---
_id: '17373'
abstract:
- lang: eng
text: Scanning Kelvin probe microscopy (SKPM) is a powerful technique for investigating
the electrostatic properties of material surfaces, enabling the imaging of variations
in work function, topology, surface charge density, or combinations thereof. Regardless
of the underlying signal source, SKPM results in a voltage image, which is spatially
distorted due to the finite size of the probe, long-range electrostatic interactions,
mechanical and electrical noise, and the finite response time of the electronics.
In order to recover the underlying signal, it is necessary to deconvolve the measurement
with an appropriate point spread function (PSF) that accounts the aforementioned
distortions, but determining this PSF is difficult. Here, we describe how such
PSFs can be determined experimentally and show how they can be used to recover
the underlying information of interest. We first consider the physical principles
that enable SKPM and discuss how these affect the system PSF. We then show how
one can experimentally measure PSFs by looking at well-defined features, and that
these compare well to simulated PSFs, provided scans are performed extremely slowly
and carefully. Next, we work at realistic scan speeds and show that the idealized
PSFs fail to capture temporal distortions in the scan direction. While simulating
PSFs for these situations would be quite challenging, we show that measuring PSFs
with similar scan conditions works well. Our approach clarifies the basic principles
and inherent challenges to SKPM measurements and gives practical methods to improve
results.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
- _id: LifeSc
- _id: ScienComp
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation program (Grant
Agreement No. 949120). This research was supported by the Scientific Service Units
of the Institute of Science and Technology Austria (ISTA) through resources provided
by the Miba Machine Shop, Nanofabrication Facility, Scientific Computing Facility,
and Lab Support Facility. The authors wish to thank Dmytro Rak and Juan Carlos Sobarzo
for letting us use their equipment. The authors wish to thank the contributions
of the whole Waitukaitis Group for useful discussions and feedback.
article_number: '045305'
article_processing_charge: No
article_type: original
author:
- first_name: Isaac C
full_name: Lenton, Isaac C
id: a550210f-223c-11ec-8182-e2d45e817efb
last_name: Lenton
orcid: 0000-0002-5010-6984
- first_name: Felix
full_name: Pertl, Felix
id: 6313aec0-15b2-11ec-abd3-ed67d16139af
last_name: Pertl
orcid: 0000-0003-0463-5794
- first_name: Lubuna B
full_name: Shafeek, Lubuna B
id: 3CD37A82-F248-11E8-B48F-1D18A9856A87
last_name: Shafeek
orcid: 0000-0001-7180-6050
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
citation:
ama: 'Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. Beyond the blur: Using experimentally
determined point spread functions to improve scanning Kelvin probe imaging. Journal
of Applied Physics. 2024;136(4). doi:10.1063/5.0215151'
apa: 'Lenton, I. C., Pertl, F., Shafeek, L. B., & Waitukaitis, S. R. (2024).
Beyond the blur: Using experimentally determined point spread functions to improve
scanning Kelvin probe imaging. Journal of Applied Physics. AIP Publishing.
https://doi.org/10.1063/5.0215151'
chicago: 'Lenton, Isaac C, Felix Pertl, Lubuna B Shafeek, and Scott R Waitukaitis.
“Beyond the Blur: Using Experimentally Determined Point Spread Functions to Improve
Scanning Kelvin Probe Imaging.” Journal of Applied Physics. AIP Publishing,
2024. https://doi.org/10.1063/5.0215151.'
ieee: 'I. C. Lenton, F. Pertl, L. B. Shafeek, and S. R. Waitukaitis, “Beyond the
blur: Using experimentally determined point spread functions to improve scanning
Kelvin probe imaging,” Journal of Applied Physics, vol. 136, no. 4. AIP
Publishing, 2024.'
ista: 'Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. 2024. Beyond the blur: Using
experimentally determined point spread functions to improve scanning Kelvin probe
imaging. Journal of Applied Physics. 136(4), 045305.'
mla: 'Lenton, Isaac C., et al. “Beyond the Blur: Using Experimentally Determined
Point Spread Functions to Improve Scanning Kelvin Probe Imaging.” Journal of
Applied Physics, vol. 136, no. 4, 045305, AIP Publishing, 2024, doi:10.1063/5.0215151.'
short: I.C. Lenton, F. Pertl, L.B. Shafeek, S.R. Waitukaitis, Journal of Applied
Physics 136 (2024).
corr_author: '1'
date_created: 2024-08-04T22:01:21Z
date_published: 2024-07-28T00:00:00Z
date_updated: 2025-09-08T08:47:42Z
day: '28'
ddc:
- '530'
department:
- _id: ScWa
- _id: NanoFab
doi: 10.1063/5.0215151
ec_funded: 1
external_id:
isi:
- '001281681100003'
file:
- access_level: open_access
checksum: 6141d05cd68d540a7446dce9490975db
content_type: application/pdf
creator: dernst
date_created: 2024-08-05T08:19:58Z
date_updated: 2024-08-05T08:19:58Z
file_id: '17386'
file_name: 2024_JourApplPhysics_Lenton.pdf
file_size: 2537502
relation: main_file
success: 1
file_date_updated: 2024-08-05T08:19:58Z
has_accepted_license: '1'
intvolume: ' 136'
isi: 1
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa
call_identifier: H2020
grant_number: '949120'
name: 'Tribocharge: a multi-scale approach to an enduring problem in physics'
publication: Journal of Applied Physics
publication_identifier:
eissn:
- 1089-7550
issn:
- 0021-8979
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Beyond the blur: Using experimentally determined point spread functions to
improve scanning Kelvin probe imaging'
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 136
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '17479'
abstract:
- lang: eng
text: Phonon polaritons (PhPs), light coupled to lattice vibrations, in the highly
anisotropic polar layered material molybdenum trioxide (α-MoO3) are currently
the focus of intense research efforts due to their extreme subwavelength field
confinement, directional propagation, and unprecedented low losses. Nevertheless,
prior research has primarily concentrated on exploiting the squeezing and steering
capabilities of α-MoO3 PhPs, without inquiring much into the dominant microscopic
mechanism that determines their long lifetimes, which is key for their implementation
in nanophotonic applications. This study delves into the fundamental processes
that govern PhP damping in α-MoO3 by combining ab initio calculations with scattering-type
scanning near-field optical microscopy (s-SNOM) and Fourier transform infrared
(FTIR) spectroscopy measurements across a broad temperature range (8–300 K). The
remarkable agreement between our theoretical predictions and experimental observations
allows us to identify third-order anharmonic phonon–phonon scattering as the main
damping mechanism of α-MoO3 PhPs. These findings shed light on the fundamental
limits of low-loss PhPs, which is a crucial factor for assessing their implementation
into nanophotonic devices.
acknowledgement: 'Funding Sources ─ A.I.F.T.-M. and G.Á.-P. acknowledge support through
the Severo Ochoa program from the Government of the Principality of Asturias (references
PA-21-PF-BP20-117 and PA20-PF-BP19-053, respectively). A.B.K. and J.T.-G. acknowledge
support from the Swiss National Science Foundation (grant # 200020_201096). J.M.-S.
acknowledges financial support from the Ramón y Cajal Program of the Government
of Spain and FSE (RYC2018-026196-I), the Spanish Ministry of Science and Innovation
(State Plan for Scientific and Technical Research and Innovation grant number PID2019-110308GA-I00/AEI/10.13039/501100011033)
and project PCI2022-132953 funded by MCIN/AEI/10.13039/501100011033 and the EU “NextGenerationEU”/PRTR”.
P.A.-G. acknowledges support from the European Research Council under starting grant
no. 715496, 2DNANOPTICA and the Spanish Ministry of Science and Innovation (State
Plan for Scientific and Technical Research and Innovation grant number PID2019-111156GB-I00).
A.Y.N. acknowledges the Spanish Ministry of Science and Innovation (grant PID2020-115221GB-C42)
and the Basque Department of Education (grant PIBA-2023-1-0007). M.V. and J.I.M.
acknowledge support by Spanish MCIN/AEI/10.13039/501100011033/FEDER, UE under grant
PID2022-136784NB and by Asturias FICYT under grant AYUD/2021/51185 with the support
of FEDER funds. I.E. acknowledges funding from the Spanish Ministry of Science and
Innovation (Grant No. PID2022-142861NA-I00) and the Department of Education, Universities,
and Research of the Eusko Jaurlaritza and the University of the Basque Country UPV/EHU
(Grant No. IT1527-22). J. Duan acknowledges the support from the Beijing Natural
Science Foundation (Grant No. Z240005), and National Natural Science Foundation
of China.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Javier
full_name: Taboada-Gutiérrez, Javier
last_name: Taboada-Gutiérrez
- first_name: Yixi
full_name: Zhou, Yixi
last_name: Zhou
- first_name: Ana I.F.
full_name: Tresguerres-Mata, Ana I.F.
last_name: Tresguerres-Mata
- first_name: Christian
full_name: Lanza, Christian
last_name: Lanza
- first_name: Abel
full_name: Martínez-Suárez, Abel
last_name: Martínez-Suárez
- first_name: Gonzalo
full_name: Álvarez-Pérez, Gonzalo
last_name: Álvarez-Pérez
- first_name: Jiahua
full_name: Duan, Jiahua
last_name: Duan
- first_name: José Ignacio
full_name: Martín, José Ignacio
last_name: Martín
- first_name: María
full_name: Vélez, María
last_name: Vélez
- first_name: Ivan
full_name: Prieto Gonzalez, Ivan
id: 2A307FE2-F248-11E8-B48F-1D18A9856A87
last_name: Prieto Gonzalez
orcid: 0000-0002-7370-5357
- first_name: Adrien
full_name: Bercher, Adrien
last_name: Bercher
- first_name: Jérémie
full_name: Teyssier, Jérémie
last_name: Teyssier
- first_name: Ion
full_name: Errea, Ion
last_name: Errea
- first_name: Alexey Y.
full_name: Nikitin, Alexey Y.
last_name: Nikitin
- first_name: Javier
full_name: Martín-Sánchez, Javier
last_name: Martín-Sánchez
- first_name: Alexey B.
full_name: Kuzmenko, Alexey B.
last_name: Kuzmenko
- first_name: Pablo
full_name: Alonso-González, Pablo
last_name: Alonso-González
citation:
ama: Taboada-Gutiérrez J, Zhou Y, Tresguerres-Mata AIF, et al. Unveiling the mechanism
of phonon-polariton damping in α‑MoO3. ACS Photonics. 2024;11(9):3570-3577.
doi:10.1021/acsphotonics.4c00485
apa: Taboada-Gutiérrez, J., Zhou, Y., Tresguerres-Mata, A. I. F., Lanza, C., Martínez-Suárez,
A., Álvarez-Pérez, G., … Alonso-González, P. (2024). Unveiling the mechanism of
phonon-polariton damping in α‑MoO3. ACS Photonics. American Chemical Society.
https://doi.org/10.1021/acsphotonics.4c00485
chicago: Taboada-Gutiérrez, Javier, Yixi Zhou, Ana I.F. Tresguerres-Mata, Christian
Lanza, Abel Martínez-Suárez, Gonzalo Álvarez-Pérez, Jiahua Duan, et al. “Unveiling
the Mechanism of Phonon-Polariton Damping in Α‑MoO3.” ACS Photonics. American
Chemical Society, 2024. https://doi.org/10.1021/acsphotonics.4c00485.
ieee: J. Taboada-Gutiérrez et al., “Unveiling the mechanism of phonon-polariton
damping in α‑MoO3,” ACS Photonics, vol. 11, no. 9. American Chemical Society,
pp. 3570–3577, 2024.
ista: Taboada-Gutiérrez J, Zhou Y, Tresguerres-Mata AIF, Lanza C, Martínez-Suárez
A, Álvarez-Pérez G, Duan J, Martín JI, Vélez M, Prieto Gonzalez I, Bercher A,
Teyssier J, Errea I, Nikitin AY, Martín-Sánchez J, Kuzmenko AB, Alonso-González
P. 2024. Unveiling the mechanism of phonon-polariton damping in α‑MoO3. ACS Photonics.
11(9), 3570–3577.
mla: Taboada-Gutiérrez, Javier, et al. “Unveiling the Mechanism of Phonon-Polariton
Damping in Α‑MoO3.” ACS Photonics, vol. 11, no. 9, American Chemical Society,
2024, pp. 3570–77, doi:10.1021/acsphotonics.4c00485.
short: J. Taboada-Gutiérrez, Y. Zhou, A.I.F. Tresguerres-Mata, C. Lanza, A. Martínez-Suárez,
G. Álvarez-Pérez, J. Duan, J.I. Martín, M. Vélez, I. Prieto Gonzalez, A. Bercher,
J. Teyssier, I. Errea, A.Y. Nikitin, J. Martín-Sánchez, A.B. Kuzmenko, P. Alonso-González,
ACS Photonics 11 (2024) 3570–3577.
date_created: 2024-09-01T22:01:09Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2025-09-08T09:05:01Z
day: '01'
ddc:
- '530'
department:
- _id: NanoFab
doi: 10.1021/acsphotonics.4c00485
external_id:
arxiv:
- '2408.09811'
isi:
- '001298164600001'
pmid:
- '39310295'
file:
- access_level: open_access
checksum: bd7e6a138c406e93eaf0a6268fc42bfe
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T14:01:06Z
date_updated: 2025-01-09T14:01:06Z
file_id: '18819'
file_name: 2024_ACSPhotonics_TaboadaGutierrez_.pdf
file_size: 2664512
relation: main_file
success: 1
file_date_updated: 2025-01-09T14:01:06Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 3570-3577
pmid: 1
publication: ACS Photonics
publication_identifier:
eissn:
- 2330-4022
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unveiling the mechanism of phonon-polariton damping in α‑MoO3
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 11
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '17885'
abstract:
- lang: eng
text: 'The formation of new ribosomes is tightly coordinated with cell growth and
proliferation. In eukaryotes, the correct assembly of all ribosomal proteins and
RNAs follows an intricate scheme of maturation and rearrangement steps across
three cellular compartments: the nucleolus, nucleoplasm, and cytoplasm. We demonstrate
that usnic acid, a lichen secondary metabolite, inhibits the maturation of the
large ribosomal subunit in yeast. We combine biochemical characterization of pre-ribosomal
particles with a quantitative single-particle cryo-EM approach to monitor changes
in nucleolar particle populations upon drug treatment. Usnic acid rapidly blocks
the transition from nucleolar state B to C of Nsa1-associated pre-ribosomes, depleting
key maturation factors such as Dbp10 and hindering pre-rRNA processing. This primary
nucleolar block rapidly rebounds on earlier stages of the pathway which highlights
the regulatory linkages between different steps. In summary, we provide an in-depth
characterization of the effect of usnic acid on ribosome biogenesis, which may
have implications for its reported anti-cancer activities.'
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: We thank Michael A. McAlear, Micheline Fromont-Racin, Philipp Milkereit,
Arlen W. Johnson, Sabine Rospert, Ed Hurt, C. Yam, Günter Daum, Wolfgang Zachariae,
Katrin Karbstein, Juan P. G. Ballesta, Mercedes Dosil, Miguel Remacha und Jesus
de la Cruz for sharing strains or providing antibodies. We thank the members of
the Bergler lab and the Haselbach lab for their helpful discussion. We thank Ellen
Zhong for helpful discussions about the quantitative cryoDRGN analysis. This research
was supported by the Scientific Service Units of IST Austria through resources provided
by the Electron Microscopy Facility. This research was funded in whole, or in part,
by the Austrian Science Foundation grants [https://doi.org/10.55776/P32977], [https://doi.org/10.55776/P29451]
and [https://doi.org/10.55776/P32536] (to H.B.). Research at the IMP is generously
supported by Boehringer Ingelheim and the Austrian Research Promotion Agency (Headquarter
grant FFG-852936). For the purpose of open access, the author has applied a CC BY
public copyright licence to any Author Accepted Manuscript version arising from
this submission.
article_number: '7511'
article_processing_charge: Yes
article_type: original
author:
- first_name: Lisa
full_name: Kofler, Lisa
last_name: Kofler
- first_name: Lorenz
full_name: Grundmann, Lorenz
last_name: Grundmann
- first_name: Magdalena
full_name: Gerhalter, Magdalena
last_name: Gerhalter
- first_name: Michael
full_name: Prattes, Michael
last_name: Prattes
- first_name: Juliane
full_name: Merl-Pham, Juliane
last_name: Merl-Pham
- first_name: Gertrude
full_name: Zisser, Gertrude
last_name: Zisser
- first_name: Irina
full_name: Grishkovskaya, Irina
last_name: Grishkovskaya
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
orcid: 0000-0003-3904-947X
- first_name: Martin
full_name: Vareka, Martin
last_name: Vareka
- first_name: Rolf
full_name: Breinbauer, Rolf
last_name: Breinbauer
- first_name: Stefanie M.
full_name: Hauck, Stefanie M.
last_name: Hauck
- first_name: David
full_name: Haselbach, David
last_name: Haselbach
- first_name: Helmut
full_name: Bergler, Helmut
last_name: Bergler
citation:
ama: Kofler L, Grundmann L, Gerhalter M, et al. The novel ribosome biogenesis inhibitor
usnic acid blocks nucleolar pre-60S maturation. Nature Communications.
2024;15. doi:10.1038/s41467-024-51754-3
apa: Kofler, L., Grundmann, L., Gerhalter, M., Prattes, M., Merl-Pham, J., Zisser,
G., … Bergler, H. (2024). The novel ribosome biogenesis inhibitor usnic acid blocks
nucleolar pre-60S maturation. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-51754-3
chicago: Kofler, Lisa, Lorenz Grundmann, Magdalena Gerhalter, Michael Prattes, Juliane
Merl-Pham, Gertrude Zisser, Irina Grishkovskaya, et al. “The Novel Ribosome Biogenesis
Inhibitor Usnic Acid Blocks Nucleolar Pre-60S Maturation.” Nature Communications.
Springer Nature, 2024. https://doi.org/10.1038/s41467-024-51754-3.
ieee: L. Kofler et al., “The novel ribosome biogenesis inhibitor usnic acid
blocks nucleolar pre-60S maturation,” Nature Communications, vol. 15. Springer
Nature, 2024.
ista: Kofler L, Grundmann L, Gerhalter M, Prattes M, Merl-Pham J, Zisser G, Grishkovskaya
I, Hodirnau V-V, Vareka M, Breinbauer R, Hauck SM, Haselbach D, Bergler H. 2024.
The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation.
Nature Communications. 15, 7511.
mla: Kofler, Lisa, et al. “The Novel Ribosome Biogenesis Inhibitor Usnic Acid Blocks
Nucleolar Pre-60S Maturation.” Nature Communications, vol. 15, 7511, Springer
Nature, 2024, doi:10.1038/s41467-024-51754-3.
short: L. Kofler, L. Grundmann, M. Gerhalter, M. Prattes, J. Merl-Pham, G. Zisser,
I. Grishkovskaya, V.-V. Hodirnau, M. Vareka, R. Breinbauer, S.M. Hauck, D. Haselbach,
H. Bergler, Nature Communications 15 (2024).
date_created: 2024-09-08T22:01:10Z
date_published: 2024-08-29T00:00:00Z
date_updated: 2025-09-08T09:13:01Z
day: '29'
ddc:
- '570'
department:
- _id: EM-Fac
doi: 10.1038/s41467-024-51754-3
external_id:
isi:
- '001457895200001'
pmid:
- '39209816'
file:
- access_level: open_access
checksum: 7c044538a47182c826d1b526c52958a2
content_type: application/pdf
creator: dernst
date_created: 2024-09-09T08:56:12Z
date_updated: 2024-09-09T08:56:12Z
file_id: '17946'
file_name: 2024_NatureComm_Kofler.pdf
file_size: 3735024
relation: main_file
success: 1
file_date_updated: 2024-09-09T08:56:12Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S
maturation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 15
year: '2024'
...
---
_id: '18052'
abstract:
- lang: eng
text: Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL)
is an electron microscope (EM) sample preparation technique which allows for high-resolution
visualization of membrane proteins with high sensitivity. However, image acquisition
of specific replica profiles such as synapses in a large field of EM view needs
a valid experience and a long time for manual searching. Here, we describe how
to utilize deep learning for automatizing image acquisition of specific profiles
of interest in replica samples. This protocol facilitates the labor-intensive
collection of EM images, in particular for rare profiles. We provide instructions
for using SerialEM image acquisition software in conjunction with object detection
by our newly developed deep learning software DarEM, to automatically acquire
tilt series of all synapses in a selected region. We then show how to perform
a mostly automated analysis of gold particle labeling in the acquired images by
utilizing Darea software.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: This research was supported by the European Research Council Advanced
Grant 694539 to RS and by the Scientific Service Units of IST Austria through resources
provided by the Electron Microscopy Facility.
alternative_title:
- Neuromethods
article_processing_charge: No
author:
- first_name: David
full_name: Kleindienst, David
id: 42E121A4-F248-11E8-B48F-1D18A9856A87
last_name: Kleindienst
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: 'Kleindienst D, Costanzo T, Shigemoto R. Automated Imaging and Analysis of
Synapses in Freeze-Fracture Replica Samples with Deep Learning. In: Lübke JHR,
Rollenhagen A, eds. New Aspects in Analyzing the Synaptic Organization of the
Brain. 1st ed. New York: Springer Nature; 2024:123-137. doi:10.1007/978-1-0716-4019-7_8'
apa: 'Kleindienst, D., Costanzo, T., & Shigemoto, R. (2024). Automated Imaging
and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning.
In J. H. R. Lübke & A. Rollenhagen (Eds.), New Aspects in Analyzing the
Synaptic Organization of the Brain (1st ed., pp. 123–137). New York: Springer
Nature. https://doi.org/10.1007/978-1-0716-4019-7_8'
chicago: 'Kleindienst, David, Tommaso Costanzo, and Ryuichi Shigemoto. “Automated
Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep
Learning.” In New Aspects in Analyzing the Synaptic Organization of the Brain,
edited by Joachim H.R. Lübke and Astrid Rollenhagen, 1st ed., 123–37. New York:
Springer Nature, 2024. https://doi.org/10.1007/978-1-0716-4019-7_8.'
ieee: 'D. Kleindienst, T. Costanzo, and R. Shigemoto, “Automated Imaging and Analysis
of Synapses in Freeze-Fracture Replica Samples with Deep Learning,” in New
Aspects in Analyzing the Synaptic Organization of the Brain, 1st ed., J. H.
R. Lübke and A. Rollenhagen, Eds. New York: Springer Nature, 2024, pp. 123–137.'
ista: 'Kleindienst D, Costanzo T, Shigemoto R. 2024.Automated Imaging and Analysis
of Synapses in Freeze-Fracture Replica Samples with Deep Learning. In: New Aspects
in Analyzing the Synaptic Organization of the Brain. Neuromethods, , 123–137.'
mla: Kleindienst, David, et al. “Automated Imaging and Analysis of Synapses in Freeze-Fracture
Replica Samples with Deep Learning.” New Aspects in Analyzing the Synaptic
Organization of the Brain, edited by Joachim H.R. Lübke and Astrid Rollenhagen,
1st ed., Springer Nature, 2024, pp. 123–37, doi:10.1007/978-1-0716-4019-7_8.
short: D. Kleindienst, T. Costanzo, R. Shigemoto, in:, J.H.R. Lübke, A. Rollenhagen
(Eds.), New Aspects in Analyzing the Synaptic Organization of the Brain, 1st ed.,
Springer Nature, New York, 2024, pp. 123–137.
corr_author: '1'
date_created: 2024-09-10T12:32:38Z
date_published: 2024-08-27T00:00:00Z
date_updated: 2025-04-14T07:27:15Z
day: '27'
department:
- _id: EM-Fac
- _id: RySh
doi: 10.1007/978-1-0716-4019-7_8
ec_funded: 1
edition: '1'
editor:
- first_name: 'Joachim H.R. '
full_name: 'Lübke, Joachim H.R. '
last_name: Lübke
- first_name: Astrid
full_name: Rollenhagen, Astrid
last_name: Rollenhagen
language:
- iso: eng
month: '08'
oa_version: None
page: 123-137
place: New York
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
publication: New Aspects in Analyzing the Synaptic Organization of the Brain
publication_identifier:
eisbn:
- '9781071640197'
eissn:
- 1940-6045
isbn:
- '9781071640180'
issn:
- 0893-2336
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples
with Deep Learning
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_id: '18168'
abstract:
- lang: eng
text: 'Despite the considerable interest in the recombinant production of synthetic
spider silk fibers that possess mechanical properties similar to those of native
spider silks, such as the cost-effectiveness, tunability, and scalability realization,
is still lacking. To address this long-standing challenge, we have constructed
an artificial spider silk gene using Golden Gate assembly for the recombinant
bacterial production of dragline-mimicking silk, incorporating all the essential
components: the N-terminal domain, a 33-residue-long major-ampullate-spidroin-inspired
segment repeated 16 times, and the C-terminal domain (N16C). This designed silk-like
protein was successfully expressed in Escherichia coli, purified, and cast into
films from formic acid. We produced uniformly 13C–15N-labeled N16C films and employed
solid-state magic-angle spinning nuclear magnetic resonance (NMR) for characterization.
Thus, we could demonstrate that our bioengineered silk-like protein self-assembles
into a film where, when hydrated, the solvent-exposed layer of the rigid, β-nanocrystalline
polyalanine core undergoes a transition to an α-helical structure, gaining mobility
to the extent that it fully dissolves in water and transforms into a highly dynamic
random coil. This hydration-induced behavior induces chain dynamics in the glycine-rich
amorphous soft segments on the microsecond time scale, contributing to the elasticity
of the solid material. Our findings not only reveal the presence of structurally
and dynamically distinct segments within the film’s superstructure but also highlight
the complexity of the self-organization responsible for the exceptional mechanical
properties observed in proteins that mimic dragline silk.'
acknowledgement: We thank Dr. Pavel Kielkowski for performing the MS/MS measurement
and providing feedback on the manuscript. We are grateful to Rodrigo Ledesma Amaro
for introducing the Golden Gate Assembly technique in our lab. We acknowledge the
support from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)─SFB
1309-325871075, the Center for NanoScience (CeNS), the Fonds der Chemischen Industrie,
and Universitätsgesellschaft München.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Dongqing
full_name: Wu, Dongqing
last_name: Wu
- first_name: Anamaria
full_name: Koscic, Anamaria
last_name: Koscic
- first_name: Sonja
full_name: Schneider, Sonja
last_name: Schneider
- first_name: Romeo C. A.
full_name: Dubini, Romeo C. A.
last_name: Dubini
- first_name: Diana C.
full_name: Rodriguez Camargo, Diana C.
last_name: Rodriguez Camargo
- first_name: Sabine
full_name: Schneider, Sabine
last_name: Schneider
- first_name: Petra
full_name: Rovo, Petra
id: c316e53f-b965-11eb-b128-bb26acc59c00
last_name: Rovo
orcid: 0000-0001-8729-7326
citation:
ama: Wu D, Koscic A, Schneider S, et al. Unveiling the dynamic self-assembly of
a recombinant dragline-silk-mimicking protein. Biomacromolecules. 2024;25(3):1759-1774.
doi:10.1021/acs.biomac.3c01239
apa: Wu, D., Koscic, A., Schneider, S., Dubini, R. C. A., Rodriguez Camargo, D.
C., Schneider, S., & Rovo, P. (2024). Unveiling the dynamic self-assembly
of a recombinant dragline-silk-mimicking protein. Biomacromolecules. American
Chemical Society. https://doi.org/10.1021/acs.biomac.3c01239
chicago: Wu, Dongqing, Anamaria Koscic, Sonja Schneider, Romeo C. A. Dubini, Diana
C. Rodriguez Camargo, Sabine Schneider, and Petra Rovo. “Unveiling the Dynamic
Self-Assembly of a Recombinant Dragline-Silk-Mimicking Protein.” Biomacromolecules.
American Chemical Society, 2024. https://doi.org/10.1021/acs.biomac.3c01239.
ieee: D. Wu et al., “Unveiling the dynamic self-assembly of a recombinant
dragline-silk-mimicking protein,” Biomacromolecules, vol. 25, no. 3. American
Chemical Society, pp. 1759–1774, 2024.
ista: Wu D, Koscic A, Schneider S, Dubini RCA, Rodriguez Camargo DC, Schneider S,
Rovo P. 2024. Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking
protein. Biomacromolecules. 25(3), 1759–1774.
mla: Wu, Dongqing, et al. “Unveiling the Dynamic Self-Assembly of a Recombinant
Dragline-Silk-Mimicking Protein.” Biomacromolecules, vol. 25, no. 3, American
Chemical Society, 2024, pp. 1759–74, doi:10.1021/acs.biomac.3c01239.
short: D. Wu, A. Koscic, S. Schneider, R.C.A. Dubini, D.C. Rodriguez Camargo, S.
Schneider, P. Rovo, Biomacromolecules 25 (2024) 1759–1774.
corr_author: '1'
date_created: 2024-10-02T10:09:53Z
date_published: 2024-03-11T00:00:00Z
date_updated: 2025-09-08T09:52:18Z
day: '11'
ddc:
- '540'
department:
- _id: NMR
doi: 10.1021/acs.biomac.3c01239
external_id:
isi:
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pmid:
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intvolume: ' 25'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1759-1774
pmid: 1
publication: Biomacromolecules
publication_identifier:
eissn:
- 1526-4602
issn:
- 1525-7797
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking
protein
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 25
year: '2024'
...
---
_id: '18296'
abstract:
- lang: eng
text: It is widely believed that information storage in neuronal circuits involves
nanoscopic structural changes at synapses, resulting in the formation of synaptic
engrams. However, direct evidence for this hypothesis is lacking. To test this
conjecture, we combined chemical potentiation, functional analysis by paired pre-postsynaptic
recordings, and structural analysis by electron microscopy (EM) and freeze-fracture
replica labeling (FRL) at the murine hippocampal mossy fiber synapse, a key synapse
in the trisynaptic circuit of the hippocampus. Biophysical analysis of synaptic
transmission revealed that forskolin-induced chemical potentiation increased the
readily releasable vesicle pool size and vesicular release probability by 146%
and 49%, respectively. Structural analysis of mossy fiber synapses by EM and FRL
demonstrated an increase in the number of vesicles close to the plasma membrane
and the number of clusters of the priming protein Munc13-1, indicating an increase
in the number of both docked and primed vesicles. Furthermore, FRL analysis revealed
a significant reduction of the distance between Munc13-1 and CaV2.1 Ca2+ channels,
suggesting reconfiguration of the channel-vesicle coupling nanotopography. Our
results indicate that presynaptic plasticity is associated with structural reorganization
of active zones. We propose that changes in potential nanoscopic organization
at synaptic vesicle release sites may be correlates of learning and memory at
a plastic central synapse.
article_processing_charge: No
author:
- first_name: Olena
full_name: Kim, Olena
id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87
last_name: Kim
orcid: 0000-0003-2344-1039
citation:
ama: Kim O. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of
synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber
boutons. 2024. doi:10.15479/AT:ISTA:18296
apa: Kim, O. (2024). Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration
of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber
boutons. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:18296
chicago: Kim, Olena. “Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration
of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber
Boutons.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:18296.
ieee: O. Kim, “Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration
of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber
boutons.” Institute of Science and Technology Austria, 2024.
ista: Kim O. 2024. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration
of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber
boutons, Institute of Science and Technology Austria, 10.15479/AT:ISTA:18296.
mla: Kim, Olena. Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration
of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber
Boutons. Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:18296.
short: O. Kim, (2024).
contributor:
- contributor_type: researcher
first_name: Olena
id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87
last_name: Kim
- contributor_type: researcher
first_name: Yuji
id: 3337E116-F248-11E8-B48F-1D18A9856A87
last_name: Okamoto
orcid: 0000-0003-0408-6094
- contributor_type: researcher
first_name: Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- contributor_type: researcher
first_name: 'Nils '
last_name: Brose
- contributor_type: researcher
first_name: Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- contributor_type: supervisor
first_name: Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
corr_author: '1'
date_created: 2024-10-11T10:12:17Z
date_published: 2024-10-11T00:00:00Z
date_updated: 2026-04-16T12:20:33Z
day: '11'
ddc:
- '570'
department:
- _id: PeJo
- _id: RySh
- _id: EM-Fac
doi: 10.15479/AT:ISTA:18296
ec_funded: 1
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date_updated: 2024-10-11T10:04:19Z
file_id: '18297'
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file_size: 164382
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file_size: 654
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success: 1
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keyword:
- Hippocampal mossy fiber synapses
- short-term potentiation
- long-term potentiation
- presynaptic plasticity
- electron microscopy
- freeze-fracture replica labeling
- paired recordings
- forskolin
- cyclic adenosine monophosphate (cAMP)
- protein kinase A (PKA)
- neuromodulation
- synaptic vesicle pools
- presynaptic Ca2+ channels
- Munc13
- docking
- priming
- active zone
month: '10'
oa: 1
oa_version: Submitted Version
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '18603'
relation: used_in_publication
status: public
status: public
title: Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic
vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2024'
...
---
OA_type: closed access
_id: '18310'
article_processing_charge: No
article_type: original
author:
- first_name: Maria
full_name: Kitsara, Maria
last_name: Kitsara
- first_name: Merima
full_name: Smajlhodžić-Deljo, Merima
last_name: Smajlhodžić-Deljo
- first_name: Lejla
full_name: Gurbeta Pokvic, Lejla
last_name: Gurbeta Pokvic
- first_name: Bettina
full_name: Bert, Bettina
last_name: Bert
- first_name: Nataliia
full_name: Bubalo, Nataliia
last_name: Bubalo
- first_name: Sevilay
full_name: Erden, Sevilay
last_name: Erden
- first_name: Nuno Henrique
full_name: Franco, Nuno Henrique
last_name: Franco
- first_name: Giuseppe
full_name: Chirico, Giuseppe
last_name: Chirico
- first_name: Jonathan
full_name: Gómez Raja, Jonathan
last_name: Gómez Raja
- first_name: Fernando
full_name: Gonzalez-Uarquin, Fernando
last_name: Gonzalez-Uarquin
- first_name: Annemarie
full_name: Lang, Annemarie
last_name: Lang
- first_name: Nicole
full_name: Linklater, Nicole
last_name: Linklater
- first_name: Sandra
full_name: Mojsova, Sandra
last_name: Mojsova
- first_name: I. Anna S.
full_name: Olsson, I. Anna S.
last_name: Olsson
- first_name: Ioanna
full_name: Sandvig, Ioanna
last_name: Sandvig
- first_name: Alexandra
full_name: Schaffert, Alexandra
last_name: Schaffert
- first_name: Marthe
full_name: Schmit, Marthe
last_name: Schmit
- first_name: Sophie
full_name: Schober, Sophie
id: 80b0a0ef-4b9f-11ec-b119-8d9d94c4a1d8
last_name: Schober
- first_name: Bogdan
full_name: Sevastre, Bogdan
last_name: Sevastre
- first_name: Doris
full_name: Wilflingseder, Doris
last_name: Wilflingseder
- first_name: Arti
full_name: Ahluwalia, Arti
last_name: Ahluwalia
- first_name: Winfried
full_name: Neuhaus, Winfried
last_name: Neuhaus
citation:
ama: Kitsara M, Smajlhodžić-Deljo M, Gurbeta Pokvic L, et al. Introducing the COST
action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE).
Alternatives to Laboratory Animals. 2024;52(6):326-333. doi:10.1177/02611929241286024
apa: Kitsara, M., Smajlhodžić-Deljo, M., Gurbeta Pokvic, L., Bert, B., Bubalo, N.,
Erden, S., … Neuhaus, W. (2024). Introducing the COST action ‘Improving the Quality
of Biomedical Science with 3Rs Concepts’ (IMPROVE). Alternatives to Laboratory
Animals. SAGE Publications. https://doi.org/10.1177/02611929241286024
chicago: Kitsara, Maria, Merima Smajlhodžić-Deljo, Lejla Gurbeta Pokvic, Bettina
Bert, Nataliia Bubalo, Sevilay Erden, Nuno Henrique Franco, et al. “Introducing
the COST Action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’
(IMPROVE).” Alternatives to Laboratory Animals. SAGE Publications, 2024.
https://doi.org/10.1177/02611929241286024.
ieee: M. Kitsara et al., “Introducing the COST action ‘Improving the Quality
of Biomedical Science with 3Rs Concepts’ (IMPROVE),” Alternatives to Laboratory
Animals, vol. 52, no. 6. SAGE Publications, pp. 326–333, 2024.
ista: Kitsara M, Smajlhodžić-Deljo M, Gurbeta Pokvic L, Bert B, Bubalo N, Erden
S, Franco NH, Chirico G, Gómez Raja J, Gonzalez-Uarquin F, Lang A, Linklater N,
Mojsova S, Olsson IAS, Sandvig I, Schaffert A, Schmit M, Schober S, Sevastre B,
Wilflingseder D, Ahluwalia A, Neuhaus W. 2024. Introducing the COST action ‘Improving
the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE). Alternatives to
Laboratory Animals. 52(6), 326–333.
mla: Kitsara, Maria, et al. “Introducing the COST Action ‘Improving the Quality
of Biomedical Science with 3Rs Concepts’ (IMPROVE).” Alternatives to Laboratory
Animals, vol. 52, no. 6, SAGE Publications, 2024, pp. 326–33, doi:10.1177/02611929241286024.
short: M. Kitsara, M. Smajlhodžić-Deljo, L. Gurbeta Pokvic, B. Bert, N. Bubalo,
S. Erden, N.H. Franco, G. Chirico, J. Gómez Raja, F. Gonzalez-Uarquin, A. Lang,
N. Linklater, S. Mojsova, I.A.S. Olsson, I. Sandvig, A. Schaffert, M. Schmit,
S. Schober, B. Sevastre, D. Wilflingseder, A. Ahluwalia, W. Neuhaus, Alternatives
to Laboratory Animals 52 (2024) 326–333.
date_created: 2024-10-13T22:01:51Z
date_published: 2024-11-01T00:00:00Z
date_updated: 2025-09-08T09:56:39Z
day: '01'
department:
- _id: PreCl
doi: 10.1177/02611929241286024
external_id:
isi:
- '001348633700007'
pmid:
- '39333027'
intvolume: ' 52'
isi: 1
issue: '6'
language:
- iso: eng
month: '11'
oa_version: None
page: 326-333
pmid: 1
publication: Alternatives to Laboratory Animals
publication_identifier:
eissn:
- 2632-3559
issn:
- 0261-1929
publication_status: published
publisher: SAGE Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Introducing the COST action ‘Improving the Quality of Biomedical Science with
3Rs Concepts’ (IMPROVE)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 52
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '14843'
abstract:
- lang: eng
text: The coupling between Ca2+ channels and release sensors is a key factor defining
the signaling properties of a synapse. However, the coupling nanotopography at
many synapses remains unknown, and it is unclear how it changes during development.
To address these questions, we examined coupling at the cerebellar inhibitory
basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission
by paired recording and intracellular pipette perfusion revealed that the effects
of exogenous Ca2+ chelators decreased during development, despite constant reliance
of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica
labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic
P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked
vesicles were only clustered at later developmental stages. Modeling suggested
a developmental transformation from a more random to a more clustered coupling
nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point
configuration, optimizing speed, reliability, and energy efficiency of synaptic
transmission.
acknowledged_ssus:
- _id: EM-Fac
- _id: PreCl
- _id: M-Shop
acknowledgement: We thank Drs. David DiGregorio and Erwin Neher for critically reading
an earlier version of the manuscript, Ralf Schneggenburger for helpful discussions,
Benjamin Suter and Katharina Lichter for support with image analysis, Chris Wojtan
for advice on numerical solution of partial differential equations, Maria Reva for
help with Ripley analysis, Alois Schlögl for programming, and Akari Hagiwara and
Toshihisa Ohtsuka for anti-ELKS antibody. We are grateful to Florian Marr, Christina
Altmutter, and Vanessa Zheden for excellent technical assistance and to Eleftheria
Kralli-Beller for manuscript editing. This research was supported by the Scientific
Services Units (SSUs) of ISTA (Electron Microscopy Facility, Preclinical Facility,
and Machine Shop). The project received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation program (grant
agreement no. 692692), the Fonds zur Förderung der Wissenschaftlichen Forschung
(Z 312-B27, Wittgenstein award; P 36232-B), all to P.J., and a DOC fellowship of
the Austrian Academy of Sciences to J.-J.C.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: JingJing
full_name: Chen, JingJing
id: 2C4E65C8-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Chong
full_name: Chen, Chong
id: 3DFD581A-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Itaru
full_name: Arai, Itaru
id: 32A73F6C-F248-11E8-B48F-1D18A9856A87
last_name: Arai
- first_name: Olena
full_name: Kim, Olena
id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87
last_name: Kim
orcid: 0000-0003-2344-1039
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Chen J, Kaufmann W, Chen C, et al. Developmental transformation of Ca2+ channel-vesicle
nanotopography at a central GABAergic synapse. Neuron. 2024;112(5):755-771.e9.
doi:10.1016/j.neuron.2023.12.002
apa: Chen, J., Kaufmann, W., Chen, C., Arai, itaru, Kim, O., Shigemoto, R., &
Jonas, P. M. (2024). Developmental transformation of Ca2+ channel-vesicle nanotopography
at a central GABAergic synapse. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.12.002
chicago: Chen, JingJing, Walter Kaufmann, Chong Chen, itaru Arai, Olena Kim, Ryuichi
Shigemoto, and Peter M Jonas. “Developmental Transformation of Ca2+ Channel-Vesicle
Nanotopography at a Central GABAergic Synapse.” Neuron. Elsevier, 2024.
https://doi.org/10.1016/j.neuron.2023.12.002.
ieee: J. Chen et al., “Developmental transformation of Ca2+ channel-vesicle
nanotopography at a central GABAergic synapse,” Neuron, vol. 112, no. 5.
Elsevier, p. 755–771.e9, 2024.
ista: Chen J, Kaufmann W, Chen C, Arai itaru, Kim O, Shigemoto R, Jonas PM. 2024.
Developmental transformation of Ca2+ channel-vesicle nanotopography at a central
GABAergic synapse. Neuron. 112(5), 755–771.e9.
mla: Chen, JingJing, et al. “Developmental Transformation of Ca2+ Channel-Vesicle
Nanotopography at a Central GABAergic Synapse.” Neuron, vol. 112, no. 5,
Elsevier, 2024, p. 755–771.e9, doi:10.1016/j.neuron.2023.12.002.
short: J. Chen, W. Kaufmann, C. Chen, itaru Arai, O. Kim, R. Shigemoto, P.M. Jonas,
Neuron 112 (2024) 755–771.e9.
corr_author: '1'
date_created: 2024-01-21T23:00:56Z
date_published: 2024-03-06T00:00:00Z
date_updated: 2026-06-24T22:30:21Z
day: '06'
ddc:
- '570'
department:
- _id: PeJo
- _id: EM-Fac
- _id: RySh
doi: 10.1016/j.neuron.2023.12.002
ec_funded: 1
external_id:
isi:
- '001202925700001'
pmid:
- '38215739'
file:
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checksum: 30098b4f0209556ddfb3540a23d07ca5
content_type: application/pdf
creator: dernst
date_created: 2025-04-23T14:02:08Z
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month: '03'
oa: 1
oa_version: Published Version
page: 755-771.e9
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
- _id: bd88be38-d553-11ed-ba76-81d5a70a6ef5
grant_number: P36232
name: Mechanisms of GABA release in hippocampal circuits
- _id: 26B66A3E-B435-11E9-9278-68D0E5697425
grant_number: '25383'
name: Development of nanodomain coupling between Ca2+ channels and release sensors
at a central inhibitory synapse
publication: Neuron
publication_identifier:
eissn:
- 1097-4199
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/synapses-brought-to-the-point/
record:
- id: '15101'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Developmental transformation of Ca2+ channel-vesicle nanotopography at a central
GABAergic synapse
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2024'
...
---
APC_amount: 804 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18601'
abstract:
- lang: eng
text: "Geometrically controlled stem cell differentiation promotes reproducible
pattern formation. Here, we present a protocol to fabricate elastomeric stencils
for patterned stem cell differentiation. We describe procedures for using photolithography
to produce molds, followed by molding polydimethylsiloxane (PDMS) to obtain stencils
with through holes. We then provide instructions for culturing cells on stencils
and, finally, removing stencils to allow colony growth and cell migration. This
approach yields reproducible two-dimensional organoids tailored for quantitative
studies of growth and pattern formation.\r\nFor complete details on the use and
execution of this protocol, please refer to Lehr et al.1"
acknowledged_ssus:
- _id: NanoFab
acknowledgement: We thank the nanofabrication facility at ISTA for technical assistance.
Work in the A.K. lab is supported by ISTA, the European Research Council under Horizon
Europe (grant 101044579), and the Austrian Science Fund (FWF) (grant https://doi.org/10.55776/F78).
S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H.
fellowship SC19-011.
article_number: '103187'
article_processing_charge: Yes
article_type: original
author:
- first_name: Stefanie
full_name: Rus, Stefanie
id: 4D9EC9B6-F248-11E8-B48F-1D18A9856A87
last_name: Rus
orcid: 0000-0001-8703-1093
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Monika Aleksandra
full_name: Kulig, Monika Aleksandra
id: 3331f5ae-e896-11ec-af79-eeb79769bcb7
last_name: Kulig
- first_name: Thomas
full_name: Minchington, Thomas
id: 7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f
last_name: Minchington
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
citation:
ama: Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. Protocol for fabricating
elastomeric stencils for patterned stem cell differentiation. STAR Protocols.
2024;5(4). doi:10.1016/j.xpro.2024.103187
apa: Rus, S., Merrin, J., Kulig, M. A., Minchington, T., & Kicheva, A. (2024).
Protocol for fabricating elastomeric stencils for patterned stem cell differentiation.
STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2024.103187
chicago: Rus, Stefanie, Jack Merrin, Monika Aleksandra Kulig, Thomas Minchington,
and Anna Kicheva. “Protocol for Fabricating Elastomeric Stencils for Patterned
Stem Cell Differentiation.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2024.103187.
ieee: S. Rus, J. Merrin, M. A. Kulig, T. Minchington, and A. Kicheva, “Protocol
for fabricating elastomeric stencils for patterned stem cell differentiation,”
STAR Protocols, vol. 5, no. 4. Elsevier, 2024.
ista: Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. 2024. Protocol for fabricating
elastomeric stencils for patterned stem cell differentiation. STAR Protocols.
5(4), 103187.
mla: Rus, Stefanie, et al. “Protocol for Fabricating Elastomeric Stencils for Patterned
Stem Cell Differentiation.” STAR Protocols, vol. 5, no. 4, 103187, Elsevier,
2024, doi:10.1016/j.xpro.2024.103187.
short: S. Rus, J. Merrin, M.A. Kulig, T. Minchington, A. Kicheva, STAR Protocols
5 (2024).
corr_author: '1'
date_created: 2024-12-01T23:01:53Z
date_published: 2024-12-20T00:00:00Z
date_updated: 2026-06-24T22:30:32Z
day: '20'
ddc:
- '570'
department:
- _id: AnKi
- _id: NanoFab
doi: 10.1016/j.xpro.2024.103187
external_id:
pmid:
- '39602310'
file:
- access_level: open_access
checksum: 0c61a6f9978608a103865905e06f4581
content_type: application/pdf
creator: dernst
date_created: 2024-12-03T10:53:23Z
date_updated: 2024-12-03T10:53:23Z
file_id: '18610'
file_name: 2024_STARProtoc_Lehr.pdf
file_size: 4989169
relation: main_file
success: 1
file_date_updated: 2024-12-03T10:53:23Z
has_accepted_license: '1'
intvolume: ' 5'
issue: '4'
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month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa
grant_number: '101044579'
name: Mechanisms of tissue size regulation in spinal cord development
- _id: 9B9B39FA-BA93-11EA-9121-9846C619BF3A
grant_number: SC19-011
name: The regulatory logic of pattern formation in the vertebrate dorsal neural
tube
publication: STAR Protocols
publication_identifier:
eissn:
- 2666-1667
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '19763'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Protocol for fabricating elastomeric stencils for patterned stem cell differentiation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2024'
...
---
_id: '12106'
abstract:
- lang: eng
text: Regulation of chromatin states involves the dynamic interplay between different
histone modifications to control gene expression. Recent advances have enabled
mapping of histone marks in single cells, but most methods are constrained to
profile only one histone mark per cell. Here, we present an integrated experimental
and computational framework, scChIX-seq (single-cell chromatin immunocleavage
and unmixing sequencing), to map several histone marks in single cells. scChIX-seq
multiplexes two histone marks together in single cells, then computationally deconvolves
the signal using training data from respective histone mark profiles. This framework
learns the cell-type-specific correlation structure between histone marks, and
therefore does not require a priori assumptions of their genomic distributions.
Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single
cells across a range of mark combinations. Modeling dynamics of in vitro macrophage
differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq
unlocks systematic interrogation of the interplay between histone modifications
in single cells.
acknowledgement: We thank M. van Loenhout for experimental advice on purifying cell
types from the bone marrow, R. van der Linden for expertise with FACS and M. Blotenburg
for help with cell typing the mouse organogenesis dataset. We thank M. Saraswat
and O. Stegle for discussions on multinomial distributions. This work was supported
by a European Research Council Advanced grant (ERC-AdG 742225-IntScOmics); Nederlandse
Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP grant (NWO CW 714.016.001)
and NWO grant (OCENW.GROOT.2019.017); the Swiss National Science Foundation Early
Postdoc Mobility (P2ELP3-184488 to P.Z. and P2BSP3-174991 to J.Y.); Marie Sklodowska-Curie
Actions Postdoc (798573 to P.Z.) and the Human Frontier for Science Program Long-Term
Fellowships (LT000209-2018-L to P.Z. and LT000097-2019-L to J.Y.). This work is
part of the Oncode Institute which is financed partly by the Dutch Cancer Society.
article_processing_charge: No
article_type: original
author:
- first_name: Jake
full_name: Yeung, Jake
id: 123012b2-db30-11eb-b4d8-a35840c0551b
last_name: Yeung
orcid: 0000-0003-1732-1559
- first_name: Maria
full_name: Florescu, Maria
last_name: Florescu
- first_name: Peter
full_name: Zeller, Peter
last_name: Zeller
- first_name: Buys Anton
full_name: De Barbanson, Buys Anton
last_name: De Barbanson
- first_name: Max D.
full_name: Wellenstein, Max D.
last_name: Wellenstein
- first_name: Alexander
full_name: Van Oudenaarden, Alexander
last_name: Van Oudenaarden
citation:
ama: Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden
A. scChIX-seq infers dynamic relationships between histone modifications in single
cells. Nature Biotechnology. 2023;41:813–823. doi:10.1038/s41587-022-01560-3
apa: Yeung, J., Florescu, M., Zeller, P., De Barbanson, B. A., Wellenstein, M. D.,
& Van Oudenaarden, A. (2023). scChIX-seq infers dynamic relationships between
histone modifications in single cells. Nature Biotechnology. Springer Nature.
https://doi.org/10.1038/s41587-022-01560-3
chicago: Yeung, Jake, Maria Florescu, Peter Zeller, Buys Anton De Barbanson, Max
D. Wellenstein, and Alexander Van Oudenaarden. “ScChIX-Seq Infers Dynamic Relationships
between Histone Modifications in Single Cells.” Nature Biotechnology. Springer
Nature, 2023. https://doi.org/10.1038/s41587-022-01560-3.
ieee: J. Yeung, M. Florescu, P. Zeller, B. A. De Barbanson, M. D. Wellenstein, and
A. Van Oudenaarden, “scChIX-seq infers dynamic relationships between histone modifications
in single cells,” Nature Biotechnology, vol. 41. Springer Nature, pp. 813–823,
2023.
ista: Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden
A. 2023. scChIX-seq infers dynamic relationships between histone modifications
in single cells. Nature Biotechnology. 41, 813–823.
mla: Yeung, Jake, et al. “ScChIX-Seq Infers Dynamic Relationships between Histone
Modifications in Single Cells.” Nature Biotechnology, vol. 41, Springer
Nature, 2023, pp. 813–823, doi:10.1038/s41587-022-01560-3.
short: J. Yeung, M. Florescu, P. Zeller, B.A. De Barbanson, M.D. Wellenstein, A.
Van Oudenaarden, Nature Biotechnology 41 (2023) 813–823.
corr_author: '1'
date_created: 2023-01-08T23:00:53Z
date_published: 2023-06-01T00:00:00Z
date_updated: 2025-04-23T08:45:24Z
day: '01'
ddc:
- '570'
department:
- _id: ScienComp
doi: 10.1038/s41587-022-01560-3
external_id:
isi:
- '000909067600003'
pmid:
- '36593403'
file:
- access_level: open_access
checksum: 668447a1c8d360b68f8aaf9e08ed644f
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T11:30:45Z
date_updated: 2023-08-16T11:30:45Z
file_id: '14066'
file_name: 2023_NatureBioTech_Yeung.pdf
file_size: 12040976
relation: main_file
success: 1
file_date_updated: 2023-08-16T11:30:45Z
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 813–823
pmid: 1
publication: Nature Biotechnology
publication_identifier:
eissn:
- 1546-1696
issn:
- 1087-0156
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: scChIX-seq infers dynamic relationships between histone modifications in single
cells
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: 41
year: '2023'
...
---
_id: '12158'
abstract:
- lang: eng
text: 'Post-translational histone modifications modulate chromatin activity to affect
gene expression. How chromatin states underlie lineage choice in single cells
is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage
(sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3)
histone modifications in the mouse bone marrow. During differentiation, hematopoietic
stem and progenitor cells (HSPCs) acquire active chromatin states mediated by
cell-type-specifying transcription factors, which are unique for each lineage.
By contrast, most alterations in repressive marks during differentiation occur
independent of the final cell type. Chromatin trajectory analysis shows that lineage
choice at the chromatin level occurs at the progenitor stage. Joint profiling
of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage
have distinct active chromatin but share similar myeloid-specific heterochromatin
states. This implies a hierarchical regulation of chromatin during hematopoiesis:
heterochromatin dynamics distinguish differentiation trajectories and lineages,
while euchromatin dynamics reflect cell types within lineages.'
acknowledgement: We thank A. Giladi for sharing mRNA abundance tables of cell types
together with J. van den Berg for critical reading of the manuscript. We thank M.
Bartosovic for sharing method comparison data. pK19pA-MN was a gift from Ulrich
Laemmli (Addgene plasmid 86973, http://n2t.net/addgene:86973; RRID:Addgene_86973).
Figure 8 is adopted from Hematopoiesis (human) diagram by A. Rad and M. Häggström
under CC-BY-SA 3.0 license. This work was supported by European Research Council
Advanced under grant ERC-AdG 742225-IntScOmics and Nederlandse Organisatie voor
Wetenschappelijk Onderzoek (NWO) TOP award NWO-CW 714.016.001. The SNF (P2BSP3-174991),
HFSP (LT000209/2018-L) and Marie Skłodowska-Curie Actions (798573) supported P.Z.
The SNF (P2ELP3_184488) and HFSP (LT000097/2019-L) supported J.Y. and the EMBO LTF
(ALTF 1197–2019) supported V.B. This work is part of the Oncode Institute, which
is partly financed by the Dutch Cancer Society. The funders had no role in study
design, data collection and analysis, decision to publish or preparation of the
manuscript.
article_processing_charge: No
article_type: review
author:
- first_name: Peter
full_name: Zeller, Peter
last_name: Zeller
- first_name: Jake
full_name: Yeung, Jake
id: 123012b2-db30-11eb-b4d8-a35840c0551b
last_name: Yeung
orcid: 0000-0003-1732-1559
- first_name: Helena
full_name: Viñas Gaza, Helena
last_name: Viñas Gaza
- first_name: Buys Anton
full_name: de Barbanson, Buys Anton
last_name: de Barbanson
- first_name: Vivek
full_name: Bhardwaj, Vivek
last_name: Bhardwaj
- first_name: Maria
full_name: Florescu, Maria
last_name: Florescu
- first_name: Reinier
full_name: van der Linden, Reinier
last_name: van der Linden
- first_name: Alexander
full_name: van Oudenaarden, Alexander
last_name: van Oudenaarden
citation:
ama: Zeller P, Yeung J, Viñas Gaza H, et al. Single-cell sortChIC identifies hierarchical
chromatin dynamics during hematopoiesis. Nature Genetics. 2023;55:333-345.
doi:10.1038/s41588-022-01260-3
apa: Zeller, P., Yeung, J., Viñas Gaza, H., de Barbanson, B. A., Bhardwaj, V., Florescu,
M., … van Oudenaarden, A. (2023). Single-cell sortChIC identifies hierarchical
chromatin dynamics during hematopoiesis. Nature Genetics. Springer Nature.
https://doi.org/10.1038/s41588-022-01260-3
chicago: Zeller, Peter, Jake Yeung, Helena Viñas Gaza, Buys Anton de Barbanson,
Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, and Alexander van Oudenaarden.
“Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.”
Nature Genetics. Springer Nature, 2023. https://doi.org/10.1038/s41588-022-01260-3.
ieee: P. Zeller et al., “Single-cell sortChIC identifies hierarchical chromatin
dynamics during hematopoiesis,” Nature Genetics, vol. 55. Springer Nature,
pp. 333–345, 2023.
ista: Zeller P, Yeung J, Viñas Gaza H, de Barbanson BA, Bhardwaj V, Florescu M,
van der Linden R, van Oudenaarden A. 2023. Single-cell sortChIC identifies hierarchical
chromatin dynamics during hematopoiesis. Nature Genetics. 55, 333–345.
mla: Zeller, Peter, et al. “Single-Cell SortChIC Identifies Hierarchical Chromatin
Dynamics during Hematopoiesis.” Nature Genetics, vol. 55, Springer Nature,
2023, pp. 333–45, doi:10.1038/s41588-022-01260-3.
short: P. Zeller, J. Yeung, H. Viñas Gaza, B.A. de Barbanson, V. Bhardwaj, M. Florescu,
R. van der Linden, A. van Oudenaarden, Nature Genetics 55 (2023) 333–345.
date_created: 2023-01-12T12:09:09Z
date_published: 2023-02-01T00:00:00Z
date_updated: 2025-04-23T08:45:00Z
day: '01'
ddc:
- '570'
- '000'
department:
- _id: ScienComp
doi: 10.1038/s41588-022-01260-3
external_id:
pmid:
- '36539617'
file:
- access_level: open_access
checksum: 6fdb8e34fbeea63edd0f2c6c2cc5823e
content_type: application/pdf
creator: dernst
date_created: 2023-02-27T07:46:45Z
date_updated: 2023-02-27T07:46:45Z
file_id: '12688'
file_name: 2023_NatureGenetics_Zeller.pdf
file_size: 21484855
relation: main_file
success: 1
file_date_updated: 2023-02-27T07:46:45Z
has_accepted_license: '1'
intvolume: ' 55'
keyword:
- Genetics
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 333-345
pmid: 1
publication: Nature Genetics
publication_identifier:
eissn:
- 1546-1718
issn:
- 1061-4036
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis
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: 55
year: '2023'
...
---
_id: '12334'
abstract:
- lang: eng
text: Regulation of the Arp2/3 complex is required for productive nucleation of
branched actin networks. An emerging aspect of regulation is the incorporation
of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit
isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity
and branch junction stability. We have combined reverse genetics and cellular
structural biology to describe how ArpC5 and ArpC5L differentially affect cell
migration. Both define the structural stability of ArpC1 in branch junctions and,
in turn, by determining protrusion characteristics, affect protein dynamics and
actin network ultrastructure. ArpC5 isoforms also affect the positioning of members
of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament
elongators, which mediate ArpC5 isoform–specific effects on the actin assembly
level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling
pathway enhancing cell migration.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: Bio
- _id: EM-Fac
acknowledgement: "We would like to thank K. von Peinen and B. Denker (Helmholtz Centre
for Infection Research, Braunschweig, Germany) for experimental and technical assistance,
respectively.\r\nThis research was supported by the Scientific Service Units (SSUs)
of ISTA through resources provided by Scientific Computing (SciComp), the Life Science
Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy
Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund
(FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz
Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and
K.R."
article_number: add6495
article_processing_charge: No
article_type: original
author:
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Manjunath
full_name: Javoor, Manjunath
id: 305ab18b-dc7d-11ea-9b2f-b58195228ea2
last_name: Javoor
orcid: 0000-0003-2311-2112
- first_name: Julia
full_name: Datler, Julia
id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87
last_name: Datler
orcid: 0000-0002-3616-8580
- first_name: Hermann
full_name: Döring, Hermann
last_name: Döring
- first_name: Florian
full_name: Hofer, Florian
id: b9d234ba-9e33-11ed-95b6-cd561df280e6
last_name: Hofer
- first_name: Georgi A
full_name: Dimchev, Georgi A
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
orcid: 0000-0001-8370-6161
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
orcid: 0000-0003-3904-947X
- first_name: Jan
full_name: Faix, Jan
last_name: Faix
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Fäßler F, Javoor M, Datler J, et al. ArpC5 isoforms regulate Arp2/3 complex–dependent
protrusion through differential Ena/VASP positioning. Science Advances.
2023;9(3). doi:10.1126/sciadv.add6495
apa: Fäßler, F., Javoor, M., Datler, J., Döring, H., Hofer, F., Dimchev, G. A.,
… Schur, F. K. (2023). ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion
through differential Ena/VASP positioning. Science Advances. American Association
for the Advancement of Science. https://doi.org/10.1126/sciadv.add6495
chicago: Fäßler, Florian, Manjunath Javoor, Julia Datler, Hermann Döring, Florian
Hofer, Georgi A Dimchev, Victor-Valentin Hodirnau, Jan Faix, Klemens Rottner,
and Florian KM Schur. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion
through Differential Ena/VASP Positioning.” Science Advances. American
Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.add6495.
ieee: F. Fäßler et al., “ArpC5 isoforms regulate Arp2/3 complex–dependent
protrusion through differential Ena/VASP positioning,” Science Advances,
vol. 9, no. 3. American Association for the Advancement of Science, 2023.
ista: Fäßler F, Javoor M, Datler J, Döring H, Hofer F, Dimchev GA, Hodirnau V-V,
Faix J, Rottner K, Schur FK. 2023. ArpC5 isoforms regulate Arp2/3 complex–dependent
protrusion through differential Ena/VASP positioning. Science Advances. 9(3),
add6495.
mla: Fäßler, Florian, et al. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion
through Differential Ena/VASP Positioning.” Science Advances, vol. 9, no.
3, add6495, American Association for the Advancement of Science, 2023, doi:10.1126/sciadv.add6495.
short: F. Fäßler, M. Javoor, J. Datler, H. Döring, F. Hofer, G.A. Dimchev, V.-V.
Hodirnau, J. Faix, K. Rottner, F.K. Schur, Science Advances 9 (2023).
corr_author: '1'
date_created: 2023-01-23T07:26:42Z
date_published: 2023-01-20T00:00:00Z
date_updated: 2026-04-07T12:59:44Z
day: '20'
ddc:
- '570'
department:
- _id: FlSc
- _id: EM-Fac
doi: 10.1126/sciadv.add6495
external_id:
isi:
- '000964550100015'
pmid:
- '36662867'
file:
- access_level: open_access
checksum: ce81a6d0b84170e5e8c62f6acfa15d9e
content_type: application/pdf
creator: dernst
date_created: 2023-01-23T07:45:54Z
date_updated: 2023-01-23T07:45:54Z
file_id: '12335'
file_name: 2023_ScienceAdvances_Faessler.pdf
file_size: 1756234
relation: main_file
success: 1
file_date_updated: 2023-01-23T07:45:54Z
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intvolume: ' 9'
isi: 1
issue: '3'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
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grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
record:
- id: '14562'
relation: research_data
status: public
- id: '18766'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential
Ena/VASP positioning
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2023'
...
---
_id: '12543'
abstract:
- lang: eng
text: Treating sick group members is a hallmark of collective disease defence in
vertebrates and invertebrates alike. Despite substantial effects on pathogen fitness
and epidemiology, it is still largely unknown how pathogens react to the selection
pressure imposed by care intervention. Using social insects and pathogenic fungi,
we here performed a serial passage experiment in the presence or absence of colony
members, which provide social immunity by grooming off infectious spores from
exposed individuals. We found specific effects on pathogen diversity, virulence
and transmission. Under selection of social immunity, pathogens invested into
higher spore production, but spores were less virulent. Notably, they also elicited
a lower grooming response in colony members, compared with spores from the individual
host selection lines. Chemical spore analysis suggested that the spores from social
selection lines escaped the caregivers’ detection by containing lower levels of
ergosterol, a key fungal membrane component. Experimental application of chemically
pure ergosterol indeed induced sanitary grooming, supporting its role as a microbe-associated
cue triggering host social immunity against fungal pathogens. By reducing this
detection cue, pathogens were able to evade the otherwise very effective collective
disease defences of their social hosts.
acknowledged_ssus:
- _id: LifeSc
acknowledgement: We thank B. M. Steinwender, N. V. Meyling and J. Eilenberg for the
fungal strains; J. Anaya-Rojas for statistical advice; the Social Immunity team
at ISTA for ant collection and experimental help, in particular H. Leitner, and
the ISTA Lab Support Facility for general laboratory support; D. Ebert, H. Schulenburg
and J. Heinze for continued project discussion; and M. Sixt, R. Roemhild and the
Social Immunity team for comments on the manuscript. The study was funded by the
German Research Foundation (CR118/3-1) within the Framework of the Priority Program
SPP 1399, and the European Research Council (ERC) under the European Union’s Horizon
2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP), both to S.C.
article_processing_charge: No
article_type: original
author:
- first_name: Miriam
full_name: Stock, Miriam
id: 42462816-F248-11E8-B48F-1D18A9856A87
last_name: Stock
- first_name: Barbara
full_name: Milutinovic, Barbara
id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87
last_name: Milutinovic
orcid: 0000-0002-8214-4758
- first_name: Michaela
full_name: Hönigsberger, Michaela
id: 953894f3-25bd-11ec-8556-f70a9d38ef60
last_name: Hönigsberger
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Florian
full_name: Wiesenhofer, Florian
id: 39523C54-F248-11E8-B48F-1D18A9856A87
last_name: Wiesenhofer
- first_name: Niklas
full_name: Kampleitner, Niklas
id: 2AC57FAC-F248-11E8-B48F-1D18A9856A87
last_name: Kampleitner
- first_name: Madhumitha
full_name: Narasimhan, Madhumitha
id: 44BF24D0-F248-11E8-B48F-1D18A9856A87
last_name: Narasimhan
orcid: 0000-0002-8600-0671
- first_name: Thomas
full_name: Schmitt, Thomas
last_name: Schmitt
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Stock M, Milutinovic B, Hönigsberger M, et al. Pathogen evasion of social immunity.
Nature Ecology and Evolution. 2023;7:450-460. doi:10.1038/s41559-023-01981-6
apa: Stock, M., Milutinovic, B., Hönigsberger, M., Grasse, A. V., Wiesenhofer, F.,
Kampleitner, N., … Cremer, S. (2023). Pathogen evasion of social immunity. Nature
Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-023-01981-6
chicago: Stock, Miriam, Barbara Milutinovic, Michaela Hönigsberger, Anna V Grasse,
Florian Wiesenhofer, Niklas Kampleitner, Madhumitha Narasimhan, Thomas Schmitt,
and Sylvia Cremer. “Pathogen Evasion of Social Immunity.” Nature Ecology and
Evolution. Springer Nature, 2023. https://doi.org/10.1038/s41559-023-01981-6.
ieee: M. Stock et al., “Pathogen evasion of social immunity,” Nature Ecology
and Evolution, vol. 7. Springer Nature, pp. 450–460, 2023.
ista: Stock M, Milutinovic B, Hönigsberger M, Grasse AV, Wiesenhofer F, Kampleitner
N, Narasimhan M, Schmitt T, Cremer S. 2023. Pathogen evasion of social immunity.
Nature Ecology and Evolution. 7, 450–460.
mla: Stock, Miriam, et al. “Pathogen Evasion of Social Immunity.” Nature Ecology
and Evolution, vol. 7, Springer Nature, 2023, pp. 450–60, doi:10.1038/s41559-023-01981-6.
short: M. Stock, B. Milutinovic, M. Hönigsberger, A.V. Grasse, F. Wiesenhofer, N.
Kampleitner, M. Narasimhan, T. Schmitt, S. Cremer, Nature Ecology and Evolution
7 (2023) 450–460.
corr_author: '1'
date_created: 2023-02-12T23:00:59Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2025-04-14T07:47:53Z
day: '01'
ddc:
- '570'
department:
- _id: SyCr
- _id: LifeSc
- _id: JiFr
doi: 10.1038/s41559-023-01981-6
ec_funded: 1
external_id:
isi:
- '000924572800001'
pmid:
- '36732670'
file:
- access_level: open_access
checksum: 8244f4650a0e7aeea488d1bcd4a31702
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T11:54:59Z
date_updated: 2023-08-16T11:54:59Z
file_id: '14069'
file_name: 2023_NatureEcoEvo_Stock.pdf
file_size: 1600499
relation: main_file
success: 1
file_date_updated: 2023-08-16T11:54:59Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 450-460
pmid: 1
project:
- _id: 2649B4DE-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771402'
name: Epidemics in ant societies on a chip
- _id: 25DAF0B2-B435-11E9-9278-68D0E5697425
grant_number: CR-118/3-1
name: Host-Parasite Coevolution
publication: Nature Ecology and Evolution
publication_identifier:
eissn:
- 2397-334X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/how-sneaky-germs-hide-from-ants/
scopus_import: '1'
status: public
title: Pathogen evasion of social immunity
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: 7
year: '2023'
...
---
_id: '12747'
abstract:
- lang: eng
text: Muscle degeneration is the most prevalent cause for frailty and dependency
in inherited diseases and ageing. Elucidation of pathophysiological mechanisms,
as well as effective treatments for muscle diseases, represents an important goal
in improving human health. Here, we show that the lipid synthesis enzyme phosphatidylethanolamine
cytidyltransferase (PCYT2/ECT) is critical to muscle health. Human deficiency
in PCYT2 causes a severe disease with failure to thrive and progressive weakness.
pcyt2-mutant zebrafish and muscle-specific Pcyt2-knockout mice recapitulate the
participant phenotypes, with failure to thrive, progressive muscle weakness and
accelerated ageing. Mechanistically, muscle Pcyt2 deficiency affects cellular
bioenergetics and membrane lipid bilayer structure and stability. PCYT2 activity
declines in ageing muscles of mice and humans, and adeno-associated virus-based
delivery of PCYT2 ameliorates muscle weakness in Pcyt2-knockout and old mice,
offering a therapy for individuals with a rare disease and muscle ageing. Thus,
PCYT2 plays a fundamental and conserved role in vertebrate muscle health, linking
PCYT2 and PCYT2-synthesized lipids to severe muscle dystrophy and ageing.
acknowledgement: 'The authors thank the participants and their families for participating
in the study. We thank all members of our laboratories for helpful discussions.
We are grateful to Vienna BioCenter Core Facilities: Mouse Phenotyping Unit, Histopathology
Unit, Bioinformatics Unit, BioOptics Unit, Electron Microscopy Unit and Comparative
Medicine Unit. We are grateful to the Lipidomics Facility, and K. Klavins and T.
Hannich at the CeMM Research Center for Molecular Medicine of the Austrian Academy
of Sciences for assistance with lipidomics analysis. We also thank T. Huan and A.
Hui (UBC Vancouver) for mouse tissue and mitochondria lipidomics analysis. We thank
A. Klymchenko (Laboratoire de Bioimagerie et Pathologies Université de Strasbourg,
Strasbourg, France) for providing the NR12S probe. We are thankful to the Sen. Paul
D. Wellstone Muscular Dystrophy Cooperative Specialized Research Center Viral Vector
Core Facility for AAV6 production. We also thank K. P. Campbell and M. E. Anderson
(University of Iowa, Carver College of Medicine) for advice on muscle tissue handling.
We thank A. Al-Qassabi from the Sultan Qaboos University for the clinical assessment
of the participants. D.C. and J.M.P. are supported by the Austrian Federal Ministry
of Education, Science and Research, the Austrian Academy of Sciences, and the City
of Vienna, and grants from the Austrian Science Fund (FWF) Wittgenstein award (Z
271-B19), the T. von Zastrow Foundation, and a Canada 150 Research Chairs Program
(F18-01336). J.S.C. is supported by grants RO1AR44533 and P50AR065139 from the US
National Institutes of Health. C.K. is supported by a grant from the Agence Nationale
de la Recherche (ANR-18-CE14-0007-01). A.V.K. is supported by European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement
no. 67544, and an Austrian Science Fund (FWF; no P-33799). A.W. is supported by
Austrian Research Promotion Agency (FFG) project no 867674. E.S. is supported by
a SciLifeLab fellowship and Karolinska Institutet Foundation Grants. Work in the
laboratory of G.S.-F. is supported by the Austrian Academy of Sciences, the European
Research Council (ERC AdG 695214 GameofGates) and the Innovative Medicines Initiative
2 Joint Undertaking (grant agreement no. 777372, ReSOLUTE). S.B., M.L. and R.Y.
acknowledge the support of the Spastic Paraplegia Foundation.'
article_processing_charge: No
article_type: original
author:
- first_name: Domagoj
full_name: Cikes, Domagoj
last_name: Cikes
- first_name: Kareem
full_name: Elsayad, Kareem
last_name: Elsayad
- first_name: Erdinc
full_name: Sezgin, Erdinc
last_name: Sezgin
- first_name: Erika
full_name: Koitai, Erika
last_name: Koitai
- first_name: Torma
full_name: Ferenc, Torma
last_name: Ferenc
- first_name: Michael
full_name: Orthofer, Michael
last_name: Orthofer
- first_name: Rebecca
full_name: Yarwood, Rebecca
last_name: Yarwood
- first_name: Leonhard X.
full_name: Heinz, Leonhard X.
last_name: Heinz
- first_name: Vitaly
full_name: Sedlyarov, Vitaly
last_name: Sedlyarov
- first_name: Nasser
full_name: Darwish-Miranda, Nasser
id: 39CD9926-F248-11E8-B48F-1D18A9856A87
last_name: Darwish-Miranda
orcid: 0000-0002-8821-8236
- first_name: Adrian
full_name: Taylor, Adrian
last_name: Taylor
- first_name: Sophie
full_name: Grapentine, Sophie
last_name: Grapentine
- first_name: Fathiya
full_name: al-Murshedi, Fathiya
last_name: al-Murshedi
- first_name: Anne
full_name: Abot, Anne
last_name: Abot
- first_name: Adelheid
full_name: Weidinger, Adelheid
last_name: Weidinger
- first_name: Candice
full_name: Kutchukian, Candice
last_name: Kutchukian
- first_name: Colline
full_name: Sanchez, Colline
last_name: Sanchez
- first_name: Shane J. F.
full_name: Cronin, Shane J. F.
last_name: Cronin
- first_name: Maria
full_name: Novatchkova, Maria
last_name: Novatchkova
- first_name: Anoop
full_name: Kavirayani, Anoop
last_name: Kavirayani
- first_name: Thomas
full_name: Schuetz, Thomas
last_name: Schuetz
- first_name: Bernhard
full_name: Haubner, Bernhard
last_name: Haubner
- first_name: Lisa
full_name: Haas, Lisa
last_name: Haas
- first_name: Astrid
full_name: Hagelkruys, Astrid
last_name: Hagelkruys
- first_name: Suzanne
full_name: Jackowski, Suzanne
last_name: Jackowski
- first_name: Andrey
full_name: Kozlov, Andrey
last_name: Kozlov
- first_name: Vincent
full_name: Jacquemond, Vincent
last_name: Jacquemond
- first_name: Claude
full_name: Knauf, Claude
last_name: Knauf
- first_name: Giulio
full_name: Superti-Furga, Giulio
last_name: Superti-Furga
- first_name: Eric
full_name: Rullman, Eric
last_name: Rullman
- first_name: Thomas
full_name: Gustafsson, Thomas
last_name: Gustafsson
- first_name: John
full_name: McDermot, John
last_name: McDermot
- first_name: Martin
full_name: Lowe, Martin
last_name: Lowe
- first_name: Zsolt
full_name: Radak, Zsolt
last_name: Radak
- first_name: Jeffrey S.
full_name: Chamberlain, Jeffrey S.
last_name: Chamberlain
- first_name: Marica
full_name: Bakovic, Marica
last_name: Bakovic
- first_name: Siddharth
full_name: Banka, Siddharth
last_name: Banka
- first_name: Josef M.
full_name: Penninger, Josef M.
last_name: Penninger
citation:
ama: Cikes D, Elsayad K, Sezgin E, et al. PCYT2-regulated lipid biosynthesis is
critical to muscle health and ageing. Nature Metabolism. 2023;5:495-515.
doi:10.1038/s42255-023-00766-2
apa: Cikes, D., Elsayad, K., Sezgin, E., Koitai, E., Ferenc, T., Orthofer, M., …
Penninger, J. M. (2023). PCYT2-regulated lipid biosynthesis is critical to muscle
health and ageing. Nature Metabolism. Springer Nature. https://doi.org/10.1038/s42255-023-00766-2
chicago: Cikes, Domagoj, Kareem Elsayad, Erdinc Sezgin, Erika Koitai, Torma Ferenc,
Michael Orthofer, Rebecca Yarwood, et al. “PCYT2-Regulated Lipid Biosynthesis
Is Critical to Muscle Health and Ageing.” Nature Metabolism. Springer Nature,
2023. https://doi.org/10.1038/s42255-023-00766-2.
ieee: D. Cikes et al., “PCYT2-regulated lipid biosynthesis is critical to
muscle health and ageing,” Nature Metabolism, vol. 5. Springer Nature,
pp. 495–515, 2023.
ista: Cikes D, Elsayad K, Sezgin E, Koitai E, Ferenc T, Orthofer M, Yarwood R, Heinz
LX, Sedlyarov V, Darwish-Miranda N, Taylor A, Grapentine S, al-Murshedi F, Abot
A, Weidinger A, Kutchukian C, Sanchez C, Cronin SJF, Novatchkova M, Kavirayani
A, Schuetz T, Haubner B, Haas L, Hagelkruys A, Jackowski S, Kozlov A, Jacquemond
V, Knauf C, Superti-Furga G, Rullman E, Gustafsson T, McDermot J, Lowe M, Radak
Z, Chamberlain JS, Bakovic M, Banka S, Penninger JM. 2023. PCYT2-regulated lipid
biosynthesis is critical to muscle health and ageing. Nature Metabolism. 5, 495–515.
mla: Cikes, Domagoj, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle
Health and Ageing.” Nature Metabolism, vol. 5, Springer Nature, 2023, pp.
495–515, doi:10.1038/s42255-023-00766-2.
short: D. Cikes, K. Elsayad, E. Sezgin, E. Koitai, T. Ferenc, M. Orthofer, R. Yarwood,
L.X. Heinz, V. Sedlyarov, N. Darwish-Miranda, A. Taylor, S. Grapentine, F. al-Murshedi,
A. Abot, A. Weidinger, C. Kutchukian, C. Sanchez, S.J.F. Cronin, M. Novatchkova,
A. Kavirayani, T. Schuetz, B. Haubner, L. Haas, A. Hagelkruys, S. Jackowski, A.
Kozlov, V. Jacquemond, C. Knauf, G. Superti-Furga, E. Rullman, T. Gustafsson,
J. McDermot, M. Lowe, Z. Radak, J.S. Chamberlain, M. Bakovic, S. Banka, J.M. Penninger,
Nature Metabolism 5 (2023) 495–515.
date_created: 2023-03-23T12:58:43Z
date_published: 2023-03-20T00:00:00Z
date_updated: 2023-11-28T07:31:33Z
day: '20'
department:
- _id: Bio
doi: 10.1038/s42255-023-00766-2
external_id:
isi:
- '000992064000002'
pmid:
- '36941451'
intvolume: ' 5'
isi: 1
keyword:
- Cell Biology
- Physiology (medical)
- Endocrinology
- Diabetes and Metabolism
- Internal Medicine
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2022.03.02.482658
month: '03'
oa: 1
oa_version: Preprint
page: 495-515
pmid: 1
publication: Nature Metabolism
publication_identifier:
issn:
- 2522-5812
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s42255-023-00791-1
scopus_import: '1'
status: public
title: PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2023'
...
---
_id: '12830'
abstract:
- lang: eng
text: Interstitial fluid (IF) accumulation between embryonic cells is thought to
be important for embryo patterning and morphogenesis. Here, we identify a positive
mechanical feedback loop between cell migration and IF relocalization and find
that it promotes embryonic axis formation during zebrafish gastrulation. We show
that anterior axial mesendoderm (prechordal plate [ppl]) cells, moving in between
the yolk cell and deep cell tissue to extend the embryonic axis, compress the
overlying deep cell layer, thereby causing IF to flow from the deep cell layer
to the boundary between the yolk cell and the deep cell layer, directly ahead
of the advancing ppl. This IF relocalization, in turn, facilitates ppl cell protrusion
formation and migration by opening up the space into which the ppl moves and,
thereby, the ability of the ppl to trigger IF relocalization by pushing against
the overlying deep cell layer. Thus, embryonic axis formation relies on a hydraulic
feedback loop between cell migration and IF relocalization.
acknowledged_ssus:
- _id: PreCl
- _id: Bio
acknowledgement: We thank Andrea Pauli (IMP) and Edouard Hannezo (ISTA) for fruitful
discussions and support with the SPIM experiments; the Heisenberg group, and especially
Feyza Nur Arslan and Alexandra Schauer, for discussions and feedback; Michaela Jović
(ISTA) for help with the quantitative real-time PCR protocol; the bioimaging and
zebrafish facilities of ISTA for continuous support; Stephan Preibisch (Janelia
Research Campus) for support with the SPIM data analysis; and Nobuhiro Nakamura
(Tokyo Institute of Technology) for sharing α1-Na+/K+-ATPase antibody. This work
was supported by funding from the European Union (European Research Council Advanced
grant 742573 to C.-P.H.), postdoctoral fellowships from EMBO (LTF-850-2017) and
HFSP (LT000429/2018-L2) to D.P., and a PhD fellowship from the Studienstiftung des
deutschen Volkes to F.P.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Karla
full_name: Huljev, Karla
id: 44C6F6A6-F248-11E8-B48F-1D18A9856A87
last_name: Huljev
- first_name: Shayan
full_name: Shamipour, Shayan
id: 40B34FE2-F248-11E8-B48F-1D18A9856A87
last_name: Shamipour
- first_name: Diana C
full_name: Nunes Pinheiro, Diana C
id: 2E839F16-F248-11E8-B48F-1D18A9856A87
last_name: Nunes Pinheiro
orcid: 0000-0003-4333-7503
- first_name: Friedrich
full_name: Preusser, Friedrich
last_name: Preusser
- first_name: Irene
full_name: Steccari, Irene
id: 2705C766-9FE2-11EA-B224-C6773DDC885E
last_name: Steccari
- 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: Suyash
full_name: Naik, Suyash
id: 2C0B105C-F248-11E8-B48F-1D18A9856A87
last_name: Naik
orcid: 0000-0001-8421-5508
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Huljev K, Shamipour S, Nunes Pinheiro DC, et al. A hydraulic feedback loop
between mesendoderm cell migration and interstitial fluid relocalization promotes
embryonic axis formation in zebrafish. Developmental Cell. 2023;58(7):582-596.e7.
doi:10.1016/j.devcel.2023.02.016
apa: Huljev, K., Shamipour, S., Nunes Pinheiro, D. C., Preusser, F., Steccari, I.,
Sommer, C. M., … Heisenberg, C.-P. J. (2023). A hydraulic feedback loop between
mesendoderm cell migration and interstitial fluid relocalization promotes embryonic
axis formation in zebrafish. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2023.02.016
chicago: Huljev, Karla, Shayan Shamipour, Diana C Nunes Pinheiro, Friedrich Preusser,
Irene Steccari, Christoph M Sommer, Suyash Naik, and Carl-Philipp J Heisenberg.
“A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial
Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” Developmental
Cell. Elsevier, 2023. https://doi.org/10.1016/j.devcel.2023.02.016.
ieee: K. Huljev et al., “A hydraulic feedback loop between mesendoderm cell
migration and interstitial fluid relocalization promotes embryonic axis formation
in zebrafish,” Developmental Cell, vol. 58, no. 7. Elsevier, p. 582–596.e7,
2023.
ista: Huljev K, Shamipour S, Nunes Pinheiro DC, Preusser F, Steccari I, Sommer CM,
Naik S, Heisenberg C-PJ. 2023. A hydraulic feedback loop between mesendoderm cell
migration and interstitial fluid relocalization promotes embryonic axis formation
in zebrafish. Developmental Cell. 58(7), 582–596.e7.
mla: Huljev, Karla, et al. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration
and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.”
Developmental Cell, vol. 58, no. 7, Elsevier, 2023, p. 582–596.e7, doi:10.1016/j.devcel.2023.02.016.
short: K. Huljev, S. Shamipour, D.C. Nunes Pinheiro, F. Preusser, I. Steccari, C.M.
Sommer, S. Naik, C.-P.J. Heisenberg, Developmental Cell 58 (2023) 582–596.e7.
corr_author: '1'
date_created: 2023-04-16T22:01:07Z
date_published: 2023-04-10T00:00:00Z
date_updated: 2025-04-23T08:51:34Z
day: '10'
ddc:
- '570'
department:
- _id: CaHe
- _id: Bio
doi: 10.1016/j.devcel.2023.02.016
ec_funded: 1
external_id:
isi:
- '000982111800001'
pmid:
- '36931269'
file:
- access_level: open_access
checksum: c80ca2ebc241232aacdb5aa4b4c80957
content_type: application/pdf
creator: dernst
date_created: 2023-04-17T07:41:25Z
date_updated: 2023-04-17T07:41:25Z
file_id: '12842'
file_name: 2023_DevelopmentalCell_Huljev.pdf
file_size: 7925886
relation: main_file
success: 1
file_date_updated: 2023-04-17T07:41:25Z
has_accepted_license: '1'
intvolume: ' 58'
isi: 1
issue: '7'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 582-596.e7
pmid: 1
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
- _id: 26520D1E-B435-11E9-9278-68D0E5697425
grant_number: ALTF 850-2017
name: Coordination of mesendoderm cell fate specification and internalization during
zebrafish gastrulation
- _id: 266BC5CE-B435-11E9-9278-68D0E5697425
grant_number: LT000429
name: Coordination of mesendoderm fate specification and internalization during
zebrafish gastrulation
publication: Developmental Cell
publication_identifier:
eissn:
- 1878-1551
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: A hydraulic feedback loop between mesendoderm cell migration and interstitial
fluid relocalization promotes embryonic axis formation in zebrafish
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: 58
year: '2023'
...
---
_id: '12863'
abstract:
- lang: eng
text: In the present study, essential and nonessential metal content and biomarker
responses were investigated in the intestine of fish collected from the areas
polluted by mining. Our objective was to determine metal and biomarker levels
in tissue responsible for dietary intake, which is rarely studied in water pollution
research. The study was conducted in the Bregalnica River, reference location,
and in the Zletovska and Kriva Rivers (the Republic of North Macedonia), which
are directly influenced by the active mines Zletovo and Toranica, respectively.
Biological responses were analyzed in Vardar chub (Squalius vardarensis; Karaman,
1928), using for the first time intestinal cytosol as a potentially toxic cell
fraction, since metal sensitivity is mostly associated with cytosol. Cytosolic
metal levels were higher in fish under the influence of mining (Tl, Li, Cs, Mo,
Sr, Cd, Rb, and Cu in the Zletovska River and Cr, Pb, and Se in the Kriva River
compared to the Bregalnica River in both seasons). The same trend was evident
for total proteins, biomarkers of general stress, and metallothioneins, biomarkers
of metal exposure, indicating cellular disturbances in the intestine, the primary
site of dietary metal uptake. The association of cytosolic Cu and Cd at all locations
pointed to similar pathways and homeostasis of these metallothionein-binding metals.
Comparison with other indicator tissues showed that metal concentrations were
higher in the intestine of fish from mining-affected areas than in the liver and
gills. In general, these results indicated the importance of dietary metal pathways,
and cytosolic metal fraction in assessing pollution impacts in freshwater ecosystems.
acknowledgement: 'The authors are grateful to Dr. Nevenka Mikac for the opportunity
to perform metal measurements on HR ICP-MS. This research was funded by the Ministry
of Science, Education and Sport of the Republic of Croatia (projects No. 098–0982934-2721
and 098–1782739-2749). The sampling was carried out as a part of two Croatian-Macedonian
bilateral projects: “The assessment of availability and effects of metals on fish
in the rivers under the impact of mining activities” and “Bacterial and parasitical
communities of chub as indicators of the status of environment exposed to mining
activities.”'
article_processing_charge: No
article_type: original
author:
- first_name: Vlatka
full_name: Filipović Marijić, Vlatka
last_name: Filipović Marijić
- first_name: Nesrete
full_name: Krasnici, Nesrete
id: cb5852d4-287f-11ed-baf0-bc1dd2d5c745
last_name: Krasnici
- first_name: Damir
full_name: Valić, Damir
last_name: Valić
- first_name: Damir
full_name: Kapetanović, Damir
last_name: Kapetanović
- first_name: Irena
full_name: Vardić Smrzlić, Irena
last_name: Vardić Smrzlić
- first_name: Maja
full_name: Jordanova, Maja
last_name: Jordanova
- first_name: Katerina
full_name: Rebok, Katerina
last_name: Rebok
- first_name: Sheriban
full_name: Ramani, Sheriban
last_name: Ramani
- first_name: Vasil
full_name: Kostov, Vasil
last_name: Kostov
- first_name: Rodne
full_name: Nastova, Rodne
last_name: Nastova
- first_name: Zrinka
full_name: Dragun, Zrinka
last_name: Dragun
citation:
ama: Filipović Marijić V, Krasnici N, Valić D, et al. Pollution impact on metal
and biomarker responses in intestinal cytosol of freshwater fish. Environmental
Science and Pollution Research. 2023;30:63510-63521. doi:10.1007/s11356-023-26844-2
apa: Filipović Marijić, V., Krasnici, N., Valić, D., Kapetanović, D., Vardić Smrzlić,
I., Jordanova, M., … Dragun, Z. (2023). Pollution impact on metal and biomarker
responses in intestinal cytosol of freshwater fish. Environmental Science and
Pollution Research. Springer Nature. https://doi.org/10.1007/s11356-023-26844-2
chicago: Filipović Marijić, Vlatka, Nesrete Krasnici, Damir Valić, Damir Kapetanović,
Irena Vardić Smrzlić, Maja Jordanova, Katerina Rebok, et al. “Pollution Impact
on Metal and Biomarker Responses in Intestinal Cytosol of Freshwater Fish.” Environmental
Science and Pollution Research. Springer Nature, 2023. https://doi.org/10.1007/s11356-023-26844-2.
ieee: V. Filipović Marijić et al., “Pollution impact on metal and biomarker
responses in intestinal cytosol of freshwater fish,” Environmental Science
and Pollution Research, vol. 30. Springer Nature, pp. 63510–63521, 2023.
ista: Filipović Marijić V, Krasnici N, Valić D, Kapetanović D, Vardić Smrzlić I,
Jordanova M, Rebok K, Ramani S, Kostov V, Nastova R, Dragun Z. 2023. Pollution
impact on metal and biomarker responses in intestinal cytosol of freshwater fish.
Environmental Science and Pollution Research. 30, 63510–63521.
mla: Filipović Marijić, Vlatka, et al. “Pollution Impact on Metal and Biomarker
Responses in Intestinal Cytosol of Freshwater Fish.” Environmental Science
and Pollution Research, vol. 30, Springer Nature, 2023, pp. 63510–21, doi:10.1007/s11356-023-26844-2.
short: V. Filipović Marijić, N. Krasnici, D. Valić, D. Kapetanović, I. Vardić Smrzlić,
M. Jordanova, K. Rebok, S. Ramani, V. Kostov, R. Nastova, Z. Dragun, Environmental
Science and Pollution Research 30 (2023) 63510–63521.
date_created: 2023-04-23T22:01:03Z
date_published: 2023-05-01T00:00:00Z
date_updated: 2023-10-04T11:23:10Z
day: '01'
department:
- _id: LifeSc
doi: 10.1007/s11356-023-26844-2
external_id:
isi:
- '000970917900012'
pmid:
- '37055686'
intvolume: ' 30'
isi: 1
language:
- iso: eng
month: '05'
oa_version: None
page: 63510-63521
pmid: 1
publication: Environmental Science and Pollution Research
publication_identifier:
eissn:
- 1614-7499
issn:
- 0944-1344
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Pollution impact on metal and biomarker responses in intestinal cytosol of
freshwater fish
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2023'
...
---
_id: '13033'
abstract:
- lang: eng
text: Current methods for assessing cell proliferation in 3D scaffolds rely on changes
in metabolic activity or total DNA, however, direct quantification of cell number
in 3D scaffolds remains a challenge. To address this issue, we developed an unbiased
stereology approach that uses systematic-random sampling and thin focal-plane
optical sectioning of the scaffolds followed by estimation of total cell number
(StereoCount). This approach was validated against an indirect method for measuring
the total DNA (DNA content); and the Bürker counting chamber, the current reference
method for quantifying cell number. We assessed the total cell number for cell
seeding density (cells per unit volume) across four values and compared the methods
in terms of accuracy, ease-of-use and time demands. The accuracy of StereoCount
markedly outperformed the DNA content for cases with ~ 10,000 and ~ 125,000 cells/scaffold.
For cases with ~ 250,000 and ~ 375,000 cells/scaffold both StereoCount and DNA
content showed lower accuracy than the Bürker but did not differ from each other.
In terms of ease-of-use, there was a strong advantage for the StereoCount due
to output in terms of absolute cell numbers along with the possibility for an
overview of cell distribution and future use of automation for high throughput
analysis. Taking together, the StereoCount method is an efficient approach for
direct cell quantification in 3D collagen scaffolds. Its major benefit is that
automated StereoCount could accelerate research using 3D scaffolds focused on
drug discovery for a wide variety of human diseases.
acknowledgement: The study was supported by Project No. CZ.02.1.01/0.0/0.0/16_019/0000787
“Fighting INfectious Diseases”, awarded by the MEYS CR, financed from EFRR, by the
Cooperatio Program, research area DIAG and research area MED/DIAG, by the profiBONE
project (TO01000309) benefitting from a € (1.433.000) grant from Iceland, Liechtenstein
and Norway through the EEA Grants and the Technology Agency of the Czech Republic
and by a Grant (#1926990) to PRM and SRC Biosciences from the National Science Foundation
(U.S. Public Health Service). The authors acknowledge the invaluable assistance
provided by Iveta Paurova via her support in terms of the provision of laboratory
services.
article_number: '7959'
article_processing_charge: No
article_type: original
author:
- first_name: Anna
full_name: Zavadakova, Anna
last_name: Zavadakova
- first_name: Lucie
full_name: Vistejnova, Lucie
last_name: Vistejnova
- first_name: Tereza
full_name: Belinova, Tereza
id: 0bf89b6a-d28b-11eb-8bd6-f43768e4d368
last_name: Belinova
- first_name: Filip
full_name: Tichanek, Filip
last_name: Tichanek
- first_name: Dagmar
full_name: Bilikova, Dagmar
last_name: Bilikova
- first_name: Peter R.
full_name: Mouton, Peter R.
last_name: Mouton
citation:
ama: Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR.
Novel stereological method for estimation of cell counts in 3D collagen scaffolds.
Scientific Reports. 2023;13(1). doi:10.1038/s41598-023-35162-z
apa: Zavadakova, A., Vistejnova, L., Belinova, T., Tichanek, F., Bilikova, D., &
Mouton, P. R. (2023). Novel stereological method for estimation of cell counts
in 3D collagen scaffolds. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-023-35162-z
chicago: Zavadakova, Anna, Lucie Vistejnova, Tereza Belinova, Filip Tichanek, Dagmar
Bilikova, and Peter R. Mouton. “Novel Stereological Method for Estimation of Cell
Counts in 3D Collagen Scaffolds.” Scientific Reports. Springer Nature,
2023. https://doi.org/10.1038/s41598-023-35162-z.
ieee: A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, and P.
R. Mouton, “Novel stereological method for estimation of cell counts in 3D collagen
scaffolds,” Scientific Reports, vol. 13, no. 1. Springer Nature, 2023.
ista: Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR.
2023. Novel stereological method for estimation of cell counts in 3D collagen
scaffolds. Scientific Reports. 13(1), 7959.
mla: Zavadakova, Anna, et al. “Novel Stereological Method for Estimation of Cell
Counts in 3D Collagen Scaffolds.” Scientific Reports, vol. 13, no. 1, 7959,
Springer Nature, 2023, doi:10.1038/s41598-023-35162-z.
short: A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, P.R.
Mouton, Scientific Reports 13 (2023).
date_created: 2023-05-19T11:12:25Z
date_published: 2023-05-17T00:00:00Z
date_updated: 2025-04-23T08:56:48Z
day: '17'
ddc:
- '570'
department:
- _id: Bio
doi: 10.1038/s41598-023-35162-z
external_id:
isi:
- '000995271600104'
pmid:
- '37198326'
file:
- access_level: open_access
checksum: 8c1b769693ff4288df8376e59ad1176d
content_type: application/pdf
creator: dernst
date_created: 2023-05-22T07:57:37Z
date_updated: 2023-05-22T07:57:37Z
file_id: '13047'
file_name: 2023_ScientificReports_Zavadakova.pdf
file_size: 3055077
relation: main_file
success: 1
file_date_updated: 2023-05-22T07:57:37Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '1'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific Reports
publication_identifier:
issn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41598-023-37265-z
scopus_import: '1'
status: public
title: Novel stereological method for estimation of cell counts in 3D collagen scaffolds
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: 13
year: '2023'
...
---
_id: '13052'
abstract:
- lang: eng
text: Imaging of the immunological synapse (IS) between dendritic cells (DCs) and
T cells in suspension is hampered by suboptimal alignment of cell-cell contacts
along the vertical imaging plane. This requires optical sectioning that often
results in unsatisfactory resolution in time and space. Here, we present a workflow
where DCs and T cells are confined between a layer of glass and polydimethylsiloxane
(PDMS) that orients the cells along one, horizontal imaging plane, allowing for
fast en-face-imaging of the DC-T cell IS.
acknowledged_ssus:
- _id: Bio
- _id: NanoFab
- _id: M-Shop
acknowledgement: 'A.L. was funded by an Erwin Schrödinger postdoctoral fellowship
of the Austrian Science Fund (FWF, project number: J4542-B) and is an EMBO non-stipendiary
postdoctoral fellow. This work was supported by a European Research Council grant
ERC-CoG-72437 to M.S. We thank the Imaging & Optics facility, the Nanofabrication
facility, and the Miba Machine Shop of ISTA for their excellent support.'
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Alexander F
full_name: Leithner, Alexander F
id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87
last_name: Leithner
orcid: 0000-0002-1073-744X
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: 'Leithner AF, Merrin J, Sixt MK. En-Face Imaging of T Cell-Dendritic Cell Immunological
Synapses. In: Baldari C, Dustin M, eds. The Immune Synapse. Vol 2654. MIMB.
New York, NY: Springer Nature; 2023:137-147. doi:10.1007/978-1-0716-3135-5_9'
apa: 'Leithner, A. F., Merrin, J., & Sixt, M. K. (2023). En-Face Imaging of
T Cell-Dendritic Cell Immunological Synapses. In C. Baldari & M. Dustin (Eds.),
The Immune Synapse (Vol. 2654, pp. 137–147). New York, NY: Springer Nature.
https://doi.org/10.1007/978-1-0716-3135-5_9'
chicago: 'Leithner, Alexander F, Jack Merrin, and Michael K Sixt. “En-Face Imaging
of T Cell-Dendritic Cell Immunological Synapses.” In The Immune Synapse,
edited by Cosima Baldari and Michael Dustin, 2654:137–47. MIMB. New York, NY:
Springer Nature, 2023. https://doi.org/10.1007/978-1-0716-3135-5_9.'
ieee: 'A. F. Leithner, J. Merrin, and M. K. Sixt, “En-Face Imaging of T Cell-Dendritic
Cell Immunological Synapses,” in The Immune Synapse, vol. 2654, C. Baldari
and M. Dustin, Eds. New York, NY: Springer Nature, 2023, pp. 137–147.'
ista: 'Leithner AF, Merrin J, Sixt MK. 2023.En-Face Imaging of T Cell-Dendritic
Cell Immunological Synapses. In: The Immune Synapse. Methods in Molecular Biology,
vol. 2654, 137–147.'
mla: Leithner, Alexander F., et al. “En-Face Imaging of T Cell-Dendritic Cell Immunological
Synapses.” The Immune Synapse, edited by Cosima Baldari and Michael Dustin,
vol. 2654, Springer Nature, 2023, pp. 137–47, doi:10.1007/978-1-0716-3135-5_9.
short: A.F. Leithner, J. Merrin, M.K. Sixt, in:, C. Baldari, M. Dustin (Eds.), The
Immune Synapse, Springer Nature, New York, NY, 2023, pp. 137–147.
date_created: 2023-05-22T08:41:48Z
date_published: 2023-04-28T00:00:00Z
date_updated: 2025-04-14T07:42:07Z
day: '28'
department:
- _id: MiSi
- _id: NanoFab
doi: 10.1007/978-1-0716-3135-5_9
ec_funded: 1
editor:
- first_name: Cosima
full_name: Baldari, Cosima
last_name: Baldari
- first_name: Michael
full_name: Dustin, Michael
last_name: Dustin
external_id:
pmid:
- '37106180'
intvolume: ' 2654'
language:
- iso: eng
month: '04'
oa_version: None
page: 137-147
place: New York, NY
pmid: 1
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular Navigation Along Spatial Gradients
publication: The Immune Synapse
publication_identifier:
eisbn:
- '9781071631355'
eissn:
- 1940-6029
isbn:
- '9781071631348'
issn:
- 1064-3745
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: MIMB
status: public
title: En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2654
year: '2023'
...
---
_id: '13126'
abstract:
- lang: eng
text: Mapping the complex and dense arrangement of cells and their connectivity
in brain tissue demands nanoscale spatial resolution imaging. Super-resolution
optical microscopy excels at visualizing specific molecules and individual cells
but fails to provide tissue context. Here, we developed Comprehensive Analysis
of Tissues across Scales (CATS), a technology to densely map brain tissue architecture
from millimeter regional to nanometer synaptic scales in diverse chemically fixed
brain preparations, including rodent and human. CATS uses fixation-compatible
extracellular labeling and optical imaging, including stimulated emission depletion
or expansion microscopy, to comprehensively delineate cellular structures. It
enables three-dimensional reconstruction of single synapses and mapping of synaptic
connectivity by identification and analysis of putative synaptic cleft regions.
Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed
and quantified the synaptic input and output structure of identified neurons.
We furthermore demonstrate applicability to clinically derived human tissue samples,
including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing
the cellular architecture of brain tissue in health and disease.
acknowledged_ssus:
- _id: ScienComp
- _id: Bio
- _id: PreCl
- _id: LifeSc
- _id: M-Shop
- _id: E-Lib
acknowledgement: "We thank Jakob Vorlaufer, Nathalie Agudelo-Dueñas, Wiebke Jahr,
Andreas Wartak for microscope maintenance and troubleshooting, Caroline Kreuzinger,
Anna Freeman, and Irene Erber for technical assistance and Matthias Tomschik for
support with obtaining human samples. We gratefully acknowledge Eder Miguel for
setting up webKnossos and Marek Šuplata for computational support and hardware control.
We are grateful to Ryuichi Shigemoto and Bernd Bickel for generous support, and
Michael Sixt and Scott Boyd (Stanford University) for discussions and critical reading
of the manuscript. PSD95-HaloTag mice were kindly provided by Seth Grant (University
of Edinburgh). We acknowledge expert support by IST Austria’s scientific computing,
imaging and optics, preclinical, and lab support facilities, and by the Library
and Miba machine shop.\r\nWe gratefully acknowledge funding by the following sources:
\r\nAustrian Science Fund (FWF) grant I3600-B27 (JGD)\r\nAustrian Science Fund (FWF)
grant DK W1232 (JGD, JMM)\r\nAustrian Science Fund (FWF) grant Z 312-B27, Wittgenstein
award (PJ)\r\nAustrian Science Funds (FWF) projects I4685-B, I6565-B (SYNABS) and
DOC 33-B27 (RH)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022
(JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European
Research Council (ERC) grant 715508 – REVERSEAUTISM (GN)\r\nEuropean Union’s Horizon
2020 research and innovation programme, European Research Council (ERC) grant 692692
– GIANTSYN (PJ)\r\nMarie Skłodowska-Curie Actions Fellowship GA no. 665385 under
the EU Horizon 2020 program (JMM, JL)\r\nMarie Skłodowska-Curie Actions Individual
Fellowship 101026635 under the EU Horizon 2020 program (JFW)"
article_processing_charge: No
author:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Danzl JG. Research data for the publication “Imaging brain tissue architecture
across millimeter to nanometer scales.” 2023. doi:10.15479/AT:ISTA:13126
apa: Danzl, J. G. (2023). Research data for the publication “Imaging brain tissue
architecture across millimeter to nanometer scales.” Institute of Science and
Technology Austria. https://doi.org/10.15479/AT:ISTA:13126
chicago: Danzl, Johann G. “Research Data for the Publication ‘Imaging Brain Tissue
Architecture across Millimeter to Nanometer Scales.’” Institute of Science and
Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:13126.
ieee: J. G. Danzl, “Research data for the publication ‘Imaging brain tissue architecture
across millimeter to nanometer scales.’” Institute of Science and Technology Austria,
2023.
ista: Danzl JG. 2023. Research data for the publication ‘Imaging brain tissue architecture
across millimeter to nanometer scales’, Institute of Science and Technology Austria,
10.15479/AT:ISTA:13126.
mla: Danzl, Johann G. Research Data for the Publication “Imaging Brain Tissue
Architecture across Millimeter to Nanometer Scales.” Institute of Science
and Technology Austria, 2023, doi:10.15479/AT:ISTA:13126.
short: J.G. Danzl, (2023).
contributor:
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last_name: Lyudchik
- first_name: Philipp
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last_name: Velicky
orcid: 0000-0002-2340-7431
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id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
corr_author: '1'
date_created: 2023-06-07T07:15:12Z
date_published: 2023-08-04T00:00:00Z
date_updated: 2026-04-14T08:34:35Z
day: '04'
ddc:
- '610'
department:
- _id: JoDa
- _id: SaSi
- _id: GaNo
- _id: PeJo
- _id: Bio
- _id: RySh
doi: 10.15479/AT:ISTA:13126
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---
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acknowledgement: Thanks to Jesse Hansen for his suggestions on improving the abstract.
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ama: 'Schlögl A, Elefante S, Hodirnau V-V. Running Windows-applications on a Linux
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EuroCC; 2023:59-59.'
apa: 'Schlögl, A., Elefante, S., & Hodirnau, V.-V. (2023). Running Windows-applications
on a Linux HPC cluster using WINE. In ASHPC23 - Austrian-Slovenian HPC Meeting
2023 (pp. 59–59). Maribor, Slovenia: EuroCC.'
chicago: Schlögl, Alois, Stefano Elefante, and Victor-Valentin Hodirnau. “Running
Windows-Applications on a Linux HPC Cluster Using WINE.” In ASHPC23 - Austrian-Slovenian
HPC Meeting 2023, 59–59. EuroCC, 2023.
ieee: A. Schlögl, S. Elefante, and V.-V. Hodirnau, “Running Windows-applications
on a Linux HPC cluster using WINE,” in ASHPC23 - Austrian-Slovenian HPC Meeting
2023, Maribor, Slovenia, 2023, pp. 59–59.
ista: 'Schlögl A, Elefante S, Hodirnau V-V. 2023. Running Windows-applications on
a Linux HPC cluster using WINE. ASHPC23 - Austrian-Slovenian HPC Meeting 2023.
ASHPC: Austrian-Slovenian HPC Meeting, 59–59.'
mla: Schlögl, Alois, et al. “Running Windows-Applications on a Linux HPC Cluster
Using WINE.” ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, 2023,
pp. 59–59.
short: A. Schlögl, S. Elefante, V.-V. Hodirnau, in:, ASHPC23 - Austrian-Slovenian
HPC Meeting 2023, EuroCC, 2023, pp. 59–59.
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date_created: 2023-06-23T11:01:23Z
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...