---
OA_place: publisher
_id: '20206'
abstract:
- lang: eng
text: "The internal structure of biomolecules and their organization in higher-order
arrangements are key factors governing the working principles of biological systems.
Bioimaging has successfully revealed arrangements across relevant spatial scales.
For example, cryo-electron tomography has become widely used for analyzing biomolecular
structures in situ due to its comprehensive structural visualization of near-natively
preserved samples, and its capability of sub-nm resolution via averaging. However,
the identification of molecules within crowded cellular environments is often
hindered by low contrast. Fluorescence microscopy, on the other hand, routinely
visualizes specifically labeled targets at single-molecule contrast against essentially
zero background. Moreover, it provides comparatively high throughput and is amenable
to multiplexing. Due to this complementarity, combining datasets from both modalities
acquired on the same region via correlative light and electron microscopy can
reveal novel types of information. \r\nThe spatial scale at which information
can be extracted depends on imaging resolution and correlation accuracy. Since
diffraction of light limits the resolution of conventional fluorescence microscopy
to few hundreds of nanometers, reaching the full potential of correlative imaging
requires super-resolution approaches. Performing imaging at cryogenic temperature
preserves structures in a near-native state and minimizes distortions between
the fluorescence and the electron microscopy datasets. Implementations of this
concept have achieved correlation on the scale of cellular organelles or bacterial
domains.\r\nWe have worked towards pushing correlative imaging to the single-molecule
scale by improving cryo-super-resolution microscopy, and devising a refined image
correlation workflow. As part of this project, I constructed a microscopy setup
and adopted it for super-resolution fluorescence microscopy at room temperature
and cryogenic conditions. I explored different cryo-stages and acquisition strategies.
Specifically, I developed a new scheme for correcting sample drift, thus increasing
mechanical stability during microscopy acquisitions.\r\n"
acknowledged_ssus:
- _id: M-Shop
- _id: EM-Fac
- _id: Bio
acknowledgement: "The project was supported by CZI grant DAF2021-234754 and grant\r\nDOI:
https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an\r\nadvised
fund of Silicon Valley Community Foundation (funder\r\nDOI: https://doi.org/10.13039/100014989),
as well as internal grants from ISTA’s Equipment\r\nInvestment Committee and Interdisciplinary
Project Committee. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Jakob
full_name: Vorlaufer, Jakob
id: 937696FA-C996-11E9-8C7C-CF13E6697425
last_name: Vorlaufer
orcid: 0009-0000-7590-3501
citation:
ama: Vorlaufer J. Construction of a cryo-super-resolution microscope to guide in
situ structure analysis. 2025. doi:10.15479/AT-ISTA-20206
apa: Vorlaufer, J. (2025). Construction of a cryo-super-resolution microscope
to guide in situ structure analysis. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT-ISTA-20206
chicago: Vorlaufer, Jakob. “Construction of a Cryo-Super-Resolution Microscope to
Guide in Situ Structure Analysis.” Institute of Science and Technology Austria,
2025. https://doi.org/10.15479/AT-ISTA-20206.
ieee: J. Vorlaufer, “Construction of a cryo-super-resolution microscope to guide
in situ structure analysis,” Institute of Science and Technology Austria, 2025.
ista: Vorlaufer J. 2025. Construction of a cryo-super-resolution microscope to guide
in situ structure analysis. Institute of Science and Technology Austria.
mla: Vorlaufer, Jakob. Construction of a Cryo-Super-Resolution Microscope to
Guide in Situ Structure Analysis. Institute of Science and Technology Austria,
2025, doi:10.15479/AT-ISTA-20206.
short: J. Vorlaufer, Construction of a Cryo-Super-Resolution Microscope to Guide
in Situ Structure Analysis, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-08-22T08:12:55Z
date_published: 2025-08-25T00:00:00Z
date_updated: 2026-10-20T08:55:33Z
day: '25'
ddc:
- '621'
- '535'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoDa
doi: 10.15479/AT-ISTA-20206
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date_created: 2025-08-25T13:49:56Z
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fulldoi: https://doi.org/10.15479/AT-ISTA-20206
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '107'
project:
- _id: 62909c6f-2b32-11ec-9570-e1476aab5308
grant_number: CZI01
name: CryoMinflux-guided in-situ molecular census and structure determination
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '19795'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
title: Construction of a cryo-super-resolution microscope to guide in situ structure
analysis
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19506'
abstract:
- lang: eng
text: 'Hippocampal reactivation of waking neuronal assemblies in sleep is a key
initial step of systems consolidation. Nevertheless, it is unclear whether reactivated
assemblies are static or whether they reorganize gradually over prolonged sleep.
We tracked reactivated CA1 assembly patterns over ∼20 h of sleep/rest periods
and related them to assemblies seen before or after in a spatial learning paradigm
using rats. We found that reactivated assembly patterns were gradually transformed
and started to resemble those seen in the subsequent recall session. Periods of
rapid eye movement (REM) sleep and non-REM (NREM) had antagonistic roles: whereas
NREM accelerated the assembly drift, REM countered it. Moreover, only a subset
of rate-changing pyramidal cells contributed to the drift, whereas stable-firing-rate
cells maintained unaltered reactivation patterns. Our data suggest that prolonged
sleep promotes the spontaneous reorganization of spatial assemblies, which can
contribute to daily cognitive map changes or encoding new learning situations.'
acknowledgement: We thank Andrea Cumpelik, Lisa Genzel, and Freya Ólafsdóttir for
comments on an earlier version of the manuscript. This work was supported by the
European Research Council (281511) and Austrian Science Fund (FWF I3713).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Lars
full_name: Bollmann, Lars
id: 47AD3038-F248-11E8-B48F-1D18A9856A87
last_name: Bollmann
- first_name: Peter
full_name: Baracskay, Peter
id: 361CC00E-F248-11E8-B48F-1D18A9856A87
last_name: Baracskay
- first_name: Federico
full_name: Stella, Federico
id: 39AF1E74-F248-11E8-B48F-1D18A9856A87
last_name: Stella
orcid: 0000-0001-9439-3148
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Bollmann L, Baracskay P, Stella F, Csicsvari JL. Sleep stages antagonistically
modulate reactivation drift. Neuron. 2025;113(9):1446-1459.e6. doi:10.1016/j.neuron.2025.02.025
apa: Bollmann, L., Baracskay, P., Stella, F., & Csicsvari, J. L. (2025). Sleep
stages antagonistically modulate reactivation drift. Neuron. Cell Press.
https://doi.org/10.1016/j.neuron.2025.02.025
chicago: Bollmann, Lars, Peter Baracskay, Federico Stella, and Jozsef L Csicsvari.
“Sleep Stages Antagonistically Modulate Reactivation Drift.” Neuron. Cell
Press, 2025. https://doi.org/10.1016/j.neuron.2025.02.025.
ieee: L. Bollmann, P. Baracskay, F. Stella, and J. L. Csicsvari, “Sleep stages antagonistically
modulate reactivation drift,” Neuron, vol. 113, no. 9. Cell Press, p. 1446–1459.e6,
2025.
ista: Bollmann L, Baracskay P, Stella F, Csicsvari JL. 2025. Sleep stages antagonistically
modulate reactivation drift. Neuron. 113(9), 1446–1459.e6.
mla: Bollmann, Lars, et al. “Sleep Stages Antagonistically Modulate Reactivation
Drift.” Neuron, vol. 113, no. 9, Cell Press, 2025, p. 1446–1459.e6, doi:10.1016/j.neuron.2025.02.025.
short: L. Bollmann, P. Baracskay, F. Stella, J.L. Csicsvari, Neuron 113 (2025) 1446–1459.e6.
corr_author: '1'
date_created: 2025-04-06T22:01:32Z
date_published: 2025-05-07T00:00:00Z
date_updated: 2026-10-20T08:54:27Z
day: '07'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1016/j.neuron.2025.02.025
ec_funded: 1
external_id:
isi:
- '001510440400001'
pmid:
- '40132588'
file:
- access_level: open_access
checksum: 5e57852a45a78a751dd3a5e807bf015f
content_type: application/pdf
creator: dernst
date_created: 2025-08-05T12:43:44Z
date_updated: 2025-08-05T12:43:44Z
file_id: '20133'
file_name: 2025_Neuron_Bollmann.pdf
file_size: 27047730
relation: main_file
success: 1
file_date_updated: 2025-08-05T12:43:44Z
fulldoi: https://doi.org/10.1016/j.neuron.2025.02.025
has_accepted_license: '1'
intvolume: ' 113'
isi: 1
issue: '9'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1446-1459.e6
pmid: 1
project:
- _id: 257A4776-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281511'
name: Memory-related information processing in neuronal circuits of the hippocampus
and entorhinal cortex
- _id: 2654F984-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 3713-B27
name: Interneuro plasticity during spatial learning
publication: Neuron
publication_identifier:
eissn:
- 1097-4199
issn:
- 0896-6273
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/how-sleep-keeps-our-memories-fresh/
scopus_import: '1'
status: public
title: Sleep stages antagonistically modulate reactivation drift
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: 113
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19443'
abstract:
- lang: eng
text: In cryo-electron microscopy, accurate particle localization and classification
are imperative. Recent deep learning solutions, though successful, require extensive
training datasets. The protracted generation time of physics-based models, often
employed to produce these datasets, limits their broad applicability. We introduce
FakET, a method based on neural style transfer, capable of simulating the forward
operator of any cryo transmission electron microscope. It can be used to adapt
a synthetic training dataset according to reference data producing high-quality
simulated micrographs or tilt-series. To assess the quality of our generated data,
we used it to train a state-of-the-art localization and classification architecture
and compared its performance with a counterpart trained on benchmark data. Remarkably,
our technique matches the performance, boosts data generation speed 750x, uses
33x less memory, and scales well to typical transmission electron microscope detector
sizes. It leverages GPU acceleration and parallel processing. The source code
is available at https://github.com/paloha/faket/.
acknowledgement: The IMP and D.H. are generously funded by Boehringer Ingelheim. We
thank Julius Berner from the Mathematical Data Science group @ UniVie, Ilja Gubins
and Marten Chaillet from the SHREC team, and the members of the Haselbach lab for
helpful discussions.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Pavol
full_name: Harar, Pavol
id: e03d953a-6e8c-11ef-99e4-f0717d385cd5
last_name: Harar
orcid: 0000-0001-5206-1794
- first_name: Lukas
full_name: Herrmann, Lukas
last_name: Herrmann
- first_name: Philipp
full_name: Grohs, Philipp
last_name: Grohs
- first_name: David
full_name: Haselbach, David
last_name: Haselbach
citation:
ama: 'Harar P, Herrmann L, Grohs P, Haselbach D. FakET: Simulating cryo-electron
tomograms with neural style transfer. Structure. 2025;33(4):820-827.e4.
doi:10.1016/j.str.2025.01.020'
apa: 'Harar, P., Herrmann, L., Grohs, P., & Haselbach, D. (2025). FakET: Simulating
cryo-electron tomograms with neural style transfer. Structure. Cell Press.
https://doi.org/10.1016/j.str.2025.01.020'
chicago: 'Harar, Pavol, Lukas Herrmann, Philipp Grohs, and David Haselbach. “FakET:
Simulating Cryo-Electron Tomograms with Neural Style Transfer.” Structure.
Cell Press, 2025. https://doi.org/10.1016/j.str.2025.01.020.'
ieee: 'P. Harar, L. Herrmann, P. Grohs, and D. Haselbach, “FakET: Simulating cryo-electron
tomograms with neural style transfer,” Structure, vol. 33, no. 4. Cell
Press, p. 820–827.e4, 2025.'
ista: 'Harar P, Herrmann L, Grohs P, Haselbach D. 2025. FakET: Simulating cryo-electron
tomograms with neural style transfer. Structure. 33(4), 820–827.e4.'
mla: 'Harar, Pavol, et al. “FakET: Simulating Cryo-Electron Tomograms with Neural
Style Transfer.” Structure, vol. 33, no. 4, Cell Press, 2025, p. 820–827.e4,
doi:10.1016/j.str.2025.01.020.'
short: P. Harar, L. Herrmann, P. Grohs, D. Haselbach, Structure 33 (2025) 820–827.e4.
corr_author: '1'
date_created: 2025-03-23T23:01:27Z
date_published: 2025-04-03T00:00:00Z
date_updated: 2026-10-20T08:54:10Z
day: '03'
ddc:
- '570'
department:
- _id: AlMi
doi: 10.1016/j.str.2025.01.020
external_id:
isi:
- '001463196100001'
pmid:
- '39947174'
file:
- access_level: open_access
checksum: f346bc357a66a88cca3d0eb95793fb73
content_type: application/pdf
creator: dernst
date_created: 2025-08-05T12:15:13Z
date_updated: 2025-08-05T12:15:13Z
file_id: '20130'
file_name: 2025_Structure_Harar.pdf
file_size: 4367530
relation: main_file
success: 1
file_date_updated: 2025-08-05T12:15:13Z
fulldoi: https://doi.org/10.1016/j.str.2025.01.020
has_accepted_license: '1'
intvolume: ' 33'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 820-827.e4
pmid: 1
publication: Structure
publication_identifier:
eissn:
- 1878-4186
issn:
- 0969-2126
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/paloha/faket/
scopus_import: '1'
status: public
title: 'FakET: Simulating cryo-electron tomograms with neural style transfer'
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: 33
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20154'
abstract:
- lang: eng
text: In long-lived mammals, including humans, brain cell homeostasis is critical
for maintaining brain function throughout life. Most neurons are generated during
development and must maintain their cellular identity and plasticity to preserve
brain function. Although extensive studies indicate the importance of recycling
and regenerating cellular molecules to maintain cellular homeostasis, recent evidence
has shown that some proteins and RNAs do not turn over for months and even years.
We propose that these long-lived cellular molecules may be the basis for maintaining
brain function in the long term, but also a potential convergent target of brain
aging. We highlight key discoveries and challenges, and propose potential directions
to unravel the mystery of brain cell longevity.
acknowledgement: The work was supported by the Deutsche Forschungsgemeinschaft (DFG,
German Research Foundation) (470322152 – T1347/3-1; 497658532 – T1347/4-1; 507965872
– T1347/5-1; and 460333672 – CRC1540 Exploring Brain Mechanics) to T.T., the Schram
Foundation (T.T.), the European Research Council (ERC-2018-STG, 804468 EAGER; ERC-2023-COG,
101125034 NEUTIME) to T.T., the Hans-Georg Geis und Xue Hong Dong-Geis Foundation
and Forschungsstiftung Medizin am Universitätsklinikum Erlangen to T.T., and the
Interdisciplinary Centre for Clinical Research Erlangen (Interdisziplinäres Zentrum
für Klinische Forschung, Universitätsklinikum Erlangen; P162 to T.T.). We thank
Dr Laura J. Harrison for editing assistance.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Martin W
full_name: Hetzer, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: Hetzer
orcid: 0000-0002-2111-992X
- first_name: Tomohisa
full_name: Toda, Tomohisa
last_name: Toda
citation:
ama: Hetzer M, Toda T. Long-lived cellular molecules in the brain. Trends in
Neurosciences. 2025;48(9):645-654. doi:10.1016/j.tins.2025.07.004
apa: Hetzer, M., & Toda, T. (2025). Long-lived cellular molecules in the brain.
Trends in Neurosciences. Cell Press. https://doi.org/10.1016/j.tins.2025.07.004
chicago: Hetzer, Martin, and Tomohisa Toda. “Long-Lived Cellular Molecules in the
Brain.” Trends in Neurosciences. Cell Press, 2025. https://doi.org/10.1016/j.tins.2025.07.004.
ieee: M. Hetzer and T. Toda, “Long-lived cellular molecules in the brain,” Trends
in Neurosciences, vol. 48, no. 9. Cell Press, pp. 645–654, 2025.
ista: Hetzer M, Toda T. 2025. Long-lived cellular molecules in the brain. Trends
in Neurosciences. 48(9), 645–654.
mla: Hetzer, Martin, and Tomohisa Toda. “Long-Lived Cellular Molecules in the Brain.”
Trends in Neurosciences, vol. 48, no. 9, Cell Press, 2025, pp. 645–54,
doi:10.1016/j.tins.2025.07.004.
short: M. Hetzer, T. Toda, Trends in Neurosciences 48 (2025) 645–654.
corr_author: '1'
date_created: 2025-08-10T22:01:29Z
date_published: 2025-09-01T00:00:00Z
date_updated: 2026-10-20T08:54:50Z
day: '01'
ddc:
- '570'
department:
- _id: MaHe
doi: 10.1016/j.tins.2025.07.004
external_id:
isi:
- '001568965400001'
pmid:
- '40744775'
file:
- access_level: open_access
checksum: 90942491b499f70b0bf48b8aec2e7387
content_type: application/pdf
creator: dernst
date_created: 2025-12-29T13:47:27Z
date_updated: 2025-12-29T13:47:27Z
file_id: '20873'
file_name: 2025_TrendsNeurosciences_Hetzer.pdf
file_size: 327847
relation: main_file
success: 1
file_date_updated: 2025-12-29T13:47:27Z
fulldoi: https://doi.org/10.1016/j.tins.2025.07.004
has_accepted_license: '1'
intvolume: ' 48'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 645-654
pmid: 1
publication: Trends in Neurosciences
publication_identifier:
eissn:
- 1878-108X
issn:
- 0166-2236
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long-lived cellular molecules in the brain
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: 48
year: '2025'
...
---
OA_type: closed access
_id: '20427'
abstract:
- lang: eng
text: Animal cells migrating up chemotactic gradients often show speed oscillations.
A new study describes a molecular circuit that switches zebrafish germ cells between
phases of straight runs, tumbling and directional reorientation.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Ziqiang
full_name: Li, Ziqiang
id: 922e68bb-1727-11ee-857c-966e8cc1b6c3
last_name: Li
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: 'LI Z, Sixt MK. Cell migration: How animal cells run and tumble. Current
Biology. 2025;35(18):R890-R892. doi:10.1016/j.cub.2025.08.016'
apa: 'LI, Z., & Sixt, M. K. (2025). Cell migration: How animal cells run and
tumble. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2025.08.016'
chicago: 'LI, ZIQIANG, and Michael K Sixt. “Cell Migration: How Animal Cells Run
and Tumble.” Current Biology. Cell Press, 2025. https://doi.org/10.1016/j.cub.2025.08.016.'
ieee: 'Z. LI and M. K. Sixt, “Cell migration: How animal cells run and tumble,”
Current Biology, vol. 35, no. 18. Cell Press, pp. R890–R892, 2025.'
ista: 'LI Z, Sixt MK. 2025. Cell migration: How animal cells run and tumble. Current
Biology. 35(18), R890–R892.'
mla: 'LI, ZIQIANG, and Michael K. Sixt. “Cell Migration: How Animal Cells Run and
Tumble.” Current Biology, vol. 35, no. 18, Cell Press, 2025, pp. R890–92,
doi:10.1016/j.cub.2025.08.016.'
short: Z. LI, M.K. Sixt, Current Biology 35 (2025) R890–R892.
corr_author: '1'
date_created: 2025-10-05T22:01:35Z
date_published: 2025-09-22T00:00:00Z
date_updated: 2026-10-20T08:55:09Z
day: '22'
department:
- _id: MiSi
doi: 10.1016/j.cub.2025.08.016
external_id:
isi:
- '001592664700001'
pmid:
- '40987270'
fulldoi: https://doi.org/10.1016/j.cub.2025.08.016
intvolume: ' 35'
isi: 1
issue: '18'
language:
- iso: eng
month: '09'
oa_version: None
page: R890-R892
pmid: 1
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Cell migration: How animal cells run and tumble'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15016'
abstract:
- lang: eng
text: Amphibians, by virtue of their phylogenetic position, provide invaluable insights
on nervous system evolution, development, and remodeling. The genetic toolkit
for amphibians, however, remains limited. Recombinant adeno-associated viral vectors
(AAVs) are a powerful alternative to transgenesis for labeling and manipulating
neurons. Although successful in mammals, AAVs have never been shown to transduce
amphibian cells efficiently. We screened AAVs in three amphibian species—the frogs
Xenopus laevis and Pelophylax bedriagae and the salamander Pleurodeles waltl—and
identified at least two AAV serotypes per species that transduce neurons. In developing
amphibians, AAVs labeled groups of neurons generated at the same time during development.
In the mature brain, AAVrg retrogradely traced long-range projections. Our study
introduces AAVs as a tool for amphibian research, establishes a generalizable
workflow for AAV screening in new species, and expands opportunities for cross-species
comparisons of nervous system development, function, and evolution.
acknowledged_ssus:
- _id: PreCl
- _id: Bio
acknowledgement: 'We thank members of the Sweeney, Tosches, Shein-Idelson, Yamaguchi,
Kelley, and Cline Labs for their contributions to this project, discussion, and
support. We additionally thank the Beckman Institute CLOVER Center and Viviana Gradinaru
(Caltech), Kimberly Ritola (UNC NeuroTools), and Flavia Gomez-Leite (ISTA Viral
Core) for AAV production and consultation; Andras Simon and Alberto Joven (Karolinska
Institute) for feedback; Elizabeth Bagnato-Cohen (Columbia) for project coordination;
our animal care and imaging facilities; the amphibian stock centers (NXR, EXRC,
and XenopusExpress); and our funding sources: NSF IOS 2110086 (D.B.K., L.B.S., M.A.T.,
A.Y., and H.T.C.); US-Israel Binational Science Foundation (BSF) 2020702 (M.S.-I.);
FTI Strategy Lower Austria Dissertation FT121-D-046 (D.V.); Horizon Europe ERC Starting
Grant 101041551 and Special Research Programme (SFB) of the Austrian Science Fund
(FWF) project F7814-B (L.B.S.); NIH grant R35GM146973, Rita Allen Foundation Award
GA_032522_FE, and CZI Ben Barres Early Career Acceleration Award 2023-331758 (M.A.T.);
EMBO Long-Term Fellowship ALTF 874-2021 (A.D.); and NSF GRFP DGE 2036197 (E.C.B.J.).'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Eliza C.B.
full_name: Jaeger, Eliza C.B.
last_name: Jaeger
- first_name: David
full_name: Vijatovic, David
id: cf391e77-ec3c-11ea-a124-d69323410b58
last_name: Vijatovic
orcid: 0000-0002-5494-0941
- first_name: Astrid
full_name: Deryckere, Astrid
last_name: Deryckere
- first_name: Nikol
full_name: Zorin, Nikol
last_name: Zorin
- first_name: Akemi L.
full_name: Nguyen, Akemi L.
last_name: Nguyen
- first_name: Georgiy
full_name: Ivanian, Georgiy
id: eaf2b366-cfd1-11ee-bbdf-c8790f800a05
last_name: Ivanian
orcid: 0009-0002-3999-3735
- first_name: Jamie
full_name: Woych, Jamie
last_name: Woych
- first_name: Rebecca C
full_name: Arnold, Rebecca C
id: d6cce458-14c9-11ed-a755-c1c8fc6fde6f
last_name: Arnold
- first_name: Alonso
full_name: Ortega Gurrola, Alonso
last_name: Ortega Gurrola
- first_name: Arik
full_name: Shvartsman, Arik
last_name: Shvartsman
- first_name: Francesca
full_name: Barbieri, Francesca
id: a9492887-8972-11ed-ae7b-bfae10998254
last_name: Barbieri
- first_name: Florina-Alexandra
full_name: Toma, Florina-Alexandra
id: 85dd99f2-15b2-11ec-abd3-d1ae4d57f3b5
last_name: Toma
- first_name: Gary J.
full_name: Gorbsky, Gary J.
last_name: Gorbsky
- first_name: Marko E.
full_name: Horb, Marko E.
last_name: Horb
- first_name: Hollis T.
full_name: Cline, Hollis T.
last_name: Cline
- first_name: Timothy F.
full_name: Shay, Timothy F.
last_name: Shay
- first_name: Darcy B.
full_name: Kelley, Darcy B.
last_name: Kelley
- first_name: Ayako
full_name: Yamaguchi, Ayako
last_name: Yamaguchi
- first_name: Mark
full_name: Shein-Idelson, Mark
last_name: Shein-Idelson
- first_name: Maria Antonietta
full_name: Tosches, Maria Antonietta
last_name: Tosches
- first_name: Lora Beatrice Jaeger
full_name: Sweeney, Lora Beatrice Jaeger
id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
last_name: Sweeney
orcid: 0000-0001-9242-5601
citation:
ama: Jaeger ECB, Vijatovic D, Deryckere A, et al. Adeno-associated viral tools to
trace neural development and connectivity across amphibians. Developmental
Cell. 2025;60(5):794-812.e6. doi:10.1016/j.devcel.2024.10.025
apa: Jaeger, E. C. B., Vijatovic, D., Deryckere, A., Zorin, N., Nguyen, A. L., Ivanian,
G., … Sweeney, L. B. (2025). Adeno-associated viral tools to trace neural development
and connectivity across amphibians. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2024.10.025
chicago: Jaeger, Eliza C.B., David Vijatovic, Astrid Deryckere, Nikol Zorin, Akemi
L. Nguyen, Georgiy Ivanian, Jamie Woych, et al. “Adeno-Associated Viral Tools
to Trace Neural Development and Connectivity across Amphibians.” Developmental
Cell. Cell Press, 2025. https://doi.org/10.1016/j.devcel.2024.10.025.
ieee: E. C. B. Jaeger et al., “Adeno-associated viral tools to trace neural
development and connectivity across amphibians,” Developmental Cell, vol.
60, no. 5. Cell Press, p. 794–812.e6, 2025.
ista: Jaeger ECB, Vijatovic D, Deryckere A, Zorin N, Nguyen AL, Ivanian G, Woych
J, Arnold RC, Ortega Gurrola A, Shvartsman A, Barbieri F, Toma F-A, Gorbsky GJ,
Horb ME, Cline HT, Shay TF, Kelley DB, Yamaguchi A, Shein-Idelson M, Tosches MA,
Sweeney LB. 2025. Adeno-associated viral tools to trace neural development and
connectivity across amphibians. Developmental Cell. 60(5), 794–812.e6.
mla: Jaeger, Eliza C. B., et al. “Adeno-Associated Viral Tools to Trace Neural Development
and Connectivity across Amphibians.” Developmental Cell, vol. 60, no. 5,
Cell Press, 2025, p. 794–812.e6, doi:10.1016/j.devcel.2024.10.025.
short: E.C.B. Jaeger, D. Vijatovic, A. Deryckere, N. Zorin, A.L. Nguyen, G. Ivanian,
J. Woych, R.C. Arnold, A. Ortega Gurrola, A. Shvartsman, F. Barbieri, F.-A. Toma,
G.J. Gorbsky, M.E. Horb, H.T. Cline, T.F. Shay, D.B. Kelley, A. Yamaguchi, M.
Shein-Idelson, M.A. Tosches, L.B. Sweeney, Developmental Cell 60 (2025) 794–812.e6.
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: 'FAMD RStudio code and raw data used for analysis of post-metamorphic
P. waltl injection outcomes are available via Dryad repository: https://doi.org/10.5061/dryad.mpg4f4r89.
Any additional information required to reanalyze the data reported in this paper
is available from the lead contact upon request.'
date_created: 2024-02-20T09:20:32Z
date_published: 2025-03-10T00:00:00Z
date_updated: 2026-10-20T08:56:33Z
day: '10'
ddc:
- '570'
department:
- _id: LoSw
- _id: MaDe
- _id: GaNo
doi: 10.1016/j.devcel.2024.10.025
external_id:
isi:
- '001444798600001'
pmid:
- '39603234'
file:
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checksum: a83a4cb58f5941096d3ad91ca0172594
content_type: application/pdf
creator: dernst
date_created: 2025-06-04T05:43:27Z
date_updated: 2025-06-04T05:43:27Z
file_id: '19790'
file_name: 2025_DevelopmentalCell_Jaeger.pdf
file_size: 11936258
relation: main_file
success: 1
file_date_updated: 2025-06-04T05:43:27Z
fulldoi: https://doi.org/10.1016/j.devcel.2024.10.025
has_accepted_license: '1'
intvolume: ' 60'
isi: 1
issue: '5'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 794-812.e6
pmid: 1
project:
- _id: bd73af52-d553-11ed-ba76-912049f0ac7a
grant_number: FTI21-D-046
name: Development of V1 interneuron diversity during swim-to-walk transition of
Xenopus metamorphosis
- _id: ebb66355-77a9-11ec-83b8-b8ac210a4dae
grant_number: '101041551'
name: Development and Evolution of Tetrapod Motor Circuits
- _id: 8da85f50-16d5-11f0-9cad-eab8b0ff6c9e
grant_number: F7814
name: 'Stem Cell Modulation in Neural Development and Regeneration/ P14-Swim-to-limb
transition: cell type to connection diversity'
publication: Developmental Cell
publication_identifier:
eissn:
- 1878-1551
issn:
- 1534-5807
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
record:
- id: '22667'
relation: dissertation_contains
status: public
- id: '22803'
relation: research_data
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Adeno-associated viral tools to trace neural development and connectivity across
amphibians
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: 60
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18619'
abstract:
- lang: eng
text: Brassinosteroids (BRs) are steroidal phytohormones indispensable for plant
growth, development, and responses to environmental stresses. The export of bioactive
BRs to the apoplast is essential for BR signalling initiation, which requires
binding of BR molecule to the extracellular domains of the plasma membrane-localized
receptor complex. We have previously shown that the Arabidopsis thaliana ATP-binding
cassette (ABC) transporter, ABCB19, functions as a BR exporter, and together with
its close homologue, ABCB1, positively regulate BR signalling. Here, we demonstrate
that ABCB1 is another BR transporter. The ATP hydrolysis activity of ABCB1 was
stimulated by bioactive BRs, and its transport activity was confirmed in proteoliposomes
and protoplasts. Structures of ABCB1 in substrate-unbound (apo), brassinolide
(BL)-bound, and ATP plus BL-bound states were determined. In the BL-bound structure,
BL was bound to the hydrophobic cavity formed by the transmembrane domain, and
triggered local conformational changes. Together, our data provide additional
insights into the ABC transporter-mediated BR export.
acknowledgement: We thank the Cryo-EM Center of the University of Science and Technology
of China for the EM facility support. We thank Yaowei Wang, Yongming Luo, and Nemanja
Vukašinović (VIB-UGhent, Belgium) for useful discussions and technical support.
L.S. is supported by an Outstanding Young Scholar Award from the Qiu Shi Science
and Technologies Foundation and a Young Scholar Award from the Cyrus Tang Foundation.
No conflict of interest is declared.
article_number: '101181'
article_processing_charge: Yes
article_type: original
author:
- first_name: H
full_name: Wei, H
last_name: Wei
- first_name: H
full_name: Zhu, H
last_name: Zhu
- first_name: W
full_name: Ying, W
last_name: Ying
- first_name: H
full_name: Janssens, H
last_name: Janssens
- first_name: M
full_name: Kvasnica, M
last_name: Kvasnica
- first_name: JM
full_name: Winne, JM
last_name: Winne
- first_name: Y
full_name: Gao, Y
last_name: Gao
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Q
full_name: Ma, Q
last_name: Ma
- first_name: S
full_name: Tan, S
last_name: Tan
- first_name: X
full_name: Liu, X
last_name: Liu
- first_name: E
full_name: Russinova, E
last_name: Russinova
- first_name: L
full_name: Sun, L
last_name: Sun
citation:
ama: Wei H, Zhu H, Ying W, et al. Structural insights into brassinosteroid export
mediated by the Arabidopsis ABC transporter ABCB1. Plant Communications.
2025;6(1). doi:10.1016/j.xplc.2024.101181
apa: Wei, H., Zhu, H., Ying, W., Janssens, H., Kvasnica, M., Winne, J., … Sun, L.
(2025). Structural insights into brassinosteroid export mediated by the Arabidopsis
ABC transporter ABCB1. Plant Communications. Cell Press. https://doi.org/10.1016/j.xplc.2024.101181
chicago: Wei, H, H Zhu, W Ying, H Janssens, M Kvasnica, JM Winne, Y Gao, et al.
“Structural Insights into Brassinosteroid Export Mediated by the Arabidopsis ABC
Transporter ABCB1.” Plant Communications. Cell Press, 2025. https://doi.org/10.1016/j.xplc.2024.101181.
ieee: H. Wei et al., “Structural insights into brassinosteroid export mediated
by the Arabidopsis ABC transporter ABCB1,” Plant Communications, vol. 6,
no. 1. Cell Press, 2025.
ista: Wei H, Zhu H, Ying W, Janssens H, Kvasnica M, Winne J, Gao Y, Friml J, Ma
Q, Tan S, Liu X, Russinova E, Sun L. 2025. Structural insights into brassinosteroid
export mediated by the Arabidopsis ABC transporter ABCB1. Plant Communications.
6(1), 101181.
mla: Wei, H., et al. “Structural Insights into Brassinosteroid Export Mediated by
the Arabidopsis ABC Transporter ABCB1.” Plant Communications, vol. 6, no.
1, 101181, Cell Press, 2025, doi:10.1016/j.xplc.2024.101181.
short: H. Wei, H. Zhu, W. Ying, H. Janssens, M. Kvasnica, J. Winne, Y. Gao, J. Friml,
Q. Ma, S. Tan, X. Liu, E. Russinova, L. Sun, Plant Communications 6 (2025).
das_tickbox: '1'
dataavailabilitystatement: The ABCB1 structures in the substrate-unbound state, BL-bound
state, and ATP plus BL-bound state have been deposited in the Protein Data Bank
under accession codes 8ZPX, 8ZPZ, and 8ZQ4, respectively. The corresponding cryo-EM
density maps have been deposited in the Electron Microscopy Data Bank under accession
codes EMD-60366, EMD-60369, and EMD-60370, respectively.
date_created: 2024-12-04T11:21:16Z
date_published: 2025-01-13T00:00:00Z
date_updated: 2026-10-20T08:56:15Z
day: '13'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.xplc.2024.101181
external_id:
isi:
- '001416757300001'
pmid:
- '39497419'
file:
- access_level: open_access
checksum: 7b0e4511e43cc0da06730c3edb7c1167
content_type: application/pdf
creator: dernst
date_created: 2025-04-16T09:02:05Z
date_updated: 2025-04-16T09:02:05Z
file_id: '19575'
file_name: 2025_PlantComm_Wei.pdf
file_size: 4443183
relation: main_file
success: 1
file_date_updated: 2025-04-16T09:02:05Z
fulldoi: https://doi.org/10.1016/j.xplc.2024.101181
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Plant Communications
publication_identifier:
issn:
- 2590-3462
publication_status: published
publisher: Cell Press
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Structural insights into brassinosteroid export mediated by the Arabidopsis
ABC transporter ABCB1
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: 6
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19003'
abstract:
- lang: eng
text: 'Super-resolution methods provide far better spatial resolution than the optical
diffraction limit of about half the wavelength of light (∼200-300 nm). Nevertheless,
they have yet to attain widespread use in plants, largely due to plants’ challenging
optical properties. Expansion microscopy improves effective resolution by isotropically
increasing the physical distances between sample structures while preserving relative
spatial arrangements and clearing the sample. However, its application to plants
has been hindered by the rigid, mechanically cohesive structure of plant tissues.
Here, we report on whole-mount expansion microscopy of thale cress (Arabidopsis
thaliana) root tissues (PlantEx), achieving a four-fold resolution increase over
conventional microscopy. Our results highlight the microtubule cytoskeleton organization
and interaction between molecularly defined cellular constituents. Combining PlantEx
with stimulated emission depletion (STED) microscopy, we increase nanoscale resolution
and visualize the complex organization of subcellular organelles from intact tissues
by example of the densely packed COPI-coated vesicles associated with the Golgi
apparatus and put these into a cellular structural context. Our results show that
expansion microscopy can be applied to increase effective imaging resolution in
Arabidopsis root specimens. '
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: E-Lib
- _id: M-Shop
acknowledgement: "We gratefully acknowledge support by the Scientific Service Units
at ISTA, including the Imaging and Optics and Lab Support facilities and the mechanical
workshop and Library. We thank Philipp Velicky for STED microscope alignment.\r\nThis
project has received funding from the European Research Council under the Horizon
2020 Framework Programme (grant agreement No 742985, J.F.). It has also received
funding from the Horizon 2020 Framework Programme under the Marie Skłodowska-Curie
Grant Agreement No. 665385 (M.G.). S.T. has received funding as an ISTplus Fellow
from the Horizon 2020 Framework Programme under Marie Skłodowska-Curie grant agreement
no. 754411 and from EMBO via a Long-Term Fellowship (grant number ALTF 679-2018).
M.R.T. received funding from the Austrian Academy of Sciences with DOC fellowship
no. 26137. The project has further received funding from the Austrian Science Fund,
via grant DK W1232 (M.R.T., N.A.D., and J.G.D). W.J. received a postdoctoral fellowship
from the Human Frontier Science Program (LT000557/2018). The funders had no role
in study design, data collection and analysis, decision to publish or preparation
of the manuscript."
article_number: koaf006
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- first_name: Sven M
full_name: Truckenbrodt, Sven M
id: 45812BD4-F248-11E8-B48F-1D18A9856A87
last_name: Truckenbrodt
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Syamala
full_name: Inumella, Syamala
id: F8660870-D756-11E9-98C5-34DFE5697425
last_name: Inumella
orcid: 0009-0002-5890-120X
- first_name: Vitali
full_name: Vistunou, Vitali
id: 7e146587-8972-11ed-ae7b-d7a32ea86a81
last_name: Vistunou
- 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: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- first_name: Nathalie
full_name: Agudelo Duenas, Nathalie
id: 40E7F008-F248-11E8-B48F-1D18A9856A87
last_name: Agudelo Duenas
- first_name: Jakob
full_name: Vorlaufer, Jakob
id: 937696FA-C996-11E9-8C7C-CF13E6697425
last_name: Vorlaufer
orcid: 0009-0000-7590-3501
- first_name: Wiebke
full_name: Jahr, Wiebke
id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
last_name: Jahr
orcid: 0000-0003-0201-2315
- first_name: Marek
full_name: Randuch, Marek
id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
last_name: Randuch
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- 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: Gallei MC, Truckenbrodt SM, Kreuzinger C, et al. Super-resolution expansion
microscopy in plant roots. The Plant Cell. 2025;37(4). doi:10.1093/plcell/koaf006
apa: Gallei, M. C., Truckenbrodt, S. M., Kreuzinger, C., Inumella, S., Vistunou,
V., Sommer, C. M., … Danzl, J. G. (2025). Super-resolution expansion microscopy
in plant roots. The Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koaf006
chicago: Gallei, Michelle C, Sven M Truckenbrodt, Caroline Kreuzinger, Syamala Inumella,
Vitali Vistunou, Christoph M Sommer, Mojtaba Tavakoli, et al. “Super-Resolution
Expansion Microscopy in Plant Roots.” The Plant Cell. Oxford University
Press, 2025. https://doi.org/10.1093/plcell/koaf006.
ieee: M. C. Gallei et al., “Super-resolution expansion microscopy in plant
roots,” The Plant Cell, vol. 37, no. 4. Oxford University Press, 2025.
ista: Gallei MC, Truckenbrodt SM, Kreuzinger C, Inumella S, Vistunou V, Sommer CM,
Tavakoli M, Agudelo Duenas N, Vorlaufer J, Jahr W, Randuch M, Johnson AJ, Benková
E, Friml J, Danzl JG. 2025. Super-resolution expansion microscopy in plant roots.
The Plant Cell. 37(4), koaf006.
mla: Gallei, Michelle C., et al. “Super-Resolution Expansion Microscopy in Plant
Roots.” The Plant Cell, vol. 37, no. 4, koaf006, Oxford University Press,
2025, doi:10.1093/plcell/koaf006.
short: M.C. Gallei, S.M. Truckenbrodt, C. Kreuzinger, S. Inumella, V. Vistunou,
C.M. Sommer, M. Tavakoli, N. Agudelo Duenas, J. Vorlaufer, W. Jahr, M. Randuch,
A.J. Johnson, E. Benková, J. Friml, J.G. Danzl, The Plant Cell 37 (2025).
corr_author: '1'
date_created: 2025-02-05T06:52:06Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2026-10-20T09:19:12Z
day: '01'
ddc:
- '580'
department:
- _id: EvBe
- _id: JoDa
- _id: JiFr
doi: 10.1093/plcell/koaf006
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issue: '4'
language:
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month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 269B5B22-B435-11E9-9278-68D0E5697425
grant_number: ALTF 679-2018
name: UltraX - achieving sub-nanometer resolution in light microscopy using iterative
X10 microscopy in combination with nanobodies and STED
- _id: 6285a163-2b32-11ec-9570-8e204ca2dba5
grant_number: '26137'
name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
Microscopy
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: The Plant Cell
publication_identifier:
eissn:
- 1532-298X
issn:
- 1040-4651
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
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scopus_import: '1'
status: public
title: Super-resolution expansion microscopy in plant roots
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: 37
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20452'
abstract:
- lang: eng
text: Accurate modeling of long-range forces is critical in atomistic simulations,
as they play a central role in determining the properties of material and chemical
systems. However, standard machine learning interatomic potentials (MLIPs) often
rely on short-range approximations, limiting their applicability to systems with
significant electrostatics and dispersion forces. We recently introduced the Latent
Ewald Summation (LES) method, which captures long-range electrostatics without
explicitly learning atomic charges or charge equilibration. We benchmark LES on
diverse and challenging systems, including charged molecules, ionic liquids, electrolyte
solutions, polar dipeptides, surface adsorption, electrolyte/solid interfaces,
and solid-solid interfaces. Here we show that LES can reproduce the exact atomic
charges for classical systems with fixed charges and can infer dipole and quadrupole
moments, as well as the dipole derivative with respect to atomic positions, for
quantum mechanical systems. Moreover, LES can achieve better accuracy in energy
and force predictions compared to methods that explicitly learn from charges.
acknowledgement: We thank Chunyi Zhang for providing the TiO2(101)/NaCl+NaOH+HCl(aq)
dataset and for useful discussions. We thank Jia-Xin Zhu for providing the Pt(111)/KF(aq)
dataset. We thank Tsz Wai Ko and Jonas Finkler for useful discussions and for the
DFT-optimized Au2-MgO(001) structures. We thank Junmin Chen for discussions. D.K
and B.C. acknowledge funding from Toyota Research Institute Synthesis Advanced Research
Challenge. D.S.K. and P.Z. acknowledge funding from BIDMaP Postdoctoral Fellowship.
article_number: '8763'
article_processing_charge: Yes
article_type: original
author:
- first_name: Daniel S.
full_name: King, Daniel S.
last_name: King
- first_name: Dongjin
full_name: Kim, Dongjin
last_name: Kim
- first_name: Peichen
full_name: Zhong, Peichen
last_name: Zhong
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: King DS, Kim D, Zhong P, Cheng B. Machine learning of charges and long-range
interactions from energies and forces. Nature Communications. 2025;16.
doi:10.1038/s41467-025-63852-x
apa: King, D. S., Kim, D., Zhong, P., & Cheng, B. (2025). Machine learning of
charges and long-range interactions from energies and forces. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-025-63852-x
chicago: King, Daniel S., Dongjin Kim, Peichen Zhong, and Bingqing Cheng. “Machine
Learning of Charges and Long-Range Interactions from Energies and Forces.” Nature
Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-025-63852-x.
ieee: D. S. King, D. Kim, P. Zhong, and B. Cheng, “Machine learning of charges and
long-range interactions from energies and forces,” Nature Communications,
vol. 16. Springer Nature, 2025.
ista: King DS, Kim D, Zhong P, Cheng B. 2025. Machine learning of charges and long-range
interactions from energies and forces. Nature Communications. 16, 8763.
mla: King, Daniel S., et al. “Machine Learning of Charges and Long-Range Interactions
from Energies and Forces.” Nature Communications, vol. 16, 8763, Springer
Nature, 2025, doi:10.1038/s41467-025-63852-x.
short: D.S. King, D. Kim, P. Zhong, B. Cheng, Nature Communications 16 (2025).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: The training sets, training scripts, MD input files, and
trained CACE potentials are available at https://github.com/BingqingCheng/cace-lr-fit;
see https://doi.org/10.5281/zenodo.16415061. Source data for all figures are provided
with this paper. Source data are provided with this paper.
date_created: 2025-10-12T22:01:25Z
date_published: 2025-10-01T00:00:00Z
date_updated: 2026-10-20T09:48:07Z
day: '01'
ddc:
- '000'
department:
- _id: BiCh
doi: 10.1038/s41467-025-63852-x
external_id:
isi:
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pmid:
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isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
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supplementarymaterial: no
title: Machine learning of charges and long-range interactions from energies and forces
tmp:
image: /images/cc_by.png
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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: 16
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19702'
abstract:
- lang: eng
text: Moran Birth-death process is a standard stochastic process that is used to
model natural selection in spatially structured populations. A newly occurring
mutation that invades a population of residents can either fixate on the whole
population or it can go extinct due to random drift. The duration of the process
depends not only on the total population size n, but also on the spatial structure
of the population. In this work, we consider the Moran process with a single type
of individuals who invade and colonize an otherwise empty environment. Mathematically,
this corresponds to the setting where the residents have zero reproduction rate,
thus they never reproduce. The spatial structure is represented by a graph. We
present two main contributions. First, in contrast to the Moran process in which
residents do reproduce, we show that the colonization time is always at most a
polynomial function of the population size n. Namely, we show that colonization
always takes at most 1/2n^3 - 1/2n^2 expected steps, and for each n, we identify
the slowest graph where it takes exactly that many steps. Moreover, we establish
a stronger bound of roughly n^2.5 steps for undirected graphs and an even stronger
bound of roughly n^2 steps for so-called regular graphs. Second, we discuss various
complications that one faces when attempting to measure fixation times and colonization
times in spatially structured populations, and we propose to measure the real
duration of the process, rather than counting the steps of the classic Moran process.
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Lenka
full_name: Kopfová, Lenka
id: 17691681-50b9-11ef-ad56-edf4cacb21b0
last_name: Kopfová
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
citation:
ama: Kopfová L, Tkadlec J. Colonization times in Moran process on graphs. PLoS
Computational Biology. 2025;21(5):e1012868. doi:10.1371/journal.pcbi.1012868
apa: Kopfová, L., & Tkadlec, J. (2025). Colonization times in Moran process
on graphs. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1012868
chicago: Kopfová, Lenka, and Josef Tkadlec. “Colonization Times in Moran Process
on Graphs.” PLoS Computational Biology. Public Library of Science, 2025.
https://doi.org/10.1371/journal.pcbi.1012868.
ieee: L. Kopfová and J. Tkadlec, “Colonization times in Moran process on graphs,”
PLoS Computational Biology, vol. 21, no. 5. Public Library of Science,
p. e1012868, 2025.
ista: Kopfová L, Tkadlec J. 2025. Colonization times in Moran process on graphs.
PLoS Computational Biology. 21(5), e1012868.
mla: Kopfová, Lenka, and Josef Tkadlec. “Colonization Times in Moran Process on
Graphs.” PLoS Computational Biology, vol. 21, no. 5, Public Library of
Science, 2025, p. e1012868, doi:10.1371/journal.pcbi.1012868.
short: L. Kopfová, J. Tkadlec, PLoS Computational Biology 21 (2025) e1012868.
date_created: 2025-05-18T22:02:50Z
date_published: 2025-05-01T00:00:00Z
date_updated: 2026-10-20T09:45:59Z
day: '01'
ddc:
- '000'
department:
- _id: GradSch
doi: 10.1371/journal.pcbi.1012868
external_id:
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- '2410.09476'
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success: 1
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issue: '5'
language:
- iso: eng
month: '05'
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oa_version: Published Version
page: e1012868
publication: PLoS Computational Biology
publication_identifier:
eissn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Colonization times in Moran process on graphs
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: 21
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '22770'
article_processing_charge: No
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Daniel
full_name: King, Daniel
last_name: King
- first_name: Dongjin
full_name: Kim, Dongjin
last_name: Kim
- first_name: Peichen
full_name: Zhong, Peichen
last_name: Zhong
citation:
ama: 'Cheng B, King D, Kim D, Zhong P. BingqingCheng/cace-lr-fit: V0. 2025. doi:10.5281/zenodo.16415060'
apa: 'Cheng, B., King, D., Kim, D., & Zhong, P. (2025). BingqingCheng/cace-lr-fit:
V0. Zenodo. https://doi.org/10.5281/zenodo.16415060'
chicago: 'Cheng, Bingqing, Daniel King, Dongjin Kim, and Peichen Zhong. “BingqingCheng/Cace-Lr-Fit:
V0.” Zenodo, 2025. https://doi.org/10.5281/zenodo.16415060.'
ieee: 'B. Cheng, D. King, D. Kim, and P. Zhong, “BingqingCheng/cace-lr-fit: V0.”
Zenodo, 2025.'
ista: 'Cheng B, King D, Kim D, Zhong P. 2025. BingqingCheng/cace-lr-fit: V0, Zenodo,
10.5281/zenodo.16415060.'
mla: 'Cheng, Bingqing, et al. BingqingCheng/Cace-Lr-Fit: V0. Zenodo, 2025,
doi:10.5281/zenodo.16415060.'
short: B. Cheng, D. King, D. Kim, P. Zhong, (2025).
date_created: 2026-08-27T12:13:55Z
date_published: 2025-07-24T00:00:00Z
date_updated: 2026-10-20T09:48:08Z
day: '24'
ddc:
- '000'
department:
- _id: BiCh
doi: 10.5281/zenodo.16415060
fulldoi: https://doi.org/10.5281/zenodo.16415060
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month: '07'
oa: 1
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title: 'BingqingCheng/cace-lr-fit: V0'
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user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20656'
abstract:
- lang: eng
text: Phytohormone auxin and its directional transport mediate much of the remarkably
plastic development of higher plants. Positive feedback between auxin signaling
and transport is a prerequisite for (1) self-organizing processes, including vascular
tissue formation, and (2) directional growth responses such as gravitropism. Here,
we identify a mechanism by which auxin signaling directly targets PIN auxin transporters.
Via the cell-surface AUXIN-BINDING PROTEIN1 (ABP1)-TRANSMEMBRANE KINASE 1 (TMK1)
receptor module, auxin rapidly induces phosphorylation and thus stabilization
of PIN2. Following gravistimulation, initial auxin asymmetry activates autophosphorylation
of the TMK1 kinase. This induces TMK1 interaction with and phosphorylation of
PIN2, stabilizing PIN2 at the lower root side, thus reinforcing asymmetric auxin
flow for root bending. Upstream of TMK1 in this regulation, ABP1 acts redundantly
with the root-expressed ABP1-LIKE 3 (ABL3) auxin receptor. Such positive feedback
between cell-surface auxin signaling and PIN-mediated polar auxin transport is
fundamental for robust root gravitropism and presumably for other self-organizing
developmental phenomena.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: We gratefully acknowledge Tongda Xu for experimental, material, and
conceptual support. We thank William Gray for providing material, Nataliia Gnyliukh
and Ema Cervenova for help with manuscript preparation, and Julia Schmid for help
with cloning. We thank Dolf Weijers, Mark Roosjen, and Andre Kuhn for discussions
and support with phospho-proteomic analyses. We thank the Bioimaging and Life Science
facilities at the Institute of Science and Technology Austria (ISTA) for their excellent
service and assistance. The research leading to these results has received funding
from the European Union (ERC, CYNIPS, 101142681) and Austrian Science Fund (FWF;
I 6123-B) to J.F., and Y.J. was funded by ERC no. 3363360-APPL under FP/2007-2013.
L.R. was supported by the FP7-PEOPLE-2011-COFUND ISTFELLOW program (IC1023FELL01)
and the European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship
(ALTF 985-2016). S.T. was supported by the National Natural Science Foundation of
China (32321001, 32570366). The work of J.H. was supported by the project JG_2024_003
implemented within the Palacký University Young Researcher Grant.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Lesia
full_name: Rodriguez Solovey, Lesia
id: 3922B506-F248-11E8-B48F-1D18A9856A87
last_name: Rodriguez Solovey
orcid: 0000-0002-7244-7237
- first_name: Lukas
full_name: Fiedler, Lukas
id: 7c417475-8972-11ed-ae7b-8b674ca26986
last_name: Fiedler
- first_name: Minxia
full_name: Zou, Minxia
id: 5c243f41-03f3-11ec-841c-96faf48a7ef9
last_name: Zou
- first_name: Caterina
full_name: Giannini, Caterina
id: e3fdddd5-f6e0-11ea-865d-ca99ee6367f4
last_name: Giannini
- first_name: Aline
full_name: Monzer, Aline
id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425
last_name: Monzer
- first_name: Dmitrii
full_name: Vladimirtsev, Dmitrii
id: 60466724-5355-11ee-ae5a-fa55e8f99c3d
last_name: Vladimirtsev
- first_name: Marek
full_name: Randuch, Marek
id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
last_name: Randuch
- first_name: Yongfan
full_name: Yu, Yongfan
last_name: Yu
- first_name: Zuzana
full_name: Gelová, Zuzana
id: 0AE74790-0E0B-11E9-ABC7-1ACFE5697425
last_name: Gelová
orcid: 0000-0003-4783-1752
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Jakub
full_name: Hajny, Jakub
id: 4800CC20-F248-11E8-B48F-1D18A9856A87
last_name: Hajny
orcid: 0000-0003-2140-7195
- first_name: Meng
full_name: Chen, Meng
last_name: Chen
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
orcid: 0000-0001-8295-2926
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Maria Mar
full_name: Marques-Bueno, Maria Mar
last_name: Marques-Bueno
- first_name: Zainab
full_name: Quddoos, Zainab
id: 32ff3c64-04a0-11f0-a50f-d0c45bfac466
last_name: Quddoos
- first_name: Gergely
full_name: Molnar, Gergely
id: 34F1AF46-F248-11E8-B48F-1D18A9856A87
last_name: Molnar
- first_name: Ivan
full_name: Kulich, Ivan
id: 57a1567c-8314-11eb-9063-c9ddc3451a54
last_name: Kulich
- first_name: Yvon
full_name: Jaillais, Yvon
last_name: Jaillais
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Rodriguez Solovey L, Fiedler L, Zou M, et al. ABP1/ABL3-TMK1 cell-surface auxin
signaling targets PIN2-mediated auxin fluxes for root gravitropism. Cell.
2025;188(22):6138-6150.e17. doi:10.1016/j.cell.2025.08.026
apa: Rodriguez Solovey, L., Fiedler, L., Zou, M., Giannini, C., Monzer, A., Vladimirtsev,
D., … Friml, J. (2025). ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated
auxin fluxes for root gravitropism. Cell. Cell Press. https://doi.org/10.1016/j.cell.2025.08.026
chicago: Rodriguez Solovey, Lesia, Lukas Fiedler, Minxia Zou, Caterina Giannini,
Aline Monzer, Dmitrii Vladimirtsev, Marek Randuch, et al. “ABP1/ABL3-TMK1 Cell-Surface
Auxin Signaling Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” Cell.
Cell Press, 2025. https://doi.org/10.1016/j.cell.2025.08.026.
ieee: L. Rodriguez Solovey et al., “ABP1/ABL3-TMK1 cell-surface auxin signaling
targets PIN2-mediated auxin fluxes for root gravitropism,” Cell, vol. 188,
no. 22. Cell Press, p. 6138–6150.e17, 2025.
ista: Rodriguez Solovey L, Fiedler L, Zou M, Giannini C, Monzer A, Vladimirtsev
D, Randuch M, Yu Y, Gelová Z, Verstraeten I, Hajny J, Chen M, Tan S, Hörmayer
L, Li L, Marques-Bueno MM, Quddoos Z, Molnar G, Kulich I, Jaillais Y, Friml J.
2025. ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin
fluxes for root gravitropism. Cell. 188(22), 6138–6150.e17.
mla: Rodriguez Solovey, Lesia, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling
Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” Cell, vol. 188,
no. 22, Cell Press, 2025, p. 6138–6150.e17, doi:10.1016/j.cell.2025.08.026.
short: L. Rodriguez Solovey, L. Fiedler, M. Zou, C. Giannini, A. Monzer, D. Vladimirtsev,
M. Randuch, Y. Yu, Z. Gelová, I. Verstraeten, J. Hajny, M. Chen, S. Tan, L. Hörmayer,
L. Li, M.M. Marques-Bueno, Z. Quddoos, G. Molnar, I. Kulich, Y. Jaillais, J. Friml,
Cell 188 (2025) 6138–6150.e17.
corr_author: '1'
date_created: 2025-11-19T09:44:31Z
date_published: 2025-10-30T00:00:00Z
date_updated: 2026-10-20T11:48:38Z
day: '30'
ddc:
- '580'
department:
- _id: JiFr
- _id: XiFe
doi: 10.1016/j.cell.2025.08.026
ec_funded: 1
external_id:
isi:
- '001616077900005'
pmid:
- '41043433'
file:
- access_level: open_access
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content_type: application/pdf
creator: dernst
date_created: 2025-11-24T10:55:18Z
date_updated: 2025-11-24T10:55:18Z
file_id: '20679'
file_name: 2025_Cell_Rodriguez.pdf
file_size: 17825465
relation: main_file
success: 1
file_date_updated: 2025-11-24T10:55:18Z
fulldoi: https://doi.org/10.1016/j.cell.2025.08.026
has_accepted_license: '1'
intvolume: ' 188'
isi: 1
issue: '22'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 6138-6150.e17
pmid: 1
project:
- _id: 8f347782-16d5-11f0-9cad-8c19706ee739
grant_number: '101142681'
name: Cyclic nucleotides as second messengers in plants
- _id: bd76d395-d553-11ed-ba76-f678c14f9033
grant_number: I06123
name: Peptide receptors for auxin canalization in Arabidopsis
- _id: 26060676-B435-11E9-9278-68D0E5697425
grant_number: ALTF 985-2016
name: Cell surface receptor complexes for auxin signaling in plants
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
record:
- id: '19399'
relation: earlier_version
status: public
- id: '23145'
relation: dissertation_contains
status: for_moderation
status: public
title: ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin fluxes
for root gravitropism
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: 188
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '23174'
abstract:
- lang: eng
text: Roots must continuously adapt their growth and have evolved the ability to
rapidly respond to diverse environmental and hormonal cues, including the phytohormone
auxin. Auxin-induced cellular responses involve membrane depolarization, cytosolic
calcium (Ca²⁺) elevation, and extracellular pH increase, but how these processes
lead to rapid growth regulation remains unclear. Here, we show that cytosolic
Ca²⁺ acts as a universal signal integrating diverse cues for rapid regulation
of root growth. Using live imaging, microfluidics, and optogenetics in Arabidopsis,
we demonstrate that a swift rise in cytosolic Ca²⁺ is the primary target of auxin
signaling affecting growth inhibition. Disruption of Ca²⁺ influx abolishes these
responses, whereas light-gated Ca²⁺ influx from the apoplast or endoplasmic reticulum
stores inhibits growth. Multiple unrelated stimuli—including auxin, extracellular
ATP, RALF peptides, and hydrogen peroxide—converge on this Ca²⁺-dependent mechanism.
Cytosolic Ca²⁺ elevation thus represents a necessary and sufficient step for rapid
growth inhibition, revealing a unifying principle of root signaling.
acknowledgement: "We gratefully acknowledge Dr. Andrea Bleckmann, creator of pBLAX000
vector and Dr. Shiqiang Gao for donation of template used in XXM-ER cloning. This
research was supported by the Laboratory Support Facility, the Plant Facility, the
IT Facility and the Imaging and Optical Facility of the Institute of Science and
Technology Austria. The graphical elements used in Fig. 5 were adapted and modified
from Servier, https://smart.servier.com, and are used under CC BY 3.0 licence. The
authors acknowledge the use of AI-tools (Microsoft Copilot, Gemini) for language
refinement. All content was critically reviewed by authors.\r\n\r\nFunder Information
Declared\r\nEuropean Research Council, 101142681 CYNIPS\r\nAustrian Science Fund,
P 37051-B"
article_processing_charge: No
author:
- first_name: Marek
full_name: Randuch, Marek
id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
last_name: Randuch
- first_name: Ivan
full_name: Kulich, Ivan
id: 57a1567c-8314-11eb-9063-c9ddc3451a54
last_name: Kulich
- first_name: Dmitrii
full_name: Vladimirtsev, Dmitrii
id: 60466724-5355-11ee-ae5a-fa55e8f99c3d
last_name: Vladimirtsev
- first_name: Shouguang
full_name: Huang, Shouguang
last_name: Huang
- first_name: Rainer
full_name: Hedrich, Rainer
last_name: Hedrich
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
biorxivid: 1
citation:
ama: Randuch M, Kulich I, Vladimirtsev D, Huang S, Hedrich R, Friml J. Cytosolic
Ca2+ as a universal signal for rapid root growth regulation. bioRxiv. doi:10.1101/2025.10.17.683082
apa: Randuch, M., Kulich, I., Vladimirtsev, D., Huang, S., Hedrich, R., & Friml,
J. (n.d.). Cytosolic Ca2+ as a universal signal for rapid root growth regulation.
bioRxiv. https://doi.org/10.1101/2025.10.17.683082
chicago: Randuch, Marek, Ivan Kulich, Dmitrii Vladimirtsev, Shouguang Huang, Rainer
Hedrich, and Jiří Friml. “Cytosolic Ca2+ as a Universal Signal for Rapid Root
Growth Regulation.” BioRxiv, n.d. https://doi.org/10.1101/2025.10.17.683082.
ieee: M. Randuch, I. Kulich, D. Vladimirtsev, S. Huang, R. Hedrich, and J. Friml,
“Cytosolic Ca2+ as a universal signal for rapid root growth regulation,” bioRxiv.
.
ista: Randuch M, Kulich I, Vladimirtsev D, Huang S, Hedrich R, Friml J. Cytosolic
Ca2+ as a universal signal for rapid root growth regulation. bioRxiv, 10.1101/2025.10.17.683082.
mla: Randuch, Marek, et al. “Cytosolic Ca2+ as a Universal Signal for Rapid Root
Growth Regulation.” BioRxiv, doi:10.1101/2025.10.17.683082.
short: M. Randuch, I. Kulich, D. Vladimirtsev, S. Huang, R. Hedrich, J. Friml, BioRxiv
(n.d.).
corr_author: '1'
date_created: 2026-10-19T11:44:48Z
date_published: 2025-10-17T00:00:00Z
date_updated: 2026-10-20T11:48:37Z
day: '17'
department:
- _id: JiFr
doi: 10.1101/2025.10.17.683082
external_id:
biorxivid:
- 10.1101/2025.10.17.683082
fulldoi: https://doi.org/10.1101/2025.10.17.683082
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2025.10.17.683082
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 8f347782-16d5-11f0-9cad-8c19706ee739
grant_number: '101142681'
name: Cyclic nucleotides as second messengers in plants
- _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6
grant_number: P37051
name: Guanylate cyclase activity of TIR1/AFBs auxin receptors
publication: bioRxiv
publication_status: draft
related_material:
record:
- id: '23145'
relation: dissertation_contains
status: for_moderation
status: public
title: Cytosolic Ca2+ as a universal signal for rapid root growth regulation
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: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
APC_amount: 2236,02 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19566'
abstract:
- lang: eng
text: "Purpose: Optic nerve crush (ONC) is a model for studying optic nerve trauma.
Unilateral ONC induces massive retinal ganglion cell (RGC) degeneration in the
affected eye, leading to vision loss within a month. A common assumption has been
that the non-injured contralateral eye is unaffected due to the minimal retino-retinal
projections of the RGCs at the chiasm. Yet, recently, microglia, the brain-resident
macrophages, have shown a responsive phenotype in the contralateral eye after
ONC. Whether RGC loss accompanies this phenotype is still controversial.\r\n\r\nMethods:
Using the available RGCode algorithm and developing our own RGC-Quant deep-learning-based
tool, we quantify RGC's total number and density across the entire retina after
ONC.\r\n\r\nResults: We confirm a short-term microglia response in the contralateral
eye after ONC, but this did not affect the microglia number. Furthermore, we cannot
confirm the previously reported RGC loss between naïve and contralateral retinas
5 weeks after ONC induction across the commonly used Cx3cr1creERT2 and C57BL6/J
mouse models. Neither sex nor the direct comparison of the RGC markers Brn3a and
RBPMS, with Brn3a co-labeling, on average, 89% of the RBPMS+-cells, explained
this discrepancy, suggesting that the early microglia-responsive phenotype does
not have immediate consequences on the RGC number.\r\n\r\nConclusions: Our results
corroborate that unilateral optic nerve injury elicits a microglial response in
the uninjured contralateral eye but without RGC loss. Therefore, the contralateral
eye should be treated separately and not as an ONC control."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
acknowledgement: "The authors thank the Scientific Service Units (SSU) of ISTA for
the provided resources, specifically the Imaging and Optics Facility (IOF), the
Lab Support Facility (LSF), and the Pre-Clinical Facility (PCF) team, specifically
Sonja Haslinger, Claudia Gold, and Michael Schunn, for mouse colony management and
support. We thank all members of the Siegert group for constant feedback on the
project and the manuscript. \r\nSupported in whole or in part by the Austrian Science
Fund (FWF) [10.55776/P37131]. For open access purposes, the author has applied a
CC BY public copyright license to any author-accepted manuscript version arising
from this submission. "
article_number: '49'
article_processing_charge: Yes
article_type: original
author:
- first_name: Florianne E
full_name: Schoot Uiterkamp, Florianne E
id: 3526230C-F248-11E8-B48F-1D18A9856A87
last_name: Schoot Uiterkamp
- 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: Mohammad
full_name: Alamalhoda, Mohammad
last_name: Alamalhoda
- first_name: Arsalan
full_name: Firoozi, Arsalan
last_name: Firoozi
- first_name: Gloria
full_name: Colombo, Gloria
id: 3483CF6C-F248-11E8-B48F-1D18A9856A87
last_name: Colombo
orcid: 0000-0001-9434-8902
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
citation:
ama: Miteva FE, Maes ME, Alamalhoda M, Firoozi A, Colombo G, Siegert S. Optic nerve
crush does not induce retinal ganglion cell loss in the contralateral eye. Investigative
Ophthalmology & Visual Science. 2025;66(3). doi:10.1167/iovs.66.3.49
apa: Miteva, F. E., Maes, M. E., Alamalhoda, M., Firoozi, A., Colombo, G., &
Siegert, S. (2025). Optic nerve crush does not induce retinal ganglion cell loss
in the contralateral eye. Investigative Ophthalmology & Visual Science.
Association for Research in Vision and Ophthalmology. https://doi.org/10.1167/iovs.66.3.49
chicago: Miteva, Florianne E, Margaret E Maes, Mohammad Alamalhoda, Arsalan Firoozi,
Gloria Colombo, and Sandra Siegert. “Optic Nerve Crush Does Not Induce Retinal
Ganglion Cell Loss in the Contralateral Eye.” Investigative Ophthalmology &
Visual Science. Association for Research in Vision and Ophthalmology, 2025.
https://doi.org/10.1167/iovs.66.3.49.
ieee: F. E. Miteva, M. E. Maes, M. Alamalhoda, A. Firoozi, G. Colombo, and S. Siegert,
“Optic nerve crush does not induce retinal ganglion cell loss in the contralateral
eye,” Investigative Ophthalmology & Visual Science, vol. 66, no. 3.
Association for Research in Vision and Ophthalmology, 2025.
ista: Miteva FE, Maes ME, Alamalhoda M, Firoozi A, Colombo G, Siegert S. 2025. Optic
nerve crush does not induce retinal ganglion cell loss in the contralateral eye.
Investigative Ophthalmology & Visual Science. 66(3), 49.
mla: Miteva, Florianne E., et al. “Optic Nerve Crush Does Not Induce Retinal Ganglion
Cell Loss in the Contralateral Eye.” Investigative Ophthalmology & Visual
Science, vol. 66, no. 3, 49, Association for Research in Vision and Ophthalmology,
2025, doi:10.1167/iovs.66.3.49.
short: F.E. Miteva, M.E. Maes, M. Alamalhoda, A. Firoozi, G. Colombo, S. Siegert,
Investigative Ophthalmology & Visual Science 66 (2025).
corr_author: '1'
date_created: 2025-04-15T13:40:35Z
date_published: 2025-03-01T00:00:00Z
date_updated: 2026-10-20T22:30:07Z
day: '01'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1167/iovs.66.3.49
external_id:
pmid:
- '40126507'
file:
- access_level: open_access
checksum: e8722ce5792f6c08fe1e191f7de6f147
content_type: application/pdf
creator: dernst
date_created: 2025-04-15T13:49:10Z
date_updated: 2025-04-15T13:49:10Z
file_id: '19567'
file_name: 2025_IOVS_SchootUiterkamp.pdf
file_size: 2721477
relation: main_file
success: 1
file_date_updated: 2025-04-15T13:49:10Z
fulldoi: https://doi.org/10.1167/iovs.66.3.49
has_accepted_license: '1'
intvolume: ' 66'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 7be82147-9f16-11ee-852c-f44682d73140
grant_number: P37131
name: Dissecting the morpho-functional relationship of microglia
- _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1
call_identifier: FWF
name: FWF Open Access Fund
publication: Investigative Ophthalmology & Visual Science
publication_identifier:
issn:
- 1552-5783
publication_status: published
publisher: Association for Research in Vision and Ophthalmology
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/siegert-lab/RGC-Quant
record:
- id: '20467'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Optic nerve crush does not induce retinal ganglion cell loss in the contralateral
eye
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: 66
year: '2025'
...
---
OA_place: publisher
_id: '19557'
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: ScienComp
acknowledgement: "The work presented in this doctoral thesis was performed at the
Institute of Science\r\nand Technology (ISTA) and financially supported by a European
Research Council\r\n(ERC) Consolidator Grant (PR1028ERC02), by SFARI (PR1028SIM02)
and by the\r\nAustrian Science Fund (FWF) to Gaia Novarino (PE1028W1232). I am very
thankful\r\nto the Doctoral Program “Molecular Drug Targets” (MolTag) for offering
me financial\r\nsupport to perform essential experiments during my PhD studies and
to participate in\r\ninternational conferences and courses."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Lena A
full_name: Schwarz, Lena A
id: 29A8453C-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
citation:
ama: Schwarz LA. Mapping developmental dynamics of autism spectrum disorder mouse
models at single-cell resolution. 2025. doi:10.15479/AT-ISTA-19557
apa: Schwarz, L. A. (2025). Mapping developmental dynamics of autism spectrum
disorder mouse models at single-cell resolution. Institute of Science and
Technology Austria. https://doi.org/10.15479/AT-ISTA-19557
chicago: Schwarz, Lena A. “Mapping Developmental Dynamics of Autism Spectrum Disorder
Mouse Models at Single-Cell Resolution.” Institute of Science and Technology Austria,
2025. https://doi.org/10.15479/AT-ISTA-19557.
ieee: L. A. Schwarz, “Mapping developmental dynamics of autism spectrum disorder
mouse models at single-cell resolution,” Institute of Science and Technology Austria,
2025.
ista: Schwarz LA. 2025. Mapping developmental dynamics of autism spectrum disorder
mouse models at single-cell resolution. Institute of Science and Technology Austria.
mla: Schwarz, Lena A. Mapping Developmental Dynamics of Autism Spectrum Disorder
Mouse Models at Single-Cell Resolution. Institute of Science and Technology
Austria, 2025, doi:10.15479/AT-ISTA-19557.
short: L.A. Schwarz, Mapping Developmental Dynamics of Autism Spectrum Disorder
Mouse Models at Single-Cell Resolution, Institute of Science and Technology Austria,
2025.
corr_author: '1'
date_created: 2025-04-14T06:59:06Z
date_published: 2025-04-14T00:00:00Z
date_updated: 2026-10-15T22:30:03Z
day: '14'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: GaNo
doi: 10.15479/AT-ISTA-19557
file:
- access_level: closed
checksum: 50290a8604edb0a720387f01e9d59fe4
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: lschwarz
date_created: 2025-04-15T08:43:36Z
date_updated: 2026-10-15T22:30:02Z
embargo_to: open_access
file_id: '19561'
file_name: Schwarz_Thesis_2025_FINAL.docx
file_size: 21783427
relation: source_file
- access_level: open_access
checksum: ed028488180ac4901e018ef1c330cf01
content_type: application/pdf
creator: lschwarz
date_created: 2025-04-15T08:43:42Z
date_updated: 2026-10-15T22:30:02Z
embargo: 2026-10-15
file_id: '19562'
file_name: Schwarz_Thesis_2025_FINALpdfa.pdf
file_size: 11432175
relation: main_file
file_date_updated: 2026-10-15T22:30:02Z
fulldoi: https://doi.org/10.15479/AT-ISTA-19557
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '124'
project:
- _id: 9B91375C-BA93-11EA-9121-9846C619BF3A
grant_number: '707964'
name: Critical windows and reversibility of ASD associated with mutations in chromatin
remodelers
- _id: 34ba8964-11ca-11ed-8bc3-e15864e7e9a6
grant_number: '101044865'
name: Toward an understanding of the brain interstitial system and the extracellular
proteome in health and autism spectrum disorders
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232
name: Molecular Drug Targets
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12802'
relation: part_of_dissertation
status: public
- id: '9429'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
title: Mapping developmental dynamics of autism spectrum disorder mouse models at
single-cell resolution
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: '2025'
...
---
OA_place: publisher
_id: '20467'
acknowledged_ssus:
- _id: Bio
- _id: SSU
- _id: PreCl
- _id: LifeSc
acknowledgement: "The work presented in this Thesis was carried out at the Institute
of Science and Technology\r\nAustria (ISTA), and was supported by the Austrian Science
Fund (FWF) [10.55776/P37131].\r\nI would like to thank the Scientific Service Units
(SSU) of ISTA for the provided resources,\r\nspecifically the Imaging and Optics
Facility (IOF), the Lab Support Facility (LSF), and the\r\nPre-Clinical Facility
(PCF) team, specifically Sonja Haslinger, Claudia Gold, and Michael\r\nSchunn, for
mouse colony management and support. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Florianne E
full_name: Miteva, Florianne E
id: 3526230C-F248-11E8-B48F-1D18A9856A87
last_name: Miteva
citation:
ama: Miteva FE. The role of cyclooxygenase 1 on microglial response to inflammatory
stressors. 2025. doi:10.15479/AT-ISTA-20467
apa: Miteva, F. E. (2025). The role of cyclooxygenase 1 on microglial response
to inflammatory stressors. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20467
chicago: Miteva, Florianne E. “The Role of Cyclooxygenase 1 on Microglial Response
to Inflammatory Stressors.” Institute of Science and Technology Austria, 2025.
https://doi.org/10.15479/AT-ISTA-20467.
ieee: F. E. Miteva, “The role of cyclooxygenase 1 on microglial response to inflammatory
stressors,” Institute of Science and Technology Austria, 2025.
ista: Miteva FE. 2025. The role of cyclooxygenase 1 on microglial response to inflammatory
stressors. Institute of Science and Technology Austria.
mla: Miteva, Florianne E. The Role of Cyclooxygenase 1 on Microglial Response
to Inflammatory Stressors. Institute of Science and Technology Austria, 2025,
doi:10.15479/AT-ISTA-20467.
short: F.E. Miteva, The Role of Cyclooxygenase 1 on Microglial Response to Inflammatory
Stressors, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-10-14T10:24:41Z
date_published: 2025-10-14T00:00:00Z
date_updated: 2026-10-14T22:30:03Z
day: '14'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: SaSi
doi: 10.15479/AT-ISTA-20467
file:
- access_level: open_access
checksum: 03537697be8c688d3a05cf948288e48f
content_type: application/pdf
creator: fschootu
date_created: 2025-10-17T11:09:11Z
date_updated: 2026-10-14T22:30:02Z
embargo: 2026-10-14
file_id: '20484'
file_name: 2025_Miteva_Florianne_thesis.pdf
file_size: 13668588
relation: main_file
- access_level: closed
checksum: df4930d7211cf9cfe1254b77204dc1d3
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: fschootu
date_created: 2025-10-23T11:33:06Z
date_updated: 2026-10-14T22:30:02Z
embargo_to: open_access
file_id: '20525'
file_name: 2025_Miteva_florianne_thesis.docx
file_size: 28991918
relation: source_file
file_date_updated: 2026-10-14T22:30:02Z
fulldoi: https://doi.org/10.15479/AT-ISTA-20467
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '99'
project:
- _id: 7be82147-9f16-11ee-852c-f44682d73140
grant_number: P37131
name: Dissecting the morpho-functional relationship of microglia
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '19566'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
title: The role of cyclooxygenase 1 on microglial response to inflammatory stressors
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: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19421'
abstract:
- lang: eng
text: The phytohormone auxin (Aux) is a principal endogenous developmental signal
in plants. It mediates transcriptional reprogramming by a well-established canonical
signalling mechanism. TIR1/AFB auxin receptors are F-box subunits of an ubiquitin
ligase complex; after auxin perception, they associate with Aux/IAA transcriptional
repressors and ubiquitinate them for degradation, thus enabling the activation
of auxin response factor (ARF) transcription factors1,2,3. Here we revise this
paradigm by showing that without TIR1 adenylate cyclase (AC) activity4, auxin-induced
degradation of Aux/IAAs is not sufficient to mediate the transcriptional auxin
response. Abolishing the TIR1 AC activity does not affect auxin-induced degradation
of Aux/IAAs but renders TIR1 non-functional in mediating transcriptional reprogramming
and auxin-regulated development, including shoot, root, root hair growth and lateral
root formation. Transgenic plants show that local cAMP production in the vicinity
of the Aux/IAA–ARF complex by unrelated AC enzymes bypasses the need for auxin
perception and is sufficient to induce ARF-mediated transcription. These discoveries
revise the canonical model of auxin signalling and establish TIR1/AFB-produced
cAMP as a second messenger essential for transcriptional reprograming.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
acknowledgement: We are grateful to J. Callis and H.-Q. Yang for sharing materials
and to M. Estelle and S. Kepinski for inspiring discussions. This research was supported
by the Laboratory Support Facility, the Plant Facility and the Imaging and Optics
Facility of the Institute of Science and Technology Austria. This project has received
funding from the European Research Council (101142681 CYNIPS) and Austrian Science
Fund (P 37051-B). L.Q. was supported by the National Natural Science Foundation
of China (grant no. 32470327). M.Z. was supported by the Interdisciplinary Project
Committee of the Institute of Science and Technology Austria, and Y.P. was supported
by an EMBO Postdoctoral Fellowship (ALTF 38-2023). Open access funding provided
by Institute of Science and Technology (IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Huihuang
full_name: Chen, Huihuang
id: 83c96512-15b2-11ec-abd3-b7eede36184f
last_name: Chen
- first_name: Linlin
full_name: Qi, Linlin
id: 44B04502-A9ED-11E9-B6FC-583AE6697425
last_name: Qi
orcid: 0000-0001-5187-8401
- first_name: Minxia
full_name: Zou, Minxia
id: 5c243f41-03f3-11ec-841c-96faf48a7ef9
last_name: Zou
- first_name: Mengting
full_name: Lu, Mengting
id: a8198a14-1ffe-11ee-8b67-d2bdff9d9178
last_name: Lu
- first_name: M
full_name: Kwiatkowski, M
last_name: Kwiatkowski
- first_name: Yuanrong
full_name: Pei, Yuanrong
id: 98605edc-6ce7-11ee-95f3-cc16b866efcd
last_name: Pei
- first_name: K
full_name: Jaworski, K
last_name: Jaworski
- 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, Qi L, Zou M, et al. TIR1-produced cAMP as a second messenger in transcriptional
auxin signalling. Nature. 2025;640:1011-1016. doi:10.1038/s41586-025-08669-w
apa: Chen, H., Qi, L., Zou, M., Lu, M., Kwiatkowski, M., Pei, Y., … Friml, J. (2025).
TIR1-produced cAMP as a second messenger in transcriptional auxin signalling.
Nature. Springer Nature. https://doi.org/10.1038/s41586-025-08669-w
chicago: Chen, Huihuang, Linlin Qi, Minxia Zou, Mengting Lu, M Kwiatkowski, Yuanrong
Pei, K Jaworski, and Jiří Friml. “TIR1-Produced CAMP as a Second Messenger in
Transcriptional Auxin Signalling.” Nature. Springer Nature, 2025. https://doi.org/10.1038/s41586-025-08669-w.
ieee: H. Chen et al., “TIR1-produced cAMP as a second messenger in transcriptional
auxin signalling,” Nature, vol. 640. Springer Nature, pp. 1011–1016, 2025.
ista: Chen H, Qi L, Zou M, Lu M, Kwiatkowski M, Pei Y, Jaworski K, Friml J. 2025.
TIR1-produced cAMP as a second messenger in transcriptional auxin signalling.
Nature. 640, 1011–1016.
mla: Chen, Huihuang, et al. “TIR1-Produced CAMP as a Second Messenger in Transcriptional
Auxin Signalling.” Nature, vol. 640, Springer Nature, 2025, pp. 1011–16,
doi:10.1038/s41586-025-08669-w.
short: H. Chen, L. Qi, M. Zou, M. Lu, M. Kwiatkowski, Y. Pei, K. Jaworski, J. Friml,
Nature 640 (2025) 1011–1016.
corr_author: '1'
date_created: 2025-03-19T09:44:39Z
date_published: 2025-04-24T00:00:00Z
date_updated: 2026-10-20T22:30:07Z
day: '24'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41586-025-08669-w
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language:
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page: 1011-1016
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grant_number: P37051
name: Guanylate cyclase activity of TIR1/AFBs auxin receptors
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
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url: https://ista.ac.at/en/news/updating-the-textbook/
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status: public
title: TIR1-produced cAMP as a second messenger in transcriptional auxin signalling
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 640
year: '2025'
...
---
OA_place: publisher
_id: '19478'
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: "This project was funded by the European Research Council Advanced
Grant (ETAP-742985),\r\nEuropean Research Council (ERC; 101142681 CYNIPS), Austrian
Science Fund (FWF; P\r\n37051-B)."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Huihuang
full_name: Chen, Huihuang
id: 83c96512-15b2-11ec-abd3-b7eede36184f
last_name: Chen
citation:
ama: Chen H. The cAMP second messenger in auxin signalling. 2025. doi:10.15479/AT-ISTA-19478
apa: Chen, H. (2025). The cAMP second messenger in auxin signalling. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19478
chicago: Chen, Huihuang. “The CAMP Second Messenger in Auxin Signalling.” Institute
of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19478.
ieee: H. Chen, “The cAMP second messenger in auxin signalling,” Institute of Science
and Technology Austria, 2025.
ista: Chen H. 2025. The cAMP second messenger in auxin signalling. Institute of
Science and Technology Austria.
mla: Chen, Huihuang. The CAMP Second Messenger in Auxin Signalling. Institute
of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19478.
short: H. Chen, The CAMP Second Messenger in Auxin Signalling, Institute of Science
and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-04-04T07:48:24Z
date_published: 2025-04-04T00:00:00Z
date_updated: 2026-10-09T22:30:04Z
day: '04'
ddc:
- '580'
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department:
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doi: 10.15479/AT-ISTA-19478
ec_funded: 1
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language:
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month: '04'
oa: 1
oa_version: Published Version
page: '118'
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6
grant_number: P37051
name: Guanylate cyclase activity of TIR1/AFBs auxin receptors
- _id: 8f347782-16d5-11f0-9cad-8c19706ee739
grant_number: '101142681'
name: Cyclic nucleotides as second messengers in plants
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '19421'
relation: part_of_dissertation
status: public
- id: '13212'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: The cAMP second messenger in auxin signalling
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_embargo: '6'
OA_place: publisher
_id: '20798'
abstract:
- lang: eng
text: "Atom interferometers measure the relative phase shifts between coherent matter-wave
paths\r\nthat arise from interactions with external fields or inertial forces.
Due to their exceptional\r\nphase sensitivity, atom interferometers became an
essential tool for precision measurements\r\nand fundamental physics experiments,
finding applications in geodesy, gravimetry, and inertial\r\nnavigation. However,
their measurement precision is limited by quantum projection noise,\r\nwhich arises
from the Heisenberg uncertainty principle, preventing the measurement of atomic\r\nstates
with absolute precision. The generation of entanglement between the atoms offers
a\r\npath to surpass this so-called standard quantum limit, thereby enhancing
the interferometer’s\r\nphase sensitivity beyond classical measurement bounds.\r\nThis
thesis reports on the development of an atom interferometer experiment designed
to\r\nrealize cavity-mediated, squeezed Mach-Zehnder-type interferometry with
ultra-cold 87Rb atoms.\r\nThe experiment combines cavity-aided spin-squeezing
with cavity-mediated Mach-Zehnder\r\ninterferometry to demonstrate entanglement-enhanced
phase sensitivity. The experiment is\r\ncentered on a triangular optical cavity
that mediates all relevant atom-light interactions. The\r\ncavity provides optical
trapping, spin-squeezing, and Raman beam-splitter operations, enabling\r\nto perform
interferometry on a continuously trapped atomic ensemble.\r\nThe thesis elaborates
on the fundamental theoretical framework, the cavity design, and the full\r\noptical
setup, including the detailed configuration of the developed laser stabilization
methods.\r\nExperimentally, continuous loading methods were explored, resulting
in an accumulation of\r\nup to 4 × 106\r\natoms in the dipole trap within a cycle
time of 500 ms. The AC Stark shift\r\ncompensation method developed for continuous
loading was further applied for in-trap cooling\r\nto 10 µK, and optical pumping
for efficient atomic state preparation. Coherent state control\r\nwas verified
via observation of microwave-driven Rabi oscillations, and used to characterize\r\natom-cavity
coupling.\r\nThese presented results establish the experimental groundwork for
the future development of\r\ncavity-mediated, entanglement-enhanced Mach-Zehnder-type
atom interferometry."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Wald, Sebastian
id: 133F200A-B015-11E9-AD41-0EDAE5697425
last_name: Wald
orcid: 0000-0002-5869-1604
citation:
ama: Wald S. Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry.
2025. doi:10.15479/AT-ISTA-20798
apa: Wald, S. (2025). Atoms in a propagating-wave cavity for squeezed Mach-Zehnder
atom interferometry. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20798
chicago: Wald, Sebastian. “Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder
Atom Interferometry.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20798.
ieee: S. Wald, “Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom
interferometry,” Institute of Science and Technology Austria, 2025.
ista: Wald S. 2025. Atoms in a propagating-wave cavity for squeezed Mach-Zehnder
atom interferometry. Institute of Science and Technology Austria.
mla: Wald, Sebastian. Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder
Atom Interferometry. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20798.
short: S. Wald, Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder Atom
Interferometry, Institute of Science and Technology Austria, 2025.
corr_author: '1'
das_tickbox: '1'
date_created: 2025-12-11T11:48:11Z
date_published: 2025-12-11T00:00:00Z
date_updated: 2026-07-24T08:07:28Z
day: '11'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: OnHo
doi: 10.15479/AT-ISTA-20798
doi_confirm: '1'
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creator: swald
date_created: 2025-12-12T11:53:42Z
date_updated: 2026-06-15T22:30:03Z
embargo: 2026-06-15
file_id: '20809'
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date_created: 2025-12-12T11:54:55Z
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fulldoi: https://doi.org/10.15479/AT-ISTA-20798
has_accepted_license: '1'
keyword:
- entanglement-enhanced atom interferometry
- cavity QED
- spin-squeezing
- dipole trap
- quantum optics
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '152'
publication_identifier:
isbn:
- 978-3-99078-075-6
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '14759'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Onur
full_name: Hosten, Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
title: Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry
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: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2025'
...
---
OA_embargo: 6 months
OA_place: publisher
OA_type: hybrid
_id: '19498'
abstract:
- lang: eng
text: A dynamic interplay between fast synaptic signals and slower neuromodulatory
signals controls the excitatory/inhibitory (E/I) balance within neuronal circuits.
The mechanisms by which neuropeptide signaling is regulated to maintain E/I balance
remain uncertain. We designed a genetic screen to isolate genes involved in the
peptidergic maintenance of the E/I balance in the C. elegans motor circuit. This
screen identified the C. elegans orthologs of the presynaptic phosphoprotein synapsin
(snn-1) and the protein phosphatase 1 (PP1) regulatory subunit PHACTR1 (phac-1).
We demonstrate that both phac-1 and snn-1 alter the motor behavior of C. elegans,
and genetic interactions suggest that SNN-1 contributes to PP1-PHAC-1 holoenzyme
signaling. De novo variants of human PHACTR1, associated with early-onset epilepsies
[developmental and epileptic encephalopathy 70 (DEE70)], when expressed in C.
elegans resulted in constitutive PP1-PHAC-1 holoenzyme activity. Unregulated PP1-PHAC-1
signaling alters the synapsin and actin cytoskeleton and increases neuropeptide
release by cholinergic motor neurons, which secondarily affects the presynaptic
vesicle cycle. Together, these results clarify the dominant mechanisms of action
of the DEE70 alleles and suggest that altered neuropeptide release may alter E/I
balance in DEE70.
acknowledgement: P.L. is a research associate of the Belgian National Fund for Scientific
Research (FRS-FNRS). K.S., M.S.-G., S.S., and P.L. are supported by grants from
the FRS-FNRS. This work was supported by an Advanced ERC Grant (269058 ACMO) to
M.D.B. We thank the team of Alexander Gottschalk for the snn-1(S9A) strain. We thank
the Imaging Facility of the Faculty of Medicine (LiMiF) of the Universite Libre
de Bruxelles, supported by FRS-FNRS. This work made use of instruments in the Electron
Microscopy Core of the University of Illinois Chicago Research Resources Center
as well as the BioCryo facility of Northwestern University's NUANCE Center, which
has received support from the SHyNE Resource (NSF ECCS-2025633), the IIN, and Northwestern's
MRSEC program (NSF DMR-2308691). Some strains were provided by the CGC, which is
funded by NIH Office of Research Infrastructure Programs (P40 OD010440).
article_number: e1767232024
article_processing_charge: No
article_type: original
author:
- first_name: Aikaterini
full_name: Stratigi, Aikaterini
last_name: Stratigi
- first_name: Miguel
full_name: Soler-García, Miguel
last_name: Soler-García
- first_name: Mia
full_name: Krout, Mia
last_name: Krout
- first_name: Shikha
full_name: Shukla, Shikha
last_name: Shukla
- first_name: Mario
full_name: De Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: De Bono
orcid: 0000-0001-8347-0443
- first_name: Janet E.
full_name: Richmond, Janet E.
last_name: Richmond
- first_name: Patrick
full_name: Laurent, Patrick
last_name: Laurent
citation:
ama: Stratigi A, Soler-García M, Krout M, et al. Neuroendocrine control of synaptic
transmission by PHAC-1 in C. elegans. Journal of Neuroscience. 2025;45(13).
doi:10.1523/JNEUROSCI.1767-23.2024
apa: Stratigi, A., Soler-García, M., Krout, M., Shukla, S., de Bono, M., Richmond,
J. E., & Laurent, P. (2025). Neuroendocrine control of synaptic transmission
by PHAC-1 in C. elegans. Journal of Neuroscience. Society for Neuroscience.
https://doi.org/10.1523/JNEUROSCI.1767-23.2024
chicago: Stratigi, Aikaterini, Miguel Soler-García, Mia Krout, Shikha Shukla, Mario
de Bono, Janet E. Richmond, and Patrick Laurent. “Neuroendocrine Control of Synaptic
Transmission by PHAC-1 in C. Elegans.” Journal of Neuroscience. Society
for Neuroscience, 2025. https://doi.org/10.1523/JNEUROSCI.1767-23.2024.
ieee: A. Stratigi et al., “Neuroendocrine control of synaptic transmission
by PHAC-1 in C. elegans,” Journal of Neuroscience, vol. 45, no. 13. Society
for Neuroscience, 2025.
ista: Stratigi A, Soler-García M, Krout M, Shukla S, de Bono M, Richmond JE, Laurent
P. 2025. Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans.
Journal of Neuroscience. 45(13), e1767232024.
mla: Stratigi, Aikaterini, et al. “Neuroendocrine Control of Synaptic Transmission
by PHAC-1 in C. Elegans.” Journal of Neuroscience, vol. 45, no. 13, e1767232024,
Society for Neuroscience, 2025, doi:10.1523/JNEUROSCI.1767-23.2024.
short: A. Stratigi, M. Soler-García, M. Krout, S. Shukla, M. de Bono, J.E. Richmond,
P. Laurent, Journal of Neuroscience 45 (2025).
date_created: 2025-04-06T22:01:32Z
date_published: 2025-03-26T00:00:00Z
date_updated: 2026-07-28T11:30:41Z
day: '26'
ddc:
- '570'
department:
- _id: MaDe
doi: 10.1523/JNEUROSCI.1767-23.2024
external_id:
isi:
- '001460952700001'
pmid:
- '39919830'
file:
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checksum: 7befc0168f4cd5bd2b0fcff9e2a94784
content_type: application/pdf
creator: dernst
date_created: 2025-04-07T11:57:19Z
date_updated: 2025-09-27T22:30:02Z
embargo: 2025-09-27
file_id: '19525'
file_name: 2025_JourNeuroscience_Stratigi.pdf
file_size: 3111735
relation: main_file
file_date_updated: 2025-09-27T22:30:02Z
fulldoi: https://doi.org/10.1523/JNEUROSCI.1767-23.2024
has_accepted_license: '1'
intvolume: ' 45'
isi: 1
issue: '13'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Neuroscience
publication_identifier:
eissn:
- 1529-2401
issn:
- 0270-6474
publication_status: published
publisher: Society for Neuroscience
quality_controlled: '1'
scopus_import: '1'
status: public
title: Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans
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: 45
year: '2025'
...