--- _id: '9794' abstract: - lang: eng text: 'Lymph nodes (LNs) comprise two main structural elements: fibroblastic reticular cells that form dedicated niches for immune cell interaction and capsular fibroblasts that build a shell around the organ. Immunological challenge causes LNs to increase more than tenfold in size within a few days. Here, we characterized the biomechanics of LN swelling on the cellular and organ scale. We identified lymphocyte trapping by influx and proliferation as drivers of an outward pressure force, causing fibroblastic reticular cells of the T-zone (TRCs) and their associated conduits to stretch. After an initial phase of relaxation, TRCs sensed the resulting strain through cell matrix adhesions, which coordinated local growth and remodeling of the stromal network. While the expanded TRC network readopted its typical configuration, a massive fibrotic reaction of the organ capsule set in and countered further organ expansion. Thus, different fibroblast populations mechanically control LN swelling in a multitier fashion.' acknowledged_ssus: - _id: Bio - _id: EM-Fac - _id: PreCl - _id: LifeSc acknowledgement: This research was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging and Optics, Electron Microscopy, Preclinical and Life Science Facilities. We thank C. Moussion for providing anti-PNAd antibody and D. Critchley for Talin1-floxed mice, and E. Papusheva for providing a custom 3D channel alignment script. This work was supported by a European Research Council grant ERC-CoG-72437 to M.S. M.H. was supported by Czech Sciencundation GACR 20-24603Y and Charles University PRIMUS/20/MED/013. article_processing_charge: No article_type: original author: - first_name: Frank P full_name: Assen, Frank P id: 3A8E7F24-F248-11E8-B48F-1D18A9856A87 last_name: Assen orcid: 0000-0003-3470-6119 - first_name: Jun full_name: Abe, Jun last_name: Abe - first_name: Miroslav full_name: Hons, Miroslav id: 4167FE56-F248-11E8-B48F-1D18A9856A87 last_name: Hons orcid: 0000-0002-6625-3348 - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Shayan full_name: Shamipour, Shayan id: 40B34FE2-F248-11E8-B48F-1D18A9856A87 last_name: Shamipour - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Tommaso full_name: Costanzo, Tommaso id: D93824F4-D9BA-11E9-BB12-F207E6697425 last_name: Costanzo orcid: 0000-0001-9732-3815 - first_name: Gabriel full_name: Krens, Gabriel id: 2B819732-F248-11E8-B48F-1D18A9856A87 last_name: Krens orcid: 0000-0003-4761-5996 - first_name: Markus full_name: Brown, Markus id: 3DAB9AFC-F248-11E8-B48F-1D18A9856A87 last_name: Brown - first_name: Burkhard full_name: Ludewig, Burkhard last_name: Ludewig - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Wolfgang full_name: Weninger, Wolfgang last_name: Weninger - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Sanjiv A. full_name: Luther, Sanjiv A. last_name: Luther - first_name: Jens V. full_name: Stein, Jens V. last_name: Stein - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-4561-241X citation: ama: Assen FP, Abe J, Hons M, et al. Multitier mechanics control stromal adaptations in swelling lymph nodes. Nature Immunology. 2022;23:1246-1255. doi:10.1038/s41590-022-01257-4 apa: Assen, F. P., Abe, J., Hons, M., Hauschild, R., Shamipour, S., Kaufmann, W., … Sixt, M. K. (2022). Multitier mechanics control stromal adaptations in swelling lymph nodes. Nature Immunology. Springer Nature. https://doi.org/10.1038/s41590-022-01257-4 chicago: Assen, Frank P, Jun Abe, Miroslav Hons, Robert Hauschild, Shayan Shamipour, Walter Kaufmann, Tommaso Costanzo, et al. “Multitier Mechanics Control Stromal Adaptations in Swelling Lymph Nodes.” Nature Immunology. Springer Nature, 2022. https://doi.org/10.1038/s41590-022-01257-4. ieee: F. P. Assen et al., “Multitier mechanics control stromal adaptations in swelling lymph nodes,” Nature Immunology, vol. 23. Springer Nature, pp. 1246–1255, 2022. ista: Assen FP, Abe J, Hons M, Hauschild R, Shamipour S, Kaufmann W, Costanzo T, Krens G, Brown M, Ludewig B, Hippenmeyer S, Heisenberg C-PJ, Weninger W, Hannezo EB, Luther SA, Stein JV, Sixt MK. 2022. Multitier mechanics control stromal adaptations in swelling lymph nodes. Nature Immunology. 23, 1246–1255. mla: Assen, Frank P., et al. “Multitier Mechanics Control Stromal Adaptations in Swelling Lymph Nodes.” Nature Immunology, vol. 23, Springer Nature, 2022, pp. 1246–55, doi:10.1038/s41590-022-01257-4. short: F.P. Assen, J. Abe, M. Hons, R. Hauschild, S. Shamipour, W. Kaufmann, T. Costanzo, G. Krens, M. Brown, B. Ludewig, S. Hippenmeyer, C.-P.J. Heisenberg, W. Weninger, E.B. Hannezo, S.A. Luther, J.V. Stein, M.K. Sixt, Nature Immunology 23 (2022) 1246–1255. date_created: 2021-08-06T09:09:11Z date_published: 2022-07-11T00:00:00Z date_updated: 2023-08-02T06:53:07Z day: '11' ddc: - '570' department: - _id: SiHi - _id: CaHe - _id: EdHa - _id: EM-Fac - _id: Bio - _id: MiSi doi: 10.1038/s41590-022-01257-4 ec_funded: 1 external_id: isi: - '000822975900002' file: - access_level: open_access checksum: 628e7b49809f22c75b428842efe70c68 content_type: application/pdf creator: dernst date_created: 2022-07-25T07:11:32Z date_updated: 2022-07-25T07:11:32Z file_id: '11642' file_name: 2022_NatureImmunology_Assen.pdf file_size: 11475325 relation: main_file success: 1 file_date_updated: 2022-07-25T07:11:32Z has_accepted_license: '1' intvolume: ' 23' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 1246-1255 project: - _id: 25FE9508-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '724373' name: Cellular navigation along spatial gradients publication: Nature Immunology publication_identifier: eissn: - 1529-2916 issn: - 1529-2908 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Multitier mechanics control stromal adaptations in swelling lymph nodes tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 23 year: '2022' ... --- _id: '8988' abstract: - lang: eng text: The differentiation of cells depends on a precise control of their internal organization, which is the result of a complex dynamic interplay between the cytoskeleton, molecular motors, signaling molecules, and membranes. For example, in the developing neuron, the protein ADAP1 (ADP-ribosylation factor GTPase-activating protein [ArfGAP] with dual pleckstrin homology [PH] domains 1) has been suggested to control dendrite branching by regulating the small GTPase ARF6. Together with the motor protein KIF13B, ADAP1 is also thought to mediate delivery of the second messenger phosphatidylinositol (3,4,5)-trisphosphate (PIP3) to the axon tip, thus contributing to PIP3 polarity. However, what defines the function of ADAP1 and how its different roles are coordinated are still not clear. Here, we studied ADAP1’s functions using in vitro reconstitutions. We found that KIF13B transports ADAP1 along microtubules, but that PIP3 as well as PI(3,4)P2 act as stop signals for this transport instead of being transported. We also demonstrate that these phosphoinositides activate ADAP1’s enzymatic activity to catalyze GTP hydrolysis by ARF6. Together, our results support a model for the cellular function of ADAP1, where KIF13B transports ADAP1 until it encounters high PIP3/PI(3,4)P2 concentrations in the plasma membrane. Here, ADAP1 disassociates from the motor to inactivate ARF6, promoting dendrite branching. acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: EM-Fac acknowledgement: "We thank Urban Bezeljak, Natalia Baranova, Mar Lopez-Pelegrin, Catarina Alcarva, and Victoria Faas for sharing reagents and helpful discussions. We thank Veronika Szentirmai for help with protein purifications. We thank Carrie Bernecky, Sascha Martens, and the M.L. lab for comments on the manuscript. We thank the bioimaging facility, the life science facility, and Armel Nicolas from the mass spec facility at the Institute of Science and Technology (IST) Austria for technical support. C.D. acknowledges funding from the IST fellowship program; this work was supported by Human Frontier Science Program Young Investigator Grant\r\nRGY0083/2016. " article_number: e2010054118 article_processing_charge: No article_type: original author: - first_name: Christian F full_name: Düllberg, Christian F id: 459064DC-F248-11E8-B48F-1D18A9856A87 last_name: Düllberg orcid: 0000-0001-6335-9748 - first_name: Albert full_name: Auer, Albert id: 3018E8C2-F248-11E8-B48F-1D18A9856A87 last_name: Auer orcid: 0000-0002-3580-2906 - first_name: Nikola full_name: Canigova, Nikola id: 3795523E-F248-11E8-B48F-1D18A9856A87 last_name: Canigova orcid: 0000-0002-8518-5926 - first_name: Katrin full_name: Loibl, Katrin id: 3760F32C-F248-11E8-B48F-1D18A9856A87 last_name: Loibl orcid: 0000-0002-2429-7668 - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 citation: ama: Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. PNAS. 2021;118(1). doi:10.1073/pnas.2010054118 apa: Düllberg, C. F., Auer, A., Canigova, N., Loibl, K., & Loose, M. (2021). In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.2010054118 chicago: Düllberg, Christian F, Albert Auer, Nikola Canigova, Katrin Loibl, and Martin Loose. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” PNAS. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2010054118. ieee: C. F. Düllberg, A. Auer, N. Canigova, K. Loibl, and M. Loose, “In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1,” PNAS, vol. 118, no. 1. National Academy of Sciences, 2021. ista: Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. 2021. In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. PNAS. 118(1), e2010054118. mla: Düllberg, Christian F., et al. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” PNAS, vol. 118, no. 1, e2010054118, National Academy of Sciences, 2021, doi:10.1073/pnas.2010054118. short: C.F. Düllberg, A. Auer, N. Canigova, K. Loibl, M. Loose, PNAS 118 (2021). date_created: 2021-01-03T23:01:23Z date_published: 2021-01-05T00:00:00Z date_updated: 2023-08-04T11:20:46Z day: '05' department: - _id: MaLo - _id: MiSi doi: 10.1073/pnas.2010054118 external_id: isi: - '000607270100018' pmid: - '33443153' intvolume: ' 118' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1073/pnas.2010054118 month: '01' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 2599F062-B435-11E9-9278-68D0E5697425 grant_number: RGY0083/2016 name: Reconstitution of cell polarity and axis determination in a cell-free system publication: PNAS publication_identifier: eissn: - '10916490' issn: - '00278424' publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1 type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 118 year: '2021' ... --- _id: '9205' abstract: - lang: eng text: Cryo-EM grid preparation is an important bottleneck in protein structure determination, especially for membrane proteins, typically requiring screening of a large number of conditions. We systematically investigated the effects of buffer components, blotting conditions and grid types on the outcome of grid preparation of five different membrane protein samples. Aggregation was the most common type of problem which was addressed by changing detergents, salt concentration or reconstitution of proteins into nanodiscs or amphipols. We show that the optimal concentration of detergent is between 0.05 and 0.4% and that the presence of a low concentration of detergent with a high critical micellar concentration protects the proteins from denaturation at the air-water interface. Furthermore, we discuss the strategies for achieving an adequate ice thickness, particle coverage and orientation distribution on free ice and on support films. Our findings provide a clear roadmap for comprehensive screening of conditions for cryo-EM grid preparation of membrane proteins. acknowledged_ssus: - _id: EM-Fac acknowledgement: We thank the Electron Microscopy Facilities at the Institute of Science and Technology Austria and at the Vienna Biocenter for providing access and training for the electron microscopes. This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement no. 665385 . article_number: '102139' article_processing_charge: No article_type: original author: - first_name: Domen full_name: Kampjut, Domen id: 37233050-F248-11E8-B48F-1D18A9856A87 last_name: Kampjut - first_name: Julia full_name: Steiner, Julia id: 3BB67EB0-F248-11E8-B48F-1D18A9856A87 last_name: Steiner - 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: Kampjut D, Steiner J, Sazanov LA. Cryo-EM grid optimization for membrane proteins. iScience. 2021;24(3). doi:10.1016/j.isci.2021.102139 apa: Kampjut, D., Steiner, J., & Sazanov, L. A. (2021). Cryo-EM grid optimization for membrane proteins. IScience. Elsevier. https://doi.org/10.1016/j.isci.2021.102139 chicago: Kampjut, Domen, Julia Steiner, and Leonid A Sazanov. “Cryo-EM Grid Optimization for Membrane Proteins.” IScience. Elsevier, 2021. https://doi.org/10.1016/j.isci.2021.102139. ieee: D. Kampjut, J. Steiner, and L. A. Sazanov, “Cryo-EM grid optimization for membrane proteins,” iScience, vol. 24, no. 3. Elsevier, 2021. ista: Kampjut D, Steiner J, Sazanov LA. 2021. Cryo-EM grid optimization for membrane proteins. iScience. 24(3), 102139. mla: Kampjut, Domen, et al. “Cryo-EM Grid Optimization for Membrane Proteins.” IScience, vol. 24, no. 3, 102139, Elsevier, 2021, doi:10.1016/j.isci.2021.102139. short: D. Kampjut, J. Steiner, L.A. Sazanov, IScience 24 (2021). date_created: 2021-02-28T23:01:24Z date_published: 2021-03-19T00:00:00Z date_updated: 2023-08-07T13:54:06Z day: '19' ddc: - '570' department: - _id: LeSa doi: 10.1016/j.isci.2021.102139 ec_funded: 1 external_id: isi: - '000631646000012' pmid: - '33665558' file: - access_level: open_access checksum: 50585447386fe5842f07ab9b3a66e7e9 content_type: application/pdf creator: dernst date_created: 2021-03-03T07:38:14Z date_updated: 2021-03-03T07:38:14Z file_id: '9219' file_name: 2021_iScience_Kampjut.pdf file_size: 7431411 relation: main_file success: 1 file_date_updated: 2021-03-03T07:38:14Z has_accepted_license: '1' intvolume: ' 24' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: iScience publication_identifier: eissn: - '25890042' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Cryo-EM grid optimization for membrane proteins tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 24 year: '2021' ... --- _id: '9301' abstract: - lang: eng text: Electrodepositing insulating lithium peroxide (Li2O2) is the key process during discharge of aprotic Li–O2 batteries and determines rate, capacity, and reversibility. Current understanding states that the partition between surface adsorbed and dissolved lithium superoxide governs whether Li2O2 grows as a conformal surface film or larger particles, leading to low or high capacities, respectively. However, better understanding governing factors for Li2O2 packing density and capacity requires structural sensitive in situ metrologies. Here, we establish in situ small- and wide-angle X-ray scattering (SAXS/WAXS) as a suitable method to record the Li2O2 phase evolution with atomic to submicrometer resolution during cycling a custom-built in situ Li–O2 cell. Combined with sophisticated data analysis, SAXS allows retrieving rich quantitative structural information from complex multiphase systems. Surprisingly, we find that features are absent that would point at a Li2O2 surface film formed via two consecutive electron transfers, even in poorly solvating electrolytes thought to be prototypical for surface growth. All scattering data can be modeled by stacks of thin Li2O2 platelets potentially forming large toroidal particles. Li2O2 solution growth is further justified by rotating ring-disk electrode measurements and electron microscopy. Higher discharge overpotentials lead to smaller Li2O2 particles, but there is no transition to an electronically passivating, conformal Li2O2 coating. Hence, mass transport of reactive species rather than electronic transport through a Li2O2 film limits the discharge capacity. Provided that species mobilities and carbon surface areas are high, this allows for high discharge capacities even in weakly solvating electrolytes. The currently accepted Li–O2 reaction mechanism ought to be reconsidered. acknowledged_ssus: - _id: EM-Fac acknowledgement: S.A.F. and C.P. are indebted to the European Research Council under the European Union's Horizon 2020 research and innovation program (Grant Agreement No. 636069), the Austrian Federal Ministry of Science, Research and Economy, and the Austrian Research Promotion Agency (Grant No. 845364). We acknowledge A. Zankel and H. Schroettner for support with SEM measurements. C.P. thanks N. Kostoglou, C. Koczwara, M. Hartmann, and M. Burian for discussions on gas sorption analysis, C++ programming, Monte Carlo modeling, and in situ SAXS experiments, respectively. We thank S. Stadlbauer for help with Karl Fischer titration, R. Riccò for gas sorption measurements, and acknowledge Graz University of Technology for support through the Lead Project LP-03. Likewise, the use of SOMAPP Lab, a core facility supported by the Austrian Federal Ministry of Education, Science and Research, the Graz University of Technology, the University of Graz, and Anton Paar GmbH is acknowledged. S.A.F. is indebted to Institute of Science and Technology Austria (IST Austria) for support. This research was supported by the Scientific Service Units of IST Austria through resources provided by the Electron Microscopy Facility. article_number: e2021893118 article_processing_charge: No article_type: original author: - first_name: Christian full_name: Prehal, Christian last_name: Prehal - first_name: Aleksej full_name: Samojlov, Aleksej last_name: Samojlov - first_name: Manfred full_name: Nachtnebel, Manfred last_name: Nachtnebel - first_name: Ludek full_name: Lovicar, Ludek id: 36DB3A20-F248-11E8-B48F-1D18A9856A87 last_name: Lovicar orcid: 0000-0001-6206-4200 - first_name: Manfred full_name: Kriechbaum, Manfred last_name: Kriechbaum - first_name: Heinz full_name: Amenitsch, Heinz last_name: Amenitsch - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Prehal C, Samojlov A, Nachtnebel M, et al. In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes. Proceedings of the National Academy of Sciences. 2021;118(14). doi:10.1073/pnas.2021893118 apa: Prehal, C., Samojlov, A., Nachtnebel, M., Lovicar, L., Kriechbaum, M., Amenitsch, H., & Freunberger, S. A. (2021). In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2021893118 chicago: Prehal, Christian, Aleksej Samojlov, Manfred Nachtnebel, Ludek Lovicar, Manfred Kriechbaum, Heinz Amenitsch, and Stefan Alexander Freunberger. “In Situ Small-Angle X-Ray Scattering Reveals Solution Phase Discharge of Li–O2 Batteries with Weakly Solvating Electrolytes.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2021893118. ieee: C. Prehal et al., “In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes,” Proceedings of the National Academy of Sciences, vol. 118, no. 14. National Academy of Sciences, 2021. ista: Prehal C, Samojlov A, Nachtnebel M, Lovicar L, Kriechbaum M, Amenitsch H, Freunberger SA. 2021. In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes. Proceedings of the National Academy of Sciences. 118(14), e2021893118. mla: Prehal, Christian, et al. “In Situ Small-Angle X-Ray Scattering Reveals Solution Phase Discharge of Li–O2 Batteries with Weakly Solvating Electrolytes.” Proceedings of the National Academy of Sciences, vol. 118, no. 14, e2021893118, National Academy of Sciences, 2021, doi:10.1073/pnas.2021893118. short: C. Prehal, A. Samojlov, M. Nachtnebel, L. Lovicar, M. Kriechbaum, H. Amenitsch, S.A. Freunberger, Proceedings of the National Academy of Sciences 118 (2021). date_created: 2021-03-31T07:00:01Z date_published: 2021-04-06T00:00:00Z date_updated: 2023-09-05T13:27:18Z day: '06' department: - _id: StFr - _id: EM-Fac doi: 10.1073/pnas.2021893118 external_id: isi: - '000637398300050' intvolume: ' 118' isi: 1 issue: '14' keyword: - small-angle X-ray scattering - oxygen reduction - disproportionation - Li-air battery language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.26434/chemrxiv.11447775 month: '04' oa: 1 oa_version: Preprint publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' status: public title: In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 118 year: '2021' ... --- _id: '9330' abstract: - lang: eng text: In nerve cells the genes encoding for α2δ subunits of voltage-gated calcium channels have been linked to synaptic functions and neurological disease. Here we show that α2δ subunits are essential for the formation and organization of glutamatergic synapses. Using a cellular α2δ subunit triple-knockout/knockdown model, we demonstrate a failure in presynaptic differentiation evidenced by defective presynaptic calcium channel clustering and calcium influx, smaller presynaptic active zones, and a strongly reduced accumulation of presynaptic vesicle-associated proteins (synapsin and vGLUT). The presynaptic defect is associated with the downscaling of postsynaptic AMPA receptors and the postsynaptic density. The role of α2δ isoforms as synaptic organizers is highly redundant, as each individual α2δ isoform can rescue presynaptic calcium channel trafficking and expression of synaptic proteins. Moreover, α2δ-2 and α2δ-3 with mutated metal ion-dependent adhesion sites can fully rescue presynaptic synapsin expression but only partially calcium channel trafficking, suggesting that the regulatory role of α2δ subunits is independent from its role as a calcium channel subunit. Our findings influence the current view on excitatory synapse formation. First, our study suggests that postsynaptic differentiation is secondary to presynaptic differentiation. Second, the dependence of presynaptic differentiation on α2δ implicates α2δ subunits as potential nucleation points for the organization of synapses. Finally, our results suggest that α2δ subunits act as transsynaptic organizers of glutamatergic synapses, thereby aligning the synaptic active zone with the postsynaptic density. acknowledged_ssus: - _id: EM-Fac acknowledgement: "We thank Arnold Schwartz for providing α2δ-1 knockout mice; Ariane Benedetti, Sabine Baumgartner, Sandra Demetz, and Irene Mahlknecht for technical support; Nadine Ortner and Andreas Lieb for electrophysiological experiments; the team of the Electron Microscopy Facility at the Institute of Science and Technology Austria for technical support related to ultrastructural analysis; Hermann Dietrich and Anja Beierfuß and her team for animal care; Jutta Engel and Jörg Striessnig for critical discussions; and Bruno Benedetti and Bernhard Flucher for critical discussions and reading the manuscript. This study was supported by Austrian Science Fund Grants P24079, F44060, F44150, and DOC30-B30 (to G.J.O.) and T855 (to M.C.), European Research Council Grant AdG 694539 (to R.S.), Deutsche Forschungsgemeinschaft\r\nGrant SFB1348-TP A03 (to M.M.), and Interdisziplinäre Zentrum für Klinische Forschung Münster Grant Mi3/004/19 (to M.M.). This work is part of the PhD theses of C.L.S., S.M.G., and C.A." article_processing_charge: No article_type: original author: - first_name: Clemens L. full_name: Schöpf, Clemens L. last_name: Schöpf - first_name: Cornelia full_name: Ablinger, Cornelia last_name: Ablinger - first_name: Stefanie M. full_name: Geisler, Stefanie M. last_name: Geisler - first_name: Ruslan I. full_name: Stanika, Ruslan I. last_name: Stanika - first_name: Marta full_name: Campiglio, Marta last_name: Campiglio - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Benedikt full_name: Nimmervoll, Benedikt last_name: Nimmervoll - first_name: Bettina full_name: Schlick, Bettina last_name: Schlick - first_name: Johannes full_name: Brockhaus, Johannes last_name: Brockhaus - first_name: Markus full_name: Missler, Markus last_name: Missler - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Gerald J. full_name: Obermair, Gerald J. last_name: Obermair citation: ama: Schöpf CL, Ablinger C, Geisler SM, et al. Presynaptic α2δ subunits are key organizers of glutamatergic synapses. PNAS. 2021;118(14). doi:10.1073/pnas.1920827118 apa: Schöpf, C. L., Ablinger, C., Geisler, S. M., Stanika, R. I., Campiglio, M., Kaufmann, W., … Obermair, G. J. (2021). Presynaptic α2δ subunits are key organizers of glutamatergic synapses. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1920827118 chicago: Schöpf, Clemens L., Cornelia Ablinger, Stefanie M. Geisler, Ruslan I. Stanika, Marta Campiglio, Walter Kaufmann, Benedikt Nimmervoll, et al. “Presynaptic Α2δ Subunits Are Key Organizers of Glutamatergic Synapses.” PNAS. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.1920827118. ieee: C. L. Schöpf et al., “Presynaptic α2δ subunits are key organizers of glutamatergic synapses,” PNAS, vol. 118, no. 14. National Academy of Sciences, 2021. ista: Schöpf CL, Ablinger C, Geisler SM, Stanika RI, Campiglio M, Kaufmann W, Nimmervoll B, Schlick B, Brockhaus J, Missler M, Shigemoto R, Obermair GJ. 2021. Presynaptic α2δ subunits are key organizers of glutamatergic synapses. PNAS. 118(14). mla: Schöpf, Clemens L., et al. “Presynaptic Α2δ Subunits Are Key Organizers of Glutamatergic Synapses.” PNAS, vol. 118, no. 14, National Academy of Sciences, 2021, doi:10.1073/pnas.1920827118. short: C.L. Schöpf, C. Ablinger, S.M. Geisler, R.I. Stanika, M. Campiglio, W. Kaufmann, B. Nimmervoll, B. Schlick, J. Brockhaus, M. Missler, R. Shigemoto, G.J. Obermair, PNAS 118 (2021). date_created: 2021-04-18T22:01:40Z date_published: 2021-04-06T00:00:00Z date_updated: 2023-08-08T13:08:47Z day: '06' ddc: - '570' department: - _id: EM-Fac - _id: RySh doi: 10.1073/pnas.1920827118 ec_funded: 1 external_id: isi: - '000637398300002' file: - access_level: open_access checksum: dd014f68ae9d7d8d8fc4139a24e04506 content_type: application/pdf creator: dernst date_created: 2021-04-19T10:10:56Z date_updated: 2021-04-19T10:10:56Z file_id: '9340' file_name: 2021_PNAS_Schoepf.pdf file_size: 2603911 relation: main_file success: 1 file_date_updated: 2021-04-19T10:10:56Z has_accepted_license: '1' intvolume: ' 118' isi: 1 issue: '14' language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 25CA28EA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694539' name: 'In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour' publication: PNAS publication_identifier: eissn: - 1091-6490 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Presynaptic α2δ subunits are key organizers of glutamatergic synapses tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 118 year: '2021' ... --- _id: '9431' abstract: - lang: eng text: Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles. acknowledged_ssus: - _id: ScienComp - _id: LifeSc - _id: EM-Fac acknowledgement: This work was funded by the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D., R01AI150454 to V.M.V, R35GM136258 in support of J-P.R.F, and the Austrian Science Fund (FWF) grant P31445 to F.K.M.S. Access to high-resolution cryo-ET data acquisition at EMBL Heidelberg was supported by iNEXT (grant no. 653706), funded by the Horizon 2020 program of the European Union (PID 4246). We thank Wim Hagen and Felix Weis at EMBL Heidelberg for support in cryo-ET data acquisition. This work made use of the Cornell Center for Materials Research Shared Facilities, which are supported through the NSF MRSEC program (DMR-179875). This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). article_number: '3226' article_processing_charge: No article_type: original author: - first_name: Martin full_name: Obr, Martin id: 4741CA5A-F248-11E8-B48F-1D18A9856A87 last_name: Obr - first_name: Clifton L. full_name: Ricana, Clifton L. last_name: Ricana - first_name: Nadia full_name: Nikulin, Nadia last_name: Nikulin - first_name: Jon-Philip R. full_name: Feathers, Jon-Philip R. last_name: Feathers - first_name: Marco full_name: Klanschnig, Marco last_name: Klanschnig - first_name: Andreas full_name: Thader, Andreas id: 3A18A7B8-F248-11E8-B48F-1D18A9856A87 last_name: Thader - first_name: Marc C. full_name: Johnson, Marc C. last_name: Johnson - first_name: Volker M. full_name: Vogt, Volker M. last_name: Vogt - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Robert A. full_name: Dick, Robert A. last_name: Dick citation: ama: Obr M, Ricana CL, Nikulin N, et al. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23506-0 apa: Obr, M., Ricana, C. L., Nikulin, N., Feathers, J.-P. R., Klanschnig, M., Thader, A., … Dick, R. A. (2021). Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. Nature Research. https://doi.org/10.1038/s41467-021-23506-0 chicago: Obr, Martin, Clifton L. Ricana, Nadia Nikulin, Jon-Philip R. Feathers, Marco Klanschnig, Andreas Thader, Marc C. Johnson, Volker M. Vogt, Florian KM Schur, and Robert A. Dick. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications. Nature Research, 2021. https://doi.org/10.1038/s41467-021-23506-0. ieee: M. Obr et al., “Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer,” Nature Communications, vol. 12, no. 1. Nature Research, 2021. ista: Obr M, Ricana CL, Nikulin N, Feathers J-PR, Klanschnig M, Thader A, Johnson MC, Vogt VM, Schur FK, Dick RA. 2021. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 12(1), 3226. mla: Obr, Martin, et al. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications, vol. 12, no. 1, 3226, Nature Research, 2021, doi:10.1038/s41467-021-23506-0. short: M. Obr, C.L. Ricana, N. Nikulin, J.-P.R. Feathers, M. Klanschnig, A. Thader, M.C. Johnson, V.M. Vogt, F.K. Schur, R.A. Dick, Nature Communications 12 (2021). date_created: 2021-05-28T14:25:50Z date_published: 2021-05-28T00:00:00Z date_updated: 2023-08-08T13:53:53Z day: '28' ddc: - '570' department: - _id: FlSc doi: 10.1038/s41467-021-23506-0 external_id: isi: - '000659145000011' file: - access_level: open_access checksum: 53ccc53d09a9111143839dbe7784e663 content_type: application/pdf creator: kschuh date_created: 2021-06-09T15:21:14Z date_updated: 2021-06-09T15:21:14Z file_id: '9538' file_name: 2021_NatureCommunications_Obr.pdf file_size: 6166295 relation: main_file success: 1 file_date_updated: 2021-06-09T15:21:14Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '1' keyword: - General Biochemistry - Genetics and Molecular Biology - General Physics and Astronomy - General Chemistry language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 26736D6A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31445 name: Structural conservation and diversity in retroviral capsid publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Nature Research quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/how-retroviruses-become-infectious/ scopus_import: '1' status: public title: Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '9540' abstract: - lang: eng text: The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1 and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown. Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism. Diazaborine forms a covalent bond to the 2′-OH of the nucleotide in D2, explaining its specificity for this site. As a consequence, the D2 domain is locked in a rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms identified include abolished drug binding and altered positioning of the nucleotide. Our results suggest nucleotide-modifying compounds as potential novel inhibitors for AAA-ATPases. acknowledged_ssus: - _id: EM-Fac acknowledgement: We are deeply grateful to the late Gregor Högenauer who built the foundation for this study with his visionary work on the inhibitor diazaborine and its bacterial target. We thank Rolf Breinbauer for insightful discussions on boron chemistry. We thank Anton Meinhart and Tim Clausen for the valuable discussion of the manuscript. We are indebted to Thomas Köcher for the MS measurement of the diazaborine-ATPγS adduct. We thank the team of the VBCF for support during early phases of this work and the IST Austria Electron Microscopy Facility for providing equipment. The lab of D.H. is supported by Boehringer Ingelheim. The work was funded by FWF projects P32536 and P32977 (to H.B.). article_number: '3483' article_processing_charge: No article_type: original author: - first_name: Michael full_name: Prattes, Michael last_name: Prattes - first_name: Irina full_name: Grishkovskaya, Irina last_name: Grishkovskaya - first_name: Victor-Valentin full_name: Hodirnau, Victor-Valentin id: 3661B498-F248-11E8-B48F-1D18A9856A87 last_name: Hodirnau - first_name: Ingrid full_name: Rössler, Ingrid last_name: Rössler - first_name: Isabella full_name: Klein, Isabella last_name: Klein - first_name: Christina full_name: Hetzmannseder, Christina last_name: Hetzmannseder - first_name: Gertrude full_name: Zisser, Gertrude last_name: Zisser - first_name: Christian C. full_name: Gruber, Christian C. last_name: Gruber - first_name: Karl full_name: Gruber, Karl last_name: Gruber - first_name: David full_name: Haselbach, David last_name: Haselbach - first_name: Helmut full_name: Bergler, Helmut last_name: Bergler citation: ama: Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23854-x apa: Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Rössler, I., Klein, I., Hetzmannseder, C., … Bergler, H. (2021). Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23854-x chicago: Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Ingrid Rössler, Isabella Klein, Christina Hetzmannseder, Gertrude Zisser, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23854-x. ieee: M. Prattes et al., “Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021. ista: Prattes M, Grishkovskaya I, Hodirnau V-V, Rössler I, Klein I, Hetzmannseder C, Zisser G, Gruber CC, Gruber K, Haselbach D, Bergler H. 2021. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 12(1), 3483. mla: Prattes, Michael, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” Nature Communications, vol. 12, no. 1, 3483, Springer Nature, 2021, doi:10.1038/s41467-021-23854-x. short: M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, I. Rössler, I. Klein, C. Hetzmannseder, G. Zisser, C.C. Gruber, K. Gruber, D. Haselbach, H. Bergler, Nature Communications 12 (2021). date_created: 2021-06-10T14:57:45Z date_published: 2021-06-09T00:00:00Z date_updated: 2023-08-08T14:05:26Z day: '09' ddc: - '570' department: - _id: EM-Fac doi: 10.1038/s41467-021-23854-x external_id: isi: - '000664874700014' pmid: - '34108481' file: - access_level: open_access checksum: 40fc24c1310930990b52a8ad1142ee97 content_type: application/pdf creator: cziletti date_created: 2021-06-15T18:55:59Z date_updated: 2021-06-15T18:55:59Z file_id: '9556' file_name: 2021_NatureComm_Prattes.pdf file_size: 3397292 relation: main_file success: 1 file_date_updated: 2021-06-15T18:55:59Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '1' keyword: - General Biochemistry - Genetics and Molecular Biology - General Physics and Astronomy - General Chemistry language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '9562' abstract: - lang: eng text: Left-right asymmetries can be considered a fundamental organizational principle of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell synaptic connection shows an input-side dependent asymmetry where the hemispheric location of the presynaptic CA3 neuron determines the synaptic properties. Left-input synapses terminating on apical dendrites in stratum radiatum have a higher density of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1 and smaller areas with less often perforated PSDs. On the other hand, left-input synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities than right-input ones. Apical and basal synapses further employ different signaling pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize synaptic membrane proteins with high sensitivity and resolution, and has been used to reveal the asymmetry at the electron microscopic level. However, it requires time-consuming manual demarcation of the synaptic surface for quantitative measurements. To facilitate the analysis of replica labeling, I first developed a software named Darea, which utilizes deep-learning to automatize this demarcation. With Darea I characterized the synaptic distribution of NMDA and AMPA receptors as well as the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I explored the role of GluN2B and its carboxy-terminus in the establishment of input-side dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were detected. We further discovered a previously unknown functional asymmetry of GluN2A, which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus plays a critical role in normal formation of input-side dependent asymmetry. acknowledged_ssus: - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: David full_name: Kleindienst, David id: 42E121A4-F248-11E8-B48F-1D18A9856A87 last_name: Kleindienst citation: ama: 'Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. 2021. doi:10.15479/at:ista:9562' apa: 'Kleindienst, D. (2021). 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9562' chicago: 'Kleindienst, David. “2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9562.' ieee: 'D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,” Institute of Science and Technology Austria, 2021.' ista: 'Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria.' mla: 'Kleindienst, David. 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9562.' short: 'D. Kleindienst, 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning, Institute of Science and Technology Austria, 2021.' date_created: 2021-06-17T14:10:47Z date_published: 2021-06-01T00:00:00Z date_updated: 2023-09-11T12:55:53Z day: '01' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: RySh doi: 10.15479/at:ista:9562 file: - access_level: open_access checksum: 659df5518db495f679cb1df9e9bd1d94 content_type: application/pdf creator: dkleindienst date_created: 2021-06-17T14:03:14Z date_updated: 2022-07-02T22:30:04Z embargo: 2022-07-01 file_id: '9563' file_name: Thesis.pdf file_size: 77299142 relation: main_file - access_level: closed checksum: 3bcf63a2b19e5b6663be051bea332748 content_type: application/zip creator: dkleindienst date_created: 2021-06-17T14:04:30Z date_updated: 2022-07-02T22:30:04Z embargo_to: open_access file_id: '9564' file_name: Thesis_source.zip file_size: 369804895 relation: source_file file_date_updated: 2022-07-02T22:30:04Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '124' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9756' relation: part_of_dissertation status: public - id: '9437' relation: part_of_dissertation status: public - id: '8532' relation: part_of_dissertation status: public - id: '612' relation: part_of_dissertation status: public status: public supervisor: - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 title: '2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning' type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '9623' abstract: - lang: eng text: "Cytoplasmic reorganizations are essential for morphogenesis. In large cells like oocytes, these reorganizations become crucial in patterning the oocyte for later stages of embryonic development. Ascidians oocytes reorganize their cytoplasm (ooplasm) in a spectacular manner. Ooplasmic reorganization is initiated at fertilization with the contraction of the actomyosin cortex along the animal-vegetal axis of the oocyte, driving the accumulation of cortical endoplasmic reticulum (cER), maternal mRNAs associated to it and a mitochondria-rich subcortical layer – the myoplasm – in a region of the vegetal pole termed contraction pole (CP). Here we have used the species Phallusia mammillata to investigate the changes in cell shape that accompany these reorganizations and the mechanochemical mechanisms underlining CP formation.\r\nWe report that the length of the animal-vegetal (AV) axis oscillates upon fertilization: it first undergoes a cycle of fast elongation-lengthening followed by a slow expansion of mainly the vegetal pole (VP) of the cell. We show that the fast oscillation corresponds to a dynamic polarization of the actin cortex as a result of a fertilization-induced increase in cortical tension in the oocyte that triggers a rupture of the cortex at the animal pole and the establishment of vegetal-directed cortical flows. These flows are responsible for the vegetal accumulation of actin causing the VP to flatten. \r\nWe find that the slow expansion of the VP, leading to CP formation, correlates with a relaxation of the vegetal cortex and that the myoplasm plays a role in the expansion. We show that the myoplasm is a solid-like layer that buckles under compression forces arising from the contracting actin cortex at the VP. Straightening of the myoplasm when actin flows stops, facilitates the expansion of the VP and the CP. Altogether, our results present a previously unrecognized role for the myoplasm in ascidian ooplasmic segregation. \r\n" acknowledged_ssus: - _id: Bio - _id: EM-Fac - _id: NanoFab - _id: M-Shop alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Silvia full_name: Caballero Mancebo, Silvia id: 2F1E1758-F248-11E8-B48F-1D18A9856A87 last_name: Caballero Mancebo orcid: 0000-0002-5223-3346 citation: ama: Caballero Mancebo S. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. 2021. doi:10.15479/at:ista:9623 apa: Caballero Mancebo, S. (2021). Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9623 chicago: Caballero Mancebo, Silvia. “Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9623. ieee: S. Caballero Mancebo, “Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes,” Institute of Science and Technology Austria, 2021. ista: Caballero Mancebo S. 2021. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria. mla: Caballero Mancebo, Silvia. Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9623. short: S. Caballero Mancebo, Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes, Institute of Science and Technology Austria, 2021. date_created: 2021-07-01T14:50:17Z date_published: 2021-07-01T00:00:00Z date_updated: 2023-09-07T13:33:27Z ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: CaHe doi: 10.15479/at:ista:9623 file: - access_level: closed checksum: e039225a47ef32666d59bf35ddd30ecf content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: scaballe date_created: 2021-07-01T14:48:54Z date_updated: 2022-07-02T22:30:06Z embargo_to: open_access file_id: '9624' file_name: PhDThesis_SCM.docx file_size: 131946790 relation: source_file - access_level: open_access checksum: dd4d78962ea94ad95e97ca7d9af08f4b content_type: application/pdf creator: scaballe date_created: 2021-07-01T14:46:25Z date_updated: 2022-07-02T22:30:06Z embargo: 2022-07-01 file_id: '9625' file_name: PhDThesis_SCM.pdf file_size: 17094958 relation: main_file file_date_updated: 2022-07-02T22:30:06Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '111' publication_identifier: isbn: - 978-3-99078-012-1 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9750' relation: part_of_dissertation status: public - id: '9006' relation: part_of_dissertation status: public status: public supervisor: - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 title: Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '10073' abstract: - lang: eng text: Thermoelectric materials enable the direct conversion between heat and electricity. SnTe is a promising candidate due to its high charge transport performance. Here, we prepared SnTe nanocomposites by employing an aqueous method to synthetize SnTe nanoparticles (NP), followed by a unique surface treatment prior NP consolidation. This synthetic approach allowed optimizing the charge and phonon transport synergistically. The novelty of this strategy was the use of a soluble PbS molecular complex prepared using a thiol-amine solvent mixture that upon blending is adsorbed on the SnTe NP surface. Upon consolidation with spark plasma sintering, SnTe-PbS nanocomposite is formed. The presence of PbS complexes significantly compensates for the Sn vacancy and increases the average grain size of the nanocomposite, thus improving the carrier mobility. Moreover, lattice thermal conductivity is also reduced by the Pb and S-induced mass and strain fluctuation. As a result, an enhanced ZT of ca. 0.8 is reached at 873 K. Our finding provides a novel strategy to conduct rational surface treatment on NP-based thermoelectrics. acknowledged_ssus: - _id: EM-Fac acknowledgement: "The authors thank the EMF facility in IST Austria for providing SEM and EDX measurements.\r\n" article_number: '5416' article_processing_charge: Yes article_type: original author: - first_name: Cheng full_name: Chang, Cheng id: 9E331C2E-9F27-11E9-AE48-5033E6697425 last_name: Chang orcid: 0000-0002-9515-4277 - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 citation: ama: Chang C, Ibáñez M. Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. 2021;14(18). doi:10.3390/ma14185416 apa: Chang, C., & Ibáñez, M. (2021). Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. MDPI. https://doi.org/10.3390/ma14185416 chicago: Chang, Cheng, and Maria Ibáñez. “Enhanced Thermoelectric Performance by Surface Engineering in SnTe-PbS Nanocomposites.” Materials. MDPI, 2021. https://doi.org/10.3390/ma14185416. ieee: C. Chang and M. Ibáñez, “Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites,” Materials, vol. 14, no. 18. MDPI, 2021. ista: Chang C, Ibáñez M. 2021. Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. 14(18), 5416. mla: Chang, Cheng, and Maria Ibáñez. “Enhanced Thermoelectric Performance by Surface Engineering in SnTe-PbS Nanocomposites.” Materials, vol. 14, no. 18, 5416, MDPI, 2021, doi:10.3390/ma14185416. short: C. Chang, M. Ibáñez, Materials 14 (2021). date_created: 2021-10-03T22:01:23Z date_published: 2021-09-19T00:00:00Z date_updated: 2023-08-14T08:00:01Z day: '19' ddc: - '540' department: - _id: MaIb doi: 10.3390/ma14185416 external_id: isi: - '000700689400001' pmid: - '34576640' file: - access_level: open_access checksum: 4929dfc673a3ae77c010b6174279cc1d content_type: application/pdf creator: cchlebak date_created: 2021-10-14T11:56:39Z date_updated: 2021-10-14T11:56:39Z file_id: '10140' file_name: 2021_Materials_Chang.pdf file_size: 4404141 relation: main_file success: 1 file_date_updated: 2021-10-14T11:56:39Z has_accepted_license: '1' intvolume: ' 14' isi: 1 issue: '18' language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A grant_number: M02889 name: Bottom-up Engineering for Thermoelectric Applications publication: Materials publication_identifier: eissn: - 1996-1944 publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 14 year: '2021' ... --- _id: '10123' abstract: - lang: eng text: Solution synthesis of particles emerged as an alternative to prepare thermoelectric materials with less demanding processing conditions than conventional solid-state synthetic methods. However, solution synthesis generally involves the presence of additional molecules or ions belonging to the precursors or added to enable solubility and/or regulate nucleation and growth. These molecules or ions can end up in the particles as surface adsorbates and interfere in the material properties. This work demonstrates that ionic adsorbates, in particular Na⁺ ions, are electrostatically adsorbed in SnSe particles synthesized in water and play a crucial role not only in directing the material nano/microstructure but also in determining the transport properties of the consolidated material. In dense pellets prepared by sintering SnSe particles, Na remains within the crystal lattice as dopant, in dislocations, precipitates, and forming grain boundary complexions. These results highlight the importance of considering all the possible unintentional impurities to establish proper structure-property relationships and control material properties in solution-processed thermoelectric materials. acknowledged_ssus: - _id: EM-Fac - _id: NanoFab acknowledgement: 'Y.L. and M.C. contributed equally to this work. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NNF). This work was financially supported by IST Austria and the Werner Siemens Foundation. Y.L. acknowledges funding from the European Union''s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. M.C. has received funding from the European Union''s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385. Y.Y. and O.C.-M. acknowledge the financial support from DFG within the project SFB 917: Nanoswitches. J.L. is a Serra Húnter Fellow and is grateful to ICREA Academia program. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N.' article_number: '2106858' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Yu full_name: Liu, Yu id: 2A70014E-F248-11E8-B48F-1D18A9856A87 last_name: Liu orcid: 0000-0001-7313-6740 - first_name: Mariano full_name: Calcabrini, Mariano id: 45D7531A-F248-11E8-B48F-1D18A9856A87 last_name: Calcabrini orcid: 0000-0003-4566-5877 - first_name: Yuan full_name: Yu, Yuan last_name: Yu - first_name: Aziz full_name: Genç, Aziz last_name: Genç - first_name: Cheng full_name: Chang, Cheng id: 9E331C2E-9F27-11E9-AE48-5033E6697425 last_name: Chang orcid: 0000-0002-9515-4277 - first_name: Tommaso full_name: Costanzo, Tommaso id: D93824F4-D9BA-11E9-BB12-F207E6697425 last_name: Costanzo orcid: 0000-0001-9732-3815 - first_name: Tobias full_name: Kleinhanns, Tobias id: 8BD9DE16-AB3C-11E9-9C8C-2A03E6697425 last_name: Kleinhanns - first_name: Seungho full_name: Lee, Seungho id: BB243B88-D767-11E9-B658-BC13E6697425 last_name: Lee orcid: 0000-0002-6962-8598 - first_name: Jordi full_name: Llorca, Jordi last_name: Llorca - first_name: Oana full_name: Cojocaru‐Mirédin, Oana last_name: Cojocaru‐Mirédin - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 citation: ama: 'Liu Y, Calcabrini M, Yu Y, et al. The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials. 2021;33(52). doi:10.1002/adma.202106858' apa: 'Liu, Y., Calcabrini, M., Yu, Y., Genç, A., Chang, C., Costanzo, T., … Ibáñez, M. (2021). The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials. Wiley. https://doi.org/10.1002/adma.202106858' chicago: 'Liu, Yu, Mariano Calcabrini, Yuan Yu, Aziz Genç, Cheng Chang, Tommaso Costanzo, Tobias Kleinhanns, et al. “The Importance of Surface Adsorbates in Solution‐processed Thermoelectric Materials: The Case of SnSe.” Advanced Materials. Wiley, 2021. https://doi.org/10.1002/adma.202106858.' ieee: 'Y. Liu et al., “The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe,” Advanced Materials, vol. 33, no. 52. Wiley, 2021.' ista: 'Liu Y, Calcabrini M, Yu Y, Genç A, Chang C, Costanzo T, Kleinhanns T, Lee S, Llorca J, Cojocaru‐Mirédin O, Ibáñez M. 2021. The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials. 33(52), 2106858.' mla: 'Liu, Yu, et al. “The Importance of Surface Adsorbates in Solution‐processed Thermoelectric Materials: The Case of SnSe.” Advanced Materials, vol. 33, no. 52, 2106858, Wiley, 2021, doi:10.1002/adma.202106858.' short: Y. Liu, M. Calcabrini, Y. Yu, A. Genç, C. Chang, T. Costanzo, T. Kleinhanns, S. Lee, J. Llorca, O. Cojocaru‐Mirédin, M. Ibáñez, Advanced Materials 33 (2021). date_created: 2021-10-11T20:07:24Z date_published: 2021-12-29T00:00:00Z date_updated: 2023-08-14T07:25:27Z day: '29' ddc: - '620' department: - _id: EM-Fac - _id: MaIb doi: 10.1002/adma.202106858 ec_funded: 1 external_id: isi: - '000709899300001' pmid: - '34626034' file: - access_level: open_access checksum: 990bccc527c64d85cf1c97885110b5f4 content_type: application/pdf creator: cchlebak date_created: 2022-02-03T13:16:14Z date_updated: 2022-02-03T13:16:14Z file_id: '10720' file_name: 2021_AdvancedMaterials_Liu.pdf file_size: 5595666 relation: main_file success: 1 file_date_updated: 2022-02-03T13:16:14Z has_accepted_license: '1' intvolume: ' 33' isi: 1 issue: '52' keyword: - mechanical engineering - mechanics of materials - general materials science language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A grant_number: M02889 name: Bottom-up Engineering for Thermoelectric Applications - _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery' publication: Advanced Materials publication_identifier: eissn: - 1521-4095 issn: - 0935-9648 publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '12885' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 33 year: '2021' ... --- _id: '10146' abstract: - lang: eng text: The enzymes of the mitochondrial electron transport chain are key players of cell metabolism. Despite being active when isolated, in vivo they associate into supercomplexes1, whose precise role is debated. Supercomplexes CIII2CIV1-2 (refs. 2,3), CICIII2 (ref. 4) and CICIII2CIV (respirasome)5,6,7,8,9,10 exist in mammals, but in contrast to CICIII2 and the respirasome, to date the only known eukaryotic structures of CIII2CIV1-2 come from Saccharomyces cerevisiae11,12 and plants13, which have different organization. Here we present the first, to our knowledge, structures of mammalian (mouse and ovine) CIII2CIV and its assembly intermediates, in different conformations. We describe the assembly of CIII2CIV from the CIII2 precursor to the final CIII2CIV conformation, driven by the insertion of the N terminus of the assembly factor SCAF1 (ref. 14) deep into CIII2, while its C terminus is integrated into CIV. Our structures (which include CICIII2 and the respirasome) also confirm that SCAF1 is exclusively required for the assembly of CIII2CIV and has no role in the assembly of the respirasome. We show that CIII2 is asymmetric due to the presence of only one copy of subunit 9, which straddles both monomers and prevents the attachment of a second copy of SCAF1 to CIII2, explaining the presence of one copy of CIV in CIII2CIV in mammals. Finally, we show that CIII2 and CIV gain catalytic advantage when assembled into the supercomplex and propose a role for CIII2CIV in fine tuning the efficiency of electron transfer in the electron transport chain. acknowledged_ssus: - _id: PreCl - _id: EM-Fac - _id: ScienComp acknowledgement: We thank the pre-clinical facility of the IST Austria and A. Venturino for assistance with the animals; and V.-V. Hodirnau for assistance during the Titan Krios data collection, performed at the IST Austria. The data processing was performed at the IST high-performance computing cluster. This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 754411. 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. Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature. 2021;598(7880):364-367. doi:10.1038/s41586-021-03927-z apa: Vercellino, I., & Sazanov, L. A. (2021). Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-03927-z chicago: Vercellino, Irene, and Leonid A Sazanov. “Structure and Assembly of the Mammalian Mitochondrial Supercomplex CIII2CIV.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-03927-z. ieee: I. Vercellino and L. A. Sazanov, “Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV,” Nature, vol. 598, no. 7880. Springer Nature, pp. 364–367, 2021. ista: Vercellino I, Sazanov LA. 2021. Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature. 598(7880), 364–367. mla: Vercellino, Irene, and Leonid A. Sazanov. “Structure and Assembly of the Mammalian Mitochondrial Supercomplex CIII2CIV.” Nature, vol. 598, no. 7880, Springer Nature, 2021, pp. 364–67, doi:10.1038/s41586-021-03927-z. short: I. Vercellino, L.A. Sazanov, Nature 598 (2021) 364–367. date_created: 2021-10-17T22:01:17Z date_published: 2021-10-14T00:00:00Z date_updated: 2023-08-14T08:01:21Z day: '14' department: - _id: LeSa doi: 10.1038/s41586-021-03927-z ec_funded: 1 external_id: isi: - '000704581600001' pmid: - '34616041' intvolume: ' 598' isi: 1 issue: '7880' language: - iso: eng month: '10' oa_version: None page: 364-367 pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Webpage relation: press_release url: https://ist.ac.at/en/news/boosting-the-cells-power-house/ scopus_import: '1' status: public title: Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 598 year: '2021' ... --- _id: '10290' abstract: - lang: eng text: A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized filamentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner. acknowledged_ssus: - _id: ScienComp - _id: LifeSc - _id: Bio - _id: EM-Fac acknowledgement: 'This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Victor-Valentin Hodirnau for help with cryo-ET data acquisition. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S.' article_number: '107808' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Georgi A full_name: Dimchev, Georgi A id: 38C393BE-F248-11E8-B48F-1D18A9856A87 last_name: Dimchev orcid: 0000-0001-8370-6161 - first_name: Behnam full_name: Amiri, Behnam last_name: Amiri - first_name: Florian full_name: Fäßler, Florian id: 404F5528-F248-11E8-B48F-1D18A9856A87 last_name: Fäßler orcid: 0000-0001-7149-769X - first_name: Martin full_name: Falcke, Martin last_name: Falcke - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 citation: ama: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. 2021;213(4). doi:10.1016/j.jsb.2021.107808 apa: Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., & Schur, F. K. (2021). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. Elsevier . https://doi.org/10.1016/j.jsb.2021.107808 chicago: Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Journal of Structural Biology. Elsevier , 2021. https://doi.org/10.1016/j.jsb.2021.107808. ieee: G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data,” Journal of Structural Biology, vol. 213, no. 4. Elsevier , 2021. ista: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2021. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. 213(4), 107808. mla: Dimchev, Georgi A., et al. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Journal of Structural Biology, vol. 213, no. 4, 107808, Elsevier , 2021, doi:10.1016/j.jsb.2021.107808. short: G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, Journal of Structural Biology 213 (2021). date_created: 2021-11-15T12:21:42Z date_published: 2021-11-03T00:00:00Z date_updated: 2023-11-21T08:36:02Z day: '03' ddc: - '572' department: - _id: FlSc doi: 10.1016/j.jsb.2021.107808 external_id: isi: - '000720259500002' file: - access_level: open_access checksum: 6b209e4d44775d4e02b50f78982c15fa content_type: application/pdf creator: cchlebak date_created: 2021-11-15T13:11:27Z date_updated: 2021-11-15T13:11:27Z file_id: '10291' file_name: 2021_JournalStructBiol_Dimchev.pdf file_size: 16818304 relation: main_file success: 1 file_date_updated: 2021-11-15T13:11:27Z has_accepted_license: '1' intvolume: ' 213' isi: 1 issue: '4' keyword: - Structural Biology language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A grant_number: P33367 name: Structure and isoform diversity of the Arp2/3 complex - _id: 2674F658-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02495 name: Protein structure and function in filopodia across scales publication: Journal of Structural Biology publication_identifier: issn: - 1047-8477 publication_status: published publisher: 'Elsevier ' quality_controlled: '1' related_material: record: - id: '14502' relation: software status: public scopus_import: '1' status: public title: Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data 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: 213 year: '2021' ... --- _id: '10307' abstract: - lang: eng text: Bacteria-host interactions represent a continuous trade-off between benefit and risk. Thus, the host immune response is faced with a non-trivial problem – accommodate beneficial commensals and remove harmful pathogens. This is especially difficult as molecular patterns, such as lipopolysaccharide or specific surface organelles such as pili, are conserved in both, commensal and pathogenic bacteria. Type 1 pili, tightly regulated by phase variation, are considered an important virulence factor of pathogenic bacteria as they facilitate invasion into host cells. While invasion represents a de facto passive mechanism for pathogens to escape the host immune response, we demonstrate a fundamental role of type 1 pili as active modulators of the innate and adaptive immune response. acknowledged_ssus: - _id: LifeSc - _id: Bio - _id: PreCl - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Kathrin full_name: Tomasek, Kathrin id: 3AEC8556-F248-11E8-B48F-1D18A9856A87 last_name: Tomasek orcid: 0000-0003-3768-877X citation: ama: Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021. doi:10.15479/at:ista:10307 apa: Tomasek, K. (2021). Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10307 chicago: Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10307. ieee: K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021. ista: Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria. mla: Tomasek, Kathrin. Pathogenic Escherichia Coli Hijack the Host Immune Response. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10307. short: K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response, Institute of Science and Technology Austria, 2021. date_created: 2021-11-18T15:05:06Z date_published: 2021-11-18T00:00:00Z date_updated: 2023-09-07T13:34:38Z day: '18' ddc: - '570' degree_awarded: PhD department: - _id: MiSi - _id: CaGu - _id: GradSch doi: 10.15479/at:ista:10307 file: - access_level: open_access checksum: b39c9e0ef18d0484d537a67551effd02 content_type: application/pdf creator: ktomasek date_created: 2021-11-18T15:07:31Z date_updated: 2022-12-20T23:30:05Z embargo: 2022-11-18 file_id: '10308' file_name: ThesisTomasekKathrin.pdf file_size: 13266088 relation: main_file - access_level: closed checksum: c0c440ee9e5ef1102a518a4f9f023e7c content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: ktomasek date_created: 2021-11-18T15:07:46Z date_updated: 2022-12-20T23:30:05Z embargo_to: open_access file_id: '10309' file_name: ThesisTomasekKathrin.docx file_size: 7539509 relation: source_file file_date_updated: 2022-12-20T23:30:05Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '73' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10316' relation: part_of_dissertation status: public status: public supervisor: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-4561-241X - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 title: Pathogenic Escherichia coli hijack the host immune response type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '10316' abstract: - lang: eng text: A key attribute of persistent or recurring bacterial infections is the ability of the pathogen to evade the host’s immune response. Many Enterobacteriaceae express type 1 pili, a pre-adapted virulence trait, to invade host epithelial cells and establish persistent infections. However, the molecular mechanisms and strategies by which bacteria actively circumvent the immune response of the host remain poorly understood. Here, we identified CD14, the major co-receptor for lipopolysaccharide detection, on dendritic cells as a previously undescribed binding partner of FimH, the protein located at the tip of the type 1 pilus of Escherichia coli. The FimH amino acids involved in CD14 binding are highly conserved across pathogenic and non-pathogenic strains. Binding of pathogenic bacteria to CD14 lead to reduced dendritic cell migration and blunted expression of co-stimulatory molecules, both rate-limiting factors of T cell activation. While defining an active molecular mechanism of immune evasion by pathogens, the interaction between FimH and CD14 represents a potential target to interfere with persistent and recurrent infections, such as urinary tract infections or Crohn’s disease. acknowledged_ssus: - _id: Bio - _id: PreCl - _id: EM-Fac acknowledgement: We thank Ulrich Dobrindt for providing UPEC strain CFT073, Vlad Gavra and Maximilian Götz, Bor Kavčič, Jonna Alanko and Eva Kiermaier for help with experiments and Robert Hauschild, Julian Stopp and Saren Tasciyan for help with data analysis. We thank the IST Austria Scientific Service Units, especially the Bioimaging facility, the Preclinical facility and the Electron microscopy facility for technical support, Jakob Wallner and all members of the Guet and Sixt lab for fruitful discussions and Daria Siekhaus for critically reading the manuscript. This work was supported by grants from the Austrian Research Promotion Agency (FEMtech 868984) to I.G., the European Research Council (CoG 724373) and the Austrian Science Fund (FWF P29911) to M.S. article_processing_charge: No author: - first_name: Kathrin full_name: Tomasek, Kathrin id: 3AEC8556-F248-11E8-B48F-1D18A9856A87 last_name: Tomasek orcid: 0000-0003-3768-877X - first_name: Alexander F full_name: Leithner, Alexander F id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87 last_name: Leithner orcid: 0000-0002-1073-744X - first_name: Ivana full_name: Glatzová, Ivana id: 727b3c7d-4939-11ec-89b3-b9b0750ab74d last_name: Glatzová - first_name: Michael S. full_name: Lukesch, Michael S. last_name: Lukesch - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-4561-241X citation: ama: Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv. doi:10.1101/2021.10.18.464770 apa: Tomasek, K., Leithner, A. F., Glatzová, I., Lukesch, M. S., Guet, C. C., & Sixt, M. K. (n.d.). Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.10.18.464770 chicago: Tomasek, Kathrin, Alexander F Leithner, Ivana Glatzová, Michael S. Lukesch, Calin C Guet, and Michael K Sixt. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2021.10.18.464770. ieee: K. Tomasek, A. F. Leithner, I. Glatzová, M. S. Lukesch, C. C. Guet, and M. K. Sixt, “Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14,” bioRxiv. Cold Spring Harbor Laboratory. ista: Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv, 10.1101/2021.10.18.464770. mla: Tomasek, Kathrin, et al. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2021.10.18.464770. short: K. Tomasek, A.F. Leithner, I. Glatzová, M.S. Lukesch, C.C. Guet, M.K. Sixt, BioRxiv (n.d.). date_created: 2021-11-19T12:24:16Z date_published: 2021-10-18T00:00:00Z date_updated: 2024-03-25T23:30:19Z day: '18' department: - _id: CaGu - _id: MiSi doi: 10.1101/2021.10.18.464770 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2021.10.18.464770v1 month: '10' oa: 1 oa_version: Preprint project: - _id: 25FE9508-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '724373' name: Cellular navigation along spatial gradients - _id: 26018E70-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29911 name: Mechanical adaptation of lamellipodial actin publication: bioRxiv publication_status: submitted publisher: Cold Spring Harbor Laboratory related_material: record: - id: '11843' relation: later_version status: public - id: '10307' relation: dissertation_contains status: public status: public title: Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14 type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2021' ... --- _id: '9887' abstract: - lang: eng text: Clathrin-mediated endocytosis is the major route of entry of cargos into cells and thus underpins many physiological processes. During endocytosis, an area of flat membrane is remodeled by proteins to create a spherical vesicle against intracellular forces. The protein machinery which mediates this membrane bending in plants is unknown. However, it is known that plant endocytosis is actin independent, thus indicating that plants utilize a unique mechanism to mediate membrane bending against high-turgor pressure compared to other model systems. Here, we investigate the TPLATE complex, a plant-specific endocytosis protein complex. It has been thought to function as a classical adaptor functioning underneath the clathrin coat. However, by using biochemical and advanced live microscopy approaches, we found that TPLATE is peripherally associated with clathrin-coated vesicles and localizes at the rim of endocytosis events. As this localization is more fitting to the protein machinery involved in membrane bending during endocytosis, we examined cells in which the TPLATE complex was disrupted and found that the clathrin structures present as flat patches. This suggests a requirement of the TPLATE complex for membrane bending during plant clathrin–mediated endocytosis. Next, we used in vitro biophysical assays to confirm that the TPLATE complex possesses protein domains with intrinsic membrane remodeling activity. These results redefine the role of the TPLATE complex and implicate it as a key component of the evolutionarily distinct plant endocytosis mechanism, which mediates endocytic membrane bending against the high-turgor pressure in plant cells. acknowledged_ssus: - _id: EM-Fac - _id: LifeSc - _id: Bio acknowledgement: 'We gratefully thank Julie Neveu and Dr. Amanda Barranco of the Grégory Vert laboratory for help preparing plants in France, Dr. Zuzana Gelova for help and advice with protoplast generation, Dr. Stéphane Vassilopoulos and Dr. Florian Schur for advice regarding EM tomography, Alejandro Marquiegui Alvaro for help with material generation, and Dr. Lukasz Kowalski for generously gifting us the mWasabi protein. This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (IST Austria) through resources provided by the Electron Microscopy Facility, Lab Support Facility (particularly Dorota Jaworska), and the Bioimaging Facility. We acknowledge the Advanced Microscopy Facility of the Vienna BioCenter Core Facilities for use of the 3D SIM. For the mass spectrometry analysis of proteins, we acknowledge the University of Natural Resources and Life Sciences (BOKU) Core Facility Mass Spectrometry. This work was supported by the following funds: A.J. is supported by funding from the Austrian Science Fund I3630B25 to J.F. P.M. and E.B. are supported by Agence Nationale de la Recherche ANR-11-EQPX-0029 Morphoscope2 and ANR-10-INBS-04 France BioImaging. S.Y.B. is supported by the NSF No. 1121998 and 1614915. J.W. and D.V.D. are supported by the European Research Council Grant 682436 (to D.V.D.), a China Scholarship Council Grant 201508440249 (to J.W.), and by a Ghent University Special Research Co-funding Grant ST01511051 (to J.W.).' article_number: e2113046118 article_processing_charge: No article_type: original author: - first_name: Alexander J full_name: Johnson, Alexander J id: 46A62C3A-F248-11E8-B48F-1D18A9856A87 last_name: Johnson orcid: 0000-0002-2739-8843 - first_name: Dana A full_name: Dahhan, Dana A last_name: Dahhan - first_name: Nataliia full_name: Gnyliukh, Nataliia id: 390C1120-F248-11E8-B48F-1D18A9856A87 last_name: Gnyliukh orcid: 0000-0002-2198-0509 - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Vanessa full_name: Zheden, Vanessa id: 39C5A68A-F248-11E8-B48F-1D18A9856A87 last_name: Zheden orcid: 0000-0002-9438-4783 - first_name: Tommaso full_name: Costanzo, Tommaso id: D93824F4-D9BA-11E9-BB12-F207E6697425 last_name: Costanzo orcid: 0000-0001-9732-3815 - first_name: Pierre full_name: Mahou, Pierre last_name: Mahou - first_name: Mónika full_name: Hrtyan, Mónika id: 45A71A74-F248-11E8-B48F-1D18A9856A87 last_name: Hrtyan - first_name: Jie full_name: Wang, Jie last_name: Wang - first_name: Juan L full_name: Aguilera Servin, Juan L id: 2A67C376-F248-11E8-B48F-1D18A9856A87 last_name: Aguilera Servin orcid: 0000-0002-2862-8372 - first_name: Daniël full_name: van Damme, Daniël last_name: van Damme - first_name: Emmanuel full_name: Beaurepaire, Emmanuel last_name: Beaurepaire - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - first_name: Sebastian Y full_name: Bednarek, Sebastian Y last_name: Bednarek - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Johnson AJ, Dahhan DA, Gnyliukh N, et al. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences. 2021;118(51). doi:10.1073/pnas.2113046118 apa: Johnson, A. J., Dahhan, D. A., Gnyliukh, N., Kaufmann, W., Zheden, V., Costanzo, T., … Friml, J. (2021). The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2113046118 chicago: Johnson, Alexander J, Dana A Dahhan, Nataliia Gnyliukh, Walter Kaufmann, Vanessa Zheden, Tommaso Costanzo, Pierre Mahou, et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2113046118. ieee: A. J. Johnson et al., “The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis,” Proceedings of the National Academy of Sciences, vol. 118, no. 51. National Academy of Sciences, 2021. ista: Johnson AJ, Dahhan DA, Gnyliukh N, Kaufmann W, Zheden V, Costanzo T, Mahou P, Hrtyan M, Wang J, Aguilera Servin JL, van Damme D, Beaurepaire E, Loose M, Bednarek SY, Friml J. 2021. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences. 118(51), e2113046118. mla: Johnson, Alexander J., et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” Proceedings of the National Academy of Sciences, vol. 118, no. 51, e2113046118, National Academy of Sciences, 2021, doi:10.1073/pnas.2113046118. short: A.J. Johnson, D.A. Dahhan, N. Gnyliukh, W. Kaufmann, V. Zheden, T. Costanzo, P. Mahou, M. Hrtyan, J. Wang, J.L. Aguilera Servin, D. van Damme, E. Beaurepaire, M. Loose, S.Y. Bednarek, J. Friml, Proceedings of the National Academy of Sciences 118 (2021). date_created: 2021-08-11T14:11:43Z date_published: 2021-12-14T00:00:00Z date_updated: 2024-02-19T11:06:09Z day: '14' ddc: - '580' department: - _id: JiFr - _id: MaLo - _id: EvBe - _id: EM-Fac - _id: NanoFab doi: 10.1073/pnas.2113046118 external_id: isi: - '000736417600043' pmid: - '34907016' file: - access_level: open_access checksum: 8d01e72e22c4fb1584e72d8601947069 content_type: application/pdf creator: cchlebak date_created: 2021-12-15T08:59:40Z date_updated: 2021-12-15T08:59:40Z file_id: '10546' file_name: 2021_PNAS_Johnson.pdf file_size: 2757340 relation: main_file success: 1 file_date_updated: 2021-12-15T08:59:40Z has_accepted_license: '1' intvolume: ' 118' isi: 1 issue: '51' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: link: - relation: earlier_version url: https://doi.org/10.1101/2021.04.26.441441 record: - id: '14510' relation: dissertation_contains status: public - id: '14988' relation: research_data status: public status: public title: The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 118 year: '2021' ... --- _id: '7814' abstract: - lang: eng text: 'Scientific research is to date largely restricted to wealthy laboratories in developed nations due to the necessity of complex and expensive equipment. This inequality limits the capacity of science to be used as a diplomatic channel. Maker movements use open-source technologies including additive manufacturing (3D printing) and laser cutting, together with low-cost computers for developing novel products. This movement is setting the groundwork for a revolution, allowing scientific equipment to be sourced at a fraction of the cost and has the potential to increase the availability of equipment for scientists around the world. Science education is increasingly recognized as another channel for science diplomacy. In this perspective, we introduce the idea that the Maker movement and open-source technologies have the potential to revolutionize science, technology, engineering and mathematics (STEM) education worldwide. We present an open-source STEM didactic tool called SCOPES (Sparking Curiosity through Open-source Platforms in Education and Science). SCOPES is self-contained, independent of local resources, and cost-effective. SCOPES can be adapted to communicate complex subjects from genetics to neurobiology, perform real-world biological experiments and explore digitized scientific samples. We envision such platforms will enhance science diplomacy by providing a means for scientists to share their findings with classrooms and for educators to incorporate didactic concepts into STEM lessons. By providing students the opportunity to design, perform, and share scientific experiments, students also experience firsthand the benefits of a multinational scientific community. We provide instructions on how to build and use SCOPES on our webpage: http://scopeseducation.org.' acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: PreCl - _id: EM-Fac article_number: '48' article_processing_charge: No article_type: original author: - first_name: Robert J full_name: Beattie, Robert J id: 2E26DF60-F248-11E8-B48F-1D18A9856A87 last_name: Beattie orcid: 0000-0002-8483-8753 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler citation: ama: 'Beattie RJ, Hippenmeyer S, Pauler F. SCOPES: Sparking curiosity through Open-Source platforms in education and science. Frontiers in Education. 2020;5. doi:10.3389/feduc.2020.00048' apa: 'Beattie, R. J., Hippenmeyer, S., & Pauler, F. (2020). SCOPES: Sparking curiosity through Open-Source platforms in education and science. Frontiers in Education. Frontiers Media. https://doi.org/10.3389/feduc.2020.00048' chicago: 'Beattie, Robert J, Simon Hippenmeyer, and Florian Pauler. “SCOPES: Sparking Curiosity through Open-Source Platforms in Education and Science.” Frontiers in Education. Frontiers Media, 2020. https://doi.org/10.3389/feduc.2020.00048.' ieee: 'R. J. Beattie, S. Hippenmeyer, and F. Pauler, “SCOPES: Sparking curiosity through Open-Source platforms in education and science,” Frontiers in Education, vol. 5. Frontiers Media, 2020.' ista: 'Beattie RJ, Hippenmeyer S, Pauler F. 2020. SCOPES: Sparking curiosity through Open-Source platforms in education and science. Frontiers in Education. 5, 48.' mla: 'Beattie, Robert J., et al. “SCOPES: Sparking Curiosity through Open-Source Platforms in Education and Science.” Frontiers in Education, vol. 5, 48, Frontiers Media, 2020, doi:10.3389/feduc.2020.00048.' short: R.J. Beattie, S. Hippenmeyer, F. Pauler, Frontiers in Education 5 (2020). date_created: 2020-05-11T08:18:48Z date_published: 2020-05-08T00:00:00Z date_updated: 2021-01-12T08:15:42Z day: '08' ddc: - '570' department: - _id: SiHi doi: 10.3389/feduc.2020.00048 ec_funded: 1 file: - access_level: open_access checksum: a24ec24e38d843341ae620ec76c53688 content_type: application/pdf creator: dernst date_created: 2020-05-11T11:34:08Z date_updated: 2020-07-14T12:48:03Z file_id: '7818' file_name: 2020_FrontiersEduc_Beattie.pdf file_size: 1402146 relation: main_file file_date_updated: 2020-07-14T12:48:03Z has_accepted_license: '1' intvolume: ' 5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 264E56E2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02416 name: Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex - _id: 260018B0-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '725780' name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development publication: Frontiers in Education publication_identifier: issn: - 2504-284X publication_status: published publisher: Frontiers Media quality_controlled: '1' status: public title: 'SCOPES: Sparking curiosity through Open-Source platforms in education and science' 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: '2020' ... --- _id: '8139' abstract: - lang: eng text: 'Clathrin-mediated endocytosis (CME) is a crucial cellular process implicated in many aspects of plant growth, development, intra- and inter-cellular signaling, nutrient uptake and pathogen defense. Despite these significant roles, little is known about the precise molecular details of how it functions in planta. In order to facilitate the direct quantitative study of plant CME, here we review current routinely used methods and present refined, standardized quantitative imaging protocols which allow the detailed characterization of CME at multiple scales in plant tissues. These include: (i) an efficient electron microscopy protocol for the imaging of Arabidopsis CME vesicles in situ, thus providing a method for the detailed characterization of the ultra-structure of clathrin-coated vesicles; (ii) a detailed protocol and analysis for quantitative live-cell fluorescence microscopy to precisely examine the temporal interplay of endocytosis components during single CME events; (iii) a semi-automated analysis to allow the quantitative characterization of global internalization of cargos in whole plant tissues; and (iv) an overview and validation of useful genetic and pharmacological tools to interrogate the molecular mechanisms and function of CME in intact plant samples.' acknowledged_ssus: - _id: EM-Fac - _id: Bio acknowledgement: "This paper is dedicated to the memory of Christien Merrifield. He pioneered quantitative\r\nimaging approaches in mammalian CME and his mentorship inspired the development of all\r\nthe analysis methods presented here. His joy in research, pure scientific curiosity and\r\nmicroscopy excellence remain a constant inspiration. We thank Daniel Van Damme for gifting\r\nus the CLC2-GFP x TPLATE-TagRFP plants used in this manuscript. We further thank the\r\nScientific Service Units at IST Austria; specifically, the Electron Microscopy Facility for\r\ntechnical assistance (in particular Vanessa Zheden) and the BioImaging Facility BioImaging\r\nFacility for access to equipment. " article_number: jcs248062 article_processing_charge: No article_type: original author: - first_name: Alexander J full_name: Johnson, Alexander J id: 46A62C3A-F248-11E8-B48F-1D18A9856A87 last_name: Johnson orcid: 0000-0002-2739-8843 - first_name: Nataliia full_name: Gnyliukh, Nataliia id: 390C1120-F248-11E8-B48F-1D18A9856A87 last_name: Gnyliukh orcid: 0000-0002-2198-0509 - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Madhumitha full_name: Narasimhan, Madhumitha id: 44BF24D0-F248-11E8-B48F-1D18A9856A87 last_name: Narasimhan orcid: 0000-0002-8600-0671 - first_name: G full_name: Vert, G last_name: Vert - first_name: SY full_name: Bednarek, SY last_name: Bednarek - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Johnson AJ, Gnyliukh N, Kaufmann W, et al. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. 2020;133(15). doi:10.1242/jcs.248062 apa: Johnson, A. J., Gnyliukh, N., Kaufmann, W., Narasimhan, M., Vert, G., Bednarek, S., & Friml, J. (2020). Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.248062 chicago: Johnson, Alexander J, Nataliia Gnyliukh, Walter Kaufmann, Madhumitha Narasimhan, G Vert, SY Bednarek, and Jiří Friml. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of Cell Science. The Company of Biologists, 2020. https://doi.org/10.1242/jcs.248062. ieee: A. J. Johnson et al., “Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis,” Journal of Cell Science, vol. 133, no. 15. The Company of Biologists, 2020. ista: Johnson AJ, Gnyliukh N, Kaufmann W, Narasimhan M, Vert G, Bednarek S, Friml J. 2020. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. 133(15), jcs248062. mla: Johnson, Alexander J., et al. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of Cell Science, vol. 133, no. 15, jcs248062, The Company of Biologists, 2020, doi:10.1242/jcs.248062. short: A.J. Johnson, N. Gnyliukh, W. Kaufmann, M. Narasimhan, G. Vert, S. Bednarek, J. Friml, Journal of Cell Science 133 (2020). date_created: 2020-07-21T08:58:19Z date_published: 2020-08-06T00:00:00Z date_updated: 2023-12-01T13:51:07Z day: '06' ddc: - '575' department: - _id: JiFr - _id: EM-Fac doi: 10.1242/jcs.248062 ec_funded: 1 external_id: isi: - '000561047900021' pmid: - '32616560' file: - access_level: open_access checksum: 2d11f79a0b4e0a380fb002b933da331a content_type: application/pdf creator: ajohnson date_created: 2020-11-26T17:12:51Z date_updated: 2021-08-08T22:30:03Z embargo: 2021-08-07 file_id: '8815' file_name: 2020 - Johnson - JSC - plant CME toolbox.pdf file_size: 15150403 relation: main_file file_date_updated: 2021-08-08T22:30:03Z has_accepted_license: '1' intvolume: ' 133' isi: 1 issue: '15' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Journal of Cell Science publication_identifier: eissn: - 1477-9137 issn: - 0021-9533 publication_status: published publisher: The Company of Biologists quality_controlled: '1' related_material: record: - id: '14510' relation: dissertation_contains status: public scopus_import: '1' status: public title: Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 133 year: '2020' ... --- _id: '8284' abstract: - lang: eng text: Multiple resistance and pH adaptation (Mrp) antiporters are multi-subunit Na+ (or K+)/H+ exchangers representing an ancestor of many essential redox-driven proton pumps, such as respiratory complex I. The mechanism of coupling between ion or electron transfer and proton translocation in this large protein family is unknown. Here, we present the structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. It is a dimer of seven-subunit protomers with 50 trans-membrane helices each. Surface charge distribution within each monomer is remarkably asymmetric, revealing probable proton and sodium translocation pathways. On the basis of the structure we propose a mechanism where the coupling between sodium and proton translocation is facilitated by a series of electrostatic interactions between a cation and key charged residues. This mechanism is likely to be applicable to the entire family of redox proton pumps, where electron transfer to substrates replaces cation movements. acknowledged_ssus: - _id: EM-Fac - _id: LifeSc acknowledgement: This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster. We thank Dr Victor-Valentin Hodirnau and Daniel Johann Gütl from IST Austria for assistance with collecting cryo-EM data. We thank Prof. Masahiro Ito (Graduate School of Life Sciences, Toyo University, Japan) for a kind provision of plasmid DNA encoding Mrp from A. flavithermus WK1. JS is a recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria. article_number: e59407 article_processing_charge: No article_type: original author: - first_name: Julia full_name: Steiner, Julia id: 3BB67EB0-F248-11E8-B48F-1D18A9856A87 last_name: Steiner orcid: 0000-0003-0493-3775 - 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: Steiner J, Sazanov LA. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 2020;9. doi:10.7554/eLife.59407 apa: Steiner, J., & Sazanov, L. A. (2020). Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.59407 chicago: Steiner, Julia, and Leonid A Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.59407. ieee: J. Steiner and L. A. Sazanov, “Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter,” eLife, vol. 9. eLife Sciences Publications, 2020. ista: Steiner J, Sazanov LA. 2020. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 9, e59407. mla: Steiner, Julia, and Leonid A. Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” ELife, vol. 9, e59407, eLife Sciences Publications, 2020, doi:10.7554/eLife.59407. short: J. Steiner, L.A. Sazanov, ELife 9 (2020). date_created: 2020-08-24T06:24:04Z date_published: 2020-07-31T00:00:00Z date_updated: 2023-09-07T13:14:08Z day: '31' ddc: - '570' department: - _id: LeSa doi: 10.7554/eLife.59407 external_id: isi: - '000562123600001' pmid: - '32735215' file: - access_level: open_access checksum: b3656d14d5ddbb9d26e3074eea2d0c15 content_type: application/pdf creator: cziletti date_created: 2020-08-24T13:31:53Z date_updated: 2020-08-24T13:31:53Z file_id: '8289' file_name: 2020_eLife_Steiner.pdf file_size: 7320493 relation: main_file success: 1 file_date_updated: 2020-08-24T13:31:53Z has_accepted_license: '1' intvolume: ' 9' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26169496-B435-11E9-9278-68D0E5697425 grant_number: '24741' name: Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I publication: eLife publication_identifier: eissn: - 2050084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/ record: - id: '8353' relation: dissertation_contains status: public scopus_import: '1' status: public title: Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2020' ... --- _id: '8340' abstract: - lang: eng text: Mitochondria are sites of oxidative phosphorylation in eukaryotic cells. Oxidative phosphorylation operates by a chemiosmotic mechanism made possible by redox-driven proton pumping machines which establish a proton motive force across the inner mitochondrial membrane. This electrochemical proton gradient is used to drive ATP synthesis, which powers the majority of cellular processes such as protein synthesis, locomotion and signalling. In this thesis I investigate the structures and molecular mechanisms of two inner mitochondrial proton pumping enzymes, respiratory complex I and transhydrogenase. I present the first high-resolution structure of the full transhydrogenase from any species, and a significantly improved structure of complex I. Improving the resolution from 3.3 Å available previously to up to 2.3 Å in this thesis allowed us to model bound water molecules, crucial in the proton pumping mechanism. For both enzymes, up to five cryo-EM datasets with different substrates and inhibitors bound were solved to delineate the catalytic cycle and understand the proton pumping mechanism. In transhydrogenase, the proton channel is gated by reversible detachment of the NADP(H)-binding domain which opens the proton channel to the opposite sites of the membrane. In complex I, the proton channels are gated by reversible protonation of key glutamate and lysine residues and breaking of the water wire connecting the proton pumps with the quinone reduction site. The tight coupling between the redox and the proton pumping reactions in transhydrogenase is achieved by controlling the NADP(H) exchange which can only happen when the NADP(H)-binding domain interacts with the membrane domain. In complex I, coupling is achieved by cycling of the whole complex between the closed state, in which quinone can get reduced, and the open state, in which NADH can induce quinol ejection from the binding pocket. On the basis of these results I propose detailed mechanisms for catalytic cycles of transhydrogenase and complex I that are consistent with a large amount of previous work. In both enzymes, conformational and electrostatic mechanisms contribute to the overall catalytic process. Results presented here could be used for better understanding of the human pathologies arising from deficiencies of complex I or transhydrogenase and could be used to develop novel therapies. acknowledged_ssus: - _id: EM-Fac acknowledgement: 'I acknowledge the support of IST facilities, especially the Electron Miscroscopy facility for providing training and resources. Special thanks also go to cryo-EM specialists who helped me to collect the data present here: Dr Valentin Hodirnau (IST Austria), Dr Tom Heuser (IMBA, Vienna), Dr Rebecca Thompson (Uni. of Leeds) and Dr Jirka Nováček (CEITEC). This work has been supported by iNEXT, project number 653706, funded by the Horizon 2020 programme of the European Union. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Domen full_name: Kampjut, Domen id: 37233050-F248-11E8-B48F-1D18A9856A87 last_name: Kampjut citation: ama: Kampjut D. Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. 2020. doi:10.15479/AT:ISTA:8340 apa: Kampjut, D. (2020). Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8340 chicago: Kampjut, Domen. “Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8340. ieee: D. Kampjut, “Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes,” Institute of Science and Technology Austria, 2020. ista: Kampjut D. 2020. Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. Institute of Science and Technology Austria. mla: Kampjut, Domen. Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8340. short: D. Kampjut, Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes, Institute of Science and Technology Austria, 2020. date_created: 2020-09-07T18:42:23Z date_published: 2020-09-09T00:00:00Z date_updated: 2023-09-07T13:26:17Z day: '09' ddc: - '572' degree_awarded: PhD department: - _id: LeSa doi: 10.15479/AT:ISTA:8340 ec_funded: 1 file: - access_level: closed checksum: dd270baf82121eb4472ad19d77bf227c content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dkampjut date_created: 2020-09-08T13:32:06Z date_updated: 2021-09-11T22:30:04Z embargo_to: open_access file_id: '8345' file_name: ThesisFull20200908.docx file_size: 166146359 relation: source_file - access_level: open_access checksum: 82fce6f95ffa47ecc4ebca67ea2cc38c content_type: application/pdf creator: dernst date_created: 2020-09-14T15:02:20Z date_updated: 2021-09-11T22:30:04Z embargo: 2021-09-10 file_id: '8393' file_name: 2020_Thesis_Kampjut.pdf file_size: 13873769 relation: main_file file_date_updated: 2021-09-11T22:30:04Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: None page: '242' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-008-4 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6848' relation: part_of_dissertation status: public status: public supervisor: - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 title: Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ...