---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19703'
abstract:
- lang: eng
text: An enlarged brain underlies the complex central nervous system of vertebrates.
The dramatic expansion of the brain that diverges its shape from the spinal cord
follows neural tube closure during embryonic development. Here, we show that this
differential deformation is encoded by a pre-pattern of tissue material properties
in chicken embryos. Using magnetic droplets and atomic force microscopy, we demonstrate
that the dorsal hindbrain is more fluid than the dorsal spinal cord, resulting
in a thinning versus a resisting response to increasing lumen pressure, respectively.
The dorsal hindbrain exhibits reduced apical actin and a disorganized laminin
matrix consistent with tissue fluidization. Blocking the activity of neural-crest-associated
matrix metalloproteinases inhibits hindbrain expansion. Transplanting dorsal hindbrain
cells to the spinal cord can locally create an expanded brain-like morphology
in some cases. Our findings raise questions in vertebrate head evolution and suggest
a general role of mechanical pre-patterning in sculpting epithelial tubes.
acknowledgement: 'We thank A. Dimitracopoulos, K. Kawaguchi, J. Vidigueira, B. Baum,
I. McLaren, D. St Johnston, and members of the Buckley, Scarpa, Steventon, Kawaguchi,
and Xiong labs for technical assistance and constructive feedback. We thank Ryan
Greenhalgh for methods developed to obtain fluidity values from AFM data. We thank
Nicola Lawrence, Alex Sossick, and Sargon Gross-Thebing from the Gurdon Institute
Imaging Facility for microscopy support. Funding: this work was supported by a Wellcome
Trust/Royal Society Sir Henry Dale Fellowship (215439/Z/19/Z) and UKRI-EPSRC Frontier
Research Grant (EP/X023761/1, originally selected as an ERC Starting Grant) to F.X.;
an ERC Consolidator Grant (772426), ERC Synergy Grant 101118729 UNFOLD, and Alexander
von Humboldt Professorship ( Alexander von Humboldt Foundation) to K.F.; and an
ERC Starting Grant (851288) to E.H.'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Susannah B.P.
full_name: Mclaren, Susannah B.P.
last_name: Mclaren
- first_name: Shi-lei
full_name: Xue, Shi-lei
id: 31D2C804-F248-11E8-B48F-1D18A9856A87
last_name: Xue
- first_name: Siyuan
full_name: Ding, Siyuan
last_name: Ding
- first_name: Alexander K.
full_name: Winkel, Alexander K.
last_name: Winkel
- first_name: Oscar
full_name: Baldwin, Oscar
last_name: Baldwin
- first_name: Shreya
full_name: Dwarakacherla, Shreya
last_name: Dwarakacherla
- first_name: Kristian
full_name: Franze, Kristian
last_name: Franze
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Fengzhu
full_name: Xiong, Fengzhu
last_name: Xiong
citation:
ama: Mclaren SBP, Xue S, Ding S, et al. Differential tissue deformability underlies
fluid pressure-driven shape divergence of the avian embryonic brain and spinal
cord. Developmental Cell. 2025;60(17):2237-2247.e4. doi:10.1016/j.devcel.2025.04.010
apa: Mclaren, S. B. P., Xue, S., Ding, S., Winkel, A. K., Baldwin, O., Dwarakacherla,
S., … Xiong, F. (2025). Differential tissue deformability underlies fluid pressure-driven
shape divergence of the avian embryonic brain and spinal cord. Developmental
Cell. Cell Press. https://doi.org/10.1016/j.devcel.2025.04.010
chicago: Mclaren, Susannah B.P., Shi-lei Xue, Siyuan Ding, Alexander K. Winkel,
Oscar Baldwin, Shreya Dwarakacherla, Kristian Franze, Edouard B Hannezo, and Fengzhu
Xiong. “Differential Tissue Deformability Underlies Fluid Pressure-Driven Shape
Divergence of the Avian Embryonic Brain and Spinal Cord.” Developmental Cell.
Cell Press, 2025. https://doi.org/10.1016/j.devcel.2025.04.010.
ieee: S. B. P. Mclaren et al., “Differential tissue deformability underlies
fluid pressure-driven shape divergence of the avian embryonic brain and spinal
cord,” Developmental Cell, vol. 60, no. 17. Cell Press, p. 2237–2247.e4,
2025.
ista: Mclaren SBP, Xue S, Ding S, Winkel AK, Baldwin O, Dwarakacherla S, Franze
K, Hannezo EB, Xiong F. 2025. Differential tissue deformability underlies fluid
pressure-driven shape divergence of the avian embryonic brain and spinal cord.
Developmental Cell. 60(17), 2237–2247.e4.
mla: Mclaren, Susannah B. P., et al. “Differential Tissue Deformability Underlies
Fluid Pressure-Driven Shape Divergence of the Avian Embryonic Brain and Spinal
Cord.” Developmental Cell, vol. 60, no. 17, Cell Press, 2025, p. 2237–2247.e4,
doi:10.1016/j.devcel.2025.04.010.
short: S.B.P. Mclaren, S. Xue, S. Ding, A.K. Winkel, O. Baldwin, S. Dwarakacherla,
K. Franze, E.B. Hannezo, F. Xiong, Developmental Cell 60 (2025) 2237–2247.e4.
date_created: 2025-05-18T22:02:50Z
date_published: 2025-09-08T00:00:00Z
date_updated: 2026-10-20T08:25:00Z
day: '08'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1016/j.devcel.2025.04.010
ec_funded: 1
external_id:
isi:
- '001570502100005'
pmid:
- '40347948'
file:
- access_level: open_access
checksum: 1ca6f0822c1cbd430686d5e2a4f96401
content_type: application/pdf
creator: dernst
date_created: 2025-12-29T13:45:05Z
date_updated: 2025-12-29T13:45:05Z
file_id: '20872'
file_name: 2025_DevelopmentalCell_McLaren.pdf
file_size: 12564806
relation: main_file
success: 1
file_date_updated: 2025-12-29T13:45:05Z
fulldoi: https://doi.org/10.1016/j.devcel.2025.04.010
has_accepted_license: '1'
intvolume: ' 60'
isi: 1
issue: '17'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 2237-2247.e4
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Developmental Cell
publication_identifier:
eissn:
- 1878-1551
issn:
- 1534-5807
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Differential tissue deformability underlies fluid pressure-driven shape divergence
of the avian embryonic brain and spinal cord
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 60
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20143'
abstract:
- lang: eng
text: Bacteria and archaea deploy diverse antiviral defense systems, many of which
remain mechanistically uncharacterized. Here, we characterize Kiwa, a widespread
two-component system composed of the transmembrane sensor KwaA and the DNA-binding
effector KwaB. Cryogenic electron microscopy (cryo-EM) analysis reveals that KwaA
and KwaB assemble into a large, membrane-associated supercomplex. Upon phage binding,
KwaA senses infection at the membrane, leading to KwaB binding of ejected phage
DNA and inhibition of replication and late transcription, without inducing host
cell death. Although KwaB can bind DNA independently, its antiviral activity requires
association with KwaA, suggesting spatial or conformational regulation. We show
that the phage-encoded DNA-mimic protein Gam directly binds and inhibits KwaB
but that co-expression with the Gam-targeted RecBCD system restores protection
by Kiwa. Our findings support a model in which Kiwa coordinates membrane-associated
detection of phage infection with downstream DNA binding by its effector, forming
a spatially coordinated antiviral mechanism.
acknowledgement: We thank Rotem Sorek (Weizmann Institute of Science) for the Lambda
Gam mutant and Ian Molineux (University of Texas) for T4Δgp2. We thank You Yu (Zhejiang
University-University of Edinburgh Institute) and J. De La Cruz (MSK) for assistance
with cryo-EM data collection and Lyuqin Zheng (MSK) for discussions on structural
analysis. We thank the Imaging and Microscopy Centre (IMC) at the University of
Southampton. This work was supported by Royal Society grant RGS\R2\222312 to F.L.N.;
Welch Foundation grant F-1938 and National Institutes of Health R35GM138348 to D.W.T.;
Wessex Medical Research Innovation grant AE06 to T.A.; and NIH grant GM145888 and
Maloris Foundation and Memorial Sloan-Kettering Core grant (P30-CA008748) to D.J.P.
In addition to MSKCC cryo-EM resources, some of this work was performed at the National
Center for CryoEM Access and Training (NCCAT) and the Simons Electron Microscopy
Center located at the New York Structural Biology Center, supported by the NIH Common
Fund Transformative High Resolution Cryo-Electron Microscopy program (U24 GM129539)
and Simons Foundation (SF349247) and NY State Assembly grants. This research used
NSLS-II MX X-ray User Resources (FMX) of the National Synchrotron Light Source II,
operated for the DOE Office of Science by Brookhaven National Laboratory under contract
no. DE-SC0012704. The Center for BioMolecular Structure (CBMS) is primarily supported
by the NIH, the National Institute of General Medical Sciences (NIGMS) through a
Center Core P30 Grant (P30GM133893), and by the DOE Office of Biological and Environmental
Research (KP1605010). R.K. and E.V.K. are supported by the Intramural Research Program
of the NIH (National Library of Medicine).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Zhiying
full_name: Zhang, Zhiying
last_name: Zhang
- first_name: Thomas C.
full_name: Todeschini, Thomas C.
last_name: Todeschini
- first_name: Yi
full_name: Wu, Yi
last_name: Wu
- first_name: Roman
full_name: Kogay, Roman
last_name: Kogay
- first_name: Ameena
full_name: Naji, Ameena
last_name: Naji
- first_name: Joaquin
full_name: Cardenas Rodriguez, Joaquin
last_name: Cardenas Rodriguez
- first_name: Rupavidhya
full_name: Mondi, Rupavidhya
last_name: Mondi
- first_name: Daniel
full_name: Kaganovich, Daniel
last_name: Kaganovich
- first_name: David W.
full_name: Taylor, David W.
last_name: Taylor
- first_name: Jack Peter Kelly
full_name: Bravo, Jack Peter Kelly
id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e
last_name: Bravo
orcid: 0000-0003-0456-0753
- first_name: Marianna
full_name: Teplova, Marianna
last_name: Teplova
- first_name: Triana
full_name: Amen, Triana
last_name: Amen
- first_name: Eugene
full_name: Koonin, Eugene
last_name: Koonin
- first_name: Dinshaw J.
full_name: Patel, Dinshaw J.
last_name: Patel
- first_name: Franklin L.
full_name: Nobrega, Franklin L.
last_name: Nobrega
citation:
ama: Zhang Z, Todeschini TC, Wu Y, et al. Kiwa is a membrane-embedded defense supercomplex
activated at phage attachment sites. Cell. 2025;188(21):5862-5877.e23.
doi:10.1016/j.cell.2025.07.002
apa: Zhang, Z., Todeschini, T. C., Wu, Y., Kogay, R., Naji, A., Cardenas Rodriguez,
J., … Nobrega, F. L. (2025). Kiwa is a membrane-embedded defense supercomplex
activated at phage attachment sites. Cell. Cell Press. https://doi.org/10.1016/j.cell.2025.07.002
chicago: Zhang, Zhiying, Thomas C. Todeschini, Yi Wu, Roman Kogay, Ameena Naji,
Joaquin Cardenas Rodriguez, Rupavidhya Mondi, et al. “Kiwa Is a Membrane-Embedded
Defense Supercomplex Activated at Phage Attachment Sites.” Cell. Cell Press,
2025. https://doi.org/10.1016/j.cell.2025.07.002.
ieee: Z. Zhang et al., “Kiwa is a membrane-embedded defense supercomplex
activated at phage attachment sites,” Cell, vol. 188, no. 21. Cell Press,
p. 5862–5877.e23, 2025.
ista: Zhang Z, Todeschini TC, Wu Y, Kogay R, Naji A, Cardenas Rodriguez J, Mondi
R, Kaganovich D, Taylor DW, Bravo JPK, Teplova M, Amen T, Koonin E, Patel DJ,
Nobrega FL. 2025. Kiwa is a membrane-embedded defense supercomplex activated at
phage attachment sites. Cell. 188(21), 5862–5877.e23.
mla: Zhang, Zhiying, et al. “Kiwa Is a Membrane-Embedded Defense Supercomplex Activated
at Phage Attachment Sites.” Cell, vol. 188, no. 21, Cell Press, 2025, p.
5862–5877.e23, doi:10.1016/j.cell.2025.07.002.
short: Z. Zhang, T.C. Todeschini, Y. Wu, R. Kogay, A. Naji, J. Cardenas Rodriguez,
R. Mondi, D. Kaganovich, D.W. Taylor, J.P.K. Bravo, M. Teplova, T. Amen, E. Koonin,
D.J. Patel, F.L. Nobrega, Cell 188 (2025) 5862–5877.e23.
date_created: 2025-08-07T05:00:04Z
date_published: 2025-10-16T00:00:00Z
date_updated: 2026-10-20T08:23:33Z
day: '16'
ddc:
- '570'
department:
- _id: JaBr
doi: 10.1016/j.cell.2025.07.002
external_id:
isi:
- '001603560700005'
pmid:
- '40730155'
file:
- access_level: open_access
checksum: b944de5fbd7455f58e1ff338ad352239
content_type: application/pdf
creator: dernst
date_created: 2025-12-29T14:15:25Z
date_updated: 2025-12-29T14:15:25Z
file_id: '20875'
file_name: 2025_Cell_Zhang.pdf
file_size: 32104588
relation: main_file
success: 1
file_date_updated: 2025-12-29T14:15:25Z
fulldoi: https://doi.org/10.1016/j.cell.2025.07.002
has_accepted_license: '1'
intvolume: ' 188'
isi: 1
issue: '21'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 5862-5877.e23
pmid: 1
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Kiwa is a membrane-embedded defense supercomplex activated at phage attachment
sites
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 188
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19846'
abstract:
- lang: eng
text: The Ca2+-release-activated Ca2+ (CRAC) channel Orai1 is activated by interaction
with the Ca2+ sensor Stromal Interaction Molecule 1 (STIM1). Owing to the lack
of structurally resolved Orai1/STIM1 complexes, the impact of their coupling on
individual Orai1 transmembrane domain (TM) movements is unclear. This study investigates
STIM1-independent and STIM1-dependent Orai1-TM dynamics using photocrosslinking
unnatural amino acids (UAAs) at each individual TM position. We primarily identify
CRAC-channel-like currents directly after UAA incorporation or additional UV-light
irradiation at TM3 sites that interface with non-pore-lining TMs. Using UAAs combined
with conventional site-directed mutagenesis and molecular dynamics simulations,
we discover that pore opening involves a widening of interfaces formed by TM3
with non-pore-lining TMs. Orai1 mutants with a UAA in TM3 exhibit weaker STIM1-induced
activation after UV exposure, possibly caused by a restricted widening of non-pore-lining
TM interfaces. We demonstrate that photocrosslinking UAAs are excellent tools
for improving our understanding of key determinants and ion channel dynamics modulating
pore opening.
acknowledgement: We thank S. Buchegger for excellent technical assistance. This research
was funded by the Austrian Science Fund (FWF) projects https://doi.org/10.55776/P32851,
https://doi.org/10.55776/P35900, and https://doi.org/10.55776/P36202 to I.D. and
https://doi.org/10.55776/PAT6871323 to A.T. N.M. is funded within the DOC program
of the OeAW (Austrian Academy of Science). For open access purposes, the author
has applied a CC BY public copyright license to any author-accepted manuscript version
arising from this submission.
article_number: '102623'
article_processing_charge: Yes
article_type: original
author:
- first_name: Hadil
full_name: Najjar, Hadil
last_name: Najjar
- first_name: Sarah
full_name: Weiß, Sarah
last_name: Weiß
- first_name: Ferdinand
full_name: Horvath, Ferdinand
id: b0dc7f61-21a3-11ef-a9b4-e6ab1aa6f21e
last_name: Horvath
- first_name: Valentina
full_name: Hopl, Valentina
last_name: Hopl
- first_name: Adéla
full_name: Tiffner, Adéla
last_name: Tiffner
- first_name: Lorenz
full_name: Höbarth, Lorenz
last_name: Höbarth
- first_name: Julia
full_name: Söllner, Julia
last_name: Söllner
- first_name: Maximilian
full_name: Fröhlich, Maximilian
last_name: Fröhlich
- first_name: Magdalena
full_name: Prantl, Magdalena
last_name: Prantl
- first_name: Nora
full_name: Müller, Nora
last_name: Müller
- first_name: Yuliia
full_name: Nazarenko, Yuliia
last_name: Nazarenko
- first_name: Selina
full_name: Harant, Selina
last_name: Harant
- first_name: Lukas
full_name: Weissenböck, Lukas
last_name: Weissenböck
- first_name: Herwig
full_name: Grabmayr, Herwig
last_name: Grabmayr
- first_name: Matthias
full_name: Sallinger, Matthias
last_name: Sallinger
- first_name: Lena
full_name: Maltan, Lena
last_name: Maltan
- first_name: Linda V.
full_name: Echefu, Linda V.
last_name: Echefu
- first_name: Tamara
full_name: Radiskovic, Tamara
last_name: Radiskovic
- first_name: Melanie
full_name: Leopold, Melanie
last_name: Leopold
- first_name: Sonja
full_name: Lindinger, Sonja
last_name: Lindinger
- first_name: Christina
full_name: Humer, Christina
last_name: Humer
- first_name: Carmen
full_name: Höglinger, Carmen
last_name: Höglinger
- first_name: Heinrich
full_name: Krobath, Heinrich
last_name: Krobath
- first_name: Thomas
full_name: Renger, Thomas
last_name: Renger
- first_name: Isabella
full_name: Derler, Isabella
last_name: Derler
citation:
ama: Najjar H, Weiß S, Horvath F, et al. STIM1-induced widening of non-pore-lining
TM interfaces is crucial for Orai1 pore opening. Cell Reports Physical Science.
2025;6(6). doi:10.1016/j.xcrp.2025.102623
apa: Najjar, H., Weiß, S., Horvath, F., Hopl, V., Tiffner, A., Höbarth, L., … Derler,
I. (2025). STIM1-induced widening of non-pore-lining TM interfaces is crucial
for Orai1 pore opening. Cell Reports Physical Science. Cell Press. https://doi.org/10.1016/j.xcrp.2025.102623
chicago: Najjar, Hadil, Sarah Weiß, Ferdinand Horvath, Valentina Hopl, Adéla Tiffner,
Lorenz Höbarth, Julia Söllner, et al. “STIM1-Induced Widening of Non-Pore-Lining
TM Interfaces Is Crucial for Orai1 Pore Opening.” Cell Reports Physical Science.
Cell Press, 2025. https://doi.org/10.1016/j.xcrp.2025.102623.
ieee: H. Najjar et al., “STIM1-induced widening of non-pore-lining TM interfaces
is crucial for Orai1 pore opening,” Cell Reports Physical Science, vol.
6, no. 6. Cell Press, 2025.
ista: Najjar H, Weiß S, Horvath F, Hopl V, Tiffner A, Höbarth L, Söllner J, Fröhlich
M, Prantl M, Müller N, Nazarenko Y, Harant S, Weissenböck L, Grabmayr H, Sallinger
M, Maltan L, Echefu LV, Radiskovic T, Leopold M, Lindinger S, Humer C, Höglinger
C, Krobath H, Renger T, Derler I. 2025. STIM1-induced widening of non-pore-lining
TM interfaces is crucial for Orai1 pore opening. Cell Reports Physical Science.
6(6), 102623.
mla: Najjar, Hadil, et al. “STIM1-Induced Widening of Non-Pore-Lining TM Interfaces
Is Crucial for Orai1 Pore Opening.” Cell Reports Physical Science, vol.
6, no. 6, 102623, Cell Press, 2025, doi:10.1016/j.xcrp.2025.102623.
short: H. Najjar, S. Weiß, F. Horvath, V. Hopl, A. Tiffner, L. Höbarth, J. Söllner,
M. Fröhlich, M. Prantl, N. Müller, Y. Nazarenko, S. Harant, L. Weissenböck, H.
Grabmayr, M. Sallinger, L. Maltan, L.V. Echefu, T. Radiskovic, M. Leopold, S.
Lindinger, C. Humer, C. Höglinger, H. Krobath, T. Renger, I. Derler, Cell Reports
Physical Science 6 (2025).
date_created: 2025-06-15T22:01:31Z
date_published: 2025-06-18T00:00:00Z
date_updated: 2026-10-20T08:25:34Z
day: '18'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1016/j.xcrp.2025.102623
external_id:
isi:
- '001516570500009'
file:
- access_level: open_access
checksum: 37ff7c396f966d0ec363e4691d63d402
content_type: application/pdf
creator: dernst
date_created: 2025-06-23T10:20:22Z
date_updated: 2025-06-23T10:20:22Z
file_id: '19868'
file_name: 2025_CellReportsPhysicalScience_Najjar.pdf
file_size: 9771117
relation: main_file
success: 1
file_date_updated: 2025-06-23T10:20:22Z
fulldoi: https://doi.org/10.1016/j.xcrp.2025.102623
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Cell Reports Physical Science
publication_identifier:
eissn:
- 2666-3864
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: STIM1-induced widening of non-pore-lining TM interfaces is crucial for Orai1
pore opening
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: 6
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '20029'
abstract:
- lang: eng
text: Vacuolar acidification is crucial for the homeostasis of intracellular pH
and the recycling of proteins and nutrients in cells, thereby playing important
roles in various physiological processes related to vacuolar function. The key
factors regulating vacuolar acidification and underlying mechanisms remain unclear.
Here, we report that Arabidopsis phospholipase Dζ2 (PLDζ2) promotes the acidification
of the vacuolar lumen to stimulate autophagic degradation under phosphorus deficiency.
The pldζ2 mutant massively accumulates autophagic structures while exhibiting
premature leaf senescence under nutrient starvation. Impaired autophagic flux,
lytic vacuole morphology, and lytic degradation in pldζ2 indicate that PLDζ2 regulates
autophagy by affecting the vacuolar function. PLDζ2 locates in both tonoplast
and cytoplasm. Genetic, structural, and biochemical studies demonstrate that PLDζ2
directly interacts with vacuolar-type ATPase (V-ATPase) subunit D (VATD) to promote
vacuolar acidification and autophagy under phosphorus starvation. These findings
reveal the importance of V-ATPase and vacuolar pH in autophagic activity and provide
clues in elucidating the regulatory mechanism of vacuolar acidification.
acknowledgement: The study was supported by National Natural Science Foundation of
China (NSFC, 92354301, 32230011, 32200274, and 91954206). The computations were
run on the Siyuan-1 cluster supported by the Center for High-Performance Computing
at Shanghai Jiao Tong University.
article_number: '116024'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Bin
full_name: Guan, Bin
id: 56aad729-cca2-11ed-a45a-9b4138991a48
last_name: Guan
- first_name: Ke Xuan
full_name: Xie, Ke Xuan
last_name: Xie
- first_name: Xin Qiao
full_name: Du, Xin Qiao
last_name: Du
- first_name: Yu Xuan
full_name: Bai, Yu Xuan
last_name: Bai
- first_name: Peng Chao
full_name: Hao, Peng Chao
last_name: Hao
- first_name: Wen Hui
full_name: Lin, Wen Hui
last_name: Lin
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Hong Wei
full_name: Xue, Hong Wei
last_name: Xue
citation:
ama: Guan B, Xie KX, Du XQ, et al. Arabidopsis phospholipase Dζ2 facilitates vacuolar
acidification and autophagy under phosphorus starvation by interacting with VATD.
Cell Reports. 2025;44(7). doi:10.1016/j.celrep.2025.116024
apa: Guan, B., Xie, K. X., Du, X. Q., Bai, Y. X., Hao, P. C., Lin, W. H., … Xue,
H. W. (2025). Arabidopsis phospholipase Dζ2 facilitates vacuolar acidification
and autophagy under phosphorus starvation by interacting with VATD. Cell Reports.
Cell Press. https://doi.org/10.1016/j.celrep.2025.116024
chicago: Guan, Bin, Ke Xuan Xie, Xin Qiao Du, Yu Xuan Bai, Peng Chao Hao, Wen Hui
Lin, Jiří Friml, and Hong Wei Xue. “Arabidopsis Phospholipase Dζ2 Facilitates
Vacuolar Acidification and Autophagy under Phosphorus Starvation by Interacting
with VATD.” Cell Reports. Cell Press, 2025. https://doi.org/10.1016/j.celrep.2025.116024.
ieee: B. Guan et al., “Arabidopsis phospholipase Dζ2 facilitates vacuolar
acidification and autophagy under phosphorus starvation by interacting with VATD,”
Cell Reports, vol. 44, no. 7. Cell Press, 2025.
ista: Guan B, Xie KX, Du XQ, Bai YX, Hao PC, Lin WH, Friml J, Xue HW. 2025. Arabidopsis
phospholipase Dζ2 facilitates vacuolar acidification and autophagy under phosphorus
starvation by interacting with VATD. Cell Reports. 44(7), 116024.
mla: Guan, Bin, et al. “Arabidopsis Phospholipase Dζ2 Facilitates Vacuolar Acidification
and Autophagy under Phosphorus Starvation by Interacting with VATD.” Cell Reports,
vol. 44, no. 7, 116024, Cell Press, 2025, doi:10.1016/j.celrep.2025.116024.
short: B. Guan, K.X. Xie, X.Q. Du, Y.X. Bai, P.C. Hao, W.H. Lin, J. Friml, H.W.
Xue, Cell Reports 44 (2025).
date_created: 2025-07-20T22:02:01Z
date_published: 2025-07-22T00:00:00Z
date_updated: 2026-10-20T08:22:53Z
day: '22'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.celrep.2025.116024
external_id:
isi:
- '001533244800001'
pmid:
- '40668679'
file:
- access_level: open_access
checksum: ee03deee47a084b0295251dc49470ad4
content_type: application/pdf
creator: dernst
date_created: 2025-07-22T08:52:17Z
date_updated: 2025-07-22T08:52:17Z
file_id: '20067'
file_name: 2025_CellReports_Guan.pdf
file_size: 37708120
relation: main_file
success: 1
file_date_updated: 2025-07-22T08:52:17Z
fulldoi: https://doi.org/10.1016/j.celrep.2025.116024
has_accepted_license: '1'
intvolume: ' 44'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
issn:
- 2639-1856
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Arabidopsis phospholipase Dζ2 facilitates vacuolar acidification and autophagy
under phosphorus starvation by interacting with VATD
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 44
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '20116'
abstract:
- lang: eng
text: Auxin regulates various aspects of plant growth and development by modulating
the transcription of target genes through the degradation of auxin/indole-3-acetic
acid (Aux/IAA) repressors via the 26S proteasome. Proteasome regulator 1 (PTRE1),
a positive regulator of proteasome activity, has been implicated in auxin-mediated
proteasome suppression; however, the mechanism by which auxin modulates PTRE1
function remains unclear. Here, we demonstrate that auxin promotes the interaction
between germin-like protein 1 (GLP1) and PTRE1, facilitating PTRE1 retention at
the plasma membrane. The relocation of PTRE1 results in reduced nuclear 26S proteasome
activity, and thus the attenuated Aux/IAA degradation and altered Aux/IAA homeostasis,
ultimately resulting in suppressed auxin-mediated transcriptional regulation.
Our findings uncover a previously uncharacterized regulatory axis in auxin signaling
that controls Aux/IAA protein stability, functioning alongside the TIR1- and TRANSMEMBRANE
KINASE 1 (TMK1)-mediated pathways, and highlight the coordination of auxin signaling
from the cell surface to the nucleus via auxin-induced PTRE1 relocation, which
fine-tunes Aux/IAA protein homeostasis and auxin responses.
acknowledgement: The study was supported by the National Natural Science Foundation
of China (NSFC; 32230011, 91954206, and 31721001). We thank Dr. Deli Lin (Shanghai
Jiao Tong University) for kind help with the laser confocal microscope observation
and the Arabidopsis Biological Resource Center (ABRC) for providing T-DNA insertional
mutants.
article_number: '116056'
article_processing_charge: Yes
article_type: original
author:
- first_name: Faqing
full_name: Xu, Faqing
last_name: Xu
- first_name: Yongqiang
full_name: Yu, Yongqiang
last_name: Yu
- first_name: Bin
full_name: Guan, Bin
id: 56aad729-cca2-11ed-a45a-9b4138991a48
last_name: Guan
- first_name: Tongda
full_name: Xu, Tongda
last_name: Xu
- first_name: Zhihong
full_name: Xu, Zhihong
last_name: Xu
- first_name: Hongwei
full_name: Xue, Hongwei
last_name: Xue
citation:
ama: Xu F, Yu Y, Guan B, Xu T, Xu Z, Xue H. Germin-like protein 1 interacts with
proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA homeostasis.
Cell Reports. 2025;44(8). doi:10.1016/j.celrep.2025.116056
apa: Xu, F., Yu, Y., Guan, B., Xu, T., Xu, Z., & Xue, H. (2025). Germin-like
protein 1 interacts with proteasome regulator 1 to regulate auxin signaling by
controlling Aux/IAA homeostasis. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2025.116056
chicago: Xu, Faqing, Yongqiang Yu, Bin Guan, Tongda Xu, Zhihong Xu, and Hongwei
Xue. “Germin-like Protein 1 Interacts with Proteasome Regulator 1 to Regulate
Auxin Signaling by Controlling Aux/IAA Homeostasis.” Cell Reports. Cell
Press, 2025. https://doi.org/10.1016/j.celrep.2025.116056.
ieee: F. Xu, Y. Yu, B. Guan, T. Xu, Z. Xu, and H. Xue, “Germin-like protein 1 interacts
with proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA
homeostasis,” Cell Reports, vol. 44, no. 8. Cell Press, 2025.
ista: Xu F, Yu Y, Guan B, Xu T, Xu Z, Xue H. 2025. Germin-like protein 1 interacts
with proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA
homeostasis. Cell Reports. 44(8), 116056.
mla: Xu, Faqing, et al. “Germin-like Protein 1 Interacts with Proteasome Regulator
1 to Regulate Auxin Signaling by Controlling Aux/IAA Homeostasis.” Cell Reports,
vol. 44, no. 8, 116056, Cell Press, 2025, doi:10.1016/j.celrep.2025.116056.
short: F. Xu, Y. Yu, B. Guan, T. Xu, Z. Xu, H. Xue, Cell Reports 44 (2025).
date_created: 2025-08-04T13:39:11Z
date_published: 2025-07-24T00:00:00Z
date_updated: 2026-10-20T08:23:15Z
day: '24'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.celrep.2025.116056
external_id:
isi:
- '001542038500001'
pmid:
- '40714631'
file:
- access_level: open_access
checksum: 3c43e040a4a7a65ec67ae1d2bb81261a
content_type: application/pdf
creator: dernst
date_created: 2025-08-05T06:15:09Z
date_updated: 2025-08-05T06:15:09Z
file_id: '20120'
file_name: 2025_CellReports_Xu.pdf
file_size: 24178018
relation: main_file
success: 1
file_date_updated: 2025-08-05T06:15:09Z
fulldoi: https://doi.org/10.1016/j.celrep.2025.116056
has_accepted_license: '1'
intvolume: ' 44'
isi: 1
issue: '8'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Germin-like protein 1 interacts with proteasome regulator 1 to regulate auxin
signaling by controlling Aux/IAA homeostasis
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 44
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20374'
abstract:
- lang: eng
text: Pioneer transcription factors (TFs) engage chromatinized DNA motifs. However,
it is unclear how the resultant TF-nucleosome complexes are decoded by co-factors.
In humans, the TF p53 regulates cell-cycle progression, apoptosis, and the DNA
damage response, with a large fraction of p53-bound sites residing in nucleosome-harboring
inaccessible chromatin. We examined the interaction of chromatin-bound p53 with
co-factors belonging to the ubiquitin proteasome system (UPS). At two distinct
motif locations on the nucleosome (super-helical location [SHL]−5.7 and SHL+5.9),
the E3 ubiquitin ligase E6-E6AP was unable to bind nucleosome-engaged p53. The
deubiquitinase USP7, on the other hand, readily engages nucleosome-bound p53 in
vitro and in cells. A corresponding cryo-electron microscopy (cryo-EM) structure
shows USP7 engaged with p53 and nucleosomes. Our work illustrates how chromatin
imposes a co-factor-selective barrier for p53 interactors, whereby flexibly tethered
interaction domains of co-factors and TFs govern compatibility between co-factors,
TFs, and chromatin.
acknowledgement: We thank M. Schütz for laboratory management, organization, and assistance
with manuscript editing. We are grateful to all Thomä and Schübeler lab members.
We thank Ulrich Hassiepen from Novartis for his support and insightful discussions
on the kinetic analysis. This work was supported by funding from the European Research
Council (ERC), under the European Union’s H2020 research program (NucEM, grant no.
884331); the Swiss National Science Foundation (SNF, grant no. 310030_301206 and
310030_214852); Krebsforschung (KFS, grant no. KFS-5933-08-2023); Novartis Research
Foundation (to N.H.T.); the Novartis Freenovation (grant no. FN23-0000000514 to
C.R.S.); the National Health and Medical Research Council CJ Martin Fellowship (APP1148380);
the EU Horizon 2020 Research and Innovation Program under the Marie Sklodowska-Curie
grant (grant no. 748760); the South Australian immunoGENomics Cancer Institute grant
funding from the Australian Government; and the Sylvia and Charles Viertel Charitable
Foundation Senior Medical Research Fellowship (to L.I.).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Deyasini
full_name: Chakraborty, Deyasini
last_name: Chakraborty
- first_name: Colby R.
full_name: Sandate, Colby R.
last_name: Sandate
- first_name: Luke
full_name: Isbel, Luke
last_name: Isbel
- first_name: Georg
full_name: Kempf, Georg
last_name: Kempf
- first_name: Joscha
full_name: Weiss, Joscha
last_name: Weiss
- first_name: Simone
full_name: Cavadini, Simone
last_name: Cavadini
- first_name: Lukas
full_name: Kater, Lukas
last_name: Kater
- first_name: Jan
full_name: Seebacher, Jan
last_name: Seebacher
- first_name: Zuzanna
full_name: Kozicka, Zuzanna
last_name: Kozicka
- first_name: Lisa
full_name: Stoos, Lisa
last_name: Stoos
- first_name: Ralph S.
full_name: Grand, Ralph S.
last_name: Grand
- first_name: Dirk
full_name: Schübeler, Dirk
last_name: Schübeler
- first_name: Alicia
full_name: Michael, Alicia
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
orcid: 0000-0002-6080-839X
- first_name: Nicolas H.
full_name: Thomä, Nicolas H.
last_name: Thomä
citation:
ama: Chakraborty D, Sandate CR, Isbel L, et al. Nucleosomes specify co-factor access
to p53. Molecular Cell. 2025;85(15):2919-2936.e12. doi:10.1016/j.molcel.2025.06.027
apa: Chakraborty, D., Sandate, C. R., Isbel, L., Kempf, G., Weiss, J., Cavadini,
S., … Thomä, N. H. (2025). Nucleosomes specify co-factor access to p53. Molecular
Cell. Cell Press. https://doi.org/10.1016/j.molcel.2025.06.027
chicago: Chakraborty, Deyasini, Colby R. Sandate, Luke Isbel, Georg Kempf, Joscha
Weiss, Simone Cavadini, Lukas Kater, et al. “Nucleosomes Specify Co-Factor Access
to P53.” Molecular Cell. Cell Press, 2025. https://doi.org/10.1016/j.molcel.2025.06.027.
ieee: D. Chakraborty et al., “Nucleosomes specify co-factor access to p53,”
Molecular Cell, vol. 85, no. 15. Cell Press, p. 2919–2936.e12, 2025.
ista: Chakraborty D, Sandate CR, Isbel L, Kempf G, Weiss J, Cavadini S, Kater L,
Seebacher J, Kozicka Z, Stoos L, Grand RS, Schübeler D, Michael AK, Thomä NH.
2025. Nucleosomes specify co-factor access to p53. Molecular Cell. 85(15), 2919–2936.e12.
mla: Chakraborty, Deyasini, et al. “Nucleosomes Specify Co-Factor Access to P53.”
Molecular Cell, vol. 85, no. 15, Cell Press, 2025, p. 2919–2936.e12, doi:10.1016/j.molcel.2025.06.027.
short: D. Chakraborty, C.R. Sandate, L. Isbel, G. Kempf, J. Weiss, S. Cavadini,
L. Kater, J. Seebacher, Z. Kozicka, L. Stoos, R.S. Grand, D. Schübeler, A.K. Michael,
N.H. Thomä, Molecular Cell 85 (2025) 2919–2936.e12.
date_created: 2025-09-23T08:56:13Z
date_published: 2025-08-07T00:00:00Z
date_updated: 2026-10-20T08:50:29Z
day: '07'
ddc:
- '570'
department:
- _id: AlMi
doi: 10.1016/j.molcel.2025.06.027
file:
- access_level: open_access
checksum: e60390ca629b350af3221d4718ca6534
content_type: application/pdf
creator: dernst
date_created: 2025-09-24T07:54:03Z
date_updated: 2025-09-24T07:54:03Z
file_id: '20386'
file_name: 2025_MolecularCell_Chakraborty.pdf
file_size: 41813494
relation: main_file
success: 1
file_date_updated: 2025-09-24T07:54:03Z
fulldoi: https://doi.org/10.1016/j.molcel.2025.06.027
has_accepted_license: '1'
intvolume: ' 85'
issue: '15'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 2919-2936.e12
publication: Molecular Cell
publication_identifier:
issn:
- 1097-2765
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nucleosomes specify co-factor access to p53
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: 85
year: '2025'
...
---
OA_type: closed access
_id: '19594'
abstract:
- lang: eng
text: In this issue of Developmental Cell, Lee et al. identify a pivotal role for
glutathione (GSH) in plant regeneration, a vital biological process enabling plants
to regrow tissues and organs after injury. Applying single-cell RNA sequencing
(scRNA-seq) and live imaging, the authors demonstrate that GSH, released upon
tissue damage, accelerates cell-cycle transitions, particularly shortening the
G1 phase, thereby facilitating efficient organ regeneration.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: 'Benková E. Unlocking plant regeneration: The role for glutathione. Developmental
Cell. 2025;60(8):1137-1139. doi:10.1016/j.devcel.2025.03.012'
apa: 'Benková, E. (2025). Unlocking plant regeneration: The role for glutathione.
Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2025.03.012'
chicago: 'Benková, Eva. “Unlocking Plant Regeneration: The Role for Glutathione.”
Developmental Cell. Cell Press, 2025. https://doi.org/10.1016/j.devcel.2025.03.012.'
ieee: 'E. Benková, “Unlocking plant regeneration: The role for glutathione,” Developmental
Cell, vol. 60, no. 8. Cell Press, pp. 1137–1139, 2025.'
ista: 'Benková E. 2025. Unlocking plant regeneration: The role for glutathione.
Developmental Cell. 60(8), 1137–1139.'
mla: 'Benková, Eva. “Unlocking Plant Regeneration: The Role for Glutathione.” Developmental
Cell, vol. 60, no. 8, Cell Press, 2025, pp. 1137–39, doi:10.1016/j.devcel.2025.03.012.'
short: E. Benková, Developmental Cell 60 (2025) 1137–1139.
corr_author: '1'
date_created: 2025-04-20T22:01:28Z
date_published: 2025-04-21T00:00:00Z
date_updated: 2026-10-20T08:24:38Z
day: '21'
department:
- _id: EvBe
doi: 10.1016/j.devcel.2025.03.012
external_id:
isi:
- '001477400800001'
pmid:
- '40262524'
fulldoi: https://doi.org/10.1016/j.devcel.2025.03.012
intvolume: ' 60'
isi: 1
issue: '8'
language:
- iso: eng
month: '04'
oa_version: None
page: 1137-1139
pmid: 1
publication: Developmental Cell
publication_identifier:
eissn:
- 1878-1551
issn:
- 1534-5807
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Unlocking plant regeneration: The role for glutathione'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 60
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19795'
abstract:
- lang: eng
text: Super-resolution microscopy often entails long acquisition times of minutes
to hours. Since drifts during the acquisition adversely affect data quality, active
sample stabilization is commonly used for some of these techniques to reach their
full potential. Although drifts in the lateral plane can often be corrected after
acquisition, this is not always possible or may come with drawbacks. Therefore,
it is appealing to stabilize sample position in three dimensions (3D) during acquisition.
Various schemes for active sample stabilization have been demonstrated previously,
with some reaching sub-nanometer stability in 3D. Here, we present a scheme for
active drift correction that delivers the nanometer-scale 3D stability demanded
by state-of-the-art super-resolution techniques and is straightforward to implement
compared to previous schemes capable of reaching this level of stabilization precision.
Using a refined algorithm that can handle various types of reference structure,
without sparse signal peaks being mandatory, we stabilized sample position to
∼1 nm in 3D using objective lenses both with high and low numerical aperture.
Our implementation requires only the addition of a simple widefield imaging path
and we provide an open-source control software with graphical user interface to
facilitate easy adoption of the module. Finally, we demonstrate how this has the
potential to enhance data collection for diffraction-limited and super-resolution
imaging techniques using single-molecule localization microscopy and cryo-confocal
imaging as showcases.
acknowledged_ssus:
- _id: M-Shop
- _id: EM-Fac
- _id: LifeSc
acknowledgement: 'We acknowledge expert support by ISTA’s scientific service units,
including the Miba Machine Shop, the Electron Microscopy Facility, and the Lab Support
Facility. This work has been made possible in part by CZI grant DAF2021-234754 and
grant DOI: https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative
DAF, an advised fund of Silicon Valley Community Foundation (funder DOI: https://doi.org/10.13039/100014989)
(F.K.M.S. and J.G.D.). We further gratefully acknowledge funding by the following
sources: Austrian Science Fund (FWF) grant DK W1232 (M.R.T. and J.G.D.); Austrian
Academy of Sciences DOC fellowship 26137 (M.R.T.); Marie Skłodowska-Curie Actions
Fellowship GA no. 665385 under the EU Horizon 2020 program (J.L.); ISTA postdoctoral
fellowship IST fellow (A.W.); and Human Frontier Science Program postdoctoral fellowship
LT000557/2018 (W.J.).'
article_number: '100211'
article_processing_charge: Yes
article_type: original
author:
- first_name: Jakob
full_name: Vorlaufer, Jakob
id: 937696FA-C996-11E9-8C7C-CF13E6697425
last_name: Vorlaufer
orcid: 0009-0000-7590-3501
- first_name: Nikolai
full_name: Semenov, Nikolai
id: e64d39c7-72ef-11ef-b75a-ee3046860d1b
last_name: Semenov
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Manjunath
full_name: Javoor, Manjunath
id: 305ab18b-dc7d-11ea-9b2f-b58195228ea2
last_name: Javoor
orcid: 0000-0003-2311-2112
- first_name: Bettina
full_name: Zens, Bettina
id: 45FD126C-F248-11E8-B48F-1D18A9856A87
last_name: Zens
orcid: 0000-0002-9561-1239
- first_name: Nathalie
full_name: Agudelo Duenas, Nathalie
id: 40E7F008-F248-11E8-B48F-1D18A9856A87
last_name: Agudelo Duenas
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- first_name: Marek
full_name: Suplata, Marek
id: EE8452B8-C26A-11E9-B157-E80CE6697425
last_name: Suplata
- first_name: Wiebke
full_name: Jahr, Wiebke
id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
last_name: Jahr
orcid: 0000-0003-0201-2315
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- first_name: Andreas
full_name: Wartak, Andreas
id: 60aaa06c-3de5-11eb-9e53-baa88e955dcb
last_name: Wartak
- first_name: Florian Km
full_name: Schur, Florian Km
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Vorlaufer J, Semenov N, Kreuzinger C, et al. Image-based 3D active sample stabilization
on the nanometer scale for optical microscopy. Biophysical Reports. 2025;5(2).
doi:10.1016/j.bpr.2025.100211
apa: Vorlaufer, J., Semenov, N., Kreuzinger, C., Javoor, M., Zens, B., Agudelo Duenas,
N., … Danzl, J. G. (2025). Image-based 3D active sample stabilization on the nanometer
scale for optical microscopy. Biophysical Reports. Cell Press. https://doi.org/10.1016/j.bpr.2025.100211
chicago: Vorlaufer, Jakob, Nikolai Semenov, Caroline Kreuzinger, Manjunath Javoor,
Bettina Zens, Nathalie Agudelo Duenas, Mojtaba Tavakoli, et al. “Image-Based 3D
Active Sample Stabilization on the Nanometer Scale for Optical Microscopy.” Biophysical
Reports. Cell Press, 2025. https://doi.org/10.1016/j.bpr.2025.100211.
ieee: J. Vorlaufer et al., “Image-based 3D active sample stabilization on
the nanometer scale for optical microscopy,” Biophysical Reports, vol.
5, no. 2. Cell Press, 2025.
ista: Vorlaufer J, Semenov N, Kreuzinger C, Javoor M, Zens B, Agudelo Duenas N,
Tavakoli M, Suplata M, Jahr W, Lyudchik J, Wartak A, Schur FK, Danzl JG. 2025.
Image-based 3D active sample stabilization on the nanometer scale for optical
microscopy. Biophysical Reports. 5(2), 100211.
mla: Vorlaufer, Jakob, et al. “Image-Based 3D Active Sample Stabilization on the
Nanometer Scale for Optical Microscopy.” Biophysical Reports, vol. 5, no.
2, 100211, Cell Press, 2025, doi:10.1016/j.bpr.2025.100211.
short: J. Vorlaufer, N. Semenov, C. Kreuzinger, M. Javoor, B. Zens, N. Agudelo Duenas,
M. Tavakoli, M. Suplata, W. Jahr, J. Lyudchik, A. Wartak, F.K. Schur, J.G. Danzl,
Biophysical Reports 5 (2025).
corr_author: '1'
date_created: 2025-06-08T22:01:22Z
date_published: 2025-06-11T00:00:00Z
date_updated: 2026-10-20T08:55:34Z
day: '11'
ddc:
- '570'
department:
- _id: JoDa
- _id: GradSch
- _id: FlSc
- _id: EM-Fac
doi: 10.1016/j.bpr.2025.100211
ec_funded: 1
file:
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checksum: 4018c833f25a3ad3b57e3577fed70334
content_type: application/pdf
creator: dernst
date_created: 2025-06-10T07:24:46Z
date_updated: 2025-06-10T07:24:46Z
file_id: '19802'
file_name: 2025_BiophysicalReports_Vorlaufer.pdf
file_size: 7238179
relation: main_file
success: 1
file_date_updated: 2025-06-10T07:24:46Z
fulldoi: https://doi.org/10.1016/j.bpr.2025.100211
has_accepted_license: '1'
intvolume: ' 5'
issue: '2'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 62909c6f-2b32-11ec-9570-e1476aab5308
grant_number: CZI01
name: CryoMinflux-guided in-situ molecular census and structure determination
- _id: 6285a163-2b32-11ec-9570-8e204ca2dba5
grant_number: '26137'
name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
Microscopy
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
- _id: 2668BFA0-B435-11E9-9278-68D0E5697425
grant_number: LT00057
name: High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration
publication: Biophysical Reports
publication_identifier:
eissn:
- 2667-0747
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
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relation: dissertation_contains
status: public
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Image-based 3D active sample stabilization on the nanometer scale for optical
microscopy
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: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18754'
abstract:
- lang: eng
text: 'Exploring the molecular correlates of metabolic health measures may identify
their shared and unique biological processes and pathways. Molecular proxies of
these traits may also provide a more objective approach to their measurement.
Here, DNA methylation (DNAm) data were used in epigenome-wide association studies
(EWASs) and for training epigenetic scores (EpiScores) of six metabolic traits:
body mass index (BMI), body fat percentage, waist-hip ratio, and blood-based measures
of glucose, high-density lipoprotein cholesterol, and total cholesterol in >17,000
volunteers from the Generation Scotland (GS) cohort. We observed a maximum of
12,033 significant findings (p < 3.6 × 10−8) for BMI in a marginal linear regression
EWAS. By contrast, a joint and conditional Bayesian penalized regression approach
yielded 27 high-confidence associations with BMI. EpiScores trained in GS performed
well in both Scottish and Singaporean test cohorts (Lothian Birth Cohort 1936
[LBC1936] and Health for Life in Singapore [HELIOS]). The EpiScores for BMI and
total cholesterol performed best in HELIOS, explaining 20.8% and 7.1% of the variance
in the measured traits, respectively. The corresponding results in LBC1936 were
14.4% and 3.2%, respectively. Differences were observed in HELIOS for body fat,
where the EpiScore explained ∼9% of the variance in Chinese and Malay -subgroups
but ∼3% in the Indian subgroup. The EpiScores also correlated with cognitive function
in LBC1936 (standardized βrange: 0.08–0.12, false discovery rate p [pFDR] < 0.05).
Accounting for the correlation structure across the methylome can vastly affect
the number of lead findings in EWASs. The EpiScores of metabolic traits are broadly
applicable across populations and can reflect differences in cognition.'
article_processing_charge: No
article_type: original
author:
- first_name: Hannah M.
full_name: Smith, Hannah M.
last_name: Smith
- first_name: Hong Kiat
full_name: Ng, Hong Kiat
last_name: Ng
- first_name: Joanna E.
full_name: Moodie, Joanna E.
last_name: Moodie
- first_name: Danni A.
full_name: Gadd, Danni A.
last_name: Gadd
- first_name: Daniel L.
full_name: Mccartney, Daniel L.
last_name: Mccartney
- first_name: Elena
full_name: Bernabeu, Elena
last_name: Bernabeu
- first_name: Archie
full_name: Campbell, Archie
last_name: Campbell
- first_name: Paul
full_name: Redmond, Paul
last_name: Redmond
- first_name: Adele
full_name: Taylor, Adele
last_name: Taylor
- first_name: Danielle
full_name: Page, Danielle
last_name: Page
- first_name: Janie
full_name: Corley, Janie
last_name: Corley
- first_name: Sarah E.
full_name: Harris, Sarah E.
last_name: Harris
- first_name: Darwin
full_name: Tay, Darwin
last_name: Tay
- first_name: Ian J.
full_name: Deary, Ian J.
last_name: Deary
- first_name: Kathryn L.
full_name: Evans, Kathryn L.
last_name: Evans
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: John C.
full_name: Chambers, John C.
last_name: Chambers
- first_name: Marie
full_name: Loh, Marie
last_name: Loh
- first_name: Simon R.
full_name: Cox, Simon R.
last_name: Cox
- first_name: Riccardo E.
full_name: Marioni, Riccardo E.
last_name: Marioni
- first_name: Robert F.
full_name: Hillary, Robert F.
last_name: Hillary
citation:
ama: Smith HM, Ng HK, Moodie JE, et al. DNA methylation-based predictors of metabolic
traits in Scottish and Singaporean cohorts. American Journal of Human Genetics.
2025;112(1):106-115. doi:10.1016/j.ajhg.2024.11.012
apa: Smith, H. M., Ng, H. K., Moodie, J. E., Gadd, D. A., Mccartney, D. L., Bernabeu,
E., … Hillary, R. F. (2025). DNA methylation-based predictors of metabolic traits
in Scottish and Singaporean cohorts. American Journal of Human Genetics.
Cell Press. https://doi.org/10.1016/j.ajhg.2024.11.012
chicago: Smith, Hannah M., Hong Kiat Ng, Joanna E. Moodie, Danni A. Gadd, Daniel
L. Mccartney, Elena Bernabeu, Archie Campbell, et al. “DNA Methylation-Based Predictors
of Metabolic Traits in Scottish and Singaporean Cohorts.” American Journal
of Human Genetics. Cell Press, 2025. https://doi.org/10.1016/j.ajhg.2024.11.012.
ieee: H. M. Smith et al., “DNA methylation-based predictors of metabolic
traits in Scottish and Singaporean cohorts,” American Journal of Human Genetics,
vol. 112, no. 1. Cell Press, pp. 106–115, 2025.
ista: Smith HM, Ng HK, Moodie JE, Gadd DA, Mccartney DL, Bernabeu E, Campbell A,
Redmond P, Taylor A, Page D, Corley J, Harris SE, Tay D, Deary IJ, Evans KL, Robinson
MR, Chambers JC, Loh M, Cox SR, Marioni RE, Hillary RF. 2025. DNA methylation-based
predictors of metabolic traits in Scottish and Singaporean cohorts. American Journal
of Human Genetics. 112(1), 106–115.
mla: Smith, Hannah M., et al. “DNA Methylation-Based Predictors of Metabolic Traits
in Scottish and Singaporean Cohorts.” American Journal of Human Genetics,
vol. 112, no. 1, Cell Press, 2025, pp. 106–15, doi:10.1016/j.ajhg.2024.11.012.
short: H.M. Smith, H.K. Ng, J.E. Moodie, D.A. Gadd, D.L. Mccartney, E. Bernabeu,
A. Campbell, P. Redmond, A. Taylor, D. Page, J. Corley, S.E. Harris, D. Tay, I.J.
Deary, K.L. Evans, M.R. Robinson, J.C. Chambers, M. Loh, S.R. Cox, R.E. Marioni,
R.F. Hillary, American Journal of Human Genetics 112 (2025) 106–115.
date_created: 2025-01-05T23:01:56Z
date_published: 2025-01-02T00:00:00Z
date_updated: 2026-10-20T08:53:52Z
day: '02'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.1016/j.ajhg.2024.11.012
external_id:
isi:
- '001412498600001'
pmid:
- '39706196'
file:
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checksum: 891d120554f07da2c35d38388c29a690
content_type: application/pdf
creator: dernst
date_created: 2025-01-08T09:26:42Z
date_updated: 2025-01-08T09:26:42Z
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file_name: 2025_AJHG_Smith.pdf
file_size: 2266488
relation: main_file
success: 1
file_date_updated: 2025-01-08T09:26:42Z
fulldoi: https://doi.org/10.1016/j.ajhg.2024.11.012
has_accepted_license: '1'
intvolume: ' 112'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 106-115
pmid: 1
publication: American Journal of Human Genetics
publication_identifier:
eissn:
- 1537-6605
issn:
- 0002-9297
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/marioni-group/Metabolic_trait
scopus_import: '1'
status: public
title: DNA methylation-based predictors of metabolic traits in Scottish and Singaporean
cohorts
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: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20099'
abstract:
- lang: eng
text: The hippocampus, critical for learning and memory, is dogmatically described
as a trisynaptic circuit where dentate gyrus granule cells (GCs), CA3 pyramidal
neurons (PNs), and CA1 PNs are serially connected. However, CA3 also forms an
autoassociative network, and its PNs have diverse morphologies, intrinsic properties,
and GC input levels. How PN subtypes compose this recurrent network is unknown.
To determine the synaptic arrangement of identified CA3 PNs, we combine multicellular
patch-clamp recording and post hoc morphological analysis in mouse hippocampal
slices. PNs can be divided into distinct “superficial” and “deep” subclasses,
the latter including previously reported “athorny” cells. Subclasses have distinct
input-output transformations and asymmetric connectivity, which is more abundant
from superficial to deep PNs, splitting CA3 locally into two parallel recurrent
networks. Coincident spontaneous inhibition occurs frequently within but not between
subclasses, implying subclass-specific inhibitory innervation. Our results suggest
two separately controlled sublayers for parallel information processing in hippocampal
CA3.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: LifeSc
- _id: M-Shop
acknowledgement: We thank Andrea Navas-Olive and Rebecca J. Morse-Mora for critically
reading an earlier version of the manuscript. We also thank Florian Marr and Christina
Altmutter for excellent technical assistance, Alois Schlögl for programming and
data-handling assistance, Todor Asenov for technical support, and Eleftheria Kralli-Beller
for manuscript editing. This research was supported by the Scientific Services Units
(SSUs) of ISTA. We are particularly grateful for assistance from the Imaging and
Optics Facility, Preclinical Facility, Lab Support Facility, and Miba 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 to P.J., Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635
to J.F.W., and an ISTplus Fellowship through Marie Skłodowska-Curie grant agreement
no. 754411 to V.V.-B.), the Austrian Science Fund (P 36232-B, PAT 4178023, and Cluster
of Excellence 10.55776/COE16 to P.J.), and a CONACyT fellowship (289638 to V.V.-B.)
and was supported by a non-stipendiary EMBO fellowship (ALTF 756–2020 to J.F.W.).
article_number: '116080'
article_processing_charge: Yes
article_type: original
author:
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Victor M
full_name: Vargas Barroso, Victor M
id: 2F55A9DE-F248-11E8-B48F-1D18A9856A87
last_name: Vargas Barroso
- 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: Watson J, Vargas Barroso VM, Jonas PM. Cell-specific wiring routes information
flow through hippocampal CA3. Cell Reports. 2025;44(8). doi:10.1016/j.celrep.2025.116080
apa: Watson, J., Vargas Barroso, V. M., & Jonas, P. M. (2025). Cell-specific
wiring routes information flow through hippocampal CA3. Cell Reports. Cell
Press. https://doi.org/10.1016/j.celrep.2025.116080
chicago: Watson, Jake, Victor M Vargas Barroso, and Peter M Jonas. “Cell-Specific
Wiring Routes Information Flow through Hippocampal CA3.” Cell Reports.
Cell Press, 2025. https://doi.org/10.1016/j.celrep.2025.116080.
ieee: J. Watson, V. M. Vargas Barroso, and P. M. Jonas, “Cell-specific wiring routes
information flow through hippocampal CA3,” Cell Reports, vol. 44, no. 8.
Cell Press, 2025.
ista: Watson J, Vargas Barroso VM, Jonas PM. 2025. Cell-specific wiring routes information
flow through hippocampal CA3. Cell Reports. 44(8), 116080.
mla: Watson, Jake, et al. “Cell-Specific Wiring Routes Information Flow through
Hippocampal CA3.” Cell Reports, vol. 44, no. 8, 116080, Cell Press, 2025,
doi:10.1016/j.celrep.2025.116080.
short: J. Watson, V.M. Vargas Barroso, P.M. Jonas, Cell Reports 44 (2025).
corr_author: '1'
date_created: 2025-08-03T22:01:30Z
date_published: 2025-08-01T00:00:00Z
date_updated: 2026-10-20T08:55:57Z
day: '01'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1016/j.celrep.2025.116080
ec_funded: 1
external_id:
isi:
- '001544472300002'
file:
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checksum: 556ff9760661ecd23949d75031043b1f
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creator: dernst
date_created: 2025-08-04T06:53:07Z
date_updated: 2025-08-04T06:53:07Z
file_id: '20106'
file_name: 2025_CellReports_Watson.pdf
file_size: 27695214
relation: main_file
success: 1
file_date_updated: 2025-08-04T06:53:07Z
fulldoi: https://doi.org/10.1016/j.celrep.2025.116080
has_accepted_license: '1'
intvolume: ' 44'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published 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
- _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9
call_identifier: H2020
grant_number: '101026635'
name: Synaptic computations of the hippocampal CA3 circuitry
- _id: bd88be38-d553-11ed-ba76-81d5a70a6ef5
grant_number: P36232
name: Mechanisms of GABA release in hippocampal circuits
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 0a6c8641-b036-11f1-bacf-e4eec62b5bb4
grant_number: COE16
name: Neuronal circuits in health and disease (Jonas)
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
issn:
- 2639-1856
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cell-specific wiring routes information flow through hippocampal CA3
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: 44
year: '2025'
...
---
OA_place: publisher
_id: '20206'
abstract:
- lang: eng
text: "The internal structure of biomolecules and their organization in higher-order
arrangements are key factors governing the working principles of biological systems.
Bioimaging has successfully revealed arrangements across relevant spatial scales.
For example, cryo-electron tomography has become widely used for analyzing biomolecular
structures in situ due to its comprehensive structural visualization of near-natively
preserved samples, and its capability of sub-nm resolution via averaging. However,
the identification of molecules within crowded cellular environments is often
hindered by low contrast. Fluorescence microscopy, on the other hand, routinely
visualizes specifically labeled targets at single-molecule contrast against essentially
zero background. Moreover, it provides comparatively high throughput and is amenable
to multiplexing. Due to this complementarity, combining datasets from both modalities
acquired on the same region via correlative light and electron microscopy can
reveal novel types of information. \r\nThe spatial scale at which information
can be extracted depends on imaging resolution and correlation accuracy. Since
diffraction of light limits the resolution of conventional fluorescence microscopy
to few hundreds of nanometers, reaching the full potential of correlative imaging
requires super-resolution approaches. Performing imaging at cryogenic temperature
preserves structures in a near-native state and minimizes distortions between
the fluorescence and the electron microscopy datasets. Implementations of this
concept have achieved correlation on the scale of cellular organelles or bacterial
domains.\r\nWe have worked towards pushing correlative imaging to the single-molecule
scale by improving cryo-super-resolution microscopy, and devising a refined image
correlation workflow. As part of this project, I constructed a microscopy setup
and adopted it for super-resolution fluorescence microscopy at room temperature
and cryogenic conditions. I explored different cryo-stages and acquisition strategies.
Specifically, I developed a new scheme for correcting sample drift, thus increasing
mechanical stability during microscopy acquisitions.\r\n"
acknowledged_ssus:
- _id: M-Shop
- _id: EM-Fac
- _id: Bio
acknowledgement: "The project was supported by CZI grant DAF2021-234754 and grant\r\nDOI:
https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an\r\nadvised
fund of Silicon Valley Community Foundation (funder\r\nDOI: https://doi.org/10.13039/100014989),
as well as internal grants from ISTA’s Equipment\r\nInvestment Committee and Interdisciplinary
Project Committee. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Jakob
full_name: Vorlaufer, Jakob
id: 937696FA-C996-11E9-8C7C-CF13E6697425
last_name: Vorlaufer
orcid: 0009-0000-7590-3501
citation:
ama: Vorlaufer J. Construction of a cryo-super-resolution microscope to guide in
situ structure analysis. 2025. doi:10.15479/AT-ISTA-20206
apa: Vorlaufer, J. (2025). Construction of a cryo-super-resolution microscope
to guide in situ structure analysis. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT-ISTA-20206
chicago: Vorlaufer, Jakob. “Construction of a Cryo-Super-Resolution Microscope to
Guide in Situ Structure Analysis.” Institute of Science and Technology Austria,
2025. https://doi.org/10.15479/AT-ISTA-20206.
ieee: J. Vorlaufer, “Construction of a cryo-super-resolution microscope to guide
in situ structure analysis,” Institute of Science and Technology Austria, 2025.
ista: Vorlaufer J. 2025. Construction of a cryo-super-resolution microscope to guide
in situ structure analysis. Institute of Science and Technology Austria.
mla: Vorlaufer, Jakob. Construction of a Cryo-Super-Resolution Microscope to
Guide in Situ Structure Analysis. Institute of Science and Technology Austria,
2025, doi:10.15479/AT-ISTA-20206.
short: J. Vorlaufer, Construction of a Cryo-Super-Resolution Microscope to Guide
in Situ Structure Analysis, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-08-22T08:12:55Z
date_published: 2025-08-25T00:00:00Z
date_updated: 2026-10-20T08:55:33Z
day: '25'
ddc:
- '621'
- '535'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoDa
doi: 10.15479/AT-ISTA-20206
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has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '107'
project:
- _id: 62909c6f-2b32-11ec-9570-e1476aab5308
grant_number: CZI01
name: CryoMinflux-guided in-situ molecular census and structure determination
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '19795'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
title: Construction of a cryo-super-resolution microscope to guide in situ structure
analysis
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19506'
abstract:
- lang: eng
text: 'Hippocampal reactivation of waking neuronal assemblies in sleep is a key
initial step of systems consolidation. Nevertheless, it is unclear whether reactivated
assemblies are static or whether they reorganize gradually over prolonged sleep.
We tracked reactivated CA1 assembly patterns over ∼20 h of sleep/rest periods
and related them to assemblies seen before or after in a spatial learning paradigm
using rats. We found that reactivated assembly patterns were gradually transformed
and started to resemble those seen in the subsequent recall session. Periods of
rapid eye movement (REM) sleep and non-REM (NREM) had antagonistic roles: whereas
NREM accelerated the assembly drift, REM countered it. Moreover, only a subset
of rate-changing pyramidal cells contributed to the drift, whereas stable-firing-rate
cells maintained unaltered reactivation patterns. Our data suggest that prolonged
sleep promotes the spontaneous reorganization of spatial assemblies, which can
contribute to daily cognitive map changes or encoding new learning situations.'
acknowledgement: We thank Andrea Cumpelik, Lisa Genzel, and Freya Ólafsdóttir for
comments on an earlier version of the manuscript. This work was supported by the
European Research Council (281511) and Austrian Science Fund (FWF I3713).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Lars
full_name: Bollmann, Lars
id: 47AD3038-F248-11E8-B48F-1D18A9856A87
last_name: Bollmann
- first_name: Peter
full_name: Baracskay, Peter
id: 361CC00E-F248-11E8-B48F-1D18A9856A87
last_name: Baracskay
- first_name: Federico
full_name: Stella, Federico
id: 39AF1E74-F248-11E8-B48F-1D18A9856A87
last_name: Stella
orcid: 0000-0001-9439-3148
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Bollmann L, Baracskay P, Stella F, Csicsvari JL. Sleep stages antagonistically
modulate reactivation drift. Neuron. 2025;113(9):1446-1459.e6. doi:10.1016/j.neuron.2025.02.025
apa: Bollmann, L., Baracskay, P., Stella, F., & Csicsvari, J. L. (2025). Sleep
stages antagonistically modulate reactivation drift. Neuron. Cell Press.
https://doi.org/10.1016/j.neuron.2025.02.025
chicago: Bollmann, Lars, Peter Baracskay, Federico Stella, and Jozsef L Csicsvari.
“Sleep Stages Antagonistically Modulate Reactivation Drift.” Neuron. Cell
Press, 2025. https://doi.org/10.1016/j.neuron.2025.02.025.
ieee: L. Bollmann, P. Baracskay, F. Stella, and J. L. Csicsvari, “Sleep stages antagonistically
modulate reactivation drift,” Neuron, vol. 113, no. 9. Cell Press, p. 1446–1459.e6,
2025.
ista: Bollmann L, Baracskay P, Stella F, Csicsvari JL. 2025. Sleep stages antagonistically
modulate reactivation drift. Neuron. 113(9), 1446–1459.e6.
mla: Bollmann, Lars, et al. “Sleep Stages Antagonistically Modulate Reactivation
Drift.” Neuron, vol. 113, no. 9, Cell Press, 2025, p. 1446–1459.e6, doi:10.1016/j.neuron.2025.02.025.
short: L. Bollmann, P. Baracskay, F. Stella, J.L. Csicsvari, Neuron 113 (2025) 1446–1459.e6.
corr_author: '1'
date_created: 2025-04-06T22:01:32Z
date_published: 2025-05-07T00:00:00Z
date_updated: 2026-10-20T08:54:27Z
day: '07'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1016/j.neuron.2025.02.025
ec_funded: 1
external_id:
isi:
- '001510440400001'
pmid:
- '40132588'
file:
- access_level: open_access
checksum: 5e57852a45a78a751dd3a5e807bf015f
content_type: application/pdf
creator: dernst
date_created: 2025-08-05T12:43:44Z
date_updated: 2025-08-05T12:43:44Z
file_id: '20133'
file_name: 2025_Neuron_Bollmann.pdf
file_size: 27047730
relation: main_file
success: 1
file_date_updated: 2025-08-05T12:43:44Z
fulldoi: https://doi.org/10.1016/j.neuron.2025.02.025
has_accepted_license: '1'
intvolume: ' 113'
isi: 1
issue: '9'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1446-1459.e6
pmid: 1
project:
- _id: 257A4776-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281511'
name: Memory-related information processing in neuronal circuits of the hippocampus
and entorhinal cortex
- _id: 2654F984-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 3713-B27
name: Interneuro plasticity during spatial learning
publication: Neuron
publication_identifier:
eissn:
- 1097-4199
issn:
- 0896-6273
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/how-sleep-keeps-our-memories-fresh/
scopus_import: '1'
status: public
title: Sleep stages antagonistically modulate reactivation drift
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19443'
abstract:
- lang: eng
text: In cryo-electron microscopy, accurate particle localization and classification
are imperative. Recent deep learning solutions, though successful, require extensive
training datasets. The protracted generation time of physics-based models, often
employed to produce these datasets, limits their broad applicability. We introduce
FakET, a method based on neural style transfer, capable of simulating the forward
operator of any cryo transmission electron microscope. It can be used to adapt
a synthetic training dataset according to reference data producing high-quality
simulated micrographs or tilt-series. To assess the quality of our generated data,
we used it to train a state-of-the-art localization and classification architecture
and compared its performance with a counterpart trained on benchmark data. Remarkably,
our technique matches the performance, boosts data generation speed 750x, uses
33x less memory, and scales well to typical transmission electron microscope detector
sizes. It leverages GPU acceleration and parallel processing. The source code
is available at https://github.com/paloha/faket/.
acknowledgement: The IMP and D.H. are generously funded by Boehringer Ingelheim. We
thank Julius Berner from the Mathematical Data Science group @ UniVie, Ilja Gubins
and Marten Chaillet from the SHREC team, and the members of the Haselbach lab for
helpful discussions.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Pavol
full_name: Harar, Pavol
id: e03d953a-6e8c-11ef-99e4-f0717d385cd5
last_name: Harar
orcid: 0000-0001-5206-1794
- first_name: Lukas
full_name: Herrmann, Lukas
last_name: Herrmann
- first_name: Philipp
full_name: Grohs, Philipp
last_name: Grohs
- first_name: David
full_name: Haselbach, David
last_name: Haselbach
citation:
ama: 'Harar P, Herrmann L, Grohs P, Haselbach D. FakET: Simulating cryo-electron
tomograms with neural style transfer. Structure. 2025;33(4):820-827.e4.
doi:10.1016/j.str.2025.01.020'
apa: 'Harar, P., Herrmann, L., Grohs, P., & Haselbach, D. (2025). FakET: Simulating
cryo-electron tomograms with neural style transfer. Structure. Cell Press.
https://doi.org/10.1016/j.str.2025.01.020'
chicago: 'Harar, Pavol, Lukas Herrmann, Philipp Grohs, and David Haselbach. “FakET:
Simulating Cryo-Electron Tomograms with Neural Style Transfer.” Structure.
Cell Press, 2025. https://doi.org/10.1016/j.str.2025.01.020.'
ieee: 'P. Harar, L. Herrmann, P. Grohs, and D. Haselbach, “FakET: Simulating cryo-electron
tomograms with neural style transfer,” Structure, vol. 33, no. 4. Cell
Press, p. 820–827.e4, 2025.'
ista: 'Harar P, Herrmann L, Grohs P, Haselbach D. 2025. FakET: Simulating cryo-electron
tomograms with neural style transfer. Structure. 33(4), 820–827.e4.'
mla: 'Harar, Pavol, et al. “FakET: Simulating Cryo-Electron Tomograms with Neural
Style Transfer.” Structure, vol. 33, no. 4, Cell Press, 2025, p. 820–827.e4,
doi:10.1016/j.str.2025.01.020.'
short: P. Harar, L. Herrmann, P. Grohs, D. Haselbach, Structure 33 (2025) 820–827.e4.
corr_author: '1'
date_created: 2025-03-23T23:01:27Z
date_published: 2025-04-03T00:00:00Z
date_updated: 2026-10-20T08:54:10Z
day: '03'
ddc:
- '570'
department:
- _id: AlMi
doi: 10.1016/j.str.2025.01.020
external_id:
isi:
- '001463196100001'
pmid:
- '39947174'
file:
- access_level: open_access
checksum: f346bc357a66a88cca3d0eb95793fb73
content_type: application/pdf
creator: dernst
date_created: 2025-08-05T12:15:13Z
date_updated: 2025-08-05T12:15:13Z
file_id: '20130'
file_name: 2025_Structure_Harar.pdf
file_size: 4367530
relation: main_file
success: 1
file_date_updated: 2025-08-05T12:15:13Z
fulldoi: https://doi.org/10.1016/j.str.2025.01.020
has_accepted_license: '1'
intvolume: ' 33'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 820-827.e4
pmid: 1
publication: Structure
publication_identifier:
eissn:
- 1878-4186
issn:
- 0969-2126
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/paloha/faket/
scopus_import: '1'
status: public
title: 'FakET: Simulating cryo-electron tomograms with neural style transfer'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20154'
abstract:
- lang: eng
text: In long-lived mammals, including humans, brain cell homeostasis is critical
for maintaining brain function throughout life. Most neurons are generated during
development and must maintain their cellular identity and plasticity to preserve
brain function. Although extensive studies indicate the importance of recycling
and regenerating cellular molecules to maintain cellular homeostasis, recent evidence
has shown that some proteins and RNAs do not turn over for months and even years.
We propose that these long-lived cellular molecules may be the basis for maintaining
brain function in the long term, but also a potential convergent target of brain
aging. We highlight key discoveries and challenges, and propose potential directions
to unravel the mystery of brain cell longevity.
acknowledgement: The work was supported by the Deutsche Forschungsgemeinschaft (DFG,
German Research Foundation) (470322152 – T1347/3-1; 497658532 – T1347/4-1; 507965872
– T1347/5-1; and 460333672 – CRC1540 Exploring Brain Mechanics) to T.T., the Schram
Foundation (T.T.), the European Research Council (ERC-2018-STG, 804468 EAGER; ERC-2023-COG,
101125034 NEUTIME) to T.T., the Hans-Georg Geis und Xue Hong Dong-Geis Foundation
and Forschungsstiftung Medizin am Universitätsklinikum Erlangen to T.T., and the
Interdisciplinary Centre for Clinical Research Erlangen (Interdisziplinäres Zentrum
für Klinische Forschung, Universitätsklinikum Erlangen; P162 to T.T.). We thank
Dr Laura J. Harrison for editing assistance.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Martin W
full_name: Hetzer, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: Hetzer
orcid: 0000-0002-2111-992X
- first_name: Tomohisa
full_name: Toda, Tomohisa
last_name: Toda
citation:
ama: Hetzer M, Toda T. Long-lived cellular molecules in the brain. Trends in
Neurosciences. 2025;48(9):645-654. doi:10.1016/j.tins.2025.07.004
apa: Hetzer, M., & Toda, T. (2025). Long-lived cellular molecules in the brain.
Trends in Neurosciences. Cell Press. https://doi.org/10.1016/j.tins.2025.07.004
chicago: Hetzer, Martin, and Tomohisa Toda. “Long-Lived Cellular Molecules in the
Brain.” Trends in Neurosciences. Cell Press, 2025. https://doi.org/10.1016/j.tins.2025.07.004.
ieee: M. Hetzer and T. Toda, “Long-lived cellular molecules in the brain,” Trends
in Neurosciences, vol. 48, no. 9. Cell Press, pp. 645–654, 2025.
ista: Hetzer M, Toda T. 2025. Long-lived cellular molecules in the brain. Trends
in Neurosciences. 48(9), 645–654.
mla: Hetzer, Martin, and Tomohisa Toda. “Long-Lived Cellular Molecules in the Brain.”
Trends in Neurosciences, vol. 48, no. 9, Cell Press, 2025, pp. 645–54,
doi:10.1016/j.tins.2025.07.004.
short: M. Hetzer, T. Toda, Trends in Neurosciences 48 (2025) 645–654.
corr_author: '1'
date_created: 2025-08-10T22:01:29Z
date_published: 2025-09-01T00:00:00Z
date_updated: 2026-10-20T08:54:50Z
day: '01'
ddc:
- '570'
department:
- _id: MaHe
doi: 10.1016/j.tins.2025.07.004
external_id:
isi:
- '001568965400001'
pmid:
- '40744775'
file:
- access_level: open_access
checksum: 90942491b499f70b0bf48b8aec2e7387
content_type: application/pdf
creator: dernst
date_created: 2025-12-29T13:47:27Z
date_updated: 2025-12-29T13:47:27Z
file_id: '20873'
file_name: 2025_TrendsNeurosciences_Hetzer.pdf
file_size: 327847
relation: main_file
success: 1
file_date_updated: 2025-12-29T13:47:27Z
fulldoi: https://doi.org/10.1016/j.tins.2025.07.004
has_accepted_license: '1'
intvolume: ' 48'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 645-654
pmid: 1
publication: Trends in Neurosciences
publication_identifier:
eissn:
- 1878-108X
issn:
- 0166-2236
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long-lived cellular molecules in the brain
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 48
year: '2025'
...
---
OA_type: closed access
_id: '20427'
abstract:
- lang: eng
text: Animal cells migrating up chemotactic gradients often show speed oscillations.
A new study describes a molecular circuit that switches zebrafish germ cells between
phases of straight runs, tumbling and directional reorientation.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Ziqiang
full_name: Li, Ziqiang
id: 922e68bb-1727-11ee-857c-966e8cc1b6c3
last_name: Li
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: 'LI Z, Sixt MK. Cell migration: How animal cells run and tumble. Current
Biology. 2025;35(18):R890-R892. doi:10.1016/j.cub.2025.08.016'
apa: 'LI, Z., & Sixt, M. K. (2025). Cell migration: How animal cells run and
tumble. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2025.08.016'
chicago: 'LI, ZIQIANG, and Michael K Sixt. “Cell Migration: How Animal Cells Run
and Tumble.” Current Biology. Cell Press, 2025. https://doi.org/10.1016/j.cub.2025.08.016.'
ieee: 'Z. LI and M. K. Sixt, “Cell migration: How animal cells run and tumble,”
Current Biology, vol. 35, no. 18. Cell Press, pp. R890–R892, 2025.'
ista: 'LI Z, Sixt MK. 2025. Cell migration: How animal cells run and tumble. Current
Biology. 35(18), R890–R892.'
mla: 'LI, ZIQIANG, and Michael K. Sixt. “Cell Migration: How Animal Cells Run and
Tumble.” Current Biology, vol. 35, no. 18, Cell Press, 2025, pp. R890–92,
doi:10.1016/j.cub.2025.08.016.'
short: Z. LI, M.K. Sixt, Current Biology 35 (2025) R890–R892.
corr_author: '1'
date_created: 2025-10-05T22:01:35Z
date_published: 2025-09-22T00:00:00Z
date_updated: 2026-10-20T08:55:09Z
day: '22'
department:
- _id: MiSi
doi: 10.1016/j.cub.2025.08.016
external_id:
isi:
- '001592664700001'
pmid:
- '40987270'
fulldoi: https://doi.org/10.1016/j.cub.2025.08.016
intvolume: ' 35'
isi: 1
issue: '18'
language:
- iso: eng
month: '09'
oa_version: None
page: R890-R892
pmid: 1
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Cell migration: How animal cells run and tumble'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15016'
abstract:
- lang: eng
text: Amphibians, by virtue of their phylogenetic position, provide invaluable insights
on nervous system evolution, development, and remodeling. The genetic toolkit
for amphibians, however, remains limited. Recombinant adeno-associated viral vectors
(AAVs) are a powerful alternative to transgenesis for labeling and manipulating
neurons. Although successful in mammals, AAVs have never been shown to transduce
amphibian cells efficiently. We screened AAVs in three amphibian species—the frogs
Xenopus laevis and Pelophylax bedriagae and the salamander Pleurodeles waltl—and
identified at least two AAV serotypes per species that transduce neurons. In developing
amphibians, AAVs labeled groups of neurons generated at the same time during development.
In the mature brain, AAVrg retrogradely traced long-range projections. Our study
introduces AAVs as a tool for amphibian research, establishes a generalizable
workflow for AAV screening in new species, and expands opportunities for cross-species
comparisons of nervous system development, function, and evolution.
acknowledged_ssus:
- _id: PreCl
- _id: Bio
acknowledgement: 'We thank members of the Sweeney, Tosches, Shein-Idelson, Yamaguchi,
Kelley, and Cline Labs for their contributions to this project, discussion, and
support. We additionally thank the Beckman Institute CLOVER Center and Viviana Gradinaru
(Caltech), Kimberly Ritola (UNC NeuroTools), and Flavia Gomez-Leite (ISTA Viral
Core) for AAV production and consultation; Andras Simon and Alberto Joven (Karolinska
Institute) for feedback; Elizabeth Bagnato-Cohen (Columbia) for project coordination;
our animal care and imaging facilities; the amphibian stock centers (NXR, EXRC,
and XenopusExpress); and our funding sources: NSF IOS 2110086 (D.B.K., L.B.S., M.A.T.,
A.Y., and H.T.C.); US-Israel Binational Science Foundation (BSF) 2020702 (M.S.-I.);
FTI Strategy Lower Austria Dissertation FT121-D-046 (D.V.); Horizon Europe ERC Starting
Grant 101041551 and Special Research Programme (SFB) of the Austrian Science Fund
(FWF) project F7814-B (L.B.S.); NIH grant R35GM146973, Rita Allen Foundation Award
GA_032522_FE, and CZI Ben Barres Early Career Acceleration Award 2023-331758 (M.A.T.);
EMBO Long-Term Fellowship ALTF 874-2021 (A.D.); and NSF GRFP DGE 2036197 (E.C.B.J.).'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Eliza C.B.
full_name: Jaeger, Eliza C.B.
last_name: Jaeger
- first_name: David
full_name: Vijatovic, David
id: cf391e77-ec3c-11ea-a124-d69323410b58
last_name: Vijatovic
orcid: 0000-0002-5494-0941
- first_name: Astrid
full_name: Deryckere, Astrid
last_name: Deryckere
- first_name: Nikol
full_name: Zorin, Nikol
last_name: Zorin
- first_name: Akemi L.
full_name: Nguyen, Akemi L.
last_name: Nguyen
- first_name: Georgiy
full_name: Ivanian, Georgiy
id: eaf2b366-cfd1-11ee-bbdf-c8790f800a05
last_name: Ivanian
orcid: 0009-0002-3999-3735
- first_name: Jamie
full_name: Woych, Jamie
last_name: Woych
- first_name: Rebecca C
full_name: Arnold, Rebecca C
id: d6cce458-14c9-11ed-a755-c1c8fc6fde6f
last_name: Arnold
- first_name: Alonso
full_name: Ortega Gurrola, Alonso
last_name: Ortega Gurrola
- first_name: Arik
full_name: Shvartsman, Arik
last_name: Shvartsman
- first_name: Francesca
full_name: Barbieri, Francesca
id: a9492887-8972-11ed-ae7b-bfae10998254
last_name: Barbieri
- first_name: Florina-Alexandra
full_name: Toma, Florina-Alexandra
id: 85dd99f2-15b2-11ec-abd3-d1ae4d57f3b5
last_name: Toma
- first_name: Gary J.
full_name: Gorbsky, Gary J.
last_name: Gorbsky
- first_name: Marko E.
full_name: Horb, Marko E.
last_name: Horb
- first_name: Hollis T.
full_name: Cline, Hollis T.
last_name: Cline
- first_name: Timothy F.
full_name: Shay, Timothy F.
last_name: Shay
- first_name: Darcy B.
full_name: Kelley, Darcy B.
last_name: Kelley
- first_name: Ayako
full_name: Yamaguchi, Ayako
last_name: Yamaguchi
- first_name: Mark
full_name: Shein-Idelson, Mark
last_name: Shein-Idelson
- first_name: Maria Antonietta
full_name: Tosches, Maria Antonietta
last_name: Tosches
- first_name: Lora Beatrice Jaeger
full_name: Sweeney, Lora Beatrice Jaeger
id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
last_name: Sweeney
orcid: 0000-0001-9242-5601
citation:
ama: Jaeger ECB, Vijatovic D, Deryckere A, et al. Adeno-associated viral tools to
trace neural development and connectivity across amphibians. Developmental
Cell. 2025;60(5):794-812.e6. doi:10.1016/j.devcel.2024.10.025
apa: Jaeger, E. C. B., Vijatovic, D., Deryckere, A., Zorin, N., Nguyen, A. L., Ivanian,
G., … Sweeney, L. B. (2025). Adeno-associated viral tools to trace neural development
and connectivity across amphibians. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2024.10.025
chicago: Jaeger, Eliza C.B., David Vijatovic, Astrid Deryckere, Nikol Zorin, Akemi
L. Nguyen, Georgiy Ivanian, Jamie Woych, et al. “Adeno-Associated Viral Tools
to Trace Neural Development and Connectivity across Amphibians.” Developmental
Cell. Cell Press, 2025. https://doi.org/10.1016/j.devcel.2024.10.025.
ieee: E. C. B. Jaeger et al., “Adeno-associated viral tools to trace neural
development and connectivity across amphibians,” Developmental Cell, vol.
60, no. 5. Cell Press, p. 794–812.e6, 2025.
ista: Jaeger ECB, Vijatovic D, Deryckere A, Zorin N, Nguyen AL, Ivanian G, Woych
J, Arnold RC, Ortega Gurrola A, Shvartsman A, Barbieri F, Toma F-A, Gorbsky GJ,
Horb ME, Cline HT, Shay TF, Kelley DB, Yamaguchi A, Shein-Idelson M, Tosches MA,
Sweeney LB. 2025. Adeno-associated viral tools to trace neural development and
connectivity across amphibians. Developmental Cell. 60(5), 794–812.e6.
mla: Jaeger, Eliza C. B., et al. “Adeno-Associated Viral Tools to Trace Neural Development
and Connectivity across Amphibians.” Developmental Cell, vol. 60, no. 5,
Cell Press, 2025, p. 794–812.e6, doi:10.1016/j.devcel.2024.10.025.
short: E.C.B. Jaeger, D. Vijatovic, A. Deryckere, N. Zorin, A.L. Nguyen, G. Ivanian,
J. Woych, R.C. Arnold, A. Ortega Gurrola, A. Shvartsman, F. Barbieri, F.-A. Toma,
G.J. Gorbsky, M.E. Horb, H.T. Cline, T.F. Shay, D.B. Kelley, A. Yamaguchi, M.
Shein-Idelson, M.A. Tosches, L.B. Sweeney, Developmental Cell 60 (2025) 794–812.e6.
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: 'FAMD RStudio code and raw data used for analysis of post-metamorphic
P. waltl injection outcomes are available via Dryad repository: https://doi.org/10.5061/dryad.mpg4f4r89.
Any additional information required to reanalyze the data reported in this paper
is available from the lead contact upon request.'
date_created: 2024-02-20T09:20:32Z
date_published: 2025-03-10T00:00:00Z
date_updated: 2026-10-20T08:56:33Z
day: '10'
ddc:
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department:
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- _id: MaDe
- _id: GaNo
doi: 10.1016/j.devcel.2024.10.025
external_id:
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pmid:
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creator: dernst
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file_date_updated: 2025-06-04T05:43:27Z
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isi: 1
issue: '5'
language:
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month: '03'
oa: 1
oa_version: Published Version
page: 794-812.e6
pmid: 1
project:
- _id: bd73af52-d553-11ed-ba76-912049f0ac7a
grant_number: FTI21-D-046
name: Development of V1 interneuron diversity during swim-to-walk transition of
Xenopus metamorphosis
- _id: ebb66355-77a9-11ec-83b8-b8ac210a4dae
grant_number: '101041551'
name: Development and Evolution of Tetrapod Motor Circuits
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grant_number: F7814
name: 'Stem Cell Modulation in Neural Development and Regeneration/ P14-Swim-to-limb
transition: cell type to connection diversity'
publication: Developmental Cell
publication_identifier:
eissn:
- 1878-1551
issn:
- 1534-5807
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
record:
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relation: dissertation_contains
status: public
- id: '22803'
relation: research_data
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Adeno-associated viral tools to trace neural development and connectivity across
amphibians
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 60
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18619'
abstract:
- lang: eng
text: Brassinosteroids (BRs) are steroidal phytohormones indispensable for plant
growth, development, and responses to environmental stresses. The export of bioactive
BRs to the apoplast is essential for BR signalling initiation, which requires
binding of BR molecule to the extracellular domains of the plasma membrane-localized
receptor complex. We have previously shown that the Arabidopsis thaliana ATP-binding
cassette (ABC) transporter, ABCB19, functions as a BR exporter, and together with
its close homologue, ABCB1, positively regulate BR signalling. Here, we demonstrate
that ABCB1 is another BR transporter. The ATP hydrolysis activity of ABCB1 was
stimulated by bioactive BRs, and its transport activity was confirmed in proteoliposomes
and protoplasts. Structures of ABCB1 in substrate-unbound (apo), brassinolide
(BL)-bound, and ATP plus BL-bound states were determined. In the BL-bound structure,
BL was bound to the hydrophobic cavity formed by the transmembrane domain, and
triggered local conformational changes. Together, our data provide additional
insights into the ABC transporter-mediated BR export.
acknowledgement: We thank the Cryo-EM Center of the University of Science and Technology
of China for the EM facility support. We thank Yaowei Wang, Yongming Luo, and Nemanja
Vukašinović (VIB-UGhent, Belgium) for useful discussions and technical support.
L.S. is supported by an Outstanding Young Scholar Award from the Qiu Shi Science
and Technologies Foundation and a Young Scholar Award from the Cyrus Tang Foundation.
No conflict of interest is declared.
article_number: '101181'
article_processing_charge: Yes
article_type: original
author:
- first_name: H
full_name: Wei, H
last_name: Wei
- first_name: H
full_name: Zhu, H
last_name: Zhu
- first_name: W
full_name: Ying, W
last_name: Ying
- first_name: H
full_name: Janssens, H
last_name: Janssens
- first_name: M
full_name: Kvasnica, M
last_name: Kvasnica
- first_name: JM
full_name: Winne, JM
last_name: Winne
- first_name: Y
full_name: Gao, Y
last_name: Gao
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Q
full_name: Ma, Q
last_name: Ma
- first_name: S
full_name: Tan, S
last_name: Tan
- first_name: X
full_name: Liu, X
last_name: Liu
- first_name: E
full_name: Russinova, E
last_name: Russinova
- first_name: L
full_name: Sun, L
last_name: Sun
citation:
ama: Wei H, Zhu H, Ying W, et al. Structural insights into brassinosteroid export
mediated by the Arabidopsis ABC transporter ABCB1. Plant Communications.
2025;6(1). doi:10.1016/j.xplc.2024.101181
apa: Wei, H., Zhu, H., Ying, W., Janssens, H., Kvasnica, M., Winne, J., … Sun, L.
(2025). Structural insights into brassinosteroid export mediated by the Arabidopsis
ABC transporter ABCB1. Plant Communications. Cell Press. https://doi.org/10.1016/j.xplc.2024.101181
chicago: Wei, H, H Zhu, W Ying, H Janssens, M Kvasnica, JM Winne, Y Gao, et al.
“Structural Insights into Brassinosteroid Export Mediated by the Arabidopsis ABC
Transporter ABCB1.” Plant Communications. Cell Press, 2025. https://doi.org/10.1016/j.xplc.2024.101181.
ieee: H. Wei et al., “Structural insights into brassinosteroid export mediated
by the Arabidopsis ABC transporter ABCB1,” Plant Communications, vol. 6,
no. 1. Cell Press, 2025.
ista: Wei H, Zhu H, Ying W, Janssens H, Kvasnica M, Winne J, Gao Y, Friml J, Ma
Q, Tan S, Liu X, Russinova E, Sun L. 2025. Structural insights into brassinosteroid
export mediated by the Arabidopsis ABC transporter ABCB1. Plant Communications.
6(1), 101181.
mla: Wei, H., et al. “Structural Insights into Brassinosteroid Export Mediated by
the Arabidopsis ABC Transporter ABCB1.” Plant Communications, vol. 6, no.
1, 101181, Cell Press, 2025, doi:10.1016/j.xplc.2024.101181.
short: H. Wei, H. Zhu, W. Ying, H. Janssens, M. Kvasnica, J. Winne, Y. Gao, J. Friml,
Q. Ma, S. Tan, X. Liu, E. Russinova, L. Sun, Plant Communications 6 (2025).
das_tickbox: '1'
dataavailabilitystatement: The ABCB1 structures in the substrate-unbound state, BL-bound
state, and ATP plus BL-bound state have been deposited in the Protein Data Bank
under accession codes 8ZPX, 8ZPZ, and 8ZQ4, respectively. The corresponding cryo-EM
density maps have been deposited in the Electron Microscopy Data Bank under accession
codes EMD-60366, EMD-60369, and EMD-60370, respectively.
date_created: 2024-12-04T11:21:16Z
date_published: 2025-01-13T00:00:00Z
date_updated: 2026-10-20T08:56:15Z
day: '13'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.xplc.2024.101181
external_id:
isi:
- '001416757300001'
pmid:
- '39497419'
file:
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checksum: 7b0e4511e43cc0da06730c3edb7c1167
content_type: application/pdf
creator: dernst
date_created: 2025-04-16T09:02:05Z
date_updated: 2025-04-16T09:02:05Z
file_id: '19575'
file_name: 2025_PlantComm_Wei.pdf
file_size: 4443183
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file_date_updated: 2025-04-16T09:02:05Z
fulldoi: https://doi.org/10.1016/j.xplc.2024.101181
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Plant Communications
publication_identifier:
issn:
- 2590-3462
publication_status: published
publisher: Cell Press
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Structural insights into brassinosteroid export mediated by the Arabidopsis
ABC transporter ABCB1
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19003'
abstract:
- lang: eng
text: 'Super-resolution methods provide far better spatial resolution than the optical
diffraction limit of about half the wavelength of light (∼200-300 nm). Nevertheless,
they have yet to attain widespread use in plants, largely due to plants’ challenging
optical properties. Expansion microscopy improves effective resolution by isotropically
increasing the physical distances between sample structures while preserving relative
spatial arrangements and clearing the sample. However, its application to plants
has been hindered by the rigid, mechanically cohesive structure of plant tissues.
Here, we report on whole-mount expansion microscopy of thale cress (Arabidopsis
thaliana) root tissues (PlantEx), achieving a four-fold resolution increase over
conventional microscopy. Our results highlight the microtubule cytoskeleton organization
and interaction between molecularly defined cellular constituents. Combining PlantEx
with stimulated emission depletion (STED) microscopy, we increase nanoscale resolution
and visualize the complex organization of subcellular organelles from intact tissues
by example of the densely packed COPI-coated vesicles associated with the Golgi
apparatus and put these into a cellular structural context. Our results show that
expansion microscopy can be applied to increase effective imaging resolution in
Arabidopsis root specimens. '
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: E-Lib
- _id: M-Shop
acknowledgement: "We gratefully acknowledge support by the Scientific Service Units
at ISTA, including the Imaging and Optics and Lab Support facilities and the mechanical
workshop and Library. We thank Philipp Velicky for STED microscope alignment.\r\nThis
project has received funding from the European Research Council under the Horizon
2020 Framework Programme (grant agreement No 742985, J.F.). It has also received
funding from the Horizon 2020 Framework Programme under the Marie Skłodowska-Curie
Grant Agreement No. 665385 (M.G.). S.T. has received funding as an ISTplus Fellow
from the Horizon 2020 Framework Programme under Marie Skłodowska-Curie grant agreement
no. 754411 and from EMBO via a Long-Term Fellowship (grant number ALTF 679-2018).
M.R.T. received funding from the Austrian Academy of Sciences with DOC fellowship
no. 26137. The project has further received funding from the Austrian Science Fund,
via grant DK W1232 (M.R.T., N.A.D., and J.G.D). W.J. received a postdoctoral fellowship
from the Human Frontier Science Program (LT000557/2018). The funders had no role
in study design, data collection and analysis, decision to publish or preparation
of the manuscript."
article_number: koaf006
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- first_name: Sven M
full_name: Truckenbrodt, Sven M
id: 45812BD4-F248-11E8-B48F-1D18A9856A87
last_name: Truckenbrodt
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Syamala
full_name: Inumella, Syamala
id: F8660870-D756-11E9-98C5-34DFE5697425
last_name: Inumella
orcid: 0009-0002-5890-120X
- first_name: Vitali
full_name: Vistunou, Vitali
id: 7e146587-8972-11ed-ae7b-d7a32ea86a81
last_name: Vistunou
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- first_name: Nathalie
full_name: Agudelo Duenas, Nathalie
id: 40E7F008-F248-11E8-B48F-1D18A9856A87
last_name: Agudelo Duenas
- first_name: Jakob
full_name: Vorlaufer, Jakob
id: 937696FA-C996-11E9-8C7C-CF13E6697425
last_name: Vorlaufer
orcid: 0009-0000-7590-3501
- first_name: Wiebke
full_name: Jahr, Wiebke
id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
last_name: Jahr
orcid: 0000-0003-0201-2315
- first_name: Marek
full_name: Randuch, Marek
id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
last_name: Randuch
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Gallei MC, Truckenbrodt SM, Kreuzinger C, et al. Super-resolution expansion
microscopy in plant roots. The Plant Cell. 2025;37(4). doi:10.1093/plcell/koaf006
apa: Gallei, M. C., Truckenbrodt, S. M., Kreuzinger, C., Inumella, S., Vistunou,
V., Sommer, C. M., … Danzl, J. G. (2025). Super-resolution expansion microscopy
in plant roots. The Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koaf006
chicago: Gallei, Michelle C, Sven M Truckenbrodt, Caroline Kreuzinger, Syamala Inumella,
Vitali Vistunou, Christoph M Sommer, Mojtaba Tavakoli, et al. “Super-Resolution
Expansion Microscopy in Plant Roots.” The Plant Cell. Oxford University
Press, 2025. https://doi.org/10.1093/plcell/koaf006.
ieee: M. C. Gallei et al., “Super-resolution expansion microscopy in plant
roots,” The Plant Cell, vol. 37, no. 4. Oxford University Press, 2025.
ista: Gallei MC, Truckenbrodt SM, Kreuzinger C, Inumella S, Vistunou V, Sommer CM,
Tavakoli M, Agudelo Duenas N, Vorlaufer J, Jahr W, Randuch M, Johnson AJ, Benková
E, Friml J, Danzl JG. 2025. Super-resolution expansion microscopy in plant roots.
The Plant Cell. 37(4), koaf006.
mla: Gallei, Michelle C., et al. “Super-Resolution Expansion Microscopy in Plant
Roots.” The Plant Cell, vol. 37, no. 4, koaf006, Oxford University Press,
2025, doi:10.1093/plcell/koaf006.
short: M.C. Gallei, S.M. Truckenbrodt, C. Kreuzinger, S. Inumella, V. Vistunou,
C.M. Sommer, M. Tavakoli, N. Agudelo Duenas, J. Vorlaufer, W. Jahr, M. Randuch,
A.J. Johnson, E. Benková, J. Friml, J.G. Danzl, The Plant Cell 37 (2025).
corr_author: '1'
date_created: 2025-02-05T06:52:06Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2026-10-20T09:19:12Z
day: '01'
ddc:
- '580'
department:
- _id: EvBe
- _id: JoDa
- _id: JiFr
doi: 10.1093/plcell/koaf006
ec_funded: 1
external_id:
isi:
- '001462763100001'
pmid:
- '39792900'
file:
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checksum: 9d3f8218ff37a29f29c48a7bbe831bd3
content_type: application/pdf
creator: dernst
date_created: 2025-07-31T07:03:43Z
date_updated: 2025-07-31T07:03:43Z
file_id: '20092'
file_name: 2025_PlantCell_Gallei.pdf
file_size: 53904111
relation: main_file
success: 1
file_date_updated: 2025-07-31T07:03:43Z
fulldoi: https://doi.org/10.1093/plcell/koaf006
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 269B5B22-B435-11E9-9278-68D0E5697425
grant_number: ALTF 679-2018
name: UltraX - achieving sub-nanometer resolution in light microscopy using iterative
X10 microscopy in combination with nanobodies and STED
- _id: 6285a163-2b32-11ec-9570-8e204ca2dba5
grant_number: '26137'
name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
Microscopy
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: The Plant Cell
publication_identifier:
eissn:
- 1532-298X
issn:
- 1040-4651
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '18837'
relation: research_data
status: public
- id: '18689'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Super-resolution expansion microscopy in plant roots
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20452'
abstract:
- lang: eng
text: Accurate modeling of long-range forces is critical in atomistic simulations,
as they play a central role in determining the properties of material and chemical
systems. However, standard machine learning interatomic potentials (MLIPs) often
rely on short-range approximations, limiting their applicability to systems with
significant electrostatics and dispersion forces. We recently introduced the Latent
Ewald Summation (LES) method, which captures long-range electrostatics without
explicitly learning atomic charges or charge equilibration. We benchmark LES on
diverse and challenging systems, including charged molecules, ionic liquids, electrolyte
solutions, polar dipeptides, surface adsorption, electrolyte/solid interfaces,
and solid-solid interfaces. Here we show that LES can reproduce the exact atomic
charges for classical systems with fixed charges and can infer dipole and quadrupole
moments, as well as the dipole derivative with respect to atomic positions, for
quantum mechanical systems. Moreover, LES can achieve better accuracy in energy
and force predictions compared to methods that explicitly learn from charges.
acknowledgement: We thank Chunyi Zhang for providing the TiO2(101)/NaCl+NaOH+HCl(aq)
dataset and for useful discussions. We thank Jia-Xin Zhu for providing the Pt(111)/KF(aq)
dataset. We thank Tsz Wai Ko and Jonas Finkler for useful discussions and for the
DFT-optimized Au2-MgO(001) structures. We thank Junmin Chen for discussions. D.K
and B.C. acknowledge funding from Toyota Research Institute Synthesis Advanced Research
Challenge. D.S.K. and P.Z. acknowledge funding from BIDMaP Postdoctoral Fellowship.
article_number: '8763'
article_processing_charge: Yes
article_type: original
author:
- first_name: Daniel S.
full_name: King, Daniel S.
last_name: King
- first_name: Dongjin
full_name: Kim, Dongjin
last_name: Kim
- first_name: Peichen
full_name: Zhong, Peichen
last_name: Zhong
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: King DS, Kim D, Zhong P, Cheng B. Machine learning of charges and long-range
interactions from energies and forces. Nature Communications. 2025;16.
doi:10.1038/s41467-025-63852-x
apa: King, D. S., Kim, D., Zhong, P., & Cheng, B. (2025). Machine learning of
charges and long-range interactions from energies and forces. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-025-63852-x
chicago: King, Daniel S., Dongjin Kim, Peichen Zhong, and Bingqing Cheng. “Machine
Learning of Charges and Long-Range Interactions from Energies and Forces.” Nature
Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-025-63852-x.
ieee: D. S. King, D. Kim, P. Zhong, and B. Cheng, “Machine learning of charges and
long-range interactions from energies and forces,” Nature Communications,
vol. 16. Springer Nature, 2025.
ista: King DS, Kim D, Zhong P, Cheng B. 2025. Machine learning of charges and long-range
interactions from energies and forces. Nature Communications. 16, 8763.
mla: King, Daniel S., et al. “Machine Learning of Charges and Long-Range Interactions
from Energies and Forces.” Nature Communications, vol. 16, 8763, Springer
Nature, 2025, doi:10.1038/s41467-025-63852-x.
short: D.S. King, D. Kim, P. Zhong, B. Cheng, Nature Communications 16 (2025).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: The training sets, training scripts, MD input files, and
trained CACE potentials are available at https://github.com/BingqingCheng/cace-lr-fit;
see https://doi.org/10.5281/zenodo.16415061. Source data for all figures are provided
with this paper. Source data are provided with this paper.
date_created: 2025-10-12T22:01:25Z
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title: Machine learning of charges and long-range interactions from energies and forces
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abstract:
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text: Moran Birth-death process is a standard stochastic process that is used to
model natural selection in spatially structured populations. A newly occurring
mutation that invades a population of residents can either fixate on the whole
population or it can go extinct due to random drift. The duration of the process
depends not only on the total population size n, but also on the spatial structure
of the population. In this work, we consider the Moran process with a single type
of individuals who invade and colonize an otherwise empty environment. Mathematically,
this corresponds to the setting where the residents have zero reproduction rate,
thus they never reproduce. The spatial structure is represented by a graph. We
present two main contributions. First, in contrast to the Moran process in which
residents do reproduce, we show that the colonization time is always at most a
polynomial function of the population size n. Namely, we show that colonization
always takes at most 1/2n^3 - 1/2n^2 expected steps, and for each n, we identify
the slowest graph where it takes exactly that many steps. Moreover, we establish
a stronger bound of roughly n^2.5 steps for undirected graphs and an even stronger
bound of roughly n^2 steps for so-called regular graphs. Second, we discuss various
complications that one faces when attempting to measure fixation times and colonization
times in spatially structured populations, and we propose to measure the real
duration of the process, rather than counting the steps of the classic Moran process.
article_processing_charge: Yes
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arxiv: 1
author:
- first_name: Lenka
full_name: Kopfová, Lenka
id: 17691681-50b9-11ef-ad56-edf4cacb21b0
last_name: Kopfová
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
citation:
ama: Kopfová L, Tkadlec J. Colonization times in Moran process on graphs. PLoS
Computational Biology. 2025;21(5):e1012868. doi:10.1371/journal.pcbi.1012868
apa: Kopfová, L., & Tkadlec, J. (2025). Colonization times in Moran process
on graphs. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1012868
chicago: Kopfová, Lenka, and Josef Tkadlec. “Colonization Times in Moran Process
on Graphs.” PLoS Computational Biology. Public Library of Science, 2025.
https://doi.org/10.1371/journal.pcbi.1012868.
ieee: L. Kopfová and J. Tkadlec, “Colonization times in Moran process on graphs,”
PLoS Computational Biology, vol. 21, no. 5. Public Library of Science,
p. e1012868, 2025.
ista: Kopfová L, Tkadlec J. 2025. Colonization times in Moran process on graphs.
PLoS Computational Biology. 21(5), e1012868.
mla: Kopfová, Lenka, and Josef Tkadlec. “Colonization Times in Moran Process on
Graphs.” PLoS Computational Biology, vol. 21, no. 5, Public Library of
Science, 2025, p. e1012868, doi:10.1371/journal.pcbi.1012868.
short: L. Kopfová, J. Tkadlec, PLoS Computational Biology 21 (2025) e1012868.
date_created: 2025-05-18T22:02:50Z
date_published: 2025-05-01T00:00:00Z
date_updated: 2026-10-20T09:45:59Z
day: '01'
ddc:
- '000'
department:
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doi: 10.1371/journal.pcbi.1012868
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language:
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oa_version: Published Version
page: e1012868
publication: PLoS Computational Biology
publication_identifier:
eissn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Colonization times in Moran process on graphs
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
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type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2025'
...