---
_id: '13126'
abstract:
- lang: eng
text: Mapping the complex and dense arrangement of cells and their connectivity
in brain tissue demands nanoscale spatial resolution imaging. Super-resolution
optical microscopy excels at visualizing specific molecules and individual cells
but fails to provide tissue context. Here, we developed Comprehensive Analysis
of Tissues across Scales (CATS), a technology to densely map brain tissue architecture
from millimeter regional to nanometer synaptic scales in diverse chemically fixed
brain preparations, including rodent and human. CATS uses fixation-compatible
extracellular labeling and optical imaging, including stimulated emission depletion
or expansion microscopy, to comprehensively delineate cellular structures. It
enables three-dimensional reconstruction of single synapses and mapping of synaptic
connectivity by identification and analysis of putative synaptic cleft regions.
Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed
and quantified the synaptic input and output structure of identified neurons.
We furthermore demonstrate applicability to clinically derived human tissue samples,
including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing
the cellular architecture of brain tissue in health and disease.
acknowledged_ssus:
- _id: ScienComp
- _id: Bio
- _id: PreCl
- _id: LifeSc
- _id: M-Shop
- _id: E-Lib
acknowledgement: "We thank Jakob Vorlaufer, Nathalie Agudelo-Dueñas, Wiebke Jahr,
Andreas Wartak for microscope maintenance and troubleshooting, Caroline Kreuzinger,
Anna Freeman, and Irene Erber for technical assistance and Matthias Tomschik for
support with obtaining human samples. We gratefully acknowledge Eder Miguel for
setting up webKnossos and Marek Šuplata for computational support and hardware control.
We are grateful to Ryuichi Shigemoto and Bernd Bickel for generous support, and
Michael Sixt and Scott Boyd (Stanford University) for discussions and critical reading
of the manuscript. PSD95-HaloTag mice were kindly provided by Seth Grant (University
of Edinburgh). We acknowledge expert support by IST Austria’s scientific computing,
imaging and optics, preclinical, and lab support facilities, and by the Library
and Miba machine shop.\r\nWe gratefully acknowledge funding by the following sources:
\r\nAustrian Science Fund (FWF) grant I3600-B27 (JGD)\r\nAustrian Science Fund (FWF)
grant DK W1232 (JGD, JMM)\r\nAustrian Science Fund (FWF) grant Z 312-B27, Wittgenstein
award (PJ)\r\nAustrian Science Funds (FWF) projects I4685-B, I6565-B (SYNABS) and
DOC 33-B27 (RH)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022
(JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European
Research Council (ERC) grant 715508 – REVERSEAUTISM (GN)\r\nEuropean Union’s Horizon
2020 research and innovation programme, European Research Council (ERC) grant 692692
– GIANTSYN (PJ)\r\nMarie Skłodowska-Curie Actions Fellowship GA no. 665385 under
the EU Horizon 2020 program (JMM, JL)\r\nMarie Skłodowska-Curie Actions Individual
Fellowship 101026635 under the EU Horizon 2020 program (JFW)"
article_processing_charge: No
author:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Danzl JG. Research data for the publication “Imaging brain tissue architecture
across millimeter to nanometer scales.” 2023. doi:10.15479/AT:ISTA:13126
apa: Danzl, J. G. (2023). Research data for the publication “Imaging brain tissue
architecture across millimeter to nanometer scales.” Institute of Science and
Technology Austria. https://doi.org/10.15479/AT:ISTA:13126
chicago: Danzl, Johann G. “Research Data for the Publication ‘Imaging Brain Tissue
Architecture across Millimeter to Nanometer Scales.’” Institute of Science and
Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:13126.
ieee: J. G. Danzl, “Research data for the publication ‘Imaging brain tissue architecture
across millimeter to nanometer scales.’” Institute of Science and Technology Austria,
2023.
ista: Danzl JG. 2023. Research data for the publication ‘Imaging brain tissue architecture
across millimeter to nanometer scales’, Institute of Science and Technology Austria,
10.15479/AT:ISTA:13126.
mla: Danzl, Johann G. Research Data for the Publication “Imaging Brain Tissue
Architecture across Millimeter to Nanometer Scales.” Institute of Science
and Technology Austria, 2023, doi:10.15479/AT:ISTA:13126.
short: J.G. Danzl, (2023).
contributor:
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last_name: Michalska
- first_name: Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- first_name: Philipp
id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
last_name: Velicky
orcid: 0000-0002-2340-7431
- first_name: Hana
id: ee3cb6ca-ec98-11ea-ae11-ff703e2254ed
last_name: Stefanickova
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last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Alban
id: 9ac8f577-2357-11eb-997a-e566c5550886
last_name: Cenameri
- first_name: Christoph M
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last_name: Sommer
orcid: 0000-0003-1216-9105
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last_name: Amberg
orcid: 0000-0002-3183-8207
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last_name: Venturino
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last_name: Siegert
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last_name: Novarino
orcid: 0000-0002-7673-7178
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id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
corr_author: '1'
date_created: 2023-06-07T07:15:12Z
date_published: 2023-08-04T00:00:00Z
date_updated: 2026-04-14T08:34:35Z
day: '04'
ddc:
- '610'
department:
- _id: JoDa
- _id: SaSi
- _id: GaNo
- _id: PeJo
- _id: Bio
- _id: RySh
doi: 10.15479/AT:ISTA:13126
ec_funded: 1
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has_accepted_license: '1'
month: '08'
oa: 1
oa_version: Published Version
project:
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call_identifier: FWF
grant_number: I03600
name: Optical control of synaptic function via adhesion molecules
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
- _id: 23889792-32DE-11EA-91FC-C7463DDC885E
grant_number: LS18-022
name: High content imaging to decode human immune cell interactions in health and
allergic disease
- _id: 25444568-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715508'
name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo
and in vitro Models
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9
call_identifier: H2020
grant_number: '101026635'
name: Synaptic computations of the hippocampal CA3 circuitry
publisher: Institute of Science and Technology Austria
related_material:
link:
- description: 'Original data for Fig. 5d, Fig. 5d (N2V) and Fig. 5f-i, provided
via an external link due to the large size (>10GB) of the datasets. '
relation: research_data
url: https://pub.ista.ac.at/group_danzl/data/CATS/
record:
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relation: used_in_publication
status: public
status: public
title: Research data for the publication "Imaging brain tissue architecture across
millimeter to nanometer scales"
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
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user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13127'
abstract:
- lang: eng
text: Cooperative disease defense emerges as group-level collective behavior, yet
how group members make the underlying individual decisions is poorly understood.
Using garden ants and fungal pathogens as an experimental model, we derive the
rules governing individual ant grooming choices and show how they produce colony-level
hygiene. Time-resolved behavioral analysis, pathogen quantification, and probabilistic
modeling reveal that ants increase grooming and preferentially target highly-infectious
individuals when perceiving high pathogen load, but transiently suppress grooming
after having been groomed by nestmates. Ants thus react to both, the infectivity
of others and the social feedback they receive on their own contagiousness. While
inferred solely from momentary ant decisions, these behavioral rules quantitatively
predict hour-long experimental dynamics, and synergistically combine into efficient
colony-wide pathogen removal. Our analyses show that noisy individual decisions
based on only local, incomplete, yet dynamically-updated information on pathogen
threat and social feedback can lead to potent collective disease defense.
acknowledged_ssus:
- _id: LifeSc
acknowledgement: We thank Mike Bidochka for the fungal strains, the ISTA Social Immunity
Team for ant collection, Hanna Leitner for experimental and molecular support, Jennifer
Robb and Lukas Lindorfer for microscopy, and the LabSupport Facility at ISTA for
general laboratory support. We further thank Victor Mireles, Iain Couzin, Fabian
Theis and the Social Immunity Team for continued feedback throughout, and Michael
Sixt, Yuko Ulrich, Koos Boomsma, Erika Dawson, Megan Kutzer and Hinrich Schulenburg
for comments on the manuscript. This project has received funding from the European
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
program (Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency
of the Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science
Program (Grant No. RGP0065/2012) to GT.
article_number: '3232'
article_processing_charge: Yes
article_type: original
author:
- first_name: Barbara E
full_name: Casillas Perez, Barbara E
id: 351ED2AA-F248-11E8-B48F-1D18A9856A87
last_name: Casillas Perez
- first_name: Katarína
full_name: Bod'Ová, Katarína
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bod'Ová
orcid: 0000-0002-7214-0171
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. Dynamic pathogen
detection and social feedback shape collective hygiene in ants. Nature Communications.
2023;14. doi:10.1038/s41467-023-38947-y
apa: Casillas Perez, B. E., Bodova, K., Grasse, A. V., Tkačik, G., & Cremer,
S. (2023). Dynamic pathogen detection and social feedback shape collective hygiene
in ants. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38947-y
chicago: Casillas Perez, Barbara E, Katarina Bodova, Anna V Grasse, Gašper Tkačik,
and Sylvia Cremer. “Dynamic Pathogen Detection and Social Feedback Shape Collective
Hygiene in Ants.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38947-y.
ieee: B. E. Casillas Perez, K. Bodova, A. V. Grasse, G. Tkačik, and S. Cremer, “Dynamic
pathogen detection and social feedback shape collective hygiene in ants,” Nature
Communications, vol. 14. Springer Nature, 2023.
ista: Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. 2023. Dynamic
pathogen detection and social feedback shape collective hygiene in ants. Nature
Communications. 14, 3232.
mla: Casillas Perez, Barbara E., et al. “Dynamic Pathogen Detection and Social Feedback
Shape Collective Hygiene in Ants.” Nature Communications, vol. 14, 3232,
Springer Nature, 2023, doi:10.1038/s41467-023-38947-y.
short: B.E. Casillas Perez, K. Bodova, A.V. Grasse, G. Tkačik, S. Cremer, Nature
Communications 14 (2023).
corr_author: '1'
date_created: 2023-06-11T22:00:40Z
date_published: 2023-06-03T00:00:00Z
date_updated: 2025-04-14T07:47:53Z
day: '03'
ddc:
- '570'
department:
- _id: SyCr
- _id: GaTk
doi: 10.1038/s41467-023-38947-y
ec_funded: 1
external_id:
isi:
- '001002562700005'
pmid:
- '37270641'
file:
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content_type: application/pdf
creator: dernst
date_created: 2023-06-13T08:05:46Z
date_updated: 2023-06-13T08:05:46Z
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file_name: 2023_NatureComm_CasillasPerez.pdf
file_size: 2358167
relation: main_file
success: 1
file_date_updated: 2023-06-13T08:05:46Z
fulldoi: https://doi.org/10.1038/s41467-023-38947-y
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2649B4DE-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771402'
name: Epidemics in ant societies on a chip
- _id: 255008E4-B435-11E9-9278-68D0E5697425
grant_number: RGP0065/2012
name: Information processing and computation in fish groups
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
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relation: research_data
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scopus_import: '1'
status: public
title: Dynamic pathogen detection and social feedback shape collective hygiene in
ants
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: 14
year: '2023'
...
---
_id: '14040'
abstract:
- lang: eng
text: Robust oxygenic photosynthesis requires a suite of accessory factors to ensure
efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex.
The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction
center polypeptide and promotes the initial steps of PSII assembly, but its binding
site is unclear. Here we use cryo-electron microscopy to determine the structure
of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached.
Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that
ultimately ligate the water-oxidising Mn4CaO5 cluster, thereby preventing the
premature binding of Mn2+ and Ca2+ ions and protecting the site from damage. Interactions
with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall,
our work provides valuable insights into the early stages of PSII assembly and
the structural changes that create the binding site for the Mn4CaO5 cluster.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: ScienComp
acknowledgement: P.J.N. and J.W.M. are grateful for the support of the Biotechnology
& Biological Sciences Research Council (awards BB/L003260/1 and BB/P00931X/1). J.
Knoppová, R.S. and J. Komenda were supported by the Czech Science Foundation (project
19-29225X) and by ERC project Photoredesign (no. 854126) and L.A.S. 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.
article_number: '4681'
article_processing_charge: Yes
article_type: original
author:
- first_name: Ziyu
full_name: Zhao, Ziyu
last_name: Zhao
- first_name: Irene
full_name: Vercellino, Irene
id: 3ED6AF16-F248-11E8-B48F-1D18A9856A87
last_name: Vercellino
orcid: 0000-0001-5618-3449
- first_name: Jana
full_name: Knoppová, Jana
last_name: Knoppová
- first_name: Roman
full_name: Sobotka, Roman
last_name: Sobotka
- first_name: James W.
full_name: Murray, James W.
last_name: Murray
- first_name: Peter J.
full_name: Nixon, Peter J.
last_name: Nixon
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
- first_name: Josef
full_name: Komenda, Josef
last_name: Komenda
citation:
ama: Zhao Z, Vercellino I, Knoppová J, et al. The Ycf48 accessory factor occupies
the site of the oxygen-evolving manganese cluster during photosystem II biogenesis.
Nature Communications. 2023;14. doi:10.1038/s41467-023-40388-6
apa: Zhao, Z., Vercellino, I., Knoppová, J., Sobotka, R., Murray, J. W., Nixon,
P. J., … Komenda, J. (2023). The Ycf48 accessory factor occupies the site of the
oxygen-evolving manganese cluster during photosystem II biogenesis. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-023-40388-6
chicago: Zhao, Ziyu, Irene Vercellino, Jana Knoppová, Roman Sobotka, James W. Murray,
Peter J. Nixon, Leonid A Sazanov, and Josef Komenda. “The Ycf48 Accessory Factor
Occupies the Site of the Oxygen-Evolving Manganese Cluster during Photosystem
II Biogenesis.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-40388-6.
ieee: Z. Zhao et al., “The Ycf48 accessory factor occupies the site of the
oxygen-evolving manganese cluster during photosystem II biogenesis,” Nature
Communications, vol. 14. Springer Nature, 2023.
ista: Zhao Z, Vercellino I, Knoppová J, Sobotka R, Murray JW, Nixon PJ, Sazanov
LA, Komenda J. 2023. The Ycf48 accessory factor occupies the site of the oxygen-evolving
manganese cluster during photosystem II biogenesis. Nature Communications. 14,
4681.
mla: Zhao, Ziyu, et al. “The Ycf48 Accessory Factor Occupies the Site of the Oxygen-Evolving
Manganese Cluster during Photosystem II Biogenesis.” Nature Communications,
vol. 14, 4681, Springer Nature, 2023, doi:10.1038/s41467-023-40388-6.
short: Z. Zhao, I. Vercellino, J. Knoppová, R. Sobotka, J.W. Murray, P.J. Nixon,
L.A. Sazanov, J. Komenda, Nature Communications 14 (2023).
corr_author: '1'
date_created: 2023-08-13T22:01:13Z
date_published: 2023-08-04T00:00:00Z
date_updated: 2025-04-23T13:05:33Z
day: '04'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1038/s41467-023-40388-6
external_id:
isi:
- '001042606700004'
pmid:
- '37542031'
file:
- access_level: open_access
checksum: 3b9043df3d51c300f9be95eac3ff9d0b
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T07:01:12Z
date_updated: 2023-08-14T07:01:12Z
file_id: '14044'
file_name: 2023_NatureComm_Zhao.pdf
file_size: 2315325
relation: main_file
success: 1
file_date_updated: 2023-08-14T07:01:12Z
fulldoi: https://doi.org/10.1038/s41467-023-40388-6
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '08'
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'
scopus_import: '1'
status: public
title: The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese
cluster during photosystem II biogenesis
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: 14
year: '2023'
...
---
_id: '14361'
abstract:
- lang: eng
text: Whether one considers swarming insects, flocking birds, or bacterial colonies,
collective motion arises from the coordination of individuals and entails the
adjustment of their respective velocities. In particular, in close confinements,
such as those encountered by dense cell populations during development or regeneration,
collective migration can only arise coordinately. Yet, how individuals unify their
velocities is often not understood. Focusing on a finite number of cells in circular
confinements, we identify waves of polymerizing actin that function as a pacemaker
governing the speed of individual cells. We show that the onset of collective
motion coincides with the synchronization of the wave nucleation frequencies across
the population. Employing a simpler and more readily accessible mechanical model
system of active spheres, we identify the synchronization of the individuals’
internal oscillators as one of the essential requirements to reach the corresponding
collective state. The mechanical ‘toy’ experiment illustrates that the global
synchronous state is achieved by nearest neighbor coupling. We suggest by analogy
that local coupling and the synchronization of actin waves are essential for the
emergent, self-organized motion of cell collectives.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: M-Shop
acknowledgement: We thank K. O’Keeffe, E. Hannezo, P. Devreotes, C. Dessalles, and
E. Martens for discussion and/or critical reading of the manuscript; the Bioimaging
Facility of ISTA for excellent support, as well as the Life Science Facility and
the Miba Machine Shop of ISTA. This work was supported by the European Research
Council (ERC StG 281556 and CoG 724373) to M.S.
article_number: '5633'
article_processing_charge: Yes
article_type: original
author:
- first_name: Michael
full_name: Riedl, Michael
id: 3BE60946-F248-11E8-B48F-1D18A9856A87
last_name: Riedl
orcid: 0000-0003-4844-6311
- first_name: Isabelle D
full_name: Mayer, Isabelle D
id: 61763940-15b2-11ec-abd3-cfaddfbc66b4
last_name: Mayer
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. Synchronization in collectively
moving inanimate and living active matter. Nature Communications. 2023;14.
doi:10.1038/s41467-023-41432-1
apa: Riedl, M., Mayer, I. D., Merrin, J., Sixt, M. K., & Hof, B. (2023). Synchronization
in collectively moving inanimate and living active matter. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-023-41432-1
chicago: Riedl, Michael, Isabelle D Mayer, Jack Merrin, Michael K Sixt, and Björn
Hof. “Synchronization in Collectively Moving Inanimate and Living Active Matter.”
Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41432-1.
ieee: M. Riedl, I. D. Mayer, J. Merrin, M. K. Sixt, and B. Hof, “Synchronization
in collectively moving inanimate and living active matter,” Nature Communications,
vol. 14. Springer Nature, 2023.
ista: Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. 2023. Synchronization in collectively
moving inanimate and living active matter. Nature Communications. 14, 5633.
mla: Riedl, Michael, et al. “Synchronization in Collectively Moving Inanimate and
Living Active Matter.” Nature Communications, vol. 14, 5633, Springer Nature,
2023, doi:10.1038/s41467-023-41432-1.
short: M. Riedl, I.D. Mayer, J. Merrin, M.K. Sixt, B. Hof, Nature Communications
14 (2023).
corr_author: '1'
date_created: 2023-09-24T22:01:10Z
date_published: 2023-09-13T00:00:00Z
date_updated: 2025-04-14T13:10:03Z
day: '13'
ddc:
- '530'
- '570'
department:
- _id: MiSi
- _id: NanoFab
- _id: BjHo
doi: 10.1038/s41467-023-41432-1
ec_funded: 1
external_id:
isi:
- '001087583700030'
pmid:
- '37704595'
file:
- access_level: open_access
checksum: 82d2d4ad736cc8493db8ce45cd313f7b
content_type: application/pdf
creator: dernst
date_created: 2023-09-25T08:32:37Z
date_updated: 2023-09-25T08:32:37Z
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file_date_updated: 2023-09-25T08:32:37Z
fulldoi: https://doi.org/10.1038/s41467-023-41432-1
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular Navigation Along Spatial Gradients
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Synchronization in collectively moving inanimate and living active matter
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: 14
year: '2023'
...
---
_id: '14363'
abstract:
- lang: eng
text: Mitochondrial networks remodel their connectivity, content, and subcellular
localization to support optimized energy production in conditions of increased
environmental or cellular stress. Microglia rely on mitochondria to respond to
these stressors, however our knowledge about mitochondrial networks and their
adaptations in microglia in vivo is limited. Here, we generate a mouse model that
selectively labels mitochondria in microglia. We identify that mitochondrial networks
are more fragmented with increased content and perinuclear localization in vitro
vs. in vivo. Mitochondrial networks adapt similarly in microglia closest to the
injury site after optic nerve crush. Preventing microglial UCP2 increase after
injury by selective knockout induces cellular stress. This results in mitochondrial
hyperfusion in male microglia, a phenotype absent in females due to circulating
estrogens. Our results establish the foundation for mitochondrial network analysis
of microglia in vivo, emphasizing the importance of mitochondrial-based sex effects
of microglia in other pathologies.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
acknowledgement: We thank the Scientific Service Units (SSU) of ISTA through resources
provided by the Imaging and Optics Facility (IOF), the Lab Support Facility (LSF),
and the Pre-Clinical Facility (PCF) team, specifically Sonja Haslinger and Michael
Schunn for excellent mouse colony management and support. This research was supported
by the FWF Sonderforschungsbereich F83 (to E.E.P). We thank Bálint Nagy, Ryan John
A. Cubero, Marco Benevento and all members of the Siegert group for constant feedback
on the project and article.
article_number: '107780'
article_processing_charge: Yes
article_type: original
author:
- first_name: Margaret E
full_name: Maes, Margaret E
id: 3838F452-F248-11E8-B48F-1D18A9856A87
last_name: Maes
orcid: 0000-0001-9642-1085
- first_name: Gloria
full_name: Colombo, Gloria
id: 3483CF6C-F248-11E8-B48F-1D18A9856A87
last_name: Colombo
orcid: 0000-0001-9434-8902
- first_name: Florianne E
full_name: Schoot Uiterkamp, Florianne E
id: 3526230C-F248-11E8-B48F-1D18A9856A87
last_name: Schoot Uiterkamp
- first_name: Felix
full_name: Sternberg, Felix
last_name: Sternberg
- first_name: Alessandro
full_name: Venturino, Alessandro
id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
last_name: Venturino
orcid: 0000-0003-2356-9403
- first_name: Elena E.
full_name: Pohl, Elena E.
last_name: Pohl
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
citation:
ama: Maes ME, Colombo G, Schoot Uiterkamp FE, et al. Mitochondrial network adaptations
of microglia reveal sex-specific stress response after injury and UCP2 knockout.
iScience. 2023;26(10). doi:10.1016/j.isci.2023.107780
apa: Maes, M. E., Colombo, G., Schoot Uiterkamp, F. E., Sternberg, F., Venturino,
A., Pohl, E. E., & Siegert, S. (2023). Mitochondrial network adaptations of
microglia reveal sex-specific stress response after injury and UCP2 knockout.
IScience. Elsevier. https://doi.org/10.1016/j.isci.2023.107780
chicago: Maes, Margaret E, Gloria Colombo, Florianne E Schoot Uiterkamp, Felix Sternberg,
Alessandro Venturino, Elena E. Pohl, and Sandra Siegert. “Mitochondrial Network
Adaptations of Microglia Reveal Sex-Specific Stress Response after Injury and
UCP2 Knockout.” IScience. Elsevier, 2023. https://doi.org/10.1016/j.isci.2023.107780.
ieee: M. E. Maes et al., “Mitochondrial network adaptations of microglia
reveal sex-specific stress response after injury and UCP2 knockout,” iScience,
vol. 26, no. 10. Elsevier, 2023.
ista: Maes ME, Colombo G, Schoot Uiterkamp FE, Sternberg F, Venturino A, Pohl EE,
Siegert S. 2023. Mitochondrial network adaptations of microglia reveal sex-specific
stress response after injury and UCP2 knockout. iScience. 26(10), 107780.
mla: Maes, Margaret E., et al. “Mitochondrial Network Adaptations of Microglia Reveal
Sex-Specific Stress Response after Injury and UCP2 Knockout.” IScience,
vol. 26, no. 10, 107780, Elsevier, 2023, doi:10.1016/j.isci.2023.107780.
short: M.E. Maes, G. Colombo, F.E. Schoot Uiterkamp, F. Sternberg, A. Venturino,
E.E. Pohl, S. Siegert, IScience 26 (2023).
corr_author: '1'
date_created: 2023-09-24T22:01:11Z
date_published: 2023-10-20T00:00:00Z
date_updated: 2024-10-09T21:07:01Z
day: '20'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1016/j.isci.2023.107780
external_id:
isi:
- '001080403500001'
pmid:
- '37731609'
file:
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content_type: application/pdf
creator: dernst
date_created: 2023-11-07T08:53:21Z
date_updated: 2023-11-07T08:53:21Z
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file_date_updated: 2023-11-07T08:53:21Z
fulldoi: https://doi.org/10.1016/j.isci.2023.107780
has_accepted_license: '1'
intvolume: ' 26'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: iScience
publication_identifier:
eissn:
- 2589-0042
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mitochondrial network adaptations of microglia reveal sex-specific stress response
after injury and UCP2 knockout
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: 26
year: '2023'
...
---
_id: '14562'
abstract:
- lang: eng
text: "Regulation of the Arp2/3 complex is required for productive nucleation of
branched actin networks. An emerging aspect of regulation is the incorporation
of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit
isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity
and branch junction stability. We have combined reverse genetics and cellular
structural biology to describe how ArpC5 and ArpC5L differentially affect cell
migration. Both define the structural stability of ArpC1 in branch junctions and,
in turn, by determining protrusion characteristics, affect protein dynamics and
actin network ultrastructure. ArpC5 isoforms also affect the positioning of members
of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament
elongators, which mediate ArpC5 isoform–specific effects on the actin assembly
level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling
pathway enhancing cell migration.\r\n"
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
- _id: ScienComp
- _id: EM-Fac
acknowledgement: "We would like to thank K. von Peinen and B. Denker (Helmholtz Centre
for Infection Research, Braunschweig, Germany) for experimental and technical assistance,
respectively.\r\nFunding: This research was supported by the Scientific Service
Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp),
the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the
Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the
Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group
GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft
(DFG) to J.F. and K.R."
article_processing_charge: No
author:
- 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: Schur FK. Research data of the publication “ArpC5 isoforms regulate Arp2/3
complex-dependent protrusion through differential Ena/VASP positioning.” 2023.
doi:10.15479/AT:ISTA:14562
apa: Schur, F. K. (2023). Research data of the publication “ArpC5 isoforms regulate
Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.”
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14562
chicago: Schur, Florian KM. “Research Data of the Publication ‘ArpC5 Isoforms Regulate
Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.’”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14562.
ieee: F. K. Schur, “Research data of the publication ‘ArpC5 isoforms regulate Arp2/3
complex-dependent protrusion through differential Ena/VASP positioning.’” Institute
of Science and Technology Austria, 2023.
ista: Schur FK. 2023. Research data of the publication ‘ArpC5 isoforms regulate
Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning’,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:14562.
mla: Schur, Florian KM. Research Data of the Publication “ArpC5 Isoforms Regulate
Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.”
Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14562.
short: F.K. Schur, (2023).
contributor:
- contributor_type: researcher
first_name: Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- contributor_type: researcher
first_name: Manjunath
id: 305ab18b-dc7d-11ea-9b2f-b58195228ea2
last_name: Javoor
- contributor_type: researcher
first_name: Julia
id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87
last_name: Datler
orcid: 0000-0002-3616-8580
- contributor_type: researcher
first_name: Hermann
last_name: Döring
- contributor_type: researcher
first_name: Florian
id: b9d234ba-9e33-11ed-95b6-cd561df280e6
last_name: Hofer
- contributor_type: researcher
first_name: Georgi A
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
orcid: 0000-0001-8370-6161
- contributor_type: researcher
first_name: Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- contributor_type: researcher
first_name: Jan
last_name: Faix
- contributor_type: researcher
first_name: Klemens
last_name: Rottner
- contributor_type: researcher
first_name: Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
corr_author: '1'
date_created: 2023-11-20T09:22:33Z
date_published: 2023-11-21T00:00:00Z
date_updated: 2025-04-23T08:46:21Z
day: '21'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.15479/AT:ISTA:14562
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fulldoi: https://doi.org/10.15479/AT:ISTA:14562
has_accepted_license: '1'
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
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12334'
relation: used_in_publication
status: public
status: public
title: Research data of the publication "ArpC5 isoforms regulate Arp2/3 complex-dependent
protrusion through differential Ena/VASP positioning"
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14644'
abstract:
- lang: eng
text: Transcription by RNA polymerase II (Pol II) can be repressed by noncoding
RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs
repress transcription remains unclear. Here we present cryo-electron microscopy
structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA
and RNA bind to Pol II during transcription elongation. Further, we show how domains
of the general transcription factor TFIIF affect complex dynamics and control
repressive activity. Together, we reveal how a non-coding RNA can regulate mammalian
gene expression.
acknowledged_ssus:
- _id: LifeSc
- _id: EM-Fac
- _id: PreCl
acknowledgement: "We thank B. Kaczmarek and other members of the Bernecky lab for
helpful discussions. We thank V.-V. Hodirnau for SerialEM data collection and support
with EPU data collection. We thank D. Slade for the wild type TFIIF expression\r\nplasmid.
We thank N. Thompson and R. Burgess for the 8WG16 hybridoma cell line. We thank
C. Plaschka and M. Loose for critical reading of the manuscript. This work was supported
by Austrian Science Fund (FWF) grant P34185. This research was further supported
by the Scientific Service Units (SSU) of IST Austria through resources provided
by the Lab Support Facility (LSF), Electron Microscopy Facility (EMF), Scientific
Computing (SciComp), and the Preclinical Facility (PCF)."
article_processing_charge: No
author:
- first_name: Katarina
full_name: Tluckova, Katarina
id: 4AC7D980-F248-11E8-B48F-1D18A9856A87
last_name: Tluckova
- first_name: Anita P
full_name: Testa Salmazo, Anita P
id: 41F1F098-F248-11E8-B48F-1D18A9856A87
last_name: Testa Salmazo
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
citation:
ama: Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional
repression by noncoding RNA. doi:10.15479/AT:ISTA:14644
apa: Tluckova, K., Testa Salmazo, A. P., & Bernecky, C. (n.d.). Mechanism of
mammalian transcriptional repression by noncoding RNA. Institute of Science and
Technology Austria. https://doi.org/10.15479/AT:ISTA:14644
chicago: Tluckova, Katarina, Anita P Testa Salmazo, and Carrie Bernecky. “Mechanism
of Mammalian Transcriptional Repression by Noncoding RNA.” Institute of Science
and Technology Austria, n.d. https://doi.org/10.15479/AT:ISTA:14644.
ieee: K. Tluckova, A. P. Testa Salmazo, and C. Bernecky, “Mechanism of mammalian
transcriptional repression by noncoding RNA.” Institute of Science and Technology
Austria.
ista: Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional
repression by noncoding RNA. 10.15479/AT:ISTA:14644.
mla: Tluckova, Katarina, et al. Mechanism of Mammalian Transcriptional Repression
by Noncoding RNA. Institute of Science and Technology Austria, doi:10.15479/AT:ISTA:14644.
short: K. Tluckova, A.P. Testa Salmazo, C. Bernecky, (n.d.).
corr_author: '1'
date_created: 2023-12-04T14:51:00Z
date_published: 2023-12-05T00:00:00Z
date_updated: 2025-11-20T10:28:37Z
day: '05'
ddc:
- '572'
doi: 10.15479/AT:ISTA:14644
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file_date_updated: 2023-12-05T10:37:02Z
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has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Submitted Version
project:
- _id: c08a6700-5a5b-11eb-8a69-82a722b2bc30
grant_number: P34185
name: Regulation of mammalian transcription by noncoding RNA
publication_status: draft
publisher: Institute of Science and Technology Austria
related_material:
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- id: '18778'
relation: later_version
status: public
status: public
title: Mechanism of mammalian transcriptional repression by noncoding RNA
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
OA_place: publisher
OA_type: hybrid
_id: '13267'
abstract:
- lang: eng
text: Three-dimensional (3D) reconstruction of living brain tissue down to an individual
synapse level would create opportunities for decoding the dynamics and structure–function
relationships of the brain’s complex and dense information processing network;
however, this has been hindered by insufficient 3D resolution, inadequate signal-to-noise
ratio and prohibitive light burden in optical imaging, whereas electron microscopy
is inherently static. Here we solved these challenges by developing an integrated
optical/machine-learning technology, LIONESS (live information-optimized nanoscopy
enabling saturated segmentation). This leverages optical modifications to stimulated
emission depletion microscopy in comprehensively, extracellularly labeled tissue
and previous information on sample structure via machine learning to simultaneously
achieve isotropic super-resolution, high signal-to-noise ratio and compatibility
with living tissue. This allows dense deep-learning-based instance segmentation
and 3D reconstruction at a synapse level, incorporating molecular, activity and
morphodynamic information. LIONESS opens up avenues for studying the dynamic functional
(nano-)architecture of living brain tissue.
acknowledged_ssus:
- _id: ScienComp
- _id: Bio
- _id: PreCl
- _id: E-Lib
- _id: LifeSc
- _id: M-Shop
acknowledgement: "We thank J. Vorlaufer, N. Agudelo and A. Wartak for microscope maintenance
and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, M. Šuplata
for hardware control support and M. Cunha dos Santos for initial exploration of
software. We\r\nthank P. Henderson for advice on deep-learning training and M. Sixt,
S. Boyd and T. Weiss for discussions and critical reading of the manuscript. L.
Lavis (Janelia Research Campus) generously provided the JF585-HaloTag ligand. We
acknowledge expert support by IST\r\nAustria’s scientific computing, imaging and
optics, preclinical, library and laboratory support facilities and by the Miba machine
shop. We gratefully acknowledge funding by the following sources: Austrian Science
Fund (F.W.F.) grant no. I3600-B27 (J.G.D.), grant no. DK W1232\r\n(J.G.D. and J.M.M.)
and grant no. Z 312-B27, Wittgenstein award (P.J.); the Gesellschaft für Forschungsförderung
NÖ grant no. LSC18-022 (J.G.D.); an ISTA Interdisciplinary project grant (J.G.D.
and B.B.); the European Union’s Horizon 2020 research and innovation programme,\r\nMarie-Skłodowska
Curie grant 665385 (J.M.M. and J.L.); the European Union’s Horizon 2020 research
and innovation programme, European Research Council grant no. 715767, MATERIALIZABLE
(B.B.); grant no. 715508, REVERSEAUTISM (G.N.); grant no. 695568, SYNNOVATE (S.G.N.G.);
and grant no. 692692, GIANTSYN (P.J.); the Simons\r\nFoundation Autism Research
Initiative grant no. 529085 (S.G.N.G.); the Wellcome Trust Technology Development
grant no. 202932 (S.G.N.G.); the Marie Skłodowska-Curie Actions Individual Fellowship
no. 101026635 under the EU Horizon 2020 program (J.F.W.);\r\nthe Human Frontier
Science Program postdoctoral fellowship LT000557/2018 (W.J.); and the National Science
Foundation grant no. IIS-1835231 (H.P.) and NCS-FO-2124179 (H.P.)."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Philipp
full_name: Velicky, Philipp
id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
last_name: Velicky
orcid: 0000-0002-2340-7431
- first_name: Eder
full_name: Miguel Villalba, Eder
id: 3FB91342-F248-11E8-B48F-1D18A9856A87
last_name: Miguel Villalba
orcid: 0000-0001-5665-0430
- first_name: Julia M
full_name: Michalska, Julia M
id: 443DB6DE-F248-11E8-B48F-1D18A9856A87
last_name: Michalska
orcid: 0000-0003-3862-1235
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- first_name: Donglai
full_name: Wei, Donglai
last_name: Wei
- first_name: Zudi
full_name: Lin, Zudi
last_name: Lin
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Jakob
full_name: Troidl, Jakob
last_name: Troidl
- first_name: Johanna
full_name: Beyer, Johanna
last_name: Beyer
- first_name: Yoav
full_name: Ben Simon, Yoav
id: 43DF3136-F248-11E8-B48F-1D18A9856A87
last_name: Ben Simon
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Wiebke
full_name: Jahr, Wiebke
id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
last_name: Jahr
orcid: 0000-0003-0201-2315
- first_name: Alban
full_name: Cenameri, Alban
id: 9ac8f577-2357-11eb-997a-e566c5550886
last_name: Cenameri
- first_name: Johannes
full_name: Broichhagen, Johannes
last_name: Broichhagen
- first_name: Seth G.N.
full_name: Grant, Seth G.N.
last_name: Grant
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Hanspeter
full_name: Pfister, Hanspeter
last_name: Pfister
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Velicky P, Miguel Villalba E, Michalska JM, et al. Dense 4D nanoscale reconstruction
of living brain tissue. Nature Methods. 2023;20:1256-1265. doi:10.1038/s41592-023-01936-6
apa: Velicky, P., Miguel Villalba, E., Michalska, J. M., Lyudchik, J., Wei, D.,
Lin, Z., … Danzl, J. G. (2023). Dense 4D nanoscale reconstruction of living brain
tissue. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-023-01936-6
chicago: Velicky, Philipp, Eder Miguel Villalba, Julia M Michalska, Julia Lyudchik,
Donglai Wei, Zudi Lin, Jake Watson, et al. “Dense 4D Nanoscale Reconstruction
of Living Brain Tissue.” Nature Methods. Springer Nature, 2023. https://doi.org/10.1038/s41592-023-01936-6.
ieee: P. Velicky et al., “Dense 4D nanoscale reconstruction of living brain
tissue,” Nature Methods, vol. 20. Springer Nature, pp. 1256–1265, 2023.
ista: Velicky P, Miguel Villalba E, Michalska JM, Lyudchik J, Wei D, Lin Z, Watson
J, Troidl J, Beyer J, Ben Simon Y, Sommer CM, Jahr W, Cenameri A, Broichhagen
J, Grant SGN, Jonas PM, Novarino G, Pfister H, Bickel B, Danzl JG. 2023. Dense
4D nanoscale reconstruction of living brain tissue. Nature Methods. 20, 1256–1265.
mla: Velicky, Philipp, et al. “Dense 4D Nanoscale Reconstruction of Living Brain
Tissue.” Nature Methods, vol. 20, Springer Nature, 2023, pp. 1256–65, doi:10.1038/s41592-023-01936-6.
short: P. Velicky, E. Miguel Villalba, J.M. Michalska, J. Lyudchik, D. Wei, Z. Lin,
J. Watson, J. Troidl, J. Beyer, Y. Ben Simon, C.M. Sommer, W. Jahr, A. Cenameri,
J. Broichhagen, S.G.N. Grant, P.M. Jonas, G. Novarino, H. Pfister, B. Bickel,
J.G. Danzl, Nature Methods 20 (2023) 1256–1265.
corr_author: '1'
date_created: 2023-07-23T22:01:13Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2026-07-06T12:49:46Z
day: '01'
ddc:
- '570'
department:
- _id: PeJo
- _id: GaNo
- _id: BeBi
- _id: JoDa
- _id: Bio
doi: 10.1038/s41592-023-01936-6
ec_funded: 1
external_id:
isi:
- '001025621500001'
pmid:
- '37429995'
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isi: 1
language:
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month: '08'
oa: 1
oa_version: Published Version
page: 1256-1265
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project:
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call_identifier: FWF
grant_number: I03600
name: Optical control of synaptic function via adhesion molecules
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232
name: Molecular Drug Targets
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call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
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grant_number: LS18-022
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allergic disease
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call_identifier: H2020
grant_number: '665385'
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call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
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call_identifier: H2020
grant_number: '715508'
name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo
and in vitro Models
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
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call_identifier: H2020
grant_number: '101026635'
name: Synaptic computations of the hippocampal CA3 circuitry
- _id: 2668BFA0-B435-11E9-9278-68D0E5697425
grant_number: LT00057
name: High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration
publication: Nature Methods
publication_identifier:
eissn:
- 1548-7105
issn:
- 1548-7091
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/danzllab/LIONESS
record:
- id: '12817'
relation: research_data
status: public
- id: '14770'
relation: shorter_version
status: public
- id: '18674'
relation: dissertation_contains
status: public
- id: '11943'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Dense 4D nanoscale reconstruction of living brain tissue
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: 20
year: '2023'
...
---
_id: '13212'
abstract:
- lang: eng
text: Auxin is the major plant hormone regulating growth and development (Friml,
2022). Forward genetic approaches in the model plant Arabidopsis thaliana have
identified major components of auxin signalling and established the canonical
mechanism mediating transcriptional and thus developmental reprogramming. In this
textbook view, TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFBs)
are auxin receptors, which act as F-box subunits determining the substrate specificity
of the Skp1-Cullin1-F box protein (SCF) type E3 ubiquitin ligase complex. Auxin
acts as a “molecular glue” increasing the affinity between TIR1/AFBs and the Aux/IAA
repressors. Subsequently, Aux/IAAs are ubiquitinated and degraded, thus releasing
auxin transcription factors from their repression making them free to mediate
transcription of auxin response genes (Yu et al., 2022). Nonetheless, accumulating
evidence suggests existence of rapid, non-transcriptional responses downstream
of TIR1/AFBs such as auxin-induced cytosolic calcium (Ca2+) transients, plasma
membrane depolarization and apoplast alkalinisation, all converging on the process
of root growth inhibition and root gravitropism (Li et al., 2022). Particularly,
these rapid responses are mostly contributed by predominantly cytosolic AFB1,
while the long-term growth responses are mediated by mainly nuclear TIR1 and AFB2-AFB5
(Li et al., 2021; Prigge et al., 2020; Serre et al., 2021). How AFB1 conducts
auxin-triggered rapid responses and how it is different from TIR1 and AFB2-AFB5
remains elusive. Here, we compare the roles of TIR1 and AFB1 in transcriptional
and rapid responses by modulating their subcellular localization in Arabidopsis
and by testing their ability to mediate transcriptional responses when part of
the minimal auxin circuit reconstituted in yeast.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
acknowledgement: We thank all the authors for sharing the published materials. This
research was supported by the Lab Support Facility and the Imaging and Optics Facility
of ISTA. We thank Lukáš Fiedler (ISTA) for critical reading of the manuscript. This
project was funded by the European Research Council Advanced Grant (ETAP-742985).
article_processing_charge: Yes (via OA deal)
article_type: letter_note
author:
- first_name: Huihuang
full_name: Chen, Huihuang
id: 83c96512-15b2-11ec-abd3-b7eede36184f
last_name: Chen
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Minxia
full_name: Zou, Minxia
id: 5c243f41-03f3-11ec-841c-96faf48a7ef9
last_name: Zou
- first_name: Linlin
full_name: Qi, Linlin
id: 44B04502-A9ED-11E9-B6FC-583AE6697425
last_name: Qi
orcid: 0000-0001-5187-8401
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Chen H, Li L, Zou M, Qi L, Friml J. Distinct functions of TIR1 and AFB1 receptors
in auxin signalling. Molecular Plant. 2023;16(7):1117-1119. doi:10.1016/j.molp.2023.06.007
apa: Chen, H., Li, L., Zou, M., Qi, L., & Friml, J. (2023). Distinct functions
of TIR1 and AFB1 receptors in auxin signalling. Molecular Plant. Elsevier.
https://doi.org/10.1016/j.molp.2023.06.007
chicago: Chen, Huihuang, Lanxin Li, Minxia Zou, Linlin Qi, and Jiří Friml. “Distinct
Functions of TIR1 and AFB1 Receptors in Auxin Signalling.” Molecular Plant.
Elsevier, 2023. https://doi.org/10.1016/j.molp.2023.06.007.
ieee: H. Chen, L. Li, M. Zou, L. Qi, and J. Friml, “Distinct functions of TIR1 and
AFB1 receptors in auxin signalling.,” Molecular Plant, vol. 16, no. 7.
Elsevier, pp. 1117–1119, 2023.
ista: Chen H, Li L, Zou M, Qi L, Friml J. 2023. Distinct functions of TIR1 and AFB1
receptors in auxin signalling. Molecular Plant. 16(7), 1117–1119.
mla: Chen, Huihuang, et al. “Distinct Functions of TIR1 and AFB1 Receptors in Auxin
Signalling.” Molecular Plant, vol. 16, no. 7, Elsevier, 2023, pp. 1117–19,
doi:10.1016/j.molp.2023.06.007.
short: H. Chen, L. Li, M. Zou, L. Qi, J. Friml, Molecular Plant 16 (2023) 1117–1119.
corr_author: '1'
das_tickbox: '1'
date_created: 2023-07-12T07:32:46Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2026-07-06T12:58:58Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.molp.2023.06.007
ec_funded: 1
external_id:
isi:
- '001044410900001'
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- '37393433'
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isi: 1
issue: '7'
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oa_version: Published Version
page: 1117-1119
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project:
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call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Molecular Plant
publication_identifier:
eissn:
- 1674-2052
issn:
- 1752-9867
publication_status: published
publisher: Elsevier
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scopus_import: '1'
status: public
title: Distinct functions of TIR1 and AFB1 receptors in auxin signalling.
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2023'
...
---
OA_place: publisher
_id: '14641'
abstract:
- lang: eng
text: "Mutation rates represent the net result of complex interactions among various\r\ncellular
processes and can dramatically influence the evolutionary fate of\r\nmicrobial
populations. However, many popular techniques used to study\r\nmutations are subject
to the confounding effects of heredity and the subtleties\r\nof adaptation to
selection, all of which make it difficult to observe any dynamic\r\nresponses
of mutation rates to fitness challenges. Furthermore, in spite of the\r\nubiquity
of quorum sensing systems across the bacterial domain and relevance\r\nfor many
physiological behaviors, the effects of such mechanisms on mutation\r\nrate and
adaptation remain poorly understood. In the following work, I\r\npresent the development
of a microfluidic droplet-based method to measure\r\nsingle base-pair mutation
rates in growing populations of the bacterium\r\nEscherichia coli. I use this
method to observe a stress-induced increase in\r\nmutation rate that is mediated
by luxS, a highly conserved bacterial quorum\r\nsensing component. I also show
that the aforementioned increase in mutation\r\nrate, and its associated control
by luxS, corresponds to a higher degree of\r\nadaptability under competitive environments."
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
- _id: CampIT
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Mike
full_name: Hennessey-Wesen, Mike
id: 3F338C72-F248-11E8-B48F-1D18A9856A87
last_name: Hennessey-Wesen
citation:
ama: Hennessey-Wesen M. Adaptive mutation in E. coli modulated by luxS. 2023. doi:10.15479/at:ista:14641
apa: Hennessey-Wesen, M. (2023). Adaptive mutation in E. coli modulated by luxS.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14641
chicago: Hennessey-Wesen, Mike. “Adaptive Mutation in E. Coli Modulated by LuxS.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14641.
ieee: M. Hennessey-Wesen, “Adaptive mutation in E. coli modulated by luxS,” Institute
of Science and Technology Austria, 2023.
ista: Hennessey-Wesen M. 2023. Adaptive mutation in E. coli modulated by luxS. Institute
of Science and Technology Austria.
mla: Hennessey-Wesen, Mike. Adaptive Mutation in E. Coli Modulated by LuxS.
Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14641.
short: M. Hennessey-Wesen, Adaptive Mutation in E. Coli Modulated by LuxS, Institute
of Science and Technology Austria, 2023.
corr_author: '1'
das_tickbox: '1'
date_created: 2023-12-04T13:17:37Z
date_published: 2023-11-30T00:00:00Z
date_updated: 2026-07-13T10:55:56Z
day: '30'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: BjHo
doi: 10.15479/at:ista:14641
doi_confirm: '1'
ec_funded: 1
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title: Print version
file_date_updated: 2026-07-13T10:55:56Z
fulldoi: https://doi.org/10.15479/at:ista:14641
has_accepted_license: '1'
keyword:
- microfluidics
- miceobiology
- mutations
- quorum sensing
language:
- iso: eng
month: '11'
oa_version: Published Version
page: '104'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
title: Adaptive mutation in E. coli modulated by luxS
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '12334'
abstract:
- lang: eng
text: Regulation of the Arp2/3 complex is required for productive nucleation of
branched actin networks. An emerging aspect of regulation is the incorporation
of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit
isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity
and branch junction stability. We have combined reverse genetics and cellular
structural biology to describe how ArpC5 and ArpC5L differentially affect cell
migration. Both define the structural stability of ArpC1 in branch junctions and,
in turn, by determining protrusion characteristics, affect protein dynamics and
actin network ultrastructure. ArpC5 isoforms also affect the positioning of members
of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament
elongators, which mediate ArpC5 isoform–specific effects on the actin assembly
level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling
pathway enhancing cell migration.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: Bio
- _id: EM-Fac
acknowledgement: "We would like to thank K. von Peinen and B. Denker (Helmholtz Centre
for Infection Research, Braunschweig, Germany) for experimental and technical assistance,
respectively.\r\nThis research was supported by the Scientific Service Units (SSUs)
of ISTA through resources provided by Scientific Computing (SciComp), the Life Science
Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy
Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund
(FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz
Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and
K.R."
article_number: add6495
article_processing_charge: No
article_type: original
author:
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Manjunath
full_name: Javoor, Manjunath
id: 305ab18b-dc7d-11ea-9b2f-b58195228ea2
last_name: Javoor
orcid: 0000-0003-2311-2112
- first_name: Julia
full_name: Datler, Julia
id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87
last_name: Datler
orcid: 0000-0002-3616-8580
- first_name: Hermann
full_name: Döring, Hermann
last_name: Döring
- first_name: Florian
full_name: Hofer, Florian
id: b9d234ba-9e33-11ed-95b6-cd561df280e6
last_name: Hofer
- 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: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
orcid: 0000-0003-3904-947X
- first_name: Jan
full_name: Faix, Jan
last_name: Faix
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
- 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: Fäßler F, Javoor M, Datler J, et al. ArpC5 isoforms regulate Arp2/3 complex–dependent
protrusion through differential Ena/VASP positioning. Science Advances.
2023;9(3). doi:10.1126/sciadv.add6495
apa: Fäßler, F., Javoor, M., Datler, J., Döring, H., Hofer, F., Dimchev, G. A.,
… Schur, F. K. (2023). ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion
through differential Ena/VASP positioning. Science Advances. American Association
for the Advancement of Science. https://doi.org/10.1126/sciadv.add6495
chicago: Fäßler, Florian, Manjunath Javoor, Julia Datler, Hermann Döring, Florian
Hofer, Georgi A Dimchev, Victor-Valentin Hodirnau, Jan Faix, Klemens Rottner,
and Florian KM Schur. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion
through Differential Ena/VASP Positioning.” Science Advances. American
Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.add6495.
ieee: F. Fäßler et al., “ArpC5 isoforms regulate Arp2/3 complex–dependent
protrusion through differential Ena/VASP positioning,” Science Advances,
vol. 9, no. 3. American Association for the Advancement of Science, 2023.
ista: Fäßler F, Javoor M, Datler J, Döring H, Hofer F, Dimchev GA, Hodirnau V-V,
Faix J, Rottner K, Schur FK. 2023. ArpC5 isoforms regulate Arp2/3 complex–dependent
protrusion through differential Ena/VASP positioning. Science Advances. 9(3),
add6495.
mla: Fäßler, Florian, et al. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion
through Differential Ena/VASP Positioning.” Science Advances, vol. 9, no.
3, add6495, American Association for the Advancement of Science, 2023, doi:10.1126/sciadv.add6495.
short: F. Fäßler, M. Javoor, J. Datler, H. Döring, F. Hofer, G.A. Dimchev, V.-V.
Hodirnau, J. Faix, K. Rottner, F.K. Schur, Science Advances 9 (2023).
corr_author: '1'
date_created: 2023-01-23T07:26:42Z
date_published: 2023-01-20T00:00:00Z
date_updated: 2026-09-03T09:36:24Z
day: '20'
ddc:
- '570'
department:
- _id: FlSc
- _id: EM-Fac
doi: 10.1126/sciadv.add6495
external_id:
isi:
- '000964550100015'
pmid:
- '36662867'
file:
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checksum: ce81a6d0b84170e5e8c62f6acfa15d9e
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file_size: 1756234
relation: main_file
success: 1
file_date_updated: 2023-01-23T07:45:54Z
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intvolume: ' 9'
isi: 1
issue: '3'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
record:
- id: '14562'
relation: research_data
status: public
- id: '18766'
relation: dissertation_contains
status: public
- id: '22744'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential
Ena/VASP positioning
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: 9
year: '2023'
...
---
OA_place: publisher
_id: '12491'
abstract:
- lang: eng
text: "The extracellular matrix (ECM) is a hydrated and complex three-dimensional
network consisting of proteins, polysaccharides, and water. It provides structural
scaffolding for the cells embedded within it and is essential in regulating numerous
physiological processes, including cell migration and proliferation, wound healing,
and stem cell fate. \r\nDespite extensive study, detailed structural knowledge
of ECM components in physiologically relevant conditions is still rudimentary.
This is due to methodological limitations in specimen preparation protocols which
are incompatible with keeping large samples, such as the ECM, in their native
state for subsequent imaging. Conventional electron microscopy (EM) techniques
rely on fixation, dehydration, contrasting, and sectioning. This results in the
alteration of a highly hydrated environment and the potential introduction of
artifacts. Other structural biology techniques, such as nuclear magnetic resonance
(NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of
protein structures but only work on homogenous and purified samples, hence lacking
contextual information. Currently, no approach exists for the ultrastructural
and structural study of extracellular components under native conditions in a
physiological, 3D environment. \r\nIn this thesis, I have developed a workflow
that allows for the ultrastructural analysis of the ECM in near-native conditions
at molecular resolution. The developments I introduced include implementing a
novel specimen preparation workflow for cell-derived matrices (CDMs) to render
them compatible with ion-beam milling and subsequent high-resolution cryo-electron
tomography (ET). \r\nTo this end, I have established protocols to generate CDMs
grown over several weeks on EM grids that are compatible with downstream cryo-EM
sample preparation and imaging techniques. Characterization of these ECMs confirmed
that they contain essential ECM components such as collagen I, collagen VI, and
fibronectin I in high abundance and hence represent a bona fide biologically-relevant
sample. I successfully optimized vitrification of these specimens by testing various
vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution
molecular insights into the ultrastructure and organization of CDMs, I established
cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging
and complex specimens. I explored different approaches for the creation of thin
cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique,
resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution
Cryo-ET of these lamellae revealed for the first time the architecture of native
CDM in the context of matrix-secreting cells. This allowed for the in situ visualization
of fibrillar matrix proteins such as collagen, laying the foundation for future
structural and ultrastructural characterization of these proteins in their near-native
environment. \r\nIn summary, in this thesis, I present a novel workflow that combines
state-of-the-art cryo-EM specimen preparation and imaging technologies to permit
characterization of the ECM, an important tissue component in higher organisms.
This innovative and highly versatile workflow will enable addressing far-reaching
questions on ECM architecture, composition, and reciprocal ECM-cell interactions."
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Bettina
full_name: Zens, Bettina
id: 45FD126C-F248-11E8-B48F-1D18A9856A87
last_name: Zens
orcid: 0000-0002-9561-1239
citation:
ama: Zens B. Ultrastructural characterization of natively preserved extracellular
matrix by cryo-electron tomography. 2023. doi:10.15479/at:ista:12491
apa: Zens, B. (2023). Ultrastructural characterization of natively preserved
extracellular matrix by cryo-electron tomography. Institute of Science and
Technology Austria. https://doi.org/10.15479/at:ista:12491
chicago: Zens, Bettina. “Ultrastructural Characterization of Natively Preserved
Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology
Austria, 2023. https://doi.org/10.15479/at:ista:12491.
ieee: B. Zens, “Ultrastructural characterization of natively preserved extracellular
matrix by cryo-electron tomography,” Institute of Science and Technology Austria,
2023.
ista: Zens B. 2023. Ultrastructural characterization of natively preserved extracellular
matrix by cryo-electron tomography. Institute of Science and Technology Austria.
mla: Zens, Bettina. Ultrastructural Characterization of Natively Preserved Extracellular
Matrix by Cryo-Electron Tomography. Institute of Science and Technology Austria,
2023, doi:10.15479/at:ista:12491.
short: B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular
Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria,
2023.
corr_author: '1'
date_created: 2023-02-02T14:50:20Z
date_published: 2023-02-02T00:00:00Z
date_updated: 2026-04-07T13:49:23Z
day: '02'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: FlSc
doi: 10.15479/at:ista:12491
file:
- access_level: open_access
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creator: bzens
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fulldoi: https://doi.org/10.15479/at:ista:12491
has_accepted_license: '1'
keyword:
- cryo-EM
- cryo-ET
- FIB milling
- method development
- FIBSEM
- extracellular matrix
- ECM
- cell-derived matrices
- CDMs
- cell culture
- high pressure freezing
- HPF
- structural biology
- tomography
- collagen
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '187'
project:
- _id: eba3b5f6-77a9-11ec-83b8-cf0905748aa3
name: Integrated visual proteomics of reciprocal cell-extracellular matrix interactions
- _id: 059B463C-7A3F-11EA-A408-12923DDC885E
name: "NÃ\x96-Fonds Preis für die Jungforscherin des Jahres am IST Austria"
publication_identifier:
isbn:
- 978-3-99078-027-5
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8586'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
title: Ultrastructural characterization of natively preserved extracellular matrix
by cryo-electron tomography
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
OA_place: publisher
_id: '13984'
abstract:
- lang: eng
text: "Social insects fight disease using their individual immune systems and the
cooperative\r\nsanitary behaviors of colony members. These social defenses are
well explored against\r\nexternally-infecting pathogens, but little is known about
defense strategies against\r\ninternally-infecting pathogens, such as viruses.
Viruses are ubiquitous and in the last decades\r\nit has become evident that also
many ant species harbor viruses. We present one of the first\r\nstudies addressing
transmission dynamics and collective disease defenses against viruses in\r\nants
on a mechanistic level. I successfully established an experimental ant host –
viral\r\npathogen system as a model for the defense strategies used by social
insects against internal\r\npathogen infections, as outlined in the third chapter.
In particular, we studied how garden ants\r\n(Lasius neglectus) defend themselves
and their colonies against the generalist insect virus\r\nCrPV (cricket paralysis
virus). We chose microinjections of virus directly into the ants’\r\nhemolymph
because it allowed us to use a defined exposure dose. Here we show that this is
a\r\ngood model system, as the virus is replicating and thus infecting the host.
The ants mount a\r\nclear individual immune response against the viral infection,
which is characterized by a\r\nspecific siRNA pattern, namely siRNAs mapping against
the viral genome with a peak of 21\r\nand 22 bp long fragments. The onset of this
immune response is consistent with the timeline\r\nof viral replication that starts
already within two days post injection. The disease manifests in\r\ndecreased
survival over a course of two to three weeks.\r\nRegarding group living, we find
that infected ants show a strong individual immune response,\r\nbut that their
course of disease is little affected by nestmate presence, as described in chapter\r\nfour.
Hence, we do not find social immunity in the context of viral infections in ants.\r\nNestmates,
however, can contract the virus. Using Drosophila S2R+ cells in culture, we\r\nshowed
that 94 % of the nestmates contract active virus within four days of social contact
to\r\nan infected individual. Virus is transmitted in low doses, thus not causing
disease\r\ntransmission within the colony. While virus can be transmitted during
short direct contacts,\r\nwe also assume transmission from deceased ants and show
that the nestmates’ immune\r\nsystem gets activated after contracting a low viral
dose. We find considerable potential for\r\nindirect transmission via the nest
space. Virus is shed to the nest, where it stays viable for one\r\nweek and is
also picked up by other ants. Apart from that, we want to underline the potential\r\nof
ant poison as antiviral agent. We determined that ant poison successfully inactivates
CrPV\r\nin vitro. However, we found no evidence for effective poison use to sanitize
the nest space.\r\nOn the other hand, local application of ant poison by oral
poison uptake, which is part of the\r\nants prophylactic behavioral repertoire,
probably contributes to keeping the gut of each\r\nindividual sanitized. We hypothesize
that oral poison uptake might be the reason why we did\r\nnot find viable virus
in the trophallactic fluid.\r\nThe fifth chapter encompasses preliminary data
on potential social immunization. However,\r\nour experiments do not confirm an
actual survival benefit for the nestmates upon pathogen\r\nchallenge under the
given experimental settings. Nevertheless, we do not want to rule out the\r\npossibility
for nestmate immunization, but rather emphasize that considering different\r\nexperimental
timelines and viral doses would provide a multitude of options for follow-up\r\nexperiments.\r\nIn
conclusion, we find that prophylactic individual behaviors, such as oral poison
uptake,\r\nmight play a role in preventing viral disease transmission. Compared
to colony defense\r\nagainst external pathogens, internal pathogen infections
require a stronger component of\r\nindividual physiological immunity than behavioral
social immunity, yet could still lead to\r\ncollective protection."
acknowledged_ssus:
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Anna
full_name: Franschitz, Anna
id: 480826C8-F248-11E8-B48F-1D18A9856A87
last_name: Franschitz
citation:
ama: Franschitz A. Individual and social immunity against viral infections in ants.
2023. doi:10.15479/at:ista:13984
apa: Franschitz, A. (2023). Individual and social immunity against viral infections
in ants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13984
chicago: Franschitz, Anna. “Individual and Social Immunity against Viral Infections
in Ants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13984.
ieee: A. Franschitz, “Individual and social immunity against viral infections in
ants,” Institute of Science and Technology Austria, 2023.
ista: Franschitz A. 2023. Individual and social immunity against viral infections
in ants. Institute of Science and Technology Austria.
mla: Franschitz, Anna. Individual and Social Immunity against Viral Infections
in Ants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13984.
short: A. Franschitz, Individual and Social Immunity against Viral Infections in
Ants, Institute of Science and Technology Austria, 2023.
corr_author: '1'
date_created: 2023-08-08T15:33:29Z
date_published: 2023-08-08T00:00:00Z
date_updated: 2026-04-07T13:51:29Z
day: '08'
ddc:
- '570'
- '577'
degree_awarded: PhD
department:
- _id: GradSch
- _id: SyCr
doi: 10.15479/at:ista:13984
file:
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date_created: 2024-03-01T08:56:06Z
date_updated: 2024-10-29T23:31:04Z
embargo_to: open_access
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file_size: 10416761
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title: Combined Version of original Thesis and Addendum
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creator: afransch
date_created: 2023-08-08T18:01:28Z
date_updated: 2024-08-09T22:30:03Z
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checksum: 40abf7ccca14a3893f72dc7fb88585d6
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
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date_updated: 2024-08-09T22:30:03Z
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content_type: application/pdf
creator: cchlebak
date_created: 2024-03-01T08:37:15Z
date_updated: 2024-10-29T23:31:04Z
description: Minor modifications and clarifications - Feb 2024
embargo: 2024-08-08
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file_name: Addendum_AnnaFranschitz202402.pdf
file_size: 85956
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title: Addendum
- access_level: closed
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content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: cchlebak
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date_updated: 2024-08-09T22:30:03Z
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file_size: 11818
relation: source_file
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file_date_updated: 2024-10-29T23:31:04Z
fulldoi: https://doi.org/10.15479/at:ista:13984
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '89'
publication_identifier:
isbn:
- 978-3-99078-034-3
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
title: Individual and social immunity against viral infections in ants
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
_id: '13116'
abstract:
- lang: eng
text: 'The emergence of large-scale order in self-organized systems relies on local
interactions between individual components. During bacterial cell division, FtsZ
-- a prokaryotic homologue of the eukaryotic protein tubulin -- polymerizes into
treadmilling filaments that further organize into a cytoskeletal ring. In vitro,
FtsZ filaments can form dynamic chiral assemblies. However, how the active and
passive properties of individual filaments relate to these large-scale self-organized
structures remains poorly understood. Here, we connect single filament properties
with the mesoscopic scale by combining minimal active matter simulations and biochemical
reconstitution experiments. We show that density and flexibility of active chiral
filaments define their global order. At intermediate densities, curved, flexible
filaments organize into chiral rings and polar bands. An effectively nematic organization
dominates for high densities and for straight, mutant filaments with increased
rigidity. Our predicted phase diagram captures these features quantitatively,
demonstrating how the flexibility, density and chirality of active filaments affect
their collective behaviour. Our findings shed light on the fundamental properties
of active chiral matter and explain how treadmilling FtsZ filaments organize during
bacterial cell division. '
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: 'This work was supported by the European Research Council through
grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607
to M.L., B. P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM
collaborative research program. Z.D. has received funding from Doctoral Programme
of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan
Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria),
Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments
on the manuscript. We are also thankful for the support by the Scientific Service
Units (SSU) of IST Austria through resources provided by the Imaging and Optics
Facility (IOF) and the Lab Support Facility (LSF). '
article_processing_charge: No
author:
- first_name: Zuzana
full_name: Dunajova, Zuzana
id: 4B39F286-F248-11E8-B48F-1D18A9856A87
last_name: Dunajova
- first_name: Batirtze
full_name: Prats Mateu, Batirtze
id: 299FE892-F248-11E8-B48F-1D18A9856A87
last_name: Prats Mateu
- first_name: Philipp
full_name: Radler, Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
- first_name: Keesiang
full_name: Lim, Keesiang
last_name: Lim
- first_name: Dörte
full_name: Brandis, Dörte
last_name: Brandis
- first_name: Philipp
full_name: Velicky, Philipp
id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
last_name: Velicky
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ama: Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible
active filaments. 2023. doi:10.15479/AT:ISTA:13116
apa: Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P.,
… Loose, M. (2023). Chiral and nematic phases of flexible active filaments. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:13116
chicago: Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte
Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of
Flexible Active Filaments.” Institute of Science and Technology Austria, 2023.
https://doi.org/10.15479/AT:ISTA:13116.
ieee: Z. Dunajova et al., “Chiral and nematic phases of flexible active filaments.”
Institute of Science and Technology Austria, 2023.
ista: Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG,
Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible
active filaments, Institute of Science and Technology Austria, 10.15479/AT:ISTA:13116.
mla: Dunajova, Zuzana, et al. Chiral and Nematic Phases of Flexible Active Filaments.
Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:13116.
short: Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G.
Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, (2023).
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title: Chiral and nematic phases of flexible active filaments
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legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
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---
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abstract:
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text: The emergence of large-scale order in self-organized systems relies on local
interactions between individual components. During bacterial cell division, FtsZ—a
prokaryotic homologue of the eukaryotic protein tubulin—polymerizes into treadmilling
filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments
can form dynamic chiral assemblies. However, how the active and passive properties
of individual filaments relate to these large-scale self-organized structures
remains poorly understood. Here we connect single-filament properties with the
mesoscopic scale by combining minimal active matter simulations and biochemical
reconstitution experiments. We show that the density and flexibility of active
chiral filaments define their global order. At intermediate densities, curved,
flexible filaments organize into chiral rings and polar bands. An effectively
nematic organization dominates for high densities and for straight, mutant filaments
with increased rigidity. Our predicted phase diagram quantitatively captures these
features, demonstrating how the flexibility, density and chirality of the active
filaments affect their collective behaviour. Our findings shed light on the fundamental
properties of active chiral matter and explain how treadmilling FtsZ filaments
organize during bacterial cell division.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: 'This work was supported by the European Research Council through
grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607
to M.L., B. P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM
collaborative research program. Z.D. has received funding from Doctoral Programme
of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan
Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria),
Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments
on the manuscript. We are also thankful for the support by the Scientific Service
Units (SSU) of IST Austria through resources provided by the Imaging and Optics
Facility (IOF) and the Lab Support Facility (LSF).'
article_processing_charge: Yes (in subscription journal)
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last_name: Velicky
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- first_name: Johann G
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last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Richard W.
full_name: Wong, Richard W.
last_name: Wong
- first_name: Jens
full_name: Elgeti, Jens
last_name: Elgeti
- 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: Martin
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last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible
active filaments. Nature Physics. 2023;19:1916-1926. doi:10.1038/s41567-023-02218-w
apa: Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P.,
… Loose, M. (2023). Chiral and nematic phases of flexible active filaments. Nature
Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02218-w
chicago: Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte
Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of
Flexible Active Filaments.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02218-w.
ieee: Z. Dunajova et al., “Chiral and nematic phases of flexible active filaments,”
Nature Physics, vol. 19. Springer Nature, pp. 1916–1926, 2023.
ista: Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG,
Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible
active filaments. Nature Physics. 19, 1916–1926.
mla: Dunajova, Zuzana, et al. “Chiral and Nematic Phases of Flexible Active Filaments.”
Nature Physics, vol. 19, Springer Nature, 2023, pp. 1916–26, doi:10.1038/s41567-023-02218-w.
short: Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G.
Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, Nature Physics 19 (2023)
1916–1926.
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call_identifier: H2020
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title: Chiral and nematic phases of flexible active filaments
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 19
year: '2023'
...
---
OA_place: publisher
_id: '14280'
abstract:
- lang: eng
text: "Cell division in Escherichia coli is performed by the divisome, a multi-protein
complex composed of more than 30 proteins. The divisome spans from the cytoplasm
through the inner membrane to the cell wall and the outer membrane. Divisome assembly
is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes
at the center of the E. coli cell and determines the position of the future cell
septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue
FtsZ, which forms treadmilling filaments. These filaments are recruited to the
inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts
with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic
components of the divisome. \r\nA previous model postulated that FtsA regulates
maturation of the divisome by switching from an oligomeric, inactive state to
a monomeric and active state. This model was based mostly on in vivo studies,
as a biochemical characterization of FtsA has been hampered by difficulties in
purifying the protein. Here, we studied FtsA using an in vitro reconstitution
approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic,
treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space
and (ii) How does FtsA regulate the maturation of the divisome?\r\nWe found that
the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact
directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments.
When we investigated the underlying mechanism by imaging single molecules of FtsNcyto,
we found the peptide to interact transiently with FtsA. An in depth analysis of
the single molecule trajectories helped to postulate a model where PG synthases
follow the dynamics of FtsZ by a diffusion and capture mechanism. \r\nFollowing
up on these findings we were interested in how the self-interaction of FtsA changes
when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer
switch. For this, we compared the behavior of the previously identified, hyperactive
mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and
transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly
however, we found that this was not due to a difference in the self-interaction
strength of the two variants, but a difference in their membrane residence time.
Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured
self-interaction of FtsA actually increased. \r\nWe propose that FtsNcyto induces
a rearrangement of the oligomeric architecture of FtsA. In further consequence
this change leads to more persistent FtsZ filaments which results in a defined
signalling zone, allowing formation of the mature divisome. The observed difference
between FtsA WT and R286W is due to the vastly different membrane turnover of
the proteins. R286W cycles 5-10x faster compared to WT which allows to sample
FtsZ filaments at faster frequencies. These findings can explain the observed
differences in toxicity for overexpression of FtsA WT and R286W and help to understand
how FtsA regulates divisome maturation."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Philipp
full_name: Radler, Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
citation:
ama: Radler P. Spatiotemporal signaling during assembly of the bacterial divisome.
2023. doi:10.15479/at:ista:14280
apa: Radler, P. (2023). Spatiotemporal signaling during assembly of the bacterial
divisome. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14280
chicago: Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial
Divisome.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14280.
ieee: P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,”
Institute of Science and Technology Austria, 2023.
ista: Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial
divisome. Institute of Science and Technology Austria.
mla: Radler, Philipp. Spatiotemporal Signaling during Assembly of the Bacterial
Divisome. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14280.
short: P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome,
Institute of Science and Technology Austria, 2023.
corr_author: '1'
date_created: 2023-09-06T10:58:25Z
date_published: 2023-09-25T00:00:00Z
date_updated: 2026-04-07T14:06:05Z
day: '25'
ddc:
- '572'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MaLo
doi: 10.15479/at:ista:14280
ec_funded: 1
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has_accepted_license: '1'
keyword:
- Cell Division
- Reconstitution
- FtsZ
- FtsA
- Divisome
- E.coli
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '156'
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
- _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d
grant_number: P34607
name: In vitro reconstitution of bacterial cell division
- _id: 2596EAB6-B435-11E9-9278-68D0E5697425
grant_number: ALTF 2015-1163
name: Synthesis of bacterial cell wall
- _id: 259B655A-B435-11E9-9278-68D0E5697425
grant_number: LT000824/2016
name: Reconstitution of bacterial cell wall synthesis
publication_identifier:
isbn:
- 978-3-99078-033-6
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10934'
relation: research_data
status: public
- id: '11373'
relation: part_of_dissertation
status: public
- id: '7387'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
title: Spatiotemporal signaling during assembly of the bacterial divisome
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
_id: '12891'
abstract:
- lang: eng
text: "The tight spatiotemporal coordination of signaling activity determining embryo\r\npatterning
and the physical processes driving embryo morphogenesis renders\r\nembryonic development
robust, such that key developmental processes can unfold\r\nrelatively normally
even outside of the full embryonic context. For instance, embryonic\r\nstem cell
cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry\r\nleading
to germ layer formation and morphogenesis, in a very reduced environment.\r\nThis
leads to questions on specific contributions of embryo-specific features, such
as\r\nthe presence of extraembryonic tissues, which are inherently involved in
gastrulation\r\nin the full embryonic context. To address this, we established
zebrafish embryonic\r\nexplants without the extraembryonic yolk cell, an important
player as a signaling\r\nsource and for morphogenesis during gastrulation, as
a model of ex vivo development.\r\nWe found that dorsal-marginal determinants
are required and sufficient in these\r\nexplants to form and pattern all three
germ layers. However, formation of tissues,\r\nwhich require the highest Nodal-signaling
levels, is variable, demonstrating a\r\ncontribution of extraembryonic tissues
for reaching peak Nodal signaling levels.\r\nBlastoderm explants also undergo
gastrulation-like axis elongation. We found that this\r\nelongation movement shows
hallmarks of oriented mesendoderm cell intercalations\r\ntypically associated
with dorsal tissues in the intact embryo. These are disrupted by\r\nuniform upregulation
of BMP signaling activity and concomitant explant ventralization,\r\nsuggesting
that tight spatial control of BMP signaling is a prerequisite for explant\r\nmorphogenesis.
This control is achieved by Nodal signaling, which is critical for\r\neffectively
downregulating BMP signaling in the mesendoderm, highlighting that Nodal\r\nsignaling
is not only directly required for mesendoderm cell fate specification and\r\nmorphogenesis,
but also by maintaining low levels of BMP signaling at the dorsal side.\r\nCollectively,
we provide insights into the capacity and organization of signaling and\r\nmorphogenetic
domains to recapitulate features of zebrafish gastrulation outside of\r\nthe full
embryonic context."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Alexandra
full_name: Schauer, Alexandra
id: 30A536BA-F248-11E8-B48F-1D18A9856A87
last_name: Schauer
orcid: 0000-0001-7659-9142
citation:
ama: 'Schauer A. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic
tissues. 2023. doi:10.15479/at:ista:12891'
apa: 'Schauer, A. (2023). Mesendoderm formation in zebrafish gastrulation: The
role of extraembryonic tissues. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:12891'
chicago: 'Schauer, Alexandra. “Mesendoderm Formation in Zebrafish Gastrulation:
The Role of Extraembryonic Tissues.” Institute of Science and Technology Austria,
2023. https://doi.org/10.15479/at:ista:12891.'
ieee: 'A. Schauer, “Mesendoderm formation in zebrafish gastrulation: The role of
extraembryonic tissues,” Institute of Science and Technology Austria, 2023.'
ista: 'Schauer A. 2023. Mesendoderm formation in zebrafish gastrulation: The role
of extraembryonic tissues. Institute of Science and Technology Austria.'
mla: 'Schauer, Alexandra. Mesendoderm Formation in Zebrafish Gastrulation: The
Role of Extraembryonic Tissues. Institute of Science and Technology Austria,
2023, doi:10.15479/at:ista:12891.'
short: 'A. Schauer, Mesendoderm Formation in Zebrafish Gastrulation: The Role of
Extraembryonic Tissues, Institute of Science and Technology Austria, 2023.'
corr_author: '1'
date_created: 2023-05-05T08:48:20Z
date_published: 2023-05-05T00:00:00Z
date_updated: 2025-06-12T06:56:58Z
day: '05'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: CaHe
doi: 10.15479/at:ista:12891
ec_funded: 1
file:
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checksum: 59b0303dc483f40a96a610a90aab7ee9
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creator: aschauer
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date_updated: 2024-05-06T22:30:03Z
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content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: aschauer
date_created: 2023-05-05T13:04:15Z
date_updated: 2024-05-06T22:30:03Z
embargo_to: open_access
file_id: '12908'
file_name: Thesis_Schauer_final.docx
file_size: 43809109
relation: source_file
file_date_updated: 2024-05-06T22:30:03Z
fulldoi: https://doi.org/10.15479/at:ista:12891
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '190'
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
- _id: 26B1E39C-B435-11E9-9278-68D0E5697425
grant_number: '25239'
name: 'Mesendoderm specification in zebrafish: The role of extraembryonic tissues'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7888'
relation: part_of_dissertation
status: public
- id: '8966'
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: 'Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic
tissues'
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
OA_place: publisher
_id: '14697'
abstract:
- lang: eng
text: "During my Ph.D. research, I managed a series of projects, each focused on
the\r\nmechanisms underlying cell migration. My work involved an in-depth examination
of\r\nthe complex strategies employed by neutrophils, with a specific focus on
their ability to\r\nsynchronize spatial-temporal cues and optimize their gradient
perception. However, it\r\nis essential to acknowledge that not all projects yielded
successful results, as some\r\nideas were discontinued and are archived for future
reference within this thesis.\r\nMy main project investigated how neutrophils
decode spatial cues for precise navigation. Human neutrophils showcased distinct
movement patterns based on source\r\ntype – linear or point-like. By combining
single-cell tracking in 3D environments with\r\nproxy dyes, this project linked
cell behaviors to gradient changes, revealing a stronger\r\nresponse to semi-exponential
gradients from point sources. In addition, neutrophils\r\nexhibited oscillating
migration speeds, using speed minima to adjust trajectories toward sources. Experiencing
continuous concentration changes, they accelerated over\r\ntime and employed a
\"Run and Fumble\" strategy, alternating between consistent runs\r\nand strategic
\"tumbles\" for efficient navigation.\r\nThe project extended to the possibility
of cells amplifying perceived gradients by\r\nenclosing their immediate surroundings,
pushing attractants forward for enrichment\r\nwhile depleting it at the cell rear.
Microfluidic devices were employed, and various experimental parameters configurations
were optimized. Although significant differences\r\nin migratory efficacy were
detected across pore sizes and device heights, quantifying\r\ngradient manipulation
effects proved challenging.\r\nThe \"Laser-Assisted Protein Adsorption by Photobleaching\"
(LAPAP) project was\r\npromising, as it allowed the printing of gradients. Initially
successful with dendritic cells,\r\nwe aimed to adapt it for neutrophils. Through
extensive experimentation with multiple\r\nparameters, we attempted to trigger
responses from neutrophils. Despite these efforts\r\nand collaboration, the project
failed due to practical challenges and limitations.\r\nFacing a lack of neutrophil-like
cells at IST, we initially established the SCF-HoxB8\r\nprimary murine cell line.
Despite their existence, their migratory behavior was largely\r\nunexplored due
to potential limitations. Through differentiation protocol refinements we\r\nenhanced
their migratory capabilities, though their capacity still lagged behind human\r\nneutrophils.
Despite this, the improved migration potential of these cells pointed toward\r\ntheir
utility for in vitro murine neutrophil migration studies."
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Julian A
full_name: Stopp, Julian A
id: 489E3F00-F248-11E8-B48F-1D18A9856A87
last_name: Stopp
citation:
ama: 'Stopp JA. Neutrophils on the hunt : Migratory strategies employed by neutrophils
to fulfill their effector function. 2023. doi:10.15479/at:ista:14697'
apa: 'Stopp, J. A. (2023). Neutrophils on the hunt : Migratory strategies employed
by neutrophils to fulfill their effector function. Institute of Science and
Technology Austria. https://doi.org/10.15479/at:ista:14697'
chicago: 'Stopp, Julian A. “Neutrophils on the Hunt : Migratory Strategies Employed
by Neutrophils to Fulfill Their Effector Function.” Institute of Science and Technology
Austria, 2023. https://doi.org/10.15479/at:ista:14697.'
ieee: 'J. A. Stopp, “Neutrophils on the hunt : Migratory strategies employed by
neutrophils to fulfill their effector function,” Institute of Science and Technology
Austria, 2023.'
ista: 'Stopp JA. 2023. Neutrophils on the hunt : Migratory strategies employed by
neutrophils to fulfill their effector function. Institute of Science and Technology
Austria.'
mla: 'Stopp, Julian A. Neutrophils on the Hunt : Migratory Strategies Employed
by Neutrophils to Fulfill Their Effector Function. Institute of Science and
Technology Austria, 2023, doi:10.15479/at:ista:14697.'
short: 'J.A. Stopp, Neutrophils on the Hunt : Migratory Strategies Employed by Neutrophils
to Fulfill Their Effector Function, Institute of Science and Technology Austria,
2023.'
corr_author: '1'
date_created: 2023-12-18T19:14:28Z
date_published: 2023-12-20T00:00:00Z
date_updated: 2026-06-18T17:34:48Z
day: '20'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MiSi
doi: 10.15479/at:ista:14697
ec_funded: 1
file:
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checksum: 457927165d5d556305d3086f6b83e5c7
content_type: application/pdf
creator: jstopp
date_created: 2023-12-20T09:35:34Z
date_updated: 2024-12-20T23:30:04Z
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date_updated: 2024-12-20T23:30:04Z
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file_size: 69625950
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language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '226'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
isbn:
- 978-3-99078-038-1
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '14360'
relation: part_of_dissertation
status: public
- id: '12272'
relation: part_of_dissertation
status: public
- id: '6328'
relation: part_of_dissertation
status: public
- id: '7885'
relation: part_of_dissertation
status: public
- id: '14274'
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: 0000-0002-6620-9179
title: 'Neutrophils on the hunt : Migratory strategies employed by neutrophils to
fulfill their effector function'
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
OA_place: publisher
_id: '13081'
abstract:
- lang: eng
text: During development, tissues undergo changes in size and shape to form functional
organs. Distinct cellular processes such as cell division and cell rearrangements
underlie tissue morphogenesis. Yet how the distinct processes are controlled and
coordinated, and how they contribute to morphogenesis is poorly understood. In
our study, we addressed these questions using the developing mouse neural tube.
This epithelial organ transforms from a flat epithelial sheet to an epithelial
tube while increasing in size and undergoing morpho-gen-mediated patterning. The
extent and mechanism of neural progenitor rearrangement within the developing
mouse neuroepithelium is unknown. To investigate this, we per-formed high resolution
lineage tracing analysis to quantify the extent of epithelial rear-rangement at
different stages of neural tube development. We quantitatively described the relationship
between apical cell size with cell cycle dependent interkinetic nuclear migra-tions
(IKNM) and performed high cellular resolution live imaging of the neuroepithelium
to study the dynamics of junctional remodeling. Furthermore, developed a vertex
model of the neuroepithelium to investigate the quantitative contribution of cell
proliferation, cell differentiation and mechanical properties to the epithelial
rearrangement dynamics and validated the model predictions through functional
experiments. Our analysis revealed that at early developmental stages, the apical
cell area kinetics driven by IKNM induce high lev-els of cell rearrangements in
a regime of high junctional tension and contractility. After E9.5, there is a
sharp decline in the extent of cell rearrangements, suggesting that the epi-thelium
transitions from a fluid-like to a solid-like state. We found that this transition
is regulated by the growth rate of the tissue, rather than by changes in cell-cell
adhesion and contractile forces. Overall, our study provides a quantitative description
of the relationship between tissue growth, cell cycle dynamics, epithelia rearrangements
and the emergent tissue material properties, and novel insights on how epithelial
cell dynamics influences tissue morphogenesis.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Laura
full_name: Bocanegra, Laura
id: 4896F754-F248-11E8-B48F-1D18A9856A87
last_name: Bocanegra
citation:
ama: Bocanegra L. Epithelial dynamics during mouse neural tube development. 2023.
doi:10.15479/at:ista:13081
apa: Bocanegra, L. (2023). Epithelial dynamics during mouse neural tube development.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13081
chicago: Bocanegra, Laura. “Epithelial Dynamics during Mouse Neural Tube Development.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13081.
ieee: L. Bocanegra, “Epithelial dynamics during mouse neural tube development,”
Institute of Science and Technology Austria, 2023.
ista: Bocanegra L. 2023. Epithelial dynamics during mouse neural tube development.
Institute of Science and Technology Austria.
mla: Bocanegra, Laura. Epithelial Dynamics during Mouse Neural Tube Development.
Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13081.
short: L. Bocanegra, Epithelial Dynamics during Mouse Neural Tube Development, Institute
of Science and Technology Austria, 2023.
corr_author: '1'
date_created: 2023-05-23T19:10:42Z
date_published: 2023-05-23T00:00:00Z
date_updated: 2026-04-14T09:50:54Z
day: '23'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: AnKi
doi: 10.15479/at:ista:13081
file:
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checksum: 74f3f89e59a0189bee53ebfad9c1b9af
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
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month: '05'
oa: 1
oa_version: Published Version
page: '93'
publication_identifier:
issn:
- 2663-337X
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related_material:
record:
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status: public
- id: '12837'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
title: Epithelial dynamics during mouse neural tube development
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
_id: '12349'
abstract:
- lang: eng
text: Statistics of natural scenes are not uniform - their structure varies dramatically
from ground to sky. It remains unknown whether these non-uniformities are reflected
in the large-scale organization of the early visual system and what benefits such
adaptations would confer. Here, by relying on the efficient coding hypothesis,
we predict that changes in the structure of receptive fields across visual space
increase the efficiency of sensory coding. We show experimentally that, in agreement
with our predictions, receptive fields of retinal ganglion cells change their
shape along the dorsoventral retinal axis, with a marked surround asymmetry at
the visual horizon. Our work demonstrates that, according to principles of efficient
coding, the panoramic structure of natural scenes is exploited by the retina across
space and cell-types.
acknowledged_ssus:
- _id: ScienComp
- _id: PreCl
- _id: LifeSc
- _id: Bio
acknowledgement: We thank Hiroki Asari for sharing the dataset of naturalistic images,
Anton Sumser for sharing visual stimulus code, Yoav Ben Simon for initial explorative
work with the generation of AAVs, and Tomas Vega-Zuñiga for help with immunostainings.
We also thank Gasper Tkacik and members of the Neuroethology group for their comments
on the manuscript. This research was supported by the Scientific Service Units of
IST Austria through resources provided by Scientific Computing, the Preclinical
Facility, the Lab Support Facility, and the Imaging and Optics Facility. This work
was supported by European Union Horizon 2020 Marie Skłodowska-Curie grant 665385
(DG), Austrian Science Fund (FWF) stand-alone grant P 34015 (WM), Human Frontiers
Science Program LT000256/2018-L (AS), EMBO ALTF 1098-2017 (AS) and the European
Research Council Starting Grant 756502 (MJ).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Divyansh
full_name: Gupta, Divyansh
id: 2A485EBE-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
orcid: 0000-0001-7400-6665
- first_name: Wiktor F
full_name: Mlynarski, Wiktor F
id: 358A453A-F248-11E8-B48F-1D18A9856A87
last_name: Mlynarski
- first_name: Anton L
full_name: Sumser, Anton L
id: 3320A096-F248-11E8-B48F-1D18A9856A87
last_name: Sumser
orcid: 0000-0002-4792-1881
- first_name: Olga
full_name: Symonova, Olga
id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87
last_name: Symonova
orcid: 0000-0003-2012-9947
- first_name: Jan
full_name: Svaton, Jan
id: f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2
last_name: Svaton
orcid: 0000-0002-6198-2939
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
citation:
ama: Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. Panoramic
visual statistics shape retina-wide organization of receptive fields. Nature
Neuroscience. 2023;26:606-614. doi:10.1038/s41593-023-01280-0
apa: Gupta, D., Mlynarski, W. F., Sumser, A. L., Symonova, O., Svaton, J., &
Jösch, M. A. (2023). Panoramic visual statistics shape retina-wide organization
of receptive fields. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-023-01280-0
chicago: Gupta, Divyansh, Wiktor F Mlynarski, Anton L Sumser, Olga Symonova, Jan
Svaton, and Maximilian A Jösch. “Panoramic Visual Statistics Shape Retina-Wide
Organization of Receptive Fields.” Nature Neuroscience. Springer Nature,
2023. https://doi.org/10.1038/s41593-023-01280-0.
ieee: D. Gupta, W. F. Mlynarski, A. L. Sumser, O. Symonova, J. Svaton, and M. A.
Jösch, “Panoramic visual statistics shape retina-wide organization of receptive
fields,” Nature Neuroscience, vol. 26. Springer Nature, pp. 606–614, 2023.
ista: Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. 2023. Panoramic
visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience.
26, 606–614.
mla: Gupta, Divyansh, et al. “Panoramic Visual Statistics Shape Retina-Wide Organization
of Receptive Fields.” Nature Neuroscience, vol. 26, Springer Nature, 2023,
pp. 606–14, doi:10.1038/s41593-023-01280-0.
short: D. Gupta, W.F. Mlynarski, A.L. Sumser, O. Symonova, J. Svaton, M.A. Jösch,
Nature Neuroscience 26 (2023) 606–614.
corr_author: '1'
date_created: 2023-01-23T14:14:19Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2026-09-15T22:30:34Z
day: '01'
ddc:
- '570'
department:
- _id: GradSch
- _id: MaJö
doi: 10.1038/s41593-023-01280-0
ec_funded: 1
external_id:
isi:
- '000955258300002'
pmid:
- '36959418'
file:
- access_level: open_access
checksum: a33d91e398e548f34003170e10988368
content_type: application/pdf
creator: dernst
date_created: 2023-10-04T11:40:51Z
date_updated: 2023-10-04T11:40:51Z
file_id: '14395'
file_name: 2023_NatureNeuroscience_Gupta.pdf
file_size: 6144866
relation: main_file
success: 1
file_date_updated: 2023-10-04T11:40:51Z
fulldoi: https://doi.org/10.1038/s41593-023-01280-0
has_accepted_license: '1'
intvolume: ' 26'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 606-614
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 626c45b5-2b32-11ec-9570-e509828c1ba6
grant_number: P34015
name: Efficient coding with biophysical realism
- _id: 2634E9D2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '756502'
name: Circuits of Visual Attention
- _id: 266D407A-B435-11E9-9278-68D0E5697425
grant_number: LT000256
name: Neuronal networks of salience and spatial detection in the murine superior
colliculus
- _id: 264FEA02-B435-11E9-9278-68D0E5697425
grant_number: ALTF 1098-2017
name: Connecting sensory with motor processing in the superior colliculus
publication: Nature Neuroscience
publication_identifier:
eissn:
- 1546-1726
issn:
- 1097-6256
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
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relation: research_data
status: public
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Panoramic visual statistics shape retina-wide organization of receptive fields
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: 26
year: '2023'
...