[{"type":"dissertation","publisher":"Institute of Science and Technology Austria","author":[{"first_name":"Christoph","orcid":"0000-0002-9033-9096","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","last_name":"Dotter","full_name":"Dotter, Christoph"}],"_id":"12364","file_date_updated":"2023-09-20T22:30:03Z","has_accepted_license":"1","citation":{"ama":"Dotter C. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12094\">10.15479/at:ista:12094</a>","ieee":"C. Dotter, “Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder,” Institute of Science and Technology Austria, 2022.","mla":"Dotter, Christoph. <i>Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12094\">10.15479/at:ista:12094</a>.","ista":"Dotter C. 2022. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. Institute of Science and Technology Austria.","chicago":"Dotter, Christoph. “Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12094\">https://doi.org/10.15479/at:ista:12094</a>.","short":"C. Dotter, Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder, Institute of Science and Technology Austria, 2022.","apa":"Dotter, C. (2022). <i>Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12094\">https://doi.org/10.15479/at:ista:12094</a>"},"department":[{"_id":"GradSch"},{"_id":"GaNo"}],"date_created":"2023-01-24T13:09:57Z","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"title":"Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder","year":"2022","project":[{"grant_number":"401299","name":"Probing development and reversibility of autism spectrum disorders","_id":"254BA948-B435-11E9-9278-68D0E5697425"},{"name":"Critical windows and reversibility of ASD associated with mutations in chromatin remodelers","_id":"9B91375C-BA93-11EA-9121-9846C619BF3A","grant_number":"707964"},{"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","grant_number":"715508"},{"_id":"2690FEAC-B435-11E9-9278-68D0E5697425","name":"Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy","grant_number":"I04205","call_identifier":"FWF"}],"page":"152","OA_place":"publisher","degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11160"},{"relation":"part_of_dissertation","id":"3","status":"public"}]},"corr_author":"1","file":[{"content_type":"application/pdf","relation":"main_file","embargo":"2023-09-19","date_updated":"2023-09-20T22:30:03Z","creator":"cchlebak","access_level":"open_access","file_size":20457465,"file_name":"220923_Thesis_CDotter_Final.pdf","date_created":"2023-01-24T13:15:45Z","file_id":"12365","checksum":"896f4cac9adb6d3f26a6605772f4e1a3"},{"creator":"cchlebak","access_level":"closed","date_updated":"2023-09-20T22:30:03Z","content_type":"application/x-zip-compressed","embargo_to":"open_access","relation":"source_file","checksum":"ad01bb20da163be6893b7af832e58419","date_created":"2023-02-02T09:15:35Z","file_id":"12482","file_size":22433512,"file_name":"latex_source_CDotter_Thesis_2022.zip"}],"day":"19","ec_funded":1,"oa":1,"language":[{"iso":"eng"}],"date_updated":"2026-04-07T14:30:57Z","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","supervisor":[{"first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}],"doi":"10.15479/at:ista:12094","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"09","date_published":"2022-09-19T00:00:00Z","status":"public","abstract":[{"text":"Autism spectrum disorders (ASDs) are a group of neurodevelopmental disorders character\u0002ized by behavioral symptoms such as problems in social communication and interaction, as\r\nwell as repetitive, restricted behaviors and interests. These disorders show a high degree\r\nof heritability and hundreds of risk genes have been identifed using high throughput\r\nsequencing technologies. This genetic heterogeneity has hampered eforts in understanding\r\nthe pathogenesis of ASD but at the same time given rise to the concept of convergent\r\nmechanisms. Previous studies have identifed that risk genes for ASD broadly converge\r\nonto specifc functional categories with transcriptional regulation being one of the biggest\r\ngroups. In this thesis, I focus on this subgroup of genes and investigate the gene regulatory\r\nconsequences of some of them in the context of neurodevelopment.\r\nFirst, we showed that mutations in the ASD and intellectual disability risk gene Setd5 lead\r\nto perturbations of gene regulatory programs in early cell fate specifcation. In addition,\r\nadult animals display abnormal learning behavior which is mirrored at the transcriptional\r\nlevel by altered activity dependent regulation of postsynaptic gene expression. Lastly,\r\nwe link the regulatory function of Setd5 to its interaction with the Paf1 and the NCoR\r\ncomplex.\r\nSecond, by modeling the heterozygous loss of the top ASD gene CHD8 in human cerebral\r\norganoids we demonstrate profound changes in the developmental trajectories of both\r\ninhibitory and excitatory neurons using single cell RNA-sequencing. While the former\r\nwere generated earlier in CHD8+/- organoids, the generation of the latter was shifted to\r\nlater times in favor of a prolonged progenitor expansion phase and ultimately increased\r\norganoid size.\r\nFinally, by modeling heterozygous mutations for four ASD associated chromatin modifers,\r\nASH1L, KDM6B, KMT5B, and SETD5 in human cortical spheroids we show evidence of\r\nregulatory convergence across three of those genes. We observe a shift from dorsal cortical\r\nexcitatory neuron fates towards partially ventralized cell types resembling cells from the\r\nlateral ganglionic eminence. As this project is still ongoing at the time of writing, future\r\nexperiments will aim at elucidating the regulatory mechanisms underlying this shift with\r\nthe aim of linking these three ASD risk genes through biological convergence.","lang":"eng"}],"publication_status":"published","ddc":["570"]},{"file_date_updated":"2023-05-17T22:30:03Z","_id":"11393","author":[{"full_name":"Jevtic, Marijo","id":"4BE3BC94-F248-11E8-B48F-1D18A9856A87","last_name":"Jevtic","first_name":"Marijo"}],"has_accepted_license":"1","citation":{"ama":"Jevtic M. Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11393\">10.15479/at:ista:11393</a>","mla":"Jevtic, Marijo. <i>Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11393\">10.15479/at:ista:11393</a>.","ieee":"M. Jevtic, “Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus,” Institute of Science and Technology Austria, 2022.","ista":"Jevtic M. 2022. Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. Institute of Science and Technology Austria.","chicago":"Jevtic, Marijo. “Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11393\">https://doi.org/10.15479/at:ista:11393</a>.","apa":"Jevtic, M. (2022). <i>Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11393\">https://doi.org/10.15479/at:ista:11393</a>","short":"M. Jevtic, Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus, Institute of Science and Technology Austria, 2022."},"type":"dissertation","publisher":"Institute of Science and Technology Austria","title":"Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus","year":"2022","degree_awarded":"PhD","OA_place":"publisher","page":"108","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7391"}]},"department":[{"_id":"GradSch"},{"_id":"RySh"}],"article_processing_charge":"No","date_created":"2022-05-17T08:57:41Z","acknowledged_ssus":[{"_id":"EM-Fac"}],"publication_identifier":{"issn":["2663-337X"]},"oa":1,"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"date_updated":"2026-04-07T14:31:19Z","oa_version":"Published Version","corr_author":"1","file":[{"file_name":"MJ thesis.docx","file_size":56427603,"checksum":"8fc695d88020d70d231dad0e9f10b138","date_created":"2022-05-17T09:08:06Z","file_id":"11395","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","embargo_to":"open_access","creator":"cchlebak","access_level":"closed","date_updated":"2023-05-17T22:30:03Z"},{"file_name":"MJ_thesis_PDFA.pdf","file_size":4351981,"date_created":"2022-05-17T12:09:25Z","file_id":"11397","checksum":"c1dd20a1aece521b3500607b00e463d6","content_type":"application/pdf","relation":"main_file","embargo":"2023-05-16","date_updated":"2023-05-17T22:30:03Z","creator":"cchlebak","access_level":"open_access"}],"day":"16","date_published":"2022-05-16T00:00:00Z","status":"public","ddc":["570"],"publication_status":"published","abstract":[{"lang":"eng","text":"AMPA receptors (AMPARs) mediate fast excitatory neurotransmission and their role is\r\nimplicated in complex processes such as learning and memory and various neurological\r\ndiseases. These receptors are composed of different subunits and the subunit composition can\r\naffect channel properties, receptor trafficking and interaction with other associated proteins.\r\nUsing the high sensitivity SDS-digested freeze-fracture replica labeling (SDS-FRL) for\r\nelectron microscopy I investigated the number, density, and localization of AMPAR subunits,\r\nGluA1, GluA2, GluA3, and GluA1-3 (panAMPA) in pyramidal cells in the CA1 area of mouse\r\nhippocampus. I have found that the immunogold labeling for all of these subunits in the\r\npostsynaptic sites was highest in stratum radiatum and lowest in stratum lacunosummoleculare. The labeling density for the all subunits in the extrasynaptic sites showed a gradual\r\nincrease from the pyramidal cell soma towards the distal part of stratum radiatum. The densities\r\nof extrasynaptic GluA1, GluA2 and panAMPA labeling reached 10-15% of synaptic densities,\r\nwhile the ratio of extrasynaptic labeling for GluA3 was significantly lower compared than those\r\nfor other subunits. The labeling patterns for GluA1, GluA2 and GluA1-3 are similar and their\r\ndensities were higher in the periphery than center of synapses. In contrast, the GluA3-\r\ncontaining receptors were more centrally localized compared to the GluA1- and GluA2-\r\ncontaining receptors.\r\nThe hippocampus plays a central role in learning and memory. Contextual learning has been\r\nshown to require the delivery of AMPA receptors to CA1 synapses in the dorsal hippocampus.\r\nHowever, proximodistal heterogeneity of this plasticity and particular contribution of different\r\nAMPA receptor subunits are not fully understood. By combining inhibitory avoidance task, a\r\nhippocampus-dependent contextual fear-learning paradigm, with SDS-FRL, I have revealed an\r\nincrease in synaptic density specific to GluA1-containing AMPA receptors in the CA1 area.\r\nThe intrasynaptic distribution of GluA1 also changed from the periphery to center-preferred\r\npattern. Furthermore, this synaptic plasticity was evident selectively in stratum radiatum but\r\nnot stratum oriens, and in the CA1 subregion proximal but not distal to CA2. These findings\r\nfurther contribute to our understanding of how specific hippocampal subregions and AMPA\r\nreceptor subunits are involved in physiological learning.\r\nAlthough the immunolabeling results above shed light on subunit-specific plasticity in\r\nAMPAR distribution, no tools to visualize and study the subunit composition at the single\r\nchannel level in situ have been available. Electron microscopy with conventional immunogold\r\nlabeling approaches has limitations in the single channel analysis because of the large size of\r\nantibodies and steric hindrance hampering multiple subunit labeling of single channels. I\r\nmanaged to develop a new chemical labeling system using a short peptide tag and small\r\nsynthetic probes, which form specific covalent bond with a cysteine residue in the tag fused to\r\nproteins of interest (reactive tag system). I additionally made substantial progress into adapting\r\nthis system for AMPA receptor subunits."}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.15479/at:ista:11393","supervisor":[{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi"}],"month":"05"},{"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"},{"_id":"EM-Fac"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-024-4"]},"article_processing_charge":"No","date_created":"2023-01-25T09:17:02Z","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"degree_awarded":"PhD","OA_place":"publisher","page":"168","project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020"},{"name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","call_identifier":"H2020"},{"grant_number":"862644","call_identifier":"H2020","name":"Quantum readout techniques and technologies","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E"}],"year":"2022","title":"Controllable states of superconducting Qubit ensembles","publisher":"Institute of Science and Technology Austria","type":"dissertation","citation":{"ama":"Redchenko E. Controllable states of superconducting Qubit ensembles. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12132\">10.15479/at:ista:12132</a>","ista":"Redchenko E. 2022. Controllable states of superconducting Qubit ensembles. Institute of Science and Technology Austria.","mla":"Redchenko, Elena. <i>Controllable States of Superconducting Qubit Ensembles</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12132\">10.15479/at:ista:12132</a>.","ieee":"E. Redchenko, “Controllable states of superconducting Qubit ensembles,” Institute of Science and Technology Austria, 2022.","chicago":"Redchenko, Elena. “Controllable States of Superconducting Qubit Ensembles.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12132\">https://doi.org/10.15479/at:ista:12132</a>.","apa":"Redchenko, E. (2022). <i>Controllable states of superconducting Qubit ensembles</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12132\">https://doi.org/10.15479/at:ista:12132</a>","short":"E. Redchenko, Controllable States of Superconducting Qubit Ensembles, Institute of Science and Technology Austria, 2022."},"has_accepted_license":"1","file_date_updated":"2023-01-26T23:30:44Z","_id":"12366","author":[{"full_name":"Redchenko, Elena","first_name":"Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"}],"month":"09","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","supervisor":[{"first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M"}],"doi":"10.15479/at:ista:12132","ddc":["530"],"abstract":[{"text":"Recent substantial advances in the feld of superconducting circuits have shown its\r\npotential as a leading platform for future quantum computing. In contrast to classical\r\ncomputers based on bits that are represented by a single binary value, 0 or 1, quantum\r\nbits (or qubits) can be in a superposition of both. Thus, quantum computers can store\r\nand handle more information at the same time and a quantum advantage has already\r\nbeen demonstrated for two types of computational tasks. Rapid progress in academic\r\nand industry labs accelerates the development of superconducting processors which may\r\nsoon fnd applications in complex computations, chemical simulations, cryptography, and\r\noptimization. Now that these machines are scaled up to tackle such problems the questions\r\nof qubit interconnects and networks becomes very relevant. How to route signals on-chip\r\nbetween diferent processor components? What is the most efcient way to entangle\r\nqubits? And how to then send and process entangled signals between distant cryostats\r\nhosting superconducting processors?\r\nIn this thesis, we are looking for solutions to these problems by studying the collective\r\nbehavior of superconducting qubit ensembles. We frst demonstrate on-demand tunable\r\ndirectional scattering of microwave photons from a pair of qubits in a waveguide. Such a\r\ndevice can route microwave photons on-chip with a high diode efciency. Then we focus\r\non studying ultra-strong coupling regimes between light (microwave photons) and matter\r\n(superconducting qubits), a regime that could be promising for extremely fast multi-qubit\r\nentanglement generation. Finally, we show coherent pulse storage and periodic revivals\r\nin a fve qubit ensemble strongly coupled to a resonator. Such a reconfgurable storage\r\ndevice could be used as part of a quantum repeater that is needed for longer-distance\r\nquantum communication.\r\nThe achieved high degree of control over multi-qubit ensembles highlights not only the\r\nbeautiful physics of circuit quantum electrodynamics, it also represents the frst step\r\ntoward new quantum simulation and communication methods, and certain techniques\r\nmay also fnd applications in future superconducting quantum computing hardware.\r\n","lang":"eng"}],"publication_status":"published","status":"public","date_published":"2022-09-26T00:00:00Z","day":"26","file":[{"file_name":"Final_Thesis_ES_Redchenko.pdf","file_size":56076868,"file_id":"12367","date_created":"2023-01-25T09:41:49Z","checksum":"39eabb1e006b41335f17f3b29af09648","relation":"main_file","content_type":"application/pdf","date_updated":"2023-01-26T23:30:44Z","embargo":"2022-12-28","access_level":"open_access","creator":"cchlebak"}],"corr_author":"1","date_updated":"2026-04-07T14:22:39Z","oa_version":"Published Version","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"ec_funded":1,"oa":1},{"type":"preprint","corr_author":"1","publisher":"Cold Spring Harbor Laboratory","day":"09","author":[{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","last_name":"Velicky","orcid":"0000-0002-2340-7431","first_name":"Philipp","full_name":"Velicky, Philipp"},{"full_name":"Miguel Villalba, Eder","orcid":"0000-0001-5665-0430","last_name":"Miguel Villalba","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","first_name":"Eder"},{"full_name":"Michalska, Julia M","orcid":"0000-0003-3862-1235","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","last_name":"Michalska","first_name":"Julia M"},{"first_name":"Donglai","last_name":"Wei","full_name":"Wei, Donglai"},{"full_name":"Lin, Zudi","last_name":"Lin","first_name":"Zudi"},{"full_name":"Watson, Jake","orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E","last_name":"Watson","first_name":"Jake"},{"full_name":"Troidl, Jakob","last_name":"Troidl","first_name":"Jakob"},{"full_name":"Beyer, Johanna","first_name":"Johanna","last_name":"Beyer"},{"full_name":"Ben Simon, Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87","last_name":"Ben Simon","first_name":"Yoav"},{"last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","first_name":"Christoph M","full_name":"Sommer, Christoph M"},{"first_name":"Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","last_name":"Jahr","orcid":"0000-0003-0201-2315","full_name":"Jahr, Wiebke"},{"full_name":"Cenameri, Alban","first_name":"Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886","last_name":"Cenameri"},{"full_name":"Broichhagen, Johannes","first_name":"Johannes","last_name":"Broichhagen"},{"last_name":"Grant","first_name":"Seth G. N.","full_name":"Grant, Seth G. N."},{"full_name":"Jonas, Peter M","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","orcid":"0000-0001-5001-4804"},{"first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","full_name":"Novarino, Gaia"},{"full_name":"Pfister, Hanspeter","last_name":"Pfister","first_name":"Hanspeter"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"},{"full_name":"Danzl, Johann G","first_name":"Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"_id":"11943","oa":1,"language":[{"iso":"eng"}],"citation":{"ista":"Velicky P, Miguel Villalba E, Michalska JM, Wei D, Lin Z, Watson J, Troidl J, Beyer J, Ben Simon Y, Sommer CM, Jahr W, Cenameri A, Broichhagen J, Grant SGN, Jonas PM, Novarino G, Pfister H, Bickel B, Danzl JG. Saturated reconstruction of living brain tissue. bioRxiv, <a href=\"https://doi.org/10.1101/2022.03.16.484431\">10.1101/2022.03.16.484431</a>.","ieee":"P. Velicky <i>et al.</i>, “Saturated reconstruction of living brain tissue,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","mla":"Velicky, Philipp, et al. “Saturated Reconstruction of Living Brain Tissue.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2022.03.16.484431\">10.1101/2022.03.16.484431</a>.","ama":"Velicky P, Miguel Villalba E, Michalska JM, et al. Saturated reconstruction of living brain tissue. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2022.03.16.484431\">10.1101/2022.03.16.484431</a>","apa":"Velicky, P., Miguel Villalba, E., Michalska, J. M., Wei, D., Lin, Z., Watson, J., … Danzl, J. G. (n.d.). Saturated reconstruction of living brain tissue. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2022.03.16.484431\">https://doi.org/10.1101/2022.03.16.484431</a>","short":"P. Velicky, E. Miguel Villalba, J.M. Michalska, D. Wei, Z. Lin, J. Watson, J. Troidl, J. Beyer, Y. Ben Simon, C.M. Sommer, W. Jahr, A. Cenameri, J. Broichhagen, S.G.N. Grant, P.M. Jonas, G. Novarino, H. Pfister, B. Bickel, J.G. Danzl, BioRxiv (n.d.).","chicago":"Velicky, Philipp, Eder Miguel Villalba, Julia M Michalska, Donglai Wei, Zudi Lin, Jake Watson, Jakob Troidl, et al. “Saturated Reconstruction of Living Brain Tissue.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2022.03.16.484431\">https://doi.org/10.1101/2022.03.16.484431</a>."},"date_updated":"2026-05-02T22:30:35Z","oa_version":"Preprint","department":[{"_id":"PeJo"},{"_id":"GaNo"},{"_id":"BeBi"},{"_id":"JoDa"}],"doi":"10.1101/2022.03.16.484431","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.1101/2022.03.16.484431","open_access":"1"}],"date_created":"2022-08-23T11:07:59Z","month":"05","article_processing_charge":"No","status":"public","year":"2022","publication":"bioRxiv","title":"Saturated reconstruction of living brain tissue","date_published":"2022-05-09T00:00:00Z","related_material":{"record":[{"status":"public","id":"13267","relation":"later_version"},{"status":"public","id":"12470","relation":"dissertation_contains"}]},"publication_status":"draft","abstract":[{"lang":"eng","text":"Complex wiring between neurons underlies the information-processing network enabling all brain functions, including cognition and memory. For understanding how the network is structured, processes information, and changes over time, comprehensive visualization of the architecture of living brain tissue with its cellular and molecular components would open up major opportunities. However, electron microscopy (EM) provides nanometre-scale resolution required for full <jats:italic>in-silico</jats:italic> reconstruction<jats:sup>1–5</jats:sup>, yet is limited to fixed specimens and static representations. Light microscopy allows live observation, with super-resolution approaches<jats:sup>6–12</jats:sup> facilitating nanoscale visualization, but comprehensive 3D-reconstruction of living brain tissue has been hindered by tissue photo-burden, photobleaching, insufficient 3D-resolution, and inadequate signal-to-noise ratio (SNR). Here we demonstrate saturated reconstruction of living brain tissue. We developed an integrated imaging and analysis technology, adapting stimulated emission depletion (STED) microscopy<jats:sup>6,13</jats:sup> in extracellularly labelled tissue<jats:sup>14</jats:sup> for high SNR and near-isotropic resolution. Centrally, a two-stage deep-learning approach leveraged previously obtained information on sample structure to drastically reduce photo-burden and enable automated volumetric reconstruction down to single synapse level. Live reconstruction provides unbiased analysis of tissue architecture across time in relation to functional activity and targeted activation, and contextual understanding of molecular labelling. This adoptable technology will facilitate novel insights into the dynamic functional architecture of living brain tissue."}],"OA_place":"repository"},{"author":[{"last_name":"Michalska","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3862-1235","first_name":"Julia M","full_name":"Michalska, Julia M"},{"full_name":"Lyudchik, Julia","last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia"},{"first_name":"Philipp","last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp"},{"first_name":"Hana","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed","last_name":"Korinkova","full_name":"Korinkova, Hana"},{"full_name":"Watson, Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","last_name":"Watson","orcid":"0000-0002-8698-3823","first_name":"Jake"},{"last_name":"Cenameri","id":"9ac8f577-2357-11eb-997a-e566c5550886","first_name":"Alban","full_name":"Cenameri, Alban"},{"first_name":"Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","full_name":"Sommer, Christoph M"},{"first_name":"Alessandro","orcid":"0000-0003-2356-9403","last_name":"Venturino","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","full_name":"Venturino, Alessandro"},{"full_name":"Roessler, Karl","last_name":"Roessler","first_name":"Karl"},{"last_name":"Czech","first_name":"Thomas","full_name":"Czech, Thomas"},{"first_name":"Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra"},{"full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","orcid":"0000-0001-5001-4804","first_name":"Peter M","full_name":"Jonas, Peter M"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","orcid":"0000-0001-8559-3973","first_name":"Johann G","full_name":"Danzl, Johann G"}],"_id":"11950","oa":1,"language":[{"iso":"eng"}],"citation":{"ama":"Michalska JM, Lyudchik J, Velicky P, et al. Uncovering brain tissue architecture across scales with super-resolution light microscopy. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2022.08.17.504272\">10.1101/2022.08.17.504272</a>","mla":"Michalska, Julia M., et al. “Uncovering Brain Tissue Architecture across Scales with Super-Resolution Light Microscopy.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2022.08.17.504272\">10.1101/2022.08.17.504272</a>.","ista":"Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer CM, Venturino A, Roessler K, Czech T, Siegert S, Novarino G, Jonas PM, Danzl JG. Uncovering brain tissue architecture across scales with super-resolution light microscopy. bioRxiv, <a href=\"https://doi.org/10.1101/2022.08.17.504272\">10.1101/2022.08.17.504272</a>.","ieee":"J. M. Michalska <i>et al.</i>, “Uncovering brain tissue architecture across scales with super-resolution light microscopy,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","chicago":"Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake Watson, Alban Cenameri, Christoph M Sommer, et al. “Uncovering Brain Tissue Architecture across Scales with Super-Resolution Light Microscopy.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2022.08.17.504272\">https://doi.org/10.1101/2022.08.17.504272</a>.","apa":"Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri, A., … Danzl, J. G. (n.d.). Uncovering brain tissue architecture across scales with super-resolution light microscopy. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2022.08.17.504272\">https://doi.org/10.1101/2022.08.17.504272</a>","short":"J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri, C.M. Sommer, A. Venturino, K. Roessler, T. Czech, S. Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, BioRxiv (n.d.)."},"oa_version":"Preprint","date_updated":"2026-05-02T22:30:35Z","type":"preprint","corr_author":"1","publisher":"Cold Spring Harbor Laboratory","day":"18","year":"2022","status":"public","publication":"bioRxiv","title":"Uncovering brain tissue architecture across scales with super-resolution light microscopy","date_published":"2022-08-18T00:00:00Z","related_material":{"record":[{"id":"12470","status":"public","relation":"dissertation_contains"}]},"abstract":[{"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 nanoscopic synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS leverages fixation-compatible extracellular labeling and advanced optical readout, in particular stimulated-emission depletion and expansion microscopy, to comprehensively delineate cellular structures. It enables 3D-reconstructing single synapses and mapping synaptic connectivity by identification and tailored analysis of putative synaptic cleft regions. Applying CATS to the hippocampal mossy fiber circuitry, we demonstrate its power to reveal the system’s molecularly informed ultrastructure across spatial scales and assess local connectivity by reconstructing and quantifying the synaptic input and output structure of identified neurons.","lang":"eng"}],"publication_status":"draft","department":[{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"JoDa"}],"doi":"10.1101/2022.08.17.504272","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.1101/2022.08.17.504272","open_access":"1"}],"date_created":"2022-08-24T08:24:52Z","article_processing_charge":"No","month":"08"},{"ec_funded":1,"oa":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","date_updated":"2026-05-02T22:30:37Z","issue":"1","file":[{"checksum":"f454212a5522a7818ba4b2892315c478","file_id":"10615","date_created":"2022-01-12T13:50:04Z","file_size":5426932,"file_name":"2022_PLOSBio_Belyaeva.pdf","success":1,"access_level":"open_access","creator":"cchlebak","date_updated":"2022-01-12T13:50:04Z","relation":"main_file","content_type":"application/pdf"}],"corr_author":"1","license":"https://creativecommons.org/licenses/by/4.0/","day":"06","status":"public","date_published":"2022-01-06T00:00:00Z","ddc":["570"],"abstract":[{"text":"The infiltration of immune cells into tissues underlies the establishment of tissue-resident macrophages and responses to infections and tumors. Yet the mechanisms immune cells utilize to negotiate tissue barriers in living organisms are not well understood, and a role for cortical actin has not been examined. Here, we find that the tissue invasion of Drosophila macrophages, also known as plasmatocytes or hemocytes, utilizes enhanced cortical F-actin levels stimulated by the Drosophila member of the fos proto oncogene transcription factor family (Dfos, Kayak). RNA sequencing analysis and live imaging show that Dfos enhances F-actin levels around the entire macrophage surface by increasing mRNA levels of the membrane spanning molecular scaffold tetraspanin TM4SF, and the actin cross-linking filamin Cheerio, which are themselves required for invasion. Both the filamin and the tetraspanin enhance the cortical activity of Rho1 and the formin Diaphanous and thus the assembly of cortical actin, which is a critical function since expressing a dominant active form of Diaphanous can rescue the Dfos macrophage invasion defect. In vivo imaging shows that Dfos enhances the efficiency of the initial phases of macrophage tissue entry. Genetic evidence argues that this Dfos-induced program in macrophages counteracts the constraint produced by the tension of surrounding tissues and buffers the properties of the macrophage nucleus from affecting tissue entry. We thus identify strengthening the cortical actin cytoskeleton through Dfos as a key process allowing efficient forward movement of an immune cell into surrounding tissues. ","lang":"eng"}],"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"doi":"10.1371/journal.pbio.3001494","month":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"_id":"10614","file_date_updated":"2022-01-12T13:50:04Z","author":[{"first_name":"Vera","last_name":"Belyaeva","id":"47F080FE-F248-11E8-B48F-1D18A9856A87","full_name":"Belyaeva, Vera"},{"first_name":"Stephanie","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","last_name":"Wachner","full_name":"Wachner, Stephanie"},{"orcid":"0000-0002-1819-198X","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","last_name":"György","first_name":"Attila","full_name":"György, Attila"},{"orcid":"0000-0001-6981-6938","last_name":"Emtenani","id":"49D32318-F248-11E8-B48F-1D18A9856A87","first_name":"Shamsi","full_name":"Emtenani, Shamsi"},{"full_name":"Gridchyn, Igor","orcid":"0000-0002-1807-1929","last_name":"Gridchyn","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","first_name":"Igor"},{"full_name":"Akhmanova, Maria","first_name":"Maria","last_name":"Akhmanova","id":"3425EC26-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1522-3162"},{"last_name":"Linder","first_name":"M","full_name":"Linder, M"},{"last_name":"Roblek","id":"3047D808-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9588-1389","first_name":"Marko","full_name":"Roblek, Marko"},{"last_name":"Sibilia","first_name":"M","full_name":"Sibilia, M"},{"full_name":"Siekhaus, Daria E","first_name":"Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353"}],"citation":{"ama":"Belyaeva V, Wachner S, György A, et al. Fos regulates macrophage infiltration against surrounding tissue resistance by a cortical actin-based mechanism in Drosophila. <i>PLoS Biology</i>. 2022;20(1):e3001494. doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001494\">10.1371/journal.pbio.3001494</a>","mla":"Belyaeva, Vera, et al. “Fos Regulates Macrophage Infiltration against Surrounding Tissue Resistance by a Cortical Actin-Based Mechanism in Drosophila.” <i>PLoS Biology</i>, vol. 20, no. 1, Public Library of Science, 2022, p. e3001494, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001494\">10.1371/journal.pbio.3001494</a>.","ista":"Belyaeva V, Wachner S, György A, Emtenani S, Gridchyn I, Akhmanova M, Linder M, Roblek M, Sibilia M, Siekhaus DE. 2022. Fos regulates macrophage infiltration against surrounding tissue resistance by a cortical actin-based mechanism in Drosophila. PLoS Biology. 20(1), e3001494.","ieee":"V. Belyaeva <i>et al.</i>, “Fos regulates macrophage infiltration against surrounding tissue resistance by a cortical actin-based mechanism in Drosophila,” <i>PLoS Biology</i>, vol. 20, no. 1. Public Library of Science, p. e3001494, 2022.","chicago":"Belyaeva, Vera, Stephanie Wachner, Attila György, Shamsi Emtenani, Igor Gridchyn, Maria Akhmanova, M Linder, Marko Roblek, M Sibilia, and Daria E Siekhaus. “Fos Regulates Macrophage Infiltration against Surrounding Tissue Resistance by a Cortical Actin-Based Mechanism in Drosophila.” <i>PLoS Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pbio.3001494\">https://doi.org/10.1371/journal.pbio.3001494</a>.","short":"V. Belyaeva, S. Wachner, A. György, S. Emtenani, I. Gridchyn, M. Akhmanova, M. Linder, M. Roblek, M. Sibilia, D.E. Siekhaus, PLoS Biology 20 (2022) e3001494.","apa":"Belyaeva, V., Wachner, S., György, A., Emtenani, S., Gridchyn, I., Akhmanova, M., … Siekhaus, D. E. (2022). Fos regulates macrophage infiltration against surrounding tissue resistance by a cortical actin-based mechanism in Drosophila. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3001494\">https://doi.org/10.1371/journal.pbio.3001494</a>"},"scopus_import":"1","quality_controlled":"1","has_accepted_license":"1","isi":1,"type":"journal_article","publisher":"Public Library of Science","intvolume":"        20","publication":"PLoS Biology","project":[{"grant_number":"P29638","call_identifier":"FWF","name":"The role of Drosophila TNF alpha in immune cell invasion","_id":"253B6E48-B435-11E9-9278-68D0E5697425"},{"_id":"26199CA4-B435-11E9-9278-68D0E5697425","name":"Implications of a TGFβ/Dpp-activated subpopulation for Drosophila macrophage migration","grant_number":"24800"},{"_id":"2536F660-B435-11E9-9278-68D0E5697425","name":"Investigating the role of transporters in invasive migration through junctions","grant_number":"334077","call_identifier":"FP7"}],"year":"2022","volume":20,"external_id":{"isi":["000971223700001"],"pmid":["34990456"]},"title":"Fos regulates macrophage infiltration against surrounding tissue resistance by a cortical actin-based mechanism in Drosophila","article_type":"original","related_material":{"record":[{"relation":"earlier_version","id":"8557","status":"public"},{"status":"public","id":"11193","relation":"dissertation_contains"}],"link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.09.18.301481","relation":"earlier_version"},{"url":"https://ista.ac.at/en/news/resisting-the-pressure/","description":"News on the ISTA Website","relation":"press_release"}]},"page":"e3001494","department":[{"_id":"DaSi"},{"_id":"JoCs"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"publication_identifier":{"issn":["1544-9173"],"eissn":["1545-7885"]},"article_processing_charge":"No","date_created":"2022-01-12T10:18:17Z","acknowledgement":"We thank the following for their contributions: Plasmids were supplied by the Drosophila Genomics Resource Center (NIH 2P40OD010949-10A1); fly stocks were provided by K. Brueckner, B. Stramer, M. Uhlirova, O. Schuldiner, the Bloomington Drosophila Stock Center (NIH P40OD018537) and the Vienna Drosophila Resource Center, FlyBase for essential genomic information, and the BDGP in situ database for data. For antibodies, we thank the Developmental Studies Hybridoma Bank, which was created by the Eunice Kennedy Shriver National Institute of Child Health and Human Development of the NIH and is maintained at the University of Iowa, as well as J. Zeitlinger for her generous gift of Dfos antibody. We thank the Vienna BioCenter Core Facilities for RNA sequencing and analysis and the Life Scientific Service Units at IST Austria for technical support and assistance with microscopy and FACS analysis. We thank C. P. Heisenberg, P. Martin, M. Sixt, and Siekhaus group members for discussions and T. Hurd, A. Ratheesh, and P. Rangan for comments on the manuscript."},{"day":"20","file":[{"file_size":8820951,"file_name":"Thesis_Stephanie_Wachner_20200414_formatted.pdf","date_created":"2022-04-20T09:03:57Z","file_id":"11195","checksum":"999ab16884c4522486136ebc5ae8dbff","content_type":"application/pdf","relation":"main_file","embargo":"2023-04-20","date_updated":"2023-04-21T22:30:03Z","creator":"cchlebak","access_level":"open_access"},{"file_name":"Thesis_Stephanie_Wachner_20200414.zip","file_size":65864612,"checksum":"fd92b1e38d53bdf8b458213882d41383","date_created":"2022-04-22T12:41:00Z","file_id":"11329","content_type":"application/x-zip-compressed","relation":"source_file","embargo_to":"open_access","creator":"cchlebak","access_level":"closed","date_updated":"2023-04-21T22:30:03Z"}],"corr_author":"1","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","date_updated":"2026-04-07T14:24:19Z","language":[{"iso":"eng"}],"oa":1,"month":"04","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","supervisor":[{"first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E"}],"doi":"10.15479/at:ista:11193","ddc":["570"],"publication_status":"published","abstract":[{"lang":"eng","text":"The infiltration of immune cells into tissues underlies the establishment of tissue-resident\r\nmacrophages and responses to infections and tumors. However, the mechanisms immune\r\ncells utilize to collectively migrate through tissue barriers in vivo are not yet well understood.\r\nIn this thesis, I describe two mechanisms that Drosophila immune cells (hemocytes) use to\r\novercome the tissue barrier of the germband in the embryo. One strategy is the strengthening\r\nof the actin cortex through developmentally controlled transcriptional regulation induced by\r\nthe Drosophila proto-oncogene family member Dfos, which I show in Chapter 2. Dfos induces\r\nexpression of the tetraspanin TM4SF and the filamin Cher leading to higher levels of the\r\nactivated formin Dia at the cortex and increased cortical F-actin. This enhanced cortical\r\nstrength allows hemocytes to overcome the physical resistance of the surrounding tissue and\r\ntranslocate their nucleus to move forward. This mechanism affects the speed of migration\r\nwhen hemocytes face a confined environment in vivo.\r\nAnother aspect of the invasion process is the initial step of the leading hemocytes entering\r\nthe tissue, which potentially guides the follower cells. In Chapter 3, I describe a novel\r\nsubpopulation of hemocytes activated by BMP signaling prior to tissue invasion that leads\r\npenetration into the germband. Hemocytes that are deficient in BMP signaling activation\r\nshow impaired persistence at the tissue entry, while their migration speed remains\r\nunaffected.\r\nThis suggests that there might be different mechanisms controlling immune cell migration\r\nwithin the confined environment in vivo, one of these being the general ability to overcome\r\nthe resistance of the surrounding tissue and another affecting the order of hemocytes that\r\ncollectively invade the tissue in a stream of individual cells.\r\nTogether, my findings provide deeper insights into transcriptional changes in immune\r\ncells that enable efficient tissue invasion and pave the way for future studies investigating the\r\nearly colonization of tissues by macrophages in higher organisms. Moreover, they extend the\r\ncurrent view of Drosophila immune cell heterogeneity and point toward a potentially\r\nconserved role for canonical BMP signaling in specifying immune cells that lead the migration\r\nof tissue resident macrophages during embryogenesis."}],"status":"public","date_published":"2022-04-20T00:00:00Z","publisher":"Institute of Science and Technology Austria","type":"dissertation","citation":{"mla":"Wachner, Stephanie. <i>Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11193\">10.15479/at:ista:11193</a>.","ista":"Wachner S. 2022. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. Institute of Science and Technology Austria.","ieee":"S. Wachner, “Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells,” Institute of Science and Technology Austria, 2022.","ama":"Wachner S. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11193\">10.15479/at:ista:11193</a>","apa":"Wachner, S. (2022). <i>Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11193\">https://doi.org/10.15479/at:ista:11193</a>","short":"S. Wachner, Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells, Institute of Science and Technology Austria, 2022.","chicago":"Wachner, Stephanie. “Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11193\">https://doi.org/10.15479/at:ista:11193</a>."},"has_accepted_license":"1","_id":"11193","file_date_updated":"2023-04-21T22:30:03Z","author":[{"first_name":"Stephanie","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","last_name":"Wachner","full_name":"Wachner, Stephanie"}],"publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"LifeSc"}],"article_processing_charge":"No","date_created":"2022-04-20T08:59:07Z","department":[{"_id":"GradSch"},{"_id":"DaSi"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"10614","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"544"}]},"degree_awarded":"PhD","page":"170","OA_place":"publisher","project":[{"grant_number":"24800","_id":"26199CA4-B435-11E9-9278-68D0E5697425","name":"Implications of a TGFβ/Dpp-activated subpopulation for Drosophila macrophage migration"}],"year":"2022","title":"Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells"},{"related_material":{"record":[{"id":"6194","status":"public","relation":"part_of_dissertation"},{"id":"10077","status":"public","relation":"part_of_dissertation"}]},"OA_place":"publisher","page":"136","degree_awarded":"PhD","year":"2022","project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"}],"title":"On the encoding, transfer, and consolidation of spatial memories","publication_identifier":{"issn":["2663-337X"]},"date_created":"2022-08-19T08:52:30Z","acknowledgement":"I acknowledge the support from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385.","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"citation":{"chicago":"Nardin, Michele. “On the Encoding, Transfer, and Consolidation of Spatial Memories.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11932\">https://doi.org/10.15479/at:ista:11932</a>.","apa":"Nardin, M. (2022). <i>On the encoding, transfer, and consolidation of spatial memories</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11932\">https://doi.org/10.15479/at:ista:11932</a>","short":"M. Nardin, On the Encoding, Transfer, and Consolidation of Spatial Memories, Institute of Science and Technology Austria, 2022.","ama":"Nardin M. On the encoding, transfer, and consolidation of spatial memories. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11932\">10.15479/at:ista:11932</a>","ista":"Nardin M. 2022. On the encoding, transfer, and consolidation of spatial memories. Institute of Science and Technology Austria.","ieee":"M. Nardin, “On the encoding, transfer, and consolidation of spatial memories,” Institute of Science and Technology Austria, 2022.","mla":"Nardin, Michele. <i>On the Encoding, Transfer, and Consolidation of Spatial Memories</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11932\">10.15479/at:ista:11932</a>."},"has_accepted_license":"1","author":[{"last_name":"Nardin","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8849-6570","first_name":"Michele","full_name":"Nardin, Michele"}],"file_date_updated":"2023-06-20T22:30:04Z","_id":"11932","publisher":"Institute of Science and Technology Austria","type":"dissertation","abstract":[{"text":"The ability to form and retrieve memories is central to survival. In mammals, the hippocampus\r\nis a brain region essential to the acquisition and consolidation of new memories. It is also\r\ninvolved in keeping track of one’s position in space and aids navigation. Although this\r\nspace-memory has been a source of contradiction, evidence supports the view that the role of\r\nthe hippocampus in navigation is memory, thanks to the formation of cognitive maps. First\r\nintroduced by Tolman in 1948, cognitive maps are generally used to organize experiences in\r\nmemory; however, the detailed mechanisms by which these maps are formed and stored are not\r\nyet agreed upon. Some influential theories describe this process as involving three fundamental\r\nsteps: initial encoding by the hippocampus, interactions between the hippocampus and other\r\ncortical areas, and long-term extra-hippocampal consolidation. In this thesis, I will show how\r\nthe investigation of cognitive maps of space helped to shed light on each of these three memory\r\nprocesses.\r\nThe first study included in this thesis deals with the initial encoding of spatial memories in\r\nthe hippocampus. Much is known about encoding at the level of single cells, but less about\r\ntheir co-activity or joint contribution to the encoding of novel spatial information. I will\r\ndescribe the structure of an interaction network that allows for efficient encoding of noisy\r\nspatial information during the first exploration of a novel environment.\r\nThe second study describes the interactions between the hippocampus and the prefrontal\r\ncortex (PFC), two areas directly and indirectly connected. It is known that the PFC, in concert\r\nwith the hippocampus, is involved in various processes, including memory storage and spatial\r\nnavigation. Nonetheless, the detailed mechanisms by which PFC receives information from the\r\nhippocampus are not clear. I will show how a transient improvement in theta phase locking of\r\nPFC cells enables interactions of cell pairs across the two regions.\r\nThe third study describes the learning of behaviorally-relevant spatial locations in the hippocampus and the medial entorhinal cortex. I will show how the accumulation of firing around\r\ngoal locations, a correlate of learning, can shed light on the transition from short- to long-term\r\nspatial memories and the speed of consolidation in different brain areas.\r\nThe studies included in this thesis represent the main scientific contributions of my Ph.D. They\r\ninvolve statistical analyses and models of neural responses of cells in different brain areas of\r\nrats executing spatial tasks. I will conclude the thesis by discussing the impact of the findings\r\non principles of memory formation and retention, including the mechanisms, the speed, and\r\nthe duration of these processes.","lang":"eng"}],"publication_status":"published","ddc":["573"],"status":"public","date_published":"2022-08-19T00:00:00Z","month":"08","supervisor":[{"first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L"}],"doi":"10.15479/at:ista:11932","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","alternative_title":["ISTA Thesis"],"date_updated":"2026-04-07T14:22:58Z","language":[{"iso":"eng"}],"ec_funded":1,"oa":1,"day":"19","file":[{"creator":"mnardin","access_level":"closed","date_updated":"2023-06-20T22:30:04Z","content_type":"application/zip","relation":"source_file","embargo_to":"open_access","checksum":"2dbb70c74aaa3b64c1f463e943baf09c","date_created":"2022-08-19T16:31:34Z","file_id":"11935","file_name":"Michele Nardin, Ph.D. Thesis - ISTA (1).zip","file_size":13515457},{"access_level":"open_access","creator":"mnardin","date_updated":"2023-06-20T22:30:04Z","embargo":"2023-06-19","relation":"main_file","content_type":"application/pdf","checksum":"0ec94035ea35a47a9f589ed168e60b48","file_id":"11941","date_created":"2022-08-22T09:43:50Z","file_name":"Michele_Nardin_Phd_Thesis_PDFA.pdf","file_size":9906458}],"corr_author":"1"},{"isi":1,"type":"journal_article","publisher":"Springer Nature","intvolume":"        25","_id":"12244","file_date_updated":"2023-01-30T08:06:56Z","author":[{"first_name":"Gloria","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","last_name":"Colombo","orcid":"0000-0001-9434-8902","full_name":"Colombo, Gloria"},{"full_name":"Cubero, Ryan J","orcid":"0000-0003-0002-1867","last_name":"Cubero","id":"850B2E12-9CD4-11E9-837F-E719E6697425","first_name":"Ryan J"},{"full_name":"Kanari, Lida","first_name":"Lida","last_name":"Kanari"},{"first_name":"Alessandro","orcid":"0000-0003-2356-9403","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","last_name":"Venturino","full_name":"Venturino, Alessandro"},{"full_name":"Schulz, Rouven","first_name":"Rouven","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","last_name":"Schulz","orcid":"0000-0001-5297-733X"},{"last_name":"Scolamiero","first_name":"Martina","full_name":"Scolamiero, Martina"},{"first_name":"Jens","last_name":"Agerberg","full_name":"Agerberg, Jens"},{"last_name":"Mathys","first_name":"Hansruedi","full_name":"Mathys, Hansruedi"},{"last_name":"Tsai","first_name":"Li-Huei","full_name":"Tsai, Li-Huei"},{"full_name":"Chachólski, Wojciech","last_name":"Chachólski","first_name":"Wojciech"},{"full_name":"Hess, Kathryn","first_name":"Kathryn","last_name":"Hess"},{"first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra"}],"keyword":["General Neuroscience"],"citation":{"chicago":"Colombo, Gloria, Ryan J Cubero, Lida Kanari, Alessandro Venturino, Rouven Schulz, Martina Scolamiero, Jens Agerberg, et al. “A Tool for Mapping Microglial Morphology, MorphOMICs, Reveals Brain-Region and Sex-Dependent Phenotypes.” <i>Nature Neuroscience</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41593-022-01167-6\">https://doi.org/10.1038/s41593-022-01167-6</a>.","short":"G. Colombo, R.J. Cubero, L. Kanari, A. Venturino, R. Schulz, M. Scolamiero, J. Agerberg, H. Mathys, L.-H. Tsai, W. Chachólski, K. Hess, S. Siegert, Nature Neuroscience 25 (2022) 1379–1393.","apa":"Colombo, G., Cubero, R. J., Kanari, L., Venturino, A., Schulz, R., Scolamiero, M., … Siegert, S. (2022). A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes. <i>Nature Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41593-022-01167-6\">https://doi.org/10.1038/s41593-022-01167-6</a>","ama":"Colombo G, Cubero RJ, Kanari L, et al. A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes. <i>Nature Neuroscience</i>. 2022;25(10):1379-1393. doi:<a href=\"https://doi.org/10.1038/s41593-022-01167-6\">10.1038/s41593-022-01167-6</a>","mla":"Colombo, Gloria, et al. “A Tool for Mapping Microglial Morphology, MorphOMICs, Reveals Brain-Region and Sex-Dependent Phenotypes.” <i>Nature Neuroscience</i>, vol. 25, no. 10, Springer Nature, 2022, pp. 1379–93, doi:<a href=\"https://doi.org/10.1038/s41593-022-01167-6\">10.1038/s41593-022-01167-6</a>.","ieee":"G. Colombo <i>et al.</i>, “A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes,” <i>Nature Neuroscience</i>, vol. 25, no. 10. Springer Nature, pp. 1379–1393, 2022.","ista":"Colombo G, Cubero RJ, Kanari L, Venturino A, Schulz R, Scolamiero M, Agerberg J, Mathys H, Tsai L-H, Chachólski W, Hess K, Siegert S. 2022. A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes. Nature Neuroscience. 25(10), 1379–1393."},"scopus_import":"1","quality_controlled":"1","has_accepted_license":"1","department":[{"_id":"SaSi"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"}],"publication_identifier":{"eissn":["1546-1726"],"issn":["1097-6256"]},"article_processing_charge":"No","acknowledgement":"We thank the scientific service units at ISTA, in particular M. Schunn’s team at the preclinical facility, and especially our colony manager S. Haslinger, for excellent support. We are also grateful to the ISTA Imaging & Optics Facility, and in particular C. Sommer for helping with the data file conversions. We thank R. Erhart from the ISTA Scientific Computing Unit for improving the script performance. We thank M. Maes, B. Nagy, S. Oakeley and M. Benevento and all members of the Siegert group for constant feedback on the project and on the manuscript. This research was supported by the European Union Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Actions program (754411 to R.J.A.C.), and by the European Research Council (grant no. 715571 to S.S.). L.K. was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne, from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology. L.-H.T. was supported by NIH (grant no. R37NS051874) and by the JPB Foundation. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","date_created":"2023-01-16T09:53:07Z","publication":"Nature Neuroscience","project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Microglia action towards neuronal circuit formation and function in health and disease","_id":"25D4A630-B435-11E9-9278-68D0E5697425","grant_number":"715571","call_identifier":"H2020"}],"year":"2022","volume":25,"title":"A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes","article_type":"original","external_id":{"pmid":["36180790"],"isi":["000862214700001"]},"related_material":{"record":[{"relation":"dissertation_contains","id":"12378","status":"public"}],"link":[{"url":"https://ista.ac.at/en/news/morphomics-revealing-the-hidden-meaning-of-microglia-shape/","description":"News on ISTA website","relation":"press_release"}]},"page":"1379-1393","file":[{"date_updated":"2023-01-30T08:06:56Z","creator":"dernst","access_level":"open_access","content_type":"application/pdf","relation":"main_file","date_created":"2023-01-30T08:06:56Z","file_id":"12437","checksum":"28431146873096f52e0107b534f178c9","success":1,"file_size":23789835,"file_name":"2022_NatureNeuroscience_Colombo.pdf"}],"corr_author":"1","day":"01","oa":1,"language":[{"iso":"eng"}],"ec_funded":1,"date_updated":"2026-05-02T22:30:38Z","oa_version":"Published Version","issue":"10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1038/s41593-022-01167-6","pmid":1,"month":"10","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","date_published":"2022-10-01T00:00:00Z","ddc":["570"],"abstract":[{"lang":"eng","text":"Environmental cues influence the highly dynamic morphology of microglia. Strategies to characterize these changes usually involve user-selected morphometric features, which preclude the identification of a spectrum of context-dependent morphological phenotypes. Here we develop MorphOMICs, a topological data analysis approach, which enables semiautomatic mapping of microglial morphology into an atlas of cue-dependent phenotypes and overcomes feature-selection biases and biological variability. We extract spatially heterogeneous and sexually dimorphic morphological phenotypes for seven adult mouse brain regions. This sex-specific phenotype declines with maturation but increases over the disease trajectories in two neurodegeneration mouse models, with females showing a faster morphological shift in affected brain regions. Remarkably, microglia morphologies reflect an adaptation upon repeated exposure to ketamine anesthesia and do not recover to control morphologies. Finally, we demonstrate that both long primary processes and short terminal processes provide distinct insights to morphological phenotypes. MorphOMICs opens a new perspective to characterize microglial morphology."}],"publication_status":"published"},{"corr_author":"1","file":[{"date_created":"2023-01-25T14:31:32Z","file_id":"12379","checksum":"8cd3ddfe9b53381dcf086023d8d8893a","file_name":"Gloria_Colombo_Thesis.docx","file_size":23890382,"date_updated":"2023-04-12T22:30:03Z","creator":"cchlebak","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","relation":"source_file"},{"file_name":"Gloria_Colombo_Thesis.pdf","file_size":13802421,"file_id":"12380","date_created":"2023-01-25T14:31:36Z","checksum":"8af4319c18b516e8758e9a6cb02b103b","relation":"main_file","content_type":"application/pdf","date_updated":"2023-04-12T22:30:03Z","embargo":"2023-04-11","access_level":"open_access","creator":"cchlebak"}],"day":"11","language":[{"iso":"eng"}],"ec_funded":1,"oa":1,"date_updated":"2026-04-07T14:29:41Z","oa_version":"Published Version","alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","supervisor":[{"orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","first_name":"Sandra","full_name":"Siegert, Sandra"}],"doi":"10.15479/at:ista:12378","month":"11","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2022-11-11T00:00:00Z","status":"public","ddc":["570"],"abstract":[{"text":"Environmental cues influence the highly dynamic morphology of microglia. Strategies to \r\ncharacterize these changes usually involve user-selected morphometric features, which \r\npreclude the identification of a spectrum of context-dependent morphological phenotypes. \r\nHere, we develop MorphOMICs, a topological data analysis approach, which enables semi\u0002automatic mapping of microglial morphology into an atlas of cue-dependent phenotypes,\r\novercomes feature-selection bias and minimizes biological variability. \r\nFirst, with MorphOMICs we derive the morphological spectrum of microglia across seven \r\nbrain regions during postnatal development and in two distinct Alzheimer’s disease \r\ndegeneration mouse models. We uncover region-specific and sexually dimorphic\r\nmorphological trajectories, with females showing an earlier morphological shift than males in \r\nthe degenerating brain. Overall, we demonstrate that both long primary- and short terminal \r\nprocesses provide distinct insights to morphological phenotypes. Moreover, using machine \r\nlearning to map novel condition on the spectrum, we observe that microglia morphologies \r\nreflect a dose-dependent adaptation upon ketamine anesthesia and do not recover to control \r\nmorphologies.\r\nNext, we took advantage of MorphOMICs to build a high-resolution and layer-specific map of \r\nmicroglial morphological spectrum in the retina, covering postnatal development and rd10 \r\ndegeneration. Here, following photoreceptor death, microglia assume an early development\u0002like morphology. Finally, we map microglial morphology following optic nerve crush on the \r\nretinal spectrum and observe a layer- and sex-dependent response. \r\nOverall, MorphOMICs opens a new perspective to analyze microglial morphology across \r\nmultiple conditions, and provides a novel tool to characterize microglial morphology beyond \r\nthe traditionally dichotomized view of microglia.","lang":"eng"}],"publication_status":"published","type":"dissertation","publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-04-12T22:30:03Z","_id":"12378","author":[{"full_name":"Colombo, Gloria","first_name":"Gloria","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","last_name":"Colombo","orcid":"0000-0001-9434-8902"}],"has_accepted_license":"1","citation":{"chicago":"Colombo, Gloria. “MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12378\">https://doi.org/10.15479/at:ista:12378</a>.","apa":"Colombo, G. (2022). <i>MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12378\">https://doi.org/10.15479/at:ista:12378</a>","short":"G. Colombo, MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes, Institute of Science and Technology Austria, 2022.","ama":"Colombo G. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12378\">10.15479/at:ista:12378</a>","ieee":"G. Colombo, “MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes,” Institute of Science and Technology Austria, 2022.","ista":"Colombo G. 2022. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. Institute of Science and Technology Austria.","mla":"Colombo, Gloria. <i>MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12378\">10.15479/at:ista:12378</a>."},"department":[{"_id":"GradSch"},{"_id":"SaSi"}],"article_processing_charge":"No","date_created":"2023-01-25T14:27:43Z","publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"}],"title":"MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes","project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020"}],"year":"2022","degree_awarded":"PhD","OA_place":"publisher","page":"142","related_material":{"record":[{"relation":"part_of_dissertation","id":"12244","status":"public"}]}},{"year":"2022","title":"The genetic basis of complex traits studied via analysis of evolve and resequence experiments","related_material":{"record":[{"relation":"part_of_dissertation","id":"6713","status":"public"}]},"degree_awarded":"PhD","page":"98","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publication_identifier":{"isbn":["978-3-99078-018-3"]},"article_processing_charge":"No","date_created":"2022-05-16T16:49:18Z","file_date_updated":"2023-05-20T22:30:03Z","_id":"11388","author":[{"full_name":"Belohlavy, Stefanie","first_name":"Stefanie","orcid":"0000-0002-9849-498X","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","last_name":"Belohlavy"}],"citation":{"apa":"Belohlavy, S. (2022). <i>The genetic basis of complex traits studied via analysis of evolve and resequence experiments</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11388\">https://doi.org/10.15479/at:ista:11388</a>","short":"S. Belohlavy, The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments, Institute of Science and Technology Austria, 2022.","chicago":"Belohlavy, Stefanie. “The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11388\">https://doi.org/10.15479/at:ista:11388</a>.","ieee":"S. Belohlavy, “The genetic basis of complex traits studied via analysis of evolve and resequence experiments,” Institute of Science and Technology Austria, 2022.","ista":"Belohlavy S. 2022. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria.","mla":"Belohlavy, Stefanie. <i>The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11388\">10.15479/at:ista:11388</a>.","ama":"Belohlavy S. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11388\">10.15479/at:ista:11388</a>"},"has_accepted_license":"1","type":"dissertation","publisher":"Institute of Science and Technology Austria","status":"public","date_published":"2022-05-18T00:00:00Z","ddc":["576"],"abstract":[{"lang":"eng","text":"In evolve and resequence experiments, a population is sequenced, subjected to selection and\r\nthen sequenced again, so that genetic changes before and after selection can be observed at\r\nthe genetic level. Here, I use these studies to better understand the genetic basis of complex\r\ntraits - traits which depend on more than a few genes.\r\nIn the first chapter, I discuss the first evolve and resequence experiment, in which a population\r\nof mice, the so-called \"Longshanks\" mice, were selected for tibia length while their body mass\r\nwas kept constant. The full pedigree is known. We observed a selection response on all\r\nchromosomes and used the infinitesimal model with linkage, a model which assumes an infinite\r\nnumber of genes with infinitesimally small effect sizes, as a null model. Results implied a very\r\npolygenic basis with a few loci of major effect standing out and changing in parallel. There\r\nwas large variability between the different chromosomes in this study, probably due to LD.\r\nIn chapter two, I go on to discuss the impact of LD, on the variability in an allele-frequency\r\nbased summary statistic, giving an equation based on the initial allele frequencies, average\r\npairwise LD, and the first four moments of the haplotype block copy number distribution. I\r\ndescribe this distribution by referring back to the founder generation. I then demonstrate\r\nhow to infer selection via a maximum likelihood scheme on the example of a single locus and\r\ndiscuss how to extend this to more realistic scenarios.\r\nIn chapter three, I discuss the second evolve and resequence experiment, in which a small\r\npopulation of Drosophila melanogaster was selected for increased pupal case size over 6\r\ngenerations. The experiment was highly replicated with 27 lines selected within family and a\r\nknown pedigree. We observed a phenotypic selection response of over one standard deviation.\r\nI describe the patterns in allele frequency data, including allele frequency changes and patterns\r\nof heterozygosity, and give ideas for future work."}],"publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","supervisor":[{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"doi":"10.15479/at:ista:11388","month":"05","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"oa":1,"alternative_title":["ISTA Thesis"],"date_updated":"2026-04-07T14:29:57Z","oa_version":"Published Version","file":[{"content_type":"application/pdf","relation":"main_file","creator":"sbelohla","access_level":"open_access","embargo":"2023-05-19","date_updated":"2023-05-20T22:30:03Z","file_name":"thesis_sb_final_pdfa.pdf","file_size":8247240,"checksum":"4d75e6a619df7e8a9d6e840aee182380","date_created":"2022-05-19T13:03:13Z","file_id":"11398"},{"content_type":"application/x-zip-compressed","embargo_to":"open_access","relation":"source_file","date_updated":"2023-05-20T22:30:03Z","creator":"sbelohla","access_level":"closed","file_name":"thesis_sb_final.zip","file_size":7094,"date_created":"2022-05-19T13:07:47Z","file_id":"11399","checksum":"7a5d8b6dd0ca00784f860075b0a7d8f0"}],"corr_author":"1","day":"18"},{"department":[{"_id":"MiSi"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"BjHo"}],"acknowledgement":"We thank N. Darwish-Miranda, F. Leite, F.P. Assen, and A. Eichner for advice and help with experiments. We thank J. Renkawitz, E. Kiermaier, A. Juanes Garcia, and M. Avellaneda for critical reading of the manuscript. We thank M. Driscoll for advice on fluorescent labeling of collagen gels. This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Molecular Biology Services/Lab Support Facility (LSF)/Bioimaging Facility/Electron Microscopy Facility. This work was funded by grants from the European Research Council ( CoG 724373 ) and the Austrian Science Foundation (FWF) to M.S. F.G. received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 747687.","date_created":"2022-01-30T23:01:33Z","article_processing_charge":"No","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"title":"WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues","article_type":"original","external_id":{"isi":["000768933800005"],"pmid":["34919802"]},"volume":57,"year":"2022","project":[{"call_identifier":"H2020","grant_number":"747687","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","_id":"260AA4E2-B435-11E9-9278-68D0E5697425"},{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular Navigation Along Spatial Gradients","call_identifier":"H2020","grant_number":"724373"}],"publication":"Developmental Cell","page":"47-62.e9","related_material":{"record":[{"id":"20149","status":"public","relation":"dissertation_contains"},{"status":"public","id":"12726","relation":"dissertation_contains"},{"status":"public","id":"14530","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"12401","status":"public"}]},"type":"journal_article","isi":1,"intvolume":"        57","publisher":"Cell Press","author":[{"last_name":"Gaertner","first_name":"Florian","full_name":"Gaertner, Florian"},{"full_name":"Dos Reis Rodrigues, Patricia","first_name":"Patricia","orcid":"0000-0003-1681-508X","id":"26E95904-5160-11E9-9C0B-C5B0DC97E90F","last_name":"Dos Reis Rodrigues"},{"full_name":"De Vries, Ingrid","last_name":"De Vries","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid"},{"first_name":"Miroslav","orcid":"0000-0002-6625-3348","last_name":"Hons","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","full_name":"Hons, Miroslav"},{"last_name":"Aguilera","first_name":"Juan","full_name":"Aguilera, Juan"},{"full_name":"Riedl, Michael","first_name":"Michael","orcid":"0000-0003-4844-6311","last_name":"Riedl","id":"3BE60946-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander F","orcid":"0000-0002-1073-744X","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","full_name":"Leithner, Alexander F"},{"full_name":"Tasciyan, Saren","orcid":"0000-0003-1671-393X","last_name":"Tasciyan","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","first_name":"Saren"},{"orcid":"0000-0002-2187-6656","last_name":"Kopf","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","first_name":"Aglaja","full_name":"Kopf, Aglaja"},{"full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"orcid":"0000-0002-9438-4783","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","last_name":"Zheden","first_name":"Vanessa","full_name":"Zheden, Vanessa"},{"last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","first_name":"Walter","full_name":"Kaufmann, Walter"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert"},{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K"}],"_id":"10703","scopus_import":"1","quality_controlled":"1","citation":{"ama":"Gaertner F, Dos Reis Rodrigues P, de Vries I, et al. WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. <i>Developmental Cell</i>. 2022;57(1):47-62.e9. doi:<a href=\"https://doi.org/10.1016/j.devcel.2021.11.024\">10.1016/j.devcel.2021.11.024</a>","mla":"Gaertner, Florian, et al. “WASp Triggers Mechanosensitive Actin Patches to Facilitate Immune Cell Migration in Dense Tissues.” <i>Developmental Cell</i>, vol. 57, no. 1, Cell Press, 2022, p. 47–62.e9, doi:<a href=\"https://doi.org/10.1016/j.devcel.2021.11.024\">10.1016/j.devcel.2021.11.024</a>.","ista":"Gaertner F, Dos Reis Rodrigues P, de Vries I, Hons M, Aguilera J, Riedl M, Leithner AF, Tasciyan S, Kopf A, Merrin J, Zheden V, Kaufmann W, Hauschild R, Sixt MK. 2022. WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. Developmental Cell. 57(1), 47–62.e9.","ieee":"F. Gaertner <i>et al.</i>, “WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues,” <i>Developmental Cell</i>, vol. 57, no. 1. Cell Press, p. 47–62.e9, 2022.","chicago":"Gaertner, Florian, Patricia Dos Reis Rodrigues, Ingrid de Vries, Miroslav Hons, Juan Aguilera, Michael Riedl, Alexander F Leithner, et al. “WASp Triggers Mechanosensitive Actin Patches to Facilitate Immune Cell Migration in Dense Tissues.” <i>Developmental Cell</i>. Cell Press, 2022. <a href=\"https://doi.org/10.1016/j.devcel.2021.11.024\">https://doi.org/10.1016/j.devcel.2021.11.024</a>.","short":"F. Gaertner, P. Dos Reis Rodrigues, I. de Vries, M. Hons, J. Aguilera, M. Riedl, A.F. Leithner, S. Tasciyan, A. Kopf, J. Merrin, V. Zheden, W. Kaufmann, R. Hauschild, M.K. Sixt, Developmental Cell 57 (2022) 47–62.e9.","apa":"Gaertner, F., Dos Reis Rodrigues, P., de Vries, I., Hons, M., Aguilera, J., Riedl, M., … Sixt, M. K. (2022). WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2021.11.024\">https://doi.org/10.1016/j.devcel.2021.11.024</a>"},"doi":"10.1016/j.devcel.2021.11.024","pmid":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"month":"01","main_file_link":[{"url":"https://www.sciencedirect.com/science/article/pii/S1534580721009497","open_access":"1"}],"date_published":"2022-01-10T00:00:00Z","status":"public","abstract":[{"text":"When crawling through the body, leukocytes often traverse tissues that are densely packed with extracellular matrix and other cells, and this raises the question: How do leukocytes overcome compressive mechanical loads? Here, we show that the actin cortex of leukocytes is mechanoresponsive and that this responsiveness requires neither force sensing via the nucleus nor adhesive interactions with a substrate. Upon global compression of the cell body as well as local indentation of the plasma membrane, Wiskott-Aldrich syndrome protein (WASp) assembles into dot-like structures, providing activation platforms for Arp2/3 nucleated actin patches. These patches locally push against the external load, which can be obstructing collagen fibers or other cells, and thereby create space to facilitate forward locomotion. We show in vitro and in vivo that this WASp function is rate limiting for ameboid leukocyte migration in dense but not in loose environments and is required for trafficking through diverse tissues such as skin and lymph nodes.","lang":"eng"}],"publication_status":"published","ddc":["570"],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","corr_author":"1","day":"10","ec_funded":1,"oa":1,"language":[{"iso":"eng"}],"issue":"1","oa_version":"Published Version","date_updated":"2026-05-02T22:30:59Z"},{"type":"dissertation","publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-12-21T23:30:03Z","_id":"12401","author":[{"full_name":"Tasciyan, Saren","last_name":"Tasciyan","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X","first_name":"Saren"}],"has_accepted_license":"1","citation":{"ama":"Tasciyan S. Role of microenvironment heterogeneity in cancer cell invasion. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12401\">10.15479/at:ista:12401</a>","ista":"Tasciyan S. 2022. Role of microenvironment heterogeneity in cancer cell invasion. Institute of Science and Technology Austria.","ieee":"S. Tasciyan, “Role of microenvironment heterogeneity in cancer cell invasion,” Institute of Science and Technology Austria, 2022.","mla":"Tasciyan, Saren. <i>Role of Microenvironment Heterogeneity in Cancer Cell Invasion</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12401\">10.15479/at:ista:12401</a>.","chicago":"Tasciyan, Saren. “Role of Microenvironment Heterogeneity in Cancer Cell Invasion.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12401\">https://doi.org/10.15479/at:ista:12401</a>.","apa":"Tasciyan, S. (2022). <i>Role of microenvironment heterogeneity in cancer cell invasion</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12401\">https://doi.org/10.15479/at:ista:12401</a>","short":"S. Tasciyan, Role of Microenvironment Heterogeneity in Cancer Cell Invasion, Institute of Science and Technology Austria, 2022."},"department":[{"_id":"GradSch"},{"_id":"MiSi"}],"article_processing_charge":"No","date_created":"2023-01-26T11:55:16Z","publication_identifier":{"issn":["2663-337X"]},"title":"Role of microenvironment heterogeneity in cancer cell invasion","year":"2022","degree_awarded":"PhD","page":"105","OA_place":"publisher","related_material":{"record":[{"relation":"part_of_dissertation","id":"7885","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"10703"},{"relation":"part_of_dissertation","id":"679","status":"public"},{"status":"public","id":"9429","relation":"part_of_dissertation"}]},"corr_author":"1","file":[{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"cchlebak","date_updated":"2023-12-21T23:30:03Z","embargo":"2023-12-20","file_name":"PhD-Thesis_Saren Tasciyan_formatted_aftercrash_fixed_600dpi_95pc_final_PDFA3b.pdf","file_size":42059787,"checksum":"cc4a2b4a7e3c4ee8ef7f2dbf909b12bd","file_id":"12402","date_created":"2023-01-26T11:58:14Z"},{"embargo_to":"open_access","relation":"source_file","content_type":"application/x-zip-compressed","access_level":"closed","creator":"cchlebak","date_updated":"2023-12-21T23:30:03Z","file_name":"Source Files - Saren Tasciyan - PhD Thesis.zip","file_size":261256696,"checksum":"f1b4ca98b8ab0cb043b1830971e9bd9c","file_id":"12403","date_created":"2023-01-26T12:00:10Z"}],"day":"22","language":[{"iso":"eng"}],"oa":1,"date_updated":"2026-04-14T09:07:14Z","oa_version":"Published Version","alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.15479/at:ista:12401","supervisor":[{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K"}],"month":"12","date_published":"2022-12-22T00:00:00Z","status":"public","ddc":["610"],"publication_status":"published","abstract":[{"text":"Detachment of the cancer cells from the bulk of the tumor is the first step of metastasis, which\r\nis the primary cause of cancer related deaths. It is unclear, which factors contribute to this step.\r\nRecent studies indicate a crucial role of the tumor microenvironment in malignant\r\ntransformation and metastasis. Studying cancer cell invasion and detachments quantitatively in\r\nthe context of its physiological microenvironment is technically challenging. Especially, precise\r\ncontrol of microenvironmental properties in vivo is currently not possible. Here, I studied the\r\nrole of microenvironment geometry in the invasion and detachment of cancer cells from the\r\nbulk with a simplistic and reductionist approach. In this approach, I engineered microfluidic\r\ndevices to mimic a pseudo 3D extracellular matrix environment, where I was able to\r\nquantitatively tune the geometrical configuration of the microenvironment and follow tumor\r\ncells with fluorescence live imaging. To aid quantitative analysis I developed a widely applicable\r\nsoftware application to automatically analyze and visualize particle tracking data.\r\nQuantitative analysis of tumor cell invasion in isotropic and anisotropic microenvironments\r\nshowed that heterogeneity in the microenvironment promotes faster invasion and more\r\nfrequent detachment of cells. These observations correlated with overall higher speed of cells at\r\nthe edge of the bulk of the cells. In heterogeneous microenvironments cells preferentially\r\npassed through larger pores, thus invading areas of least resistance and generating finger-like\r\ninvasive structures. The detachments occurred mostly at the tips of these structures.\r\nTo investigate the potential mechanism, we established a two dimensional model to simulate\r\nactive Brownian particles representing the cell nuclei dynamics. These simulations backed our in\r\nvitro observations without the need of precise fitting the simulation parameters. Our model\r\nsuggests the importance of the pore heterogeneity in the direction perpendicular to the\r\norientation of bias field (lateral heterogeneity), which causes the interface roughening.","lang":"eng"}]},{"file":[{"checksum":"f79ff5383e882ea3f95f3da47a78029d","date_created":"2023-01-30T08:59:58Z","file_id":"12440","success":1,"file_size":1347136,"file_name":"2022_Genetics_Elkrewi.pdf","creator":"dernst","access_level":"open_access","date_updated":"2023-01-30T08:59:58Z","content_type":"application/pdf","relation":"main_file"}],"corr_author":"1","day":"01","oa":1,"ec_funded":1,"language":[{"iso":"eng"}],"date_updated":"2026-05-02T22:31:09Z","oa_version":"Published Version","issue":"2","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"doi":"10.1093/genetics/iyac123","month":"10","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","date_published":"2022-10-01T00:00:00Z","ddc":["570"],"publication_status":"published","abstract":[{"lang":"eng","text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species Artemia sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species Artemia sp. Kazakhstan and several asexual lineages of Artemia parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality."}],"isi":1,"type":"journal_article","publisher":"Oxford University Press","intvolume":"       222","file_date_updated":"2023-01-30T08:59:58Z","_id":"12248","author":[{"first_name":"Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N"},{"last_name":"Khauratovich","id":"5eba06f4-97d8-11ed-9f8f-d826ebdd9434","first_name":"Uladzislava","full_name":"Khauratovich, Uladzislava"},{"orcid":"0000-0002-9752-7380","last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","full_name":"Toups, Melissa A"},{"first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425","last_name":"Bett","full_name":"Bett, Vincent K"},{"full_name":"Mrnjavac, Andrea","first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","last_name":"Mrnjavac"},{"full_name":"Macon, Ariana","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon"},{"orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle","full_name":"Fraisse, Christelle"},{"full_name":"Sax, Luca","first_name":"Luca","last_name":"Sax","id":"701c5602-97d8-11ed-96b5-b52773c70189"},{"first_name":"Ann K","last_name":"Huylmans","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961","full_name":"Huylmans, Ann K"},{"full_name":"Hontoria, Francisco","first_name":"Francisco","last_name":"Hontoria"},{"full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"keyword":["Genetics"],"citation":{"apa":"Elkrewi, M. N., Khauratovich, U., Toups, M. A., Bett, V. K., Mrnjavac, A., Macon, A., … Vicoso, B. (2022). ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyac123\">https://doi.org/10.1093/genetics/iyac123</a>","short":"M.N. Elkrewi, U. Khauratovich, M.A. Toups, V.K. Bett, A. Mrnjavac, A. Macon, C. Fraisse, L. Sax, A.K. Huylmans, F. Hontoria, B. Vicoso, Genetics 222 (2022).","chicago":"Elkrewi, Marwan N, Uladzislava Khauratovich, Melissa A Toups, Vincent K Bett, Andrea Mrnjavac, Ariana Macon, Christelle Fraisse, et al. “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” <i>Genetics</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/genetics/iyac123\">https://doi.org/10.1093/genetics/iyac123</a>.","ieee":"M. N. Elkrewi <i>et al.</i>, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp,” <i>Genetics</i>, vol. 222, no. 2. Oxford University Press, 2022.","mla":"Elkrewi, Marwan N., et al. “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” <i>Genetics</i>, vol. 222, no. 2, iyac123, Oxford University Press, 2022, doi:<a href=\"https://doi.org/10.1093/genetics/iyac123\">10.1093/genetics/iyac123</a>.","ista":"Elkrewi MN, Khauratovich U, Toups MA, Bett VK, Mrnjavac A, Macon A, Fraisse C, Sax L, Huylmans AK, Hontoria F, Vicoso B. 2022. ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. Genetics. 222(2), iyac123.","ama":"Elkrewi MN, Khauratovich U, Toups MA, et al. ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. <i>Genetics</i>. 2022;222(2). doi:<a href=\"https://doi.org/10.1093/genetics/iyac123\">10.1093/genetics/iyac123</a>"},"article_number":"iyac123","quality_controlled":"1","scopus_import":"1","has_accepted_license":"1","department":[{"_id":"BeVi"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"publication_identifier":{"issn":["1943-2631"]},"article_processing_charge":"No","date_created":"2023-01-16T09:56:10Z","acknowledgement":"This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 715257) and by the Austrian Science Foundation (FWF SFB F88-10).\r\nWe thank the Vicoso group for comments on the manuscript and the ISTA Scientific computing team and the Vienna Biocenter Sequencing facility for technical support.","publication":"Genetics","project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257","call_identifier":"H2020"},{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810"}],"year":"2022","volume":222,"title":"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp","article_type":"original","external_id":{"isi":["000850270300001"],"pmid":["35977389"]},"related_material":{"record":[{"id":"11653","status":"public","relation":"research_data"},{"status":"public","id":"19386","relation":"dissertation_contains"}]}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"doi":"10.1098/rspb.2021.1985","month":"02","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","date_published":"2022-02-09T00:00:00Z","ddc":["570"],"publication_status":"published","abstract":[{"text":"The t-haplotype of mice is a classical model for autosomal transmission distortion. A largely non-recombining variant of the proximal region of chromosome 17, it is transmitted to more than 90% of the progeny of heterozygous males through the disabling of sperm carrying a standard chromosome. While extensive genetic and functional work has shed light on individual genes involved in drive, much less is known about the evolution and function of the rest of its hundreds of genes. Here, we characterize the sequence and expression of dozens of t-specific transcripts and of their chromosome 17 homologues. Many genes showed reduced expression of the t-allele, but an equal number of genes showed increased expression of their t-copy, consistent with increased activity or a newly evolved function. Genes on the t-haplotype had a significantly higher non-synonymous substitution rate than their homologues on the standard chromosome, with several genes harbouring dN/dS ratios above 1. Finally, the t-haplotype has acquired at least two genes from other chromosomes, which show high and tissue-specific expression. These results provide a first overview of the gene content of this selfish element, and support a more dynamic evolutionary scenario than expected of a large genomic region with almost no recombination.","lang":"eng"}],"file":[{"success":1,"file_size":2366976,"file_name":"2022_ProceedingsRoyalSocB_Kelemen.pdf","checksum":"27042a3706ae52a919fed1ac114bf7bb","date_created":"2022-02-21T08:17:38Z","file_id":"10779","content_type":"application/pdf","relation":"main_file","creator":"dernst","access_level":"open_access","date_updated":"2022-02-21T08:17:38Z"}],"corr_author":"1","day":"09","ec_funded":1,"language":[{"iso":"eng"}],"oa":1,"date_updated":"2026-05-02T22:31:09Z","oa_version":"Published Version","issue":"1968","department":[{"_id":"BeVi"}],"publication_identifier":{"eissn":["1471-2954"]},"article_processing_charge":"No","date_created":"2022-02-20T23:01:31Z","acknowledgement":"This project has received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 715257) and from the Swiss National Science Foundation (grant no. 310030_189145).\r\nWe thank Jari Garbely of the Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland, for conducting the PCR verification. Barbara\r\nKonig, Gabi Stichel and A.K.L. collected mouse tissue samples, from the field study led by R.K.K. ","publication":"Proceedings of the Royal Society B: Biological Sciences","project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715257"}],"year":"2022","volume":289,"article_type":"original","external_id":{"isi":["000752812800012"],"pmid":["35135349"]},"title":"Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome","related_material":{"record":[{"relation":"dissertation_contains","id":"17119","status":"public"},{"id":"19386","status":"public","relation":"dissertation_contains"}]},"page":"20211985","isi":1,"type":"journal_article","publisher":"The Royal Society","intvolume":"       289","_id":"10767","file_date_updated":"2022-02-21T08:17:38Z","author":[{"first_name":"Réka K","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","last_name":"Kelemen","orcid":"0000-0002-8489-9281","full_name":"Kelemen, Réka K"},{"first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N"},{"first_name":"Anna K.","last_name":"Lindholm","full_name":"Lindholm, Anna K."},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz"}],"citation":{"mla":"Kelemen, Réka K., et al. “Novel Patterns of Expression and Recruitment of New Genes on the T-Haplotype, a Mouse Selfish Chromosome.” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 289, no. 1968, The Royal Society, 2022, p. 20211985, doi:<a href=\"https://doi.org/10.1098/rspb.2021.1985\">10.1098/rspb.2021.1985</a>.","ista":"Kelemen RK, Elkrewi MN, Lindholm AK, Vicoso B. 2022. Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. Proceedings of the Royal Society B: Biological Sciences. 289(1968), 20211985.","ieee":"R. K. Kelemen, M. N. Elkrewi, A. K. Lindholm, and B. Vicoso, “Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome,” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 289, no. 1968. The Royal Society, p. 20211985, 2022.","ama":"Kelemen RK, Elkrewi MN, Lindholm AK, Vicoso B. Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. <i>Proceedings of the Royal Society B: Biological Sciences</i>. 2022;289(1968):20211985. doi:<a href=\"https://doi.org/10.1098/rspb.2021.1985\">10.1098/rspb.2021.1985</a>","short":"R.K. Kelemen, M.N. Elkrewi, A.K. Lindholm, B. Vicoso, Proceedings of the Royal Society B: Biological Sciences 289 (2022) 20211985.","apa":"Kelemen, R. K., Elkrewi, M. N., Lindholm, A. K., &#38; Vicoso, B. (2022). Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2021.1985\">https://doi.org/10.1098/rspb.2021.1985</a>","chicago":"Kelemen, Réka K, Marwan N Elkrewi, Anna K. Lindholm, and Beatriz Vicoso. “Novel Patterns of Expression and Recruitment of New Genes on the T-Haplotype, a Mouse Selfish Chromosome.” <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society, 2022. <a href=\"https://doi.org/10.1098/rspb.2021.1985\">https://doi.org/10.1098/rspb.2021.1985</a>."},"quality_controlled":"1","scopus_import":"1","has_accepted_license":"1"},{"year":"2022","publication":"Nature Communications","project":[{"_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020","grant_number":"758053"},{"grant_number":"899354","call_identifier":"H2020","name":"Quantum Local Area Networks with Superconducting Qubits","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A"},{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"},{"_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","name":"Quantum readout techniques and technologies","call_identifier":"H2020","grant_number":"862644"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","grant_number":"F07105"}],"article_type":"original","title":"Quantum-enabled operation of a microwave-optical interface","external_id":{"pmid":["35277488"],"isi":["000767892300013"],"arxiv":["2107.08303"]},"volume":13,"related_material":{"record":[{"status":"public","id":"13175","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"12900"},{"status":"public","id":"18871","relation":"dissertation_contains"}]},"department":[{"_id":"JoFi"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"publication_identifier":{"eissn":["2041-1723"]},"date_created":"2022-03-27T22:01:45Z","acknowledgement":"The authors thank S. Wald and F. Diorico for their help with optical filtering, O. Hosten\r\nand M. Aspelmeyer for equipment, H.G.L. Schwefel for materials and discussions, L.\r\nDrmic and P. Zielinski for software support, and the MIBA workshop at IST Austria for\r\nmachining the microwave cavity. This work was supported by the European Research\r\nCouncil under grant agreement no. 758053 (ERC StG QUNNECT) and the European\r\nUnion’s Horizon 2020 research and innovation program under grant agreement no.\r\n899354 (FETopen SuperQuLAN). W.H. is the recipient of an ISTplus postdoctoral fellowship\r\nwith funding from the European Union’s Horizon 2020 research and innovation\r\nprogram under the Marie Skłodowska-Curie grant agreement no. 754411. G.A. is the\r\nrecipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F.\r\nacknowledges support from the Austrian Science Fund (FWF) through BeyondC (F7105)\r\nand the European Union’s Horizon 2020 research and innovation programs under grant\r\nagreement no. 862644 (FETopen QUARTET).","article_processing_charge":"No","author":[{"first_name":"Rishabh","last_name":"Sahu","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6264-2162","full_name":"Sahu, Rishabh"},{"id":"29705398-F248-11E8-B48F-1D18A9856A87","last_name":"Hease","orcid":"0000-0001-9868-2166","first_name":"William J","full_name":"Hease, William J"},{"full_name":"Rueda Sanchez, Alfredo R","first_name":"Alfredo R","orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez"},{"first_name":"Georg M","orcid":"0000-0003-1397-7876","last_name":"Arnold","id":"3770C838-F248-11E8-B48F-1D18A9856A87","full_name":"Arnold, Georg M"},{"first_name":"Liu","orcid":"0000-0003-4345-4267","last_name":"Qiu","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","full_name":"Qiu, Liu"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","orcid":"0000-0001-8112-028X","first_name":"Johannes M","full_name":"Fink, Johannes M"}],"_id":"10924","file_date_updated":"2022-03-28T08:02:12Z","citation":{"ama":"Sahu R, Hease WJ, Rueda Sanchez AR, Arnold GM, Qiu L, Fink JM. Quantum-enabled operation of a microwave-optical interface. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-28924-2\">10.1038/s41467-022-28924-2</a>","mla":"Sahu, Rishabh, et al. “Quantum-Enabled Operation of a Microwave-Optical Interface.” <i>Nature Communications</i>, vol. 13, 1276, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-28924-2\">10.1038/s41467-022-28924-2</a>.","ieee":"R. Sahu, W. J. Hease, A. R. Rueda Sanchez, G. M. Arnold, L. Qiu, and J. M. Fink, “Quantum-enabled operation of a microwave-optical interface,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","ista":"Sahu R, Hease WJ, Rueda Sanchez AR, Arnold GM, Qiu L, Fink JM. 2022. Quantum-enabled operation of a microwave-optical interface. Nature Communications. 13, 1276.","chicago":"Sahu, Rishabh, William J Hease, Alfredo R Rueda Sanchez, Georg M Arnold, Liu Qiu, and Johannes M Fink. “Quantum-Enabled Operation of a Microwave-Optical Interface.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-28924-2\">https://doi.org/10.1038/s41467-022-28924-2</a>.","apa":"Sahu, R., Hease, W. J., Rueda Sanchez, A. R., Arnold, G. M., Qiu, L., &#38; Fink, J. M. (2022). Quantum-enabled operation of a microwave-optical interface. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-28924-2\">https://doi.org/10.1038/s41467-022-28924-2</a>","short":"R. Sahu, W.J. Hease, A.R. Rueda Sanchez, G.M. Arnold, L. Qiu, J.M. Fink, Nature Communications 13 (2022)."},"has_accepted_license":"1","scopus_import":"1","article_number":"1276","quality_controlled":"1","type":"journal_article","isi":1,"publisher":"Springer Nature","intvolume":"        13","status":"public","date_published":"2022-03-11T00:00:00Z","publication_status":"published","abstract":[{"lang":"eng","text":"Solid-state microwave systems offer strong interactions for fast quantum logic and sensing but photons at telecom wavelength are the ideal choice for high-density low-loss quantum interconnects. A general-purpose interface that can make use of single photon effects requires < 1 input noise quanta, which has remained elusive due to either low efficiency or pump induced heating. Here we demonstrate coherent electro-optic modulation on nanosecond-timescales with only 0.16+0.02−0.01 microwave input noise photons with a total bidirectional transduction efficiency of 8.7% (or up to 15% with 0.41+0.02−0.02), as required for near-term heralded quantum network protocols. The use of short and high-power optical pump pulses also enables near-unity cooperativity of the electro-optic interaction leading to an internal pure conversion efficiency of up to 99.5%. Together with the low mode occupancy this provides evidence for electro-optic laser cooling and vacuum amplification as predicted a decade ago."}],"ddc":["530"],"pmid":1,"doi":"10.1038/s41467-022-28924-2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"03","language":[{"iso":"eng"}],"oa":1,"ec_funded":1,"arxiv":1,"date_updated":"2026-05-02T22:31:10Z","oa_version":"Published Version","file":[{"checksum":"7c5176db7b8e2ed18a4e0c5aca70a72c","date_created":"2022-03-28T08:02:12Z","file_id":"10929","success":1,"file_size":1167492,"file_name":"2022_NatureCommunications_Sahu.pdf","creator":"dernst","access_level":"open_access","date_updated":"2022-03-28T08:02:12Z","content_type":"application/pdf","relation":"main_file"}],"corr_author":"1","day":"11"},{"day":"01","corr_author":"1","oa_version":"Published Version","date_updated":"2025-04-14T07:43:57Z","arxiv":1,"oa":1,"language":[{"iso":"eng"}],"ec_funded":1,"month":"12","main_file_link":[{"url":"https://proceedings.neurips.cc/paper/2021/file/1680e9fa7b4dd5d62ece800239bb53bd-Paper.pdf","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We study efficient distributed algorithms for the fundamental problem of principal component analysis and leading eigenvector computation on the sphere, when the data are randomly distributed among a set of computational nodes. We propose a new quantized variant of Riemannian gradient descent to solve this problem, and prove that the algorithm converges with high probability under a set of necessary spherical-convexity properties. We give bounds on the number of bits transmitted by the algorithm under common initialization schemes, and investigate the dependency on the problem dimension in each case."}],"publication_status":"published","date_published":"2021-12-01T00:00:00Z","status":"public","intvolume":"         4","publisher":"Neural Information Processing Systems Foundation","type":"conference","quality_controlled":"1","scopus_import":"1","citation":{"ista":"Alimisis F, Davies P, Vandereycken B, Alistarh D-A. 2021. Distributed principal component analysis with limited communication. Advances in Neural Information Processing Systems - 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 4, 2823–2834.","ieee":"F. Alimisis, P. Davies, B. Vandereycken, and D.-A. Alistarh, “Distributed principal component analysis with limited communication,” in <i>Advances in Neural Information Processing Systems - 35th Conference on Neural Information Processing Systems</i>, Virtual, Online, 2021, vol. 4, pp. 2823–2834.","mla":"Alimisis, Foivos, et al. “Distributed Principal Component Analysis with Limited Communication.” <i>Advances in Neural Information Processing Systems - 35th Conference on Neural Information Processing Systems</i>, vol. 4, Neural Information Processing Systems Foundation, 2021, pp. 2823–34.","ama":"Alimisis F, Davies P, Vandereycken B, Alistarh D-A. Distributed principal component analysis with limited communication. In: <i>Advances in Neural Information Processing Systems - 35th Conference on Neural Information Processing Systems</i>. Vol 4. Neural Information Processing Systems Foundation; 2021:2823-2834.","short":"F. Alimisis, P. Davies, B. Vandereycken, D.-A. Alistarh, in:, Advances in Neural Information Processing Systems - 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021, pp. 2823–2834.","apa":"Alimisis, F., Davies, P., Vandereycken, B., &#38; Alistarh, D.-A. (2021). Distributed principal component analysis with limited communication. In <i>Advances in Neural Information Processing Systems - 35th Conference on Neural Information Processing Systems</i> (Vol. 4, pp. 2823–2834). Virtual, Online: Neural Information Processing Systems Foundation.","chicago":"Alimisis, Foivos, Peter Davies, Bart Vandereycken, and Dan-Adrian Alistarh. “Distributed Principal Component Analysis with Limited Communication.” In <i>Advances in Neural Information Processing Systems - 35th Conference on Neural Information Processing Systems</i>, 4:2823–34. Neural Information Processing Systems Foundation, 2021."},"author":[{"full_name":"Alimisis, Foivos","last_name":"Alimisis","first_name":"Foivos"},{"full_name":"Davies, Peter","last_name":"Davies","id":"11396234-BB50-11E9-B24C-90FCE5697425","orcid":"0000-0002-5646-9524","first_name":"Peter"},{"last_name":"Vandereycken","first_name":"Bart","full_name":"Vandereycken, Bart"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X"}],"_id":"11452","acknowledgement":"We would like to thank the anonymous reviewers for helpful comments and suggestions. We also thank Aurelien Lucchi and Antonio Orvieto for fruitful discussions at an early stage of this work. FA is partially supported by the SNSF under research project No. 192363 and conducted part of this work while at IST Austria under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 805223 ScaleML). PD partly conducted this work while at IST Austria and was supported by the European Union’s Horizon 2020 programme under the Marie Skłodowska-Curie grant agreement No. 754411.","date_created":"2022-06-19T22:01:58Z","article_processing_charge":"No","publication_identifier":{"isbn":["9781713845393"],"issn":["1049-5258"]},"conference":{"location":"Virtual, Online","end_date":"2021-12-14","start_date":"2021-12-06","name":"NeurIPS: Neural Information Processing Systems"},"department":[{"_id":"DaAl"}],"page":"2823-2834","title":"Distributed principal component analysis with limited communication","external_id":{"arxiv":["2110.14391"]},"volume":4,"year":"2021","project":[{"call_identifier":"H2020","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"}],"publication":"Advances in Neural Information Processing Systems - 35th Conference on Neural Information Processing Systems"},{"date_created":"2022-06-19T22:01:59Z","acknowledgement":"We would like to thank Professor Dr. Henning Sprekeler for his valuable suggestions and Dr. Andrew Saxe, Milan Klöwer and Anna Wallis for their constructive feedback on the manuscript. Lukas Braun was supported by the Network of European Neuroscience Schools through their NENS Exchange Grant program, by the European Union through their European Community Action Scheme for the Mobility of University Students, the Woodward Scholarship awarded by Wadham College, Oxford and the Medical Research Council [MR/N013468/1]. Tim P. Vogels was supported by a Wellcome Trust Senior Research Fellowship [214316/Z/18/Z].","article_processing_charge":"No","publication_identifier":{"isbn":["9781713845393"],"issn":["1049-5258"]},"conference":{"end_date":"2021-12-14","start_date":"2021-12-06","location":"Virtual, Online","name":"NeurIPS: Neural Information Processing Systems"},"department":[{"_id":"TiVo"}],"page":"16437-16450","title":"Online learning of neural computations from sparse temporal feedback","volume":20,"year":"2021","publication":"Advances in Neural Information Processing Systems - 35th Conference on Neural Information Processing Systems","project":[{"_id":"c084a126-5a5b-11eb-8a69-d75314a70a87","name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks.","grant_number":"214316/Z/18/Z"}],"intvolume":"        20","publisher":"Neural Information Processing Systems Foundation","type":"conference","scopus_import":"1","quality_controlled":"1","citation":{"chicago":"Braun, Lukas, and Tim P Vogels. “Online Learning of Neural Computations from Sparse Temporal Feedback.” In <i>Advances in Neural Information Processing Systems - 35th Conference on Neural Information Processing Systems</i>, 20:16437–50. Neural Information Processing Systems Foundation, 2021.","apa":"Braun, L., &#38; Vogels, T. P. (2021). Online learning of neural computations from sparse temporal feedback. In <i>Advances in Neural Information Processing Systems - 35th Conference on Neural Information Processing Systems</i> (Vol. 20, pp. 16437–16450). Virtual, Online: Neural Information Processing Systems Foundation.","short":"L. Braun, T.P. Vogels, in:, Advances in Neural Information Processing Systems - 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021, pp. 16437–16450.","ama":"Braun L, Vogels TP. Online learning of neural computations from sparse temporal feedback. In: <i>Advances in Neural Information Processing Systems - 35th Conference on Neural Information Processing Systems</i>. Vol 20. Neural Information Processing Systems Foundation; 2021:16437-16450.","ista":"Braun L, Vogels TP. 2021. Online learning of neural computations from sparse temporal feedback. Advances in Neural Information Processing Systems - 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 20, 16437–16450.","ieee":"L. Braun and T. P. Vogels, “Online learning of neural computations from sparse temporal feedback,” in <i>Advances in Neural Information Processing Systems - 35th Conference on Neural Information Processing Systems</i>, Virtual, Online, 2021, vol. 20, pp. 16437–16450.","mla":"Braun, Lukas, and Tim P. Vogels. “Online Learning of Neural Computations from Sparse Temporal Feedback.” <i>Advances in Neural Information Processing Systems - 35th Conference on Neural Information Processing Systems</i>, vol. 20, Neural Information Processing Systems Foundation, 2021, pp. 16437–50."},"author":[{"last_name":"Braun","first_name":"Lukas","full_name":"Braun, Lukas"},{"full_name":"Vogels, Tim P","first_name":"Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181"}],"_id":"11453","month":"12","main_file_link":[{"url":"https://proceedings.neurips.cc/paper/2021/file/88e1ce84f9feef5a08d0df0334c53468-Paper.pdf","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Neuronal computations depend on synaptic connectivity and intrinsic electrophysiological properties. Synaptic connectivity determines which inputs from presynaptic neurons are integrated, while cellular properties determine how inputs are filtered over time. Unlike their biological counterparts, most computational approaches to learning in simulated neural networks are limited to changes in synaptic connectivity. However, if intrinsic parameters change, neural computations are altered drastically. Here, we include the parameters that determine the intrinsic properties,\r\ne.g., time constants and reset potential, into the learning paradigm. Using sparse feedback signals that indicate target spike times, and gradient-based parameter updates, we show that the intrinsic parameters can be learned along with the synaptic weights to produce specific input-output functions. Specifically, we use a teacher-student paradigm in which a randomly initialised leaky integrate-and-fire or resonate-and-fire neuron must recover the parameters of a teacher neuron. We show that complex temporal functions can be learned online and without backpropagation through time, relying on event-based updates only. Our results are a step towards online learning of neural computations from ungraded and unsigned sparse feedback signals with a biologically inspired learning mechanism.","lang":"eng"}],"publication_status":"published","date_published":"2021-12-01T00:00:00Z","status":"public","day":"01","corr_author":"1","oa_version":"Published Version","date_updated":"2025-04-14T09:44:14Z","oa":1,"language":[{"iso":"eng"}]},{"day":"06","corr_author":"1","date_updated":"2025-05-14T11:28:00Z","alternative_title":["Advances in Neural Information Processing Systems"],"oa_version":"Published Version","arxiv":1,"oa":1,"ec_funded":1,"language":[{"iso":"eng"}],"month":"12","main_file_link":[{"open_access":"1","url":"https://proceedings.neurips.cc/paper/2021/file/7cfd5df443b4eb0d69886a583b33de4c-Paper.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"text":"Efficiently approximating local curvature information of the loss function is a key tool for optimization and compression of deep neural networks. Yet, most existing methods to approximate second-order information have high computational\r\nor storage costs, which limits their practicality. In this work, we investigate matrix-free, linear-time approaches for estimating Inverse-Hessian Vector Products (IHVPs) for the case when the Hessian can be approximated as a sum of rank-one matrices, as in the classic approximation of the Hessian by the empirical Fisher matrix. We propose two new algorithms: the first is tailored towards network compression and can compute the IHVP for dimension d, if the Hessian is given as a sum of m rank-one matrices, using O(dm2) precomputation, O(dm) cost for computing the IHVP, and query cost O(m) for any single element of the inverse Hessian. The second algorithm targets an optimization setting, where we wish to compute the product between the inverse Hessian, estimated over a sliding window of optimization steps, and a given gradient direction, as required for preconditioned SGD. We give an algorithm with cost O(dm + m2) for computing the IHVP and O(dm + m3) for adding or removing any gradient from the sliding window. These\r\ntwo algorithms yield state-of-the-art results for network pruning and optimization with lower computational overhead relative to existing second-order methods. Implementations are available at [9] and [17].","lang":"eng"}],"date_published":"2021-12-06T00:00:00Z","status":"public","intvolume":"        34","publisher":"Neural Information Processing Systems Foundation","type":"conference","quality_controlled":"1","scopus_import":"1","citation":{"ama":"Frantar E, Kurtic E, Alistarh D-A. M-FAC: Efficient matrix-free approximations of second-order information. In: <i>35th Conference on Neural Information Processing Systems</i>. Vol 34. Neural Information Processing Systems Foundation; 2021:14873-14886.","mla":"Frantar, Elias, et al. “M-FAC: Efficient Matrix-Free Approximations of Second-Order Information.” <i>35th Conference on Neural Information Processing Systems</i>, vol. 34, Neural Information Processing Systems Foundation, 2021, pp. 14873–86.","ieee":"E. Frantar, E. Kurtic, and D.-A. Alistarh, “M-FAC: Efficient matrix-free approximations of second-order information,” in <i>35th Conference on Neural Information Processing Systems</i>, Virtual, Online, 2021, vol. 34, pp. 14873–14886.","ista":"Frantar E, Kurtic E, Alistarh D-A. 2021. M-FAC: Efficient matrix-free approximations of second-order information. 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 34, 14873–14886.","chicago":"Frantar, Elias, Eldar Kurtic, and Dan-Adrian Alistarh. “M-FAC: Efficient Matrix-Free Approximations of Second-Order Information.” In <i>35th Conference on Neural Information Processing Systems</i>, 34:14873–86. Neural Information Processing Systems Foundation, 2021.","apa":"Frantar, E., Kurtic, E., &#38; Alistarh, D.-A. (2021). M-FAC: Efficient matrix-free approximations of second-order information. In <i>35th Conference on Neural Information Processing Systems</i> (Vol. 34, pp. 14873–14886). Virtual, Online: Neural Information Processing Systems Foundation.","short":"E. Frantar, E. Kurtic, D.-A. Alistarh, in:, 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021, pp. 14873–14886."},"author":[{"first_name":"Elias","last_name":"Frantar","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","full_name":"Frantar, Elias"},{"full_name":"Kurtic, Eldar","first_name":"Eldar","last_name":"Kurtic","id":"47beb3a5-07b5-11eb-9b87-b108ec578218"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"}],"_id":"11463","acknowledgement":"We gratefully acknowledge funding the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML), as well as computational support from Amazon Web Services (AWS) EC2.","date_created":"2022-06-26T22:01:35Z","article_processing_charge":"No","publication_identifier":{"issn":["1049-5258"],"isbn":["9781713845393"]},"conference":{"name":"NeurIPS: Neural Information Processing Systems","location":"Virtual, Online","start_date":"2021-12-06","end_date":"2021-12-14"},"department":[{"_id":"DaAl"}],"page":"14873-14886","title":"M-FAC: Efficient matrix-free approximations of second-order information","external_id":{"arxiv":["2010.08222"]},"volume":34,"year":"2021","project":[{"call_identifier":"H2020","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"publication":"35th Conference on Neural Information Processing Systems"},{"page":"7254-7266","project":[{"name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"805223"}],"publication":"35th Conference on Neural Information Processing Systems","year":"2021","volume":34,"title":"Towards tight communication lower bounds for distributed optimisation","external_id":{"arxiv":["2010.08222"]},"publication_identifier":{"issn":["1049-5258"],"isbn":["9781713845393"]},"article_processing_charge":"No","acknowledgement":"We thank the NeurIPS reviewers for insightful comments that helped us improve the positioning of our results, as well as for pointing out the subsampling approach for complementing the randomised lower bound. We also thank Foivos Alimisis and Peter Davies for useful discussions. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML).","date_created":"2022-06-26T22:01:35Z","department":[{"_id":"DaAl"}],"conference":{"name":"NeurIPS: Neural Information Processing Systems","end_date":"2021-12-14","start_date":"2021-12-06","location":"Virtual, Online"},"citation":{"chicago":"Alistarh, Dan-Adrian, and Janne Korhonen. “Towards Tight Communication Lower Bounds for Distributed Optimisation.” In <i>35th Conference on Neural Information Processing Systems</i>, 34:7254–66. Neural Information Processing Systems Foundation, 2021.","apa":"Alistarh, D.-A., &#38; Korhonen, J. (2021). Towards tight communication lower bounds for distributed optimisation. In <i>35th Conference on Neural Information Processing Systems</i> (Vol. 34, pp. 7254–7266). Virtual, Online: Neural Information Processing Systems Foundation.","short":"D.-A. Alistarh, J. Korhonen, in:, 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021, pp. 7254–7266.","ama":"Alistarh D-A, Korhonen J. Towards tight communication lower bounds for distributed optimisation. In: <i>35th Conference on Neural Information Processing Systems</i>. Vol 34. Neural Information Processing Systems Foundation; 2021:7254-7266.","mla":"Alistarh, Dan-Adrian, and Janne Korhonen. “Towards Tight Communication Lower Bounds for Distributed Optimisation.” <i>35th Conference on Neural Information Processing Systems</i>, vol. 34, Neural Information Processing Systems Foundation, 2021, pp. 7254–66.","ieee":"D.-A. Alistarh and J. Korhonen, “Towards tight communication lower bounds for distributed optimisation,” in <i>35th Conference on Neural Information Processing Systems</i>, Virtual, Online, 2021, vol. 34, pp. 7254–7266.","ista":"Alistarh D-A, Korhonen J. 2021. Towards tight communication lower bounds for distributed optimisation. 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 34, 7254–7266."},"quality_controlled":"1","scopus_import":"1","_id":"11464","author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"},{"full_name":"Korhonen, Janne","first_name":"Janne","id":"C5402D42-15BC-11E9-A202-CA2BE6697425","last_name":"Korhonen"}],"publisher":"Neural Information Processing Systems Foundation","intvolume":"        34","type":"conference","publication_status":"published","abstract":[{"text":"We consider a standard distributed optimisation setting where N machines, each holding a d-dimensional function\r\nfi, aim to jointly minimise the sum of the functions ∑Ni=1fi(x). This problem arises naturally in large-scale distributed optimisation, where a standard solution is to apply variants of (stochastic) gradient descent. We focus on the communication complexity of this problem: our main result provides the first fully unconditional bounds on total number of bits which need to be sent and received by the N machines to solve this problem under point-to-point communication, within a given error-tolerance. Specifically, we show that Ω(Ndlogd/Nε) total bits need to be communicated between the machines to find an additive ϵ-approximation to the minimum of ∑Ni=1fi(x). The result holds for both deterministic and randomised algorithms, and, importantly, requires no assumptions on the algorithm structure. The lower bound is tight under certain restrictions on parameter values, and is matched within constant factors for quadratic objectives by a new variant of quantised gradient descent, which we describe and analyse. Our results bring over tools from communication complexity to distributed optimisation, which has potential for further applications.","lang":"eng"}],"status":"public","date_published":"2021-12-06T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://proceedings.neurips.cc/paper/2021/file/3b92d18aa7a6176dd37d372bc2f1eb71-Paper.pdf"}],"month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"date_updated":"2025-05-14T11:27:51Z","alternative_title":["Advances in Neural Information Processing Systems"],"oa_version":"Published Version","ec_funded":1,"oa":1,"language":[{"iso":"eng"}],"day":"06","corr_author":"1"}]