--- OA_place: publisher _id: '15352' abstract: - lang: eng text: "Epilepsy affects about 50 to 65 million people globally. It summarizes a spectrum of neurological\r\ndisorders that have in common a hyperactivity of the neuronal network resulting in seizures. A common\r\nassumption is that an imbalance between neuronal excitation and inhibition is a key mechanism in\r\nseizure generation and epileptogeneisis. In at least one-third of the patients, current therapies have\r\nproven unsuccessful in treating seizure progression. One potential reason could be that the therapies\r\nonly focus on neurons. Recent studies suggest that neuronal hyperactivity causes a microglial\r\nresponse, which reinstates brain homeostasis. Additionally, interactions between microglia and neurons\r\nhave been shown to inhibit neuronal firing and dampen seizure activity. However, the exact relationship\r\nbetween microglia and seizure progression in epilepsy is yet to be elucidated. A main bottleneck is that\r\nseveral studies investigate microglia dynamics in ex vivo slice models, which can severely affect the\r\nmicroglia dynamics due to their rapid response to environmental changes. On the other hand, in vivo\r\nstudies focus mostly on behavior characterization of the epileptic seizure phenotype and their long-term\r\nconsequences on microglia activity leaving out the direct consequences of acute seizure activity on\r\nmicroglia dynamics.\r\nHere, we perform a pilot study to combine electroencephalography (EEG) and in vivo live imaging to\r\ndirectly monitor and correlate the onset of seizure activity with microglia response. To induce seizures,\r\nwe take advantage of the kainic acid (KA) model, which represents similar neuropathological and\r\nelectroencephalographic features seen in human patients with temporal lobe epilepsy (TLE). After\r\nconfirmation of induction of the seizure and microglia activity in the hippocampus as a focal point, we\r\ninvestigated whether these changes also reached the primary visual cortex (V1) as a secondary\r\ngeneralized seizure activity. Indeed, we found that microglia changed their morphology at high doses\r\nof KA in the V1. Next, we optimized each of the two methodological components: for the EEG recording,\r\nour initial attempts under the microscope suffered from extensive electrical noise, which overlaid the\r\nactual signal. Thus, we built a customized Faraday-cage and confirmed that the signal-to-noise ratio\r\nwas sufficiently reduced to be able to record brain oscillatory activity. For the in vivo live imaging of\r\nmicroglia, we had to optimize the imaging parameters, so that we would be able to detect microglial\r\nprocesses in a sufficient resolution to track their process changes. Finally, we combined both\r\nmethodologies with the KA model. We confirmed that KA induced seizure activity and found first\r\nindication that those correlate with microglia volume changes.\r\nOverall, we have developed a first methodological approach, which allows the analysis of the acute\r\neffects of seizure onset on microglia. Future studies will have to continue to optimize the drift during\r\nimaging recording and the post-image analysis. " acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: PreCl alternative_title: - ISTA Master's Thesis article_processing_charge: No author: - first_name: Julie Stefanie full_name: Murmann, Julie Stefanie id: 1d390868-f128-11eb-9611-a0ca5f7833b5 last_name: Murmann citation: ama: 'Murmann JS. Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. 2024. doi:10.15479/at:ista:15352' apa: 'Murmann, J. S. (2024). Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15352' chicago: 'Murmann, Julie Stefanie. “Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15352.' ieee: 'J. S. Murmann, “Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording,” Institute of Science and Technology Austria, 2024.' ista: 'Murmann JS. 2024. Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. Institute of Science and Technology Austria.' mla: 'Murmann, Julie Stefanie. Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15352.' short: 'J.S. Murmann, Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording, Institute of Science and Technology Austria, 2024.' corr_author: '1' date_created: 2024-05-02T08:31:38Z date_published: 2024-05-02T00:00:00Z date_updated: 2026-04-07T13:05:00Z day: '02' ddc: - '570' degree_awarded: MS department: - _id: SaSi - _id: GradSch doi: 10.15479/at:ista:15352 file: - access_level: open_access checksum: 095817a6c944954ac3f277e547031a33 content_type: application/pdf creator: cchlebak date_created: 2024-05-02T12:26:13Z date_updated: 2025-05-02T22:30:04Z embargo: 2025-05-02 file_id: '15354' file_name: Murmann_Thesis_final_2024_2.pdf file_size: 5936142 relation: main_file - access_level: closed checksum: 43b632255372973a437ac87739cfd4db content_type: application/x-zip-compressed creator: cchlebak date_created: 2024-05-02T12:37:56Z date_updated: 2025-05-02T22:30:04Z embargo_to: open_access file_id: '15355' file_name: Murmann_Thesis_final_2024.zip file_size: 20645510 relation: source_file file_date_updated: 2025-05-02T22:30:04Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '54' publication_identifier: issn: - 2791-4585 publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 title: 'Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '14843' abstract: - lang: eng text: The coupling between Ca2+ channels and release sensors is a key factor defining the signaling properties of a synapse. However, the coupling nanotopography at many synapses remains unknown, and it is unclear how it changes during development. To address these questions, we examined coupling at the cerebellar inhibitory basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission by paired recording and intracellular pipette perfusion revealed that the effects of exogenous Ca2+ chelators decreased during development, despite constant reliance of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked vesicles were only clustered at later developmental stages. Modeling suggested a developmental transformation from a more random to a more clustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic transmission. acknowledged_ssus: - _id: EM-Fac - _id: PreCl - _id: M-Shop acknowledgement: We thank Drs. David DiGregorio and Erwin Neher for critically reading an earlier version of the manuscript, Ralf Schneggenburger for helpful discussions, Benjamin Suter and Katharina Lichter for support with image analysis, Chris Wojtan for advice on numerical solution of partial differential equations, Maria Reva for help with Ripley analysis, Alois Schlögl for programming, and Akari Hagiwara and Toshihisa Ohtsuka for anti-ELKS antibody. We are grateful to Florian Marr, Christina Altmutter, and Vanessa Zheden for excellent technical assistance and to Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA (Electron Microscopy Facility, Preclinical Facility, and Machine Shop). The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 692692), the Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award; P 36232-B), all to P.J., and a DOC fellowship of the Austrian Academy of Sciences to J.-J.C. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: JingJing full_name: Chen, JingJing id: 2C4E65C8-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Chong full_name: Chen, Chong id: 3DFD581A-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Itaru full_name: Arai, Itaru id: 32A73F6C-F248-11E8-B48F-1D18A9856A87 last_name: Arai - first_name: Olena full_name: Kim, Olena id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87 last_name: Kim orcid: 0000-0003-2344-1039 - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Chen J, Kaufmann W, Chen C, et al. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. 2024;112(5):755-771.e9. doi:10.1016/j.neuron.2023.12.002 apa: Chen, J., Kaufmann, W., Chen, C., Arai, itaru, Kim, O., Shigemoto, R., & Jonas, P. M. (2024). Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.12.002 chicago: Chen, JingJing, Walter Kaufmann, Chong Chen, itaru Arai, Olena Kim, Ryuichi Shigemoto, and Peter M Jonas. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” Neuron. Elsevier, 2024. https://doi.org/10.1016/j.neuron.2023.12.002. ieee: J. Chen et al., “Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse,” Neuron, vol. 112, no. 5. Elsevier, p. 755–771.e9, 2024. ista: Chen J, Kaufmann W, Chen C, Arai itaru, Kim O, Shigemoto R, Jonas PM. 2024. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. 112(5), 755–771.e9. mla: Chen, JingJing, et al. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” Neuron, vol. 112, no. 5, Elsevier, 2024, p. 755–771.e9, doi:10.1016/j.neuron.2023.12.002. short: J. Chen, W. Kaufmann, C. Chen, itaru Arai, O. Kim, R. Shigemoto, P.M. Jonas, Neuron 112 (2024) 755–771.e9. corr_author: '1' date_created: 2024-01-21T23:00:56Z date_published: 2024-03-06T00:00:00Z date_updated: 2026-07-16T22:30:20Z day: '06' ddc: - '570' department: - _id: PeJo - _id: EM-Fac - _id: RySh doi: 10.1016/j.neuron.2023.12.002 ec_funded: 1 external_id: isi: - '001202925700001' pmid: - '38215739' file: - access_level: open_access checksum: 30098b4f0209556ddfb3540a23d07ca5 content_type: application/pdf creator: dernst date_created: 2025-04-23T14:02:08Z date_updated: 2025-04-23T14:02:08Z file_id: '19614' file_name: 2024_Neuron_Chen.pdf file_size: 8192355 relation: main_file success: 1 file_date_updated: 2025-04-23T14:02:08Z has_accepted_license: '1' intvolume: ' 112' isi: 1 issue: '5' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 755-771.e9 pmid: 1 project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glutamatergic synapse - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: Synaptic communication in neuronal microcircuits - _id: bd88be38-d553-11ed-ba76-81d5a70a6ef5 grant_number: P36232 name: Mechanisms of GABA release in hippocampal circuits - _id: 26B66A3E-B435-11E9-9278-68D0E5697425 grant_number: '25383' name: Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse publication: Neuron publication_identifier: eissn: - 1097-4199 issn: - 0896-6273 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on ISTA Website relation: press_release url: https://ista.ac.at/en/news/synapses-brought-to-the-point/ record: - id: '15101' relation: dissertation_contains status: public scopus_import: '1' status: public title: Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2024' ... --- OA_place: publisher _id: '14821' abstract: - lang: eng text: "The hippocampus is central to memory formation, storage and retrieval over many\r\ntimescales. Neurons in this brain area are highly selective to spatial position as well as to many\r\nother variables of the environment. It is believed that the selectivity patterns of hippocampal\r\nneurons reflect the structure of tasks an animal performs. However, especially at timescales\r\nlonger than a few minutes or hours it is not fully known how these representations evolve, nor\r\nhow they map to behaviour in the process. In this thesis, I monitored the evolution of\r\nhippocampal representations in a novel spatial-associative memory task for rats. Reward\r\nlocations were associated with global sensory cues (i.e. context); animals had to remember the\r\nassociations and dig for food in those locations only. I used in vivo electrophysiology to record\r\nthe activity of the hippocampus dorsal CA1 neurons during the learning period of a few days.\r\nI report here a novel and simple method to classify behaviour performance to account\r\nfor individual variability in learning speed and spurious performance unrelated to true task rule\r\nlearning. Using this classification I was then able to investigate neural responses on different\r\nstages of learning matched across animals. On the first day of learning, I observed a fast\r\nformation of single-cell selectivity to task variables which remained stable over days. I also\r\nobserved that reward tuning was not a single process but dependent on task-related cognitive\r\nload. At the population level, a linear decoding approach revealed a hierarchy in the\r\nrepresentation of task variables that changed with learning. In the high-dimensional space of\r\npopulation activity, the representation of contexts was specific to each position in the maze, and\r\ncould thus be better decoded if the position was known. The decoding of position did not improve\r\nwith knowledge of other variables. As learning progressed, the hippocampal code underwent a\r\nreorganisation of high-variance directions in population activity, identified by principal\r\ncomponent analysis. I found that dominant dimensions started carrying increasing amounts of\r\ninformation about task context specifically at those positions where it mattered for task\r\nperformance. When I contrasted this with variables less relevant to task performance (e.g.\r\nmovement direction), I did not observe differences in decoding quality over positions nor a\r\nreduction of dimensionality with learning.\r\nOverall, the largest changes in CA1 neural response with task learning happened in a\r\nmatter of a few trials; over days, changes undetectable in single-cell statistics were responsible\r\nfor re-structuring the hierarchy of neural representations at the population level; these changes\r\nwere task-specific and reflected different stages of learning. This indicates that complex task\r\nlearning may involve different magnitudes of response modulation in CA1, which happen at\r\nspecific time scales linked to behaviour." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Heloisa full_name: Chiossi, Heloisa id: 2BBA502C-F248-11E8-B48F-1D18A9856A87 last_name: Chiossi orcid: 0009-0004-2973-278X citation: ama: Chiossi HSC. Adaptive hierarchical representations in the hippocampus. 2024. doi:10.15479/at:ista:14821 apa: Chiossi, H. S. C. (2024). Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14821 chicago: Chiossi, Heloisa S. C. “Adaptive Hierarchical Representations in the Hippocampus.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:14821. ieee: H. S. C. Chiossi, “Adaptive hierarchical representations in the hippocampus,” Institute of Science and Technology Austria, 2024. ista: Chiossi HSC. 2024. Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria. mla: Chiossi, Heloisa S. C. Adaptive Hierarchical Representations in the Hippocampus. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:14821. short: H.S.C. Chiossi, Adaptive Hierarchical Representations in the Hippocampus, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-01-16T14:25:21Z date_published: 2024-01-19T00:00:00Z date_updated: 2026-04-07T13:21:56Z day: '19' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: JoCs doi: 10.15479/at:ista:14821 ec_funded: 1 file: - access_level: closed checksum: d3fa3de1abd5af5204c13e9d55375615 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: hchiossi date_created: 2024-01-19T11:04:05Z date_updated: 2025-01-19T23:30:04Z embargo_to: open_access file_id: '14838' file_name: PhD_Thesis_190124.docx file_size: 8656268 relation: source_file - access_level: open_access checksum: 13adc8dcfb5b6b18107f89f0a98fa8bd content_type: application/pdf creator: hchiossi date_created: 2024-01-19T11:03:59Z date_updated: 2025-01-19T23:30:04Z embargo: 2025-01-19 file_id: '14839' file_name: PhD_Thesis_190124.pdf file_size: 6567275 relation: main_file file_date_updated: 2025-01-19T23:30:04Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '89' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 title: Adaptive hierarchical representations in the hippocampus type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher _id: '15101' abstract: - lang: eng text: "The coupling between presynaptic Ca2+ channels and release sensors is a key factor that\r\ndetermines speed and efficacy of synapse transmission. At some excitatory synapses,\r\nchannel–sensor coupling becomes tighter during development, and tightening is often\r\nassociated with a switch in the reliance on different Ca2+ channel subtypes. However, the\r\ncoupling topography at many synapses remains unknown, and it is unclear how it changes\r\nduring development. To address this question, we analyzed the coupling configuration at the\r\ncerebellar basket cell (BC) to Purkinje cell (PC) synapse at different developmental stages,\r\ncombining biophysical analysis, structural analysis, and modeling.\r\nQuantal analysis of BC–PC indicated that release probability decreased, while the\r\nnumber of functional sites increased during development. Although transmitter release\r\npersistently relied on P/Q-type Ca2+ channels in the time period postnatal day 7–23, effects\r\nof the Ca2+ chelator EGTA and BAPTA applied by intracellular pipette perfusion decreased\r\nduring development, indicative of tightening of source-sensor coupling. Furthermore,\r\npresynaptic action potentials became shorter during development, suggesting reduced\r\nefficacy of Ca2+ channel activation.\r\nStructural analysis by freeze-fracture replica labeling (FRL) and transmission electron\r\nmicroscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters\r\nthroughout development, whereas docked vesicles were only clustered at later\r\ndevelopmental stages. The number of functional release sites correlated better with the AZ\r\nnumber early in development, but match better with the Ca2+ channel cluster number at later\r\nstages.\r\nModeling suggested a developmental transformation from a more random to a more\r\nclustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches\r\na point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic\r\ntransmission." acknowledged_ssus: - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: JingJing full_name: Chen, JingJing id: 2C4E65C8-F248-11E8-B48F-1D18A9856A87 last_name: Chen citation: ama: Chen J. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. 2024. doi:10.15479/at:ista:15101 apa: Chen, J. (2024). Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15101 chicago: Chen, JingJing. “Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15101. ieee: J. Chen, “Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse,” Institute of Science and Technology Austria, 2024. ista: Chen J. 2024. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria. mla: Chen, JingJing. Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15101. short: J. Chen, Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-03-11T10:09:54Z date_published: 2024-03-11T00:00:00Z date_updated: 2026-04-07T13:24:22Z day: '11' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: PeJo doi: 10.15479/at:ista:15101 ec_funded: 1 file: - access_level: closed checksum: db4947474ffa271e66c254b6fe876a55 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: jchen date_created: 2024-03-11T14:10:58Z date_updated: 2024-04-02T22:30:03Z embargo_to: open_access file_id: '15104' file_name: Thesis_Jingjing CHEN.docx file_size: 11271363 relation: source_file - access_level: open_access checksum: a5eeae8b5702cd540f5d03469bc33dde content_type: application/pdf creator: jchen date_created: 2024-03-11T14:11:06Z date_updated: 2024-04-02T22:30:03Z embargo: 2024-04-01 file_id: '15105' file_name: Thesis_Jingjing CHEN_merged.pdf file_size: 16627311 relation: main_file file_date_updated: 2024-04-02T22:30:03Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '84' project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glutamatergic synapse - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: Synaptic communication in neuronal microcircuits - _id: bd88be38-d553-11ed-ba76-81d5a70a6ef5 grant_number: P36232 name: Mechanisms of GABA release in hippocampal circuits - _id: 26B66A3E-B435-11E9-9278-68D0E5697425 grant_number: '25383' name: Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '14843' relation: part_of_dissertation status: public status: public supervisor: - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 title: Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher _id: '18471' abstract: - lang: eng text: "Spatial omics technologies are enriching our understanding of complex biological samples, by\r\nallowing us to study their molecular composition while preserving the spatial relationships\r\nbetween molecules in their native context. As the field continues to advance, there are\r\ntechnical challenges that need to be addressed in order to take full advantage of the spatial\r\ncapabilities of these methods. In this work, I present two technical developments that I\r\nestablished for multiplexed error robust FISH (MERFISH) throughout my PhD: (1) pushing the\r\nspatial resolution limits to the nanoscale, and (2) adding rich tissue context to the mouse brain\r\ntranscriptome. To achieve nanoscale resolution with MERFISH in cultured cells, I combined it\r\nwith stimulated emission depletion (STED) and expansion microscopy (ExM) to achieve a\r\nspatial resolution as low as ~20 nm, and explored the compatibility of MERFISH with singlemolecule localization microscopy (SMLM) techniques. To visualize targeted mRNAs in mouse\r\nbrain tissue, I applied the comprehensive analysis of tissues across scales (CATS) toolbox, which\r\nprovides an unbiased morphological readout by labeling the extracellular domain. I\r\nsuccessfully established this method, which we call CATS-MERFISH-ExM, to work with thick\r\nmouse brain slices, being able to extract transcriptomics information with 3D tissue context.\r\nCATS-MERFISH-ExM enabled us to identify cell types and further visualize the subcellular\r\ndistribution of transcripts in mouse brain tissue, shedding light on the neuropil-specific\r\ntranscriptome. This method provides integrated information on cellular structure and\r\ntranscriptomes in situ, and could potentially be applied with other modalities, opening new\r\navenues for scientific discovery. " acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: PreCl - _id: M-Shop - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Nathalie full_name: Agudelo Duenas, Nathalie id: 40E7F008-F248-11E8-B48F-1D18A9856A87 last_name: Agudelo Duenas citation: ama: Agudelo Duenas N. Visualizing the neuronal transcriptional landscape with tissue context. 2024. doi:10.15479/at:ista:18471 apa: Agudelo Duenas, N. (2024). Visualizing the neuronal transcriptional landscape with tissue context. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18471 chicago: Agudelo Duenas, Nathalie. “Visualizing the Neuronal Transcriptional Landscape with Tissue Context.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18471. ieee: N. Agudelo Duenas, “Visualizing the neuronal transcriptional landscape with tissue context,” Institute of Science and Technology Austria, 2024. ista: Agudelo Duenas N. 2024. Visualizing the neuronal transcriptional landscape with tissue context. Institute of Science and Technology Austria. mla: Agudelo Duenas, Nathalie. Visualizing the Neuronal Transcriptional Landscape with Tissue Context. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18471. short: N. Agudelo Duenas, Visualizing the Neuronal Transcriptional Landscape with Tissue Context, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-10-26T20:02:42Z date_published: 2024-10-28T00:00:00Z date_updated: 2026-04-14T08:34:37Z day: '28' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: JoDa doi: 10.15479/at:ista:18471 ec_funded: 1 file: - access_level: closed checksum: 6d7c7725d040d8debc070dcb35ac965d content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: nagudelo date_created: 2024-10-26T22:29:06Z date_updated: 2025-05-05T22:30:04Z embargo_to: open_access file_id: '18475' file_name: PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.docx file_size: 183077763 relation: source_file - access_level: open_access checksum: 52f9c0bf2bdafa3baf827b73814a53ff content_type: application/pdf creator: nagudelo date_created: 2024-10-26T23:13:33Z date_updated: 2025-05-05T22:30:04Z embargo: 2025-05-05 file_id: '18476' file_name: PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.pdf file_size: 47027710 relation: main_file file_date_updated: 2025-05-05T22:30:04Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '97' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 2548AE96-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232 name: Molecular Drug Targets publication_identifier: isbn: - 978-3-99078-044-2 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 title: Visualizing the neuronal transcriptional landscape with tissue context tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_embargo: '12' OA_place: publisher _id: '18574' abstract: - lang: eng text: "Biological vision is unlike a camera; rather than transmitting light information faithfully, early\r\nvisual circuits process the visual scene to convey only the relevant information in an efficient\r\nmanner. Consequentially, the nature of this visual processing then depends on what is the\r\nrelevant information in a scene and on the notion of efficiency. In this work, I study how visual\r\nprocessing is modulated by two different variations in the visual scene. First, I discovered that\r\nin the mouse (Mus musculus) retina, Retinal Ganglion Cells in the upper and lower visual\r\nfield have differences in the center surround structure of their receptive fields. Comparison\r\nwith models of efficient coding show that this adaptation likely evolved to cope with the\r\nbrightness gradient from the sky to the ground that is pervasive in natural scenes. In the\r\nsecond project, I study how the downstream neurons in the Superior Colliculus dynamically\r\nchange their temporal selectivity depending on the ambient luminance and behavioral state.\r\nAs the scene gets darker or when the animal is is less aroused, the neuronal responses get\r\nlaggier, while still maintaining their relative timing with respect to the population. Overall, this\r\nwork emphasises the need to understand visual processing in the context of specific demands\r\nof the animal in its the environment. The adaptive changes in the visual system, from the\r\nretinal ganglion cells to the superior colliculus, highlight the intricate ways in which biological\r\nvision optimizes the processing of visual information.\r\n" acknowledged_ssus: - _id: Bio - _id: ScienComp - _id: PreCl - _id: LifeSc - _id: M-Shop - _id: E-Lib acknowledgement: "This work would have been impossible without the Scientific Service Units of IST Austria. The resources and expertise provided by Scientific Computing (especially Alois Schlögl), the MIBA Machine Shop (especially Todor Asenov), the Preclinical Facility (especially Freyja Langer), the Library, the Lab Support Facility and the Imaging and Optics Facility were the essential bedrock I could build upon. I would also like to thank IT support at ISTA for powering through remote work and a cyberattack.\r\nI am grateful for having been funded initially by the European Union Horizon 2020 Marie Skłodowska-Curie grant 665385 and later by Prof. Maximilian Joesch's the European Research Council Starting (756502) and Consolidator (101086580) Grants." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Divyansh full_name: Gupta, Divyansh id: 2A485EBE-F248-11E8-B48F-1D18A9856A87 last_name: Gupta orcid: 0000-0001-7400-6665 citation: ama: Gupta D. Visual adaptations to natural statistics. 2024. doi:10.15479/at:ista:18574 apa: Gupta, D. (2024). Visual adaptations to natural statistics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18574 chicago: Gupta, Divyansh. “Visual Adaptations to Natural Statistics.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18574. ieee: D. Gupta, “Visual adaptations to natural statistics,” Institute of Science and Technology Austria, 2024. ista: Gupta D. 2024. Visual adaptations to natural statistics. Institute of Science and Technology Austria. mla: Gupta, Divyansh. Visual Adaptations to Natural Statistics. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18574. short: D. Gupta, Visual Adaptations to Natural Statistics, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-11-20T21:30:44Z date_published: 2024-11-22T00:00:00Z date_updated: 2026-04-07T13:24:48Z day: '22' ddc: - '573' degree_awarded: PhD department: - _id: GradSch - _id: MaJö doi: 10.15479/at:ista:18574 ec_funded: 1 file: - access_level: closed checksum: ebb000d361c36b22ed6e639a931c6b7c content_type: application/zip creator: dgupta date_created: 2024-11-25T14:44:03Z date_updated: 2025-11-11T23:30:02Z embargo_to: open_access file_id: '18589' file_name: PhD Thesis - Divyansh Gupta.zip file_size: 75512262 relation: source_file - access_level: open_access checksum: 1282401eb71598bc311058b0fcefc6a1 content_type: application/pdf creator: dgupta date_created: 2024-11-26T11:43:19Z date_updated: 2025-11-11T23:30:02Z embargo: 2025-11-11 file_id: '18591' file_name: PDFA_PhD_Thesis___Divyansh_Gupta-26_11_24.pdf file_size: 6412619 relation: main_file file_date_updated: 2025-11-11T23:30:02Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '86' project: - _id: bdaf81a8-d553-11ed-ba76-c95961984540 grant_number: '101086580' name: 'Action Selection in the Midbrain: Neuromodulation of Visuomotor Senses' - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 2634E9D2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '756502' name: Circuits of Visual Attention publication_identifier: isbn: - 978-3-99078-050-3 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12349' relation: part_of_dissertation status: public - id: '12370' relation: research_data status: public status: public supervisor: - first_name: Maximilian A full_name: Jösch, Maximilian A id: 2BD278E6-F248-11E8-B48F-1D18A9856A87 last_name: Jösch orcid: 0000-0002-3937-1330 title: Visual adaptations to natural statistics tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- _id: '15323' abstract: - lang: eng text: Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies have shown that different tissues/organs are equipped with specific sets of supercomplexes, depending on their metabolic needs, the notion that supercomplexes have a role in the regulation of metabolism has been challenged. However, irrespective of the mechanistic conclusions, the composition of various high molecular weight supercomplexes remains uncertain. Here, using cryogenic electron microscopy, we demonstrate that mammalian (mouse) tissues contain three defined types of ‘respirasome’, supercomplexes made of CI, CIII2 and CIV. The stoichiometry and position of CIV differs in the three respirasomes, of which only one contains the supercomplex-associated factor SCAF1, whose involvement in respirasome formation has long been contended. Our structures confirm that the ‘canonical’ respirasome (the C-respirasome, CICIII2CIV) does not contain SCAF1, which is instead associated to a different respirasome (the CS-respirasome), containing a second copy of CIV. We also identify an alternative respirasome (A-respirasome), with CIV bound to the ‘back’ of CI, instead of the ‘toe’. This structural characterization of mouse mitochondrial supercomplexes allows us to hypothesize a mechanistic basis for their specific role in different metabolic conditions. acknowledged_ssus: - _id: EM-Fac - _id: LifeSc - _id: PreCl - _id: ScienComp acknowledgement: Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies have shown that different tissues/organs are equipped with specific sets of supercomplexes, depending on their metabolic needs, the notion that supercomplexes have a role in the regulation of metabolism has been challenged. However, irrespective of the mechanistic conclusions, the composition of various high molecular weight supercomplexes remains uncertain. Here, using cryogenic electron microscopy, we demonstrate that mammalian (mouse) tissues contain three defined types of ‘respirasome’, supercomplexes made of CI, CIII2 and CIV. The stoichiometry and position of CIV differs in the three respirasomes, of which only one contains the supercomplex-associated factor SCAF1, whose involvement in respirasome formation has long been contended. Our structures confirm that the ‘canonical’ respirasome (the C-respirasome, CICIII2CIV) does not contain SCAF1, which is instead associated to a different respirasome (the CS-respirasome), containing a second copy of CIV. We also identify an alternative respirasome (A-respirasome), with CIV bound to the ‘back’ of CI, instead of the ‘toe’. This structural characterization of mouse mitochondrial supercomplexes allows us to hypothesize a mechanistic basis for their specific role in different metabolic conditions. article_processing_charge: No article_type: original author: - first_name: Irene full_name: Vercellino, Irene id: 3ED6AF16-F248-11E8-B48F-1D18A9856A87 last_name: Vercellino orcid: 0000-0001-5618-3449 - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Vercellino I, Sazanov LA. SCAF1 drives the compositional diversity of mammalian respirasomes. Nature Structural and Molecular Biology. 2024;31:1061-1071. doi:10.1038/s41594-024-01255-0 apa: Vercellino, I., & Sazanov, L. A. (2024). SCAF1 drives the compositional diversity of mammalian respirasomes. Nature Structural and Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-024-01255-0 chicago: Vercellino, Irene, and Leonid A Sazanov. “SCAF1 Drives the Compositional Diversity of Mammalian Respirasomes.” Nature Structural and Molecular Biology. Springer Nature, 2024. https://doi.org/10.1038/s41594-024-01255-0. ieee: I. Vercellino and L. A. Sazanov, “SCAF1 drives the compositional diversity of mammalian respirasomes,” Nature Structural and Molecular Biology, vol. 31. Springer Nature, pp. 1061–1071, 2024. ista: Vercellino I, Sazanov LA. 2024. SCAF1 drives the compositional diversity of mammalian respirasomes. Nature Structural and Molecular Biology. 31, 1061–1071. mla: Vercellino, Irene, and Leonid A. Sazanov. “SCAF1 Drives the Compositional Diversity of Mammalian Respirasomes.” Nature Structural and Molecular Biology, vol. 31, Springer Nature, 2024, pp. 1061–71, doi:10.1038/s41594-024-01255-0. short: I. Vercellino, L.A. Sazanov, Nature Structural and Molecular Biology 31 (2024) 1061–1071. corr_author: '1' date_created: 2024-04-14T22:01:03Z date_published: 2024-07-01T00:00:00Z date_updated: 2025-11-24T08:35:04Z day: '01' ddc: - '572' department: - _id: LeSa doi: 10.1038/s41594-024-01255-0 ec_funded: 1 external_id: isi: - '001196897300001' pmid: - '38575788' file: - access_level: open_access checksum: 21f05d188762acd7f49a97f3d09c8d9f content_type: application/pdf creator: lsazanov date_created: 2024-05-14T11:57:56Z date_updated: 2025-01-01T23:30:03Z embargo: 2025-01-01 file_id: '15392' file_name: megacomplex_submit_NSMB_withFigures.pdf file_size: 24424729 relation: main_file file_date_updated: 2025-01-01T23:30:03Z has_accepted_license: '1' intvolume: ' 31' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 1061-1071 pmid: 1 project: - _id: 627abdeb-2b32-11ec-9570-ec31a97243d3 call_identifier: H2020 grant_number: '101020697' name: Structure and mechanism of respiratory chain molecular machines publication: Nature Structural and Molecular Biology publication_identifier: eissn: - 1545-9985 issn: - 1545-9993 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41594-025-01721-3 scopus_import: '1' status: public title: SCAF1 drives the compositional diversity of mammalian respirasomes tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2024' ... --- OA_embargo: '6' OA_place: publisher _id: '18531' abstract: - lang: eng text: "Sex chromosomes and autosomes exhibit very different evolutionary dynamics.\r\nThe Y chromosome usually degenerates, leaving many X-linked loci hemizygous in\r\nmales. Since recessive X-linked mutations are always exposed to selection in males,\r\nselection is more efficient on the X chromosome than on autosomes on recessive\r\nmutations, leading to faster adaptation on the X chromosome than other genomic\r\nregions, if beneficial mutations are on average recessive (known as the Faster-X\r\neffect). In the presence of the functional, but non-recombining gametolog on the Y (as\r\nis often the case in young non-recombining regions), recessive mutations are\r\nsheltered from selection on the X chromosome. We model this scenario and show that\r\nthe efficiency of selection is reduced on diploid X loci due to sheltering by the Y\r\nchromosome. Reduced efficiency of selection leads to slower adaptation and\r\nincreased accumulation of deleterious mutations (Slower-X effect). We extended this\r\nmodel to explore the effect of sex-specific selection on degeneration of sex\r\nchromosomes, showing theoretically that male-limited genes degenerate on the X\r\nchromosome and female-biased genes degenerate on the Y chromosome. This\r\nprediction depends on the effective population size and the mutation rate, explaining\r\nthe variety of sex chromosome degeneration patterns observed in nature.\r\nTo test for direct evidence of a Slower-X (or Slower-Z) effect, we analyzed the\r\nZW sex chromosomes of the flatworm Schistosoma japonicum, which have a very\r\nyoung non-recombining region with non-degenerated W. Diploid Z-linked genes have\r\nhigher ratios of non-synonymous to synonymous polymorphisms than autosomal\r\ngenes, supporting reduced efficiency of selection on the diploid Z region. These results\r\nprovide evidence of sheltering by the W chromosome, a mechanism that could\r\ncontribute to Z (X) chromosome degeneration, and illustrate contrasting evolutionary\r\npatterns in old and young sex chromosome regions. In addition, genes with sexspecific patterns of expression show opposite patterns of selection in the young\r\n(diploid) and old (hemizygous) Z, showing the complex manner in which sex-specific selection shapes the evolutionary patterns of sex chromosomes. " acknowledged_ssus: - _id: ScienComp - _id: CampIT alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Andrea full_name: Mrnjavac, Andrea id: 353FAC84-AE61-11E9-8BFC-00D3E5697425 last_name: Mrnjavac citation: ama: Mrnjavac A. Early stages of sex chromosome evolution. 2024. doi:10.15479/at:ista:18531 apa: Mrnjavac, A. (2024). Early stages of sex chromosome evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18531 chicago: Mrnjavac, Andrea. “Early Stages of Sex Chromosome Evolution.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18531. ieee: A. Mrnjavac, “Early stages of sex chromosome evolution,” Institute of Science and Technology Austria, 2024. ista: Mrnjavac A. 2024. Early stages of sex chromosome evolution. Institute of Science and Technology Austria. mla: Mrnjavac, Andrea. Early Stages of Sex Chromosome Evolution. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18531. short: A. Mrnjavac, Early Stages of Sex Chromosome Evolution, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-11-11T08:40:45Z date_published: 2024-11-11T00:00:00Z date_updated: 2026-04-07T13:22:45Z day: '11' ddc: - '576' degree_awarded: PhD department: - _id: GradSch - _id: BeVi doi: 10.15479/at:ista:18531 file: - access_level: closed checksum: 3e48b163c22114ef5d5371f758668289 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: amrnjava date_created: 2024-11-13T12:15:28Z date_updated: 2025-05-11T22:30:04Z embargo_to: open_access file_id: '18551' file_name: AMrnjavac_thesis_library.docx file_size: 26870629 relation: source_file title: Early stages of sex chromosome evolution - access_level: open_access checksum: 3ead60c1b678e7dcf018043aef3b5db2 content_type: application/pdf creator: amrnjava date_created: 2024-11-13T12:15:54Z date_updated: 2025-05-11T22:30:04Z embargo: 2025-05-11 file_id: '18552' file_name: AMrnjavac_thesis_library.pdf file_size: 4228766 relation: main_file title: Early stages of sex chromosome evolution file_date_updated: 2025-05-11T22:30:04Z has_accepted_license: '1' keyword: - Sex chromosomes - evolution - selection - sheltering language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '181' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12521' relation: part_of_dissertation status: public - id: '18549' relation: part_of_dissertation status: public status: public supervisor: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 title: Early stages of sex chromosome evolution tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: repository _id: '18549' abstract: - lang: eng text: "Sex-linked and autosomal loci experience different selective pressures and\r\nevolutionary dynamics. X (or Z) chromosomes are often hemizygous, as Y (or W)\r\nchromosomes often degenerate. Such hemizygous regions can be under greater\r\nefficacy of selection, as recessive mutations are immediately exposed to selection in\r\nthe heterogametic sex (the so-called Faster-X or Faster-Z effect). However, in young\r\nnon-recombining regions, Y/W chromosomes often have many functional genes, and\r\nmany X/Z-linked loci are therefore diploid. The sheltering of recessive mutations on\r\nthe X/Z by the Y/W homolog is expected to drive a Slower-X (Slower-Z) effect for\r\ndiploid X/Z loci, i.e. a reduction in the efficacy of selection. While the Faster-X effect\r\nhas been studied extensively, much less is known empirically about the evolutionary\r\ndynamics of diploid X or Z chromosomes. Here, we took advantage of published\r\npopulation genomic data in the female-heterogametic human parasite Schistosoma\r\njaponicum to characterize the gene content and diversity levels of the diploid and\r\nhemizygous regions of the Z chromosome. We used different metrics of selective\r\npressures acting on genes to test for differences in the efficacy of selection in\r\nhemizygous and diploid Z regions, relative to autosomes. We found consistent\r\npatterns suggesting reduced Ne, and reduced efficacy of purifying selection, on both\r\nhemizygous and diploid Z regions. Moreover, relaxed selection was particularly\r\npronounced for female-biased genes on the diploid Z, as predicted by Slower-Z\r\ntheory.\r\n" article_processing_charge: No author: - first_name: Andrea full_name: Mrnjavac, Andrea id: 353FAC84-AE61-11E9-8BFC-00D3E5697425 last_name: Mrnjavac - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Mrnjavac A, Vicoso B. Evidence of a Slower-Z effect in Schistosoma japonicum. bioRxiv. doi:10.1101/2024.07.02.601697 apa: Mrnjavac, A., & Vicoso, B. (n.d.). Evidence of a Slower-Z effect in Schistosoma japonicum. bioRxiv. https://doi.org/10.1101/2024.07.02.601697 chicago: Mrnjavac, Andrea, and Beatriz Vicoso. “Evidence of a Slower-Z Effect in Schistosoma Japonicum.” BioRxiv, n.d. https://doi.org/10.1101/2024.07.02.601697. ieee: A. Mrnjavac and B. Vicoso, “Evidence of a Slower-Z effect in Schistosoma japonicum,” bioRxiv. . ista: Mrnjavac A, Vicoso B. Evidence of a Slower-Z effect in Schistosoma japonicum. bioRxiv, 10.1101/2024.07.02.601697. mla: Mrnjavac, Andrea, and Beatriz Vicoso. “Evidence of a Slower-Z Effect in Schistosoma Japonicum.” BioRxiv, doi:10.1101/2024.07.02.601697. short: A. Mrnjavac, B. Vicoso, BioRxiv (n.d.). corr_author: '1' date_created: 2024-11-13T09:12:08Z date_published: 2024-07-04T00:00:00Z date_updated: 2026-07-16T22:30:22Z day: '04' department: - _id: BeVi doi: 10.1101/2024.07.02.601697 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2024.07.02.601697 month: '07' oa: 1 oa_version: Preprint publication: bioRxiv publication_status: draft related_material: record: - id: '19370' relation: later_version status: public - id: '18531' relation: dissertation_contains status: public status: public title: Evidence of a Slower-Z effect in Schistosoma japonicum tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: publisher _id: '18642' abstract: - lang: eng text: "This thesis consists of two pieces of work in the broader feld of computational biology,\r\nboth of which are methods for the analysis of large scale biological data, implemented in\r\nefcient software.\r\nChapter 2 introduces a statistical software for causal discovery and inference from observed\r\ngenetic marker and phenotypic trait data. We explore in simulation how well the method\r\ncan fne-map genetic efects, fnd the correct causal structure among tens of traits and\r\nmillions of genetic markers, and infer the causal efect size for the discovered causal\r\nrelations. We then apply the method to 8 million markers and 17 traits from the UK\r\nBiobank and show that many relationships found with other methods are likely due to\r\nthe efects of hidden confounders.\r\nChapter 3 describes how this method can be applied to longitudinal data. I show how one\r\ncan incorporate the background knowledge present in the known order of measurements to\r\nimprove the accuracy of the causal discovery process, and explore the method’s ability to\r\nidentify age specifc genetic efects, and how the error rates of this recovery are infuenced\r\nby missing data due to diferent censoring mechanisms.\r\nChapter 4 introduces a statistical software for the comparison of chromatin contact maps\r\nbased on the structural similarity index. We explore the robustness of the method to\r\nnoise and size diferences of the compared maps, show how it can measure evolutionary\r\nconservation of topological features by providing a similarity ranking of syntenic regions,\r\nand fnally how it can detect alterations in 3D genome structure due to genetic mutations\r\nin samples of medical relevance.\r\n" acknowledgement: "I would like to thank the Swiss National Science Foundation for funding parts of this work\r\nthrough the Eccellenza Grant \"Improving estimation and prediction of common complex\r\ndisease risk\" with grant number PCEGP3_181181." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Nick N full_name: Machnik, Nick N id: 3591A0AA-F248-11E8-B48F-1D18A9856A87 last_name: Machnik orcid: 0000-0001-6617-9742 citation: ama: Machnik NN. Algorithms for causal learning and comparative analysis for genomic data. 2024. doi:10.15479/at:ista:18642 apa: Machnik, N. N. (2024). Algorithms for causal learning and comparative analysis for genomic data. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18642 chicago: Machnik, Nick N. “Algorithms for Causal Learning and Comparative Analysis for Genomic Data.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18642. ieee: N. N. Machnik, “Algorithms for causal learning and comparative analysis for genomic data,” Institute of Science and Technology Austria, 2024. ista: Machnik NN. 2024. Algorithms for causal learning and comparative analysis for genomic data. Institute of Science and Technology Austria. mla: Machnik, Nick N. Algorithms for Causal Learning and Comparative Analysis for Genomic Data. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18642. short: N.N. Machnik, Algorithms for Causal Learning and Comparative Analysis for Genomic Data, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-12-10T13:49:15Z date_published: 2024-12-11T00:00:00Z date_updated: 2026-04-07T13:23:06Z day: '11' ddc: - '576' degree_awarded: PhD department: - _id: GradSch - _id: MaRo doi: 10.15479/at:ista:18642 file: - access_level: open_access checksum: d45e4d170f9a70a1f69b44b99bd058e4 content_type: application/pdf creator: nmachnik date_created: 2024-12-11T11:59:54Z date_updated: 2025-06-12T22:30:02Z embargo: 2025-06-12 file_id: '18649' file_name: NickMachnikThesisFinal_pdfa_conv.pdf file_size: 12845009 relation: main_file - access_level: closed checksum: f88c9acc62002395ec4dcbdb5eea8b82 content_type: application/zip creator: nmachnik date_created: 2024-12-11T11:59:34Z date_updated: 2025-06-12T22:30:02Z embargo_to: open_access file_id: '18650' file_name: thesis.zip file_size: 14189810 relation: source_file file_date_updated: 2025-06-12T22:30:02Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '138' project: - _id: 9B8D11D6-BA93-11EA-9121-9846C619BF3A grant_number: PCEGP3_181181 name: Improving estimation and prediction of common complex disease risk publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18648' relation: part_of_dissertation status: public - id: '8707' relation: part_of_dissertation status: public status: public supervisor: - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 title: Algorithms for causal learning and comparative analysis for genomic data type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: repository OA_type: free access _id: '18648' abstract: - lang: eng text: "Statistical causal learning in genomics relies on the instrumental variable method of\r\nMendelian Randomization (MR). Currently, an overwhelming number of MR studies\r\npurport to show causal relationships among a wide range of risk factors and outcomes.\r\nHere, we show that selecting instrument variables from genome-wide association study\r\nestimates leads to high false discovery rates for many MR approaches, which can be\r\ngreatly reduced by employing a graphical inference approach which: (i) explicitly tests\r\ninstrumental variable assumptions; (ii) distinguishes direct from indirect factors in very\r\nhigh-dimensional data; (iii) discriminates pleiotropic from trait-specific markers, controlling for LD genome-wide; (iv) accommodates rare variants and binary outcomes in a\r\nprincipled way; and (v) identifies potential unobserved latent confounding. For 17 traits\r\nand 8.4M variants recorded for 458,747 individuals in the UK Biobank, we show that\r\nstandard MR analysis gives an abundance of findings that disappear under stringent\r\nassumption checks, with many relationships reflecting potential unmeasured confounding. This implies that mixtures of temporal precedence and potential for reverse-causality\r\nprohibit understanding the underlying nature of phenotypic and genetic correlations in\r\nbiobank data. We propose that well-curated longitudinal records are likely needed and\r\nthat our approach provides a first-step toward robust principled screening for potential\r\ncausal links.\r\n" acknowledged_ssus: - _id: ScienComp acknowledgement: "We thank Zoltan Kutalik and members of the Robinson group \r\nat ISTA for their comments, which improved this manuscript. This work was funded \r\nby a research collaboration agreement between Boehringer Ingelheim and the research \r\ngroup of MRR at the Institute of Science and Technology Austria. Additional funding \r\nwas also provided by an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and by \r\ncore funding from the Institute of Science and Technology Austria. We would like \r\nto acknowledge the participants and investigators of the UK Biobank study. High- \r\nperformance computing was supported by the Scientific Service Units (SSU) of IST \r\nAustria through resources provided by Scientific Computing (SciComp). " article_processing_charge: No author: - first_name: Nick N full_name: Machnik, Nick N id: 3591A0AA-F248-11E8-B48F-1D18A9856A87 last_name: Machnik orcid: 0000-0001-6617-9742 - first_name: Seyed Mahdi full_name: Mahmoudi, Seyed Mahdi id: b9f6d5ef-7774-11eb-a47f-df2c75c02ee7 last_name: Mahmoudi - first_name: Malgorzata full_name: Borczyk, Malgorzata last_name: Borczyk - first_name: Ilse full_name: Krätschmer, Ilse id: 30d4014e-7753-11eb-b44b-db6d61112e73 last_name: Krätschmer orcid: 0000-0002-5636-9259 - first_name: Markus J. full_name: Bauer, Markus J. last_name: Bauer - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 citation: ama: Machnik NN, Mahmoudi SM, Borczyk M, Krätschmer I, Bauer MJ, Robinson MR. Causal inference for multiple risk factors and diseases from genomics data. bioRxiv. 2024. doi:10.1101/2023.12.06.570392 apa: Machnik, N. N., Mahmoudi, S. M., Borczyk, M., Krätschmer, I., Bauer, M. J., & Robinson, M. R. (2024). Causal inference for multiple risk factors and diseases from genomics data. bioRxiv. https://doi.org/10.1101/2023.12.06.570392 chicago: Machnik, Nick N, Seyed Mahdi Mahmoudi, Malgorzata Borczyk, Ilse Krätschmer, Markus J. Bauer, and Matthew Richard Robinson. “Causal Inference for Multiple Risk Factors and Diseases from Genomics Data.” BioRxiv, 2024. https://doi.org/10.1101/2023.12.06.570392. ieee: N. N. Machnik, S. M. Mahmoudi, M. Borczyk, I. Krätschmer, M. J. Bauer, and M. R. Robinson, “Causal inference for multiple risk factors and diseases from genomics data,” bioRxiv. 2024. ista: Machnik NN, Mahmoudi SM, Borczyk M, Krätschmer I, Bauer MJ, Robinson MR. 2024. Causal inference for multiple risk factors and diseases from genomics data. bioRxiv, 10.1101/2023.12.06.570392. mla: Machnik, Nick N., et al. “Causal Inference for Multiple Risk Factors and Diseases from Genomics Data.” BioRxiv, 2024, doi:10.1101/2023.12.06.570392. short: N.N. Machnik, S.M. Mahmoudi, M. Borczyk, I. Krätschmer, M.J. Bauer, M.R. Robinson, BioRxiv (2024). corr_author: '1' date_created: 2024-12-11T10:42:59Z date_published: 2024-08-10T00:00:00Z date_updated: 2026-07-16T22:30:22Z day: '10' department: - _id: MaRo doi: 10.1101/2023.12.06.570392 language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ main_file_link: - open_access: '1' url: https://doi.org/10.1101/2023.12.06.570392 month: '08' oa: 1 oa_version: Preprint project: - _id: 9B8D11D6-BA93-11EA-9121-9846C619BF3A grant_number: PCEGP3_181181 name: Improving estimation and prediction of common complex disease risk - _id: bd936e6f-d553-11ed-ba76-a82299f63e8c grant_number: '590359' name: Advanced statistical modelling to facilitate more accurate characterisation of disease phenotypes, improved genetic mapping, and effective therapeutic hypothesis generation publication: bioRxiv publication_status: published related_material: record: - id: '18642' relation: dissertation_contains status: public status: public title: Causal inference for multiple risk factors and diseases from genomics data tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2024' ... --- OA_place: publisher _id: '18661' abstract: - lang: eng text: "Across the tree of life, distinct designs of cellular membranes have evolved that are both stable\r\nand flexible. In bacteria and eukaryotes this trade-off is accomplished by single-headed lipids\r\nthat self-assemble into flexible bilayer membranes. By contrast, archaea in many cases possess\r\nboth bilayer and double-headed, monolayer spanning bolalipids. This composition is believed\r\nto enable extremophile archaea to survive harsh environments. Here, through the creation of a\r\nminimal computational model for bolalipid membranes, we discover trade-offs when forming\r\nmembranes using lipids of a single type. Similar to living archaea, we can tune the stiffness of\r\nbolalipid molecules. We find that membranes made out of flexible bolalipid molecules resemble\r\nbilayer membranes as they can adopt U-shaped conformations to enable higher curvatures.\r\nConversely, rigid bolalipid molecules, like those found in archaea at higher temperatures,\r\npreferentially take on a straight conformation to self-assemble into liquid membranes that are\r\nstable, stiff, prone to pore formation, and which tear during membrane reshaping. Strikingly,\r\nhowever, our analysis reveals that it is possible to achieve the best of both worlds – membranes\r\nthat are fluid, stable at high temperatures and flexible enough to be reshaped without leaking –\r\nthrough the inclusion of a small fraction of bilayer lipids into a bolalipid membrane. Additionally,\r\nthe curvature-dependent softening of bolalipid membranes made of lipids with tension-sensitive\r\nconformation can also enable high rigidity at low curvatures while softening at high curvatures,\r\nmaking the membrane effectively a plastic material. Taken together, our study compares the\r\ndifferent membrane designs across the tree of life and indicates how combining lipids can be\r\nused to resolve trade-offs when generating membranes for (bio)technological applications.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Miguel full_name: Santana de Freitas Amaral, Miguel id: 4f2d02dd-47a9-11ec-ad10-82820ed3f501 last_name: Santana de Freitas Amaral citation: ama: 'Santana de Freitas Amaral M. Archaeal membranes : In silico modelling and design. 2024. doi:10.15479/at:ista:18661' apa: 'Santana de Freitas Amaral, M. (2024). Archaeal membranes : In silico modelling and design. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18661' chicago: 'Santana de Freitas Amaral, Miguel. “Archaeal Membranes : In Silico Modelling and Design.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18661.' ieee: 'M. Santana de Freitas Amaral, “Archaeal membranes : In silico modelling and design,” Institute of Science and Technology Austria, 2024.' ista: 'Santana de Freitas Amaral M. 2024. Archaeal membranes : In silico modelling and design. Institute of Science and Technology Austria.' mla: 'Santana de Freitas Amaral, Miguel. Archaeal Membranes : In Silico Modelling and Design. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18661.' short: 'M. Santana de Freitas Amaral, Archaeal Membranes : In Silico Modelling and Design, Institute of Science and Technology Austria, 2024.' corr_author: '1' date_created: 2024-12-16T10:53:39Z date_published: 2024-12-17T00:00:00Z date_updated: 2026-04-07T13:22:29Z day: '17' ddc: - '572' - '530' degree_awarded: PhD department: - _id: GradSch - _id: AnSa doi: 10.15479/at:ista:18661 file: - access_level: closed checksum: eca06497a29078558395455c890a32d9 content_type: application/zip creator: mamaral date_created: 2024-12-18T12:27:01Z date_updated: 2025-06-18T22:30:03Z embargo_to: open_access file_id: '18671' file_name: 2024_msfa_thesis.zip file_size: 19161387 relation: source_file - access_level: open_access checksum: 2dc30ea46c5daf48d07e4cccb3c3de00 content_type: application/pdf creator: mamaral date_created: 2024-12-18T12:26:30Z date_updated: 2025-06-18T22:30:03Z embargo: 2025-06-18 file_id: '18672' file_name: 2024_msfa_thesis.pdf file_size: 16530084 relation: main_file file_date_updated: 2025-06-18T22:30:03Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-sa/4.0/ month: '12' oa: 1 oa_version: Published Version page: '57' publication_identifier: isbn: - 978-3-99078-046-6 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18670' relation: part_of_dissertation status: public status: public supervisor: - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 title: 'Archaeal membranes : In silico modelling and design' tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: repository _id: '18670' abstract: - lang: eng text: Across the tree of life, distinct designs of cellular membranes have evolved. In bacteria and eukaryotes single-headed lipids self-assemble into flexible bilayer membranes. By contrast, archaea often possess double-headed, monolayer spanning bolalipids, mixed with bilayer lipids, enabling them to survive in harsh environments. Here, using a minimal computational model for bolalipid membranes, we discover trade-offs when forming membranes. We find that membranes made out of flexible bolalipids resemble bilayer membranes as bolalipids exhibit conformational switch into U-shaped conformations to enable higher curvatures. Conversely, stiffer bolalipids, resembling those in extremophile archaea, take on straight conformations and form liquid membranes that are stiff, and prone to pore formation during membrane reshaping. Strikingly, we show how to achieve fluid bolalipid membranes that are both stable and flexible – by including small amounts of bilayer lipids, as archaea do. Our study explains how different organisms resolve trade-offs when generating membranes of desired material properties. acknowledgement: "MA, BB, and AŠ acknowledge funding by the\r\nVolkswagen Foundation Grant Az 96727. FF\r\nacknowledges fnancial support by the NOMIS\r\nfoundation. AŠ acknowledges funding by ERC\r\nStarting Grant “NEPA” 802960. We thank\r\nClaudia Flandoli for help with illustrations." article_processing_charge: No author: - first_name: Miguel full_name: Santana de Freitas Amaral, Miguel id: 4f2d02dd-47a9-11ec-ad10-82820ed3f501 last_name: Santana de Freitas Amaral - first_name: Felix F full_name: Frey, Felix F id: a0270b37-8f1a-11ec-95c7-8e710c59a4f3 last_name: Frey orcid: 0000-0001-8501-6017 - first_name: Xiuyun full_name: Jiang, Xiuyun last_name: Jiang - first_name: Buzz full_name: Baum, Buzz last_name: Baum - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 citation: ama: 'Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability vs flexibility: Reshaping archaeal membranes in silico. bioRxiv. doi:10.1101/2024.10.18.619072' apa: 'Santana de Freitas Amaral, M., Frey, F. F., Jiang, X., Baum, B., & Šarić, A. (n.d.). Stability vs flexibility: Reshaping archaeal membranes in silico. bioRxiv. https://doi.org/10.1101/2024.10.18.619072' chicago: 'Santana de Freitas Amaral, Miguel, Felix F Frey, Xiuyun Jiang, Buzz Baum, and Anđela Šarić. “Stability vs Flexibility: Reshaping Archaeal Membranes in Silico.” BioRxiv, n.d. https://doi.org/10.1101/2024.10.18.619072.' ieee: 'M. Santana de Freitas Amaral, F. F. Frey, X. Jiang, B. Baum, and A. Šarić, “Stability vs flexibility: Reshaping archaeal membranes in silico,” bioRxiv. .' ista: 'Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability vs flexibility: Reshaping archaeal membranes in silico. bioRxiv, 10.1101/2024.10.18.619072.' mla: 'Santana de Freitas Amaral, Miguel, et al. “Stability vs Flexibility: Reshaping Archaeal Membranes in Silico.” BioRxiv, doi:10.1101/2024.10.18.619072.' short: M. Santana de Freitas Amaral, F.F. Frey, X. Jiang, B. Baum, A. Šarić, BioRxiv (n.d.). corr_author: '1' date_created: 2024-12-18T10:07:45Z date_published: 2024-11-27T00:00:00Z date_updated: 2026-07-16T22:30:24Z day: '27' department: - _id: AnSa doi: 10.1101/2024.10.18.619072 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2024.10.18.619072 month: '11' oa: 1 oa_version: Preprint project: - _id: eba2549b-77a9-11ec-83b8-a81e493eae4e call_identifier: H2020 grant_number: '802960' name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines' publication: bioRxiv publication_status: draft related_material: record: - id: '18661' relation: dissertation_contains status: public status: public title: 'Stability vs flexibility: Reshaping archaeal membranes in silico' tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- APC_amount: 5887,8 EUR OA_place: publisher OA_type: hybrid _id: '15084' abstract: - lang: eng text: "GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles (SVs) at the presynaptic active zone (AZ). Strikingly, the depressing phasic release exhibits looser coupling distance than the tonic release. Furthermore, the tonic and phasic release are selectively affected by deletion of synaptoporin (SPO) and Ca\r\n 2+\r\n -dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. The cytosolic protein CAPS2 showed a SV-associated distribution similar to the vesicular transmembrane protein SPO, and they were colocalized in the same terminals. We developed the “Flash and Freeze-fracture” method, and revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to persistency of the RRP increase. Thus, we identified structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals." acknowledged_ssus: - _id: M-Shop - _id: PreCl - _id: EM-Fac acknowledgement: We thank Erwin Neher and Ipe Ninan for critical comments on the manuscript. This project has received funding from the European Research Council (ERC) and European Commission, under the European Union’s Horizon 2020 research and innovation program (ERC grant agreement no. 694539 to R.S. and the Marie Skłodowska-Curie grant agreement no. 665385 to C.Ö.). This study was supported by the Cooperative Study Program of Center for Animal Resources and Collaborative Study of NINS. We thank Kohgaku Eguchi for statistical analysis, Yu Kasugai for additional EM imaging, Robert Beattie for the design of the slice recovery chamber for Flash and Freeze experiments, Todor Asenov from the ISTA machine shop for custom part preparations for high-pressure freezing, the ISTA preclinical facility for animal caretaking, and the ISTA EM facilities for technical support. article_number: e2301449121 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Peter full_name: Koppensteiner, Peter id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87 last_name: Koppensteiner orcid: 0000-0002-3509-1948 - first_name: Pradeep full_name: Bhandari, Pradeep id: 45EDD1BC-F248-11E8-B48F-1D18A9856A87 last_name: Bhandari orcid: 0000-0003-0863-4481 - first_name: Hüseyin C full_name: Önal, Hüseyin C id: 4659D740-F248-11E8-B48F-1D18A9856A87 last_name: Önal orcid: 0000-0002-2771-2011 - first_name: Carolina full_name: Borges Merjane, Carolina id: 4305C450-F248-11E8-B48F-1D18A9856A87 last_name: Borges Merjane orcid: 0000-0003-0005-401X - first_name: Elodie full_name: Le Monnier, Elodie id: 3B59276A-F248-11E8-B48F-1D18A9856A87 last_name: Le Monnier - first_name: Utsa full_name: Roy, Utsa id: 4d26cf11-5355-11ee-ae5a-eb05e255b9b2 last_name: Roy - first_name: Yukihiro full_name: Nakamura, Yukihiro last_name: Nakamura - first_name: Tetsushi full_name: Sadakata, Tetsushi last_name: Sadakata - first_name: Makoto full_name: Sanbo, Makoto last_name: Sanbo - first_name: Masumi full_name: Hirabayashi, Masumi last_name: Hirabayashi - first_name: JeongSeop full_name: Rhee, JeongSeop last_name: Rhee - first_name: Nils full_name: Brose, Nils last_name: Brose - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 citation: ama: Koppensteiner P, Bhandari P, Önal C, et al. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(8). doi:10.1073/pnas.2301449121 apa: Koppensteiner, P., Bhandari, P., Önal, C., Borges Merjane, C., Le Monnier, E., Roy, U., … Shigemoto, R. (2024). GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2301449121 chicago: Koppensteiner, Peter, Pradeep Bhandari, Cihan Önal, Carolina Borges Merjane, Elodie Le Monnier, Utsa Roy, Yukihiro Nakamura, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2301449121. ieee: P. Koppensteiner et al., “GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 8. National Academy of Sciences, 2024. ista: Koppensteiner P, Bhandari P, Önal C, Borges Merjane C, Le Monnier E, Roy U, Nakamura Y, Sadakata T, Sanbo M, Hirabayashi M, Rhee J, Brose N, Jonas PM, Shigemoto R. 2024. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences of the United States of America. 121(8), e2301449121. mla: Koppensteiner, Peter, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 8, e2301449121, National Academy of Sciences, 2024, doi:10.1073/pnas.2301449121. short: P. Koppensteiner, P. Bhandari, C. Önal, C. Borges Merjane, E. Le Monnier, U. Roy, Y. Nakamura, T. Sadakata, M. Sanbo, M. Hirabayashi, J. Rhee, N. Brose, P.M. Jonas, R. Shigemoto, Proceedings of the National Academy of Sciences of the United States of America 121 (2024). corr_author: '1' date_created: 2024-03-05T09:23:55Z date_published: 2024-02-20T00:00:00Z date_updated: 2026-07-16T22:30:25Z day: '20' ddc: - '570' department: - _id: RySh - _id: PeJo doi: 10.1073/pnas.2301449121 ec_funded: 1 external_id: isi: - '001208567300006' pmid: - '38346189' file: - access_level: open_access checksum: b25b2a057c266ff317a48b0d54d6fc8a content_type: application/pdf creator: dernst date_created: 2024-03-12T13:42:42Z date_updated: 2024-03-12T13:42:42Z file_id: '15110' file_name: 2024_PNAS_Koppensteiner.pdf file_size: 13648221 relation: main_file success: 1 file_date_updated: 2024-03-12T13:42:42Z has_accepted_license: '1' intvolume: ' 121' isi: 1 issue: '8' language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25CA28EA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694539' name: 'In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour' - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: link: - description: News on ISTA Website relation: press_release url: https://ista.ac.at/en/news/neuronal-insights-flash-and-freeze-fracture/ record: - id: '13173' relation: research_data status: public - id: '19271' relation: dissertation_contains status: public scopus_import: '1' status: public title: GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 121 year: '2024' ... --- APC_amount: 3782,54 DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '17183' abstract: - lang: eng text: "The photon blockade breakdown in a continuously driven cavity QED system has been proposed as a prime example for a first-order driven-dissipative quantum phase transition. However, the predicted scaling from a microscopic behavior—dominated by quantum fluctuations—to a macroscopic one—characterized by stable phases—and the associated exponents and phase diagram have not been observed so far. In this work we couple a single transmon qubit with a fixed coupling strength \U0001D454 to a superconducting cavity that is in situ bandwidth \U0001D705 tunable to controllably approach this thermodynamic limit. Even though the system remains microscopic, we observe its behavior becoming increasingly macroscopic as a function of \U0001D454/\U0001D705. For the highest realized \U0001D454/\U0001D705 of approximately 287, the system switches with a characteristic timescale as long as 6 s between a bright coherent state with approximately 8×103 intracavity photons and the vacuum state. This exceeds the microscopic timescales by 6 orders of magnitude and approaches the perfect hysteresis expected between two macroscopic attractors in the thermodynamic limit. These findings and interpretation are qualitatively supported by neoclassical theory and large-scale quantum-jump Monte Carlo simulations. Besides shedding more light on driven-dissipative physics in the limit of strong light-matter coupling, this system might also find applications in quantum sensing and metrology." acknowledged_ssus: - _id: M-Shop acknowledgement: This work has received funding from the Austrian Science Fund (FWF) through BeyondC (F7105) and the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 862644 (FETopen QUARTET). A.V. acknowledges support from the National Research, Development and Innovation Office of Hungary (NKFIH) within the Quantum Information National Laboratory of Hungary. The authors thank the MIBA workshop and the Institute of Science and Technology Austria nanofabrication facility for technical support. We are grateful to HUN-REN Cloud for providing us with suitable computational infrastructure for the simulations. article_number: '010327' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Riya full_name: Sett, Riya id: 2E6D040E-F248-11E8-B48F-1D18A9856A87 last_name: Sett orcid: 0000-0001-7641-8348 - first_name: Farid full_name: Hassani, Farid id: 2AED110C-F248-11E8-B48F-1D18A9856A87 last_name: Hassani orcid: 0000-0001-6937-5773 - first_name: Duc T full_name: Phan, Duc T id: 29C8C0B4-F248-11E8-B48F-1D18A9856A87 last_name: Phan - first_name: Shabir full_name: Barzanjeh, Shabir id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87 last_name: Barzanjeh orcid: 0000-0003-0415-1423 - first_name: Andras full_name: Vukics, Andras last_name: Vukics - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. Emergent macroscopic bistability induced by a single superconducting qubit. PRX Quantum. 2024;5(1). doi:10.1103/prxquantum.5.010327 apa: Sett, R., Hassani, F., Phan, D. T., Barzanjeh, S., Vukics, A., & Fink, J. M. (2024). Emergent macroscopic bistability induced by a single superconducting qubit. PRX Quantum. American Physical Society. https://doi.org/10.1103/prxquantum.5.010327 chicago: Sett, Riya, Farid Hassani, Duc T Phan, Shabir Barzanjeh, Andras Vukics, and Johannes M Fink. “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” PRX Quantum. American Physical Society, 2024. https://doi.org/10.1103/prxquantum.5.010327. ieee: R. Sett, F. Hassani, D. T. Phan, S. Barzanjeh, A. Vukics, and J. M. Fink, “Emergent macroscopic bistability induced by a single superconducting qubit,” PRX Quantum, vol. 5, no. 1. American Physical Society, 2024. ista: Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. 2024. Emergent macroscopic bistability induced by a single superconducting qubit. PRX Quantum. 5(1), 010327. mla: Sett, Riya, et al. “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” PRX Quantum, vol. 5, no. 1, 010327, American Physical Society, 2024, doi:10.1103/prxquantum.5.010327. short: R. Sett, F. Hassani, D.T. Phan, S. Barzanjeh, A. Vukics, J.M. Fink, PRX Quantum 5 (2024). corr_author: '1' date_created: 2024-06-27T10:58:06Z date_published: 2024-02-16T00:00:00Z date_updated: 2026-07-16T22:30:27Z day: '16' ddc: - '530' department: - _id: JoFi - _id: AnHi doi: 10.1103/prxquantum.5.010327 ec_funded: 1 external_id: arxiv: - '2210.14182' isi: - '001171652500001' file: - access_level: open_access checksum: 0833880d47f74ad1deda93a1d8ffa5a7 content_type: application/pdf creator: cchlebak date_created: 2024-06-28T12:04:43Z date_updated: 2024-06-28T12:04:43Z file_id: '17185' file_name: 2024_PRXQuantum_Sett.pdf file_size: 1443351 relation: main_file success: 1 file_date_updated: 2024-06-28T12:04:43Z has_accepted_license: '1' intvolume: ' 5' isi: 1 issue: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version project: - _id: 237CBA6C-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '862644' name: Quantum readout techniques and technologies - _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1 call_identifier: FWF name: FWF Open Access Fund - _id: bdb108fd-d553-11ed-ba76-83dc74a9864f grant_number: F07105 name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits publication: PRX Quantum publication_identifier: eissn: - 2691-3399 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '18978' relation: research_data status: public - id: '19533' relation: dissertation_contains status: public scopus_import: '1' status: public title: Emergent macroscopic bistability induced by a single superconducting qubit tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2024' ... --- OA_place: repository OA_type: gold _id: '18978' abstract: - lang: eng text: "Data analysis files for the manuscript \"Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit\".\r\n\r\nThis contains the raw data and the data analysis files for generating the figures in the manuscript.\r\n\r\n Figure1 file - The raw data of cavity transmission spectra for 6 different kappas are there. They are fitted with input-output theory in the python file.\r\n Figure2 file - The raw data at 8 MHz kappa are included. all hte figures in figure 2 are generated in the python file\r\n Figure3 file - The raw data of PBB single shot measurements at all kappas are included. The detailed analysis and the Figure3 generated for the paper are all in the python analysis file. Also, thefiles containing the time-evolution of the intensity from Master Equation solution are included.\r\nFigure4 file - The raw data at 2.6 MHz for different drive detunings and the corresponding analyses are included. And the python file includes the analysis of the experimental data as well as approximate neoclassical equations solutions for 2-level and 3-level transmons are included. " article_processing_charge: No author: - first_name: Riya full_name: Sett, Riya id: 2E6D040E-F248-11E8-B48F-1D18A9856A87 last_name: Sett orcid: 0000-0001-7641-8348 - first_name: Farid full_name: Hassani, Farid id: 2AED110C-F248-11E8-B48F-1D18A9856A87 last_name: Hassani orcid: 0000-0001-6937-5773 - first_name: Duc T full_name: Phan, Duc T id: 29C8C0B4-F248-11E8-B48F-1D18A9856A87 last_name: Phan - first_name: Shabir full_name: Barzanjeh, Shabir id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87 last_name: Barzanjeh orcid: 0000-0003-0415-1423 - first_name: Andras full_name: Vukics, Andras last_name: Vukics - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. Data Analysis files for “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” 2024. doi:10.5281/ZENODO.10518320 apa: Sett, R., Hassani, F., Phan, D. T., Barzanjeh, S., Vukics, A., & Fink, J. M. (2024). Data Analysis files for “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” Zenodo. https://doi.org/10.5281/ZENODO.10518320 chicago: Sett, Riya, Farid Hassani, Duc T Phan, Shabir Barzanjeh, Andras Vukics, and Johannes M Fink. “Data Analysis Files for ‘Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.’” Zenodo, 2024. https://doi.org/10.5281/ZENODO.10518320. ieee: R. Sett, F. Hassani, D. T. Phan, S. Barzanjeh, A. Vukics, and J. M. Fink, “Data Analysis files for ‘Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.’” Zenodo, 2024. ista: Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. 2024. Data Analysis files for ‘Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit’, Zenodo, 10.5281/ZENODO.10518320. mla: Sett, Riya, et al. Data Analysis Files for “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” Zenodo, 2024, doi:10.5281/ZENODO.10518320. short: R. Sett, F. Hassani, D.T. Phan, S. Barzanjeh, A. Vukics, J.M. Fink, (2024). corr_author: '1' date_created: 2025-01-30T08:30:03Z date_published: 2024-01-16T00:00:00Z date_updated: 2026-07-16T22:30:27Z day: '16' ddc: - '530' department: - _id: JoFi - _id: AnHi doi: 10.5281/ZENODO.10518320 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.10518320 month: '01' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '17183' relation: used_in_publication status: public - id: '19533' relation: used_in_publication status: public status: public title: Data Analysis files for "Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit" tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '17148' abstract: - lang: eng text: During neural tube (NT) development, the notochord induces an organizer, the floorplate, which secretes Sonic Hedgehog (SHH) to pattern neural progenitors. Conversely, NT organoids (NTOs) from embryonic stem cells (ESCs) spontaneously form floorplates without the notochord, demonstrating that stem cells can self-organize without embryonic inducers. Here, we investigated floorplate self-organization in clonal mouse NTOs. Expression of the floorplate marker FOXA2 was initially spatially scattered before resolving into multiple clusters, which underwent competition and sorting, resulting in a stable “winning” floorplate. We identified that BMP signaling governed long-range cluster competition. FOXA2+ clusters expressed BMP4, suppressing FOXA2 in receiving cells while simultaneously expressing the BMP-inhibitor NOGGIN, promoting cluster persistence. Noggin mutation perturbed floorplate formation in NTOs and in the NT in vivo at mid/hindbrain regions, demonstrating how the floorplate can form autonomously without the notochord. Identifying the pathways governing organizer self-organization is critical for harnessing the developmental plasticity of stem cells in tissue engineering. acknowledgement: We thank P. Pasierbek, A.C. Moreno, T. Lendl, and K. Aumayr for microscopy support; G. Schmauss for FACS support; M. Novatchkova for assistance with Bioinformatic analyses; J. Ahel, A. Polikarpova, S. Horer, E. Cesare, and E. Norouzi for technical assistance; A. Meinhardt for supervision; DRESDEN-concept Genome Center, A. Vogt, A. Sommer, and the Vienna BioCenter NGS facility for RNA sequencing. We are grateful to M. Placzek and E. Martí for discussions about the floorplate; to S. Shvartsman for valuable input; to A. Aszodi, W. Masselink, and S. Raiders for advice on statistical analyses; to J. Cornwall Scoones, G. Martello, and Tanaka lab members for critical reading of the manuscript; E. Bassat and E. Chatzidaki for contributing schematics; and to K. Lust for support. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement ERC AdG 742046) to E.M.T. This research was funded in whole or in part by the Austrian Science Fund (FWF) (10.55776/F7803-B) (Stem Cell Modulation) to E.M.T. and A.K., Sir Henry Wellcome postdoctoral fellowship to H.T.S., ELBE fellowship to K.I., and National Science Foundation (US) Phy 2013131 to E.S. The A.K. lab is also supported by ISTA and the European Research Council under Horizon Europe grant 101044579, and S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011. This work was supported in part by the Francis Crick Institute, which receives its core funding from Cancer Research UK (CC001051), the UK Medical Research Council (CC001051), and the Wellcome Trust (CC001051). For the purpose of open access, the authors have applied a CC BY public copyright license to any author accepted manuscript (AAM) version arising from this submission. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Teresa full_name: Krammer, Teresa last_name: Krammer - first_name: Hannah T. full_name: Stuart, Hannah T. last_name: Stuart - first_name: Elena full_name: Gromberg, Elena last_name: Gromberg - first_name: Keisuke full_name: Ishihara, Keisuke last_name: Ishihara - first_name: Dillon full_name: Cislo, Dillon last_name: Cislo - first_name: Manuela full_name: Melchionda, Manuela last_name: Melchionda - first_name: Fernando full_name: Becerril Perez, Fernando last_name: Becerril Perez - first_name: Jingkui full_name: Wang, Jingkui last_name: Wang - first_name: Elena full_name: Costantini, Elena last_name: Costantini - first_name: Stefanie full_name: Rus, Stefanie id: 4D9EC9B6-F248-11E8-B48F-1D18A9856A87 last_name: Rus orcid: 0000-0001-8703-1093 - first_name: Laura full_name: Arbanas, Laura last_name: Arbanas - first_name: Alexandra full_name: Hörmann, Alexandra last_name: Hörmann - first_name: Ralph A. full_name: Neumüller, Ralph A. last_name: Neumüller - first_name: Nicola full_name: Elvassore, Nicola last_name: Elvassore - first_name: Eric full_name: Siggia, Eric last_name: Siggia - first_name: James full_name: Briscoe, James last_name: Briscoe - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: Elly M. full_name: Tanaka, Elly M. last_name: Tanaka citation: ama: Krammer T, Stuart HT, Gromberg E, et al. Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. Developmental Cell. 2024;59(15):1940-1953.e10. doi:10.1016/j.devcel.2024.04.021 apa: Krammer, T., Stuart, H. T., Gromberg, E., Ishihara, K., Cislo, D., Melchionda, M., … Tanaka, E. M. (2024). Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2024.04.021 chicago: Krammer, Teresa, Hannah T. Stuart, Elena Gromberg, Keisuke Ishihara, Dillon Cislo, Manuela Melchionda, Fernando Becerril Perez, et al. “Mouse Neural Tube Organoids Self-Organize Floorplate through BMP-Mediated Cluster Competition.” Developmental Cell. Elsevier, 2024. https://doi.org/10.1016/j.devcel.2024.04.021. ieee: T. Krammer et al., “Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition,” Developmental Cell, vol. 59, no. 15. Elsevier, p. 1940–1953.e10, 2024. ista: Krammer T, Stuart HT, Gromberg E, Ishihara K, Cislo D, Melchionda M, Becerril Perez F, Wang J, Costantini E, Rus S, Arbanas L, Hörmann A, Neumüller RA, Elvassore N, Siggia E, Briscoe J, Kicheva A, Tanaka EM. 2024. Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. Developmental Cell. 59(15), 1940–1953.e10. mla: Krammer, Teresa, et al. “Mouse Neural Tube Organoids Self-Organize Floorplate through BMP-Mediated Cluster Competition.” Developmental Cell, vol. 59, no. 15, Elsevier, 2024, p. 1940–1953.e10, doi:10.1016/j.devcel.2024.04.021. short: T. Krammer, H.T. Stuart, E. Gromberg, K. Ishihara, D. Cislo, M. Melchionda, F. Becerril Perez, J. Wang, E. Costantini, S. Rus, L. Arbanas, A. Hörmann, R.A. Neumüller, N. Elvassore, E. Siggia, J. Briscoe, A. Kicheva, E.M. Tanaka, Developmental Cell 59 (2024) 1940–1953.e10. date_created: 2024-06-16T22:01:07Z date_published: 2024-08-01T00:00:00Z date_updated: 2026-07-16T22:30:29Z day: '01' ddc: - '570' department: - _id: AnKi doi: 10.1016/j.devcel.2024.04.021 external_id: isi: - '001289684800001' pmid: - '38776925' file: - access_level: open_access checksum: fefdea9c02862b4bb74de49b65ce638a content_type: application/pdf creator: dernst date_created: 2025-01-13T10:59:12Z date_updated: 2025-01-13T10:59:12Z file_id: '18841' file_name: 2024_DevelopmentalCell_Krammer.pdf file_size: 6249076 relation: main_file success: 1 file_date_updated: 2025-01-13T10:59:12Z has_accepted_license: '1' intvolume: ' 59' isi: 1 issue: '15' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 1940-1953.e10 pmid: 1 project: - _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa grant_number: '101044579' name: Mechanisms of tissue size regulation in spinal cord development - _id: 9B9B39FA-BA93-11EA-9121-9846C619BF3A grant_number: SC19-011 name: The regulatory logic of pattern formation in the vertebrate dorsal neural tube publication: Developmental Cell publication_identifier: eissn: - 1878-1551 issn: - 1534-5807 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '19763' relation: dissertation_contains status: public scopus_import: '1' status: public title: Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 59 year: '2024' ... --- APC_amount: 804 EUR DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18601' abstract: - lang: eng text: "Geometrically controlled stem cell differentiation promotes reproducible pattern formation. Here, we present a protocol to fabricate elastomeric stencils for patterned stem cell differentiation. We describe procedures for using photolithography to produce molds, followed by molding polydimethylsiloxane (PDMS) to obtain stencils with through holes. We then provide instructions for culturing cells on stencils and, finally, removing stencils to allow colony growth and cell migration. This approach yields reproducible two-dimensional organoids tailored for quantitative studies of growth and pattern formation.\r\nFor complete details on the use and execution of this protocol, please refer to Lehr et al.1" acknowledged_ssus: - _id: NanoFab acknowledgement: We thank the nanofabrication facility at ISTA for technical assistance. Work in the A.K. lab is supported by ISTA, the European Research Council under Horizon Europe (grant 101044579), and the Austrian Science Fund (FWF) (grant https://doi.org/10.55776/F78). S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011. article_number: '103187' article_processing_charge: Yes article_type: original author: - first_name: Stefanie full_name: Rus, Stefanie id: 4D9EC9B6-F248-11E8-B48F-1D18A9856A87 last_name: Rus orcid: 0000-0001-8703-1093 - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Monika Aleksandra full_name: Kulig, Monika Aleksandra id: 3331f5ae-e896-11ec-af79-eeb79769bcb7 last_name: Kulig - first_name: Thomas full_name: Minchington, Thomas id: 7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f last_name: Minchington - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 citation: ama: Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. STAR Protocols. 2024;5(4). doi:10.1016/j.xpro.2024.103187 apa: Rus, S., Merrin, J., Kulig, M. A., Minchington, T., & Kicheva, A. (2024). Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2024.103187 chicago: Rus, Stefanie, Jack Merrin, Monika Aleksandra Kulig, Thomas Minchington, and Anna Kicheva. “Protocol for Fabricating Elastomeric Stencils for Patterned Stem Cell Differentiation.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2024.103187. ieee: S. Rus, J. Merrin, M. A. Kulig, T. Minchington, and A. Kicheva, “Protocol for fabricating elastomeric stencils for patterned stem cell differentiation,” STAR Protocols, vol. 5, no. 4. Elsevier, 2024. ista: Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. 2024. Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. STAR Protocols. 5(4), 103187. mla: Rus, Stefanie, et al. “Protocol for Fabricating Elastomeric Stencils for Patterned Stem Cell Differentiation.” STAR Protocols, vol. 5, no. 4, 103187, Elsevier, 2024, doi:10.1016/j.xpro.2024.103187. short: S. Rus, J. Merrin, M.A. Kulig, T. Minchington, A. Kicheva, STAR Protocols 5 (2024). corr_author: '1' date_created: 2024-12-01T23:01:53Z date_published: 2024-12-20T00:00:00Z date_updated: 2026-07-16T22:30:29Z day: '20' ddc: - '570' department: - _id: AnKi - _id: NanoFab doi: 10.1016/j.xpro.2024.103187 external_id: pmid: - '39602310' file: - access_level: open_access checksum: 0c61a6f9978608a103865905e06f4581 content_type: application/pdf creator: dernst date_created: 2024-12-03T10:53:23Z date_updated: 2024-12-03T10:53:23Z file_id: '18610' file_name: 2024_STARProtoc_Lehr.pdf file_size: 4989169 relation: main_file success: 1 file_date_updated: 2024-12-03T10:53:23Z has_accepted_license: '1' intvolume: ' 5' issue: '4' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa grant_number: '101044579' name: Mechanisms of tissue size regulation in spinal cord development - _id: 9B9B39FA-BA93-11EA-9121-9846C619BF3A grant_number: SC19-011 name: The regulatory logic of pattern formation in the vertebrate dorsal neural tube publication: STAR Protocols publication_identifier: eissn: - 2666-1667 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '19763' relation: dissertation_contains status: public scopus_import: '1' status: public title: Protocol for fabricating elastomeric stencils for patterned stem cell differentiation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2024' ... --- OA_place: repository OA_type: green _id: '14796' abstract: - lang: eng text: Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer–specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer–specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step. acknowledgement: "We thank J. Galindo, M. Montaño-Rendón, N. Mikhailova, A. Blakeslee, E. Arnason, and P. Kemppainen for providing samples; R. Turney, G. Sotelo, J. Larsson, T. Broquet, and S. Loisel for help collecting samples; Science Animated for providing the snail cartoons shown in Fig. 1; M. Dunning for help in developing bioinformatic pipelines; R. Faria, H. Morales, and V. Sousa for advice; and M. Hahn, J. Slate, M. Ravinet, J. Raeymaekers, A. Comeault, and N. Barton for feedback on a draft manuscript.\r\nThis work was supported by the Natural Environment Research Council (grant NE/P001610/1 to R.K.B.), the European Research Council (grant ERC-2015-AdG693030-BARRIERS to R.K.B.), the Norwegian Research Council (RCN Project 315287 to A.M.W.), and the Swedish Research Council (grant 2020-05385 to E.L.)." article_processing_charge: No article_type: original author: - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski - first_name: Zuzanna B. full_name: Zagrodzka, Zuzanna B. last_name: Zagrodzka - first_name: Martin D. full_name: Garlovsky, Martin D. last_name: Garlovsky - first_name: Arka full_name: Pal, Arka id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425 last_name: Pal orcid: 0000-0002-4530-8469 - first_name: Daria full_name: Shipilina, Daria id: 428A94B0-F248-11E8-B48F-1D18A9856A87 last_name: Shipilina orcid: 0000-0002-1145-9226 - first_name: Diego Fernando full_name: Garcia Castillo, Diego Fernando id: ae681a14-dc74-11ea-a0a7-c6ef18161701 last_name: Garcia Castillo - first_name: Hila full_name: Lifchitz, Hila id: d6ab5470-2fb3-11ed-8633-986a9b84edac last_name: Lifchitz - first_name: Alan full_name: Le Moan, Alan last_name: Le Moan - first_name: Erica full_name: Leder, Erica last_name: Leder - first_name: James full_name: Reeve, James last_name: Reeve - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin citation: ama: Stankowski S, Zagrodzka ZB, Garlovsky MD, et al. The genetic basis of a recent transition to live-bearing in marine snails. Science. 2024;383(6678):114-119. doi:10.1126/science.adi2982 apa: Stankowski, S., Zagrodzka, Z. B., Garlovsky, M. D., Pal, A., Shipilina, D., Garcia Castillo, D. F., … Butlin, R. K. (2024). The genetic basis of a recent transition to live-bearing in marine snails. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adi2982 chicago: Stankowski, Sean, Zuzanna B. Zagrodzka, Martin D. Garlovsky, Arka Pal, Daria Shipilina, Diego Fernando Garcia Castillo, Hila Lifchitz, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” Science. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/science.adi2982. ieee: S. Stankowski et al., “The genetic basis of a recent transition to live-bearing in marine snails,” Science, vol. 383, no. 6678. American Association for the Advancement of Science, pp. 114–119, 2024. ista: Stankowski S, Zagrodzka ZB, Garlovsky MD, Pal A, Shipilina D, Garcia Castillo DF, Lifchitz H, Le Moan A, Leder E, Reeve J, Johannesson K, Westram AM, Butlin RK. 2024. The genetic basis of a recent transition to live-bearing in marine snails. Science. 383(6678), 114–119. mla: Stankowski, Sean, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” Science, vol. 383, no. 6678, American Association for the Advancement of Science, 2024, pp. 114–19, doi:10.1126/science.adi2982. short: S. Stankowski, Z.B. Zagrodzka, M.D. Garlovsky, A. Pal, D. Shipilina, D.F. Garcia Castillo, H. Lifchitz, A. Le Moan, E. Leder, J. Reeve, K. Johannesson, A.M. Westram, R.K. Butlin, Science 383 (2024) 114–119. corr_author: '1' date_created: 2024-01-14T23:00:56Z date_published: 2024-01-05T00:00:00Z date_updated: 2026-07-16T22:30:38Z day: '05' department: - _id: NiBa - _id: GradSch doi: 10.1126/science.adi2982 external_id: isi: - '001138156400003' pmid: - '38175895' intvolume: ' 383' isi: 1 issue: '6678' language: - iso: eng main_file_link: - open_access: '1' url: https://figshare.com/articles/journal_contribution/The_genetic_basis_of_a_recent_transition_to_live-bearing_in_marine_snails/26356054?file=47868241 month: '01' oa: 1 oa_version: Submitted Version page: 114-119 pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' related_material: link: - description: News on ISTA Website relation: press_release url: https://ista.ac.at/en/news/the-snail-or-the-egg/ record: - id: '14812' relation: research_data status: public - id: '20694' relation: dissertation_contains status: public scopus_import: '1' status: public title: The genetic basis of a recent transition to live-bearing in marine snails type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 383 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18706' abstract: - lang: eng text: "We prove discrete-to-continuum convergence for dynamical optimal transport on Zd\r\n -periodic graphs with cost functional having linear growth at infinity. This result provides an answer to a problem left open by Gladbach, Kopfer, Maas, and Portinale (Calc Var Partial Differential Equations 62(5), 2023), where the convergence behaviour of discrete boundary-value dynamical transport problems is proved under the stronger assumption of superlinear growth. Our result extends the known literature to some important classes of examples, such as scaling limits of 1 -Wasserstein transport problems. Similarly to what happens in the quadratic case, the geometry of the graph plays a crucial role in the structure of the limit cost function, as we discuss in the final part of this work, which includes some visual representations." acknowledgement: L.P. gratefully acknowledges fundings from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – GZ 2047/1, Projekt-ID 390685813. F.Q. gratefully acknowledges support from the Austrian Science Fund (FWF) project 10.55776/F65. article_processing_charge: Yes article_type: original author: - first_name: Lorenzo full_name: Portinale, Lorenzo id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87 last_name: Portinale - first_name: Filippo full_name: Quattrocchi, Filippo id: 3ebd6ba8-edfb-11eb-afb5-91a9745ba308 last_name: Quattrocchi orcid: 0009-0000-9773-1931 citation: ama: Portinale L, Quattrocchi F. Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. European Journal of Applied Mathematics. 2024:1-29. doi:10.1017/s0956792524000810 apa: Portinale, L., & Quattrocchi, F. (2024). Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. European Journal of Applied Mathematics. Cambridge University Press. https://doi.org/10.1017/s0956792524000810 chicago: Portinale, Lorenzo, and Filippo Quattrocchi. “Discrete-to-Continuum Limits of Optimal Transport with Linear Growth on Periodic Graphs.” European Journal of Applied Mathematics. Cambridge University Press, 2024. https://doi.org/10.1017/s0956792524000810. ieee: L. Portinale and F. Quattrocchi, “Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs,” European Journal of Applied Mathematics. Cambridge University Press, pp. 1–29, 2024. ista: Portinale L, Quattrocchi F. 2024. Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. European Journal of Applied Mathematics., 1–29. mla: Portinale, Lorenzo, and Filippo Quattrocchi. “Discrete-to-Continuum Limits of Optimal Transport with Linear Growth on Periodic Graphs.” European Journal of Applied Mathematics, Cambridge University Press, 2024, pp. 1–29, doi:10.1017/s0956792524000810. short: L. Portinale, F. Quattrocchi, European Journal of Applied Mathematics (2024) 1–29. date_created: 2024-12-23T11:03:59Z date_published: 2024-12-20T00:00:00Z date_updated: 2026-07-16T22:30:39Z day: '20' ddc: - '500' department: - _id: GradSch - _id: JaMa doi: 10.1017/s0956792524000810 external_id: isi: - '001381435800001' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1017/S0956792524000810 month: '12' oa: 1 oa_version: Published Version page: 1-29 project: - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems publication: European Journal of Applied Mathematics publication_identifier: eissn: - 1469-4425 issn: - 0956-7925 publication_status: epub_ahead publisher: Cambridge University Press quality_controlled: '1' related_material: record: - id: '20563' relation: dissertation_contains status: public scopus_import: '1' status: public title: Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ...