[{"day":"11","OA_type":"gold","fulldoi":"https://doi.org/10.1126/sciadv.adp2102","publication_status":"published","file_date_updated":"2024-11-04T09:35:49Z","date_published":"2024-10-11T00:00:00Z","article_type":"original","scopus_import":"1","das_tickbox":"1","PlanS_conform":"1","OA_place":"publisher","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"type":"journal_article","author":[{"full_name":"Garcia Castillo, Diego Fernando","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","last_name":"Garcia Castillo","first_name":"Diego Fernando"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"full_name":"Larsson, Jenny","first_name":"Jenny","last_name":"Larsson"},{"full_name":"Stankowski, Sean","first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"full_name":"Butlin, Roger","first_name":"Roger","last_name":"Butlin"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"}],"month":"10","article_number":"eadp2102","date_created":"2024-11-03T23:01:44Z","publication_identifier":{"eissn":["2375-2548"]},"citation":{"mla":"Garcia Castillo, Diego Fernando, et al. “Predicting Rapid Adaptation in Time from Adaptation in Space: A 30-Year Field Experiment in Marine Snails.” <i>Science Advances</i>, vol. 10, no. 41, eadp2102, AAAS, 2024, doi:<a href=\"https://doi.org/10.1126/sciadv.adp2102\">10.1126/sciadv.adp2102</a>.","ama":"Garcia Castillo DF, Barton NH, Faria R, et al. Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails. <i>Science Advances</i>. 2024;10(41). doi:<a href=\"https://doi.org/10.1126/sciadv.adp2102\">10.1126/sciadv.adp2102</a>","ista":"Garcia Castillo DF, Barton NH, Faria R, Larsson J, Stankowski S, Butlin R, Johannesson K, Westram AM. 2024. Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails. Science Advances. 10(41), eadp2102.","apa":"Garcia Castillo, D. F., Barton, N. H., Faria, R., Larsson, J., Stankowski, S., Butlin, R., … Westram, A. M. (2024). Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails. <i>Science Advances</i>. AAAS. <a href=\"https://doi.org/10.1126/sciadv.adp2102\">https://doi.org/10.1126/sciadv.adp2102</a>","ieee":"D. F. Garcia Castillo <i>et al.</i>, “Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails,” <i>Science Advances</i>, vol. 10, no. 41. AAAS, 2024.","chicago":"Garcia Castillo, Diego Fernando, Nicholas H Barton, Rui Faria, Jenny Larsson, Sean Stankowski, Roger Butlin, Kerstin Johannesson, and Anja M Westram. “Predicting Rapid Adaptation in Time from Adaptation in Space: A 30-Year Field Experiment in Marine Snails.” <i>Science Advances</i>. AAAS, 2024. <a href=\"https://doi.org/10.1126/sciadv.adp2102\">https://doi.org/10.1126/sciadv.adp2102</a>.","short":"D.F. Garcia Castillo, N.H. Barton, R. Faria, J. Larsson, S. Stankowski, R. Butlin, K. Johannesson, A.M. Westram, Science Advances 10 (2024)."},"doi":"10.1126/sciadv.adp2102","title":"Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails","publication":"Science Advances","APC_amount":"4569,23 EUR","DOAJ_listed":"1","issue":"41","quality_controlled":"1","project":[{"name":"Understanding the evolution of continuous genomes","grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"},{"grant_number":"P32166","name":"Snapdragon Speciation","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"},{"name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF"}],"isi":1,"file":[{"creator":"dernst","date_created":"2024-11-04T09:35:49Z","date_updated":"2024-11-04T09:35:49Z","file_size":1154107,"file_name":"2024_ScienceAdv_Castillo.pdf","success":1,"file_id":"18499","content_type":"application/pdf","checksum":"96aa0d3640fa9401975138e59054f84e","access_level":"open_access","relation":"main_file"}],"corr_author":"1","dataavailabilitystatement":"All analysis scripts and data needed to evaluate the conclusions of the paper are present in the paper and/or the Supplementary Materials and have been archived on Zenodo (63) at https://zenodo.org/doi/10.5281/zenodo.12159343 and are available on Github at https://github.com/fernandoGarcia21/littorina_saxatilis_skerry.","abstract":[{"lang":"eng","text":"Predicting the outcomes of adaptation is a major goal of evolutionary biology. When temporal changes in the environment mirror spatial gradients, it opens up the potential for predicting the course of adaptive evolution over time based on patterns of spatial genetic and phenotypic variation. We assessed this approach in a 30-year transplant experiment in the intertidal snail Littorina saxatilis. In 1992, snails were transplanted from a predation-dominated environment to one dominated by wave action. On the basis of spatial patterns, we predicted transitions in shell size and morphology, allele frequencies at positions throughout the genome, and chromosomal rearrangement frequencies. Observed changes closely agreed with predictions and transformation was both dramatic and rapid. Hence, adaptation can be predicted from knowledge of the phenotypic and genetic variation among populations."}],"language":[{"iso":"eng"}],"oa_version":"Published Version","year":"2024","researchdata_availability":"yes (supplementary data)","volume":10,"external_id":{"isi":["001354405400018"]},"department":[{"_id":"NiBa"}],"intvolume":"        10","_id":"18491","article_processing_charge":"Yes","related_material":{"link":[{"url":"https://github.com/fernandoGarcia21/littorina_saxatilis_skerry","relation":"software"}],"record":[{"status":"public","relation":"research_data","id":"18498"},{"status":"public","id":"20991","relation":"dissertation_contains"}]},"date_updated":"2026-10-21T08:18:22Z","status":"public","publisher":"AAAS","has_accepted_license":"1","supplementarymaterial":"yes","acknowledgement":"This work was received funding from the following: Norwegian Research Council RCN project 315287 (A.M.W.), Swedish Research Council 2021-04191 (K.J.), European Research Council grant 101055327 HaplotypeStructure (N.B.), Austrian Science Fund FWF; P 32166-B32 Snapdragon Speciation (N.B.), European Research Council (R.B.), and Portuguese Foundation for Science and Technology FCT: 2020.00275.CEECIND and PTDC/BIA-EVL/1614/2021 (R.F.).","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["570"],"oa":1},{"oa_version":"Published Version","language":[{"iso":"eng"}],"external_id":{"pmid":["37843465"],"isi":["001085119000001"]},"year":"2024","volume":33,"researchdata_availability":"yes","isi":1,"abstract":[{"lang":"eng","text":"Inversions are thought to play a key role in adaptation and speciation, suppressing recombination between diverging populations. Genes influencing adaptive traits cluster in inversions, and changes in inversion frequencies are associated with environmental differences. However, in many organisms, it is unclear if inversions are geographically and taxonomically widespread. The intertidal snail, Littorina saxatilis, is one such example. Strong associations between putative polymorphic inversions and phenotypic differences have been demonstrated between two ecotypes of L. saxatilis in Sweden and inferred elsewhere, but no direct evidence for inversion polymorphism currently exists across the species range. Using whole genome data from 107 snails, most inversion polymorphisms were found to be widespread across the species range. The frequencies of some inversion arrangements were significantly different among ecotypes, suggesting a parallel adaptive role. Many inversions were also polymorphic in the sister species, L. arcana, hinting at an ancient origin."}],"dataavailabilitystatement":"All raw sequence data were uploaded to the NCBI short read archive (PRJNA626520). All scripts used for this project are uploaded to GitHub (https://github.com/ja-Reeve/Littorina_inversion_identification.git).","file":[{"file_size":6228700,"success":1,"file_name":"2024_MolecularEcology_Reeve.pdf","date_created":"2025-01-09T07:52:12Z","date_updated":"2025-01-09T07:52:12Z","creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"686576036663f489c2d079df3079d126","content_type":"application/pdf","file_id":"18785"}],"_id":"14463","date_updated":"2026-10-21T08:19:22Z","status":"public","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"NiBa"}],"intvolume":"        33","supplementarymaterial":"yes","has_accepted_license":"1","publisher":"Wiley","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"We would like to thank members of the Littorina team for their advice and feedback during this project. In particular, we thank Alan Le Moan, who inspired us to look at heterozygosity differences to identify inversions, and Katherine Hearn for helping with the PCA scripts. We thank Edinburgh Genomics for library preparation and sequencing. Sample collections, sequencing and data preparation were supported by the European Research Council (ERC-2015-AdG-693030- BARRIERS) and the Natural Environment Research Council (NE/P001610/1). The analysis was supported by the Swedish Research Council (vetenskaprådet; 2018-03695_VR) and the Portuguese Foundation for Science and Technology (Fundación para a Ciência e Tecnologia) through a research project (PTDC/BIA-EVL/1614/2021) and CEEC contract (2020.00275.CEECIND).","oa":1,"ddc":["570"],"das_tickbox":"1","OA_place":"publisher","fulldoi":"https://doi.org/10.1111/mec.17160","day":"01","OA_type":"hybrid","scopus_import":"1","publication_status":"published","date_published":"2024-12-01T00:00:00Z","article_type":"original","file_date_updated":"2025-01-09T07:52:12Z","article_number":"e17160","month":"12","author":[{"full_name":"Reeve, James","last_name":"Reeve","first_name":"James"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."},{"full_name":"Koch, Eva L.","first_name":"Eva L.","last_name":"Koch"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean","full_name":"Stankowski, Sean"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"}],"date_created":"2023-10-29T23:01:17Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"type":"journal_article","title":"Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana)","publication":"Molecular Ecology","citation":{"mla":"Reeve, James, et al. “Chromosomal Inversion Polymorphisms Are Widespread across the Species Ranges of Rough Periwinkles (Littorina Saxatilis and L. Arcana).” <i>Molecular Ecology</i>, vol. 33, no. 24, e17160, Wiley, 2024, doi:<a href=\"https://doi.org/10.1111/mec.17160\">10.1111/mec.17160</a>.","apa":"Reeve, J., Butlin, R. K., Koch, E. L., Stankowski, S., &#38; Faria, R. (2024). Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.17160\">https://doi.org/10.1111/mec.17160</a>","ama":"Reeve J, Butlin RK, Koch EL, Stankowski S, Faria R. Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). <i>Molecular Ecology</i>. 2024;33(24). doi:<a href=\"https://doi.org/10.1111/mec.17160\">10.1111/mec.17160</a>","ista":"Reeve J, Butlin RK, Koch EL, Stankowski S, Faria R. 2024. Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Molecular Ecology. 33(24), e17160.","ieee":"J. Reeve, R. K. Butlin, E. L. Koch, S. Stankowski, and R. Faria, “Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana),” <i>Molecular Ecology</i>, vol. 33, no. 24. Wiley, 2024.","chicago":"Reeve, James, Roger K. Butlin, Eva L. Koch, Sean Stankowski, and Rui Faria. “Chromosomal Inversion Polymorphisms Are Widespread across the Species Ranges of Rough Periwinkles (Littorina Saxatilis and L. Arcana).” <i>Molecular Ecology</i>. Wiley, 2024. <a href=\"https://doi.org/10.1111/mec.17160\">https://doi.org/10.1111/mec.17160</a>.","short":"J. Reeve, R.K. Butlin, E.L. Koch, S. Stankowski, R. Faria, Molecular Ecology 33 (2024)."},"publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"doi":"10.1111/mec.17160","issue":"24","quality_controlled":"1","pmid":1},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"publisher":"Inter-Research Science Center","supplementarymaterial":"yes","department":[{"_id":"NiBa"}],"intvolume":"       740","_id":"18944","page":"23-42","date_updated":"2026-10-21T08:20:48Z","status":"public","article_processing_charge":"No","corr_author":"1","abstract":[{"text":"Understanding connectivity patterns exhibited by endangered species living in fragmented habitats is fundamental to improving management and conservation actions. Such improvements can be particularly pressing at the trailing edges of these habitats, where populations are facing the greatest challenges from climate change, and appear even more crucial if the species is commercially harvested. Seascape genetics have been increasingly used to meet these needs. In this study, we examined connectivity patterns among 32 populations of the oarweed kelp <jats:italic>Lam</jats:italic><jats:italic>inaria digitata</jats:italic> located at the species’ southern range limit. The distance (or sampling gap) between neighboring populations ranged from a few km to a few 100s of km. By genotyping 11 microsatellite markers, we aimed to (1) refine analyses of population structure; (2) test whether on-shelf islands are genetically more differentiated than mainland populations; (3) evaluate the relative importance of various abiotic conditions in shaping the genetic structure; and (4) evaluate if the relative importance of each environmental factor varied according to sampling schemes. Our analyses revealed a positive relationship between connectivity links and genetic diversity: populations with high levels of connectivity were genetically enriched while isolated populations showed signs of genetic erosion. The genetically impoverished populations corresponded to the southernmost populations as well as populations along the northern coast of Brittany (Locquirec, Saint-Malo Bay) and the northernmost population in Pas-de-Calais. By performing distance-based redundancy analysis on various sampling schemes, geographic distance appeared as the dominant factor influencing connectivity between populations separated by great distances, while hydrodynamic processes were the main factor when analyzing at a final spatial resolution.","lang":"eng"}],"oa_version":"Submitted Version","language":[{"iso":"eng"}],"year":"2024","volume":740,"researchdata_availability":"unclear","quality_controlled":"1","citation":{"short":"L. Fouqueau, L. Reynes, F. Tempera, T. Bajjouk, A. Blanfuné, C. Chevalier, M. Laurans, S. Mauger, M. Sourisseau, J. Assis, L. Lévêque, M. Valero, Marine Ecology Progress Series 740 (2024) 23–42.","chicago":"Fouqueau, Louise, L Reynes, F Tempera, T Bajjouk, A Blanfuné, C Chevalier, M Laurans, et al. “Seascape Genetic Study on Laminaria Digitata Underscores the Critical Role of Sampling Schemes.” <i>Marine Ecology Progress Series</i>. Inter-Research Science Center, 2024. <a href=\"https://doi.org/10.3354/meps14640\">https://doi.org/10.3354/meps14640</a>.","ieee":"L. Fouqueau <i>et al.</i>, “Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes,” <i>Marine Ecology Progress Series</i>, vol. 740. Inter-Research Science Center, pp. 23–42, 2024.","mla":"Fouqueau, Louise, et al. “Seascape Genetic Study on Laminaria Digitata Underscores the Critical Role of Sampling Schemes.” <i>Marine Ecology Progress Series</i>, vol. 740, Inter-Research Science Center, 2024, pp. 23–42, doi:<a href=\"https://doi.org/10.3354/meps14640\">10.3354/meps14640</a>.","ama":"Fouqueau L, Reynes L, Tempera F, et al. Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes. <i>Marine Ecology Progress Series</i>. 2024;740:23-42. doi:<a href=\"https://doi.org/10.3354/meps14640\">10.3354/meps14640</a>","ista":"Fouqueau L, Reynes L, Tempera F, Bajjouk T, Blanfuné A, Chevalier C, Laurans M, Mauger S, Sourisseau M, Assis J, Lévêque L, Valero M. 2024. Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes. Marine Ecology Progress Series. 740, 23–42.","apa":"Fouqueau, L., Reynes, L., Tempera, F., Bajjouk, T., Blanfuné, A., Chevalier, C., … Valero, M. (2024). Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes. <i>Marine Ecology Progress Series</i>. Inter-Research Science Center. <a href=\"https://doi.org/10.3354/meps14640\">https://doi.org/10.3354/meps14640</a>"},"publication_identifier":{"issn":["0171-8630"],"eissn":["1616-1599"]},"doi":"10.3354/meps14640","title":"Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes","main_file_link":[{"url":"https://inria.hal.science/hal-04624490/","open_access":"1"}],"publication":"Marine Ecology Progress Series","type":"journal_article","month":"07","author":[{"last_name":"Fouqueau","id":"1676e173-8143-11ed-8927-fe165216a93f","first_name":"Louise","orcid":"0000-0003-0371-9339","full_name":"Fouqueau, Louise"},{"full_name":"Reynes, L","first_name":"L","last_name":"Reynes"},{"full_name":"Tempera, F","last_name":"Tempera","first_name":"F"},{"full_name":"Bajjouk, T","first_name":"T","last_name":"Bajjouk"},{"full_name":"Blanfuné, A","first_name":"A","last_name":"Blanfuné"},{"last_name":"Chevalier","first_name":"C","full_name":"Chevalier, C"},{"full_name":"Laurans, M","last_name":"Laurans","first_name":"M"},{"last_name":"Mauger","first_name":"S","full_name":"Mauger, S"},{"full_name":"Sourisseau, M","first_name":"M","last_name":"Sourisseau"},{"full_name":"Assis, J","first_name":"J","last_name":"Assis"},{"last_name":"Lévêque","first_name":"L","full_name":"Lévêque, L"},{"full_name":"Valero, M","first_name":"M","last_name":"Valero"}],"date_created":"2025-01-29T09:09:10Z","fulldoi":"https://doi.org/10.3354/meps14640","day":"25","OA_type":"green","scopus_import":"1","date_published":"2024-07-25T00:00:00Z","publication_status":"published","article_type":"original","OA_place":"repository"},{"status":"public","date_created":"2026-09-09T10:39:08Z","date_updated":"2026-10-21T08:20:20Z","related_material":{"record":[{"id":"18908","relation":"used_in_publication","status":"public"}]},"article_processing_charge":"No","_id":"22870","contributor":[{"last_name":"Le Moan","contributor_type":"contact_person","first_name":"Alan"}],"month":"03","author":[{"full_name":"Le Moan, Alan","first_name":"Alan","last_name":"Le Moan"}],"department":[{"_id":"NiBa"}],"type":"research_data_reference","OA_place":"repository","year":"2024","oa_version":"None","abstract":[{"lang":"eng","text":"Abstract: Chromosomal rearrangements can lead to the coupling of reproductive barriers, but whether and how they contribute to completion of speciation remains unclear. Marine snails of the genus Littorina repeatedly form hybrid zones between populations segregating for multiple inversion arrangements, providing opportunities to study their barrier effects. Here, we analysed two adjacent transects across hybrid zones between two ecotypes of Littorina fabalis (‘large’ and ‘dwarf’) adapted to different wave exposure conditions on a Swedish island. Applying whole-genome sequencing, we found 12 putative inversions on nine of 17 chromosomes. Nine of the putative inversions reached near differential fixation between the two ecotypes, and all were in strong linkage disequilibrium. These inversions cover 20% of the genome and carry 93% of divergent single nucleotide polymorphisms (SNPs). Bimodal hybrid zones in both transects indicated that the two ecotypes of Littorina fabalis maintain their genetic and phenotypic integrity following contact. The bimodality reflects the strong coupling between inversion clines and the extension of the barrier effect across the whole genome. Demographic inference suggests that coupling arose during a period of allopatry and has been maintained for >1000 generations after secondary contact. Overall, this study shows that the coupling of multiple chromosomal inversions contributes to strong reproductive isolation. Notably, two of the putative inversions overlap with inverted genomic regions associated with ecotype differences in a closely-related species (Littorina saxatilis), suggesting the same regions, with similar structural variants, repeatedly contribute to ecotype evolution in distinct species."}],"date_published":"2024-03-06T00:00:00Z","fulldoi":"https://doi.org/10.5281/zenodo.10790257","OA_type":"green","day":"06","oa":1,"ddc":["570"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes","publisher":"Repository","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.10790257","open_access":"1"}],"doi":"10.5281/zenodo.10790257","citation":{"short":"A. Le Moan, (2024).","chicago":"Le Moan, Alan. “Coupling of Twelve Putative Chromosomal Inversions Maintains a Strong Barrier to Gene Flow between Snail Ecotypes.” Repository, 2024. <a href=\"https://doi.org/10.5281/zenodo.10790257\">https://doi.org/10.5281/zenodo.10790257</a>.","ieee":"A. Le Moan, “Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes.” Repository, 2024.","ista":"Le Moan A. 2024. Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes, Repository, <a href=\"https://doi.org/10.5281/zenodo.10790257\">10.5281/zenodo.10790257</a>.","ama":"Le Moan A. Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes. 2024. doi:<a href=\"https://doi.org/10.5281/zenodo.10790257\">10.5281/zenodo.10790257</a>","apa":"Le Moan, A. (2024). Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes. Repository. <a href=\"https://doi.org/10.5281/zenodo.10790257\">https://doi.org/10.5281/zenodo.10790257</a>","mla":"Le Moan, Alan. <i>Coupling of Twelve Putative Chromosomal Inversions Maintains a Strong Barrier to Gene Flow between Snail Ecotypes</i>. Repository, 2024, doi:<a href=\"https://doi.org/10.5281/zenodo.10790257\">10.5281/zenodo.10790257</a>."}},{"day":"19","fulldoi":"https://doi.org/10.5281/ZENODO.12159343","date_published":"2024-06-19T00:00:00Z","abstract":[{"text":"Scripts and data used in the research study Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails. https://doi.org/10.1101/2023.09.27.559715","lang":"eng"}],"corr_author":"1","oa_version":"Published Version","year":"2024","OA_place":"repository","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"type":"research_data_reference","department":[{"_id":"NiBa"}],"author":[{"full_name":"Garcia Castillo, Diego Fernando","first_name":"Diego Fernando","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","last_name":"Garcia Castillo"},{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"first_name":"Jenny","last_name":"Larsson","full_name":"Larsson, Jenny"},{"first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"},{"last_name":"Butlin","first_name":"Roger","full_name":"Butlin, Roger"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"}],"_id":"18498","month":"06","article_processing_charge":"No","date_created":"2024-11-04T09:33:17Z","related_material":{"record":[{"id":"20991","relation":"used_in_publication","status":"public"},{"status":"public","relation":"used_in_publication","id":"18491"}]},"status":"public","date_updated":"2026-10-21T08:18:21Z","citation":{"ieee":"D. F. Garcia Castillo <i>et al.</i>, “Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails.” Zenodo, 2024.","ama":"Garcia Castillo DF, Barton NH, Faria R, et al. Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails. 2024. doi:<a href=\"https://doi.org/10.5281/ZENODO.12159343\">10.5281/ZENODO.12159343</a>","apa":"Garcia Castillo, D. F., Barton, N. H., Faria, R., Larsson, J., Stankowski, S., Butlin, R., … Westram, A. M. (2024). Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.12159343\">https://doi.org/10.5281/ZENODO.12159343</a>","ista":"Garcia Castillo DF, Barton NH, Faria R, Larsson J, Stankowski S, Butlin R, Johannesson K, Westram AM. 2024. Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.12159343\">10.5281/ZENODO.12159343</a>.","mla":"Garcia Castillo, Diego Fernando, et al. <i>Data and Code for: Predicting Rapid Adaptation in Time from Adaptation in Space: A 30-Year Field Experiment in Marine Snails</i>. Zenodo, 2024, doi:<a href=\"https://doi.org/10.5281/ZENODO.12159343\">10.5281/ZENODO.12159343</a>.","short":"D.F. Garcia Castillo, N.H. Barton, R. Faria, J. Larsson, S. Stankowski, R. Butlin, K. Johannesson, A.M. Westram, (2024).","chicago":"Garcia Castillo, Diego Fernando, Nicholas H Barton, Rui Faria, Jenny Larsson, Sean Stankowski, Roger Butlin, Kerstin Johannesson, and Anja M Westram. “Data and Code for: Predicting Rapid Adaptation in Time from Adaptation in Space: A 30-Year Field Experiment in Marine Snails.” Zenodo, 2024. <a href=\"https://doi.org/10.5281/ZENODO.12159343\">https://doi.org/10.5281/ZENODO.12159343</a>."},"doi":"10.5281/ZENODO.12159343","title":"Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails","publisher":"Zenodo","has_accepted_license":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.12159344"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"ddc":["570"]},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["576"],"oa":1,"supplementarymaterial":"yes","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","doi_confirm":"1","alternative_title":["ISTA Thesis"],"supervisor":[{"full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"},{"last_name":"Polechova","first_name":"Jitka","full_name":"Polechova, Jitka"},{"full_name":"Sachdeva, Himani","first_name":"Himani","last_name":"Sachdeva"}],"department":[{"_id":"NiBa"},{"_id":"GradSch"}],"page":"183","_id":"14711","article_processing_charge":"No","status":"public","date_updated":"2026-10-21T08:24:47Z","related_material":{"record":[{"status":"public","id":"10787","relation":"part_of_dissertation"},{"status":"public","id":"10658","relation":"part_of_dissertation"},{"id":"14732","relation":"part_of_dissertation","status":"public"}]},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"},{"grant_number":"P32896","name":"Causes and consequences of population fragmentation","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8"},{"grant_number":"26380","name":"Polygenic Adaptation in a Metapopulation","_id":"34c872fe-11ca-11ed-8bc3-8534b82131e6"}],"file":[{"creator":"oolusany","date_created":"2024-01-03T18:30:13Z","date_updated":"2024-01-03T18:30:13Z","file_name":"FinalSubmission_Thesis_OLUSANYA.zip","file_size":16986244,"file_id":"14730","content_type":"application/zip","checksum":"de179b1c6758f182ff0c70d8b38c1501","access_level":"closed","relation":"source_file"},{"creator":"oolusany","date_created":"2024-01-03T18:31:34Z","date_updated":"2024-01-03T18:31:34Z","success":1,"file_size":6460403,"file_name":"FinalSubmission2_Thesis_OLUSANYA.pdf","file_id":"14731","content_type":"application/pdf","checksum":"0e331585e3cd4823320aab4e69e64ccf","access_level":"open_access","relation":"main_file"}],"corr_author":"1","abstract":[{"text":"In nature, different species find their niche in a range of environments, each with its unique characteristics. While some thrive in uniform (homogeneous) landscapes where environmental conditions stay relatively consistent across space, others traverse the complexities of spatially heterogeneous terrains. Comprehending how species are distributed and how they interact within these landscapes holds the key to gaining insights into their evolutionary dynamics while also informing conservation and management strategies.\r\n\r\nFor species inhabiting heterogeneous landscapes, when the rate of dispersal is low compared to spatial fluctuations in selection pressure, localized adaptations may emerge. Such adaptation in response to varying selection strengths plays an important role in the persistence of populations in our rapidly changing world. Hence, species in nature are continuously in a struggle to adapt to local environmental conditions, to ensure their continued survival. Natural populations can often adapt in time scales short enough for evolutionary changes to influence ecological dynamics and vice versa, thereby creating a feedback between evolution and demography. The analysis of this feedback and the relative contributions of gene flow, demography, drift, and natural selection to genetic variation and differentiation has remained a recurring theme in evolutionary biology. Nevertheless, the effective role of these forces in maintaining variation and shaping patterns of diversity is not fully understood. Even in homogeneous environments devoid of local adaptations, such understanding remains elusive. Understanding this feedback is crucial, for example in determining the conditions under which extinction risk can be mitigated in peripheral populations subject to deleterious mutation accumulation at the edges of species’ ranges\r\nas well as in highly fragmented populations.\r\n\r\nIn this thesis we explore both uniform and spatially heterogeneous metapopulations, investigating and providing theoretical insights into the dynamics of local adaptation in the latter and examining the dynamics of load and extinction as well as the impact of joint ecological and evolutionary (eco-evolutionary) dynamics in the former. The thesis is divided into 5 chapters.\r\n\r\nChapter 1 provides a general introduction into the subject matter, clarifying concepts and ideas used throughout the thesis. In chapter 2, we explore how fast a species distributed across a heterogeneous landscape adapts to changing conditions marked by alterations in carrying capacity, selection pressure, and migration rate.\r\n\r\nIn chapter 3, we investigate how migration selection and drift influences adaptation and the maintenance of variation in a metapopulation with three habitats, an extension of previous models of adaptation in two habitats. We further develop analytical approximations for the critical threshold required for polymorphism to persist.\r\n\r\nThe focus of chapter 4 of the thesis is on understanding the interplay between ecology and evolution as coupled processes. We investigate how eco-evolutionary feedback between migration, selection, drift, and demography influences eco-evolutionary outcomes in marginal populations subject to deleterious mutation accumulation. Using simulations as well as theoretical approximations of the coupled dynamics of population size and allele frequency, we analyze how gene flow from a large mainland source influences genetic load and population size on an island (i.e., in a marginal population) under genetically realistic assumptions. Analyses of this sort are important because small isolated populations, are repeatedly affected by complex interactions between ecological and evolutionary processes, which can lead to their death. Understanding these interactions can therefore provide an insight into the conditions under which extinction risk can be mitigated in peripheral populations thus, contributing to conservation and restoration efforts.\r\n\r\nChapter 5 extends the analysis in chapter 4 to consider the dynamics of load (due to deleterious mutation accumulation) and extinction risk in a metapopulation. We explore the role of gene flow, selection, and dominance on load and extinction risk and further pinpoint critical thresholds required for metapopulation persistence.\r\n\r\nOverall this research contributes to our understanding of ecological and evolutionary mechanisms that shape species’ persistence in fragmented landscapes, a crucial foundation for successful conservation efforts and biodiversity management.","lang":"eng"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","year":"2024","researchdata_availability":"no","citation":{"ieee":"O. O. Olusanya, “Local adaptation, genetic load and extinction in metapopulations,” Institute of Science and Technology Austria, 2024.","ista":"Olusanya OO. 2024. Local adaptation, genetic load and extinction in metapopulations. Institute of Science and Technology Austria.","apa":"Olusanya, O. O. (2024). <i>Local adaptation, genetic load and extinction in metapopulations</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14711\">https://doi.org/10.15479/at:ista:14711</a>","ama":"Olusanya OO. Local adaptation, genetic load and extinction in metapopulations. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:14711\">10.15479/at:ista:14711</a>","mla":"Olusanya, Oluwafunmilola O. <i>Local Adaptation, Genetic Load and Extinction in Metapopulations</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:14711\">10.15479/at:ista:14711</a>.","short":"O.O. Olusanya, Local Adaptation, Genetic Load and Extinction in Metapopulations, Institute of Science and Technology Austria, 2024.","chicago":"Olusanya, Oluwafunmilola O. “Local Adaptation, Genetic Load and Extinction in Metapopulations.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:14711\">https://doi.org/10.15479/at:ista:14711</a>."},"publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:14711","title":"Local adaptation, genetic load and extinction in metapopulations","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","type":"dissertation","tmp":{"short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"acknowledged_ssus":[{"_id":"SSU"}],"ec_funded":1,"author":[{"full_name":"Olusanya, Oluwafunmilola O","orcid":"0000-0003-1971-8314","first_name":"Oluwafunmilola O","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","last_name":"Olusanya"}],"month":"01","date_created":"2023-12-26T22:49:53Z","degree_awarded":"PhD","day":"19","fulldoi":"https://doi.org/10.15479/at:ista:14711","date_published":"2024-01-19T00:00:00Z","file_date_updated":"2024-01-03T18:31:34Z","publication_status":"published","das_tickbox":"0","OA_place":"publisher"},{"month":"06","article_number":"e3002668","author":[{"full_name":"Burnett, Laura","orcid":"0000-0002-8937-410X","first_name":"Laura","last_name":"Burnett","id":"3B717F68-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter","orcid":"0000-0002-3509-1948","last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","full_name":"Koppensteiner, Peter"},{"orcid":"0000-0003-2012-9947","first_name":"Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","last_name":"Symonova","full_name":"Symonova, Olga"},{"full_name":"Masson, Tomas","orcid":"0000-0002-2634-6283","first_name":"Tomas","id":"93ac43e8-8599-11eb-9b86-f6efb0a4c207","last_name":"Masson"},{"id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","last_name":"Vega Zuniga","first_name":"Tomas A","full_name":"Vega Zuniga, Tomas A"},{"full_name":"Contreras, Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","last_name":"Contreras","first_name":"Ximena"},{"last_name":"Rülicke","first_name":"Thomas","full_name":"Rülicke, Thomas"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-3937-1330","first_name":"Maximilian A","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","full_name":"Jösch, Maximilian A"}],"date_created":"2024-06-16T22:01:05Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"type":"journal_article","ec_funded":1,"das_tickbox":"1","OA_place":"publisher","fulldoi":"https://doi.org/10.1371/journal.pbio.3002668","day":"10","OA_type":"gold","scopus_import":"1","publication_status":"published","article_type":"original","file_date_updated":"2025-01-09T10:39:41Z","date_published":"2024-06-10T00:00:00Z","quality_controlled":"1","pmid":1,"title":"Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice","APC_amount":"6081,83 EUR","DOAJ_listed":"1","publication":"PLoS Biology","citation":{"ieee":"L. Burnett <i>et al.</i>, “Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice,” <i>PLoS Biology</i>, vol. 22. Public Library of Science, 2024.","mla":"Burnett, Laura, et al. “Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice.” <i>PLoS Biology</i>, vol. 22, e3002668, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002668\">10.1371/journal.pbio.3002668</a>.","ama":"Burnett L, Koppensteiner P, Symonova O, et al. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. <i>PLoS Biology</i>. 2024;22. doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002668\">10.1371/journal.pbio.3002668</a>","apa":"Burnett, L., Koppensteiner, P., Symonova, O., Masson, T., Vega Zuniga, T. A., Contreras, X., … Jösch, M. A. (2024). Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3002668\">https://doi.org/10.1371/journal.pbio.3002668</a>","ista":"Burnett L, Koppensteiner P, Symonova O, Masson T, Vega Zuniga TA, Contreras X, Rülicke T, Shigemoto R, Novarino G, Jösch MA. 2024. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. PLoS Biology. 22, e3002668.","short":"L. Burnett, P. Koppensteiner, O. Symonova, T. Masson, T.A. Vega Zuniga, X. Contreras, T. Rülicke, R. Shigemoto, G. Novarino, M.A. Jösch, PLoS Biology 22 (2024).","chicago":"Burnett, Laura, Peter Koppensteiner, Olga Symonova, Tomas Masson, Tomas A Vega Zuniga, Ximena Contreras, Thomas Rülicke, Ryuichi Shigemoto, Gaia Novarino, and Maximilian A Jösch. “Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice.” <i>PLoS Biology</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pbio.3002668\">https://doi.org/10.1371/journal.pbio.3002668</a>."},"publication_identifier":{"eissn":["1545-7885"],"issn":["1544-9173"]},"doi":"10.1371/journal.pbio.3002668","_id":"17142","status":"public","date_updated":"2026-10-21T08:31:42Z","related_material":{"record":[{"id":"15385","relation":"research_data","status":"public"}],"link":[{"relation":"software","url":"https://doi.org/10.5281/zenodo.11130587"}]},"article_processing_charge":"Yes","department":[{"_id":"RySh"},{"_id":"GaNo"},{"_id":"MaJö"}],"intvolume":"        22","oa_version":"Published Version","language":[{"iso":"eng"}],"external_id":{"pmid":["38857283"],"isi":["001246176800003"]},"year":"2024","volume":22,"researchdata_availability":"yes","isi":1,"project":[{"_id":"2634E9D2-B435-11E9-9278-68D0E5697425","name":"Circuits of Visual Attention","grant_number":"756502","call_identifier":"H2020"}],"abstract":[{"text":"Despite the diverse genetic origins of autism spectrum disorders (ASDs), affected individuals share strikingly similar and correlated behavioural traits that include perceptual and sensory processing challenges. Notably, the severity of these sensory symptoms is often predictive of the expression of other autistic traits. However, the origin of these perceptual deficits remains largely elusive. Here, we show a recurrent impairment in visual threat perception that is similarly impaired in 3 independent mouse models of ASD with different molecular aetiologies. Interestingly, this deficit is associated with reduced avoidance of threatening environments—a nonperceptual trait. Focusing on a common cause of ASDs, the Setd5 gene mutation, we define the molecular mechanism. We show that the perceptual impairment is caused by a potassium channel (Kv1)-mediated hypoexcitability in a subcortical node essential for the initiation of escape responses, the dorsal periaqueductal grey (dPAG). Targeted pharmacological Kv1 blockade rescued both perceptual and place avoidance deficits, causally linking seemingly unrelated trait deficits to the dPAG. Furthermore, we show that different molecular mechanisms converge on similar behavioural phenotypes by demonstrating that the autism models Cul3 and Ptchd1, despite having similar behavioural phenotypes, differ in their functional and molecular alteration. Our findings reveal a link between rapid perception controlled by subcortical pathways and appropriate learned interactions with the environment and define a nondevelopmental source of such deficits in ASD.","lang":"eng"}],"corr_author":"1","dataavailabilitystatement":"The mass spectrometry proteomics data have been deposited at the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD051022. The data used in the analysis can be found in the ISTA data repository DOI: 10.15479/AT:ISTA:15385. The code used to generate the results is available at: https://zenodo.org/records/11130588.","file":[{"checksum":"496e1aa4fd5b92b7e4087ecc2c964133","content_type":"application/pdf","file_id":"18805","relation":"main_file","access_level":"open_access","date_created":"2025-01-09T10:39:41Z","date_updated":"2025-01-09T10:39:41Z","creator":"dernst","file_size":4016568,"file_name":"2024_PloS_Burnett.pdf","success":1}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"This work was supported by a European Research Council Starting Grant 756502 (MJ). ","ddc":["570"],"oa":1,"publisher":"Public Library of Science","supplementarymaterial":"yes","has_accepted_license":"1"},{"file":[{"file_size":6597227,"success":1,"file_name":"2024_BioMacromolecules_Wu.pdf","creator":"dernst","date_created":"2024-10-07T08:33:35Z","date_updated":"2024-10-07T08:33:35Z","access_level":"open_access","relation":"main_file","file_id":"18180","content_type":"application/pdf","checksum":"9552b6d52f1e8a350764849a535fc13e"}],"corr_author":"1","abstract":[{"lang":"eng","text":"Despite the considerable interest in the recombinant production of synthetic spider silk fibers that possess mechanical properties similar to those of native spider silks, such as the cost-effectiveness, tunability, and scalability realization, is still lacking. To address this long-standing challenge, we have constructed an artificial spider silk gene using Golden Gate assembly for the recombinant bacterial production of dragline-mimicking silk, incorporating all the essential components: the N-terminal domain, a 33-residue-long major-ampullate-spidroin-inspired segment repeated 16 times, and the C-terminal domain (N16C). This designed silk-like protein was successfully expressed in Escherichia coli, purified, and cast into films from formic acid. We produced uniformly 13C–15N-labeled N16C films and employed solid-state magic-angle spinning nuclear magnetic resonance (NMR) for characterization. Thus, we could demonstrate that our bioengineered silk-like protein self-assembles into a film where, when hydrated, the solvent-exposed layer of the rigid, β-nanocrystalline polyalanine core undergoes a transition to an α-helical structure, gaining mobility to the extent that it fully dissolves in water and transforms into a highly dynamic random coil. This hydration-induced behavior induces chain dynamics in the glycine-rich amorphous soft segments on the microsecond time scale, contributing to the elasticity of the solid material. Our findings not only reveal the presence of structurally and dynamically distinct segments within the film’s superstructure but also highlight the complexity of the self-organization responsible for the exceptional mechanical properties observed in proteins that mimic dragline silk."}],"isi":1,"researchdata_availability":"no","volume":25,"year":"2024","external_id":{"pmid":["38343096"],"isi":["001166501000001"]},"language":[{"iso":"eng"}],"oa_version":"Published Version","intvolume":"        25","department":[{"_id":"NMR"}],"article_processing_charge":"Yes (via OA deal)","status":"public","date_updated":"2026-10-21T08:25:57Z","page":"1759-1774","_id":"18168","supplementarymaterial":"yes","publisher":"American Chemical Society","has_accepted_license":"1","ddc":["540"],"oa":1,"acknowledgement":"We thank Dr. Pavel Kielkowski for performing the MS/MS measurement and providing feedback on the manuscript. We are grateful to Rodrigo Ledesma Amaro for introducing the Golden Gate Assembly technique in our lab. We acknowledge the support from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)─SFB 1309-325871075, the Center for NanoScience (CeNS), the Fonds der Chemischen Industrie, and Universitätsgesellschaft München.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original","date_published":"2024-03-11T00:00:00Z","file_date_updated":"2024-10-07T08:33:35Z","publication_status":"published","scopus_import":"1","day":"11","fulldoi":"https://doi.org/10.1021/acs.biomac.3c01239","das_tickbox":"0","type":"journal_article","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"date_created":"2024-10-02T10:09:53Z","author":[{"last_name":"Wu","first_name":"Dongqing","full_name":"Wu, Dongqing"},{"full_name":"Koscic, Anamaria","first_name":"Anamaria","last_name":"Koscic"},{"full_name":"Schneider, Sonja","last_name":"Schneider","first_name":"Sonja"},{"full_name":"Dubini, Romeo C. A.","last_name":"Dubini","first_name":"Romeo C. A."},{"full_name":"Rodriguez Camargo, Diana C.","last_name":"Rodriguez Camargo","first_name":"Diana C."},{"first_name":"Sabine","last_name":"Schneider","full_name":"Schneider, Sabine"},{"full_name":"Rovo, Petra","id":"c316e53f-b965-11eb-b128-bb26acc59c00","last_name":"Rovo","first_name":"Petra","orcid":"0000-0001-8729-7326"}],"month":"03","doi":"10.1021/acs.biomac.3c01239","citation":{"ieee":"D. Wu <i>et al.</i>, “Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking protein,” <i>Biomacromolecules</i>, vol. 25, no. 3. American Chemical Society, pp. 1759–1774, 2024.","mla":"Wu, Dongqing, et al. “Unveiling the Dynamic Self-Assembly of a Recombinant Dragline-Silk-Mimicking Protein.” <i>Biomacromolecules</i>, vol. 25, no. 3, American Chemical Society, 2024, pp. 1759–74, doi:<a href=\"https://doi.org/10.1021/acs.biomac.3c01239\">10.1021/acs.biomac.3c01239</a>.","ista":"Wu D, Koscic A, Schneider S, Dubini RCA, Rodriguez Camargo DC, Schneider S, Rovo P. 2024. Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking protein. Biomacromolecules. 25(3), 1759–1774.","ama":"Wu D, Koscic A, Schneider S, et al. Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking protein. <i>Biomacromolecules</i>. 2024;25(3):1759-1774. doi:<a href=\"https://doi.org/10.1021/acs.biomac.3c01239\">10.1021/acs.biomac.3c01239</a>","apa":"Wu, D., Koscic, A., Schneider, S., Dubini, R. C. A., Rodriguez Camargo, D. C., Schneider, S., &#38; Rovo, P. (2024). Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking protein. <i>Biomacromolecules</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.biomac.3c01239\">https://doi.org/10.1021/acs.biomac.3c01239</a>","short":"D. Wu, A. Koscic, S. Schneider, R.C.A. Dubini, D.C. Rodriguez Camargo, S. Schneider, P. Rovo, Biomacromolecules 25 (2024) 1759–1774.","chicago":"Wu, Dongqing, Anamaria Koscic, Sonja Schneider, Romeo C. A. Dubini, Diana C. Rodriguez Camargo, Sabine Schneider, and Petra Rovo. “Unveiling the Dynamic Self-Assembly of a Recombinant Dragline-Silk-Mimicking Protein.” <i>Biomacromolecules</i>. American Chemical Society, 2024. <a href=\"https://doi.org/10.1021/acs.biomac.3c01239\">https://doi.org/10.1021/acs.biomac.3c01239</a>."},"publication_identifier":{"issn":["1525-7797"],"eissn":["1526-4602"]},"publication":"Biomacromolecules","title":"Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking protein","pmid":1,"quality_controlled":"1","issue":"3"},{"file":[{"file_name":"Lauritsen-thesis-final.pdf","success":1,"file_size":3648831,"creator":"alaurits","date_updated":"2024-09-26T13:11:24Z","date_created":"2024-09-26T13:11:24Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"18147","checksum":"c7bc3b31e430d57c65393051ca439575"},{"creator":"alaurits","date_updated":"2024-09-26T13:12:55Z","date_created":"2024-09-26T13:12:55Z","file_name":"Lauritsen-thesis-source.zip","file_size":1625888,"file_id":"18148","content_type":"application/x-zip-compressed","checksum":"39f6b1b7f83e25a3bf9f933f1ea0bc06","access_level":"closed","relation":"source_file"}],"corr_author":"1","abstract":[{"lang":"eng","text":"This thesis consists of two separate parts. In the first part we consider a dilute Fermi gas interacting through a repulsive interaction in dimensions $d=1,2,3$. Our focus is mostly on the physically most relevant dimension $d=3$ \r\nand the setting of a spin-polarized (equivalently spinless) gas, where the Pauli exclusion principle plays a key role. We show that, at zero temperature, the ground state energy density of the interacting spin-polarized gas differs (to leading order) from that of the free (i.e. non-interacting) gas by a term of order $a_p^d\\rho^{2+2/d}$  with $a_p$ the $p$-wave scattering length of the repulsive interaction and $\\rho$ the density. Further, we extend this to positive temperature and show that the pressure of an interacting spin-polarized gas differs from that of the free gas by a now temperature dependent term, again of order $a_p^d\\rho^{2+2/d}$. Lastly, we consider the setting of a spin-$\\frac{1}{2}$ Fermi gas in $d=3$ dimensions and show that here, as an upper bound, the ground state energy density differs from that of the free system by a term of order $a_s \\rho^2$ with an error smaller than $a_s \\rho^2 (a_s\\rho^{1/3})^{1-\\eps}$ for any $\\eps > 0$, where $a_s$ is the $s$-wave scattering length of the repulsive interaction. \r\n\r\nThese asymptotic formulas complement the similar formulas in the literature for the dilute Bose and spin-$\\frac{1}{2}$ Fermi gas, where the ground state energies or pressures differ from that of the corresponding free systems by a term of order $a_s \\rho^2$ in dimension $d=3$. In the spin-polarized setting, the corrections, of order $a_p^3\\rho^{8/3}$ in dimension $d=3$, are thus much smaller and requires a more delicate analysis.\r\n\r\nIn the second part of the thesis we consider the Bardeen--Cooper--Schrieffer (BCS) theory of superconductivity and in particular its associated critical temperature and energy gap. We prove that the ratio of the zero-temperature energy gap and critical temperature $\\Xi(T=0)/T_c$ approaches a universal constant $\\pi e^{-\\gamma}\\approx 1.76$ in both the limit of high density in dimension $d=3$ and in the limit of weak coupling in dimensions $d=1,2$. This complements the proofs in the literature of this universal behaviour in the limit of weak coupling or low density in dimension $d=3$. Secondly, we prove that the ratio of the energy gap at positive temperature and critical temperature $\\Xi(T)/T_c$ approaches a universal function of the relative temperature $T/T_c$ in the limit of weak coupling in dimensions $d=1,2,3$."}],"project":[{"_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","grant_number":"I06427","name":"Mathematical Challenges in BCS Theory of Superconductivity"},{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"researchdata_availability":"no","year":"2024","language":[{"iso":"eng"}],"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"article_processing_charge":"No","date_updated":"2026-10-21T08:29:08Z","status":"public","related_material":{"record":[{"relation":"part_of_dissertation","id":"11732","status":"public"},{"relation":"part_of_dissertation","id":"14542","status":"public"},{"relation":"part_of_dissertation","id":"18107","status":"public"},{"status":"public","id":"17240","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"14931","status":"public"}]},"page":"353","_id":"18135","doi_confirm":"1","supervisor":[{"full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521"}],"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","supplementarymaterial":"no","oa":1,"ddc":["515","539"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-09-23T00:00:00Z","file_date_updated":"2024-09-26T13:12:55Z","publication_status":"published","day":"23","fulldoi":"https://doi.org/10.15479/at:ista:18135","OA_place":"publisher","das_tickbox":"0","ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"type":"dissertation","date_created":"2024-09-24T10:56:25Z","degree_awarded":"PhD","author":[{"orcid":"0000-0003-4476-2288","first_name":"Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","last_name":"Lauritsen","full_name":"Lauritsen, Asbjørn Bækgaard"}],"month":"09","doi":"10.15479/at:ista:18135","publication_identifier":{"isbn":["978-3-99078-042-8"],"issn":["2663-337X"]},"citation":{"chicago":"Lauritsen, Asbjørn Bækgaard. “Energies of Dilute Fermi Gases and Universalities in BCS Theory.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18135\">https://doi.org/10.15479/at:ista:18135</a>.","short":"A.B. Lauritsen, Energies of Dilute Fermi Gases and Universalities in BCS Theory, Institute of Science and Technology Austria, 2024.","mla":"Lauritsen, Asbjørn Bækgaard. <i>Energies of Dilute Fermi Gases and Universalities in BCS Theory</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18135\">10.15479/at:ista:18135</a>.","ama":"Lauritsen AB. Energies of dilute Fermi gases and universalities in BCS theory. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18135\">10.15479/at:ista:18135</a>","apa":"Lauritsen, A. B. (2024). <i>Energies of dilute Fermi gases and universalities in BCS theory</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18135\">https://doi.org/10.15479/at:ista:18135</a>","ista":"Lauritsen AB. 2024. Energies of dilute Fermi gases and universalities in BCS theory. Institute of Science and Technology Austria.","ieee":"A. B. Lauritsen, “Energies of dilute Fermi gases and universalities in BCS theory,” Institute of Science and Technology Austria, 2024."},"title":"Energies of dilute Fermi gases and universalities in BCS theory"},{"department":[{"_id":"PreCl"}],"intvolume":"       126","_id":"15164","article_processing_charge":"Yes (in subscription journal)","status":"public","date_updated":"2026-10-21T08:26:38Z","isi":1,"file":[{"creator":"dernst","date_created":"2024-03-25T08:29:52Z","date_updated":"2024-03-25T08:29:52Z","file_size":10039402,"file_name":"2024_MedEngineeringPhysics_SilvaHenao.pdf","success":1,"file_id":"15177","content_type":"application/pdf","checksum":"974acbf2731e7382dcf5920ac762e551","access_level":"open_access","relation":"main_file"}],"abstract":[{"lang":"eng","text":"Primary implant stability, which refers to the stability of the implant during the initial healing period is a crucial factor in determining the long-term success of the implant and lays the foundation for secondary implant stability achieved through osseointegration. Factors affecting primary stability include implant design, surgical technique, and patient-specific factors like bone quality and morphology. In vivo, the cyclic nature of anatomical loading puts osteosynthesis locking screws under dynamic loads, which can lead to the formation of micro cracks and defects that slowly degrade the mechanical connection between the bone and screw, thus compromising the initial stability and secondary stability of the implant. Monotonic quasi-static loading used for testing the holding capacity of implanted screws is not well suited to capture this behavior since it cannot capture the progressive deterioration of peri‑implant bone at small displacements. In order to address this issue, this study aims to determine a critical point of loss of primary implant stability in osteosynthesis locking screws under cyclic overloading by investigating the evolution of damage, dissipated energy, and permanent deformation. A custom-made test setup was used to test implanted 2.5 mm locking screws under cyclic overloading test. For each loading cycle, maximum forces and displacement were recorded as well as initial and final cycle displacements and used to calculate damage and energy dissipation evolution. The results of this study demonstrate that for axial, shear, and mixed loading significant damage and energy dissipation can be observed at approximately 20 % of the failure force. Additionally, at this load level, permanent deformations on the screw-bone interface were found to be in the range of 50 to 150 mm which promotes osseointegration and secondary implant stability. This research can assist surgeons in making informed preoperative decisions by providing a better understanding of the critical point of loss of primary implant stability, thus improving the long-term success of the implant and overall patient satisfaction."}],"language":[{"iso":"eng"}],"oa_version":"Published Version","researchdata_availability":"no","year":"2024","volume":126,"external_id":{"isi":["001219145400001"],"pmid":["38621845"]},"acknowledgement":"The authors declare no conflict of interest related to this study. This project was funded by the Gesellschaft fuer Forschungsfoerderung Niederoesterreich m.b.H. Life Science Call 2017 Grant No. LS17004 and Science call 2019 Dissertationen Grant No. SC19014. No ethical approval was required for this study.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["610"],"oa":1,"supplementarymaterial":"no","publisher":"Elsevier","has_accepted_license":"1","type":"journal_article","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"author":[{"first_name":"Juan D.","last_name":"Silva-Henao","full_name":"Silva-Henao, Juan D."},{"full_name":"Schober, Sophie","first_name":"Sophie","id":"80b0a0ef-4b9f-11ec-b119-8d9d94c4a1d8","last_name":"Schober"},{"full_name":"Pahr, Dieter H.","first_name":"Dieter H.","last_name":"Pahr"},{"last_name":"Reisinger","first_name":"Andreas G.","full_name":"Reisinger, Andreas G."}],"article_number":"104143","month":"04","date_created":"2024-03-24T23:00:58Z","day":"01","fulldoi":"https://doi.org/10.1016/j.medengphy.2024.104143","file_date_updated":"2024-03-25T08:29:52Z","date_published":"2024-04-01T00:00:00Z","publication_status":"published","article_type":"original","scopus_import":"1","das_tickbox":"0","pmid":1,"quality_controlled":"1","publication_identifier":{"issn":["1350-4533"],"eissn":["1873-4030"]},"citation":{"ieee":"J. D. Silva-Henao, S. Schober, D. H. Pahr, and A. G. Reisinger, “Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading,” <i>Medical Engineering and Physics</i>, vol. 126. Elsevier, 2024.","ista":"Silva-Henao JD, Schober S, Pahr DH, Reisinger AG. 2024. Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. Medical Engineering and Physics. 126, 104143.","ama":"Silva-Henao JD, Schober S, Pahr DH, Reisinger AG. Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. <i>Medical Engineering and Physics</i>. 2024;126. doi:<a href=\"https://doi.org/10.1016/j.medengphy.2024.104143\">10.1016/j.medengphy.2024.104143</a>","apa":"Silva-Henao, J. D., Schober, S., Pahr, D. H., &#38; Reisinger, A. G. (2024). Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. <i>Medical Engineering and Physics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.medengphy.2024.104143\">https://doi.org/10.1016/j.medengphy.2024.104143</a>","mla":"Silva-Henao, Juan D., et al. “Critical Loss of Primary Implant Stability in Osteosynthesis Locking Screws under Cyclic Overloading.” <i>Medical Engineering and Physics</i>, vol. 126, 104143, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.medengphy.2024.104143\">10.1016/j.medengphy.2024.104143</a>.","short":"J.D. Silva-Henao, S. Schober, D.H. Pahr, A.G. Reisinger, Medical Engineering and Physics 126 (2024).","chicago":"Silva-Henao, Juan D., Sophie Schober, Dieter H. Pahr, and Andreas G. Reisinger. “Critical Loss of Primary Implant Stability in Osteosynthesis Locking Screws under Cyclic Overloading.” <i>Medical Engineering and Physics</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.medengphy.2024.104143\">https://doi.org/10.1016/j.medengphy.2024.104143</a>."},"doi":"10.1016/j.medengphy.2024.104143","title":"Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading","publication":"Medical Engineering and Physics"},{"issue":"1","quality_controlled":"1","title":"Laser-cavity locking utilizing beam ellipticity: accessing the 10<sup>−7</sup> instability scale relative to cavity linewidth","DOAJ_listed":"1","APC_amount":"3393,38 EUR","publication":"Optica","citation":{"chicago":"Diorico, Fritz R, Artem Zhutov, and Onur Hosten. “Laser-Cavity Locking Utilizing Beam Ellipticity: Accessing the 10<sup>−7</sup> Instability Scale Relative to Cavity Linewidth.” <i>Optica</i>. Optica Publishing Group, 2024. <a href=\"https://doi.org/10.1364/optica.507451\">https://doi.org/10.1364/optica.507451</a>.","short":"F.R. Diorico, A. Zhutov, O. Hosten, Optica 11 (2024) 26–31.","mla":"Diorico, Fritz R., et al. “Laser-Cavity Locking Utilizing Beam Ellipticity: Accessing the 10<sup>−7</sup> Instability Scale Relative to Cavity Linewidth.” <i>Optica</i>, vol. 11, no. 1, Optica Publishing Group, 2024, pp. 26–31, doi:<a href=\"https://doi.org/10.1364/optica.507451\">10.1364/optica.507451</a>.","apa":"Diorico, F. R., Zhutov, A., &#38; Hosten, O. (2024). Laser-cavity locking utilizing beam ellipticity: accessing the 10<sup>−7</sup> instability scale relative to cavity linewidth. <i>Optica</i>. Optica Publishing Group. <a href=\"https://doi.org/10.1364/optica.507451\">https://doi.org/10.1364/optica.507451</a>","ama":"Diorico FR, Zhutov A, Hosten O. Laser-cavity locking utilizing beam ellipticity: accessing the 10<sup>−7</sup> instability scale relative to cavity linewidth. <i>Optica</i>. 2024;11(1):26-31. doi:<a href=\"https://doi.org/10.1364/optica.507451\">10.1364/optica.507451</a>","ista":"Diorico FR, Zhutov A, Hosten O. 2024. Laser-cavity locking utilizing beam ellipticity: accessing the 10<sup>−7</sup> instability scale relative to cavity linewidth. Optica. 11(1), 26–31.","ieee":"F. R. Diorico, A. Zhutov, and O. Hosten, “Laser-cavity locking utilizing beam ellipticity: accessing the 10<sup>−7</sup> instability scale relative to cavity linewidth,” <i>Optica</i>, vol. 11, no. 1. Optica Publishing Group, pp. 26–31, 2024."},"publication_identifier":{"issn":["2334-2536"]},"doi":"10.1364/optica.507451","month":"01","author":[{"orcid":"0000-0002-4947-8924","first_name":"Fritz R","id":"2E054C4C-F248-11E8-B48F-1D18A9856A87","last_name":"Diorico","full_name":"Diorico, Fritz R"},{"full_name":"Zhutov, Artem","id":"0f02ed6a-b514-11ee-b891-8379c5f19cb7","last_name":"Zhutov","first_name":"Artem"},{"last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X","first_name":"Onur","full_name":"Hosten, Onur"}],"date_created":"2024-01-15T10:25:38Z","type":"journal_article","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"das_tickbox":"1","OA_place":"publisher","fulldoi":"https://doi.org/10.1364/optica.507451","day":"20","OA_type":"gold","scopus_import":"1","publication_status":"published","article_type":"original","file_date_updated":"2024-01-17T08:53:16Z","date_published":"2024-01-20T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"We thank Rishabh Sahu and Sebastian Wald for technical contributions to the experiment. Funding by Institute of Science and Technology Austria.","oa":1,"ddc":["530"],"supplementarymaterial":"no","publisher":"Optica Publishing Group","has_accepted_license":"1","_id":"14802","page":"26-31","status":"public","date_updated":"2026-10-21T08:26:22Z","article_processing_charge":"Yes","department":[{"_id":"OnHo"}],"intvolume":"        11","oa_version":"Published Version","language":[{"iso":"eng"}],"external_id":{"isi":["001202817000004"]},"keyword":["Atomic and Molecular Physics","and Optics","Electronic","Optical and Magnetic Materials"],"year":"2024","volume":11,"researchdata_availability":"upon request","isi":1,"abstract":[{"text":"Frequency-stable lasers form the back bone of precision measurements in science and technology. Such lasers typically attain their stability through frequency locking to reference cavities. State-of-the-art locking performances to date had been achieved using frequency modulation based methods, complemented with active drift cancellation systems. We demonstrate an all passive, modulation-free laser-cavity locking technique (squash locking) that utilizes changes in spatial beam ellipticity for error signal generation, and a coherent polarization post-selection for noise resilience. By comparing two identically built proof-of-principle systems, we show a frequency locking instability of 5×10<jats:sup>−7</jats:sup> relative to the cavity linewidth at 10 s averaging. The results surpass the demonstrated performances of methods engineered over the last five decades, potentially enabling an advancement in the precision control of lasers, while creating avenues for bridging the performance gaps between industrial grade lasers with scientific ones due to the afforded simplicity and scalability.","lang":"eng"}],"corr_author":"1","dataavailabilitystatement":"Data underlying the results presented in this paper are not publicly available at this time but may be obtained from the authors upon reasonable request.","file":[{"success":1,"file_name":"2023_Optica_Diorico.pdf","file_size":4558986,"date_updated":"2024-01-17T08:53:16Z","date_created":"2024-01-17T08:53:16Z","creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"eb99ca7d0fe73e22f121875175546ed7","file_id":"14824","content_type":"application/pdf"}]},{"supplementarymaterial":"no","publisher":"Elsevier","has_accepted_license":"1","acknowledgement":"A.B.L. would like to thank Johannes Agerskov and Jan Philip Solovej for valuable discussions. We thank Alessandro Giuliani for helpful discussions and for pointing out the reference [18]. Funding from the European Union's Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is acknowledged. Financial support by the Austrian Science Fund (FWF) through project number I 6427-N (as part of the SFB/TRR 352) is gratefully acknowledged.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"ddc":["510"],"language":[{"iso":"eng"}],"oa_version":"Published Version","volume":286,"year":"2024","researchdata_availability":"not applicable","external_id":{"isi":["001170294000001"],"arxiv":["2301.04894"]},"project":[{"call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"name":"Mathematical Challenges in BCS Theory of Superconductivity","grant_number":"I06427","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b"}],"isi":1,"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"17305","checksum":"ee203cf2dc4420ad90d3c9970d246a78","success":1,"file_size":1381063,"file_name":"2024_JourFunctAnalysis_Lauritsen.pdf","creator":"dernst","date_created":"2024-07-22T11:11:56Z","date_updated":"2024-07-22T11:11:56Z"}],"abstract":[{"text":"We prove an upper bound on the ground state energy of the dilute spin-polarized Fermi gas capturing the leading correction to the kinetic energy resulting from repulsive interactions. One of the main ingredients in the proof is a rigorous implementation of the fermionic cluster expansion of Gaudin et al. (1971) [15].","lang":"eng"}],"corr_author":"1","dataavailabilitystatement":"No data was used for the research described in the article.","_id":"14931","article_processing_charge":"Yes (via OA deal)","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"18135"}]},"date_updated":"2026-10-21T08:29:09Z","status":"public","department":[{"_id":"RoSe"}],"intvolume":"       286","title":"Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion","publication":"Journal of Functional Analysis","publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"citation":{"ieee":"A. B. Lauritsen and R. Seiringer, “Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion,” <i>Journal of Functional Analysis</i>, vol. 286, no. 7. Elsevier, 2024.","ama":"Lauritsen AB, Seiringer R. Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. <i>Journal of Functional Analysis</i>. 2024;286(7). doi:<a href=\"https://doi.org/10.1016/j.jfa.2024.110320\">10.1016/j.jfa.2024.110320</a>","apa":"Lauritsen, A. B., &#38; Seiringer, R. (2024). Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2024.110320\">https://doi.org/10.1016/j.jfa.2024.110320</a>","ista":"Lauritsen AB, Seiringer R. 2024. Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis. 286(7), 110320.","mla":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” <i>Journal of Functional Analysis</i>, vol. 286, no. 7, 110320, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.jfa.2024.110320\">10.1016/j.jfa.2024.110320</a>.","short":"A.B. Lauritsen, R. Seiringer, Journal of Functional Analysis 286 (2024).","chicago":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” <i>Journal of Functional Analysis</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.jfa.2024.110320\">https://doi.org/10.1016/j.jfa.2024.110320</a>."},"arxiv":1,"doi":"10.1016/j.jfa.2024.110320","issue":"7","quality_controlled":"1","das_tickbox":"1","day":"01","fulldoi":"https://doi.org/10.1016/j.jfa.2024.110320","date_published":"2024-04-01T00:00:00Z","publication_status":"published","article_type":"original","file_date_updated":"2024-07-22T11:11:56Z","scopus_import":"1","author":[{"full_name":"Lauritsen, Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","first_name":"Asbjørn Bækgaard","last_name":"Lauritsen","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1"},{"last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","full_name":"Seiringer, Robert"}],"article_number":"110320","month":"04","date_created":"2024-02-04T23:00:53Z","type":"journal_article","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"ec_funded":1},{"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","oa":1,"ddc":["570"],"acknowledgement":"We thank Armel Nicolas, Bella Bruszel and Ewelina Dutkiewicz from the ISTA Mass Spectrometry Service (Lab Services Facilities) for all Proteomics work, including samples preparation, LC/MS data acquisition, searches and data evaluation. We thank Prof. Peter Jonas for his suggestion on the involvement of potassium channels and members of the Neuroethology group for their comments on the manuscript. Katalin Szigeti and Julie Murmann for experimental help. This research was supported by the Scientific Service Units of ISTA through resources provided by the Lab Support Facility, the Imaging and Optics Facility, the Machine Shop Unit and the Preclinical Facility, especially Freyja Langer and Michael Schunn. ","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","year":"2024","keyword":["ASD","periaqueductal gray","perception","behavior","potassium channels"],"oa_version":"Published Version","file":[{"success":1,"file_size":"1149617663","file_name":"PatchClamp.zip","creator":"mjoesch","date_created":"2024-05-15T06:09:17Z","date_updated":"2024-05-15T06:09:17Z","access_level":"open_access","relation":"main_file","file_id":"15396","content_type":"application/zip","checksum":"9205eb0876f0f08552dbad80d6884b4b"},{"file_id":"15397","content_type":"application/zip","relation":"main_file","access_level":"open_access","date_created":"2024-05-15T06:09:12Z","date_updated":"2024-05-15T06:09:12Z","creator":"mjoesch","file_size":"564903112","success":1,"file_name":"SiliconProbe.zip"},{"relation":"main_file","access_level":"open_access","checksum":"49a807bbab06b5fada38f532e2176e2e","content_type":"application/zip","file_id":"15398","file_size":"11685703","success":1,"file_name":"WesternBlot.zip","date_updated":"2024-05-15T06:09:14Z","date_created":"2024-05-15T06:09:14Z","creator":"mjoesch"},{"file_name":"Behaviour.zip","success":1,"file_size":"1335626779","date_created":"2024-05-15T06:09:38Z","date_updated":"2024-05-15T06:09:38Z","creator":"mjoesch","relation":"main_file","access_level":"open_access","checksum":"beeeeaa43770090f3b291209ed6b0623","content_type":"application/zip","file_id":"15399"},{"creator":"mjoesch","date_updated":"2024-05-16T09:08:20Z","date_created":"2024-05-16T09:08:20Z","file_name":"Readme_Data.txt","success":1,"file_size":18841,"content_type":"text/plain","file_id":"15400","checksum":"8862ad7719388304d1d19f8e7db8bb00","access_level":"open_access","relation":"main_file"}],"corr_author":"1","abstract":[{"lang":"eng","text":"Relevant information about the data can be found in the 'Readme_Data.txt' file. \r\nA previous version of the publication can be found on BioRxiv: https://www.biorxiv.org/content/10.1101/2022.10.11.511691v4\r\nand published in Plos Biology (2024)"}],"article_processing_charge":"No","status":"public","date_updated":"2026-10-21T08:31:42Z","related_material":{"record":[{"id":"17142","relation":"used_in_publication","status":"public"}]},"_id":"15385","department":[{"_id":"MaJö"},{"_id":"PreCl"},{"_id":"SiHi"},{"_id":"RySh"},{"_id":"GaNo"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","title":"Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice","doi":"10.15479/AT:ISTA:15385","citation":{"mla":"Burnett, Laura, et al. <i>Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:15385\">10.15479/AT:ISTA:15385</a>.","apa":"Burnett, L., Koppensteiner, P., Symonova, O., Masson, T., Vega Zuniga, T. A., Contreras, X., … Jösch, M. A. (2024). Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:15385\">https://doi.org/10.15479/AT:ISTA:15385</a>","ama":"Burnett L, Koppensteiner P, Symonova O, et al. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:15385\">10.15479/AT:ISTA:15385</a>","ista":"Burnett L, Koppensteiner P, Symonova O, Masson T, Vega Zuniga TA, Contreras X, Rülicke T, Shigemoto R, Novarino G, Jösch MA. 2024. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:15385\">10.15479/AT:ISTA:15385</a>.","ieee":"L. Burnett <i>et al.</i>, “Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice.” Institute of Science and Technology Austria, 2024.","chicago":"Burnett, Laura, Peter Koppensteiner, Olga Symonova, Tomas Masson, Tomas A Vega Zuniga, Ximena Contreras, Thomas Rülicke, Ryuichi Shigemoto, Gaia Novarino, and Maximilian A Jösch. “Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:15385\">https://doi.org/10.15479/AT:ISTA:15385</a>.","short":"L. Burnett, P. Koppensteiner, O. Symonova, T. Masson, T.A. Vega Zuniga, X. Contreras, T. Rülicke, R. Shigemoto, G. Novarino, M.A. Jösch, (2024)."},"date_published":"2024-05-15T00:00:00Z","file_date_updated":"2024-05-16T09:08:20Z","day":"15","fulldoi":"https://doi.org/10.15479/AT:ISTA:15385","date_created":"2024-05-13T15:04:04Z","author":[{"full_name":"Burnett, Laura","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","last_name":"Burnett","first_name":"Laura","orcid":"0000-0002-8937-410X"},{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner","orcid":"0000-0002-3509-1948","first_name":"Peter","full_name":"Koppensteiner, Peter"},{"full_name":"Symonova, Olga","first_name":"Olga","orcid":"0000-0003-2012-9947","last_name":"Symonova","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Masson, Tomas","first_name":"Tomas","orcid":"0000-0002-2634-6283","last_name":"Masson","id":"93ac43e8-8599-11eb-9b86-f6efb0a4c207"},{"id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","last_name":"Vega Zuniga","first_name":"Tomas A","full_name":"Vega Zuniga, Tomas A"},{"full_name":"Contreras, Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","last_name":"Contreras","first_name":"Ximena"},{"last_name":"Rülicke","first_name":"Thomas","full_name":"Rülicke, Thomas"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino"},{"full_name":"Jösch, Maximilian A","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"month":"05","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png"},"type":"research_data","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"Bio"}]},{"publication":"Nature Biotechnology","title":"Imaging brain tissue architecture across millimeter to nanometer scales","doi":"10.1038/s41587-023-01911-8","citation":{"short":"J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri, C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S. Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology 42 (2024) 1051–1064.","chicago":"Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake Watson, Alban Cenameri, Christoph M Sommer, et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” <i>Nature Biotechnology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41587-023-01911-8\">https://doi.org/10.1038/s41587-023-01911-8</a>.","ieee":"J. M. Michalska <i>et al.</i>, “Imaging brain tissue architecture across millimeter to nanometer scales,” <i>Nature Biotechnology</i>, vol. 42. Springer Nature, pp. 1051–1064, 2024.","mla":"Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” <i>Nature Biotechnology</i>, vol. 42, Springer Nature, 2024, pp. 1051–64, doi:<a href=\"https://doi.org/10.1038/s41587-023-01911-8\">10.1038/s41587-023-01911-8</a>.","ama":"Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture across millimeter to nanometer scales. <i>Nature Biotechnology</i>. 2024;42:1051-1064. doi:<a href=\"https://doi.org/10.1038/s41587-023-01911-8\">10.1038/s41587-023-01911-8</a>","apa":"Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri, A., … Danzl, J. G. (2024). Imaging brain tissue architecture across millimeter to nanometer scales. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-023-01911-8\">https://doi.org/10.1038/s41587-023-01911-8</a>","ista":"Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer CM, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino G, Jonas PM, Danzl JG. 2024. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. 42, 1051–1064."},"publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"quality_controlled":"1","pmid":1,"OA_place":"publisher","das_tickbox":"1","scopus_import":"1","file_date_updated":"2025-01-09T07:48:01Z","article_type":"original","date_published":"2024-07-01T00:00:00Z","publication_status":"published","fulldoi":"https://doi.org/10.1038/s41587-023-01911-8","day":"01","OA_type":"hybrid","date_created":"2023-09-03T22:01:15Z","month":"07","author":[{"full_name":"Michalska, Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","last_name":"Michalska","orcid":"0000-0003-3862-1235","first_name":"Julia M"},{"last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","full_name":"Lyudchik, Julia"},{"full_name":"Velicky, Philipp","last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","orcid":"0000-0002-2340-7431"},{"full_name":"Korinkova, Hana","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed","last_name":"Korinkova","first_name":"Hana"},{"full_name":"Watson, Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","last_name":"Watson","first_name":"Jake","orcid":"0000-0002-8698-3823"},{"first_name":"Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886","last_name":"Cenameri","full_name":"Cenameri, Alban"},{"full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer"},{"last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","first_name":"Nicole","full_name":"Amberg, Nicole"},{"first_name":"Alessandro","orcid":"0000-0003-2356-9403","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","last_name":"Venturino","full_name":"Venturino, Alessandro"},{"last_name":"Roessler","first_name":"Karl","full_name":"Roessler, Karl"},{"first_name":"Thomas","last_name":"Czech","full_name":"Czech, Thomas"},{"last_name":"Höftberger","first_name":"Romana","full_name":"Höftberger, Romana"},{"full_name":"Siegert, Sandra","first_name":"Sandra","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"},{"first_name":"Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M"},{"full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl"}],"ec_funded":1,"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"type":"journal_article","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"publisher":"Springer Nature","has_accepted_license":"1","supplementarymaterial":"yes","oa":1,"ddc":["570"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I. Erber for technical assistance; and M. Tomschik for support with obtaining human samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata for computational support and hardware control. We are grateful to R. Shigemoto and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University) for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly provided by S. Grant (University of Edinburgh). We acknowledge expert support by Institute of Science and Technology Austria’s scientific computing, imaging and optics, preclinical and lab support facilities and by the Miba machine shop and library. We gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).","external_id":{"pmid":["37653226"],"isi":["001065254200001"]},"volume":42,"researchdata_availability":"yes","year":"2024","oa_version":"Published Version","language":[{"iso":"eng"}],"corr_author":"1","abstract":[{"lang":"eng","text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease."}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"18784","checksum":"57d5fafb16f02dcb9f7dddb1bd7e2a71","file_size":26065165,"success":1,"file_name":"2024_NatureBiotech_Michalska.pdf","creator":"dernst","date_created":"2025-01-09T07:48:01Z","date_updated":"2025-01-09T07:48:01Z"}],"isi":1,"project":[{"call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232","call_identifier":"FWF"},{"name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"High content imaging to decode human immune cell interactions in health and allergic disease","grant_number":"LS18-022","_id":"23889792-32DE-11EA-91FC-C7463DDC885E"},{"call_identifier":"H2020","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"call_identifier":"H2020","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","grant_number":"101026635","name":"Synaptic computations of the hippocampal CA3 circuitry"}],"related_material":{"link":[{"relation":"software","url":"https://github.com/danzllab/CATS"}],"record":[{"id":"18660","relation":"dissertation_contains","status":"deleted"},{"id":"13126","relation":"research_data","status":"public"},{"status":"public","id":"18674","relation":"dissertation_contains"}]},"date_updated":"2026-10-21T08:36:20Z","status":"public","article_processing_charge":"Yes (in subscription journal)","_id":"14257","page":"1051-1064","intvolume":"        42","department":[{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"JoDa"},{"_id":"Bio"},{"_id":"RySh"}]},{"supplementarymaterial":"yes","publisher":"American Association for the Advancement of Science","has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"Ajap1HA/HA and Ajap1W183C/+ mice were generated in collaboration with Pawel Pelczar at the center for transgenic models at the University of Basel, Switzerland. We thank the imaging core facility (IMCF, University of Basel) and in particular A. Ferrand for the technical assistance provided on the OMX 3D-SIM microscope.\r\nThis work was supported by a grant from the Swiss National Science Foundation (SNF) to B.B. (31003A-152970, 310030B-201291), an NIH grant to E.A. and E.H.S. (R01NS058721), DFG grants to B.F. (TRR 152 project ID 239283807, FA 332/15-1, 16-1), and grants to P.S. from AIMS-2-TRIALS, which are supported by the Innovative Medicines Initiatives from the European Commission joint undertaking under grant agreement No 777394.","ddc":["570"],"oa":1,"oa_version":"Published Version","language":[{"iso":"eng"}],"external_id":{"pmid":["38985877"],"isi":["001280159000022"]},"researchdata_availability":"yes (supplementary data)","volume":10,"year":"2024","isi":1,"dataavailabilitystatement":"All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials.","abstract":[{"text":"Adherens junction–associated protein 1 (AJAP1) has been implicated in brain diseases; however, a pathogenic mechanism has not been identified. AJAP1 is widely expressed in neurons and binds to γ-aminobutyric acid type B receptors (GBRs), which inhibit neurotransmitter release at most synapses in the brain. Here, we show that AJAP1 is selectively expressed in dendrites and trans-synaptically recruits GBRs to presynaptic sites of neurons expressing AJAP1. We have identified several monoallelic AJAP1 variants in individuals with epilepsy and/or neurodevelopmental disorders. Specifically, we show that the variant p.(W183C) lacks binding to GBRs, resulting in the inability to recruit them. Ultrastructural analysis revealed significantly decreased presynaptic GBR levels in Ajap1−/− and Ajap1W183C/+ mice. Consequently, these mice exhibited reduced GBR-mediated presynaptic inhibition at excitatory and inhibitory synapses, along with impaired synaptic plasticity. Our study reveals that AJAP1 enables the postsynaptic neuron to regulate the level of presynaptic GBR-mediated inhibition, supporting the clinical relevance of loss-of-function AJAP1 variants.","lang":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"17287","checksum":"9cbc4501fcd4ba1c0811fd244031422b","file_name":"2024_ScienceAdv_Früh.pdf","success":1,"file_size":7241489,"creator":"dernst","date_created":"2024-07-22T06:29:27Z","date_updated":"2024-07-22T06:29:27Z"}],"_id":"17280","date_updated":"2026-10-21T08:35:21Z","status":"public","article_processing_charge":"Yes","department":[{"_id":"RySh"},{"_id":"PreCl"}],"intvolume":"        10","title":"Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release","DOAJ_listed":"1","publication":"Science Advances","citation":{"short":"S. Früh, S. Boudkkazi, P. Koppensteiner, V. Sereikaite, L.Y. Chen, D. Fernandez-Fernandez, P.D. Rem, D. Ulrich, J. Schwenk, Z. Chen, E.L. Monnier, T. Fritzius, S.M. Innocenti, V. Besseyrias, L. Trovò, M. Stawarski, E. Argilli, E.H. Sherr, B. Van Bon, E.J. Kamsteeg, M. Iascone, A. Pilotta, M.R. Cutrì, M.S. Azamian, A. Hernández-García, S.R. Lalani, J.A. Rosenfeld, X. Zhao, T.P. Vogel, H. Ona, D.A. Scott, P. Scheiffele, K. Strømgaard, M. Tafti, M. Gassmann, B. Fakler, R. Shigemoto, B. Bettler, Science Advances 10 (2024).","chicago":"Früh, Simon, Sami Boudkkazi, Peter Koppensteiner, Vita Sereikaite, Li Yuan Chen, Diego Fernandez-Fernandez, Pascal D. Rem, et al. “Monoallelic de Novo AJAP1 Loss-of- Function Variants Disrupt Trans-Synaptic Control of Neurotransmitter Release.” <i>Science Advances</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/sciadv.adk5462\">https://doi.org/10.1126/sciadv.adk5462</a>.","ieee":"S. Früh <i>et al.</i>, “Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release,” <i>Science Advances</i>, vol. 10, no. 28. American Association for the Advancement of Science, 2024.","apa":"Früh, S., Boudkkazi, S., Koppensteiner, P., Sereikaite, V., Chen, L. Y., Fernandez-Fernandez, D., … Bettler, B. (2024). Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.adk5462\">https://doi.org/10.1126/sciadv.adk5462</a>","ama":"Früh S, Boudkkazi S, Koppensteiner P, et al. Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release. <i>Science Advances</i>. 2024;10(28). doi:<a href=\"https://doi.org/10.1126/sciadv.adk5462\">10.1126/sciadv.adk5462</a>","ista":"Früh S, Boudkkazi S, Koppensteiner P, Sereikaite V, Chen LY, Fernandez-Fernandez D, Rem PD, Ulrich D, Schwenk J, Chen Z, Monnier EL, Fritzius T, Innocenti SM, Besseyrias V, Trovò L, Stawarski M, Argilli E, Sherr EH, Van Bon B, Kamsteeg EJ, Iascone M, Pilotta A, Cutrì MR, Azamian MS, Hernández-García A, Lalani SR, Rosenfeld JA, Zhao X, Vogel TP, Ona H, Scott DA, Scheiffele P, Strømgaard K, Tafti M, Gassmann M, Fakler B, Shigemoto R, Bettler B. 2024. Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release. Science Advances. 10(28), adk5462.","mla":"Früh, Simon, et al. “Monoallelic de Novo AJAP1 Loss-of- Function Variants Disrupt Trans-Synaptic Control of Neurotransmitter Release.” <i>Science Advances</i>, vol. 10, no. 28, adk5462, American Association for the Advancement of Science, 2024, doi:<a href=\"https://doi.org/10.1126/sciadv.adk5462\">10.1126/sciadv.adk5462</a>."},"publication_identifier":{"eissn":["2375-2548"]},"doi":"10.1126/sciadv.adk5462","issue":"28","quality_controlled":"1","pmid":1,"das_tickbox":"1","OA_place":"publisher","fulldoi":"https://doi.org/10.1126/sciadv.adk5462","day":"12","OA_type":"gold","scopus_import":"1","article_type":"original","publication_status":"published","file_date_updated":"2024-07-22T06:29:27Z","date_published":"2024-07-12T00:00:00Z","month":"07","article_number":"adk5462","author":[{"first_name":"Simon","last_name":"Früh","full_name":"Früh, Simon"},{"last_name":"Boudkkazi","first_name":"Sami","full_name":"Boudkkazi, Sami"},{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner","orcid":"0000-0002-3509-1948","first_name":"Peter","full_name":"Koppensteiner, Peter"},{"full_name":"Sereikaite, Vita","first_name":"Vita","last_name":"Sereikaite"},{"full_name":"Chen, Li Yuan","first_name":"Li Yuan","last_name":"Chen"},{"first_name":"Diego","last_name":"Fernandez-Fernandez","full_name":"Fernandez-Fernandez, Diego"},{"last_name":"Rem","first_name":"Pascal D.","full_name":"Rem, Pascal D."},{"full_name":"Ulrich, Daniel","last_name":"Ulrich","first_name":"Daniel"},{"last_name":"Schwenk","first_name":"Jochen","full_name":"Schwenk, Jochen"},{"last_name":"Chen","first_name":"Ziyang","full_name":"Chen, Ziyang"},{"first_name":"Elodie Le","last_name":"Monnier","full_name":"Monnier, Elodie Le"},{"last_name":"Fritzius","first_name":"Thorsten","full_name":"Fritzius, Thorsten"},{"full_name":"Innocenti, Sabrina M.","first_name":"Sabrina M.","last_name":"Innocenti"},{"full_name":"Besseyrias, Valérie","last_name":"Besseyrias","first_name":"Valérie"},{"last_name":"Trovò","first_name":"Luca","full_name":"Trovò, Luca"},{"last_name":"Stawarski","first_name":"Michal","full_name":"Stawarski, Michal"},{"full_name":"Argilli, Emanuela","first_name":"Emanuela","last_name":"Argilli"},{"last_name":"Sherr","first_name":"Elliott H.","full_name":"Sherr, Elliott H."},{"full_name":"Van Bon, Bregje","first_name":"Bregje","last_name":"Van Bon"},{"last_name":"Kamsteeg","first_name":"Erik Jan","full_name":"Kamsteeg, Erik Jan"},{"full_name":"Iascone, Maria","last_name":"Iascone","first_name":"Maria"},{"last_name":"Pilotta","first_name":"Alba","full_name":"Pilotta, Alba"},{"full_name":"Cutrì, Maria R.","first_name":"Maria R.","last_name":"Cutrì"},{"full_name":"Azamian, Mahshid S.","last_name":"Azamian","first_name":"Mahshid S."},{"full_name":"Hernández-García, Andrés","first_name":"Andrés","last_name":"Hernández-García"},{"last_name":"Lalani","first_name":"Seema R.","full_name":"Lalani, Seema R."},{"full_name":"Rosenfeld, Jill A.","first_name":"Jill A.","last_name":"Rosenfeld"},{"full_name":"Zhao, Xiaonan","first_name":"Xiaonan","last_name":"Zhao"},{"last_name":"Vogel","first_name":"Tiphanie P.","full_name":"Vogel, Tiphanie P."},{"full_name":"Ona, Herda","last_name":"Ona","first_name":"Herda"},{"last_name":"Scott","first_name":"Daryl A.","full_name":"Scott, Daryl A."},{"first_name":"Peter","last_name":"Scheiffele","full_name":"Scheiffele, Peter"},{"first_name":"Kristian","last_name":"Strømgaard","full_name":"Strømgaard, Kristian"},{"full_name":"Tafti, Mehdi","last_name":"Tafti","first_name":"Mehdi"},{"last_name":"Gassmann","first_name":"Martin","full_name":"Gassmann, Martin"},{"last_name":"Fakler","first_name":"Bernd","full_name":"Fakler, Bernd"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi"},{"last_name":"Bettler","first_name":"Bernhard","full_name":"Bettler, Bernhard"}],"date_created":"2024-07-21T22:01:01Z","type":"journal_article","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"}},{"citation":{"ama":"Lyudchik J. Image analysis for brain tissue reconstruction with super-resolution light microscopy. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18674\">10.15479/at:ista:18674</a>","apa":"Lyudchik, J. (2024). <i>Image analysis for brain tissue reconstruction with super-resolution light microscopy</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18674\">https://doi.org/10.15479/at:ista:18674</a>","ista":"Lyudchik J. 2024. Image analysis for brain tissue reconstruction with super-resolution light microscopy. Institute of Science and Technology Austria.","mla":"Lyudchik, Julia. <i>Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18674\">10.15479/at:ista:18674</a>.","ieee":"J. Lyudchik, “Image analysis for brain tissue reconstruction with super-resolution light microscopy,” Institute of Science and Technology Austria, 2024.","chicago":"Lyudchik, Julia. “Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18674\">https://doi.org/10.15479/at:ista:18674</a>.","short":"J. Lyudchik, Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy, Institute of Science and Technology Austria, 2024."},"publication_identifier":{"isbn":[" 978-3-99078-051-0"],"issn":["2663-337X"]},"doi":"10.15479/at:ista:18674","title":"Image analysis for brain tissue reconstruction with super-resolution light microscopy","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"acknowledged_ssus":[{"_id":"Bio"}],"ec_funded":1,"author":[{"first_name":"Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik","full_name":"Lyudchik, Julia"}],"month":"12","date_created":"2024-12-18T14:24:43Z","degree_awarded":"PhD","day":"18","fulldoi":"https://doi.org/10.15479/at:ista:18674","file_date_updated":"2024-12-18T14:41:53Z","date_published":"2024-12-18T00:00:00Z","publication_status":"published","das_tickbox":"0","OA_place":"publisher","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"ddc":["004"],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","supplementarymaterial":"no","doi_confirm":"1","supervisor":[{"first_name":"Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G"}],"alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"JoDa"}],"page":"217","_id":"18674","article_processing_charge":"No","related_material":{"record":[{"status":"public","id":"11160","relation":"part_of_dissertation"},{"status":"public","id":"13267","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"18677"},{"relation":"part_of_dissertation","id":"14257","status":"public"}]},"date_updated":"2026-10-21T08:36:19Z","status":"public","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"file":[{"access_level":"open_access","relation":"main_file","file_id":"18675","content_type":"application/pdf","checksum":"1b42b8073e2bc09fc504da52372248c1","file_size":160536833,"success":1,"file_name":"18122024_PhDthesis_corrected_final_pdfa.pdf","creator":"jlyudchi","date_created":"2024-12-18T14:17:34Z","date_updated":"2024-12-18T14:17:34Z"},{"file_name":"18122024_PhDthesis_corrected_final_JL_markup.docx","file_size":99172203,"date_updated":"2024-12-18T14:41:53Z","date_created":"2024-12-18T14:21:06Z","creator":"jlyudchi","relation":"source_file","access_level":"closed","checksum":"b4da84624060745519723698f7ddf54b","file_id":"18676","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"abstract":[{"text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue requires volumetric imaging at nanoscale spatial resolution. While light microscopy excels at visualizing specific molecules and individual cells, achieving dense, synapse-level circuit reconstruction has not been possible with any light microscopy technique. Thus, the goal of my work was to develop image and data analysis pipelines for brain tissue visualization and reconstruction with light microscopy. To achieve dense circuit reconstruction with single-synapse resolution, I developed both conventional and deep-learning-based synapse detection algorithms, as well as connectivity analysis pipelines that integrate synapse detection with volumetric segmentation of brain tissue.","lang":"eng"}],"corr_author":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","researchdata_availability":"no","year":"2024"},{"doi":"10.1063/5.0215151","publication_identifier":{"eissn":["1089-7550"],"issn":["0021-8979"]},"citation":{"mla":"Lenton, Isaac C., et al. “Beyond the Blur: Using Experimentally Determined Point Spread Functions to Improve Scanning Kelvin Probe Imaging.” <i>Journal of Applied Physics</i>, vol. 136, no. 4, 045305, AIP Publishing, 2024, doi:<a href=\"https://doi.org/10.1063/5.0215151\">10.1063/5.0215151</a>.","ama":"Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging. <i>Journal of Applied Physics</i>. 2024;136(4). doi:<a href=\"https://doi.org/10.1063/5.0215151\">10.1063/5.0215151</a>","ista":"Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. 2024. Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging. Journal of Applied Physics. 136(4), 045305.","apa":"Lenton, I. C., Pertl, F., Shafeek, L. B., &#38; Waitukaitis, S. R. (2024). Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging. <i>Journal of Applied Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0215151\">https://doi.org/10.1063/5.0215151</a>","ieee":"I. C. Lenton, F. Pertl, L. B. Shafeek, and S. R. Waitukaitis, “Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging,” <i>Journal of Applied Physics</i>, vol. 136, no. 4. AIP Publishing, 2024.","chicago":"Lenton, Isaac C, Felix Pertl, Lubuna B Shafeek, and Scott R Waitukaitis. “Beyond the Blur: Using Experimentally Determined Point Spread Functions to Improve Scanning Kelvin Probe Imaging.” <i>Journal of Applied Physics</i>. AIP Publishing, 2024. <a href=\"https://doi.org/10.1063/5.0215151\">https://doi.org/10.1063/5.0215151</a>.","short":"I.C. Lenton, F. Pertl, L.B. Shafeek, S.R. Waitukaitis, Journal of Applied Physics 136 (2024)."},"publication":"Journal of Applied Physics","title":"Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging","quality_controlled":"1","issue":"4","scopus_import":"1","publication_status":"published","article_type":"original","file_date_updated":"2024-08-05T08:19:58Z","date_published":"2024-07-28T00:00:00Z","fulldoi":"https://doi.org/10.1063/5.0215151","day":"28","das_tickbox":"1","ec_funded":1,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"type":"journal_article","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"date_created":"2024-08-04T22:01:21Z","month":"07","article_number":"045305","author":[{"full_name":"Lenton, Isaac C","last_name":"Lenton","id":"a550210f-223c-11ec-8182-e2d45e817efb","first_name":"Isaac C","orcid":"0000-0002-5010-6984"},{"orcid":"0000-0003-0463-5794","first_name":"Felix","id":"6313aec0-15b2-11ec-abd3-ed67d16139af","last_name":"Pertl","full_name":"Pertl, Felix"},{"full_name":"Shafeek, Lubuna B","first_name":"Lubuna B","orcid":"0000-0001-7180-6050","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","last_name":"Shafeek"},{"last_name":"Waitukaitis","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176","first_name":"Scott R","full_name":"Waitukaitis, Scott R"}],"has_accepted_license":"1","publisher":"AIP Publishing","supplementarymaterial":"yes","oa":1,"ddc":["530"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 949120). This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine Shop, Nanofabrication Facility, Scientific Computing Facility, and Lab Support Facility. The authors wish to thank Dmytro Rak and Juan Carlos Sobarzo for letting us use their equipment. The authors wish to thank the contributions of the whole Waitukaitis Group for useful discussions and feedback.","dataavailabilitystatement":"The data that support the findings of this study are available from the corresponding author upon reasonable request.","corr_author":"1","abstract":[{"text":"Scanning Kelvin probe microscopy (SKPM) is a powerful technique for investigating the electrostatic properties of material surfaces, enabling the imaging of variations in work function, topology, surface charge density, or combinations thereof. Regardless of the underlying signal source, SKPM results in a voltage image, which is spatially distorted due to the finite size of the probe, long-range electrostatic interactions, mechanical and electrical noise, and the finite response time of the electronics. In order to recover the underlying signal, it is necessary to deconvolve the measurement with an appropriate point spread function (PSF) that accounts the aforementioned distortions, but determining this PSF is difficult. Here, we describe how such PSFs can be determined experimentally and show how they can be used to recover the underlying information of interest. We first consider the physical principles that enable SKPM and discuss how these affect the system PSF. We then show how one can experimentally measure PSFs by looking at well-defined features, and that these compare well to simulated PSFs, provided scans are performed extremely slowly and carefully. Next, we work at realistic scan speeds and show that the idealized PSFs fail to capture temporal distortions in the scan direction. While simulating PSFs for these situations would be quite challenging, we show that measuring PSFs with similar scan conditions works well. Our approach clarifies the basic principles and inherent challenges to SKPM measurements and gives practical methods to improve results.","lang":"eng"}],"file":[{"creator":"dernst","date_updated":"2024-08-05T08:19:58Z","date_created":"2024-08-05T08:19:58Z","file_size":2537502,"success":1,"file_name":"2024_JourApplPhysics_Lenton.pdf","file_id":"17386","content_type":"application/pdf","checksum":"6141d05cd68d540a7446dce9490975db","access_level":"open_access","relation":"main_file"}],"isi":1,"project":[{"call_identifier":"H2020","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","grant_number":"949120","name":"Tribocharge: a multi-scale approach to an enduring problem in physics"}],"external_id":{"isi":["001281681100003"]},"volume":136,"researchdata_availability":"upon request","year":"2024","oa_version":"Published Version","language":[{"iso":"eng"}],"intvolume":"       136","department":[{"_id":"ScWa"},{"_id":"NanoFab"}],"status":"public","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"22684"}]},"date_updated":"2026-10-21T08:39:25Z","article_processing_charge":"No","_id":"17373"},{"supplementarymaterial":"no","publisher":"Elsevier","has_accepted_license":"1","ddc":["570"],"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Imaging & Optics Facility (IOF) and Preclinical Facilities (PCF). N.A. received support from FWF Firnberg-Programme (T 1031). G.C. received support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411 as an ISTplus postdoctoral fellow. This work was also supported by IST Austria institutional funds, FWF SFB F78 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H.","dataavailabilitystatement":"No custom code or dataset was generated in this protocol.","corr_author":"1","abstract":[{"lang":"eng","text":"Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice and high-resolution phenotyping at the individual cell level. Here, we present a protocol for isolating MADM-labeled cells with high yield for downstream molecular analyses using fluorescence-activated cell sorting (FACS). We describe steps for generating MADM-labeled mice, perfusion, single-cell suspension, and debris removal. We then detail procedures for cell sorting by FACS and downstream analysis. This protocol is suitable for embryonic to adult mice.\r\nFor complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).1"}],"file":[{"success":1,"file_size":8871807,"file_name":"2024_STARProtoc_Amberg.pdf","creator":"dernst","date_created":"2024-07-16T11:50:03Z","date_updated":"2024-07-16T11:50:03Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"17260","checksum":"3f0ee62e04bf5a44b45b035662826e95"}],"project":[{"call_identifier":"FWF","grant_number":"T01031","name":"Role of Eed in neural stem cell lineage progression","_id":"268F8446-B435-11E9-9278-68D0E5697425"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"},{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression"},{"call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780"}],"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"external_id":{"pmid":["38070137"]},"researchdata_availability":"not applicable","year":"2024","volume":5,"oa_version":"Published Version","language":[{"iso":"eng"}],"intvolume":"         5","department":[{"_id":"SiHi"}],"status":"public","date_updated":"2026-10-21T08:40:15Z","article_processing_charge":"Yes (in subscription journal)","_id":"14683","doi":"10.1016/j.xpro.2023.102771","citation":{"short":"N. Amberg, G.T. Cheung, S. Hippenmeyer, STAR Protocols 5 (2024).","chicago":"Amberg, Nicole, Giselle T Cheung, and Simon Hippenmeyer. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">https://doi.org/10.1016/j.xpro.2023.102771</a>.","ieee":"N. Amberg, G. T. Cheung, and S. Hippenmeyer, “Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry,” <i>STAR Protocols</i>, vol. 5, no. 1. Elsevier, 2024.","mla":"Amberg, Nicole, et al. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” <i>STAR Protocols</i>, vol. 5, no. 1, 102771, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">10.1016/j.xpro.2023.102771</a>.","ama":"Amberg N, Cheung GT, Hippenmeyer S. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. <i>STAR Protocols</i>. 2024;5(1). doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">10.1016/j.xpro.2023.102771</a>","apa":"Amberg, N., Cheung, G. T., &#38; Hippenmeyer, S. (2024). Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">https://doi.org/10.1016/j.xpro.2023.102771</a>","ista":"Amberg N, Cheung GT, Hippenmeyer S. 2024. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. 5(1), 102771."},"publication_identifier":{"issn":["2666-1667"]},"publication":"STAR Protocols","title":"Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry","quality_controlled":"1","pmid":1,"issue":"1","scopus_import":"1","file_date_updated":"2024-07-16T11:50:03Z","article_type":"review","publication_status":"published","date_published":"2024-03-15T00:00:00Z","fulldoi":"https://doi.org/10.1016/j.xpro.2023.102771","day":"15","das_tickbox":"1","ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"type":"journal_article","date_created":"2023-12-13T11:48:05Z","month":"03","article_number":"102771","author":[{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg","orcid":"0000-0002-3183-8207","first_name":"Nicole","full_name":"Amberg, Nicole"},{"orcid":"0000-0001-8457-2572","first_name":"Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87","last_name":"Cheung","full_name":"Cheung, Giselle T"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","full_name":"Hippenmeyer, Simon"}]},{"publisher":"Elsevier","supplementarymaterial":"yes","has_accepted_license":"1","oa":1,"ddc":["570"],"acknowledgement":"We thank A. Heger for mouse breeding support. This work was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging & Optics and Preclinical facilities. G.C. received funding from the European Commission (IST plus postdoctoral fellowship); S.H. was funded by ISTA institutional funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro Stem Modulation).","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"checksum":"d8a8cdba82a394e731aa699ace1ae433","content_type":"application/pdf","file_id":"18809","relation":"main_file","access_level":"open_access","date_updated":"2025-01-09T12:12:40Z","date_created":"2025-01-09T12:12:40Z","creator":"dernst","file_size":5186071,"success":1,"file_name":"2024_STARProtoc_Cheung.pdf"}],"abstract":[{"text":"The generation of diverse cell types during development is fundamental to brain\r\nfunctions. We outline a protocol to quantitatively assess the clonal output of individual neural progenitors using mosaic analysis with double markers (MADM) in\r\nmice. We first describe steps to acquire and reconstruct adult MADM clones in\r\nthe superior colliculus. Then we detail analysis pipelines to determine clonal\r\ncomposition and architecture. This protocol enables the buildup of quantitative\r\nframeworks of lineage progression with precise spatial resolution in the brain.\r\nFor complete details on the use and execution of this protocol, please refer to\r\nCheung et al.1","lang":"eng"}],"corr_author":"1","dataavailabilitystatement":"No dataset was generated while composing this protocol. A FIJI macro script “3DSerialSectionAlignmentLineROI.ijm” and a Microsoft Excel template used in this protocol are provided as supplementary materials.","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F7805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"}],"volume":5,"year":"2024","researchdata_availability":"yes (supplementary data)","external_id":{"pmid":["38935508"]},"language":[{"iso":"eng"}],"oa_version":"Published Version","intvolume":"         5","department":[{"_id":"SiHi"}],"article_processing_charge":"Yes","status":"public","date_updated":"2026-10-21T09:14:52Z","_id":"17187","doi":"10.1016/j.xpro.2024.103157","citation":{"ieee":"G. T. Cheung, C. Streicher, and S. Hippenmeyer, “Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice,” <i>STAR Protocols</i>, vol. 5, no. 3. Elsevier, 2024.","mla":"Cheung, Giselle T., et al. “Protocol for Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double Markers in Mice.” <i>STAR Protocols</i>, vol. 5, no. 3, 103157, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">10.1016/j.xpro.2024.103157</a>.","ista":"Cheung GT, Streicher C, Hippenmeyer S. 2024. Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. STAR Protocols. 5(3), 103157.","apa":"Cheung, G. T., Streicher, C., &#38; Hippenmeyer, S. (2024). Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">https://doi.org/10.1016/j.xpro.2024.103157</a>","ama":"Cheung GT, Streicher C, Hippenmeyer S. Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. <i>STAR Protocols</i>. 2024;5(3). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">10.1016/j.xpro.2024.103157</a>","short":"G.T. Cheung, C. Streicher, S. Hippenmeyer, STAR Protocols 5 (2024).","chicago":"Cheung, Giselle T, Carmen Streicher, and Simon Hippenmeyer. “Protocol for Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double Markers in Mice.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">https://doi.org/10.1016/j.xpro.2024.103157</a>."},"publication_identifier":{"eissn":["2666-1667"]},"publication":"STAR Protocols","APC_amount":"804 EUR","title":"Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice","pmid":1,"quality_controlled":"1","issue":"3","date_published":"2024-09-20T00:00:00Z","article_type":"original","file_date_updated":"2025-01-09T12:12:40Z","publication_status":"published","scopus_import":"1","day":"20","OA_type":"gold","fulldoi":"https://doi.org/10.1016/j.xpro.2024.103157","OA_place":"publisher","das_tickbox":"1","ec_funded":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"type":"journal_article","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"date_created":"2024-06-30T22:01:04Z","author":[{"full_name":"Cheung, Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87","last_name":"Cheung","first_name":"Giselle T","orcid":"0000-0001-8457-2572"},{"full_name":"Streicher, Carmen","last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"}],"article_number":"103157","month":"09"},{"das_tickbox":"1","OA_place":"publisher","fulldoi":"https://doi.org/10.1016/j.xpro.2024.103168","OA_type":"gold","day":"20","scopus_import":"1","publication_status":"published","article_type":"original","file_date_updated":"2025-01-09T12:16:53Z","date_published":"2024-09-20T00:00:00Z","month":"09","article_number":"103168","author":[{"full_name":"Cheung, Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87","last_name":"Cheung","orcid":"0000-0001-8457-2572","first_name":"Giselle T"},{"last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","first_name":"Florian","full_name":"Pauler, Florian"},{"orcid":"0000-0002-3509-1948","first_name":"Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner","full_name":"Koppensteiner, Peter"},{"orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"}],"date_created":"2024-07-14T22:01:10Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"PreCl"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"type":"journal_article","title":"Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq","APC_amount":"804 EUR","publication":"STAR Protocols","citation":{"short":"G.T. Cheung, F. Pauler, P. Koppensteiner, S. Hippenmeyer, STAR Protocols 5 (2024).","chicago":"Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, and Simon Hippenmeyer. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>.","ieee":"G. T. Cheung, F. Pauler, P. Koppensteiner, and S. Hippenmeyer, “Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq,” <i>STAR Protocols</i>, vol. 5, no. 3. Elsevier, 2024.","mla":"Cheung, Giselle T., et al. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>, vol. 5, no. 3, 103168, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>.","ista":"Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. 2024. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. STAR Protocols. 5(3), 103168.","ama":"Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. 2024;5(3). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>","apa":"Cheung, G. T., Pauler, F., Koppensteiner, P., &#38; Hippenmeyer, S. (2024). Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>"},"publication_identifier":{"eissn":["2666-1667"]},"doi":"10.1016/j.xpro.2024.103168","issue":"3","quality_controlled":"1","pmid":1,"oa_version":"Published Version","language":[{"iso":"eng"}],"external_id":{"pmid":["38968076"]},"volume":5,"year":"2024","researchdata_availability":"not applicable","project":[{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression"}],"dataavailabilitystatement":"No dataset or new code was generated while composing this protocol.","abstract":[{"text":"The lineage relationship of clonally-related cells offers important insights into the ontogeny and cytoarchitecture of the brain in health and disease. Here, we provide a protocol to concurrently assess cell lineage relationship and cell-type identity among clonally-related cells in situ. We first describe the preparation and screening of acute brain slices containing clonally-related cells labeled using mosaic analysis with double markers (MADM). We then outline steps to collect RNA from individual cells for downstream applications and cell-type identification using RNA sequencing.\r\nFor complete details on the use and execution of this protocol, please refer to Cheung et al.\r\n1","lang":"eng"}],"corr_author":"1","file":[{"file_size":6445556,"file_name":"2024_STARProtoc_Cheung2.pdf","success":1,"creator":"dernst","date_created":"2025-01-09T12:16:53Z","date_updated":"2025-01-09T12:16:53Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"18810","checksum":"464f52ecc6ec92f509552823bb82bf79"}],"_id":"17232","status":"public","date_updated":"2026-10-21T09:15:51Z","article_processing_charge":"Yes","department":[{"_id":"SiHi"},{"_id":"PreCl"}],"intvolume":"         5","has_accepted_license":"1","supplementarymaterial":"no","publisher":"Elsevier","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"We thank R. Beattie and T. Asenov for designing and producing components of the multi-well slice recover chamber. We thank R. Shigemoto for providing equipment access. We thank C. Streicher and A. Heger for mouse breeding support. This work was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging & Optics, Miba Machine Shop, and Preclinical facilities. G.C. received funding from the European Commission (IST plus postdoctoral fellowship) and S.H. was funded by ISTA institutional funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro Stem Modulation).","ddc":["570"],"oa":1}]