---
_id: '11448'
abstract:
- lang: eng
text: Studies of protein fitness landscapes reveal biophysical constraints guiding
protein evolution and empower prediction of functional proteins. However, generalisation
of these findings is limited due to scarceness of systematic data on fitness landscapes
of proteins with a defined evolutionary relationship. We characterized the fitness
peaks of four orthologous fluorescent proteins with a broad range of sequence
divergence. While two of the four studied fitness peaks were sharp, the other
two were considerably flatter, being almost entirely free of epistatic interactions.
Mutationally robust proteins, characterized by a flat fitness peak, were not optimal
templates for machine-learning-driven protein design – instead, predictions were
more accurate for fragile proteins with epistatic landscapes. Our work paves insights
for practical application of fitness landscape heterogeneity in protein engineering.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
acknowledgement: "We thank Ondřej Draganov, Rodrigo Redondo, Bor Kavčič, Mia Juračić
and Andrea Pauli for discussion and technical advice. We thank Anita Testa Salmazo
for advice on resin protein purification, Dmitry Bolotin and the Milaboratory (milaboratory.com)
for access to computing and storage infrastructure, and Josef Houser and Eva Fujdiarova
for technical assistance and data interpretation. Core facility Biomolecular Interactions
and Crystallization of CEITEC Masaryk University is gratefully acknowledged for
the obtaining of the scientific data presented in this paper. This research was
supported by the Scientific Service Units (SSU) of IST-Austria\r\nthrough resources
provided by the Bioimaging Facility (BIF), and the Life Science Facility (LSF).
MiSeq and HiSeq NGS sequencing was performed by the Next Generation Sequencing Facility
at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC),
Austria. FACS was performed at the BioOptics Facility of the Institute of Molecular
Pathology (IMP), Austria. We also thank the Biomolecular Crystallography Facility
in the Vanderbilt University Center for Structural Biology. We are grateful to Joel
M Harp for help with X-ray data collection. This work was supported by the ERC Consolidator
grant to FAK (771209—CharFL). KSS acknowledges support by President’s Grant МК–5405.2021.1.4,
the Imperial College Research Fellowship and the MRC London Institute of Medical
Sciences (UKRI MC-A658-5QEA0).\r\nAF is supported by the Marie Skłodowska-Curie
Fellowship (H2020-MSCA-IF-2019, Grant Agreement No. 898203, Project acronym \"FLINDIP\").
Experiments were partially carried out using equipment provided by the Institute
of Bioorganic Chemistry of the Russian Academy of Sciences Сore Facility (CKP IBCH).
This work was supported by a Russian Science Foundation grant 19-74-10102.This project
has received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 665,385."
article_number: '75842'
article_processing_charge: No
article_type: original
author:
- first_name: Louisa
full_name: Gonzalez Somermeyer, Louisa
id: 4720D23C-F248-11E8-B48F-1D18A9856A87
last_name: Gonzalez Somermeyer
orcid: 0000-0001-9139-5383
- first_name: Aubin
full_name: Fleiss, Aubin
last_name: Fleiss
- first_name: Alexander S
full_name: Mishin, Alexander S
last_name: Mishin
- first_name: Nina G
full_name: Bozhanova, Nina G
last_name: Bozhanova
- first_name: Anna A
full_name: Igolkina, Anna A
last_name: Igolkina
- first_name: Jens
full_name: Meiler, Jens
last_name: Meiler
- first_name: Maria-Elisenda
full_name: Alaball Pujol, Maria-Elisenda
last_name: Alaball Pujol
- first_name: Ekaterina V
full_name: Putintseva, Ekaterina V
last_name: Putintseva
- first_name: Karen S
full_name: Sarkisyan, Karen S
last_name: Sarkisyan
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Gonzalez Somermeyer L, Fleiss A, Mishin AS, et al. Heterogeneity of the GFP
fitness landscape and data-driven protein design. eLife. 2022;11. doi:10.7554/elife.75842
apa: Gonzalez Somermeyer, L., Fleiss, A., Mishin, A. S., Bozhanova, N. G., Igolkina,
A. A., Meiler, J., … Kondrashov, F. (2022). Heterogeneity of the GFP fitness landscape
and data-driven protein design. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.75842
chicago: Gonzalez Somermeyer, Louisa, Aubin Fleiss, Alexander S Mishin, Nina G Bozhanova,
Anna A Igolkina, Jens Meiler, Maria-Elisenda Alaball Pujol, Ekaterina V Putintseva,
Karen S Sarkisyan, and Fyodor Kondrashov. “Heterogeneity of the GFP Fitness Landscape
and Data-Driven Protein Design.” ELife. eLife Sciences Publications, 2022.
https://doi.org/10.7554/elife.75842.
ieee: L. Gonzalez Somermeyer et al., “Heterogeneity of the GFP fitness landscape
and data-driven protein design,” eLife, vol. 11. eLife Sciences Publications,
2022.
ista: Gonzalez Somermeyer L, Fleiss A, Mishin AS, Bozhanova NG, Igolkina AA, Meiler
J, Alaball Pujol M-E, Putintseva EV, Sarkisyan KS, Kondrashov F. 2022. Heterogeneity
of the GFP fitness landscape and data-driven protein design. eLife. 11, 75842.
mla: Gonzalez Somermeyer, Louisa, et al. “Heterogeneity of the GFP Fitness Landscape
and Data-Driven Protein Design.” ELife, vol. 11, 75842, eLife Sciences
Publications, 2022, doi:10.7554/elife.75842.
short: L. Gonzalez Somermeyer, A. Fleiss, A.S. Mishin, N.G. Bozhanova, A.A. Igolkina,
J. Meiler, M.-E. Alaball Pujol, E.V. Putintseva, K.S. Sarkisyan, F. Kondrashov,
ELife 11 (2022).
corr_author: '1'
date_created: 2022-06-18T09:06:59Z
date_published: 2022-05-05T00:00:00Z
date_updated: 2026-04-07T13:25:01Z
day: '05'
ddc:
- '570'
department:
- _id: GradSch
- _id: FyKo
doi: 10.7554/elife.75842
ec_funded: 1
external_id:
isi:
- '000799197200001'
pmid:
- '35510622'
file:
- access_level: open_access
checksum: 7573c28f44028ab0cc81faef30039e44
content_type: application/pdf
creator: dernst
date_created: 2022-06-20T07:44:19Z
date_updated: 2022-06-20T07:44:19Z
file_id: '11454'
file_name: 2022_eLife_Somermeyer.pdf
file_size: 5297213
relation: main_file
success: 1
file_date_updated: 2022-06-20T07:44:19Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/aequorea238/Orthologous_GFP_Fitness_Peaks
record:
- id: '17850'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Heterogeneity of the GFP fitness landscape and data-driven protein design
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: 11
year: '2022'
...
---
_id: '11734'
abstract:
- lang: eng
text: Mineral nutrition is one of the key environmental factors determining plant
development and growth. Nitrate is the major form of macronutrient nitrogen that
plants take up from the soil. Fluctuating availability or deficiency of this element
severely limits plant growth and negatively affects crop production in the agricultural
system. To cope with the heterogeneity of nitrate distribution in soil, plants
evolved a complex regulatory mechanism that allows rapid adjustment of physiological
and developmental processes to the status of this nutrient. The root, as a major
exploitation organ that controls the uptake of nitrate to the plant body, acts
as a regulatory hub that, according to nitrate availability, coordinates the growth
and development of other plant organs. Here, we identified a regulatory framework,
where cytokinin response factors (CRFs) play a central role as a molecular readout
of the nitrate status in roots to guide shoot adaptive developmental response.
We show that nitrate-driven activation of NLP7, a master regulator of nitrate
response in plants, fine tunes biosynthesis of cytokinin in roots and its translocation
to shoots where it enhances expression of CRFs. CRFs, through direct transcriptional
regulation of PIN auxin transporters, promote the flow of auxin and thereby stimulate
the development of shoot organs.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: "We acknowledge Hana Semeradova, Juan Carlos Montesinos, Nicola Cavallari,
Marc¸al Gallem\x03ı, Kaori Tabata, Andrej Hurn\x03y, and Sascha Waidmann for sharing
materials; and Marina Borges Osorio for critical reading of the manuscript. Work
in the E. Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S)
to K.O., R.A., and E. Benkova. We acknowledge the Bioimaging Facility and Life Science
Facilities of the Institute of Science\r\nand Technology Austria. We give sincere
thanks to Hana Martınkova and Petra Amakorova for their help with cytokinin analyses.
This work was funded by the Czech Science Foundation (Project No. 19-00973S)."
article_number: e2122460119
article_processing_charge: No
article_type: original
author:
- first_name: Rashed
full_name: Abualia, Rashed
id: 4827E134-F248-11E8-B48F-1D18A9856A87
last_name: Abualia
orcid: 0000-0002-9357-9415
- first_name: Krisztina
full_name: Ötvös, Krisztina
id: 29B901B0-F248-11E8-B48F-1D18A9856A87
last_name: Ötvös
orcid: 0000-0002-5503-4983
- first_name: Ondřej
full_name: Novák, Ondřej
last_name: Novák
- first_name: Eleonore
full_name: Bouguyon, Eleonore
last_name: Bouguyon
- first_name: Kevin
full_name: Domanegg, Kevin
id: a24c7829-16e8-11ed-8527-c4d36ffb7539
last_name: Domanegg
orcid: 0000-0002-1215-4264
- first_name: Anne
full_name: Krapp, Anne
last_name: Krapp
- first_name: Philip
full_name: Nacry, Philip
last_name: Nacry
- first_name: Alain
full_name: Gojon, Alain
last_name: Gojon
- first_name: Benoit
full_name: Lacombe, Benoit
last_name: Lacombe
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Abualia R, Ötvös K, Novák O, et al. Molecular framework integrating nitrate
sensing in root and auxin-guided shoot adaptive responses. Proceedings of the
National Academy of Sciences of the United States of America. 2022;119(31).
doi:10.1073/pnas.2122460119
apa: Abualia, R., Ötvös, K., Novák, O., Bouguyon, E., Domanegg, K., Krapp, A., …
Benková, E. (2022). Molecular framework integrating nitrate sensing in root and
auxin-guided shoot adaptive responses. Proceedings of the National Academy
of Sciences of the United States of America. National Academy of Sciences.
https://doi.org/10.1073/pnas.2122460119
chicago: Abualia, Rashed, Krisztina Ötvös, Ondřej Novák, Eleonore Bouguyon, Kevin
Domanegg, Anne Krapp, Philip Nacry, Alain Gojon, Benoit Lacombe, and Eva Benková.
“Molecular Framework Integrating Nitrate Sensing in Root and Auxin-Guided Shoot
Adaptive Responses.” Proceedings of the National Academy of Sciences of the
United States of America. National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2122460119.
ieee: R. Abualia et al., “Molecular framework integrating nitrate sensing
in root and auxin-guided shoot adaptive responses,” Proceedings of the National
Academy of Sciences of the United States of America, vol. 119, no. 31. National
Academy of Sciences, 2022.
ista: Abualia R, Ötvös K, Novák O, Bouguyon E, Domanegg K, Krapp A, Nacry P, Gojon
A, Lacombe B, Benková E. 2022. Molecular framework integrating nitrate sensing
in root and auxin-guided shoot adaptive responses. Proceedings of the National
Academy of Sciences of the United States of America. 119(31), e2122460119.
mla: Abualia, Rashed, et al. “Molecular Framework Integrating Nitrate Sensing in
Root and Auxin-Guided Shoot Adaptive Responses.” Proceedings of the National
Academy of Sciences of the United States of America, vol. 119, no. 31, e2122460119,
National Academy of Sciences, 2022, doi:10.1073/pnas.2122460119.
short: R. Abualia, K. Ötvös, O. Novák, E. Bouguyon, K. Domanegg, A. Krapp, P. Nacry,
A. Gojon, B. Lacombe, E. Benková, Proceedings of the National Academy of Sciences
of the United States of America 119 (2022).
corr_author: '1'
date_created: 2022-08-07T22:01:57Z
date_published: 2022-07-25T00:00:00Z
date_updated: 2025-05-14T11:00:29Z
day: '25'
ddc:
- '570'
department:
- _id: EvBe
doi: 10.1073/pnas.2122460119
external_id:
isi:
- '000881496900007'
pmid:
- '35878040'
file:
- access_level: open_access
checksum: 6e97dedc281247fc3fe238a209f14af0
content_type: application/pdf
creator: dernst
date_created: 2022-08-08T07:09:58Z
date_updated: 2022-08-08T07:09:58Z
file_id: '11744'
file_name: 2022_PNAS_Abualia.pdf
file_size: 3092330
relation: main_file
success: 1
file_date_updated: 2022-08-08T07:09:58Z
has_accepted_license: '1'
intvolume: ' 119'
isi: 1
issue: '31'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2542D156-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 1774-B16
name: Hormone cross-talk drives nutrient dependent plant development
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Molecular framework integrating nitrate sensing in root and auxin-guided shoot
adaptive responses
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: 119
year: '2022'
...
---
OA_place: publisher
_id: '11945'
abstract:
- lang: eng
text: "G protein-coupled receptors (GPCRs) respond to specific ligands and regulate
multiple processes ranging from cell growth and immune responses to neuronal signal
transmission. However, ligands for many GPCRs remain unknown, suffer from off-target
effects or have poor bioavailability. Additional challenges exist to dissect cell-type
specific responses when the same GPCR is expressed on several cell types within
the body. Here, we overcome these limitations by engineering DREADD-based GPCR
chimeras that selectively bind their agonist clozapine-N-oxide (CNO) and mimic
a GPCR-of-interest in a desired cell type.\r\nWe validated our approach with β2-adrenergic
receptor (β2AR/ADRB2) and show that our chimeric DREADD-β2AR triggers comparable
responses on second messenger and kinase activity, post-translational modifications,
and protein-protein interactions. Since β2AR is also enriched in microglia, which
can drive inflammation in the central nervous system, we expressed chimeric DREADD-β2AR
in primary microglia and successfully recapitulate β2AR-mediated filopodia formation
through CNO stimulation. To dissect the role of selected GPCRs during microglial
inflammation, we additionally generated DREADD-based chimeras for microglia-enriched
GPR65 and GPR109A/HCAR2. In a microglia cell line, DREADD-β2AR and DREADD-GPR65
both modulated the inflammatory response with a similar profile as endogenously
expressed β2AR, while DREADD-GPR109A showed no impact.\r\nOur DREADD-based approach
provides the means to obtain mechanistic and functional insights into GPCR signaling
on a cell-type specific level."
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Rouven
full_name: Schulz, Rouven
id: 4C5E7B96-F248-11E8-B48F-1D18A9856A87
last_name: Schulz
orcid: 0000-0001-5297-733X
citation:
ama: Schulz R. Chimeric G protein-coupled receptors mimic distinct signaling pathways
and modulate microglia function. 2022. doi:10.15479/at:ista:11945
apa: Schulz, R. (2022). Chimeric G protein-coupled receptors mimic distinct signaling
pathways and modulate microglia function. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:11945
chicago: Schulz, Rouven. “Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling
Pathways and Modulate Microglia Function.” Institute of Science and Technology
Austria, 2022. https://doi.org/10.15479/at:ista:11945.
ieee: R. Schulz, “Chimeric G protein-coupled receptors mimic distinct signaling
pathways and modulate microglia function,” Institute of Science and Technology
Austria, 2022.
ista: Schulz R. 2022. Chimeric G protein-coupled receptors mimic distinct signaling
pathways and modulate microglia function. Institute of Science and Technology
Austria.
mla: Schulz, Rouven. Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling
Pathways and Modulate Microglia Function. Institute of Science and Technology
Austria, 2022, doi:10.15479/at:ista:11945.
short: R. Schulz, Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling
Pathways and Modulate Microglia Function, Institute of Science and Technology
Austria, 2022.
corr_author: '1'
date_created: 2022-08-23T11:33:11Z
date_published: 2022-08-23T00:00:00Z
date_updated: 2026-04-07T14:17:59Z
day: '23'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: SaSi
doi: 10.15479/at:ista:11945
file:
- access_level: open_access
checksum: 61b1b666a210ff7cdd0e95ea75207a13
content_type: application/pdf
creator: rschulz
date_created: 2022-08-25T08:59:57Z
date_updated: 2022-08-25T08:59:57Z
file_id: '11970'
file_name: Thesis_Rouven_Schulz_2022_final.pdf
file_size: 28079331
relation: main_file
success: 1
- access_level: closed
checksum: 2b8f95ea1c134dbdb927b41b1dbeeeb5
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: rschulz
date_created: 2022-08-25T09:00:11Z
date_updated: 2022-08-25T09:33:31Z
file_id: '11971'
file_name: Thesis_Rouven_Schulz_2022_final.docx
file_size: 27226963
relation: source_file
file_date_updated: 2022-08-25T09:33:31Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '133'
project:
- _id: 267F75D8-B435-11E9-9278-68D0E5697425
name: Modulating microglia through G protein-coupled receptor (GPCR) signaling
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11995'
relation: dissertation_contains
status: public
status: public
supervisor:
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
title: Chimeric G protein-coupled receptors mimic distinct signaling pathways and
modulate microglia function
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2022'
...
---
_id: '11951'
abstract:
- lang: eng
text: The mammalian hippocampal formation (HF) plays a key role in several higher
brain functions, such as spatial coding, learning and memory. Its simple circuit
architecture is often viewed as a trisynaptic loop, processing input originating
from the superficial layers of the entorhinal cortex (EC) and sending it back
to its deeper layers. Here, we show that excitatory neurons in layer 6b of the
mouse EC project to all sub-regions comprising the HF and receive input from the
CA1, thalamus and claustrum. Furthermore, their output is characterized by unique
slow-decaying excitatory postsynaptic currents capable of driving plateau-like
potentials in their postsynaptic targets. Optogenetic inhibition of the EC-6b
pathway affects spatial coding in CA1 pyramidal neurons, while cell ablation impairs
not only acquisition of new spatial memories, but also degradation of previously
acquired ones. Our results provide evidence of a functional role for cortical
layer 6b neurons in the adult brain.
acknowledged_ssus:
- _id: Bio
- _id: SSU
acknowledgement: We thank F. Marr and A. Schlögl for technical assistance, E. Kralli-Beller
for manuscript editing, as well as C. Sommer and the Imaging and Optics Facility
of the Institute of Science and Technology Austria (ISTA) for image analysis scripts
and microscopy support. We extend our gratitude to J. Wallenschus and D. Rangel
Guerrero for technical assistance acquiring single-unit data and I. Gridchyn for
help with single-unit clustering. Finally, we also thank B. Suter for discussions,
A. Saunders, M. Jösch, and H. Monyer for critically reading earlier versions of
the manuscript, C. Petersen for sharing clearing protocols, and the Scientific Service
Units of ISTA for efficient support. This project was funded by the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
(ERC advanced grant No 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen
Forschung (Z 312-B27, Wittgenstein award for P.J. and I3600-B27 for J.G.D. and P.V.).
article_number: '4826'
article_processing_charge: No
article_type: original
author:
- first_name: Yoav
full_name: Ben Simon, Yoav
id: 43DF3136-F248-11E8-B48F-1D18A9856A87
last_name: Ben Simon
- first_name: Karola
full_name: Käfer, Karola
id: 2DAA49AA-F248-11E8-B48F-1D18A9856A87
last_name: Käfer
- first_name: Philipp
full_name: Velicky, Philipp
id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
last_name: Velicky
orcid: 0000-0002-2340-7431
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- 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: Ben Simon Y, Käfer K, Velicky P, Csicsvari JL, Danzl JG, Jonas PM. A direct
excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes
to spatial coding and memory. Nature Communications. 2022;13. doi:10.1038/s41467-022-32559-8
apa: Ben Simon, Y., Käfer, K., Velicky, P., Csicsvari, J. L., Danzl, J. G., &
Jonas, P. M. (2022). A direct excitatory projection from entorhinal layer 6b neurons
to the hippocampus contributes to spatial coding and memory. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-022-32559-8
chicago: Ben Simon, Yoav, Karola Käfer, Philipp Velicky, Jozsef L Csicsvari, Johann
G Danzl, and Peter M Jonas. “A Direct Excitatory Projection from Entorhinal Layer
6b Neurons to the Hippocampus Contributes to Spatial Coding and Memory.” Nature
Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-32559-8.
ieee: Y. Ben Simon, K. Käfer, P. Velicky, J. L. Csicsvari, J. G. Danzl, and P. M.
Jonas, “A direct excitatory projection from entorhinal layer 6b neurons to the
hippocampus contributes to spatial coding and memory,” Nature Communications,
vol. 13. Springer Nature, 2022.
ista: Ben Simon Y, Käfer K, Velicky P, Csicsvari JL, Danzl JG, Jonas PM. 2022. A
direct excitatory projection from entorhinal layer 6b neurons to the hippocampus
contributes to spatial coding and memory. Nature Communications. 13, 4826.
mla: Ben Simon, Yoav, et al. “A Direct Excitatory Projection from Entorhinal Layer
6b Neurons to the Hippocampus Contributes to Spatial Coding and Memory.” Nature
Communications, vol. 13, 4826, Springer Nature, 2022, doi:10.1038/s41467-022-32559-8.
short: Y. Ben Simon, K. Käfer, P. Velicky, J.L. Csicsvari, J.G. Danzl, P.M. Jonas,
Nature Communications 13 (2022).
corr_author: '1'
date_created: 2022-08-24T08:25:50Z
date_published: 2022-08-16T00:00:00Z
date_updated: 2025-06-12T06:10:44Z
day: '16'
ddc:
- '570'
department:
- _id: JoCs
- _id: PeJo
- _id: JoDa
doi: 10.1038/s41467-022-32559-8
ec_funded: 1
external_id:
isi:
- '000841396400008'
pmid:
- '35974109'
file:
- access_level: open_access
checksum: 405936d9e4d33625d80c093c9713a91f
content_type: application/pdf
creator: dernst
date_created: 2022-08-26T11:51:40Z
date_updated: 2022-08-26T11:51:40Z
file_id: '11990'
file_name: 2022_NatureCommunications_BenSimon.pdf
file_size: 5910357
relation: main_file
success: 1
file_date_updated: 2022-08-26T11:51:40Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 265CB4D0-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03600
name: Optical control of synaptic function via adhesion molecules
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus
contributes to spatial coding and memory
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2022'
...
---
_id: '11995'
abstract:
- lang: eng
text: G protein-coupled receptors (GPCRs) regulate processes ranging from immune
responses to neuronal signaling. However, ligands for many GPCRs remain unknown,
suffer from off-target effects or have poor bioavailability. Additionally, dissecting
cell type-specific responses is challenging when the same GPCR is expressed on
different cells within a tissue. Here, we overcome these limitations by engineering
DREADD-based GPCR chimeras that bind clozapine-N-oxide and mimic a GPCR-of-interest.
We show that chimeric DREADD-β2AR triggers responses comparable to β2AR on second
messenger and kinase activity, post-translational modifications, and protein-protein
interactions. Moreover, we successfully recapitulate β2AR-mediated filopodia formation
in microglia, an immune cell capable of driving central nervous system inflammation.
When dissecting microglial inflammation, we included two additional DREADD-based
chimeras mimicking microglia-enriched GPR65 and GPR109A. DREADD-β2AR and DREADD-GPR65
modulate the inflammatory response with high similarity to endogenous β2AR, while
DREADD-GPR109A shows no impact. Our DREADD-based approach allows investigation
of cell type-dependent pathways without known endogenous ligands.
acknowledged_ssus:
- _id: PreCl
- _id: Bio
- _id: LifeSc
acknowledgement: The authors thank the Scientific Service Units at ISTA, in particular
the Molecular Biology Service of the Lab Support Facility, Imaging & Optics Facility,
and the Preclinical Facility, and the Novarino group, Harald Janoviak, and Marco
Benevento for sharing reagents and expertise. This research was supported by a DOC
Fellowship (24979) awarded to R.S. by the Austrian Academy of Sciences.
article_number: '4728'
article_processing_charge: No
article_type: original
author:
- first_name: Rouven
full_name: Schulz, Rouven
id: 4C5E7B96-F248-11E8-B48F-1D18A9856A87
last_name: Schulz
orcid: 0000-0001-5297-733X
- first_name: Medina
full_name: Korkut, Medina
id: 4B51CE74-F248-11E8-B48F-1D18A9856A87
last_name: Korkut
orcid: 0000-0003-4309-2251
- first_name: Alessandro
full_name: Venturino, Alessandro
id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
last_name: Venturino
orcid: 0000-0003-2356-9403
- first_name: Gloria
full_name: Colombo, Gloria
id: 3483CF6C-F248-11E8-B48F-1D18A9856A87
last_name: Colombo
orcid: 0000-0001-9434-8902
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
citation:
ama: Schulz R, Korkut M, Venturino A, Colombo G, Siegert S. Chimeric GPCRs mimic
distinct signaling pathways and modulate microglia responses. Nature Communications.
2022;13. doi:10.1038/s41467-022-32390-1
apa: Schulz, R., Korkut, M., Venturino, A., Colombo, G., & Siegert, S. (2022).
Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses.
Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-32390-1
chicago: Schulz, Rouven, Medina Korkut, Alessandro Venturino, Gloria Colombo, and
Sandra Siegert. “Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate
Microglia Responses.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-32390-1.
ieee: R. Schulz, M. Korkut, A. Venturino, G. Colombo, and S. Siegert, “Chimeric
GPCRs mimic distinct signaling pathways and modulate microglia responses,” Nature
Communications, vol. 13. Springer Nature, 2022.
ista: Schulz R, Korkut M, Venturino A, Colombo G, Siegert S. 2022. Chimeric GPCRs
mimic distinct signaling pathways and modulate microglia responses. Nature Communications.
13, 4728.
mla: Schulz, Rouven, et al. “Chimeric GPCRs Mimic Distinct Signaling Pathways and
Modulate Microglia Responses.” Nature Communications, vol. 13, 4728, Springer
Nature, 2022, doi:10.1038/s41467-022-32390-1.
short: R. Schulz, M. Korkut, A. Venturino, G. Colombo, S. Siegert, Nature Communications
13 (2022).
corr_author: '1'
date_created: 2022-08-28T22:01:59Z
date_published: 2022-08-15T00:00:00Z
date_updated: 2026-04-07T14:17:58Z
day: '15'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1038/s41467-022-32390-1
external_id:
isi:
- '000840984400032'
pmid:
- '35970889'
file:
- access_level: open_access
checksum: 191d9db0266e14a28d3a56dc7f65da84
content_type: application/pdf
creator: cchlebak
date_created: 2022-08-29T06:44:30Z
date_updated: 2022-08-29T06:44:30Z
file_id: '12002'
file_name: 2022_NatComm_Schulz.pdf
file_size: 7317396
relation: main_file
success: 1
file_date_updated: 2022-08-29T06:44:30Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 267F75D8-B435-11E9-9278-68D0E5697425
name: Modulating microglia through G protein-coupled receptor (GPCR) signaling
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/dreaddful-mimicry/
record:
- id: '11542'
relation: research_data
status: public
- id: '11945'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13
year: '2022'
...
---
_id: '12082'
abstract:
- lang: eng
text: Proximity-dependent protein labeling provides a powerful in vivo strategy
to characterize the interactomes of specific proteins. We previously optimized
a proximity labeling protocol for Caenorhabditis elegans using the highly active
biotin ligase TurboID. A significant constraint on the sensitivity of TurboID
is the presence of abundant endogenously biotinylated proteins that take up bandwidth
in the mass spectrometer, notably carboxylases that use biotin as a cofactor.
In C. elegans, these comprise POD-2/acetyl-CoA carboxylase alpha, PCCA-1/propionyl-CoA
carboxylase alpha, PYC-1/pyruvate carboxylase, and MCCC-1/methylcrotonyl-CoA carboxylase
alpha. Here, we developed ways to remove these carboxylases prior to streptavidin
purification and mass spectrometry by engineering their corresponding genes to
add a C-terminal His10 tag. This allows us to deplete them from C. elegans lysates
using immobilized metal affinity chromatography. To demonstrate the method's efficacy,
we use it to expand the interactome map of the presynaptic active zone protein
ELKS-1. We identify many known active zone proteins, including UNC-10/RIM, SYD-2/liprin-alpha,
SAD-1/BRSK1, CLA-1/CLArinet, C16E9.2/Sentryn, as well as previously uncharacterized
potentially synaptic proteins such as the ortholog of human angiomotin, F59C12.3
and the uncharacterized protein R148.3. Our approach provides a quick and inexpensive
solution to a common contaminant problem in biotin-dependent proximity labeling.
The approach may be applicable to other model organisms and will enable deeper
and more complete analysis of interactors for proteins of interest.
acknowledged_ssus:
- _id: Bio
acknowledgement: "We thank de Bono laboratory members for helpful comments on the
article and the Mass Spec Facilities at IST Austria and Max Perutz Labs for invaluable
discussions and comments on how to optimize mass spec analyses of worm samples.
We are grateful to Ekaterina Lashmanova for designing the degron knock-in constructs
and preparing the injection mixes for CRISPR/Cas9-mediated genome editing. All LC–MS/MS
analyses were performed on instruments of the Vienna BioCenter Core Facilities instrument
pool.\r\nThis work was supported by a Wellcome Investigator Award (grant no.: 209504/Z/17/Z
) to M.d.B. and an ISTplus Fellowship to M.A. (Marie Sklodowska-Curie agreement
no.: 754411)."
article_number: '102343'
article_processing_charge: No
article_type: original
author:
- first_name: Murat
full_name: Artan, Murat
id: C407B586-6052-11E9-B3AE-7006E6697425
last_name: Artan
orcid: 0000-0001-8945-6992
- first_name: Markus
full_name: Hartl, Markus
last_name: Hartl
- first_name: Weiqiang
full_name: Chen, Weiqiang
last_name: Chen
- first_name: Mario
full_name: De Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: De Bono
orcid: 0000-0001-8347-0443
citation:
ama: Artan M, Hartl M, Chen W, de Bono M. Depletion of endogenously biotinylated
carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in
Caenorhabditis elegans. Journal of Biological Chemistry. 2022;298(9). doi:10.1016/j.jbc.2022.102343
apa: Artan, M., Hartl, M., Chen, W., & de Bono, M. (2022). Depletion of endogenously
biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity
labeling in Caenorhabditis elegans. Journal of Biological Chemistry. Elsevier.
https://doi.org/10.1016/j.jbc.2022.102343
chicago: Artan, Murat, Markus Hartl, Weiqiang Chen, and Mario de Bono. “Depletion
of Endogenously Biotinylated Carboxylases Enhances the Sensitivity of TurboID-Mediated
Proximity Labeling in Caenorhabditis Elegans.” Journal of Biological Chemistry.
Elsevier, 2022. https://doi.org/10.1016/j.jbc.2022.102343.
ieee: M. Artan, M. Hartl, W. Chen, and M. de Bono, “Depletion of endogenously biotinylated
carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in
Caenorhabditis elegans,” Journal of Biological Chemistry, vol. 298, no.
9. Elsevier, 2022.
ista: Artan M, Hartl M, Chen W, de Bono M. 2022. Depletion of endogenously biotinylated
carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in
Caenorhabditis elegans. Journal of Biological Chemistry. 298(9), 102343.
mla: Artan, Murat, et al. “Depletion of Endogenously Biotinylated Carboxylases Enhances
the Sensitivity of TurboID-Mediated Proximity Labeling in Caenorhabditis Elegans.”
Journal of Biological Chemistry, vol. 298, no. 9, 102343, Elsevier, 2022,
doi:10.1016/j.jbc.2022.102343.
short: M. Artan, M. Hartl, W. Chen, M. de Bono, Journal of Biological Chemistry
298 (2022).
corr_author: '1'
date_created: 2022-09-11T22:01:55Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2025-04-14T07:44:00Z
day: '01'
ddc:
- '570'
department:
- _id: MaDe
doi: 10.1016/j.jbc.2022.102343
ec_funded: 1
external_id:
isi:
- '000884241800011'
pmid:
- '35933017'
file:
- access_level: open_access
checksum: e726c7b9315230e6710e0b1f1d1677e9
content_type: application/pdf
creator: dernst
date_created: 2022-09-12T08:14:50Z
date_updated: 2022-09-12T08:14:50Z
file_id: '12092'
file_name: 2022_JBC_Artan.pdf
file_size: 2101656
relation: main_file
success: 1
file_date_updated: 2022-09-12T08:14:50Z
has_accepted_license: '1'
intvolume: ' 298'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 23870BE8-32DE-11EA-91FC-C7463DDC885E
grant_number: 209504/A/17/Z
name: Molecular mechanisms of neural circuit function
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of Biological Chemistry
publication_identifier:
eissn:
- 1083-351X
issn:
- 0021-9258
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Depletion of endogenously biotinylated carboxylases enhances the sensitivity
of TurboID-mediated proximity labeling in Caenorhabditis elegans
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 298
year: '2022'
...
---
_id: '12117'
abstract:
- lang: eng
text: "To understand how potential gene manipulations affect in vitro microglia,
we provide a set of short protocols to evaluate microglia identity and function.
We detail steps for immunostaining to determine microglia identity. We describe
three functional assays for microglia: phagocytosis, calcium response following
ATP stimulation, and cytokine expression upon inflammatory stimuli. We apply these
protocols to human induced-pluripotent-stem-cell (hiPSC)-derived microglia, but
they can be also applied to other in vitro microglial models including primary
mouse microglia.\r\nFor complete details on the use and execution of this protocol,
please refer to Bartalska et al. (2022).1"
acknowledged_ssus:
- _id: Bio
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation program (grant
No. 715571 to S.S.) and from the Gesellschaft für Forschungsförderung Niederösterreich
(grant No. Sc19-017 to V.H.). We thank Rouven Schulz and Alessandro Venturino for
their insights into functional assays and data analysis, Verena Seiboth for insights
into necessary institutional permission, and ISTA imaging & optics facility (IOF)
especially Bernhard Hochreiter for their support.
article_number: '101866'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Verena
full_name: Hübschmann, Verena
id: 32B7C918-F248-11E8-B48F-1D18A9856A87
last_name: Hübschmann
- first_name: Medina
full_name: Korkut, Medina
id: 4B51CE74-F248-11E8-B48F-1D18A9856A87
last_name: Korkut
orcid: 0000-0003-4309-2251
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
citation:
ama: Hübschmann V, Korkut M, Siegert S. Assessing human iPSC-derived microglia identity
and function by immunostaining, phagocytosis, calcium activity, and inflammation
assay. STAR Protocols. 2022;3(4). doi:10.1016/j.xpro.2022.101866
apa: Hübschmann, V., Korkut, M., & Siegert, S. (2022). Assessing human iPSC-derived
microglia identity and function by immunostaining, phagocytosis, calcium activity,
and inflammation assay. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2022.101866
chicago: Hübschmann, Verena, Medina Korkut, and Sandra Siegert. “Assessing Human
IPSC-Derived Microglia Identity and Function by Immunostaining, Phagocytosis,
Calcium Activity, and Inflammation Assay.” STAR Protocols. Elsevier, 2022.
https://doi.org/10.1016/j.xpro.2022.101866.
ieee: V. Hübschmann, M. Korkut, and S. Siegert, “Assessing human iPSC-derived microglia
identity and function by immunostaining, phagocytosis, calcium activity, and inflammation
assay,” STAR Protocols, vol. 3, no. 4. Elsevier, 2022.
ista: Hübschmann V, Korkut M, Siegert S. 2022. Assessing human iPSC-derived microglia
identity and function by immunostaining, phagocytosis, calcium activity, and inflammation
assay. STAR Protocols. 3(4), 101866.
mla: Hübschmann, Verena, et al. “Assessing Human IPSC-Derived Microglia Identity
and Function by Immunostaining, Phagocytosis, Calcium Activity, and Inflammation
Assay.” STAR Protocols, vol. 3, no. 4, 101866, Elsevier, 2022, doi:10.1016/j.xpro.2022.101866.
short: V. Hübschmann, M. Korkut, S. Siegert, STAR Protocols 3 (2022).
corr_author: '1'
date_created: 2023-01-12T11:56:38Z
date_published: 2022-12-16T00:00:00Z
date_updated: 2025-06-11T13:58:47Z
day: '16'
ddc:
- '570'
department:
- _id: SaSi
- _id: GradSch
doi: 10.1016/j.xpro.2022.101866
ec_funded: 1
external_id:
pmid:
- '36595902'
file:
- access_level: open_access
checksum: 3c71b8a60633d42c2f77c49025d5559b
content_type: application/pdf
creator: dernst
date_created: 2023-01-23T09:50:51Z
date_updated: 2023-01-23T09:50:51Z
file_id: '12340'
file_name: 2022_STARProtocols_Huebschmann.pdf
file_size: 6251945
relation: main_file
success: 1
file_date_updated: 2023-01-23T09:50:51Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '4'
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Neuroscience
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25D4A630-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715571'
name: Microglia action towards neuronal circuit formation and function in health
and disease
- _id: 9B99D380-BA93-11EA-9121-9846C619BF3A
grant_number: SC19-017
name: How human microglia shape developing neurons during health and inflammation
publication: STAR Protocols
publication_identifier:
issn:
- 2666-1667
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '11478'
relation: other
status: public
scopus_import: '1'
status: public
title: Assessing human iPSC-derived microglia identity and function by immunostaining,
phagocytosis, calcium activity, and inflammation assay
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: 3
year: '2022'
...
---
_id: '12144'
abstract:
- lang: eng
text: The phytohormone auxin is the major coordinative signal in plant development1,
mediating transcriptional reprogramming by a well-established canonical signalling
pathway. TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFB) auxin
receptors are F-box subunits of ubiquitin ligase complexes. In response to auxin,
they associate with Aux/IAA transcriptional repressors and target them for degradation
via ubiquitination2,3. Here we identify adenylate cyclase (AC) activity as an
additional function of TIR1/AFB receptors across land plants. Auxin, together
with Aux/IAAs, stimulates cAMP production. Three separate mutations in the AC
motif of the TIR1 C-terminal region, all of which abolish the AC activity, each
render TIR1 ineffective in mediating gravitropism and sustained auxin-induced
root growth inhibition, and also affect auxin-induced transcriptional regulation.
These results highlight the importance of TIR1/AFB AC activity in canonical auxin
signalling. They also identify a unique phytohormone receptor cassette combining
F-box and AC motifs, and the role of cAMP as a second messenger in plants.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
acknowledgement: This research was supported by the Lab Support Facility (LSF) and
the Imaging and Optics Facility (IOF) of IST Austria. We thank C. Gehring for suggestions
and advice; and K. U. Torii and G. Stacey for seeds and plasmids. This project was
funded by a European Research Council Advanced Grant (ETAP-742985). M.F.K. and R.N.
acknowledge the support of the EU MSCA-IF project CrysPINs (792329). M.K. was supported
by the project POWR.03.05.00-00-Z302/17 Universitas Copernicana Thoruniensis in
Futuro–IDS “Academia Copernicana”. CIDG acknowledges support from UKRI under Future
Leaders Fellowship grant number MR/T020652/1.
article_processing_charge: No
article_type: original
author:
- first_name: Linlin
full_name: Qi, Linlin
id: 44B04502-A9ED-11E9-B6FC-583AE6697425
last_name: Qi
orcid: 0000-0001-5187-8401
- first_name: Mateusz
full_name: Kwiatkowski, Mateusz
last_name: Kwiatkowski
- first_name: Huihuang
full_name: Chen, Huihuang
id: 83c96512-15b2-11ec-abd3-b7eede36184f
last_name: Chen
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
orcid: 0000-0001-8295-2926
- first_name: Scott A
full_name: Sinclair, Scott A
id: 2D99FE6A-F248-11E8-B48F-1D18A9856A87
last_name: Sinclair
orcid: 0000-0002-4566-0593
- first_name: Minxia
full_name: Zou, Minxia
id: 5c243f41-03f3-11ec-841c-96faf48a7ef9
last_name: Zou
- first_name: Charo I.
full_name: del Genio, Charo I.
last_name: del Genio
- first_name: Martin F.
full_name: Kubeš, Martin F.
last_name: Kubeš
- first_name: Richard
full_name: Napier, Richard
last_name: Napier
- first_name: Krzysztof
full_name: Jaworski, Krzysztof
last_name: Jaworski
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Qi L, Kwiatkowski M, Chen H, et al. Adenylate cyclase activity of TIR1/AFB
auxin receptors in plants. Nature. 2022;611(7934):133-138. doi:10.1038/s41586-022-05369-7
apa: Qi, L., Kwiatkowski, M., Chen, H., Hörmayer, L., Sinclair, S. A., Zou, M.,
… Friml, J. (2022). Adenylate cyclase activity of TIR1/AFB auxin receptors in
plants. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-05369-7
chicago: Qi, Linlin, Mateusz Kwiatkowski, Huihuang Chen, Lukas Hörmayer, Scott A
Sinclair, Minxia Zou, Charo I. del Genio, et al. “Adenylate Cyclase Activity of
TIR1/AFB Auxin Receptors in Plants.” Nature. Springer Nature, 2022. https://doi.org/10.1038/s41586-022-05369-7.
ieee: L. Qi et al., “Adenylate cyclase activity of TIR1/AFB auxin receptors
in plants,” Nature, vol. 611, no. 7934. Springer Nature, pp. 133–138, 2022.
ista: Qi L, Kwiatkowski M, Chen H, Hörmayer L, Sinclair SA, Zou M, del Genio CI,
Kubeš MF, Napier R, Jaworski K, Friml J. 2022. Adenylate cyclase activity of TIR1/AFB
auxin receptors in plants. Nature. 611(7934), 133–138.
mla: Qi, Linlin, et al. “Adenylate Cyclase Activity of TIR1/AFB Auxin Receptors
in Plants.” Nature, vol. 611, no. 7934, Springer Nature, 2022, pp. 133–38,
doi:10.1038/s41586-022-05369-7.
short: L. Qi, M. Kwiatkowski, H. Chen, L. Hörmayer, S.A. Sinclair, M. Zou, C.I.
del Genio, M.F. Kubeš, R. Napier, K. Jaworski, J. Friml, Nature 611 (2022) 133–138.
corr_author: '1'
date_created: 2023-01-12T12:06:05Z
date_published: 2022-11-03T00:00:00Z
date_updated: 2025-04-14T07:45:02Z
day: '03'
department:
- _id: JiFr
doi: 10.1038/s41586-022-05369-7
ec_funded: 1
external_id:
isi:
- '000875061600013'
pmid:
- '36289340'
intvolume: ' 611'
isi: 1
issue: '7934'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://wrap.warwick.ac.uk/168325/1/WRAP-denylate-cyclase-activity-TIR1-AFB-auxin-receptors-root-growth-22.pdf
month: '11'
oa: 1
oa_version: Submitted Version
page: 133-138
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
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Adenylate cyclase activity of TIR1/AFB auxin receptors in plants
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 611
year: '2022'
...
---
_id: '12209'
abstract:
- lang: eng
text: Embryo development requires biochemical signalling to generate patterns of
cell fates and active mechanical forces to drive tissue shape changes. However,
how these processes are coordinated, and how tissue patterning is preserved despite
the cellular flows occurring during morphogenesis, remains poorly understood.
Gastrulation is a crucial embryonic stage that involves both patterning and internalization
of the mesendoderm germ layer tissue. Here we show that, in zebrafish embryos,
a gradient in Nodal signalling orchestrates pattern-preserving internalization
movements by triggering a motility-driven unjamming transition. In addition to
its role as a morphogen determining embryo patterning, graded Nodal signalling
mechanically subdivides the mesendoderm into a small fraction of highly protrusive
leader cells, able to autonomously internalize via local unjamming, and less protrusive
followers, which need to be pulled inwards by the leaders. The Nodal gradient
further enforces a code of preferential adhesion coupling leaders to their immediate
followers, resulting in a collective and ordered mode of internalization that
preserves mesendoderm patterning. Integrating this dual mechanical role of Nodal
signalling into minimal active particle simulations quantitatively predicts both
physiological and experimentally perturbed internalization movements. This provides
a quantitative framework for how a morphogen-encoded unjamming transition can
bidirectionally couple tissue mechanics with patterning during complex three-dimensional
morphogenesis.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: "We thank K. Sampath, A. Pauli and Y. Bellaїche for feedback on the
manuscript. We also thank the members of the Heisenberg group, in particular A.
Schauer and F. Nur Arslan, for help, technical advice and discussions, and the Bioimaging
and Life Science facilities at IST\r\nAustria for continuous support. We thank C.
Flandoli for the artwork in the figures. This work was supported by postdoctoral
fellowships from EMBO (LTF-850-2017) and HFSP (LT000429/2018-L2) to D.P. and the
European Union (European Research Council starting grant 851288 to É.H. and European
Research Council advanced grant 742573 to C.-P.H.)."
article_processing_charge: No
article_type: original
author:
- first_name: Diana C
full_name: Nunes Pinheiro, Diana C
id: 2E839F16-F248-11E8-B48F-1D18A9856A87
last_name: Nunes Pinheiro
orcid: 0000-0003-4333-7503
- first_name: Roland
full_name: Kardos, Roland
id: 4039350E-F248-11E8-B48F-1D18A9856A87
last_name: Kardos
- 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: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Nunes Pinheiro DC, Kardos R, Hannezo EB, Heisenberg C-PJ. Morphogen gradient
orchestrates pattern-preserving tissue morphogenesis via motility-driven unjamming.
Nature Physics. 2022;18(12):1482-1493. doi:10.1038/s41567-022-01787-6
apa: Nunes Pinheiro, D. C., Kardos, R., Hannezo, E. B., & Heisenberg, C.-P.
J. (2022). Morphogen gradient orchestrates pattern-preserving tissue morphogenesis
via motility-driven unjamming. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-022-01787-6
chicago: Nunes Pinheiro, Diana C, Roland Kardos, Edouard B Hannezo, and Carl-Philipp
J Heisenberg. “Morphogen Gradient Orchestrates Pattern-Preserving Tissue Morphogenesis
via Motility-Driven Unjamming.” Nature Physics. Springer Nature, 2022.
https://doi.org/10.1038/s41567-022-01787-6.
ieee: D. C. Nunes Pinheiro, R. Kardos, E. B. Hannezo, and C.-P. J. Heisenberg, “Morphogen
gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven
unjamming,” Nature Physics, vol. 18, no. 12. Springer Nature, pp. 1482–1493,
2022.
ista: Nunes Pinheiro DC, Kardos R, Hannezo EB, Heisenberg C-PJ. 2022. Morphogen
gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven
unjamming. Nature Physics. 18(12), 1482–1493.
mla: Nunes Pinheiro, Diana C., et al. “Morphogen Gradient Orchestrates Pattern-Preserving
Tissue Morphogenesis via Motility-Driven Unjamming.” Nature Physics, vol.
18, no. 12, Springer Nature, 2022, pp. 1482–93, doi:10.1038/s41567-022-01787-6.
short: D.C. Nunes Pinheiro, R. Kardos, E.B. Hannezo, C.-P.J. Heisenberg, Nature
Physics 18 (2022) 1482–1493.
corr_author: '1'
date_created: 2023-01-16T09:45:19Z
date_published: 2022-12-01T00:00:00Z
date_updated: 2025-04-14T07:46:59Z
day: '01'
ddc:
- '570'
department:
- _id: CaHe
- _id: EdHa
doi: 10.1038/s41567-022-01787-6
ec_funded: 1
external_id:
isi:
- '000871319900002'
file:
- access_level: open_access
checksum: c86a8e8d80d1bfc46d56a01e88a2526a
content_type: application/pdf
creator: dernst
date_created: 2023-01-27T07:32:01Z
date_updated: 2023-01-27T07:32:01Z
file_id: '12412'
file_name: 2022_NaturePhysics_Pinheiro.pdf
file_size: 36703569
relation: main_file
success: 1
file_date_updated: 2023-01-27T07:32:01Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '12'
keyword:
- General Physics and Astronomy
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 1482-1493
project:
- _id: 26520D1E-B435-11E9-9278-68D0E5697425
grant_number: ALTF 850-2017
name: Coordination of mesendoderm cell fate specification and internalization during
zebrafish gastrulation
- _id: 26520D1E-B435-11E9-9278-68D0E5697425
grant_number: ALTF 850-2017
name: Coordination of mesendoderm cell fate specification and internalization during
zebrafish gastrulation
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Morphogen gradient orchestrates pattern-preserving tissue morphogenesis via
motility-driven unjamming
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 18
year: '2022'
...
---
_id: '12239'
abstract:
- lang: eng
text: Biological systems are the sum of their dynamic three-dimensional (3D) parts.
Therefore, it is critical to study biological structures in 3D and at high resolution
to gain insights into their physiological functions. Electron microscopy of metal
replicas of unroofed cells and isolated organelles has been a key technique to
visualize intracellular structures at nanometer resolution. However, many of these
methods require specialized equipment and personnel to complete them. Here, we
present novel accessible methods to analyze biological structures in unroofed
cells and biochemically isolated organelles in 3D and at nanometer resolution,
focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential
trafficking organelles, their detailed structural information is lacking due to
their poor preservation when observed via classical electron microscopy protocols
experiments. First, we establish a method to visualize CCVs in unroofed cells
using scanning transmission electron microscopy tomography, providing sufficient
resolution to define the clathrin coat arrangements. Critically, the samples are
prepared directly on electron microscopy grids, removing the requirement to use
extremely corrosive acids, thereby enabling the use of this method in any electron
microscopy lab. Secondly, we demonstrate that this standardized sample preparation
allows the direct comparison of isolated CCV samples with those visualized in
cells. Finally, to facilitate the high-throughput and robust screening of metal
replicated samples, we provide a deep learning analysis method to screen the “pseudo
3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes
accessible ways to examine the 3D structure of biological samples and provide
novel insights into the structure of plant CCVs.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: Bio
acknowledgement: A.J. is supported by funding from the Austrian Science Fund I3630B25
(to J.F.). This research was supported by the Scientific Service Units of Institute
of Science and Technology Austria (ISTA) through resources provided by the Electron
Microscopy Facility, Lab Support Facility, and the Imaging and Optics Facility.
We acknowledge Prof. David Robinson (Heidelberg) and Prof. Jan Traas (Lyon) for
making us aware of previously published classical on-grid preparation methods. No
conflict of interest declared.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- 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: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Dana A.
full_name: Dahhan, Dana A.
last_name: Dahhan
- first_name: Sebastian Y.
full_name: Bednarek, Sebastian Y.
last_name: Bednarek
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Johnson AJ, Kaufmann W, Sommer CM, et al. Three-dimensional visualization of
planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant.
2022;15(10):1533-1542. doi:10.1016/j.molp.2022.09.003
apa: Johnson, A. J., Kaufmann, W., Sommer, C. M., Costanzo, T., Dahhan, D. A., Bednarek,
S. Y., & Friml, J. (2022). Three-dimensional visualization of planta clathrin-coated
vesicles at ultrastructural resolution. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2022.09.003
chicago: Johnson, Alexander J, Walter Kaufmann, Christoph M Sommer, Tommaso Costanzo,
Dana A. Dahhan, Sebastian Y. Bednarek, and Jiří Friml. “Three-Dimensional Visualization
of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” Molecular
Plant. Elsevier, 2022. https://doi.org/10.1016/j.molp.2022.09.003.
ieee: A. J. Johnson et al., “Three-dimensional visualization of planta clathrin-coated
vesicles at ultrastructural resolution,” Molecular Plant, vol. 15, no.
10. Elsevier, pp. 1533–1542, 2022.
ista: Johnson AJ, Kaufmann W, Sommer CM, Costanzo T, Dahhan DA, Bednarek SY, Friml
J. 2022. Three-dimensional visualization of planta clathrin-coated vesicles at
ultrastructural resolution. Molecular Plant. 15(10), 1533–1542.
mla: Johnson, Alexander J., et al. “Three-Dimensional Visualization of Planta Clathrin-Coated
Vesicles at Ultrastructural Resolution.” Molecular Plant, vol. 15, no.
10, Elsevier, 2022, pp. 1533–42, doi:10.1016/j.molp.2022.09.003.
short: A.J. Johnson, W. Kaufmann, C.M. Sommer, T. Costanzo, D.A. Dahhan, S.Y. Bednarek,
J. Friml, Molecular Plant 15 (2022) 1533–1542.
corr_author: '1'
date_created: 2023-01-16T09:51:49Z
date_published: 2022-10-03T00:00:00Z
date_updated: 2025-04-15T07:32:09Z
day: '03'
ddc:
- '580'
department:
- _id: JiFr
- _id: EM-Fac
- _id: Bio
doi: 10.1016/j.molp.2022.09.003
external_id:
isi:
- '000882769800009'
pmid:
- '36081349'
file:
- access_level: open_access
checksum: 04d5c12490052d03e4dc4412338a43dd
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T07:46:51Z
date_updated: 2023-01-30T07:46:51Z
file_id: '12435'
file_name: 2022_MolecularPlant_Johnson.pdf
file_size: 2307251
relation: main_file
success: 1
file_date_updated: 2023-01-30T07:46:51Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '10'
keyword:
- Plant Science
- Molecular Biology
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 1533-1542
pmid: 1
project:
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: Molecular Plant
publication_identifier:
issn:
- 1674-2052
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural
resolution
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2022'
...
---
_id: '12288'
abstract:
- lang: eng
text: To understand the function of neuronal circuits, it is crucial to disentangle
the connectivity patterns within the network. However, most tools currently used
to explore connectivity have low throughput, low selectivity, or limited accessibility.
Here, we report the development of an improved packaging system for the production
of the highly neurotropic RVdGenvA-CVS-N2c rabies viral vectors, yielding titers
orders of magnitude higher with no background contamination, at a fraction of
the production time, while preserving the efficiency of transsynaptic labeling.
Along with the production pipeline, we developed suites of ‘starter’ AAV and bicistronic
RVdG-CVS-N2c vectors, enabling retrograde labeling from a wide range of neuronal
populations, tailored for diverse experimental requirements. We demonstrate the
power and flexibility of the new system by uncovering hidden local and distal
inhibitory connections in the mouse hippocampal formation and by imaging the functional
properties of a cortical microcircuit across weeks. Our novel production pipeline
provides a convenient approach to generate new rabies vectors, while our toolkit
flexibly and efficiently expands the current capacity to label, manipulate and
image the neuronal activity of interconnected neuronal circuits in vitro and in
vivo.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: We thank F Marr for technical assistance, A Murray for RVdG-CVS-N2c
viruses and Neuro2A packaging cell-lines and J Watson for reading the manuscript.
This research was supported by the Scientific Service Units (SSU) of IST-Austria
through resources provided by the Imaging and Optics Facility (IOF) and the Preclinical
Facility (PCF). This project was funded by the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation programme (ERC advanced
grant No 692692, PJ, ERC starting grant No 756502, MJ), the Fond zur Förderung der
Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award, PJ), the Human Frontier
Science Program (LT000256/2018-L, AS) and EMBO (ALTF 1098-2017, AS).
article_number: '79848'
article_processing_charge: No
article_type: original
author:
- first_name: Anton L
full_name: Sumser, Anton L
id: 3320A096-F248-11E8-B48F-1D18A9856A87
last_name: Sumser
orcid: 0000-0002-4792-1881
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Yoav
full_name: Ben Simon, Yoav
id: 43DF3136-F248-11E8-B48F-1D18A9856A87
last_name: Ben Simon
citation:
ama: Sumser AL, Jösch MA, Jonas PM, Ben Simon Y. Fast, high-throughput production
of improved rabies viral vectors for specific, efficient and versatile transsynaptic
retrograde labeling. eLife. 2022;11. doi:10.7554/elife.79848
apa: Sumser, A. L., Jösch, M. A., Jonas, P. M., & Ben Simon, Y. (2022). Fast,
high-throughput production of improved rabies viral vectors for specific, efficient
and versatile transsynaptic retrograde labeling. ELife. eLife Sciences
Publications. https://doi.org/10.7554/elife.79848
chicago: Sumser, Anton L, Maximilian A Jösch, Peter M Jonas, and Yoav Ben Simon.
“Fast, High-Throughput Production of Improved Rabies Viral Vectors for Specific,
Efficient and Versatile Transsynaptic Retrograde Labeling.” ELife. eLife
Sciences Publications, 2022. https://doi.org/10.7554/elife.79848.
ieee: A. L. Sumser, M. A. Jösch, P. M. Jonas, and Y. Ben Simon, “Fast, high-throughput
production of improved rabies viral vectors for specific, efficient and versatile
transsynaptic retrograde labeling,” eLife, vol. 11. eLife Sciences Publications,
2022.
ista: Sumser AL, Jösch MA, Jonas PM, Ben Simon Y. 2022. Fast, high-throughput production
of improved rabies viral vectors for specific, efficient and versatile transsynaptic
retrograde labeling. eLife. 11, 79848.
mla: Sumser, Anton L., et al. “Fast, High-Throughput Production of Improved Rabies
Viral Vectors for Specific, Efficient and Versatile Transsynaptic Retrograde Labeling.”
ELife, vol. 11, 79848, eLife Sciences Publications, 2022, doi:10.7554/elife.79848.
short: A.L. Sumser, M.A. Jösch, P.M. Jonas, Y. Ben Simon, ELife 11 (2022).
corr_author: '1'
date_created: 2023-01-16T10:04:15Z
date_published: 2022-09-15T00:00:00Z
date_updated: 2025-04-15T08:29:05Z
day: '15'
ddc:
- '570'
department:
- _id: MaJö
- _id: PeJo
doi: 10.7554/elife.79848
ec_funded: 1
external_id:
isi:
- '000892204300001'
pmid:
- '36040301'
file:
- access_level: open_access
checksum: 5a2a65e3e7225090c3d8199f3bbd7b7b
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T11:50:53Z
date_updated: 2023-01-30T11:50:53Z
file_id: '12463'
file_name: 2022_eLife_Sumser.pdf
file_size: 8506811
relation: main_file
success: 1
file_date_updated: 2023-01-30T11:50:53Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 2634E9D2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '756502'
name: Circuits of Visual Attention
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
- _id: 266D407A-B435-11E9-9278-68D0E5697425
grant_number: LT000256
name: Neuronal networks of salience and spatial detection in the murine superior
colliculus
- _id: 264FEA02-B435-11E9-9278-68D0E5697425
grant_number: ALTF 1098-2017
name: Connecting sensory with motor processing in the superior colliculus
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fast, high-throughput production of improved rabies viral vectors for specific,
efficient and versatile transsynaptic retrograde labeling
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2022'
...
---
OA_place: publisher
_id: '12368'
abstract:
- lang: eng
text: "Metazoan development relies on the formation and remodeling of cell-cell
contacts. The \r\nbinding of adhesion receptors and remodeling of the actomyosin
cell cortex at cell-cell \r\ninteraction sites have been implicated in cell-cell
contact formation. Yet, how these two \r\nprocesses functionally interact to drive
cell-cell contact expansion and strengthening \r\nremains unclear. Here, we study
how primary germ layer progenitor cells from zebrafish \r\nbind to supported lipid
bilayers (SLB) functionalized with E-cadherin ectodomains as an \r\nassay system
for monitoring cell-cell contact formation at high spatiotemporal resolution.
\r\nWe show that cell-cell contact formation represents a two-tiered process:
E-cadherin\x02mediated downregulation of the small GTPase RhoA at the forming
contact leads to both \r\ndepletion of Myosin-2 and decrease of F-actin. This
is followed by centrifugal actin \r\nnetwork flows at the contact triggered by
a sharp gradient of Myosin-2 at the rim of the \r\ncontact zone, with Myosin-2
displaying higher cortical localization outside than inside of \r\nthe contact.
These centrifugal cortical actin flows, in turn, not only further dilute the actin
\r\nnetwork at the contact disc, but also lead to an accumulation of both F-actin
and E\x02cadherin at the contact rim. Eventually, this combination of actomyosin
downregulation \r\nand flows at the contact contribute to the characteristic molecular
organization implicated \r\nin contact formation and maintenance: depletion of
cortical actomyosin at the contact disc, \r\ndriving contact expansion by lowering
interfacial tension at the contact, and accumulation \r\nof both E-cadherin and
F-actin at the contact rim, mechanically linking the contractile \r\ncortices
of the adhering cells. Thus, using a biomimetic assay, we exemplify how \r\nadhesion
signaling and cell mechanics function together to modulate the spatial \r\norganization
of cell-cell contacts."
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
- _id: NanoFab
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Feyza N
full_name: Arslan, Feyza N
id: 49DA7910-F248-11E8-B48F-1D18A9856A87
last_name: Arslan
orcid: 0000-0001-5809-9566
citation:
ama: Arslan FN. Remodeling of E-cadherin-mediated contacts via cortical flows.
2022. doi:10.15479/at:ista:12153
apa: Arslan, F. N. (2022). Remodeling of E-cadherin-mediated contacts via cortical
flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12153
chicago: Arslan, Feyza N. “Remodeling of E-Cadherin-Mediated Contacts via Cortical
Flows.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12153.
ieee: F. N. Arslan, “Remodeling of E-cadherin-mediated contacts via cortical flows,”
Institute of Science and Technology Austria, 2022.
ista: Arslan FN. 2022. Remodeling of E-cadherin-mediated contacts via cortical
flows. Institute of Science and Technology Austria.
mla: Arslan, Feyza N. Remodeling of E-Cadherin-Mediated Contacts via Cortical
Flows. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12153.
short: F.N. Arslan, Remodeling of E-Cadherin-Mediated Contacts via Cortical Flows,
Institute of Science and Technology Austria, 2022.
corr_author: '1'
date_created: 2023-01-25T10:43:24Z
date_published: 2022-09-29T00:00:00Z
date_updated: 2026-06-18T19:47:50Z
day: '29'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: CaHe
doi: 10.15479/at:ista:12153
ec_funded: 1
file:
- access_level: open_access
checksum: e54a3e69b83ebf166544164afd25608e
content_type: application/pdf
creator: cchlebak
date_created: 2023-01-25T10:52:46Z
date_updated: 2023-01-25T10:52:46Z
file_id: '12369'
file_name: THESIS_FINAL_FArslan_pdfa.pdf
file_size: 14581024
relation: main_file
success: 1
file_date_updated: 2023-01-25T10:52:46Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '113'
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
publication_identifier:
isbn:
- '978-3-99078-025-1 '
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9350'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
title: Remodeling of E-cadherin-mediated contacts via cortical flows
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2022'
...
---
_id: '10712'
abstract:
- lang: eng
text: Solute carriers are increasingly recognized as participating in a plethora
of pathologies, including cancer. We describe here the involvement of the orphan
solute carrier MFSD1 in the regulation of tumor cell migration. Loss of MFSD1
enabled higher levels of metastasis in a mouse model. We identified an increased
migratory potential in MFSD1-/- tumor cells which was mediated by increased focal
adhesion turn-over, reduced stability of mature inactive β1 integrin, and the
resulting increased integrin activation index. We show that MFSD1 promoted recycling
to the cell surface of endocytosed inactive β1 integrin and thereby protected
β1 integrin from proteolytic degradation; this led to dampening of the integrin
activation index. Furthermore, down-regulation of MFSD1 expression was observed
during early steps of tumorigenesis and higher MFSD1 expression levels correlate
with a better cancer patient prognosis. In sum, we describe a requirement for
endolysosomal MFSD1 in efficient β1 integrin recycling to suppress tumor spread.
acknowledged_ssus:
- _id: Bio
acknowledgement: We thank M. Sixt, A. Leithner, and J. Alanko for helpful advice and
the BioImaging Facility at IST Austria for technical support and assistance. We
thank the Siekhaus Lab for the careful review of the manuscript and their input.
MR and DS were funded by the NO Forschungs- und Bildungsges.m.b.H. (LS16-021) and
IST core funding. MD was funded by Deutsche Forschungsgemeinschaft (DA 1785-1).
article_number: '777634'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Marko
full_name: Roblek, Marko
id: 3047D808-F248-11E8-B48F-1D18A9856A87
last_name: Roblek
orcid: 0000-0001-9588-1389
- first_name: Julia
full_name: Bicher, Julia
id: 3CCBB46E-F248-11E8-B48F-1D18A9856A87
last_name: Bicher
- first_name: Merel
full_name: van Gogh, Merel
last_name: van Gogh
- first_name: Attila
full_name: György, Attila
id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87
last_name: György
orcid: 0000-0002-1819-198X
- first_name: Rita
full_name: Seeböck, Rita
last_name: Seeböck
- first_name: Bozena
full_name: Szulc, Bozena
last_name: Szulc
- first_name: Markus
full_name: Damme, Markus
last_name: Damme
- first_name: Mariusz
full_name: Olczak, Mariusz
last_name: Olczak
- first_name: Lubor
full_name: Borsig, Lubor
last_name: Borsig
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
citation:
ama: Roblek M, Bicher J, van Gogh M, et al. The solute carrier MFSD1 decreases β1
integrin’s activation status and thus tumor metastasis. Frontiers in Oncology.
2022;12. doi:10.3389/fonc.2022.777634
apa: Roblek, M., Bicher, J., van Gogh, M., György, A., Seeböck, R., Szulc, B., …
Siekhaus, D. E. (2022). The solute carrier MFSD1 decreases β1 integrin’s activation
status and thus tumor metastasis. Frontiers in Oncology. Frontiers. https://doi.org/10.3389/fonc.2022.777634
chicago: Roblek, Marko, Julia Bicher, Merel van Gogh, Attila György, Rita Seeböck,
Bozena Szulc, Markus Damme, Mariusz Olczak, Lubor Borsig, and Daria E Siekhaus.
“The Solute Carrier MFSD1 Decreases Β1 Integrin’s Activation Status and Thus Tumor
Metastasis.” Frontiers in Oncology. Frontiers, 2022. https://doi.org/10.3389/fonc.2022.777634.
ieee: M. Roblek et al., “The solute carrier MFSD1 decreases β1 integrin’s
activation status and thus tumor metastasis,” Frontiers in Oncology, vol.
12. Frontiers, 2022.
ista: Roblek M, Bicher J, van Gogh M, György A, Seeböck R, Szulc B, Damme M, Olczak
M, Borsig L, Siekhaus DE. 2022. The solute carrier MFSD1 decreases β1 integrin’s
activation status and thus tumor metastasis. Frontiers in Oncology. 12, 777634.
mla: Roblek, Marko, et al. “The Solute Carrier MFSD1 Decreases Β1 Integrin’s Activation
Status and Thus Tumor Metastasis.” Frontiers in Oncology, vol. 12, 777634,
Frontiers, 2022, doi:10.3389/fonc.2022.777634.
short: M. Roblek, J. Bicher, M. van Gogh, A. György, R. Seeböck, B. Szulc, M. Damme,
M. Olczak, L. Borsig, D.E. Siekhaus, Frontiers in Oncology 12 (2022).
corr_author: '1'
date_created: 2022-02-01T10:33:50Z
date_published: 2022-02-08T00:00:00Z
date_updated: 2025-06-11T13:56:08Z
day: '08'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.3389/fonc.2022.777634
external_id:
isi:
- '000760618800001'
pmid:
- '35211397'
file:
- access_level: open_access
checksum: 63dfecf30c5bbf9408b3512bd603f78c
content_type: application/pdf
creator: cchlebak
date_created: 2022-02-08T13:26:40Z
date_updated: 2022-02-08T13:26:40Z
file_id: '10751'
file_name: 2022_FrontiersOncol_Roblek.pdf
file_size: 6303227
relation: main_file
success: 1
file_date_updated: 2022-02-08T13:26:40Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2637E9C0-B435-11E9-9278-68D0E5697425
grant_number: LSC16-021
name: Investigating the role of the novel major superfamily facilitator transporter
family member MFSD1 in metastasis
publication: Frontiers in Oncology
publication_identifier:
issn:
- 2234-943X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: confirmation
url: https://ist.ac.at/en/news/suppressing-the-spread-of-tumors/
scopus_import: '1'
status: public
title: The solute carrier MFSD1 decreases β1 integrin’s activation status and thus
tumor metastasis
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: 12
year: '2022'
...
---
_id: '10713'
abstract:
- lang: eng
text: Cells migrate through crowded microenvironments within tissues during normal
development, immune response, and cancer metastasis. Although migration through
pores and tracks in the extracellular matrix (ECM) has been well studied, little
is known about cellular traversal into confining cell-dense tissues. We find that
embryonic tissue invasion by Drosophila macrophages requires division of an epithelial
ectodermal cell at the site of entry. Dividing ectodermal cells disassemble ECM
attachment formed by integrin-mediated focal adhesions next to mesodermal cells,
allowing macrophages to move their nuclei ahead and invade between two immediately
adjacent tissues. Invasion efficiency depends on division frequency, but reduction
of adhesion strength allows macrophage entry independently of division. This work
demonstrates that tissue dynamics can regulate cellular infiltration.
acknowledged_ssus:
- _id: Bio
acknowledgement: 'We thank J. Friml, C. Guet, T. Hurd, M. Fendrych and members of
the laboratory for comments on the manuscript; the Bioimaging Facility of IST Austria
for excellent support and T. Lecuit, E. Hafen, R. Levayer and A. Martin for fly
strains. This work was supported by a grant from the Austrian Science Fund FWF:
Lise Meitner Fellowship M2379-B28 to M.A and D.S., and internal funding from IST
Austria to D.S. and EMBL to S.D.R.'
article_processing_charge: No
article_type: original
author:
- first_name: Maria
full_name: Akhmanova, Maria
id: 3425EC26-F248-11E8-B48F-1D18A9856A87
last_name: Akhmanova
orcid: 0000-0003-1522-3162
- first_name: Shamsi
full_name: Emtenani, Shamsi
id: 49D32318-F248-11E8-B48F-1D18A9856A87
last_name: Emtenani
orcid: 0000-0001-6981-6938
- first_name: Daniel
full_name: Krueger, Daniel
last_name: Krueger
- first_name: Attila
full_name: György, Attila
id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87
last_name: György
orcid: 0000-0002-1819-198X
- first_name: Mariana
full_name: Pereira Guarda, Mariana
id: 6de81d9d-e2f2-11eb-945a-af8bc2a60b26
last_name: Pereira Guarda
orcid: 0000-0001-8238-480X
- first_name: Mikhail
full_name: Vlasov, Mikhail
last_name: Vlasov
- first_name: Fedor
full_name: Vlasov, Fedor
last_name: Vlasov
- first_name: Andrei
full_name: Akopian, Andrei
last_name: Akopian
- first_name: Aparna
full_name: Ratheesh, Aparna
id: 2F064CFE-F248-11E8-B48F-1D18A9856A87
last_name: Ratheesh
orcid: 0000-0001-7190-0776
- first_name: Stefano
full_name: De Renzis, Stefano
last_name: De Renzis
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
citation:
ama: Akhmanova M, Emtenani S, Krueger D, et al. Cell division in tissues enables
macrophage infiltration. Science. 2022;376(6591):394-396. doi:10.1126/science.abj0425
apa: Akhmanova, M., Emtenani, S., Krueger, D., György, A., Pereira Guarda, M., Vlasov,
M., … Siekhaus, D. E. (2022). Cell division in tissues enables macrophage infiltration.
Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.abj0425
chicago: Akhmanova, Maria, Shamsi Emtenani, Daniel Krueger, Attila György, Mariana
Pereira Guarda, Mikhail Vlasov, Fedor Vlasov, et al. “Cell Division in Tissues
Enables Macrophage Infiltration.” Science. American Association for the
Advancement of Science, 2022. https://doi.org/10.1126/science.abj0425.
ieee: M. Akhmanova et al., “Cell division in tissues enables macrophage infiltration,”
Science, vol. 376, no. 6591. American Association for the Advancement of
Science, pp. 394–396, 2022.
ista: Akhmanova M, Emtenani S, Krueger D, György A, Pereira Guarda M, Vlasov M,
Vlasov F, Akopian A, Ratheesh A, De Renzis S, Siekhaus DE. 2022. Cell division
in tissues enables macrophage infiltration. Science. 376(6591), 394–396.
mla: Akhmanova, Maria, et al. “Cell Division in Tissues Enables Macrophage Infiltration.”
Science, vol. 376, no. 6591, American Association for the Advancement of
Science, 2022, pp. 394–96, doi:10.1126/science.abj0425.
short: M. Akhmanova, S. Emtenani, D. Krueger, A. György, M. Pereira Guarda, M. Vlasov,
F. Vlasov, A. Akopian, A. Ratheesh, S. De Renzis, D.E. Siekhaus, Science 376 (2022)
394–396.
corr_author: '1'
date_created: 2022-02-01T11:23:18Z
date_published: 2022-04-22T00:00:00Z
date_updated: 2025-04-15T07:25:41Z
day: '22'
department:
- _id: DaSi
doi: 10.1126/science.abj0425
external_id:
isi:
- '000788553700039'
pmid:
- '35446632'
intvolume: ' 376'
isi: 1
issue: '6591'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2021.04.19.438995
month: '04'
oa: 1
oa_version: Preprint
page: 394-396
pmid: 1
project:
- _id: 264CBBAC-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02379
name: Modeling epithelial tissue mechanics during cell invasion
publication: Science
publication_identifier:
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cell division in tissues enables macrophage infiltration
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 376
year: '2022'
...
---
_id: '10791'
abstract:
- lang: eng
text: The mammalian neocortex is composed of diverse neuronal and glial cell classes
that broadly arrange in six distinct laminae. Cortical layers emerge during development
and defects in the developmental programs that orchestrate cortical lamination
are associated with neurodevelopmental diseases. The developmental principle of
cortical layer formation depends on concerted radial projection neuron migration,
from their birthplace to their final target position. Radial migration occurs
in defined sequential steps, regulated by a large array of signaling pathways.
However, based on genetic loss-of-function experiments, most studies have thus
far focused on the role of cell-autonomous gene function. Yet, cortical neuron
migration in situ is a complex process and migrating neurons traverse along diverse
cellular compartments and environments. The role of tissue-wide properties and
genetic state in radial neuron migration is however not clear. Here we utilized
mosaic analysis with double markers (MADM) technology to either sparsely or globally
delete gene function, followed by quantitative single-cell phenotyping. The MADM-based
gene ablation paradigms in combination with computational modeling demonstrated
that global tissue-wide effects predominate cell-autonomous gene function albeit
in a gene-specific manner. Our results thus suggest that the genetic landscape
in a tissue critically affects the overall migration phenotype of individual cortical
projection neurons. In a broader context, our findings imply that global tissue-wide
effects represent an essential component of the underlying etiology associated
with focal malformations of cortical development in particular, and neurological
diseases in general.
acknowledged_ssus:
- _id: LifeSc
- _id: PreCl
- _id: Bio
acknowledgement: "A.H.H. was a recipient of a DOC Fellowship (24812) of the Austrian
Academy of Sciences. This work also received support from IST Austria institutional
funds; the People Programme (Marie Curie Actions) of the European Union’s Seventh
Framework Programme (FP7/2007–2013) under REA grant agreement No 618444 to S.H.\r\nAPC
funding was obtained by IST Austria institutional funds.\r\nWe thank A. Sommer and
C. Czepe (VBCF GmbH, NGS Unit), L. Andersen, J. Sonntag and J. Renno for technical
support and/or initial experiments; M. Sixt, J. Nimpf and all members of the Hippenmeyer
lab for discussion. This research was supported by the Scientific Service Units
of IST Austria through resources provided by the Imaging and Optics Facility, Lab
Support Facility and Preclinical Facility."
article_number: kvac009
article_processing_charge: No
article_type: original
author:
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Michael
full_name: Riedl, Michael
id: 3BE60946-F248-11E8-B48F-1D18A9856A87
last_name: Riedl
orcid: 0000-0003-4844-6311
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Anna-Magdalena
full_name: Heger, Anna-Magdalena
id: 4B76FFD2-F248-11E8-B48F-1D18A9856A87
last_name: Heger
- first_name: Susanne
full_name: Laukoter, Susanne
id: 2D6B7A9A-F248-11E8-B48F-1D18A9856A87
last_name: Laukoter
orcid: 0000-0002-7903-3010
- 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: Armel
full_name: Nicolas, Armel
id: 2A103192-F248-11E8-B48F-1D18A9856A87
last_name: Nicolas
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Li Huei
full_name: Tsai, Li Huei
last_name: Tsai
- first_name: Thomas
full_name: Rülicke, Thomas
last_name: Rülicke
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Hansen AH, Pauler F, Riedl M, et al. Tissue-wide effects override cell-intrinsic
gene function in radial neuron migration. Oxford Open Neuroscience. 2022;1(1).
doi:10.1093/oons/kvac009
apa: Hansen, A. H., Pauler, F., Riedl, M., Streicher, C., Heger, A.-M., Laukoter,
S., … Hippenmeyer, S. (2022). Tissue-wide effects override cell-intrinsic gene
function in radial neuron migration. Oxford Open Neuroscience. Oxford University
Press. https://doi.org/10.1093/oons/kvac009
chicago: Hansen, Andi H, Florian Pauler, Michael Riedl, Carmen Streicher, Anna-Magdalena
Heger, Susanne Laukoter, Christoph M Sommer, et al. “Tissue-Wide Effects Override
Cell-Intrinsic Gene Function in Radial Neuron Migration.” Oxford Open Neuroscience.
Oxford University Press, 2022. https://doi.org/10.1093/oons/kvac009.
ieee: A. H. Hansen et al., “Tissue-wide effects override cell-intrinsic gene
function in radial neuron migration,” Oxford Open Neuroscience, vol. 1,
no. 1. Oxford University Press, 2022.
ista: Hansen AH, Pauler F, Riedl M, Streicher C, Heger A-M, Laukoter S, Sommer CM,
Nicolas A, Hof B, Tsai LH, Rülicke T, Hippenmeyer S. 2022. Tissue-wide effects
override cell-intrinsic gene function in radial neuron migration. Oxford Open
Neuroscience. 1(1), kvac009.
mla: Hansen, Andi H., et al. “Tissue-Wide Effects Override Cell-Intrinsic Gene Function
in Radial Neuron Migration.” Oxford Open Neuroscience, vol. 1, no. 1, kvac009,
Oxford University Press, 2022, doi:10.1093/oons/kvac009.
short: A.H. Hansen, F. Pauler, M. Riedl, C. Streicher, A.-M. Heger, S. Laukoter,
C.M. Sommer, A. Nicolas, B. Hof, L.H. Tsai, T. Rülicke, S. Hippenmeyer, Oxford
Open Neuroscience 1 (2022).
corr_author: '1'
date_created: 2022-02-25T07:52:11Z
date_published: 2022-07-07T00:00:00Z
date_updated: 2026-04-07T13:29:13Z
day: '07'
ddc:
- '570'
department:
- _id: SiHi
- _id: BjHo
- _id: LifeSc
- _id: EM-Fac
doi: 10.1093/oons/kvac009
ec_funded: 1
external_id:
pmid:
- '38596707'
file:
- access_level: open_access
checksum: 822e76e056c07099d1fb27d1ece5941b
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T08:00:30Z
date_updated: 2023-08-16T08:00:30Z
file_id: '14061'
file_name: 2023_OxfordOpenNeuroscience_Hansen.pdf
file_size: 4846551
relation: main_file
success: 1
file_date_updated: 2023-08-16T08:00:30Z
has_accepted_license: '1'
intvolume: ' 1'
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25D61E48-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618444'
name: Molecular Mechanisms of Cerebral Cortex Development
- _id: 2625A13E-B435-11E9-9278-68D0E5697425
grant_number: '24812'
name: Molecular mechanisms of radial neuronal migration
publication: Oxford Open Neuroscience
publication_identifier:
eissn:
- 2753-149X
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '12726'
relation: dissertation_contains
status: public
- id: '14530'
relation: dissertation_contains
status: public
status: public
title: Tissue-wide effects override cell-intrinsic gene function in radial neuron
migration
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: 1
year: '2022'
...
---
_id: '9794'
abstract:
- lang: eng
text: 'Lymph nodes (LNs) comprise two main structural elements: fibroblastic reticular
cells that form dedicated niches for immune cell interaction and capsular fibroblasts
that build a shell around the organ. Immunological challenge causes LNs to increase
more than tenfold in size within a few days. Here, we characterized the biomechanics
of LN swelling on the cellular and organ scale. We identified lymphocyte trapping
by influx and proliferation as drivers of an outward pressure force, causing fibroblastic
reticular cells of the T-zone (TRCs) and their associated conduits to stretch.
After an initial phase of relaxation, TRCs sensed the resulting strain through
cell matrix adhesions, which coordinated local growth and remodeling of the stromal
network. While the expanded TRC network readopted its typical configuration, a
massive fibrotic reaction of the organ capsule set in and countered further organ
expansion. Thus, different fibroblast populations mechanically control LN swelling
in a multitier fashion.'
acknowledged_ssus:
- _id: Bio
- _id: EM-Fac
- _id: PreCl
- _id: LifeSc
acknowledgement: This research was supported by the Scientific Service Units of IST
Austria through resources provided by the Imaging and Optics, Electron Microscopy,
Preclinical and Life Science Facilities. We thank C. Moussion for providing anti-PNAd
antibody and D. Critchley for Talin1-floxed mice, and E. Papusheva for providing
a custom 3D channel alignment script. This work was supported by a European Research
Council grant ERC-CoG-72437 to M.S. M.H. was supported by Czech Sciencundation GACR
20-24603Y and Charles University PRIMUS/20/MED/013.
article_processing_charge: No
article_type: original
author:
- first_name: Frank P
full_name: Assen, Frank P
id: 3A8E7F24-F248-11E8-B48F-1D18A9856A87
last_name: Assen
orcid: 0000-0003-3470-6119
- first_name: Jun
full_name: Abe, Jun
last_name: Abe
- first_name: Miroslav
full_name: Hons, Miroslav
id: 4167FE56-F248-11E8-B48F-1D18A9856A87
last_name: Hons
orcid: 0000-0002-6625-3348
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Shayan
full_name: Shamipour, Shayan
id: 40B34FE2-F248-11E8-B48F-1D18A9856A87
last_name: Shamipour
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Markus
full_name: Brown, Markus
id: 3DAB9AFC-F248-11E8-B48F-1D18A9856A87
last_name: Brown
- first_name: Burkhard
full_name: Ludewig, Burkhard
last_name: Ludewig
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Wolfgang
full_name: Weninger, Wolfgang
last_name: Weninger
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Sanjiv A.
full_name: Luther, Sanjiv A.
last_name: Luther
- first_name: Jens V.
full_name: Stein, Jens V.
last_name: Stein
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-4561-241X
citation:
ama: Assen FP, Abe J, Hons M, et al. Multitier mechanics control stromal adaptations
in swelling lymph nodes. Nature Immunology. 2022;23:1246-1255. doi:10.1038/s41590-022-01257-4
apa: Assen, F. P., Abe, J., Hons, M., Hauschild, R., Shamipour, S., Kaufmann, W.,
… Sixt, M. K. (2022). Multitier mechanics control stromal adaptations in swelling
lymph nodes. Nature Immunology. Springer Nature. https://doi.org/10.1038/s41590-022-01257-4
chicago: Assen, Frank P, Jun Abe, Miroslav Hons, Robert Hauschild, Shayan Shamipour,
Walter Kaufmann, Tommaso Costanzo, et al. “Multitier Mechanics Control Stromal
Adaptations in Swelling Lymph Nodes.” Nature Immunology. Springer Nature,
2022. https://doi.org/10.1038/s41590-022-01257-4.
ieee: F. P. Assen et al., “Multitier mechanics control stromal adaptations
in swelling lymph nodes,” Nature Immunology, vol. 23. Springer Nature,
pp. 1246–1255, 2022.
ista: Assen FP, Abe J, Hons M, Hauschild R, Shamipour S, Kaufmann W, Costanzo T,
Krens G, Brown M, Ludewig B, Hippenmeyer S, Heisenberg C-PJ, Weninger W, Hannezo
EB, Luther SA, Stein JV, Sixt MK. 2022. Multitier mechanics control stromal adaptations
in swelling lymph nodes. Nature Immunology. 23, 1246–1255.
mla: Assen, Frank P., et al. “Multitier Mechanics Control Stromal Adaptations in
Swelling Lymph Nodes.” Nature Immunology, vol. 23, Springer Nature, 2022,
pp. 1246–55, doi:10.1038/s41590-022-01257-4.
short: F.P. Assen, J. Abe, M. Hons, R. Hauschild, S. Shamipour, W. Kaufmann, T.
Costanzo, G. Krens, M. Brown, B. Ludewig, S. Hippenmeyer, C.-P.J. Heisenberg,
W. Weninger, E.B. Hannezo, S.A. Luther, J.V. Stein, M.K. Sixt, Nature Immunology
23 (2022) 1246–1255.
corr_author: '1'
date_created: 2021-08-06T09:09:11Z
date_published: 2022-07-11T00:00:00Z
date_updated: 2025-06-11T13:52:43Z
day: '11'
ddc:
- '570'
department:
- _id: SiHi
- _id: CaHe
- _id: EdHa
- _id: EM-Fac
- _id: Bio
- _id: MiSi
doi: 10.1038/s41590-022-01257-4
ec_funded: 1
external_id:
isi:
- '000822975900002'
pmid:
- '35817845'
file:
- access_level: open_access
checksum: 628e7b49809f22c75b428842efe70c68
content_type: application/pdf
creator: dernst
date_created: 2022-07-25T07:11:32Z
date_updated: 2022-07-25T07:11:32Z
file_id: '11642'
file_name: 2022_NatureImmunology_Assen.pdf
file_size: 11475325
relation: main_file
success: 1
file_date_updated: 2022-07-25T07:11:32Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1246-1255
pmid: 1
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular Navigation Along Spatial Gradients
publication: Nature Immunology
publication_identifier:
eissn:
- 1529-2916
issn:
- 1529-2908
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Multitier mechanics control stromal adaptations in swelling lymph nodes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2022'
...
---
_id: '10766'
abstract:
- lang: eng
text: Tension of the actomyosin cell cortex plays a key role in determining cell–cell
contact growth and size. The level of cortical tension outside of the cell–cell
contact, when pulling at the contact edge, scales with the total size to which
a cell–cell contact can grow [J.-L. Maître et al., Science 338, 253–256 (2012)].
Here, we show in zebrafish primary germ-layer progenitor cells that this monotonic
relationship only applies to a narrow range of cortical tension increase and that
above a critical threshold, contact size inversely scales with cortical tension.
This switch from cortical tension increasing to decreasing progenitor cell–cell
contact size is caused by cortical tension promoting E-cadherin anchoring to the
actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin
at the contact. After tension-mediated E-cadherin stabilization at the contact
exceeds a critical threshold level, the rate by which the contact expands in response
to pulling forces from the cortex sharply drops, leading to smaller contacts at
physiologically relevant timescales of contact formation. Thus, the activity of
cortical tension in expanding cell–cell contact size is limited by tension-stabilizing
E-cadherin–actin complexes at the contact.
acknowledged_ssus:
- _id: Bio
- _id: EM-Fac
- _id: PreCl
acknowledgement: 'We thank Guillaume Salbreaux, Silvia Grigolon, Edouard Hannezo,
and Vanessa Barone for discussions and comments on the manuscript and Shayan Shamipour
and Daniel Capek for help with data analysis. We also thank the Imaging & Optics,
Electron Microscopy, and Zebrafish Facility Scientific Service Units at the Institute
of Science and Technology Austria (ISTA)Nasser Darwish-Miranda for continuous support.
We acknowledge Hitoshi Morita for the gift of VinculinB-GFP plasmid. This research
was supported by an ISTA Fellow Marie-Curie Co-funding of regional, national, and
international programmes Grant P_IST_EU01 (to J.S.), European Molecular Biology
Organization Long-Term Fellowship Grant, ALTF reference number: 187-2013 (to M.S.),
Schroedinger Fellowship J4332-B28 (to M.S.), and European Research Council Advanced
Grant (MECSPEC; to C.-P.H.).'
article_number: e2122030119
article_processing_charge: No
article_type: original
author:
- first_name: Jana
full_name: Slovakova, Jana
id: 30F3F2F0-F248-11E8-B48F-1D18A9856A87
last_name: Slovakova
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Feyza N
full_name: Arslan, Feyza N
id: 49DA7910-F248-11E8-B48F-1D18A9856A87
last_name: Arslan
orcid: 0000-0001-5809-9566
- first_name: Silvia
full_name: Caballero Mancebo, Silvia
id: 2F1E1758-F248-11E8-B48F-1D18A9856A87
last_name: Caballero Mancebo
orcid: 0000-0002-5223-3346
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Slovakova J, Sikora MK, Arslan FN, et al. Tension-dependent stabilization of
E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor
cells. Proceedings of the National Academy of Sciences of the United States
of America. 2022;119(8). doi:10.1073/pnas.2122030119
apa: Slovakova, J., Sikora, M. K., Arslan, F. N., Caballero Mancebo, S., Krens,
G., Kaufmann, W., … Heisenberg, C.-P. J. (2022). Tension-dependent stabilization
of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor
cells. Proceedings of the National Academy of Sciences of the United States
of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2122030119
chicago: Slovakova, Jana, Mateusz K Sikora, Feyza N Arslan, Silvia Caballero Mancebo,
Gabriel Krens, Walter Kaufmann, Jack Merrin, and Carl-Philipp J Heisenberg. “Tension-Dependent
Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer
Progenitor Cells.” Proceedings of the National Academy of Sciences of the United
States of America. National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2122030119.
ieee: J. Slovakova et al., “Tension-dependent stabilization of E-cadherin
limits cell-cell contact expansion in zebrafish germ-layer progenitor cells,”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 119, no. 8. National Academy of Sciences, 2022.
ista: Slovakova J, Sikora MK, Arslan FN, Caballero Mancebo S, Krens G, Kaufmann
W, Merrin J, Heisenberg C-PJ. 2022. Tension-dependent stabilization of E-cadherin
limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings
of the National Academy of Sciences of the United States of America. 119(8), e2122030119.
mla: Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits
Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” Proceedings
of the National Academy of Sciences of the United States of America, vol.
119, no. 8, e2122030119, National Academy of Sciences, 2022, doi:10.1073/pnas.2122030119.
short: J. Slovakova, M.K. Sikora, F.N. Arslan, S. Caballero Mancebo, G. Krens, W.
Kaufmann, J. Merrin, C.-P.J. Heisenberg, Proceedings of the National Academy of
Sciences of the United States of America 119 (2022).
corr_author: '1'
date_created: 2022-02-20T23:01:31Z
date_published: 2022-02-14T00:00:00Z
date_updated: 2026-07-06T12:45:39Z
day: '14'
ddc:
- '570'
department:
- _id: CaHe
- _id: EM-Fac
- _id: Bio
doi: 10.1073/pnas.2122030119
ec_funded: 1
external_id:
isi:
- '000766926900009'
pmid:
- '35165179'
file:
- access_level: open_access
checksum: d49f83c3580613966f71768ddb9a55a5
content_type: application/pdf
creator: dernst
date_created: 2022-02-21T08:45:11Z
date_updated: 2022-02-21T08:45:11Z
file_id: '10780'
file_name: 2022_PNAS_Slovakova.pdf
file_size: 1609678
relation: main_file
success: 1
file_date_updated: 2022-02-21T08:45:11Z
has_accepted_license: '1'
intvolume: ' 119'
isi: 1
issue: '8'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
- _id: 2521E28E-B435-11E9-9278-68D0E5697425
grant_number: 187-2013
name: Modulation of adhesion function in cell-cell contact formation by cortical
tension
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
record:
- id: '9750'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion
in zebrafish germ-layer progenitor cells
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 119
year: '2022'
...
---
_id: '11843'
abstract:
- lang: eng
text: A key attribute of persistent or recurring bacterial infections is the ability
of the pathogen to evade the host’s immune response. Many Enterobacteriaceae express
type 1 pili, a pre-adapted virulence trait, to invade host epithelial cells and
establish persistent infections. However, the molecular mechanisms and strategies
by which bacteria actively circumvent the immune response of the host remain poorly
understood. Here, we identified CD14, the major co-receptor for lipopolysaccharide
detection, on mouse dendritic cells (DCs) as a binding partner of FimH, the protein
located at the tip of the type 1 pilus of Escherichia coli. The FimH amino acids
involved in CD14 binding are highly conserved across pathogenic and non-pathogenic
strains. Binding of the pathogenic strain CFT073 to CD14 reduced DC migration
by overactivation of integrins and blunted expression of co-stimulatory molecules
by overactivating the NFAT (nuclear factor of activated T-cells) pathway, both
rate-limiting factors of T cell activation. This response was binary at the single-cell
level, but averaged in larger populations exposed to both piliated and non-piliated
pathogens, presumably via the exchange of immunomodulatory cytokines. While defining
an active molecular mechanism of immune evasion by pathogens, the interaction
between FimH and CD14 represents a potential target to interfere with persistent
and recurrent infections, such as urinary tract infections or Crohn’s disease.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: EM-Fac
acknowledgement: We thank Ulrich Dobrindt for providing UPEC strains CFT073, UTI89,
and 536, Frank Assen, Vlad Gavra, Maximilian Götz, Bor Kavčič, Jonna Alanko, and
Eva Kiermaier for help with experiments and Robert Hauschild, Julian Stopp, and
Saren Tasciyan for help with data analysis. We thank the IST Austria Scientific
Service Units, especially the Bioimaging facility, the Preclinical facility and
the Electron microscopy facility for technical support, Jakob Wallner and all members
of the Guet and Sixt lab for fruitful discussions and Daria Siekhaus for critically
reading the manuscript. This work was supported by grants from the Austrian Research
Promotion Agency (FEMtech 868984) to IG, the European Research Council (CoG 724373),
and the Austrian Science Fund (FWF P29911) to MS.
article_number: e78995
article_processing_charge: Yes
article_type: original
author:
- first_name: Kathrin
full_name: Tomasek, Kathrin
id: 3AEC8556-F248-11E8-B48F-1D18A9856A87
last_name: Tomasek
orcid: 0000-0003-3768-877X
- first_name: Alexander F
full_name: Leithner, Alexander F
id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87
last_name: Leithner
orcid: 0000-0002-1073-744X
- first_name: Ivana
full_name: Glatzová, Ivana
id: 727b3c7d-4939-11ec-89b3-b9b0750ab74d
last_name: Glatzová
- first_name: Michael S.
full_name: Lukesch, Michael S.
last_name: Lukesch
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated
uropathogenic Escherichia coli hijack the host immune response by binding to CD14.
eLife. 2022;11. doi:10.7554/eLife.78995
apa: Tomasek, K., Leithner, A. F., Glatzová, I., Lukesch, M. S., Guet, C. C., &
Sixt, M. K. (2022). Type 1 piliated uropathogenic Escherichia coli hijack the
host immune response by binding to CD14. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.78995
chicago: Tomasek, Kathrin, Alexander F Leithner, Ivana Glatzová, Michael S. Lukesch,
Calin C Guet, and Michael K Sixt. “Type 1 Piliated Uropathogenic Escherichia Coli
Hijack the Host Immune Response by Binding to CD14.” ELife. eLife Sciences
Publications, 2022. https://doi.org/10.7554/eLife.78995.
ieee: K. Tomasek, A. F. Leithner, I. Glatzová, M. S. Lukesch, C. C. Guet, and M.
K. Sixt, “Type 1 piliated uropathogenic Escherichia coli hijack the host immune
response by binding to CD14,” eLife, vol. 11. eLife Sciences Publications,
2022.
ista: Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. 2022. Type
1 piliated uropathogenic Escherichia coli hijack the host immune response by binding
to CD14. eLife. 11, e78995.
mla: Tomasek, Kathrin, et al. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack
the Host Immune Response by Binding to CD14.” ELife, vol. 11, e78995, eLife
Sciences Publications, 2022, doi:10.7554/eLife.78995.
short: K. Tomasek, A.F. Leithner, I. Glatzová, M.S. Lukesch, C.C. Guet, M.K. Sixt,
ELife 11 (2022).
corr_author: '1'
date_created: 2022-08-14T22:01:46Z
date_published: 2022-07-26T00:00:00Z
date_updated: 2026-07-06T12:48:19Z
day: '26'
ddc:
- '570'
department:
- _id: MiSi
- _id: CaGu
doi: 10.7554/eLife.78995
ec_funded: 1
external_id:
isi:
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pmid:
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oa_version: Published Version
pmid: 1
project:
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call_identifier: H2020
grant_number: '724373'
name: Cellular Navigation Along Spatial Gradients
- _id: 26018E70-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29911
name: Mechanical adaptation of lamellipodial actin
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
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title: Type 1 piliated uropathogenic Escherichia coli hijack the host immune response
by binding to CD14
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: 11
year: '2022'
...
---
_id: '11478'
abstract:
- lang: eng
text: Cerebral organoids differentiated from human-induced pluripotent stem cells
(hiPSC) provide a unique opportunity to investigate brain development. However,
organoids usually lack microglia, brain-resident immune cells, which are present
in the early embryonic brain and participate in neuronal circuit development.
Here, we find IBA1+ microglia-like cells alongside retinal cups between week 3
and 4 in 2.5D culture with an unguided retinal organoid differentiation protocol.
Microglia do not infiltrate the neuroectoderm and instead enrich within non-pigmented,
3D-cystic compartments that develop in parallel to the 3D-retinal organoids. When
we guide the retinal organoid differentiation with low-dosed BMP4, we prevent
cup development and enhance microglia and 3D-cysts formation. Mass spectrometry
identifies these 3D-cysts to express mesenchymal and epithelial markers. We confirmed
this microglia-preferred environment also within the unguided protocol, providing
insight into microglial behavior and migration and offer a model to study how
they enter and distribute within the human brain.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: We thank the scientific service units at ISTA, specifically the lab
support facility and imaging & optics facility for their support; Nicolas Armel
for performing the Mass Spectrometry. We thank Alexandra Lang and Tanja Peilnsteiner
for their help in human brain tissue collection, Rouven Schulz for his insights
into the functional assays We thank all members of the Siegert group for constant
feedback on the project and Margaret Maes, Rouven Schulz, and Marco Benevento for
feedback on the manuscript. This project has received funding from the European
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
program (grant No. 715571 to S.S.) and from the Gesellschaft für Forschungsförderung
Niederösterreich (grant No. Sc19-017 to V.H.).
article_number: '104580'
article_processing_charge: Yes
article_type: original
author:
- first_name: Katarina
full_name: Bartalska, Katarina
id: 4D883232-F248-11E8-B48F-1D18A9856A87
last_name: Bartalska
- first_name: Verena
full_name: Hübschmann, Verena
id: 32B7C918-F248-11E8-B48F-1D18A9856A87
last_name: Hübschmann
- first_name: Medina
full_name: Korkut, Medina
id: 4B51CE74-F248-11E8-B48F-1D18A9856A87
last_name: Korkut
orcid: 0000-0003-4309-2251
- first_name: Ryan J
full_name: Cubero, Ryan J
id: 850B2E12-9CD4-11E9-837F-E719E6697425
last_name: Cubero
orcid: 0000-0003-0002-1867
- first_name: Alessandro
full_name: Venturino, Alessandro
id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
last_name: Venturino
orcid: 0000-0003-2356-9403
- first_name: Karl
full_name: Rössler, Karl
last_name: Rössler
- first_name: Thomas
full_name: Czech, Thomas
last_name: Czech
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
citation:
ama: Bartalska K, Hübschmann V, Korkut M, et al. A systematic characterization of
microglia-like cell occurrence during retinal organoid differentiation. iScience.
2022;25(7). doi:10.1016/j.isci.2022.104580
apa: Bartalska, K., Hübschmann, V., Korkut, M., Cubero, R. J., Venturino, A., Rössler,
K., … Siegert, S. (2022). A systematic characterization of microglia-like cell
occurrence during retinal organoid differentiation. IScience. Elsevier.
https://doi.org/10.1016/j.isci.2022.104580
chicago: Bartalska, Katarina, Verena Hübschmann, Medina Korkut, Ryan J Cubero, Alessandro
Venturino, Karl Rössler, Thomas Czech, and Sandra Siegert. “A Systematic Characterization
of Microglia-like Cell Occurrence during Retinal Organoid Differentiation.” IScience.
Elsevier, 2022. https://doi.org/10.1016/j.isci.2022.104580.
ieee: K. Bartalska et al., “A systematic characterization of microglia-like
cell occurrence during retinal organoid differentiation,” iScience, vol.
25, no. 7. Elsevier, 2022.
ista: Bartalska K, Hübschmann V, Korkut M, Cubero RJ, Venturino A, Rössler K, Czech
T, Siegert S. 2022. A systematic characterization of microglia-like cell occurrence
during retinal organoid differentiation. iScience. 25(7), 104580.
mla: Bartalska, Katarina, et al. “A Systematic Characterization of Microglia-like
Cell Occurrence during Retinal Organoid Differentiation.” IScience, vol.
25, no. 7, 104580, Elsevier, 2022, doi:10.1016/j.isci.2022.104580.
short: K. Bartalska, V. Hübschmann, M. Korkut, R.J. Cubero, A. Venturino, K. Rössler,
T. Czech, S. Siegert, IScience 25 (2022).
corr_author: '1'
date_created: 2022-07-03T22:01:33Z
date_published: 2022-07-15T00:00:00Z
date_updated: 2026-08-12T08:45:16Z
day: '15'
ddc:
- '610'
department:
- _id: SaSi
doi: 10.1016/j.isci.2022.104580
ec_funded: 1
external_id:
isi:
- '000830428500005'
pmid:
- '35789843'
file:
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checksum: a470b74e1b3796c710189c81a4cd4329
content_type: application/pdf
creator: cchlebak
date_created: 2022-07-04T08:19:25Z
date_updated: 2022-07-04T08:19:25Z
file_id: '11480'
file_name: 2022_iScience_Bartalska.pdf
file_size: 19400048
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file_date_updated: 2022-07-04T08:19:25Z
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intvolume: ' 25'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25D4A630-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715571'
name: Microglia action towards neuronal circuit formation and function in health
and disease
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
- _id: 9B99D380-BA93-11EA-9121-9846C619BF3A
grant_number: SC19-017
name: How human microglia shape developing neurons during health and inflammation
publication: iScience
publication_identifier:
eissn:
- 2589-0042
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
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relation: other
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: A systematic characterization of microglia-like cell occurrence during retinal
organoid differentiation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2022'
...
---
_id: '12291'
abstract:
- lang: eng
text: The phytohormone auxin triggers transcriptional reprogramming through a well-characterized
perception machinery in the nucleus. By contrast, mechanisms that underlie fast
effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation
of proteins or auxin feedback on its transport, remain unclear1,2,3. Whether auxin-binding
protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4.
Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds
auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its
plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required
for the auxin-induced ultrafast global phospho-response and for downstream processes
that include the activation of H+-ATPase and accelerated cytoplasmic streaming.
abp1 and tmk mutants cannot establish auxin-transporting channels and show defective
auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that
lacks the capacity to bind auxin is unable to complement these defects in abp1
mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface
signalling, which mediates the global phospho-response and auxin canalization.
acknowledged_ssus:
- _id: Bio
- _id: EM-Fac
- _id: LifeSc
acknowledgement: We acknowledge K. Kubiasová for excellent technical assistance, J.
Neuhold, A. Lehner and A. Sedivy for technical assistance with protein production
and purification at Vienna Biocenter Core Facilities; Creoptix for performing GCI;
and the Bioimaging, Electron Microscopy and Life Science Facilities at ISTA, the
Plant Sciences Core Facility of CEITEC Masaryk University, the Core Facility CELLIM
(MEYS CR, LM2018129 Czech-BioImaging) and J. Sprakel for their assistance. J.F.
is grateful to R. Napier for many insightful suggestions and support. We thank all
past and present members of the Friml group for their support and for other contributions
to this effort to clarify the controversial role of ABP1 over the past seven years.
The project received funding from the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation program (grant agreement no.
742985 to J.F. and 833867 to D.W.); the Austrian Science Fund (FWF; P29988 to J.F.);
the Netherlands Organization for Scientific Research (NWO; VICI grant 865.14.001
to D.W. and VENI grant VI.Veni.212.003 to A.K.); the Ministry of Education, Science
and Technological Development of the Republic of Serbia (contract no. 451-03-68/2022-14/200053
to B.D.Ž.); and the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and
20H05910).
article_processing_charge: No
article_type: original
author:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- 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: Zuzana
full_name: Gelová, Zuzana
id: 0AE74790-0E0B-11E9-ABC7-1ACFE5697425
last_name: Gelová
orcid: 0000-0003-4783-1752
- 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: Ewa
full_name: Mazur, Ewa
last_name: Mazur
- first_name: Aline
full_name: Monzer, Aline
id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425
last_name: Monzer
- first_name: Lesia
full_name: Rodriguez Solovey, Lesia
id: 3922B506-F248-11E8-B48F-1D18A9856A87
last_name: Rodriguez Solovey
orcid: 0000-0002-7244-7237
- first_name: Mark
full_name: Roosjen, Mark
last_name: Roosjen
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Branka D.
full_name: Živanović, Branka D.
last_name: Živanović
- first_name: Minxia
full_name: Zou, Minxia
id: 5c243f41-03f3-11ec-841c-96faf48a7ef9
last_name: Zou
- first_name: Lukas
full_name: Fiedler, Lukas
id: 7c417475-8972-11ed-ae7b-8b674ca26986
last_name: Fiedler
- first_name: Caterina
full_name: Giannini, Caterina
id: e3fdddd5-f6e0-11ea-865d-ca99ee6367f4
last_name: Giannini
- first_name: Peter
full_name: Grones, Peter
last_name: Grones
- first_name: Mónika
full_name: Hrtyan, Mónika
id: 45A71A74-F248-11E8-B48F-1D18A9856A87
last_name: Hrtyan
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Andre
full_name: Kuhn, Andre
last_name: Kuhn
- first_name: Madhumitha
full_name: Narasimhan, Madhumitha
id: 44BF24D0-F248-11E8-B48F-1D18A9856A87
last_name: Narasimhan
orcid: 0000-0002-8600-0671
- first_name: Marek
full_name: Randuch, Marek
id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
last_name: Randuch
- first_name: Nikola
full_name: Rýdza, Nikola
last_name: Rýdza
- first_name: Koji
full_name: Takahashi, Koji
last_name: Takahashi
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Anastasiia
full_name: Teplova, Anastasiia
id: e3736151-106c-11ec-b916-c2558e2762c6
last_name: Teplova
- first_name: Toshinori
full_name: Kinoshita, Toshinori
last_name: Kinoshita
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Hana
full_name: Rakusová, Hana
last_name: Rakusová
citation:
ama: Friml J, Gallei MC, Gelová Z, et al. ABP1–TMK auxin perception for global phosphorylation
and auxin canalization. Nature. 2022;609(7927):575-581. doi:10.1038/s41586-022-05187-x
apa: Friml, J., Gallei, M. C., Gelová, Z., Johnson, A. J., Mazur, E., Monzer, A.,
… Rakusová, H. (2022). ABP1–TMK auxin perception for global phosphorylation and
auxin canalization. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-05187-x
chicago: Friml, Jiří, Michelle C Gallei, Zuzana Gelová, Alexander J Johnson, Ewa
Mazur, Aline Monzer, Lesia Rodriguez Solovey, et al. “ABP1–TMK Auxin Perception
for Global Phosphorylation and Auxin Canalization.” Nature. Springer Nature,
2022. https://doi.org/10.1038/s41586-022-05187-x.
ieee: J. Friml et al., “ABP1–TMK auxin perception for global phosphorylation
and auxin canalization,” Nature, vol. 609, no. 7927. Springer Nature, pp.
575–581, 2022.
ista: Friml J, Gallei MC, Gelová Z, Johnson AJ, Mazur E, Monzer A, Rodriguez Solovey
L, Roosjen M, Verstraeten I, Živanović BD, Zou M, Fiedler L, Giannini C, Grones
P, Hrtyan M, Kaufmann W, Kuhn A, Narasimhan M, Randuch M, Rýdza N, Takahashi K,
Tan S, Teplova A, Kinoshita T, Weijers D, Rakusová H. 2022. ABP1–TMK auxin perception
for global phosphorylation and auxin canalization. Nature. 609(7927), 575–581.
mla: Friml, Jiří, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and
Auxin Canalization.” Nature, vol. 609, no. 7927, Springer Nature, 2022,
pp. 575–81, doi:10.1038/s41586-022-05187-x.
short: J. Friml, M.C. Gallei, Z. Gelová, A.J. Johnson, E. Mazur, A. Monzer, L. Rodriguez
Solovey, M. Roosjen, I. Verstraeten, B.D. Živanović, M. Zou, L. Fiedler, C. Giannini,
P. Grones, M. Hrtyan, W. Kaufmann, A. Kuhn, M. Narasimhan, M. Randuch, N. Rýdza,
K. Takahashi, S. Tan, A. Teplova, T. Kinoshita, D. Weijers, H. Rakusová, Nature
609 (2022) 575–581.
corr_author: '1'
date_created: 2023-01-16T10:04:48Z
date_published: 2022-09-15T00:00:00Z
date_updated: 2026-08-14T09:33:45Z
day: '15'
ddc:
- '580'
department:
- _id: JiFr
- _id: GradSch
- _id: EvBe
- _id: EM-Fac
doi: 10.1038/s41586-022-05187-x
ec_funded: 1
external_id:
isi:
- '000851357500002'
pmid:
- '36071161'
file:
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checksum: a6055c606aefb900bf62ae3e7d15f921
content_type: application/pdf
creator: amally
date_created: 2023-11-02T17:12:37Z
date_updated: 2023-11-02T17:12:37Z
file_id: '14483'
file_name: Friml Nature 2022_merged.pdf
file_size: 79774945
relation: main_file
success: 1
file_date_updated: 2023-11-02T17:12:37Z
has_accepted_license: '1'
intvolume: ' 609'
isi: 1
issue: '7927'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 575-581
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: 262EF96E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29988
name: RNA-directed DNA methylation in plant development
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
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scopus_import: '1'
status: public
title: ABP1–TMK auxin perception for global phosphorylation and auxin canalization
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 609
year: '2022'
...