, Nano Letters 19 (2019) 5476–5482. date_created: 2022-01-13T15:11:14Z date_published: 2019-06-27T00:00:00Z date_updated: 2022-01-13T15:41:24Z day: '27' doi: 10.1021/acs.nanolett.9b01983 extern: '1' external_id: arxiv: - '1905.06303' pmid: - '31246034' intvolume: ' 19' issue: '8' keyword: - mechanical engineering - condensed matter physics - general materials science - general chemistry - bioengineering language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1905.06303 month: '06' oa: 1 oa_version: Preprint page: 5476-5482 pmid: 1 publication: Nano Letters publication_identifier: eissn: - 1530-6992 issn: - 1530-6984 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Manipulating multivortex states in superconducting structures type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 19 year: '2019' ... --- _id: '10625' abstract: - lang: eng text: The discovery of superconductivity and exotic insulating phases in twisted bilayer graphene has established this material as a model system of strongly correlated electrons. To achieve superconductivity, the two layers of graphene need to be at a very precise angle with respect to each other. Yankowitz et al. now show that another experimental knob, hydrostatic pressure, can be used to tune the phase diagram of twisted bilayer graphene (see the Perspective by Feldman). Applying pressure increased the coupling between the layers, which shifted the superconducting transition to higher angles and somewhat higher temperatures. acknowledgement: We thank J. Zhu and H. Zhou for experimental assistance and D. Shahar, A. Millis, O. Vafek, M. Zaletel, L. Balents, C. Xu, A. Bernevig, L. Fu, M. Koshino, and P. Moon for helpful discussions. article_processing_charge: No article_type: original author: - first_name: Matthew full_name: Yankowitz, Matthew last_name: Yankowitz - first_name: Shaowen full_name: Chen, Shaowen last_name: Chen - first_name: Hryhoriy full_name: Polshyn, Hryhoriy id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48 last_name: Polshyn orcid: 0000-0001-8223-8896 - first_name: Yuxuan full_name: Zhang, Yuxuan last_name: Zhang - first_name: K. full_name: Watanabe, K. last_name: Watanabe - first_name: T. full_name: Taniguchi, T. last_name: Taniguchi - first_name: David full_name: Graf, David last_name: Graf - first_name: Andrea F. full_name: Young, Andrea F. last_name: Young - first_name: Cory R. full_name: Dean, Cory R. last_name: Dean citation: ama: Yankowitz M, Chen S, Polshyn H, et al. Tuning superconductivity in twisted bilayer graphene. Science. 2019;363(6431):1059-1064. doi:10.1126/science.aav1910 apa: Yankowitz, M., Chen, S., Polshyn, H., Zhang, Y., Watanabe, K., Taniguchi, T., … Dean, C. R. (2019). Tuning superconductivity in twisted bilayer graphene. Science. American Association for the Advancement of Science (AAAS). https://doi.org/10.1126/science.aav1910 chicago: Yankowitz, Matthew, Shaowen Chen, Hryhoriy Polshyn, Yuxuan Zhang, K. Watanabe, T. Taniguchi, David Graf, Andrea F. Young, and Cory R. Dean. “Tuning Superconductivity in Twisted Bilayer Graphene.” Science. American Association for the Advancement of Science (AAAS), 2019. https://doi.org/10.1126/science.aav1910. ieee: M. Yankowitz et al., “Tuning superconductivity in twisted bilayer graphene,” Science, vol. 363, no. 6431. American Association for the Advancement of Science (AAAS), pp. 1059–1064, 2019. ista: Yankowitz M, Chen S, Polshyn H, Zhang Y, Watanabe K, Taniguchi T, Graf D, Young AF, Dean CR. 2019. Tuning superconductivity in twisted bilayer graphene. Science. 363(6431), 1059–1064. mla: Yankowitz, Matthew, et al. “Tuning Superconductivity in Twisted Bilayer Graphene.” Science, vol. 363, no. 6431, American Association for the Advancement of Science (AAAS), 2019, pp. 1059–64, doi:10.1126/science.aav1910. short: M. Yankowitz, S. Chen, H. Polshyn, Y. Zhang, K. Watanabe, T. Taniguchi, D. Graf, A.F. Young, C.R. Dean, Science 363 (2019) 1059–1064. date_created: 2022-01-14T12:14:58Z date_published: 2019-01-24T00:00:00Z date_updated: 2022-01-14T13:48:32Z day: '24' doi: 10.1126/science.aav1910 extern: '1' external_id: arxiv: - '1808.07865' pmid: - '30679385 ' intvolume: ' 363' issue: '6431' keyword: - multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1808.07865 month: '01' oa: 1 oa_version: Preprint page: 1059-1064 pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science (AAAS) quality_controlled: '1' scopus_import: '1' status: public title: Tuning superconductivity in twisted bilayer graphene type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 363 year: '2019' ... --- _id: '10664' abstract: - lang: eng text: "Since the discovery of correlated insulators and superconductivity in magic-angle twisted bilayer graphene (tBLG) ([1, 2], JCCM April 2018), theorists have been excitedly pursuing the alluring mix of band topology, symmetry breaking, Mott insulators and superconductivity at play, as well as the potential relation (if any) to high-Tc physics. Now a new stream\r\nof experimental work is arriving which further enriches the story. To briefly recap Episodes 1 and 2 (JCCM April and November 2018), when two graphene layers are stacked with a small rotational mismatch θ, the resulting long-wavelength moire pattern leads to a superlattice potential which reconstructs the low energy band structure. When θ approaches the “magic-angle” θM ∼ 1 ◦, the band structure features eight nearly-flat bands which fill when the electron number per moire unit cell, n/n0, lies between −4 < n/n0 < 4. The bands can be counted as 8 = 2 × 2 × 2: for each spin (2×) and valley (2×) characteristic of monolayergraphene, tBLG has has 2× flat bands which cross at mini-Dirac points." article_processing_charge: No article_type: original author: - first_name: Mathew full_name: Yankowitz, Mathew last_name: Yankowitz - first_name: Shaowen full_name: Chen, Shaowen last_name: Chen - first_name: Hryhoriy full_name: Polshyn, Hryhoriy id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48 last_name: Polshyn orcid: 0000-0001-8223-8896 - first_name: K. full_name: Watanabe, K. last_name: Watanabe - first_name: T. full_name: Taniguchi, T. last_name: Taniguchi - first_name: David full_name: Graf, David last_name: Graf - first_name: Andrea F. full_name: Young, Andrea F. last_name: Young - first_name: Cory R. full_name: Dean, Cory R. last_name: Dean - first_name: Aaron L. full_name: Sharpe, Aaron L. last_name: Sharpe - first_name: E.J. full_name: Fox, E.J. last_name: Fox - first_name: A.W. full_name: Barnard, A.W. last_name: Barnard - first_name: Joe full_name: Finney, Joe last_name: Finney citation: ama: Yankowitz M, Chen S, Polshyn H, et al. New correlated phenomena in magic-angle twisted bilayer graphene/s. Journal Club for Condensed Matter Physics. 2019;03. doi:10.36471/jccm_february_2019_03 apa: Yankowitz, M., Chen, S., Polshyn, H., Watanabe, K., Taniguchi, T., Graf, D., … Finney, J. (2019). New correlated phenomena in magic-angle twisted bilayer graphene/s. Journal Club for Condensed Matter Physics. Simons Foundation ; University of California, Riverside. https://doi.org/10.36471/jccm_february_2019_03 chicago: Yankowitz, Mathew, Shaowen Chen, Hryhoriy Polshyn, K. Watanabe, T. Taniguchi, David Graf, Andrea F. Young, et al. “New Correlated Phenomena in Magic-Angle Twisted Bilayer Graphene/S.” Journal Club for Condensed Matter Physics. Simons Foundation ; University of California, Riverside, 2019. https://doi.org/10.36471/jccm_february_2019_03. ieee: M. Yankowitz et al., “New correlated phenomena in magic-angle twisted bilayer graphene/s,” Journal Club for Condensed Matter Physics, vol. 03. Simons Foundation ; University of California, Riverside, 2019. ista: Yankowitz M, Chen S, Polshyn H, Watanabe K, Taniguchi T, Graf D, Young AF, Dean CR, Sharpe AL, Fox EJ, Barnard AW, Finney J. 2019. New correlated phenomena in magic-angle twisted bilayer graphene/s. Journal Club for Condensed Matter Physics. 03. mla: Yankowitz, Mathew, et al. “New Correlated Phenomena in Magic-Angle Twisted Bilayer Graphene/S.” Journal Club for Condensed Matter Physics, vol. 03, Simons Foundation ; University of California, Riverside, 2019, doi:10.36471/jccm_february_2019_03. short: M. Yankowitz, S. Chen, H. Polshyn, K. Watanabe, T. Taniguchi, D. Graf, A.F. Young, C.R. Dean, A.L. Sharpe, E.J. Fox, A.W. Barnard, J. Finney, Journal Club for Condensed Matter Physics 03 (2019). date_created: 2022-01-25T15:09:58Z date_published: 2019-02-28T00:00:00Z date_updated: 2022-01-25T15:56:39Z day: '28' doi: 10.36471/jccm_february_2019_03 intvolume: ' 3' language: - iso: eng main_file_link: - open_access: '1' url: https://www.condmatjclub.org/?p=3541 month: '02' oa: 1 oa_version: Published Version publication: Journal Club for Condensed Matter Physics publication_status: published publisher: Simons Foundation ; University of California, Riverside quality_controlled: '1' status: public title: New correlated phenomena in magic-angle twisted bilayer graphene/s type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: '03' year: '2019' ...