[{"project":[{"call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"},{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"article_number":"94","title":"Water surface wavelets","publist_id":"7789","author":[{"id":"44D6411A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","full_name":"Jeschke, Stefan","last_name":"Jeschke"},{"full_name":"Skrivan, Tomas","last_name":"Skrivan","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas"},{"first_name":"Matthias","full_name":"Mueller Fischer, Matthias","last_name":"Mueller Fischer"},{"last_name":"Chentanez","full_name":"Chentanez, Nuttapong","first_name":"Nuttapong"},{"last_name":"Macklin","full_name":"Macklin, Miles","first_name":"Miles"},{"last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"}],"external_id":{"isi":["000448185000055"]},"article_processing_charge":"No","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Jeschke, Stefan, Tomas Skrivan, Matthias Mueller Fischer, Nuttapong Chentanez, Miles Macklin, and Chris Wojtan. “Water Surface Wavelets.” ACM Transactions on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201336.","ista":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. 2018. Water surface wavelets. ACM Transactions on Graphics. 37(4), 94.","mla":"Jeschke, Stefan, et al. “Water Surface Wavelets.” ACM Transactions on Graphics, vol. 37, no. 4, 94, ACM, 2018, doi:10.1145/3197517.3201336.","short":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, C. Wojtan, ACM Transactions on Graphics 37 (2018).","ieee":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, and C. Wojtan, “Water surface wavelets,” ACM Transactions on Graphics, vol. 37, no. 4. ACM, 2018.","ama":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. Water surface wavelets. ACM Transactions on Graphics. 2018;37(4). doi:10.1145/3197517.3201336","apa":"Jeschke, S., Skrivan, T., Mueller Fischer, M., Chentanez, N., Macklin, M., & Wojtan, C. (2018). Water surface wavelets. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3197517.3201336"},"quality_controlled":"1","publisher":"ACM","oa":1,"date_published":"2018-07-30T00:00:00Z","doi":"10.1145/3197517.3201336","date_created":"2018-12-11T11:44:48Z","day":"30","publication":"ACM Transactions on Graphics","has_accepted_license":"1","isi":1,"year":"2018","status":"public","type":"journal_article","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"_id":"134","file_date_updated":"2020-07-14T12:44:45Z","department":[{"_id":"ChWo"}],"ddc":["000"],"date_updated":"2024-02-28T13:58:51Z","month":"07","intvolume":" 37","scopus_import":"1","alternative_title":["SIGGRAPH"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The current state of the art in real-time two-dimensional water wave simulation requires developers to choose between efficient Fourier-based methods, which lack interactions with moving obstacles, and finite-difference or finite element methods, which handle environmental interactions but are significantly more expensive. This paper attempts to bridge this long-standing gap between complexity and performance, by proposing a new wave simulation method that can faithfully simulate wave interactions with moving obstacles in real time while simultaneously preserving minute details and accommodating very large simulation domains.\r\n\r\nPrevious methods for simulating 2D water waves directly compute the change in height of the water surface, a strategy which imposes limitations based on the CFL condition (fast moving waves require small time steps) and Nyquist's limit (small wave details require closely-spaced simulation variables). This paper proposes a novel wavelet transformation that discretizes the liquid motion in terms of amplitude-like functions that vary over space, frequency, and direction, effectively generalizing Fourier-based methods to handle local interactions. Because these new variables change much more slowly over space than the original water height function, our change of variables drastically reduces the limitations of the CFL condition and Nyquist limit, allowing us to simulate highly detailed water waves at very large visual resolutions. Our discretization is amenable to fast summation and easy to parallelize. We also present basic extensions like pre-computed wave paths and two-way solid fluid coupling. Finally, we argue that our discretization provides a convenient set of variables for artistic manipulation, which we illustrate with a novel wave-painting interface."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"volume":37,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/new-water-simulation-captures-small-details-even-in-large-scenes/","description":"News on IST Homepage"}]},"issue":"4","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"db75ebabe2ec432bf41389e614d6ef62","file_id":"5744","creator":"dernst","date_updated":"2020-07-14T12:44:45Z","file_size":22185016,"date_created":"2018-12-18T09:59:23Z","file_name":"2018_ACM_Jeschke.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published"},{"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/description-of-rotating-molecules-made-easy/","relation":"press_release"}]},"issue":"16","volume":121,"language":[{"iso":"eng"}],"publication_status":"published","month":"10","intvolume":" 121","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1803.07990","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We introduce a diagrammatic Monte Carlo approach to angular momentum properties of quantum many-particle systems possessing a macroscopic number of degrees of freedom. The treatment is based on a diagrammatic expansion that merges the usual Feynman diagrams with the angular momentum diagrams known from atomic and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent to quantum rotations. Our approach is applicable at arbitrary coupling, is free of systematic errors and of finite-size effects, and naturally provides access to the impurity Green function. We exemplify the technique by obtaining an all-coupling solution of the angulon model; however, the method is quite general and can be applied to a broad variety of systems in which particles exchange quantum angular momentum with their many-body environment."}],"department":[{"_id":"MiLe"}],"date_updated":"2024-02-28T13:15:09Z","status":"public","type":"journal_article","_id":"6339","date_published":"2018-10-16T00:00:00Z","doi":"10.1103/physrevlett.121.165301","date_created":"2019-04-17T10:53:38Z","day":"16","publication":"Physical Review Letters","isi":1,"year":"2018","quality_controlled":"1","publisher":"American Physical Society","oa":1,"title":"Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems","author":[{"id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo","last_name":"Bighin","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777"},{"full_name":"Tscherbul, Timur","last_name":"Tscherbul","first_name":"Timur"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"}],"article_processing_charge":"No","external_id":{"isi":["000447468400008"],"arxiv":["1803.07990"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review Letters, vol. 121, no. 16, 165301, American Physical Society, 2018, doi:10.1103/physrevlett.121.165301.","ama":"Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. 2018;121(16). doi:10.1103/physrevlett.121.165301","apa":"Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.121.165301","ieee":"G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018.","short":"G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018).","chicago":"Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/physrevlett.121.165301.","ista":"Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. 121(16), 165301."},"project":[{"name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425"}],"article_number":"165301"},{"type":"journal_article","status":"public","_id":"417","department":[{"_id":"MiLe"}],"date_updated":"2024-02-28T13:14:53Z","main_file_link":[{"url":"https://arxiv.org/abs/1803.07990","open_access":"1"}],"scopus_import":"1","intvolume":" 121","month":"10","abstract":[{"lang":"eng","text":"We introduce a Diagrammatic Monte Carlo (DiagMC) approach to complex molecular impurities with rotational degrees of freedom interacting with a many-particle environment. The treatment is based on the diagrammatic expansion that merges the usual Feynman diagrams with the angular momentum diagrams known from atomic and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent to quantum rotations. Our approach works at arbitrary coupling, is free of systematic errors and of finite size effects, and naturally provides access to the impurity Green function. We exemplify the technique by obtaining an all-coupling solution of the angulon model, however, the method is quite general and can be applied to a broad variety of quantum impurities possessing angular momentum degrees of freedom. "}],"oa_version":"Preprint","volume":121,"issue":"16","publication_status":"published","language":[{"iso":"eng"}],"project":[{"name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"165301","article_processing_charge":"No","external_id":{"arxiv":["1803.07990"]},"publist_id":"8025","author":[{"first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","last_name":"Bighin","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo"},{"first_name":"Timur","last_name":"Tscherbul","full_name":"Tscherbul, Timur"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"}],"title":"Diagrammatic Monte Carlo approach to rotating molecular impurities","citation":{"mla":"Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Rotating Molecular Impurities.” Physical Review Letters, vol. 121, no. 16, 165301, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.165301.","ieee":"G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach to rotating molecular impurities,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018.","short":"G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018).","apa":"Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.165301","ama":"Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. 2018;121(16). doi:10.1103/PhysRevLett.121.165301","chicago":"Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo Approach to Rotating Molecular Impurities.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.165301.","ista":"Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. 121(16), 165301."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"American Physical Society","quality_controlled":"1","date_created":"2018-12-11T11:46:22Z","date_published":"2018-10-16T00:00:00Z","doi":"10.1103/PhysRevLett.121.165301","year":"2018","publication":"Physical Review Letters","day":"16"},{"day":"01","publication":"2018 IEEE Information Theory Workshop","language":[{"iso":"eng"}],"publication_status":"published","year":"2018","related_material":{"record":[{"id":"9002","status":"public","relation":"later_version"}]},"doi":"10.1109/itw.2018.8613428","date_published":"2018-11-01T00:00:00Z","date_created":"2019-07-23T11:01:42Z","page":"1-5","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We prove that, at least for the binary erasure channel, the polar-coding paradigm gives rise to codes that not only approach the Shannon limit but, in fact, do so under the best possible scaling of their block length as a function of the gap to capacity. This result exhibits the first known family of binary codes that attain both optimal scaling and quasi-linear complexity of encoding and decoding. Specifically, for any fixed δ > 0, we exhibit binary linear codes that ensure reliable communication at rates within ε > 0 of capacity with block length n = O(1/ε 2+δ ), construction complexity Θ(n), and encoding/decoding complexity Θ(n log n)."}],"month":"11","quality_controlled":"1","publisher":"IEEE","main_file_link":[{"url":"https://arxiv.org/abs/1711.01339","open_access":"1"}],"oa":1,"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Fazeli, Arman, et al. “Binary Linear Codes with Optimal Scaling: Polar Codes with Large Kernels.” 2018 IEEE Information Theory Workshop, IEEE, 2018, pp. 1–5, doi:10.1109/itw.2018.8613428.","ieee":"A. Fazeli, H. Hassani, M. Mondelli, and A. Vardy, “Binary linear codes with optimal scaling: Polar codes with large kernels,” in 2018 IEEE Information Theory Workshop, Guangzhou, China, 2018, pp. 1–5.","short":"A. Fazeli, H. Hassani, M. Mondelli, A. Vardy, in:, 2018 IEEE Information Theory Workshop, IEEE, 2018, pp. 1–5.","ama":"Fazeli A, Hassani H, Mondelli M, Vardy A. Binary linear codes with optimal scaling: Polar codes with large kernels. In: 2018 IEEE Information Theory Workshop. IEEE; 2018:1-5. doi:10.1109/itw.2018.8613428","apa":"Fazeli, A., Hassani, H., Mondelli, M., & Vardy, A. (2018). Binary linear codes with optimal scaling: Polar codes with large kernels. In 2018 IEEE Information Theory Workshop (pp. 1–5). Guangzhou, China: IEEE. https://doi.org/10.1109/itw.2018.8613428","chicago":"Fazeli, Arman, Hamed Hassani, Marco Mondelli, and Alexander Vardy. “Binary Linear Codes with Optimal Scaling: Polar Codes with Large Kernels.” In 2018 IEEE Information Theory Workshop, 1–5. IEEE, 2018. https://doi.org/10.1109/itw.2018.8613428.","ista":"Fazeli A, Hassani H, Mondelli M, Vardy A. 2018. Binary linear codes with optimal scaling: Polar codes with large kernels. 2018 IEEE Information Theory Workshop. ITW: Information Theory Workshop, 1–5."},"date_updated":"2024-03-07T12:18:50Z","title":"Binary linear codes with optimal scaling: Polar codes with large kernels","author":[{"last_name":"Fazeli","full_name":"Fazeli, Arman","first_name":"Arman"},{"first_name":"Hamed","last_name":"Hassani","full_name":"Hassani, Hamed"},{"orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","last_name":"Mondelli","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"full_name":"Vardy, Alexander","last_name":"Vardy","first_name":"Alexander"}],"external_id":{"arxiv":["1711.01339"]},"_id":"6665","status":"public","type":"conference","conference":{"location":"Guangzhou, China","end_date":"2018-11-29","start_date":"2018-11-25","name":"ITW: Information Theory Workshop"}},{"_id":"15143","status":"public","keyword":["Genetics"],"article_type":"original","type":"journal_article","extern":"1","date_updated":"2024-03-20T11:10:56Z","pmid":1,"oa_version":"Published Version","abstract":[{"text":"To maintain genome integrity, segmented double-stranded RNA viruses of the Reoviridae family must accurately select and package a complete set of up to a dozen distinct genomic RNAs. It is thought that the high fidelity segmented genome assembly involves multiple sequence-specific RNA–RNA interactions between single-stranded RNA segment precursors. These are mediated by virus-encoded non-structural proteins with RNA chaperone-like activities, such as rotavirus (RV) NSP2 and avian reovirus σNS. Here, we compared the abilities of NSP2 and σNS to mediate sequence-specific interactions between RV genomic segment precursors. Despite their similar activities, NSP2 successfully promotes inter-segment association, while σNS fails to do so. To understand the mechanisms underlying such selectivity in promoting inter-molecular duplex formation, we compared RNA-binding and helix-unwinding activities of both proteins. We demonstrate that octameric NSP2 binds structured RNAs with high affinity, resulting in efficient intramolecular RNA helix disruption. Hexameric σNS oligomerizes into an octamer that binds two RNAs, yet it exhibits only limited RNA-unwinding activity compared to NSP2. Thus, the formation of intersegment RNA–RNA interactions is governed by both helix-unwinding capacity of the chaperones and stability of RNA structure. We propose that this protein-mediated RNA selection mechanism may underpin the high fidelity assembly of multi-segmented RNA genomes in Reoviridae.","lang":"eng"}],"month":"09","intvolume":" 46","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1093/nar/gky394","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0305-1048"],"eissn":["1362-4962"]},"publication_status":"published","volume":46,"issue":"15","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Bravo, Jack Peter Kelly, et al. “Stability of Local Secondary Structure Determines Selectivity of Viral RNA Chaperones.” Nucleic Acids Research, vol. 46, no. 15, Oxford University Press, 2018, pp. 7924–37, doi:10.1093/nar/gky394.","ieee":"J. P. K. Bravo et al., “Stability of local secondary structure determines selectivity of viral RNA chaperones,” Nucleic Acids Research, vol. 46, no. 15. Oxford University Press, pp. 7924–7937, 2018.","short":"J.P.K. Bravo, A. Borodavka, A. Barth, A.N. Calabrese, P. Mojzes, J.J.B. Cockburn, D.C. Lamb, R. Tuma, Nucleic Acids Research 46 (2018) 7924–7937.","apa":"Bravo, J. P. K., Borodavka, A., Barth, A., Calabrese, A. N., Mojzes, P., Cockburn, J. J. B., … Tuma, R. (2018). Stability of local secondary structure determines selectivity of viral RNA chaperones. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gky394","ama":"Bravo JPK, Borodavka A, Barth A, et al. Stability of local secondary structure determines selectivity of viral RNA chaperones. Nucleic Acids Research. 2018;46(15):7924-7937. doi:10.1093/nar/gky394","chicago":"Bravo, Jack Peter Kelly, Alexander Borodavka, Anders Barth, Antonio N Calabrese, Peter Mojzes, Joseph J B Cockburn, Don C Lamb, and Roman Tuma. “Stability of Local Secondary Structure Determines Selectivity of Viral RNA Chaperones.” Nucleic Acids Research. Oxford University Press, 2018. https://doi.org/10.1093/nar/gky394.","ista":"Bravo JPK, Borodavka A, Barth A, Calabrese AN, Mojzes P, Cockburn JJB, Lamb DC, Tuma R. 2018. Stability of local secondary structure determines selectivity of viral RNA chaperones. Nucleic Acids Research. 46(15), 7924–7937."},"title":"Stability of local secondary structure determines selectivity of viral RNA chaperones","author":[{"first_name":"Jack Peter Kelly","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","full_name":"Bravo, Jack Peter Kelly","orcid":"0000-0003-0456-0753","last_name":"Bravo"},{"first_name":"Alexander","last_name":"Borodavka","full_name":"Borodavka, Alexander"},{"full_name":"Barth, Anders","last_name":"Barth","first_name":"Anders"},{"first_name":"Antonio N","last_name":"Calabrese","full_name":"Calabrese, Antonio N"},{"first_name":"Peter","full_name":"Mojzes, Peter","last_name":"Mojzes"},{"last_name":"Cockburn","full_name":"Cockburn, Joseph J B","first_name":"Joseph J B"},{"last_name":"Lamb","full_name":"Lamb, Don C","first_name":"Don C"},{"last_name":"Tuma","full_name":"Tuma, Roman","first_name":"Roman"}],"external_id":{"pmid":["29796667"]},"article_processing_charge":"Yes","publisher":"Oxford University Press","quality_controlled":"1","oa":1,"day":"06","publication":"Nucleic Acids Research","year":"2018","date_published":"2018-09-06T00:00:00Z","doi":"10.1093/nar/gky394","date_created":"2024-03-20T10:43:13Z","page":"7924-7937"},{"issue":"3","volume":30,"related_material":{"record":[{"id":"6269","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"file":[{"success":1,"checksum":"4e165e653b67d3f0684697f21aace5a1","file_id":"11406","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_PlantCell_Adamowski.pdf","date_created":"2022-05-23T09:12:38Z","file_size":4407538,"date_updated":"2022-05-23T09:12:38Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"publication_status":"published","month":"04","intvolume":" 30","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Clathrin-mediated endocytosis (CME) is a cellular trafficking process in which cargoes and lipids are internalized from the plasma membrane into vesicles coated with clathrin and adaptor proteins. CME is essential for many developmental and physiological processes in plants, but its underlying mechanism is not well characterised compared to that in yeast and animal systems. Here, we searched for new factors involved in CME in Arabidopsis thaliana by performing Tandem Affinity Purification of proteins that interact with clathrin light chain, a principal component of the clathrin coat. Among the confirmed interactors, we found two putative homologues of the clathrin-coat uncoating factor auxilin previously described in non-plant systems. Overexpression of AUXILIN-LIKE1 and AUXILIN-LIKE2 in A. thaliana caused an arrest of seedling growth and development. This was concomitant with inhibited endocytosis due to blocking of clathrin recruitment after the initial step of adaptor protein binding to the plasma membrane. By contrast, auxilin-like(1/2) loss-of-function lines did not present endocytosis-related developmental or cellular phenotypes under normal growth conditions. This work contributes to the on-going characterization of the endocytotic machinery in plants and provides a robust tool for conditionally and specifically interfering with CME in A. thaliana.","lang":"eng"}],"file_date_updated":"2022-05-23T09:12:38Z","department":[{"_id":"JiFr"}],"ddc":["580"],"date_updated":"2024-03-27T23:30:06Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"412","date_published":"2018-04-09T00:00:00Z","doi":"10.1105/tpc.17.00785","date_created":"2018-12-11T11:46:20Z","page":"700 - 716","day":"09","publication":"The Plant Cell","has_accepted_license":"1","isi":1,"year":"2018","publisher":"American Society of Plant Biologists","quality_controlled":"1","oa":1,"acknowledgement":"We thank James Matthew Watson, Monika Borowska, and Peggy Stolt-Bergner at ProTech Facility of the Vienna Biocenter Core Facilities for the CRISPR/CAS9 construct; Anna Müller for assistance with molecular cloning; Sebastian Bednarek, Liwen Jiang, and Daniël Van Damme for sharing published material; Matyáš Fendrych, Daniël Van Damme, and Lindy Abas for valuable discussions; and Martine De Cock for help with correcting the manuscript. This work was supported by the European Research Council under the European Union Seventh Framework Programme (FP7/2007-2013)/ERC Grant 282300 and by the Ministry of Education of the Czech Republic/MŠMT project NPUI-LO1417.","title":"A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis","publist_id":"7417","author":[{"full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","last_name":"Adamowski","first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Narasimhan","orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha","first_name":"Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87"},{"id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","first_name":"Urszula","full_name":"Kania, Urszula","last_name":"Kania"},{"orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous","last_name":"Glanc","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous"},{"last_name":"De Jaeger","full_name":"De Jaeger, Geert","first_name":"Geert"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"article_processing_charge":"No","external_id":{"isi":["000429441400018"],"pmid":["29511054"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Adamowski, Maciek, et al. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell, vol. 30, no. 3, American Society of Plant Biologists, 2018, pp. 700–16, doi:10.1105/tpc.17.00785.","ieee":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, and J. Friml, “A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis,” The Plant Cell, vol. 30, no. 3. American Society of Plant Biologists, pp. 700–716, 2018.","short":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, J. Friml, The Plant Cell 30 (2018) 700–716.","ama":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 2018;30(3):700-716. doi:10.1105/tpc.17.00785","apa":"Adamowski, M., Narasimhan, M., Kania, U., Glanc, M., De Jaeger, G., & Friml, J. (2018). A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.17.00785","chicago":"Adamowski, Maciek, Madhumitha Narasimhan, Urszula Kania, Matous Glanc, Geert De Jaeger, and Jiří Friml. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell. American Society of Plant Biologists, 2018. https://doi.org/10.1105/tpc.17.00785.","ista":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. 2018. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 30(3), 700–716."},"project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}]},{"author":[{"orcid":"0000-0002-8602-4374","full_name":"Rangel Guerrero, Dámaris K","last_name":"Rangel Guerrero","first_name":"Dámaris K","id":"4871BCE6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"James G.","last_name":"Donnett","full_name":"Donnett, James G."},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036"},{"last_name":"Kovács","orcid":"0000-0001-6251-1007","full_name":"Kovács, Krisztián","id":"2AB5821E-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztián"}],"article_processing_charge":"No","external_id":{"isi":["000443994700007"]},"title":"Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning","citation":{"mla":"Rangel Guerrero, Dámaris K., et al. “Tetrode Recording from the Hippocampus of Behaving Mice Coupled with Four-Point-Irradiation Closed-Loop Optogenetics: A Technique to Study the Contribution of Hippocampal SWR Events to Learning.” ENeuro, vol. 5, no. 4, e0087, Society of Neuroscience, 2018, doi:10.1523/ENEURO.0087-18.2018.","ieee":"D. K. Rangel Guerrero, J. G. Donnett, J. L. Csicsvari, and K. Kovács, “Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning,” eNeuro, vol. 5, no. 4. Society of Neuroscience, 2018.","short":"D.K. Rangel Guerrero, J.G. Donnett, J.L. Csicsvari, K. Kovács, ENeuro 5 (2018).","ama":"Rangel Guerrero DK, Donnett JG, Csicsvari JL, Kovács K. Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. eNeuro. 2018;5(4). doi:10.1523/ENEURO.0087-18.2018","apa":"Rangel Guerrero, D. K., Donnett, J. G., Csicsvari, J. L., & Kovács, K. (2018). Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. ENeuro. Society of Neuroscience. https://doi.org/10.1523/ENEURO.0087-18.2018","chicago":"Rangel Guerrero, Dámaris K, James G. Donnett, Jozsef L Csicsvari, and Krisztián Kovács. “Tetrode Recording from the Hippocampus of Behaving Mice Coupled with Four-Point-Irradiation Closed-Loop Optogenetics: A Technique to Study the Contribution of Hippocampal SWR Events to Learning.” ENeuro. Society of Neuroscience, 2018. https://doi.org/10.1523/ENEURO.0087-18.2018.","ista":"Rangel Guerrero DK, Donnett JG, Csicsvari JL, Kovács K. 2018. Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. eNeuro. 5(4), e0087."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"name":"Interneuron plasticity during spatial learning","grant_number":"I2072-B27","_id":"257D4372-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"e0087","date_published":"2018-07-27T00:00:00Z","doi":"10.1523/ENEURO.0087-18.2018","date_created":"2019-02-03T22:59:16Z","has_accepted_license":"1","isi":1,"year":"2018","day":"27","publication":"eNeuro","quality_controlled":"1","publisher":"Society of Neuroscience","oa":1,"file_date_updated":"2020-07-14T12:47:13Z","department":[{"_id":"JoCs"}],"date_updated":"2024-03-27T23:30:10Z","ddc":["570"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"5914","related_material":{"record":[{"id":"6849","status":"public","relation":"dissertation_contains"}]},"volume":5,"issue":"4","ec_funded":1,"publication_status":"published","file":[{"file_id":"5921","checksum":"f4915d45fc7ad4648b7b7a13fdecca01","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_ENeuro_Guerrero.pdf","date_created":"2019-02-05T12:48:36Z","creator":"dernst","file_size":3746884,"date_updated":"2020-07-14T12:47:13Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"07","intvolume":" 5","abstract":[{"text":"With the advent of optogenetics, it became possible to change the activity of a targeted population of neurons in a temporally controlled manner. To combine the advantages of 60-channel in vivo tetrode recording and laser-based optogenetics, we have developed a closed-loop recording system that allows for the actual electrophysiological signal to be used as a trigger for the laser light mediating the optogenetic intervention. We have optimized the weight, size, and shape of the corresponding implant to make it compatible with the size, force, and movements of a behaving mouse, and we have shown that the system can efficiently block sharp wave ripple (SWR) events using those events themselves as a trigger. To demonstrate the full potential of the optogenetic recording system we present a pilot study addressing the contribution of SWR events to learning in a complex behavioral task.","lang":"eng"}],"oa_version":"Published Version"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Brown, Markus, Frank P Assen, Alexander F Leithner, Jun Abe, Helga Schachner, Gabriele Asfour, Zsuzsanna Bagó Horváth, et al. “Lymph Node Blood Vessels Provide Exit Routes for Metastatic Tumor Cell Dissemination in Mice.” Science. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/science.aal3662.","ista":"Brown M, Assen FP, Leithner AF, Abe J, Schachner H, Asfour G, Bagó Horváth Z, Stein J, Uhrin P, Sixt MK, Kerjaschki D. 2018. Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. 359(6382), 1408–1411.","mla":"Brown, Markus, et al. “Lymph Node Blood Vessels Provide Exit Routes for Metastatic Tumor Cell Dissemination in Mice.” Science, vol. 359, no. 6382, American Association for the Advancement of Science, 2018, pp. 1408–11, doi:10.1126/science.aal3662.","short":"M. Brown, F.P. Assen, A.F. Leithner, J. Abe, H. Schachner, G. Asfour, Z. Bagó Horváth, J. Stein, P. Uhrin, M.K. Sixt, D. Kerjaschki, Science 359 (2018) 1408–1411.","ieee":"M. Brown et al., “Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice,” Science, vol. 359, no. 6382. American Association for the Advancement of Science, pp. 1408–1411, 2018.","apa":"Brown, M., Assen, F. P., Leithner, A. F., Abe, J., Schachner, H., Asfour, G., … Kerjaschki, D. (2018). Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aal3662","ama":"Brown M, Assen FP, Leithner AF, et al. Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. 2018;359(6382):1408-1411. doi:10.1126/science.aal3662"},"title":"Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice","publist_id":"7428","author":[{"first_name":"Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Markus","last_name":"Brown"},{"orcid":"0000-0003-3470-6119","full_name":"Assen, Frank P","last_name":"Assen","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","first_name":"Frank P"},{"first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X"},{"last_name":"Abe","full_name":"Abe, Jun","first_name":"Jun"},{"first_name":"Helga","full_name":"Schachner, Helga","last_name":"Schachner"},{"first_name":"Gabriele","full_name":"Asfour, Gabriele","last_name":"Asfour"},{"first_name":"Zsuzsanna","last_name":"Bagó Horváth","full_name":"Bagó Horváth, Zsuzsanna"},{"last_name":"Stein","full_name":"Stein, Jens","first_name":"Jens"},{"last_name":"Uhrin","full_name":"Uhrin, Pavel","first_name":"Pavel"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"},{"first_name":"Dontscho","last_name":"Kerjaschki","full_name":"Kerjaschki, Dontscho"}],"article_processing_charge":"No","external_id":{"isi":["000428043600047"],"pmid":["29567714"]},"project":[{"grant_number":"Y 564-B12","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","call_identifier":"FWF","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425"},{"grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"day":"23","publication":"Science","isi":1,"year":"2018","date_published":"2018-03-23T00:00:00Z","doi":"10.1126/science.aal3662","date_created":"2018-12-11T11:46:16Z","page":"1408 - 1411","acknowledgement":"M.B. was supported by the Cell Communication in Health and Disease graduate study program of the Austrian Science Fund (FWF) and the Medical University of Vienna. M.S. was supported by the European Research Council (grant ERC GA 281556) and an FWF START award.\r\nWe thank C. Moussion for establishing the intralymphatic injection at IST Austria and for providing anti-PNAd hybridoma supernatant, R. Förster and A. Braun for sharing the intralymphatic injection technology, K. Vaahtomeri for the lentiviral constructs, M. Hons for establishing in vivo multiphoton imaging, the Sixt lab for intellectual input, M. Schunn for help with the design of the in vivo experiments, F. Langer for technical assistance with the in vivo experiments, the bioimaging facility of IST Austria for support, and R. Efferl for providing the CT26 cell line.","quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"date_updated":"2024-03-27T23:30:09Z","department":[{"_id":"MiSi"}],"_id":"402","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","volume":359,"issue":"6382","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6947"}]},"ec_funded":1,"oa_version":"Published Version","pmid":1,"acknowledged_ssus":[{"_id":"Bio"}],"abstract":[{"text":"During metastasis, malignant cells escape the primary tumor, intravasate lymphatic vessels, and reach draining sentinel lymph nodes before they colonize distant organs via the blood circulation. Although lymph node metastasis in cancer patients correlates with poor prognosis, evidence is lacking as to whether and how tumor cells enter the bloodstream via lymph nodes. To investigate this question, we delivered carcinoma cells into the lymph nodes of mice by microinfusing the cells into afferent lymphatic vessels. We found that tumor cells rapidly infiltrated the lymph node parenchyma, invaded blood vessels, and seeded lung metastases without involvement of the thoracic duct. These results suggest that the lymph node blood vessels can serve as an exit route for systemic dissemination of cancer cells in experimental mouse models. Whether this form of tumor cell spreading occurs in cancer patients remains to be determined.","lang":"eng"}],"month":"03","intvolume":" 359","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/science.aal3662"}]},{"oa_version":"Published Version","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"}],"abstract":[{"text":"Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. Despite the remarkable number of scientific breakthroughs of the last 100 years, the treatment of neurodevelopmental disorders (e.g. autism spectrum disorder, intellectual disability, epilepsy) remains a great challenge. Recent advancements in geno mics, like whole-exome or whole-genome sequencing, have enabled scientists to identify numerous mutations underlying neurodevelopmental disorders. Given the few hundred risk genes that were discovered, the etiological variability and the heterogeneous phenotypic outcomes, the need for genotype -along with phenotype- based diagnosis of individual patients becomes a requisite. Driven by this rationale, in a previous study our group described mutations, identified via whole - exome sequencing, in the gene BCKDK – encoding for a key regulator of branched chain amin o acid (BCAA) catabolism - as a cause of ASD. Following up on the role of BCAAs, in the study described here we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized mainly at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation and severe neurolo gical abnormalities. Additionally, deletion of Slc7a5 from the neural progenitor cell population leads to microcephaly. Interestingly, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Furthermore, whole - exome sequencing of patients diagnosed with neurological dis o r ders helped us identify several patients with autistic traits, microcephaly and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. In conclusion, our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for t he BCAA s in human bra in function. Together with r ecent studies (described in chapter two) that have successfully made the transition into clinical practice, our findings on the role of B CAAs might have a crucial impact on the development of novel individualized therapeutic strategies for ASD. ","lang":"eng"}],"month":"03","alternative_title":["ISTA Thesis"],"file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file","file_id":"6217","checksum":"9f5231c96e0ad945040841a8630232da","date_updated":"2021-02-11T23:30:15Z","file_size":43684035,"creator":"dernst","date_created":"2019-04-05T09:19:17Z","file_name":"2018_Thesis_Tarlungeanu_source.docx"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2018-03-15","file_id":"6218","checksum":"0c33c370aa2010df5c552db57a6d01e9","creator":"dernst","file_size":30511532,"date_updated":"2021-02-11T11:17:16Z","file_name":"2018_Thesis_Tarlungeanu.pdf","date_created":"2019-04-05T09:19:17Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"id":"1183","status":"public","relation":"part_of_dissertation"}]},"_id":"395","status":"public","pubrep_id":"992","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570","616"],"supervisor":[{"last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"}],"date_updated":"2023-09-07T12:38:59Z","department":[{"_id":"GaNo"}],"file_date_updated":"2021-02-11T23:30:15Z","publisher":"Institute of Science and Technology Austria","oa":1,"day":"01","has_accepted_license":"1","year":"2018","doi":"10.15479/AT:ISTA:th_992","date_published":"2018-03-01T00:00:00Z","date_created":"2018-12-11T11:46:14Z","page":"88","project":[{"call_identifier":"FWF","_id":"25473368-B435-11E9-9278-68D0E5697425","grant_number":"F03523","name":"Transmembrane Transporters in Health and Disease"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Tarlungeanu, Dora-Clara. “The Branched Chain Amino Acids in Autism Spectrum Disorders .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_992.","ista":"Tarlungeanu D-C. 2018. The branched chain amino acids in autism spectrum disorders . Institute of Science and Technology Austria.","mla":"Tarlungeanu, Dora-Clara. The Branched Chain Amino Acids in Autism Spectrum Disorders . Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_992.","apa":"Tarlungeanu, D.-C. (2018). The branched chain amino acids in autism spectrum disorders . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_992","ama":"Tarlungeanu D-C. The branched chain amino acids in autism spectrum disorders . 2018. doi:10.15479/AT:ISTA:th_992","short":"D.-C. Tarlungeanu, The Branched Chain Amino Acids in Autism Spectrum Disorders , Institute of Science and Technology Austria, 2018.","ieee":"D.-C. Tarlungeanu, “The branched chain amino acids in autism spectrum disorders ,” Institute of Science and Technology Austria, 2018."},"title":"The branched chain amino acids in autism spectrum disorders ","author":[{"first_name":"Dora-Clara","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","full_name":"Tarlungeanu, Dora-Clara","last_name":"Tarlungeanu"}],"publist_id":"7434","article_processing_charge":"No"},{"related_material":{"record":[{"relation":"part_of_dissertation","id":"682","status":"public"}]},"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2021-02-11T23:30:13Z","file_size":141270528,"date_created":"2019-04-09T07:16:26Z","file_name":"2018_Thesis_Case_Source.doc","access_level":"closed","relation":"source_file","content_type":"application/msword","embargo_to":"open_access","file_id":"6251","checksum":"dcc7b55619d8509dd62b8e99d6cdee44"},{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","embargo":"2019-07-05","file_id":"6252","checksum":"f69fdd5c8709c4e618aa8c1a1221153d","file_size":15193621,"date_updated":"2021-02-11T11:17:14Z","creator":"dernst","file_name":"2018_Thesis_Case.pdf","date_created":"2019-04-09T07:16:23Z"}],"alternative_title":["ISTA Thesis"],"month":"06","abstract":[{"text":"Asymmetries have long been known about in the central nervous system. From gross anatomical differences, such as the presence of the parapineal organ in only one hemisphere of the developing zebrafish, to more subtle differences in activity between both hemispheres, as seen in freely roaming animals or human participants under PET and fMRI imaging analysis. The presence of asymmetries has been demonstrated to have huge behavioural implications, with their disruption often leading to the generation of neurological disorders, memory problems, changes in personality, and in an organism's health and well-being. For my Ph.D. work I aimed to tackle two important avenues of research. The first being the process of input-side dependency in the hippocampus, with the goal of finding a key gene responsible for its development (Gene X). The second project was to do with experience-induced laterality formation in the hippocampus. Specifically, how laterality in the synapse density of the CA1 stratum radiatum (s.r.) could be induced purely through environmental enrichment. Through unilateral tracer injections into the CA3, I was able to selectively measure the properties of synapses within the CA1 and investigate how they differed based upon which hemisphere the presynaptic neurone originated. Having found the existence of a previously unreported reversed (left-isomerism) i.v. mutant, through morpholocal examination of labelled terminals in the CA1 s.r., I aimed to elucidate a key gene responsible for the process of left or right determination of inputs to the CA1 s.r.. This work relates to the previous finding of input-side dependent asymmetry in the wild-type rodent, where the origin of the projecting neurone to the CA1 will determine the morphology of a synapse, to a greater degree than the hemisphere in which the projection terminates. Using left- and right-isomerism i.v. mice, in combination with whole genome sequence analysis, I highlight Ena/VASP-like (Evl) as a potential target for Gene X. In relation to this topic, I also highlight my work in the recently published paper of how knockout of PirB can lead to a lack of input-side dependency in the murine hippocampus. For the second question, I show that the environmental enrichment paradigm will lead to an asymmetry in the synapse densities in the hippocampus of mice. I also highlight that the nature of the enrichment is of less consequence than the process of enrichment itself. I demonstrate that the CA3 region will dramatically alter its projection targets, in relation to environmental stimulation, with the asymmetry in synaptic density, caused by enrichment, relying heavily on commissural fibres. I also highlight the vital importance of input-side dependent asymmetry, as a necessary component of experience-dependent laterality formation in the CA1 s.r.. However, my results suggest that it isn't the only cause, as there appears to be a CA1 dependent mechanism also at play. Upon further investigation, I highlight the significant, and highly important, finding that the changes seen in the CA1 s.r. were predominantly caused through projections from the left-CA3, with the right-CA3 having less involvement in this mechanism.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2021-02-11T23:30:13Z","department":[{"_id":"RySh"}],"date_updated":"2023-09-07T12:39:22Z","supervisor":[{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"ddc":["571","576"],"type":"dissertation","pubrep_id":"1032","status":"public","_id":"51","page":"186","date_created":"2018-12-11T11:44:22Z","doi":"10.15479/AT:ISTA:th_1032","date_published":"2018-06-27T00:00:00Z","year":"2018","has_accepted_license":"1","day":"27","oa":1,"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","author":[{"last_name":"Case","full_name":"Case, Matthew J","id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Matthew J"}],"publist_id":"8003","title":"From the left to the right: A tale of asymmetries, environments, and hippocampal development","citation":{"mla":"Case, Matthew J. From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1032.","short":"M.J. Case, From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development, Institute of Science and Technology Austria, 2018.","ieee":"M. J. Case, “From the left to the right: A tale of asymmetries, environments, and hippocampal development,” Institute of Science and Technology Austria, 2018.","apa":"Case, M. J. (2018). From the left to the right: A tale of asymmetries, environments, and hippocampal development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1032","ama":"Case MJ. From the left to the right: A tale of asymmetries, environments, and hippocampal development. 2018. doi:10.15479/AT:ISTA:th_1032","chicago":"Case, Matthew J. “From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1032.","ista":"Case MJ. 2018. From the left to the right: A tale of asymmetries, environments, and hippocampal development. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"article_processing_charge":"No","publist_id":"8046","author":[{"last_name":"Laukoter","full_name":"Laukoter, Susanne","orcid":"0000-0002-7903-3010","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","first_name":"Susanne"}],"title":"Role of genomic imprinting in cerebral cortex development","citation":{"mla":"Laukoter, Susanne. Role of Genomic Imprinting in Cerebral Cortex Development. Institute of Science and Technology Austria, 2018, pp. 1–139, doi:10.15479/AT:ISTA:th1057.","ama":"Laukoter S. Role of genomic imprinting in cerebral cortex development. 2018:1-139. doi:10.15479/AT:ISTA:th1057","apa":"Laukoter, S. (2018). Role of genomic imprinting in cerebral cortex development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1057","ieee":"S. Laukoter, “Role of genomic imprinting in cerebral cortex development,” Institute of Science and Technology Austria, 2018.","short":"S. Laukoter, Role of Genomic Imprinting in Cerebral Cortex Development, Institute of Science and Technology Austria, 2018.","chicago":"Laukoter, Susanne. “Role of Genomic Imprinting in Cerebral Cortex Development.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1057.","ista":"Laukoter S. 2018. Role of genomic imprinting in cerebral cortex development. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"1 - 139","date_created":"2018-12-11T11:44:08Z","doi":"10.15479/AT:ISTA:th1057","date_published":"2018-11-21T00:00:00Z","year":"2018","has_accepted_license":"1","day":"21","oa":1,"publisher":"Institute of Science and Technology Austria","file_date_updated":"2021-02-11T11:17:16Z","department":[{"_id":"SiHi"}],"date_updated":"2023-09-07T12:40:44Z","supervisor":[{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"ddc":["570"],"type":"dissertation","pubrep_id":"1057","status":"public","_id":"10","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2019-05-10T07:47:04Z","file_name":"Thesis_LaukoterSusanne_FINAL.docx","date_updated":"2019-11-23T23:30:03Z","file_size":17949175,"creator":"dernst","file_id":"6396","checksum":"41fdbf5fdce312802935d88a8ad9932c","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file"},{"file_size":21187245,"date_updated":"2021-02-11T11:17:16Z","creator":"dernst","file_name":"Thesis_LaukoterSusanne_FINAL.pdf","date_created":"2019-05-10T07:47:04Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","embargo":"2019-11-21","file_id":"6397","checksum":"53001a9a0c9e570e598d861bb0af28aa"}],"alternative_title":["ISTA Thesis"],"month":"11","abstract":[{"text":"Genomic imprinting is an epigenetic process that leads to parent of origin-specific gene expression in a subset of genes. Imprinted genes are essential for brain development, and deregulation of imprinting is associated with neurodevelopmental diseases and the pathogenesis of psychiatric disorders. However, the cell-type specificity of imprinting at single cell resolution, and how imprinting and thus gene dosage regulates neuronal circuit assembly is still largely unknown. Here, MADM (Mosaic Analysis with Double Markers) technology was employed to assess genomic imprinting at single cell level. By visualizing MADM-induced uniparental disomies (UPDs) in distinct colors at single cell level in genetic mosaic animals, this experimental paradigm provides a unique quantitative platform to systematically assay the UPD-mediated imbalances in imprinted gene expression at unprecedented resolution. An experimental pipeline based on FACS, RNA-seq and bioinformatics analysis was established and applied to systematically map cell-type-specific ‘imprintomes’ in the mouse brain. The results revealed that parental-specific expression of imprinted genes per se is rarely cell-type-specific even at the individual cell level. Conversely, when we extended the comparison to downstream responses resulting from imbalanced imprinted gene expression, we discovered an unexpectedly high degree of cell-type specificity. Furthermore, we determined a novel function of genomic imprinting in cortical astrocyte production and in olfactory bulb (OB) granule cell generation. These results suggest important functional implication of genomic imprinting for generating cell-type diversity in the brain. In addition, MADM provides a powerful tool to study candidate genes by concomitant genetic manipulation and fluorescent labelling of single cells. MADM-based candidate gene approach was utilized to identify potential imprinted genes involved in the generation of cortical astrocytes and OB granule cells. We investigated p57Kip2, a maternally expressed gene and known cell cycle regulator. Although we found that p57Kip2 does not play a role in these processes, we detected an unexpected function of the paternal allele previously thought to be silent. Finally, we took advantage of a key property of MADM which is to allow unambiguous investigation of environmental impact on single cells. The experimental pipeline based on FACS and RNA-seq analysis of MADM-labeled cells was established to probe the functional differences of single cell loss of gene function compared to global loss of function on a transcriptional level. With this method, both common and distinct responses were isolated due to cell-autonomous and non-autonomous effects acting on genotypically identical cells. As a result, transcriptional changes were identified which result solely from the surrounding environment. Using the MADM technology to study genomic imprinting at single cell resolution, we have identified cell-type-specific gene expression, novel gene function and the impact of environment on single cell transcriptomes. Together, these provide important insights to the understanding of mechanisms regulating cell-type specificity and thus diversity in the brain.","lang":"eng"}],"oa_version":"Published Version"},{"has_accepted_license":"1","year":"2018","day":"12","page":"99","date_published":"2018-04-12T00:00:00Z","doi":"10.15479/AT:ISTA:th_998","date_created":"2018-12-11T11:45:49Z","acknowledgement":"First of all I would like to thank Michael Sixt for giving me the opportunity to work in \r\nhis group and for his support throughout the years. He is a truly inspiring person and \r\nthe best boss one can imagine. I would also like to thank all current and past \r\nmembers of the Sixt group for their help and the great working atmosphere in the lab. \r\nIt is a true privilege to work with such a bright, funny and friendly group of people and \r\nI’m proud that I could be part of it. Furthermore, I would like to say ‘thank you’ to Daria Siekhaus for all the meetings and discussion we had throughout the years \r\nand to Federica Benvenuti for being part of my committee. I am also grateful to Jack \r\nMerrin in the nanofabrication facility and all the people working in the bioimaging-\r\n, the electron microscopy- and the preclinical facilities.","publisher":"Institute of Science and Technology Austria","oa":1,"citation":{"ista":"Leithner AF. 2018. Branched actin networks in dendritic cell biology. Institute of Science and Technology Austria.","chicago":"Leithner, Alexander F. “Branched Actin Networks in Dendritic Cell Biology.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_998.","ama":"Leithner AF. Branched actin networks in dendritic cell biology. 2018. doi:10.15479/AT:ISTA:th_998","apa":"Leithner, A. F. (2018). Branched actin networks in dendritic cell biology. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_998","ieee":"A. F. Leithner, “Branched actin networks in dendritic cell biology,” Institute of Science and Technology Austria, 2018.","short":"A.F. Leithner, Branched Actin Networks in Dendritic Cell Biology, Institute of Science and Technology Austria, 2018.","mla":"Leithner, Alexander F. Branched Actin Networks in Dendritic Cell Biology. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_998."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander F","orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F","last_name":"Leithner"}],"publist_id":"7542","article_processing_charge":"No","title":"Branched actin networks in dendritic cell biology","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"d5e3edbac548c26c1fa43a4b37a54a4c","file_id":"6219","creator":"dernst","file_size":29027671,"date_updated":"2021-02-11T23:30:17Z","file_name":"PhD_thesis_AlexLeithner_final_version.docx","date_created":"2019-04-05T09:23:11Z"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2019-04-15","checksum":"071f7476db29e41146824ebd0697cb10","file_id":"6220","creator":"dernst","file_size":66045341,"date_updated":"2021-02-11T11:17:16Z","file_name":"PhD_thesis_AlexLeithner.pdf","date_created":"2019-04-05T09:23:11Z"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1321"}]},"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"abstract":[{"lang":"eng","text":"In the here presented thesis, we explore the role of branched actin networks in cell migration and antigen presentation, the two most relevant processes in dendritic cell biology. Branched actin networks construct lamellipodial protrusions at the leading edge of migrating cells. These are typically seen as adhesive structures, which mediate force transduction to the extracellular matrix that leads to forward locomotion. We ablated Arp2/3 nucleation promoting factor WAVE in DCs and found that the resulting cells lack lamellipodial protrusions. Instead, depending on the maturation state, one or multiple filopodia were formed. By challenging these cells in a variety of migration assays we found that lamellipodial protrusions are dispensable for the locomotion of leukocytes and actually dampen the speed of migration. However, lamellipodia are critically required to negotiate complex environments that DCs experience while they travel to the next draining lymph node. Taken together our results suggest that leukocyte lamellipodia have rather a sensory- than a force transducing function. Furthermore, we show for the first time structure and dynamics of dendritic cell F-actin at the immunological synapse with naïve T cells. Dendritic cell F-actin appears as dynamic foci that are nucleated by the Arp2/3 complex. WAVE ablated dendritic cells show increased membrane tension, leading to an altered ultrastructure of the immunological synapse and severe T cell priming defects. These results point towards a previously unappreciated role of the cellular mechanics of dendritic cells in T cell activation. Additionally, we present a novel cell culture based system for the differentiation of dendritic cells from conditionally immortalized hematopoietic precursors. These precursor cells are genetically tractable via the CRISPR/Cas9 system while they retain their ability to differentiate into highly migratory dendritic cells and other immune cells. This will foster the study of all aspects of dendritic cell biology and beyond. "}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"04","supervisor":[{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T12:39:44Z","ddc":["571","599","610"],"department":[{"_id":"MiSi"}],"file_date_updated":"2021-02-11T23:30:17Z","_id":"323","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"998"},{"alternative_title":["ISTA Thesis"],"month":"01","abstract":[{"lang":"eng","text":"The whole life cycle of plants as well as their responses to environmental stimuli is governed by a complex network of hormonal regulations. A number of studies have demonstrated an essential role of both auxin and cytokinin in the regulation of many aspects of plant growth and development including embryogenesis, postembryonic organogenic processes such as root, and shoot branching, root and shoot apical meristem activity and phyllotaxis. Over the last decades essential knowledge on the key molecular factors and pathways that spatio-temporally define auxin and cytokinin activities in the plant body has accumulated. However, how both hormonal pathways are interconnected by a complex network of interactions and feedback circuits that determines the final outcome of the individual hormone actions is still largely unknown. Root system architecture establishment and in particular formation of lateral organs is prime example of developmental process at whose regulation both auxin and cytokinin pathways converge. To dissect convergence points and pathways that tightly balance auxin - cytokinin antagonistic activities that determine the root branching pattern transcriptome profiling was applied. Genome wide expression analyses of the xylem pole pericycle, a tissue giving rise to lateral roots, led to identification of genes that are highly responsive to combinatorial auxin and cytokinin treatments and play an essential function in the auxin-cytokinin regulated root branching. SYNERGISTIC AUXIN CYTOKININ 1 (SYAC1) gene, which encodes for a protein of unknown function, was detected among the top candidate genes of which expression was synergistically up-regulated by simultaneous hormonal treatment. Plants with modulated SYAC1 activity exhibit severe defects in the root system establishment and attenuate developmental responses to both auxin and cytokinin. To explore the biological function of the SYAC1, we employed different strategies including expression pattern analysis, subcellular localization and phenotypic analyses of the syac1 loss-of-function and gain-of-function transgenic lines along with the identification of the SYAC1 interaction partners. Detailed functional characterization revealed that SYAC1 acts as a developmentally specific regulator of the secretory pathway to control deposition of cell wall components and thereby rapidly fine tune elongation growth."}],"oa_version":"Published Version","related_material":{"record":[{"id":"1024","status":"public","relation":"part_of_dissertation"}]},"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"checksum":"0c9d6d1c80d9857e6e545213467bbcb2","file_id":"6226","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"2018_Hurny_thesis_source.docx","date_created":"2019-04-05T09:37:56Z","creator":"dernst","file_size":28112114,"date_updated":"2020-12-02T23:30:08Z"},{"date_updated":"2020-12-02T09:52:16Z","file_size":12524427,"creator":"dernst","date_created":"2019-04-05T09:37:55Z","file_name":"2018_Hurny_thesis.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"ecbe481a1413d270bd501b872c7ed54f","file_id":"6227","embargo":"2019-07-10"}],"language":[{"iso":"eng"}],"type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"930","_id":"539","file_date_updated":"2020-12-02T23:30:08Z","department":[{"_id":"EvBe"}],"supervisor":[{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"}],"date_updated":"2023-09-07T12:41:06Z","ddc":["570"],"publisher":"Institute of Science and Technology Austria","oa":1,"page":"147","doi":"10.15479/AT:ISTA:th_930","date_published":"2018-01-01T00:00:00Z","date_created":"2018-12-11T11:47:03Z","has_accepted_license":"1","year":"2018","day":"01","publist_id":"7277","author":[{"first_name":"Andrej","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","last_name":"Hurny","full_name":"Hurny, Andrej","orcid":"0000-0003-3638-1426"}],"article_processing_charge":"No","title":"Identification and characterization of novel auxin-cytokinin cross-talk components","citation":{"ista":"Hurny A. 2018. Identification and characterization of novel auxin-cytokinin cross-talk components. Institute of Science and Technology Austria.","chicago":"Hurny, Andrej. “Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_930.","short":"A. Hurny, Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components, Institute of Science and Technology Austria, 2018.","ieee":"A. Hurny, “Identification and characterization of novel auxin-cytokinin cross-talk components,” Institute of Science and Technology Austria, 2018.","ama":"Hurny A. Identification and characterization of novel auxin-cytokinin cross-talk components. 2018. doi:10.15479/AT:ISTA:th_930","apa":"Hurny, A. (2018). Identification and characterization of novel auxin-cytokinin cross-talk components. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_930","mla":"Hurny, Andrej. Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_930."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"oa":1,"publisher":"Institute of Science and Technology Austria","day":"27","year":"2018","has_accepted_license":"1","date_created":"2018-12-11T11:44:21Z","doi":"10.15479/AT:ISTA:th_1042","date_published":"2018-08-27T00:00:00Z","page":"104","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Gridchyn, Igor. Reactivation Content Is Important for Consolidation of Spatial Memory. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1042.","apa":"Gridchyn, I. (2018). Reactivation content is important for consolidation of spatial memory. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1042","ama":"Gridchyn I. Reactivation content is important for consolidation of spatial memory. 2018. doi:10.15479/AT:ISTA:th_1042","short":"I. Gridchyn, Reactivation Content Is Important for Consolidation of Spatial Memory, Institute of Science and Technology Austria, 2018.","ieee":"I. Gridchyn, “Reactivation content is important for consolidation of spatial memory,” Institute of Science and Technology Austria, 2018.","chicago":"Gridchyn, Igor. “Reactivation Content Is Important for Consolidation of Spatial Memory.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1042.","ista":"Gridchyn I. 2018. Reactivation content is important for consolidation of spatial memory. Institute of Science and Technology Austria."},"title":"Reactivation content is important for consolidation of spatial memory","article_processing_charge":"No","author":[{"orcid":"0000-0002-1807-1929","full_name":"Gridchyn, Igor","last_name":"Gridchyn","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","first_name":"Igor"}],"publist_id":"8006","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The hippocampus is a key brain region for spatial memory and navigation and is needed at all stages of memory, including encoding, consolidation, and recall. Hippocampal place cells selectively discharge at specific locations of the environment to form a cognitive map of the space. During the rest period and sleep following spatial navigation and/or learning, the waking activity of the place cells is reactivated within high synchrony events. This reactivation is thought to be important for memory consolidation and stabilization of the spatial representations. The aim of my thesis was to directly test whether the reactivation content encoded in firing patterns of place cells is important for consolidation of spatial memories. In particular, I aimed to test whether, in cases when multiple spatial memory traces are acquired during learning, the specific disruption of the reactivation of a subset of these memories leads to the selective disruption of the corresponding memory traces or through memory interference the other learned memories are disrupted as well. In this thesis, using a modified cheeseboard paradigm and a closed-loop recording setup with feedback optogenetic stimulation, I examined how the disruption of the reactivation of specific spiking patterns affects consolidation of the corresponding memory traces. To obtain multiple distinctive memories, animals had to perform a spatial task in two distinct cheeseboard environments and the reactivation of spiking patterns associated with one of the environments (target) was disrupted after learning during four hours rest period using a real-time decoding method. This real-time decoding method was capable of selectively affecting the firing rates and cofiring correlations of the target environment-encoding cells. The selective disruption led to behavioural impairment in the memory tests after the rest periods in the target environment but not in the other undisrupted control environment. In addition, the map of the target environment was less stable in the impaired memory tests compared to the learning session before than the map of the control environment. However, when the animal relearned the task, the same map recurred in the target environment that was present during learning before the disruption. Altogether my work demonstrated that the reactivation content is important: assembly-related disruption of reactivation can lead to a selective memory impairment and deficiency in map stability. These findings indeed suggest that reactivated assembly patterns reflect processes associated with the consolidation of memory traces. "}],"month":"08","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":7666687,"date_updated":"2021-02-11T23:30:22Z","file_name":"2018_Thesis_Gridchyn_source.docx","date_created":"2019-04-08T13:36:01Z","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"7db4415e435590fa33542c7b0a0321d7","file_id":"6236"},{"checksum":"f96f3fe8979f7b1e6db6acaca962b10c","file_id":"6237","embargo":"2019-08-29","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-04-08T13:36:01Z","file_name":"2018_Thesis_Gridchyn.pdf","creator":"dernst","date_updated":"2021-02-11T11:17:18Z","file_size":6034153}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"_id":"48","pubrep_id":"1042","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","ddc":["573"],"date_updated":"2023-09-07T12:42:44Z","supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036"}],"file_date_updated":"2021-02-11T23:30:22Z","department":[{"_id":"JoCs"}]},{"doi":"10.15479/AT:ISTA:th1064","date_published":"2018-07-01T00:00:00Z","date_created":"2018-12-11T11:44:08Z","page":"96","day":"01","has_accepted_license":"1","year":"2018","publisher":"Institute of Science and Technology Austria","oa":1,"title":"Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ","publist_id":"8047","author":[{"first_name":"Vera","id":"47F080FE-F248-11E8-B48F-1D18A9856A87","full_name":"Belyaeva, Vera","last_name":"Belyaeva"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Belyaeva, Vera. Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo . Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1064.","apa":"Belyaeva, V. (2018). Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1064","ama":"Belyaeva V. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . 2018. doi:10.15479/AT:ISTA:th1064","short":"V. Belyaeva, Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo , Institute of Science and Technology Austria, 2018.","ieee":"V. Belyaeva, “Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ,” Institute of Science and Technology Austria, 2018.","chicago":"Belyaeva, Vera. “Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1064.","ista":"Belyaeva V. 2018. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . Institute of Science and Technology Austria."},"file":[{"file_name":"2018_Thesis_Belyaeva_source.docx","date_created":"2019-04-08T14:13:12Z","creator":"dernst","file_size":102737483,"date_updated":"2020-07-14T12:48:14Z","checksum":"d27b2465cb70d0c9678a0381b9b6ced1","file_id":"6243","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"creator":"dernst","file_size":88077843,"date_updated":"2021-02-11T11:17:16Z","file_name":"2018_Thesis_Belyaeva.pdf","date_created":"2019-04-08T14:14:08Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2019-11-19","checksum":"a2939b61bde2de7b8ced77bbae0eaaed","file_id":"6244"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","month":"07","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"Immune cells migrating to the sites of infection navigate through diverse tissue architectures and switch their migratory mechanisms upon demand. However, little is known about systemic regulators that could allow the acquisition of these mechanisms. We performed a genetic screen in Drosophila melanogaster to identify regulators of germband invasion by embryonic macrophages into the confined space between the ectoderm and mesoderm. We have found that bZIP circadian transcription factors (TFs) Kayak (dFos) and Vrille (dNFIL3) have opposite effects on macrophage germband infiltration: Kayak facilitated and Vrille inhibited it. These TFs are enriched in the macrophages during migration and genetically interact to control it. Kayak sets a less coordinated mode of migration of the macrophage group and increases the probability and length of Levy walks. Intriguingly, the motility of kayak mutant macrophages was also strongly affected during initial germband invasion but not along another less confined route. Inhibiting Rho1 signaling within the tail ectoderm partially rescued the Kayak mutant phenotype, strongly suggesting that migrating macrophages have to overcome a barrier imposed by the stiffness of the ectoderm. Also, Kayak appeared to be important for the maintenance of the round cell shape and the rear edge translocation of the macrophages invading the germband. Complementary to this, the cortical actin cytoskeleton of Kayak- deficient macrophages was strongly affected. RNA sequencing revealed the filamin Cheerio and tetraspanin TM4SF to be downstream of Kayak. Chromatin immunoprecipitation and immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Indeed, Cheerio, TM4SF and Diaphanous are required within macrophages for germband invasion, and expression of constitutively active Diaphanous in macrophages was able to rescue the kayak mutant phenotype. Moreover, Cher and Diaphanous are also reduced in the macrophages overexpressing Vrille. We hypothesize that Kayak, through its targets, increases actin polymerization and cortical tension in macrophages and thus allows extra force generation necessary for macrophage dissemination and migration through confined stiff tissues, while Vrille counterbalances it.","lang":"eng"}],"department":[{"_id":"DaSi"}],"file_date_updated":"2021-02-11T11:17:16Z","ddc":["570"],"supervisor":[{"first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","last_name":"Siekhaus"}],"date_updated":"2023-09-07T12:43:10Z","status":"public","pubrep_id":"1064","type":"dissertation","_id":"9"},{"alternative_title":["ISTA Thesis"],"month":"10","abstract":[{"text":"A major challenge in neuroscience research is to dissect the circuits that orchestrate behavior in health and disease. Proteins from a wide range of non-mammalian species, such as microbial opsins, have been successfully transplanted to specific neuronal targets to override their natural communication patterns. The goal of our work is to manipulate synaptic communication in a manner that closely incorporates the functional intricacies of synapses by preserving temporal encoding (i.e. the firing pattern of the presynaptic neuron) and connectivity (i.e. target specific synapses rather than specific neurons). Our strategy to achieve this goal builds on the use of non-mammalian transplants to create a synthetic synapse. The mode of modulation comes from pre-synaptic uptake of a synthetic neurotransmitter (SN) into synaptic vesicles by means of a genetically targeted transporter selective for the SN. Upon natural vesicular release, exposure of the SN to the synaptic cleft will modify the post-synaptic potential through an orthogonal ligand gated ion channel. To achieve this goal we have functionally characterized a mixed cationic methionine-gated ion channel from Arabidopsis thaliana, designed a method to functionally characterize a synthetic transporter in isolated synaptic vesicles without the need for transgenic animals, identified and extracted multiple prokaryotic uptake systems that are substrate specific for methionine (Met), and established a primary/cell line co-culture system that would allow future combinatorial testing of this orthogonal transmitter-transporter-channel trifecta. Synthetic synapses will provide a unique opportunity to manipulate synaptic communication while maintaining the electrophysiological integrity of the pre-synaptic cell. In this way, information may be preserved that was generated in upstream circuits and that could be essential for concerted function and information processing. ","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"new_edition","status":"public","id":"7132"}]},"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"9d2c2dca04b00e485470c28b262af59a","file_id":"6267","embargo":"2019-11-24","creator":"dernst","date_updated":"2021-02-11T11:17:16Z","file_size":4906420,"date_created":"2019-04-09T14:12:40Z","file_name":"2018_Thesis_McKenzie.pdf"},{"embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","checksum":"50b58c272899601bc6fd9642c4dc97f1","file_id":"6268","file_size":5053545,"date_updated":"2020-07-14T12:47:25Z","creator":"dernst","file_name":"2018_Thesis_McKenzie_source.docx","date_created":"2019-04-09T14:12:40Z"}],"language":[{"iso":"eng"}],"type":"dissertation","status":"public","pubrep_id":"1055","_id":"6266","file_date_updated":"2021-02-11T11:17:16Z","department":[{"_id":"HaJa"}],"supervisor":[{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","last_name":"Janovjak"}],"date_updated":"2023-09-07T13:02:37Z","ddc":["571","573"],"publisher":"Institute of Science and Technology Austria","oa":1,"page":"95","doi":"10.15479/at:ista:th_1055","date_published":"2018-10-31T00:00:00Z","date_created":"2019-04-09T14:13:39Z","has_accepted_license":"1","year":"2018","day":"31","author":[{"full_name":"Mckenzie, Catherine","last_name":"Mckenzie","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","first_name":"Catherine"}],"article_processing_charge":"No","title":"Design and characterization of methods and biological components to realize synthetic neurotransmission ","citation":{"ista":"Mckenzie C. 2018. Design and characterization of methods and biological components to realize synthetic neurotransmission . Institute of Science and Technology Austria.","chicago":"Mckenzie, Catherine. “Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/at:ista:th_1055.","short":"C. Mckenzie, Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission , Institute of Science and Technology Austria, 2018.","ieee":"C. Mckenzie, “Design and characterization of methods and biological components to realize synthetic neurotransmission ,” Institute of Science and Technology Austria, 2018.","ama":"Mckenzie C. Design and characterization of methods and biological components to realize synthetic neurotransmission . 2018. doi:10.15479/at:ista:th_1055","apa":"Mckenzie, C. (2018). Design and characterization of methods and biological components to realize synthetic neurotransmission . Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th_1055","mla":"Mckenzie, Catherine. Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission . Institute of Science and Technology Austria, 2018, doi:10.15479/at:ista:th_1055."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"_id":"50","type":"dissertation","status":"public","pubrep_id":"1031","supervisor":[{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"date_updated":"2023-09-07T12:48:16Z","ddc":["570","591","596"],"file_date_updated":"2021-02-11T23:30:21Z","department":[{"_id":"CaHe"}],"abstract":[{"text":"The Wnt/planar cell polarity (Wnt/PCP) pathway determines planar polarity of epithelial cells in both vertebrates and invertebrates. The role that Wnt/PCP signaling plays in mesenchymal contexts, however, is only poorly understood. While previous studies have demonstrated the capacity of Wnt/PCP signaling to polarize and guide directed migration of mesenchymal cells, it remains unclear whether endogenous Wnt/PCP signaling performs these functions instructively, as it does in epithelial cells. Here we developed a light-switchable version of the Wnt/PCP receptor Frizzled 7 (Fz7) to unambiguously distinguish between an instructive and a permissive role of Wnt/PCP signaling for the directional collective migration of mesendoderm progenitor cells during zebrafish gastrulation. We show that prechordal plate (ppl) cell migration is defective in maternal-zygotic fz7a and fz7b (MZ fz7a,b) double mutant embryos, and that Fz7 functions cell-autonomously in this process by promoting ppl cell protrusion formation and directed migration. We further show that local activation of Fz7 can direct ppl cell migration both in vitro and in vivo. Surprisingly, however, uniform Fz7 activation is sufficient to fully rescue the ppl cell migration defect in MZ fz7a,b mutant embryos, indicating that Wnt/PCP signaling functions permissively rather than instructively in directed mesendoderm cell migration during zebrafish gastrulation.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"06","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"creator":"dernst","file_size":31576521,"date_updated":"2021-02-11T11:17:17Z","file_name":"2018_Thesis_Capek.pdf","date_created":"2019-04-08T13:42:26Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2019-06-25","checksum":"d3eca3dcacb67bffdde6e6609c31cdd0","file_id":"6238"},{"file_name":"2018_Thesis_Capek_source.docx","date_created":"2019-04-08T13:42:27Z","creator":"dernst","file_size":38992956,"date_updated":"2021-02-11T23:30:21Z","file_id":"6239","checksum":"876deb14067e638aba65d209668bd821","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1100"},{"relation":"part_of_dissertation","id":"661","status":"public"},{"relation":"part_of_dissertation","id":"676","status":"public"}]},"citation":{"ista":"Capek D. 2018. Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. Institute of Science and Technology Austria.","chicago":"Capek, Daniel. “Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1031.","apa":"Capek, D. (2018). Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1031","ama":"Capek D. Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. 2018. doi:10.15479/AT:ISTA:TH_1031","ieee":"D. Capek, “Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration,” Institute of Science and Technology Austria, 2018.","short":"D. Capek, Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration, Institute of Science and Technology Austria, 2018.","mla":"Capek, Daniel. Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1031."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Capek","full_name":"Capek, Daniel","orcid":"0000-0001-5199-9940","first_name":"Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"8004","article_processing_charge":"No","title":"Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration","publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2018","day":"22","page":"95","doi":"10.15479/AT:ISTA:TH_1031","date_published":"2018-06-22T00:00:00Z","date_created":"2018-12-11T11:44:21Z"},{"department":[{"_id":"CaGu"}],"file_date_updated":"2021-02-11T11:17:14Z","ddc":["576","579"],"supervisor":[{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"}],"date_updated":"2023-09-07T12:48:43Z","status":"public","pubrep_id":"1059","type":"dissertation","_id":"26","related_material":{"record":[{"status":"public","id":"704","relation":"part_of_dissertation"}]},"file":[{"file_size":9190845,"date_updated":"2020-07-14T12:45:43Z","creator":"dernst","file_name":"Thesis_Steinrueck_final.docx","date_created":"2019-02-08T10:51:22Z","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_id":"5941","checksum":"413cbce1cd1debeae3abe2a25dbc70d1"},{"file_name":"Thesis_Steinrueck_final.pdf","date_created":"2019-02-08T10:51:22Z","file_size":7521973,"date_updated":"2021-02-11T11:17:14Z","creator":"dernst","embargo":"2019-11-02","file_id":"5942","checksum":"3def8b7854c8b42d643597ce0215efac","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","month":"10","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"Expression of genes is a fundamental molecular phenotype that is subject to evolution by different types of mutations. Both the rate and the effect of mutations may depend on the DNA sequence context of a particular gene or a particular promoter sequence. In this thesis I investigate the nature of this dependence using simple genetic systems in Escherichia coli. With these systems I explore the evolution of constitutive gene expression from random starting sequences at different loci on the chromosome and at different locations in sequence space. First, I dissect chromosomal neighborhood effects that underlie locus-dependent differences in the potential of a gene under selection to become more highly expressed. Next, I find that the effects of point mutations in promoter sequences are dependent on sequence context, and that an existing energy matrix model performs poorly in predicting relative expression of unrelated sequences. Finally, I show that a substantial fraction of random sequences contain functional promoters and I present an extended thermodynamic model that predicts promoter strength in full sequence space. Taken together, these results provide new insights and guides on how to integrate information on sequence context to improve our qualitative and quantitative understanding of bacterial gene expression, with implications for rapid evolution of drug resistance, de novo evolution of genes, and horizontal gene transfer.","lang":"eng"}],"title":"The influence of sequence context on the evolution of bacterial gene expression","author":[{"id":"2C023F40-F248-11E8-B48F-1D18A9856A87","first_name":"Magdalena","last_name":"Steinrück","orcid":"0000-0003-1229-9719","full_name":"Steinrück, Magdalena"}],"publist_id":"8029","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Steinrück M. 2018. The influence of sequence context on the evolution of bacterial gene expression. Institute of Science and Technology Austria.","chicago":"Steinrück, Magdalena. “The Influence of Sequence Context on the Evolution of Bacterial Gene Expression.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1059.","apa":"Steinrück, M. (2018). The influence of sequence context on the evolution of bacterial gene expression. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1059","ama":"Steinrück M. The influence of sequence context on the evolution of bacterial gene expression. 2018. doi:10.15479/AT:ISTA:th1059","short":"M. Steinrück, The Influence of Sequence Context on the Evolution of Bacterial Gene Expression, Institute of Science and Technology Austria, 2018.","ieee":"M. Steinrück, “The influence of sequence context on the evolution of bacterial gene expression,” Institute of Science and Technology Austria, 2018.","mla":"Steinrück, Magdalena. The Influence of Sequence Context on the Evolution of Bacterial Gene Expression. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1059."},"doi":"10.15479/AT:ISTA:th1059","date_published":"2018-10-30T00:00:00Z","date_created":"2018-12-11T11:44:14Z","page":"109","day":"30","has_accepted_license":"1","year":"2018","publisher":"Institute of Science and Technology Austria","oa":1},{"_id":"5816","status":"public","type":"journal_article","date_updated":"2024-03-27T23:30:26Z","department":[{"_id":"GeKa"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Solid-state qubit manipulation and read-out fidelities are reaching fault-tolerance, but quantum error correction requires millions of physical qubits and therefore a scalable quantum computer architecture. To solve signal-line bandwidth and fan-out problems, microwave sources required for qubit manipulation might be embedded close to the qubit chip, typically operating at temperatures below 4 K. Here, we perform the first low temperature measurements of a 130 nm BiCMOS based SiGe voltage controlled oscillator at cryogenic temperature. We determined the frequency and output power dependence on temperature and magnetic field up to 5 T and measured the temperature influence on its noise performance. The device maintains its full functionality from 300 K to 4 K. The carrier frequency at 4 K increases by 3% with respect to the carrier frequency at 300 K, and the output power at 4 K increases by 10 dB relative to the output power at 300 K. The frequency tuning range of approximately 20% remains unchanged between 300 K and 4 K. In an in-plane magnetic field of 5 T, the carrier frequency shifts by only 0.02% compared to the frequency at zero magnetic field."}],"month":"11","intvolume":" 89","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.09522"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00346748"]},"publication_status":"published","volume":89,"related_material":{"record":[{"id":"10058","status":"public","relation":"dissertation_contains"}]},"issue":"11","article_number":"114701","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Hollmann, Arne, et al. “30 GHz-Voltage Controlled Oscillator Operating at 4 K.” Review of Scientific Instruments, vol. 89, no. 11, 114701, AIP Publishing, 2018, doi:10.1063/1.5038258.","ama":"Hollmann A, Jirovec D, Kucharski M, Kissinger D, Fischer G, Schreiber LR. 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments. 2018;89(11). doi:10.1063/1.5038258","apa":"Hollmann, A., Jirovec, D., Kucharski, M., Kissinger, D., Fischer, G., & Schreiber, L. R. (2018). 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments. AIP Publishing. https://doi.org/10.1063/1.5038258","ieee":"A. Hollmann, D. Jirovec, M. Kucharski, D. Kissinger, G. Fischer, and L. R. Schreiber, “30 GHz-voltage controlled oscillator operating at 4 K,” Review of Scientific Instruments, vol. 89, no. 11. AIP Publishing, 2018.","short":"A. Hollmann, D. Jirovec, M. Kucharski, D. Kissinger, G. Fischer, L.R. Schreiber, Review of Scientific Instruments 89 (2018).","chicago":"Hollmann, Arne, Daniel Jirovec, Maciej Kucharski, Dietmar Kissinger, Gunter Fischer, and Lars R. Schreiber. “30 GHz-Voltage Controlled Oscillator Operating at 4 K.” Review of Scientific Instruments. AIP Publishing, 2018. https://doi.org/10.1063/1.5038258.","ista":"Hollmann A, Jirovec D, Kucharski M, Kissinger D, Fischer G, Schreiber LR. 2018. 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments. 89(11), 114701."},"title":"30 GHz-voltage controlled oscillator operating at 4 K","author":[{"first_name":"Arne","last_name":"Hollmann","full_name":"Hollmann, Arne"},{"id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel","last_name":"Jirovec"},{"last_name":"Kucharski","full_name":"Kucharski, Maciej","first_name":"Maciej"},{"first_name":"Dietmar","last_name":"Kissinger","full_name":"Kissinger, Dietmar"},{"first_name":"Gunter","full_name":"Fischer, Gunter","last_name":"Fischer"},{"last_name":"Schreiber","full_name":"Schreiber, Lars R.","first_name":"Lars R."}],"article_processing_charge":"No","external_id":{"isi":["000451735700054"],"arxiv":["1804.09522"]},"publisher":"AIP Publishing","quality_controlled":"1","oa":1,"day":"01","publication":"Review of Scientific Instruments","isi":1,"year":"2018","doi":"10.1063/1.5038258","date_published":"2018-11-01T00:00:00Z","date_created":"2019-01-10T14:22:23Z"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Antibiotic resistance can emerge spontaneously through genomic mutation and render treatment ineffective. To counteract this process, in addition to the discovery and description of resistance mechanisms,a deeper understanding of resistanceevolvabilityand its determinantsis needed. To address this challenge, this thesisuncoversnew genetic determinants of resistance evolvability using a customized robotic setup, exploressystematic ways in which resistance evolution is perturbed due to dose-responsecharacteristics of drugs and mutation rate differences,and mathematically investigates the evolutionary fate of one specific type of evolvability modifier -a stress-induced mutagenesis allele.We find severalgenes which strongly inhibit or potentiate resistance evolution. In order to identify them, we first developedan automated high-throughput feedback-controlled protocol whichkeeps the population size and selection pressure approximately constant for hundreds of cultures by dynamically re-diluting the cultures and adjusting the antibiotic concentration. We implementedthis protocol on a customized liquid handling robot and propagated 100 different gene deletion strains of Escherichia coliin triplicate for over 100 generations in tetracycline and in chloramphenicol, and comparedtheir adaptation rates.We find a diminishing returns pattern, where initially sensitive strains adapted more compared to less sensitive ones. Our data uncover that deletions of certain genes which do not affect mutation rate,including efflux pump components, a chaperone and severalstructural and regulatory genes can strongly and reproducibly alterresistance evolution. Sequencing analysis of evolved populations indicates that epistasis with resistance mutations is the most likelyexplanation. This work could inspire treatment strategies in which targeted inhibitors of evolvability mechanisms will be given alongside antibiotics to slow down resistance evolution and extend theefficacy of antibiotics.We implemented astochasticpopulation genetics model, toverifyways in which general properties, namely, dose-response characteristics of drugs and mutation rates, influence evolutionary dynamics. In particular, under the exposure to antibiotics with shallow dose-response curves,bacteria have narrower distributions of fitness effects of new mutations. We show that in silicothis also leads to slower resistance evolution. We see and confirm with experiments that increased mutation rates, apart from speeding up evolution, also leadto high reproducibility of phenotypic adaptation in a context of continually strong selection pressure.Knowledge of these patterns can aid in predicting the dynamics of antibiotic resistance evolutionand adapting treatment schemes accordingly.Focusing on a previously described type of evolvability modifier –a stress-induced mutagenesis allele –we find conditions under which it can persist in a population under periodic selectionakin to clinical treatment. We set up a deterministic infinite populationcontinuous time model tracking the frequencies of a mutator and resistance allele and evaluate various treatment schemes in how well they maintain a stress-induced mutator allele. In particular,a high diversity of stresses is crucial for the persistence of the mutator allele. This leads to a general trade-off where exactly those diversifying treatment schemes which are likely to decrease levels of resistance could lead to stronger selection of highly evolvable genotypes.In the long run, this work will lead to a deeper understanding of the genetic and cellular mechanisms involved in antibiotic resistance evolution and could inspire new strategies for slowing down its rate. 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