---
OA_place: publisher
_id: '10083'
abstract:
- lang: eng
text: "Plant motions occur across a wide spectrum of timescales, ranging from seed
dispersal through bursting (milliseconds) and stomatal opening (minutes) to long-term
adaptation of gross architecture. Relatively fast motions include water-driven
growth as exemplified by root cell expansion under abiotic/biotic stresses or
during gravitropism. A showcase is a root growth inhibition in 30 seconds triggered
by the phytohormone auxin. However, the cellular and molecular mechanisms are
still largely unknown. This thesis covers the studies about this topic as follows.
By taking advantage of microfluidics combined with live imaging, pharmaceutical
tools, and transgenic lines, we examined the kinetics of and causal relationship
among various auxininduced rapid cellular changes in root growth, apoplastic pH,
cytosolic Ca2+, cortical microtubule (CMT) orientation, and vacuolar morphology.
We revealed that CMT reorientation and vacuolar constriction are the consequence
of growth itself instead of responding directly to auxin. In contrast, auxin induces
apoplast alkalinization to rapidly inhibit root growth in 30 seconds. This auxin-triggered
apoplast alkalinization results from rapid H+- influx that is contributed by Ca2+
inward channel CYCLIC NUCLEOTIDE-GATED CHANNEL 14 (CNGC14)-dependent Ca2+ signaling.
To dissect which auxin signaling mediates the rapid apoplast alkalinization, we\r\ncombined
microfluidics and genetic engineering to verify that TIR1/AFB receptors conduct
a non-transcriptional regulation on Ca2+ and H+ -influx. This non-canonical pathway
is mostly mediated by the cytosolic portion of TIR1/AFB. On the other hand, we
uncovered, using biochemical and phospho-proteomic analysis, that auxin cell surface
signaling component TRANSMEMBRANE KINASE 1 (TMK1) plays a negative role during
auxin-trigger apoplast\r\nalkalinization and root growth inhibition through directly
activating PM H+ -ATPases. Therefore, we discovered that PM H+ -ATPases counteract
instead of mediate the auxintriggered rapid H+ -influx, and that TIR1/AFB and
TMK1 regulate root growth antagonistically. This opposite effect of TIR1/AFB and
TMK1 is consistent during auxin-induced hypocotyl elongation, leading us to explore
the relation of two signaling pathways. Assisted with biochemistry and fluorescent
imaging, we verified for the first time that TIR1/AFB and TMK1 can interact with
each other. The ability of TIR1/AFB binding to membrane lipid provides a basis
for the interaction of plasma membrane- and cytosol-localized proteins.\r\nBesides,
transgenic analysis combined with genetic engineering and biochemistry showed
that vi\r\nthey do function in the same pathway. Particularly, auxin-induced
TMK1 increase is TIR1/AFB dependent, suggesting TIR1/AFB regulation on TMK1. Conversely,
TMK1 also regulates TIR1/AFB protein levels and thus auxin canonical signaling.
To follow the study of rapid growth regulation, we analyzed another rapid growth
regulator, signaling peptide RALF1. We showed that RALF1 also triggers a rapid
and reversible growth inhibition caused by H + influx, highly resembling but not
dependent on auxin. Besides, RALF1 promotes auxin biosynthesis by increasing expression
of auxin biosynthesis enzyme YUCCAs and thus induces auxin signaling in ca. 1
hour, contributing to the sustained RALF1-triggered growth inhibition. These studies
collectively contribute to understanding rapid regulation on plant cell\r\ngrowth,
novel auxin signaling pathway as well as auxin-peptide crosstalk. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
citation:
ama: Li L. Rapid cell growth regulation in Arabidopsis. 2021. doi:10.15479/at:ista:10083
apa: Li, L. (2021). Rapid cell growth regulation in Arabidopsis. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:10083
chicago: Li, Lanxin. “Rapid Cell Growth Regulation in Arabidopsis.” Institute of
Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10083.
ieee: L. Li, “Rapid cell growth regulation in Arabidopsis,” Institute of Science
and Technology Austria, 2021.
ista: Li L. 2021. Rapid cell growth regulation in Arabidopsis. Institute of Science
and Technology Austria.
mla: Li, Lanxin. Rapid Cell Growth Regulation in Arabidopsis. Institute of
Science and Technology Austria, 2021, doi:10.15479/at:ista:10083.
short: L. Li, Rapid Cell Growth Regulation in Arabidopsis, Institute of Science
and Technology Austria, 2021.
corr_author: '1'
date_created: 2021-10-04T13:33:10Z
date_published: 2021-10-06T00:00:00Z
date_updated: 2026-04-16T12:20:41Z
day: '06'
ddc:
- '575'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JiFr
doi: 10.15479/at:ista:10083
ec_funded: 1
file:
- access_level: open_access
checksum: 3b2f55b3b8ae05337a0dcc1cd8595b10
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-14T08:00:07Z
date_updated: 2022-12-20T23:30:03Z
embargo: 2022-10-14
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file_name: 0._IST_Austria_Thesis_Lanxin_Li_1014_pdftron.pdf
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relation: main_file
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content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: cchlebak
date_created: 2021-10-14T08:00:13Z
date_updated: 2022-12-20T23:30:03Z
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file_id: '10139'
file_name: 0._IST_Austria_Thesis_Lanxin_Li_1014.docx
file_size: 15058499
relation: source_file
file_date_updated: 2022-12-20T23:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 26B4D67E-B435-11E9-9278-68D0E5697425
grant_number: '25351'
name: 'A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated
Rapid Growth Inhibition in Arabidopsis Root'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '442'
relation: part_of_dissertation
status: public
- id: '6627'
relation: part_of_dissertation
status: public
- id: '8931'
relation: part_of_dissertation
status: public
- id: '8986'
relation: part_of_dissertation
status: public
- id: '10095'
relation: part_of_dissertation
status: public
- id: '8283'
relation: part_of_dissertation
status: public
- id: '9287'
relation: part_of_dissertation
status: public
- id: '10015'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: Rapid cell growth regulation in Arabidopsis
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2021'
...
---
_id: '10015'
abstract:
- lang: eng
text: "Auxin plays a dual role in growth regulation and, depending on the tissue
and concentration of the hormone, it can either promote or inhibit division and
expansion processes in plants. Recent studies have revealed that, beyond transcriptional
reprogramming, alternative auxincontrolled mechanisms regulate root growth. Here,
we explored the impact of different concentrations of the synthetic auxin NAA
that establish growth-promoting and -repressing conditions on the root tip proteome
and phosphoproteome, generating a unique resource. From the phosphoproteome data,
we pinpointed (novel) growth regulators, such as the RALF34-THE1 module. Our results,
together with previously published studies, suggest that auxin, H+-ATPases, cell
wall modifications and cell wall sensing receptor-like kinases are tightly embedded
in a pathway regulating cell elongation. Furthermore, our study assigned a novel
role to MKK2 as a regulator of primary root growth and a (potential) regulator
of auxin biosynthesis and signalling, and suggests the importance of the MKK2\r\nThr31
phosphorylation site for growth regulation in the Arabidopsis root tip."
acknowledgement: We thank the Nottingham Stock Centre for seeds, Frank Van Breusegem
for the phb3 mutant, and Herman Höfte for the the1 mutant. Open Access Funding by
the Austrian Science Fund (FWF).
alternative_title:
- Protein Phosphorylation and Cell Signaling in Plants
article_number: '1665 '
article_processing_charge: Yes
article_type: original
author:
- first_name: N
full_name: Nikonorova, N
last_name: Nikonorova
- first_name: E
full_name: Murphy, E
last_name: Murphy
- first_name: CF
full_name: Fonseca de Lima, CF
last_name: Fonseca de Lima
- first_name: S
full_name: Zhu, S
last_name: Zhu
- first_name: B
full_name: van de Cotte, B
last_name: van de Cotte
- first_name: LD
full_name: Vu, LD
last_name: Vu
- first_name: D
full_name: Balcerowicz, D
last_name: Balcerowicz
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: X
full_name: Kong, X
last_name: Kong
- first_name: G
full_name: De Rop, G
last_name: De Rop
- first_name: T
full_name: Beeckman, T
last_name: Beeckman
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: K
full_name: Vissenberg, K
last_name: Vissenberg
- first_name: PC
full_name: Morris, PC
last_name: Morris
- first_name: Z
full_name: Ding, Z
last_name: Ding
- first_name: I
full_name: De Smet, I
last_name: De Smet
citation:
ama: Nikonorova N, Murphy E, Fonseca de Lima C, et al. The Arabidopsis root tip
(phospho)proteomes at growth-promoting versus growth-repressing conditions reveal
novel root growth regulators. Cells. 2021;10. doi:10.3390/cells10071665
apa: Nikonorova, N., Murphy, E., Fonseca de Lima, C., Zhu, S., van de Cotte, B.,
Vu, L., … De Smet, I. (2021). The Arabidopsis root tip (phospho)proteomes at growth-promoting
versus growth-repressing conditions reveal novel root growth regulators. Cells.
MDPI. https://doi.org/10.3390/cells10071665
chicago: Nikonorova, N, E Murphy, CF Fonseca de Lima, S Zhu, B van de Cotte, LD
Vu, D Balcerowicz, et al. “The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting
versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators.” Cells.
MDPI, 2021. https://doi.org/10.3390/cells10071665.
ieee: N. Nikonorova et al., “The Arabidopsis root tip (phospho)proteomes
at growth-promoting versus growth-repressing conditions reveal novel root growth
regulators,” Cells, vol. 10. MDPI, 2021.
ista: Nikonorova N, Murphy E, Fonseca de Lima C, Zhu S, van de Cotte B, Vu L, Balcerowicz
D, Li L, Kong X, De Rop G, Beeckman T, Friml J, Vissenberg K, Morris P, Ding Z,
De Smet I. 2021. The Arabidopsis root tip (phospho)proteomes at growth-promoting
versus growth-repressing conditions reveal novel root growth regulators. Cells.
10, 1665.
mla: Nikonorova, N., et al. “The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting
versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators.” Cells,
vol. 10, 1665, MDPI, 2021, doi:10.3390/cells10071665.
short: N. Nikonorova, E. Murphy, C. Fonseca de Lima, S. Zhu, B. van de Cotte, L.
Vu, D. Balcerowicz, L. Li, X. Kong, G. De Rop, T. Beeckman, J. Friml, K. Vissenberg,
P. Morris, Z. Ding, I. De Smet, Cells 10 (2021).
date_created: 2021-09-14T11:36:20Z
date_published: 2021-07-02T00:00:00Z
date_updated: 2026-07-02T22:30:44Z
day: '02'
ddc:
- '575'
department:
- _id: JiFr
doi: 10.3390/cells10071665
ec_funded: 1
external_id:
isi:
- '000676604700001'
pmid:
- '34359847'
file:
- access_level: open_access
checksum: 2a9f534b9c2200e72e2cde95afaf4eed
content_type: application/pdf
creator: cchlebak
date_created: 2021-09-16T09:07:06Z
date_updated: 2021-09-16T09:07:06Z
file_id: '10021'
file_name: 2021_Cells_Nikonorova.pdf
file_size: 2667848
relation: main_file
success: 1
file_date_updated: 2021-09-16T09:07:06Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
keyword:
- primary root
- (phospho)proteomics
- auxin
- (receptor) kinase
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1
call_identifier: FWF
name: FWF Open Access Fund
publication: Cells
publication_identifier:
issn:
- 2073-4409
publication_status: published
publisher: MDPI
quality_controlled: '1'
related_material:
record:
- id: '10083'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing
conditions reveal novel root growth regulators
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: 10
year: '2021'
...
---
_id: '10095'
abstract:
- lang: eng
text: Growth regulation tailors plant development to its environment. A showcase
is response to gravity, where shoots bend up and roots down1. This paradox is
based on opposite effects of the phytohormone auxin, which promotes cell expansion
in shoots, while inhibiting it in roots via a yet unknown cellular mechanism2.
Here, by combining microfluidics, live imaging, genetic engineering and phospho-proteomics
in Arabidopsis thaliana, we advance our understanding how auxin inhibits root
growth. We show that auxin activates two distinct, antagonistically acting signalling
pathways that converge on the rapid regulation of the apoplastic pH, a causative
growth determinant. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts
with and mediates phosphorylation and activation of plasma membrane H+-ATPases
for apoplast acidification, while intracellular canonical auxin signalling promotes
net cellular H+-influx, causing apoplast alkalinisation. The simultaneous activation
of these two counteracting mechanisms poises the root for a rapid, fine-tuned
growth modulation while navigating complex soil environment.
acknowledged_ssus:
- _id: LifeSc
- _id: M-Shop
- _id: Bio
acknowledgement: We thank Nataliia Gnyliukh and Lukas Hörmayer for technical assistance
and Nadine Paris for sharing PM-Cyto seeds. We gratefully acknowledge Life Science,
Machine Shop and Bioimaging Facilities of IST Austria. This project has received
funding from the European Research Council Advanced Grant (ETAP-742985) and the
Austrian Science Fund (FWF) I 3630-B25 to J.F., the National Institutes of Health
(GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO;
VIDI-864.13.001.), the Research Foundation-Flanders (FWO; Odysseus II G0D0515N)
and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R.,
the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research
to M.R and D.W., the Australian Research Council and China National Distinguished
Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685)
and T.K. (20H05687 and 20H05910), the European Union’s Horizon 2020 research and
innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385
and the DOC Fellowship of the Austrian Academy of Sciences to L.L., the China Scholarship
Council to J.C.
article_number: '266395'
article_processing_charge: No
author:
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Mark
full_name: Roosjen, Mark
last_name: Roosjen
- first_name: Koji
full_name: Takahashi, Koji
last_name: Takahashi
- 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: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Jian
full_name: Chen, Jian
last_name: Chen
- first_name: Lana
full_name: Shabala, Lana
last_name: Shabala
- first_name: Wouter
full_name: Smet, Wouter
last_name: Smet
- first_name: Hong
full_name: Ren, Hong
last_name: Ren
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Sergey
full_name: Shabala, Sergey
last_name: Shabala
- first_name: Bert
full_name: De Rybel, Bert
last_name: De Rybel
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Toshinori
full_name: Kinoshita, Toshinori
last_name: Kinoshita
- first_name: William M.
full_name: Gray, William M.
last_name: Gray
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin
signalling for H+-fluxes in root growth. Research Square. doi:10.21203/rs.3.rs-266395/v3
apa: Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L.,
Merrin, J., … Friml, J. (n.d.). Cell surface and intracellular auxin signalling
for H+-fluxes in root growth. Research Square. https://doi.org/10.21203/rs.3.rs-266395/v3
chicago: Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez
Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin
Signalling for H+-Fluxes in Root Growth.” Research Square, n.d. https://doi.org/10.21203/rs.3.rs-266395/v3.
ieee: L. Li et al., “Cell surface and intracellular auxin signalling for
H+-fluxes in root growth,” Research Square. .
ista: Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J,
Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D,
Kinoshita T, Gray WM, Friml J. Cell surface and intracellular auxin signalling
for H+-fluxes in root growth. Research Square, 266395.
mla: Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes
in Root Growth.” Research Square, 266395, doi:10.21203/rs.3.rs-266395/v3.
short: L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J.
Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel,
D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Research Square (n.d.).
corr_author: '1'
date_created: 2021-10-06T08:56:22Z
date_published: 2021-09-09T00:00:00Z
date_updated: 2026-07-02T22:30:44Z
day: '09'
department:
- _id: JiFr
- _id: NanoFab
doi: 10.21203/rs.3.rs-266395/v3
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.doi.org/10.21203/rs.3.rs-266395/v3
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
- _id: 26B4D67E-B435-11E9-9278-68D0E5697425
grant_number: '25351'
name: 'A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated
Rapid Growth Inhibition in Arabidopsis Root'
publication: Research Square
publication_identifier:
issn:
- 2693-5015
publication_status: draft
related_material:
record:
- id: '10223'
relation: later_version
status: public
- id: '10083'
relation: dissertation_contains
status: public
status: public
title: Cell surface and intracellular auxin signalling for H+-fluxes in root growth
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
OA_place: publisher
_id: '10293'
abstract:
- lang: eng
text: "Indirect reciprocity in evolutionary game theory is a prominent mechanism
for explaining the evolution of cooperation among unrelated individuals. In contrast
to direct reciprocity, which is based on individuals meeting repeatedly, and conditionally
cooperating by using their own experiences, indirect reciprocity is based on individuals’
reputations. If a player helps another, this increases the helper’s public standing,
benefitting them in the future. This lets cooperation in the population emerge
without individuals having to meet more than once. While the two modes of reciprocity
are intertwined, they are difficult to compare. Thus, they are usually studied
in isolation. Direct reciprocity can maintain cooperation with simple strategies,
and is robust against noise even when players do not remember more\r\nthan their
partner’s last action. Meanwhile, indirect reciprocity requires its successful
strategies, or social norms, to be more complex. Exhaustive search previously
identified eight such norms, called the “leading eight”, which excel at maintaining
cooperation. However, as the first result of this thesis, we show that the leading
eight break down once we remove the fundamental assumption that information is
synchronized and public, such that everyone agrees on reputations. Once we consider
a more realistic scenario of imperfect information, where reputations are private,
and individuals occasionally misinterpret or miss observations, the leading eight
do not promote cooperation anymore. Instead, minor initial disagreements can proliferate,
fragmenting populations into subgroups. In a next step, we consider ways to mitigate
this issue. We first explore whether introducing “generosity” can stabilize cooperation
when players use the leading eight strategies in noisy environments. This approach
of modifying strategies to include probabilistic elements for coping with errors
is known to work well in direct reciprocity. However, as we show here, it fails
for the more complex norms of indirect reciprocity. Imperfect information still
prevents cooperation from evolving. On the other hand, we succeeded to show in
this thesis that modifying the leading eight to use “quantitative assessment”,
i.e. tracking reputation scores on a scale beyond good and bad, and making overall
judgments of others based on a threshold, is highly successful, even when noise
increases in the environment. Cooperation can flourish when reputations\r\nare
more nuanced, and players have a broader understanding what it means to be “good.”
Finally, we present a single theoretical framework that unites the two modes of
reciprocity despite their differences. Within this framework, we identify a novel
simple and successful strategy for indirect reciprocity, which can cope with noisy
environments and has an analogue in direct reciprocity. We can also analyze decision
making when different sources of information are available. Our results help highlight
that for sustaining cooperation, already the most simple rules of reciprocity
can be sufficient."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Laura
full_name: Schmid, Laura
id: 38B437DE-F248-11E8-B48F-1D18A9856A87
last_name: Schmid
orcid: 0000-0002-6978-7329
citation:
ama: Schmid L. Evolution of cooperation via (in)direct reciprocity under imperfect
information. 2021. doi:10.15479/at:ista:10293
apa: Schmid, L. (2021). Evolution of cooperation via (in)direct reciprocity under
imperfect information. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10293
chicago: Schmid, Laura. “Evolution of Cooperation via (in)Direct Reciprocity under
Imperfect Information.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10293.
ieee: L. Schmid, “Evolution of cooperation via (in)direct reciprocity under imperfect
information,” Institute of Science and Technology Austria, 2021.
ista: Schmid L. 2021. Evolution of cooperation via (in)direct reciprocity under
imperfect information. Institute of Science and Technology Austria.
mla: Schmid, Laura. Evolution of Cooperation via (in)Direct Reciprocity under
Imperfect Information. Institute of Science and Technology Austria, 2021,
doi:10.15479/at:ista:10293.
short: L. Schmid, Evolution of Cooperation via (in)Direct Reciprocity under Imperfect
Information, Institute of Science and Technology Austria, 2021.
corr_author: '1'
date_created: 2021-11-15T17:12:57Z
date_published: 2021-11-17T00:00:00Z
date_updated: 2026-04-08T07:11:20Z
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department:
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- _id: KrCh
doi: 10.15479/at:ista:10293
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language:
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month: '11'
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oa_version: Published Version
page: '171'
project:
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call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9997'
relation: part_of_dissertation
status: public
- id: '9402'
relation: part_of_dissertation
status: public
- id: '2'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
title: Evolution of cooperation via (in)direct reciprocity under imperfect information
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2021'
...
---
_id: '9997'
abstract:
- lang: eng
text: Indirect reciprocity is a mechanism for the evolution of cooperation based
on social norms. This mechanism requires that individuals in a population observe
and judge each other’s behaviors. Individuals with a good reputation are more
likely to receive help from others. Previous work suggests that indirect reciprocity
is only effective when all relevant information is reliable and publicly available.
Otherwise, individuals may disagree on how to assess others, even if they all
apply the same social norm. Such disagreements can lead to a breakdown of cooperation.
Here we explore whether the predominantly studied ‘leading eight’ social norms
of indirect reciprocity can be made more robust by equipping them with an element
of generosity. To this end, we distinguish between two kinds of generosity. According
to assessment generosity, individuals occasionally assign a good reputation to
group members who would usually be regarded as bad. According to action generosity,
individuals occasionally cooperate with group members with whom they would usually
defect. Using individual-based simulations, we show that the two kinds of generosity
have a very different effect on the resulting reputation dynamics. Assessment
generosity tends to add to the overall noise and allows defectors to invade. In
contrast, a limited amount of action generosity can be beneficial in a few cases.
However, even when action generosity is beneficial, the respective simulations
do not result in full cooperation. Our results suggest that while generosity can
favor cooperation when individuals use the most simple strategies of reciprocity,
it is disadvantageous when individuals use more complex social norms.
acknowledgement: 'This work was supported by the European Research Council CoG 863818
(ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529:
E-DIRECT (to C.H.). L.S. received additional partial support by the Austrian Science
Fund (FWF) under Grant Z211-N23 (Wittgenstein Award).'
article_number: '17443'
article_processing_charge: Yes
article_type: original
author:
- first_name: Laura
full_name: Schmid, Laura
id: 38B437DE-F248-11E8-B48F-1D18A9856A87
last_name: Schmid
orcid: 0000-0002-6978-7329
- first_name: Pouya
full_name: Shati, Pouya
last_name: Shati
- first_name: Christian
full_name: Hilbe, Christian
last_name: Hilbe
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: Schmid L, Shati P, Hilbe C, Chatterjee K. The evolution of indirect reciprocity
under action and assessment generosity. Scientific Reports. 2021;11(1).
doi:10.1038/s41598-021-96932-1
apa: Schmid, L., Shati, P., Hilbe, C., & Chatterjee, K. (2021). The evolution
of indirect reciprocity under action and assessment generosity. Scientific
Reports. Springer Nature. https://doi.org/10.1038/s41598-021-96932-1
chicago: Schmid, Laura, Pouya Shati, Christian Hilbe, and Krishnendu Chatterjee.
“The Evolution of Indirect Reciprocity under Action and Assessment Generosity.”
Scientific Reports. Springer Nature, 2021. https://doi.org/10.1038/s41598-021-96932-1.
ieee: L. Schmid, P. Shati, C. Hilbe, and K. Chatterjee, “The evolution of indirect
reciprocity under action and assessment generosity,” Scientific Reports,
vol. 11, no. 1. Springer Nature, 2021.
ista: Schmid L, Shati P, Hilbe C, Chatterjee K. 2021. The evolution of indirect
reciprocity under action and assessment generosity. Scientific Reports. 11(1),
17443.
mla: Schmid, Laura, et al. “The Evolution of Indirect Reciprocity under Action and
Assessment Generosity.” Scientific Reports, vol. 11, no. 1, 17443, Springer
Nature, 2021, doi:10.1038/s41598-021-96932-1.
short: L. Schmid, P. Shati, C. Hilbe, K. Chatterjee, Scientific Reports 11 (2021).
corr_author: '1'
date_created: 2021-09-11T16:22:02Z
date_published: 2021-08-31T00:00:00Z
date_updated: 2026-07-02T22:30:45Z
day: '31'
ddc:
- '003'
department:
- _id: GradSch
- _id: KrCh
doi: 10.1038/s41598-021-96932-1
ec_funded: 1
external_id:
isi:
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pmid:
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file_date_updated: 2021-09-13T10:31:21Z
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intvolume: ' 11'
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issue: '1'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
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call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication: Scientific Reports
publication_identifier:
eissn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The evolution of indirect reciprocity under action and assessment generosity
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: '2021'
...
---
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_id: '10135'
abstract:
- lang: eng
text: "Plants maintain the capacity to develop new organs e.g. lateral roots post-embryonically
throughout their whole life and thereby flexibly adapt to ever-changing environmental
conditions. Plant hormones auxin and cytokinin are the main regulators of the
lateral root organogenesis. Additionally to their solo activities, the interaction
between auxin and\r\ncytokinin plays crucial role in fine-tuning of lateral root
development and growth. In particular, cytokinin modulates auxin distribution
within the developing lateral root by affecting the endomembrane trafficking of
auxin transporter PIN1 and promoting its vacuolar degradation (Marhavý et al.,
2011, 2014). This effect is independent of transcription and\r\ntranslation. Therefore,
it suggests novel, non-canonical cytokinin activity occuring possibly on the posttranslational
level. Impact of cytokinin and other plant hormones on auxin transporters (including
PIN1) on the posttranslational level is described in detail in the introduction
part of this thesis in a form of a review (Semeradova et al., 2020). To gain insights
into the molecular machinery underlying cytokinin effect on the endomembrane trafficking
in the plant cell, in particular on the PIN1 degradation, we conducted two large
proteomic screens: 1) Identification of cytokinin binding proteins using\r\nchemical
proteomics. 2) Monitoring of proteomic and phosphoproteomic changes upon cytokinin
treatment. In the first screen, we identified DYNAMIN RELATED PROTEIN 2A (DRP2A).
We found that DRP2A plays a role in cytokinin regulated processes during the plant
growth and that cytokinin treatment promotes destabilization of DRP2A protein.
However, the role of DRP2A in the PIN1 degradation remains to be elucidated. In
the second screen, we found VACUOLAR PROTEIN SORTING 9A (VPS9A). VPS9a plays crucial
role in plant’s response to cytokin and in cytokinin mediated PIN1 degradation.
Altogether, we identified proteins, which bind to cytokinin and proteins that
in response to\r\ncytokinin exhibit significantly changed abundance or phosphorylation
pattern. By combining information from these two screens, we can pave our way
towards understanding of noncanonical cytokinin effects."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Hana
full_name: Semerádová, Hana
id: 42FE702E-F248-11E8-B48F-1D18A9856A87
last_name: Semerádová
citation:
ama: Semerádová H. Molecular mechanisms of the cytokinin-regulated endomembrane
trafficking to coordinate plant organogenesis. 2021. doi:10.15479/at:ista:10135
apa: Semerádová, H. (2021). Molecular mechanisms of the cytokinin-regulated endomembrane
trafficking to coordinate plant organogenesis. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:10135
chicago: Semerádová, Hana. “Molecular Mechanisms of the Cytokinin-Regulated Endomembrane
Trafficking to Coordinate Plant Organogenesis.” Institute of Science and Technology
Austria, 2021. https://doi.org/10.15479/at:ista:10135.
ieee: H. Semerádová, “Molecular mechanisms of the cytokinin-regulated endomembrane
trafficking to coordinate plant organogenesis,” Institute of Science and Technology
Austria, 2021.
ista: Semerádová H. 2021. Molecular mechanisms of the cytokinin-regulated endomembrane
trafficking to coordinate plant organogenesis. Institute of Science and Technology
Austria.
mla: Semerádová, Hana. Molecular Mechanisms of the Cytokinin-Regulated Endomembrane
Trafficking to Coordinate Plant Organogenesis. Institute of Science and Technology
Austria, 2021, doi:10.15479/at:ista:10135.
short: H. Semerádová, Molecular Mechanisms of the Cytokinin-Regulated Endomembrane
Trafficking to Coordinate Plant Organogenesis, Institute of Science and Technology
Austria, 2021.
corr_author: '1'
date_created: 2021-10-13T13:42:48Z
date_published: 2021-10-13T00:00:00Z
date_updated: 2026-04-08T07:12:06Z
day: '13'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: EvBe
doi: 10.15479/at:ista:10135
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grant_number: '24746'
name: Molecular mechanisms of the cytokinin regulated endomembrane trafficking to
coordinate plant organogenesis
publication_identifier:
isbn:
- 978-3-99078-014-5
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9160'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
title: Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to
coordinate plant organogenesis
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2021'
...
---
_id: '9402'
abstract:
- lang: eng
text: Direct and indirect reciprocity are key mechanisms for the evolution of cooperation.
Direct reciprocity means that individuals use their own experience to decide whether
to cooperate with another person. Indirect reciprocity means that they also consider
the experiences of others. Although these two mechanisms are intertwined, they
are typically studied in isolation. Here, we introduce a mathematical framework
that allows us to explore both kinds of reciprocity simultaneously. We show that
the well-known ‘generous tit-for-tat’ strategy of direct reciprocity has a natural
analogue in indirect reciprocity, which we call ‘generous scoring’. Using an equilibrium
analysis, we characterize under which conditions either of the two strategies
can maintain cooperation. With simulations, we additionally explore which kind
of reciprocity evolves when members of a population engage in social learning
to adapt to their environment. Our results draw unexpected connections between
direct and indirect reciprocity while highlighting important differences regarding
their evolvability.
acknowledgement: 'This work was supported by the European Research Council CoG 863818
(ForM-SMArt) (to K.C.), the European Research Council Start Grant 279307: Graph
Games (to K.C.), and the European Research Council Starting Grant 850529: E-DIRECT
(to C.H.). The funders had no role in study design, data collection and analysis,
decision to publish or preparation of the manuscript.'
article_processing_charge: No
article_type: original
author:
- first_name: Laura
full_name: Schmid, Laura
id: 38B437DE-F248-11E8-B48F-1D18A9856A87
last_name: Schmid
orcid: 0000-0002-6978-7329
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Martin A.
full_name: Nowak, Martin A.
last_name: Nowak
citation:
ama: Schmid L, Chatterjee K, Hilbe C, Nowak MA. A unified framework of direct and
indirect reciprocity. Nature Human Behaviour. 2021;5(10):1292–1302. doi:10.1038/s41562-021-01114-8
apa: Schmid, L., Chatterjee, K., Hilbe, C., & Nowak, M. A. (2021). A unified
framework of direct and indirect reciprocity. Nature Human Behaviour. Springer
Nature. https://doi.org/10.1038/s41562-021-01114-8
chicago: Schmid, Laura, Krishnendu Chatterjee, Christian Hilbe, and Martin A. Nowak.
“A Unified Framework of Direct and Indirect Reciprocity.” Nature Human Behaviour.
Springer Nature, 2021. https://doi.org/10.1038/s41562-021-01114-8.
ieee: L. Schmid, K. Chatterjee, C. Hilbe, and M. A. Nowak, “A unified framework
of direct and indirect reciprocity,” Nature Human Behaviour, vol. 5, no.
10. Springer Nature, pp. 1292–1302, 2021.
ista: Schmid L, Chatterjee K, Hilbe C, Nowak MA. 2021. A unified framework of direct
and indirect reciprocity. Nature Human Behaviour. 5(10), 1292–1302.
mla: Schmid, Laura, et al. “A Unified Framework of Direct and Indirect Reciprocity.”
Nature Human Behaviour, vol. 5, no. 10, Springer Nature, 2021, pp. 1292–1302,
doi:10.1038/s41562-021-01114-8.
short: L. Schmid, K. Chatterjee, C. Hilbe, M.A. Nowak, Nature Human Behaviour 5
(2021) 1292–1302.
corr_author: '1'
date_created: 2021-05-18T16:56:57Z
date_published: 2021-05-13T00:00:00Z
date_updated: 2026-07-02T22:30:45Z
day: '13'
ddc:
- '000'
department:
- _id: KrCh
- _id: GradSch
doi: 10.1038/s41562-021-01114-8
ec_funded: 1
external_id:
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page: 1292–1302
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call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
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call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Nature Human Behaviour
publication_identifier:
eissn:
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publisher: Springer Nature
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related_material:
link:
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url: https://ist.ac.at/en/news/the-emergence-of-cooperation/
record:
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status: public
scopus_import: '1'
status: public
title: A unified framework of direct and indirect reciprocity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2021'
...
---
_id: '9010'
abstract:
- lang: eng
text: Availability of the essential macronutrient nitrogen in soil plays a critical
role in plant growth, development, and impacts agricultural productivity. Plants
have evolved different strategies for sensing and responding to heterogeneous
nitrogen distribution. Modulation of root system architecture, including primary
root growth and branching, is among the most essential plant adaptions to ensure
adequate nitrogen acquisition. However, the immediate molecular pathways coordinating
the adjustment of root growth in response to distinct nitrogen sources, such as
nitrate or ammonium, are poorly understood. Here, we show that growth as manifested
by cell division and elongation is synchronized by coordinated auxin flux between
two adjacent outer tissue layers of the root. This coordination is achieved by
nitrate‐dependent dephosphorylation of the PIN2 auxin efflux carrier at a previously
uncharacterized phosphorylation site, leading to subsequent PIN2 lateralization
and thereby regulating auxin flow between adjacent tissues. A dynamic computer
model based on our experimental data successfully recapitulates experimental observations.
Our study provides mechanistic insights broadening our understanding of root growth
mechanisms in dynamic environments.
acknowledged_ssus:
- _id: Bio
acknowledgement: 'We acknowledge Gergely Molnar for critical reading of the manuscript,
Alexander Johnson for language editing and Yulija Salanenka for technical assistance.
Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S)
to KO, RA and EB. Work in the Benkova laboratory was supported by the Austrian Science
Fund (FWF01_I1774S) to KO, RA and EB and by the DOC Fellowship Programme of the
AustrianAcademy of Sciences (25008) to C.A. Work in the Wabnik laboratory was supported
by the Programa de Atraccion de Talento 2017 (Comunidad deMadrid, 2017-T1/BIO-5654
to K.W.), Severo Ochoa Programme for Centres of Excellence in R&D from the Agencia
Estatal de Investigacion of Spain (grantSEV-2016-0672 (2017-2021) to K.W. via the
CBGP) and Programa Estatal de Generacion del Conocimiento y Fortalecimiento Científico
y Tecnologico del Sistema de I+D+I 2019 (PGC2018-093387-A-I00) from MICIU (to K.W.).
M.M.was supported by a postdoctoral contract associated to SEV-2016-0672.We acknowledge
the Bioimaging Facility in IST-Austria and the Advanced Microscopy Facility of the
Vienna Bio Center Core Facilities, member of the Vienna Bio Center Austria, for
use of the OMX v43D SIM microscope. AJ was supported by the Austrian Science Fund
(FWF): I03630 to J.F'
article_number: e106862
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Krisztina
full_name: Ötvös, Krisztina
id: 29B901B0-F248-11E8-B48F-1D18A9856A87
last_name: Ötvös
orcid: 0000-0002-5503-4983
- first_name: Marco
full_name: Marconi, Marco
last_name: Marconi
- first_name: Andrea
full_name: Vega, Andrea
last_name: Vega
- first_name: Jose
full_name: O’Brien, Jose
last_name: O’Brien
- 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: Rashed
full_name: Abualia, Rashed
id: 4827E134-F248-11E8-B48F-1D18A9856A87
last_name: Abualia
orcid: 0000-0002-9357-9415
- first_name: Livio
full_name: Antonielli, Livio
last_name: Antonielli
- first_name: Juan C
full_name: Montesinos López, Juan C
id: 310A8E3E-F248-11E8-B48F-1D18A9856A87
last_name: Montesinos López
orcid: 0000-0001-9179-6099
- first_name: Yuzhou
full_name: Zhang, Yuzhou
id: 3B6137F2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0003-2627-6956
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Candela
full_name: Cuesta, Candela
id: 33A3C818-F248-11E8-B48F-1D18A9856A87
last_name: Cuesta
orcid: 0000-0003-1923-2410
- first_name: Christina
full_name: Artner, Christina
id: 45DF286A-F248-11E8-B48F-1D18A9856A87
last_name: Artner
- first_name: Eleonore
full_name: Bouguyon, Eleonore
last_name: Bouguyon
- first_name: Alain
full_name: Gojon, Alain
last_name: Gojon
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Rodrigo A.
full_name: Gutiérrez, Rodrigo A.
last_name: Gutiérrez
- first_name: Krzysztof T
full_name: Wabnik, Krzysztof T
id: 4DE369A4-F248-11E8-B48F-1D18A9856A87
last_name: Wabnik
orcid: 0000-0001-7263-0560
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Ötvös K, Marconi M, Vega A, et al. Modulation of plant root growth by nitrogen
source-defined regulation of polar auxin transport. EMBO Journal. 2021;40(3).
doi:10.15252/embj.2020106862
apa: Ötvös, K., Marconi, M., Vega, A., O’Brien, J., Johnson, A. J., Abualia, R.,
… Benková, E. (2021). Modulation of plant root growth by nitrogen source-defined
regulation of polar auxin transport. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2020106862
chicago: Ötvös, Krisztina, Marco Marconi, Andrea Vega, Jose O’Brien, Alexander J
Johnson, Rashed Abualia, Livio Antonielli, et al. “Modulation of Plant Root Growth
by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” EMBO Journal.
Embo Press, 2021. https://doi.org/10.15252/embj.2020106862.
ieee: K. Ötvös et al., “Modulation of plant root growth by nitrogen source-defined
regulation of polar auxin transport,” EMBO Journal, vol. 40, no. 3. Embo
Press, 2021.
ista: Ötvös K, Marconi M, Vega A, O’Brien J, Johnson AJ, Abualia R, Antonielli L,
Montesinos López JC, Zhang Y, Tan S, Cuesta C, Artner C, Bouguyon E, Gojon A,
Friml J, Gutiérrez RA, Wabnik KT, Benková E. 2021. Modulation of plant root growth
by nitrogen source-defined regulation of polar auxin transport. EMBO Journal.
40(3), e106862.
mla: Ötvös, Krisztina, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined
Regulation of Polar Auxin Transport.” EMBO Journal, vol. 40, no. 3, e106862,
Embo Press, 2021, doi:10.15252/embj.2020106862.
short: K. Ötvös, M. Marconi, A. Vega, J. O’Brien, A.J. Johnson, R. Abualia, L. Antonielli,
J.C. Montesinos López, Y. Zhang, S. Tan, C. Cuesta, C. Artner, E. Bouguyon, A.
Gojon, J. Friml, R.A. Gutiérrez, K.T. Wabnik, E. Benková, EMBO Journal 40 (2021).
corr_author: '1'
date_created: 2021-01-17T23:01:12Z
date_published: 2021-02-01T00:00:00Z
date_updated: 2026-07-02T22:30:48Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
- _id: EvBe
doi: 10.15252/embj.2020106862
external_id:
isi:
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pmid:
- ' 33399250'
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oa: 1
oa_version: Published Version
pmid: 1
project:
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call_identifier: FWF
grant_number: I 1774-B16
name: Hormone cross-talk drives nutrient dependent plant development
- _id: 2685A872-B435-11E9-9278-68D0E5697425
name: Hormonal regulation of plant adaptive responses to environmental signals
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: EMBO Journal
publication_identifier:
eissn:
- 1460-2075
issn:
- 0261-4189
publication_status: published
publisher: Embo Press
quality_controlled: '1'
related_material:
link:
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relation: press_release
url: https://ist.ac.at/en/news/a-plants-way-to-its-favorite-food/
record:
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status: public
scopus_import: '1'
status: public
title: Modulation of plant root growth by nitrogen source-defined regulation of polar
auxin transport
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 40
year: '2021'
...
---
_id: '10816'
abstract:
- lang: eng
text: Pattern separation is a fundamental brain computation that converts small
differences in input patterns into large differences in output patterns. Several
synaptic mechanisms of pattern separation have been proposed, including code expansion,
inhibition and plasticity; however, which of these mechanisms play a role in the
entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation
circuit, remains unclear. Here we show that a biologically realistic, full-scale
EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive
inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator.
Both external gamma-modulated inhibition and internal lateral inhibition mediated
by PV+-INs substantially contributed to pattern separation. Both local connectivity
and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness.
Similarly, mossy fiber synapses with conditional detonator properties contributed
to pattern separation. By contrast, perforant path synapses with Hebbian synaptic
plasticity and direct EC–CA3 connection shifted the network towards pattern completion.
Our results demonstrate that the specific properties of cells and synapses optimize
higher-order computations in biological networks and might be useful to improve
the deep learning capabilities of technical networks.
acknowledged_ssus:
- _id: SSU
acknowledgement: We thank A. Aertsen, N. Kopell, W. Maass, A. Roth, F. Stella and
T. Vogels for critically reading earlier versions of the manuscript. We are grateful
to F. Marr and C. Altmutter for excellent technical assistance, E. Kralli-Beller
for manuscript editing, and the Scientific Service Units of IST Austria for efficient
support. Finally, we thank T. Carnevale, L. Erdös, M. Hines, D. Nykamp and D. Schröder
for useful discussions, and R. Friedrich and S. Wiechert for sharing unpublished
data. This project received funding from the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation programme (grant agreement
no. 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z
312-B27, Wittgenstein award to P.J. and P 31815 to S.J.G.).
article_processing_charge: No
article_type: original
author:
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
orcid: 0000-0003-2209-5242
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: 'Claudia '
full_name: 'Espinoza Martinez, Claudia '
id: 31FFEE2E-F248-11E8-B48F-1D18A9856A87
last_name: Espinoza Martinez
orcid: 0000-0003-4710-2082
- first_name: Xiaomin
full_name: Zhang, Xiaomin
id: 423EC9C2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0003-0256-6529
- first_name: Benjamin
full_name: Suter, Benjamin
id: 4952F31E-F248-11E8-B48F-1D18A9856A87
last_name: Suter
orcid: 0000-0002-9885-6936
- 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: Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity
rules and synaptic properties shape the efficacy of pattern separation in the
entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science.
2021;1(12):830-842. doi:10.1038/s43588-021-00157-1
apa: Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., &
Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the
efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network.
Nature Computational Science. Springer Nature. https://doi.org/10.1038/s43588-021-00157-1
chicago: Guzmán, José, Alois Schlögl, Claudia Espinoza Martinez, Xiaomin Zhang,
Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties
Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3
Network.” Nature Computational Science. Springer Nature, 2021. https://doi.org/10.1038/s43588-021-00157-1.
ieee: J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M.
Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern
separation in the entorhinal cortex–dentate gyrus–CA3 network,” Nature Computational
Science, vol. 1, no. 12. Springer Nature, pp. 830–842, 2021.
ista: Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021.
How connectivity rules and synaptic properties shape the efficacy of pattern separation
in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science.
1(12), 830–842.
mla: Guzmán, José, et al. “How Connectivity Rules and Synaptic Properties Shape
the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3
Network.” Nature Computational Science, vol. 1, no. 12, Springer Nature,
2021, pp. 830–42, doi:10.1038/s43588-021-00157-1.
short: J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas,
Nature Computational Science 1 (2021) 830–842.
corr_author: '1'
date_created: 2022-03-04T08:32:36Z
date_published: 2021-12-16T00:00:00Z
date_updated: 2025-10-09T22:30:54Z
day: '16'
ddc:
- '610'
department:
- _id: PeJo
doi: 10.1038/s43588-021-00157-1
ec_funded: 1
external_id:
isi:
- '000888567500015'
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relation: supplementary_material
title: Supplementary Material
file_date_updated: 2022-06-18T22:30:03Z
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intvolume: ' 1'
isi: 1
issue: '12'
keyword:
- general medicine
language:
- iso: eng
main_file_link:
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url: https://www.biorxiv.org/content/10.1101/647800
month: '12'
oa: 1
oa_version: Submitted Version
page: 830-842
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
publication: Nature Computational Science
publication_identifier:
issn:
- 2662-8457
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
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url: https://ista.ac.at/en/news/spot-the-difference/
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relation: software
status: public
scopus_import: '1'
status: public
title: How connectivity rules and synaptic properties shape the efficacy of pattern
separation in the entorhinal cortex–dentate gyrus–CA3 network
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 1
year: '2021'
...
---
_id: '9913'
abstract:
- lang: eng
text: Nitrate commands genome-wide gene expression changes that impact metabolism,
physiology, plant growth, and development. In an effort to identify new components
involved in nitrate responses in plants, we analyze the Arabidopsis thaliana root
phosphoproteome in response to nitrate treatments via liquid chromatography coupled
to tandem mass spectrometry. 176 phosphoproteins show significant changes at 5
or 20 min after nitrate treatments. Proteins identified by 5 min include signaling
components such as kinases or transcription factors. In contrast, by 20 min, proteins
identified were associated with transporter activity or hormone metabolism functions,
among others. The phosphorylation profile of NITRATE TRANSPORTER 1.1 (NRT1.1)
mutant plants was significantly altered as compared to wild-type plants, confirming
its key role in nitrate signaling pathways that involves phosphorylation changes.
Integrative bioinformatics analysis highlights auxin transport as an important
mechanism modulated by nitrate signaling at the post-translational level. We validated
a new phosphorylation site in PIN2 and provide evidence that it functions in primary
and lateral root growth responses to nitrate.
acknowledgement: This work was supported by ANID—Millennium Science Initiative Program—ICN17_022,
Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation
(15090007), ANID—Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT)
1180759 (to RAG) and 1171631 (to AV). We would like to thank Unidad de Microscopía
Avanzada UC (UMA UC).
article_number: e51813
article_processing_charge: Yes
article_type: original
author:
- first_name: Andrea
full_name: Vega, Andrea
last_name: Vega
- first_name: Isabel
full_name: Fredes, Isabel
last_name: Fredes
- first_name: José
full_name: O’Brien, José
last_name: O’Brien
- first_name: Zhouxin
full_name: Shen, Zhouxin
last_name: Shen
- first_name: Krisztina
full_name: Ötvös, Krisztina
id: 29B901B0-F248-11E8-B48F-1D18A9856A87
last_name: Ötvös
orcid: 0000-0002-5503-4983
- first_name: Rashed
full_name: Abualia, Rashed
id: 4827E134-F248-11E8-B48F-1D18A9856A87
last_name: Abualia
orcid: 0000-0002-9357-9415
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Steven P.
full_name: Briggs, Steven P.
last_name: Briggs
- first_name: Rodrigo A.
full_name: Gutiérrez, Rodrigo A.
last_name: Gutiérrez
citation:
ama: Vega A, Fredes I, O’Brien J, et al. Nitrate triggered phosphoproteome changes
and a PIN2 phosphosite modulating root system architecture. EMBO Reports.
2021;22(9). doi:10.15252/embr.202051813
apa: Vega, A., Fredes, I., O’Brien, J., Shen, Z., Ötvös, K., Abualia, R., … Gutiérrez,
R. A. (2021). Nitrate triggered phosphoproteome changes and a PIN2 phosphosite
modulating root system architecture. EMBO Reports. Wiley. https://doi.org/10.15252/embr.202051813
chicago: Vega, Andrea, Isabel Fredes, José O’Brien, Zhouxin Shen, Krisztina Ötvös,
Rashed Abualia, Eva Benková, Steven P. Briggs, and Rodrigo A. Gutiérrez. “Nitrate
Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System
Architecture.” EMBO Reports. Wiley, 2021. https://doi.org/10.15252/embr.202051813.
ieee: A. Vega et al., “Nitrate triggered phosphoproteome changes and a PIN2
phosphosite modulating root system architecture,” EMBO Reports, vol. 22,
no. 9. Wiley, 2021.
ista: Vega A, Fredes I, O’Brien J, Shen Z, Ötvös K, Abualia R, Benková E, Briggs
SP, Gutiérrez RA. 2021. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite
modulating root system architecture. EMBO Reports. 22(9), e51813.
mla: Vega, Andrea, et al. “Nitrate Triggered Phosphoproteome Changes and a PIN2
Phosphosite Modulating Root System Architecture.” EMBO Reports, vol. 22,
no. 9, e51813, Wiley, 2021, doi:10.15252/embr.202051813.
short: A. Vega, I. Fredes, J. O’Brien, Z. Shen, K. Ötvös, R. Abualia, E. Benková,
S.P. Briggs, R.A. Gutiérrez, EMBO Reports 22 (2021).
date_created: 2021-08-15T22:01:30Z
date_published: 2021-09-06T00:00:00Z
date_updated: 2026-07-02T22:30:48Z
day: '06'
ddc:
- '580'
department:
- _id: EvBe
- _id: GradSch
doi: 10.15252/embr.202051813
external_id:
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pmid:
- '34357701 '
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pmid: 1
publication: EMBO Reports
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eissn:
- 1469-3178
issn:
- 1469-221X
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating
root system architecture
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: 22
year: '2021'
...
---
OA_place: publisher
_id: '10303'
abstract:
- lang: eng
text: 'Nitrogen is an essential macronutrient determining plant growth, development
and affecting agricultural productivity. Root, as a hub that perceives and integrates
local and systemic signals on the plant’s external and endogenous nitrogen resources,
communicates with other plant organs to consolidate their physiology and development
in accordance with actual nitrogen balance. Over the last years, numerous studies
demonstrated that these comprehensive developmental adaptations rely on the interaction
between pathways controlling nitrogen homeostasis and hormonal networks acting
globally in the plant body. However, molecular insights into how the information
about the nitrogen status is translated through hormonal pathways into specific
developmental output are lacking. In my work, I addressed so far poorly understood
mechanisms underlying root-to-shoot communication that lead to a rapid re-adjustment
of shoot growth and development after nitrate provision. Applying a combination
of molecular, cell, and developmental biology approaches, genetics and grafting
experiments as well as hormonal analytics, I identified and characterized an unknown
molecular framework orchestrating shoot development with a root nitrate sensory
system. '
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Rashed
full_name: Abualia, Rashed
id: 4827E134-F248-11E8-B48F-1D18A9856A87
last_name: Abualia
orcid: 0000-0002-9357-9415
citation:
ama: Abualia R. Role of hormones in nitrate regulated growth. 2021. doi:10.15479/at:ista:10303
apa: Abualia, R. (2021). Role of hormones in nitrate regulated growth. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:10303
chicago: Abualia, Rashed. “Role of Hormones in Nitrate Regulated Growth.” Institute
of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10303.
ieee: R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science
and Technology Austria, 2021.
ista: Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of
Science and Technology Austria.
mla: Abualia, Rashed. Role of Hormones in Nitrate Regulated Growth. Institute
of Science and Technology Austria, 2021, doi:10.15479/at:ista:10303.
short: R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science
and Technology Austria, 2021.
corr_author: '1'
date_created: 2021-11-18T11:20:59Z
date_published: 2021-11-22T00:00:00Z
date_updated: 2026-04-08T07:20:07Z
day: '22'
ddc:
- '580'
- '581'
degree_awarded: PhD
department:
- _id: GradSch
- _id: EvBe
doi: 10.15479/at:ista:10303
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supervisor:
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
title: Role of hormones in nitrate regulated growth
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: '2021'
...
---
OA_place: publisher
_id: '10307'
abstract:
- lang: eng
text: Bacteria-host interactions represent a continuous trade-off between benefit
and risk. Thus, the host immune response is faced with a non-trivial problem –
accommodate beneficial commensals and remove harmful pathogens. This is especially
difficult as molecular patterns, such as lipopolysaccharide or specific surface
organelles such as pili, are conserved in both, commensal and pathogenic bacteria.
Type 1 pili, tightly regulated by phase variation, are considered an important
virulence factor of pathogenic bacteria as they facilitate invasion into host
cells. While invasion represents a de facto passive mechanism for pathogens to
escape the host immune response, we demonstrate a fundamental role of type 1 pili
as active modulators of the innate and adaptive immune response.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
- _id: PreCl
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Kathrin
full_name: Tomasek, Kathrin
id: 3AEC8556-F248-11E8-B48F-1D18A9856A87
last_name: Tomasek
orcid: 0000-0003-3768-877X
citation:
ama: Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021.
doi:10.15479/at:ista:10307
apa: Tomasek, K. (2021). Pathogenic Escherichia coli hijack the host immune response.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10307
chicago: Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.”
Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10307.
ieee: K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,”
Institute of Science and Technology Austria, 2021.
ista: Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response.
Institute of Science and Technology Austria.
mla: Tomasek, Kathrin. Pathogenic Escherichia Coli Hijack the Host Immune Response.
Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10307.
short: K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response,
Institute of Science and Technology Austria, 2021.
corr_author: '1'
date_created: 2021-11-18T15:05:06Z
date_published: 2021-11-18T00:00:00Z
date_updated: 2026-04-08T07:14:01Z
day: '18'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: MiSi
- _id: CaGu
- _id: GradSch
doi: 10.15479/at:ista:10307
file:
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checksum: b39c9e0ef18d0484d537a67551effd02
content_type: application/pdf
creator: ktomasek
date_created: 2021-11-18T15:07:31Z
date_updated: 2022-12-20T23:30:05Z
embargo: 2022-11-18
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file_size: 13266088
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creator: ktomasek
date_created: 2021-11-18T15:07:46Z
date_updated: 2022-12-20T23:30:05Z
embargo_to: open_access
file_id: '10309'
file_name: ThesisTomasekKathrin.docx
file_size: 7539509
relation: source_file
file_date_updated: 2022-12-20T23:30:05Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '73'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10316'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-4561-241X
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
title: Pathogenic Escherichia coli hijack the host immune response
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2021'
...
---
_id: '10316'
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 dendritic cells as a previously undescribed 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 pathogenic bacteria to CD14 lead to reduced
dendritic cell migration and blunted expression of co-stimulatory molecules, both
rate-limiting factors of T cell activation. 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 strain CFT073, Vlad Gavra
and 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 I.G.,
the European Research Council (CoG 724373) and the Austrian Science Fund (FWF P29911)
to M.S.
article_processing_charge: No
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: 0000-0002-4561-241X
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.
bioRxiv. doi:10.1101/2021.10.18.464770
apa: Tomasek, K., Leithner, A. F., Glatzová, I., Lukesch, M. S., Guet, C. C., &
Sixt, M. K. (n.d.). Type 1 piliated uropathogenic Escherichia coli hijack the
host immune response by binding to CD14. bioRxiv. Cold Spring Harbor Laboratory.
https://doi.org/10.1101/2021.10.18.464770
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.” BioRxiv. Cold Spring
Harbor Laboratory, n.d. https://doi.org/10.1101/2021.10.18.464770.
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,” bioRxiv. Cold Spring Harbor Laboratory.
ista: 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.
bioRxiv, 10.1101/2021.10.18.464770.
mla: Tomasek, Kathrin, et al. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack
the Host Immune Response by Binding to CD14.” BioRxiv, Cold Spring Harbor
Laboratory, doi:10.1101/2021.10.18.464770.
short: K. Tomasek, A.F. Leithner, I. Glatzová, M.S. Lukesch, C.C. Guet, M.K. Sixt,
BioRxiv (n.d.).
corr_author: '1'
date_created: 2021-11-19T12:24:16Z
date_published: 2021-10-18T00:00:00Z
date_updated: 2026-07-02T22:30:48Z
day: '18'
department:
- _id: CaGu
- _id: MiSi
doi: 10.1101/2021.10.18.464770
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2021.10.18.464770v1
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
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: bioRxiv
publication_status: draft
publisher: Cold Spring Harbor Laboratory
related_material:
record:
- id: '11843'
relation: later_version
status: public
- id: '10307'
relation: dissertation_contains
status: public
status: public
title: Type 1 piliated uropathogenic Escherichia coli hijack the host immune response
by binding to CD14
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '10110'
abstract:
- lang: eng
text: Pattern separation is a fundamental brain computation that converts small
differences in input patterns into large differences in output patterns. Several
synaptic mechanisms of pattern separation have been proposed, including code expansion,
inhibition and plasticity; however, which of these mechanisms play a role in the
entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation
circuit, remains unclear. Here we show that a biologically realistic, full-scale
EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive
inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator.
Both external gamma-modulated inhibition and internal lateral inhibition mediated
by PV+-INs substantially contributed to pattern separation. Both local connectivity
and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness.
Similarly, mossy fiber synapses with conditional detonator properties contributed
to pattern separation. By contrast, perforant path synapses with Hebbian synaptic
plasticity and direct EC–CA3 connection shifted the network towards pattern completion.
Our results demonstrate that the specific properties of cells and synapses optimize
higher-order computations in biological networks and might be useful to improve
the deep learning capabilities of technical networks.
author:
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
orcid: 0000-0003-2209-5242
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: 'Claudia '
full_name: 'Espinoza Martinez, Claudia '
id: 31FFEE2E-F248-11E8-B48F-1D18A9856A87
last_name: Espinoza Martinez
orcid: 0000-0003-4710-2082
- first_name: Xiaomin
full_name: Zhang, Xiaomin
id: 423EC9C2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0003-0256-6529
- first_name: Benjamin
full_name: Suter, Benjamin
id: 4952F31E-F248-11E8-B48F-1D18A9856A87
last_name: Suter
orcid: 0000-0002-9885-6936
- 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: Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity
rules and synaptic properties shape the efficacy of pattern separation in the
entorhinal cortex–dentate gyrus–CA3 network. 2021. doi:10.15479/AT:ISTA:10110
apa: Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., &
Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the
efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network.
IST Austria. https://doi.org/10.15479/AT:ISTA:10110
chicago: Guzmán, José, Alois Schlögl, Claudia Espinoza Martinez, Xiaomin Zhang,
Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties
Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3
Network.” IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:10110.
ieee: J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M.
Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern
separation in the entorhinal cortex–dentate gyrus–CA3 network.” IST Austria, 2021.
ista: Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021.
How connectivity rules and synaptic properties shape the efficacy of pattern separation
in the entorhinal cortex–dentate gyrus–CA3 network, IST Austria, 10.15479/AT:ISTA:10110.
mla: Guzmán, José, et al. How Connectivity Rules and Synaptic Properties Shape
the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3
Network. IST Austria, 2021, doi:10.15479/AT:ISTA:10110.
short: J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas,
(2021).
date_created: 2021-10-08T06:44:22Z
date_published: 2021-12-16T00:00:00Z
date_updated: 2026-07-02T22:30:47Z
day: '16'
ddc:
- '005'
department:
- _id: PeJo
- _id: ScienComp
doi: 10.15479/AT:ISTA:10110
file:
- access_level: open_access
checksum: f92f8931cad0aa7e411c1715337bf408
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2021-10-08T08:46:04Z
date_updated: 2021-10-08T08:46:04Z
file_id: '10114'
file_name: patternseparation-main (1).zip
file_size: 332990101
relation: main_file
success: 1
file_date_updated: 2021-10-08T08:46:04Z
has_accepted_license: '1'
license: https://opensource.org/licenses/GPL-3.0
month: '12'
oa: 1
publisher: IST Austria
related_material:
link:
- description: News on IST Webpage
relation: press_release
url: https://ist.ac.at/en/news/spot-the-difference/
record:
- id: '10816'
relation: used_for_analysis_in
status: public
status: public
title: How connectivity rules and synaptic properties shape the efficacy of pattern
separation in the entorhinal cortex–dentate gyrus–CA3 network
tmp:
legal_code_url: https://www.gnu.org/licenses/gpl-3.0.en.html
name: GNU General Public License 3.0
short: GPL 3.0
type: software
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '9887'
abstract:
- lang: eng
text: Clathrin-mediated endocytosis is the major route of entry of cargos into cells
and thus underpins many physiological processes. During endocytosis, an area of
flat membrane is remodeled by proteins to create a spherical vesicle against intracellular
forces. The protein machinery which mediates this membrane bending in plants is
unknown. However, it is known that plant endocytosis is actin independent, thus
indicating that plants utilize a unique mechanism to mediate membrane bending
against high-turgor pressure compared to other model systems. Here, we investigate
the TPLATE complex, a plant-specific endocytosis protein complex. It has been
thought to function as a classical adaptor functioning underneath the clathrin
coat. However, by using biochemical and advanced live microscopy approaches, we
found that TPLATE is peripherally associated with clathrin-coated vesicles and
localizes at the rim of endocytosis events. As this localization is more fitting
to the protein machinery involved in membrane bending during endocytosis, we examined
cells in which the TPLATE complex was disrupted and found that the clathrin structures
present as flat patches. This suggests a requirement of the TPLATE complex for
membrane bending during plant clathrin–mediated endocytosis. Next, we used in
vitro biophysical assays to confirm that the TPLATE complex possesses protein
domains with intrinsic membrane remodeling activity. These results redefine the
role of the TPLATE complex and implicate it as a key component of the evolutionarily
distinct plant endocytosis mechanism, which mediates endocytic membrane bending
against the high-turgor pressure in plant cells.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: Bio
acknowledgement: 'We gratefully thank Julie Neveu and Dr. Amanda Barranco of the Grégory
Vert laboratory for help preparing plants in France, Dr. Zuzana Gelova for help
and advice with protoplast generation, Dr. Stéphane Vassilopoulos and Dr. Florian
Schur for advice regarding EM tomography, Alejandro Marquiegui Alvaro for help with
material generation, and Dr. Lukasz Kowalski for generously gifting us the mWasabi
protein. This research was supported by the Scientific Service Units of Institute
of Science and Technology Austria (IST Austria) through resources provided by the
Electron Microscopy Facility, Lab Support Facility (particularly Dorota Jaworska),
and the Bioimaging Facility. We acknowledge the Advanced Microscopy Facility of
the Vienna BioCenter Core Facilities for use of the 3D SIM. For the mass spectrometry
analysis of proteins, we acknowledge the University of Natural Resources and Life
Sciences (BOKU) Core Facility Mass Spectrometry. This work was supported by the
following funds: A.J. is supported by funding from the Austrian Science Fund I3630B25
to J.F. P.M. and E.B. are supported by Agence Nationale de la Recherche ANR-11-EQPX-0029
Morphoscope2 and ANR-10-INBS-04 France BioImaging. S.Y.B. is supported by the NSF
No. 1121998 and 1614915. J.W. and D.V.D. are supported by the European Research
Council Grant 682436 (to D.V.D.), a China Scholarship Council Grant 201508440249
(to J.W.), and by a Ghent University Special Research Co-funding Grant ST01511051
(to J.W.).'
article_number: e2113046118
article_processing_charge: No
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: Dana A
full_name: Dahhan, Dana A
last_name: Dahhan
- first_name: Nataliia
full_name: Gnyliukh, Nataliia
id: 390C1120-F248-11E8-B48F-1D18A9856A87
last_name: Gnyliukh
orcid: 0000-0002-2198-0509
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Vanessa
full_name: Zheden, Vanessa
id: 39C5A68A-F248-11E8-B48F-1D18A9856A87
last_name: Zheden
orcid: 0000-0002-9438-4783
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Pierre
full_name: Mahou, Pierre
last_name: Mahou
- first_name: Mónika
full_name: Hrtyan, Mónika
id: 45A71A74-F248-11E8-B48F-1D18A9856A87
last_name: Hrtyan
- first_name: Jie
full_name: Wang, Jie
last_name: Wang
- first_name: Juan L
full_name: Aguilera Servin, Juan L
id: 2A67C376-F248-11E8-B48F-1D18A9856A87
last_name: Aguilera Servin
orcid: 0000-0002-2862-8372
- first_name: Daniël
full_name: van Damme, Daniël
last_name: van Damme
- first_name: Emmanuel
full_name: Beaurepaire, Emmanuel
last_name: Beaurepaire
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- 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, Dahhan DA, Gnyliukh N, et al. The TPLATE complex mediates membrane
bending during plant clathrin-mediated endocytosis. Proceedings of the National
Academy of Sciences of the United States of America. 2021;118(51). doi:10.1073/pnas.2113046118
apa: Johnson, A. J., Dahhan, D. A., Gnyliukh, N., Kaufmann, W., Zheden, V., Costanzo,
T., … Friml, J. (2021). The TPLATE complex mediates membrane bending during plant
clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences
of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2113046118
chicago: Johnson, Alexander J, Dana A Dahhan, Nataliia Gnyliukh, Walter Kaufmann,
Vanessa Zheden, Tommaso Costanzo, Pierre Mahou, et al. “The TPLATE Complex Mediates
Membrane Bending during Plant Clathrin-Mediated Endocytosis.” Proceedings of
the National Academy of Sciences of the United States of America. National
Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2113046118.
ieee: A. J. Johnson et al., “The TPLATE complex mediates membrane bending
during plant clathrin-mediated endocytosis,” Proceedings of the National Academy
of Sciences of the United States of America, vol. 118, no. 51. National Academy
of Sciences, 2021.
ista: Johnson AJ, Dahhan DA, Gnyliukh N, Kaufmann W, Zheden V, Costanzo T, Mahou
P, Hrtyan M, Wang J, Aguilera Servin JL, van Damme D, Beaurepaire E, Loose M,
Bednarek SY, Friml J. 2021. The TPLATE complex mediates membrane bending during
plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences
of the United States of America. 118(51), e2113046118.
mla: Johnson, Alexander J., et al. “The TPLATE Complex Mediates Membrane Bending
during Plant Clathrin-Mediated Endocytosis.” Proceedings of the National Academy
of Sciences of the United States of America, vol. 118, no. 51, e2113046118,
National Academy of Sciences, 2021, doi:10.1073/pnas.2113046118.
short: A.J. Johnson, D.A. Dahhan, N. Gnyliukh, W. Kaufmann, V. Zheden, T. Costanzo,
P. Mahou, M. Hrtyan, J. Wang, J.L. Aguilera Servin, D. van Damme, E. Beaurepaire,
M. Loose, S.Y. Bednarek, J. Friml, Proceedings of the National Academy of Sciences
of the United States of America 118 (2021).
corr_author: '1'
date_created: 2021-08-11T14:11:43Z
date_published: 2021-12-14T00:00:00Z
date_updated: 2026-07-02T22:30:55Z
day: '14'
ddc:
- '580'
department:
- _id: JiFr
- _id: MaLo
- _id: EvBe
- _id: EM-Fac
- _id: NanoFab
doi: 10.1073/pnas.2113046118
external_id:
isi:
- '000736417600043'
pmid:
- '34907016'
file:
- access_level: open_access
checksum: 8d01e72e22c4fb1584e72d8601947069
content_type: application/pdf
creator: cchlebak
date_created: 2021-12-15T08:59:40Z
date_updated: 2021-12-15T08:59:40Z
file_id: '10546'
file_name: 2021_PNAS_Johnson.pdf
file_size: 2757340
relation: main_file
success: 1
file_date_updated: 2021-12-15T08:59:40Z
has_accepted_license: '1'
intvolume: ' 118'
isi: 1
issue: '51'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
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: 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:
link:
- relation: earlier_version
url: https://doi.org/10.1101/2021.04.26.441441
record:
- id: '14988'
relation: research_data
status: public
- id: '14510'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The TPLATE complex mediates membrane bending during plant clathrin-mediated
endocytosis
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: 118
year: '2021'
...
---
_id: '9250'
abstract:
- lang: eng
text: Aprotic alkali metal–O2 batteries face two major obstacles to their chemistry
occurring efficiently, the insulating nature of the formed alkali superoxides/peroxides
and parasitic reactions that are caused by the highly reactive singlet oxygen
(1O2). Redox mediators are recognized to be key for improving rechargeability.
However, it is unclear how they affect 1O2 formation, which hinders strategies
for their improvement. Here we clarify the mechanism of mediated peroxide and
superoxide oxidation and thus explain how redox mediators either enhance or suppress
1O2 formation. We show that charging commences with peroxide oxidation to a superoxide
intermediate and that redox potentials above ~3.5 V versus Li/Li+ drive 1O2 evolution
from superoxide oxidation, while disproportionation always generates some 1O2.
We find that 1O2 suppression requires oxidation to be faster than the generation
of 1O2 from disproportionation. Oxidation rates decrease with growing driving
force following Marcus inverted-region behaviour, establishing a region of maximum
rate.
acknowledged_ssus:
- _id: M-Shop
acknowledgement: S.A.F. is indebted to the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation programme (grant agreement
No. 636069) as well as IST Austria. O.F thanks the French National Research Agency
(STORE-EX Labex Project ANR-10-LABX-76-01). We thank EL-Cell GmbH (Hamburg, Germany)
for the pressure test cell. We thank R. Saf for help with the mass spectrometry,
J. Schlegl for manufacturing instrumentation, M. Winkler of Acib GmbH, G. Strohmeier
and R. Fürst for HPLC measurements and S. Mondal and S. Stadlbauer for kinetic measurements.
article_processing_charge: No
article_type: original
author:
- first_name: Yann K.
full_name: Petit, Yann K.
last_name: Petit
- first_name: Eléonore
full_name: Mourad, Eléonore
last_name: Mourad
- first_name: Christian
full_name: Prehal, Christian
last_name: Prehal
- first_name: Christian
full_name: Leypold, Christian
last_name: Leypold
- first_name: Andreas
full_name: Windischbacher, Andreas
last_name: Windischbacher
- first_name: Daniel
full_name: Mijailovic, Daniel
last_name: Mijailovic
- first_name: Christian
full_name: Slugovc, Christian
last_name: Slugovc
- first_name: Sergey M.
full_name: Borisov, Sergey M.
last_name: Borisov
- first_name: Egbert
full_name: Zojer, Egbert
last_name: Zojer
- first_name: Sergio
full_name: Brutti, Sergio
last_name: Brutti
- first_name: Olivier
full_name: Fontaine, Olivier
last_name: Fontaine
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Petit YK, Mourad E, Prehal C, et al. Mechanism of mediated alkali peroxide
oxidation and triplet versus singlet oxygen formation. Nature Chemistry.
2021;13(5):465-471. doi:10.1038/s41557-021-00643-z
apa: Petit, Y. K., Mourad, E., Prehal, C., Leypold, C., Windischbacher, A., Mijailovic,
D., … Freunberger, S. A. (2021). Mechanism of mediated alkali peroxide oxidation
and triplet versus singlet oxygen formation. Nature Chemistry. Springer
Nature. https://doi.org/10.1038/s41557-021-00643-z
chicago: Petit, Yann K., Eléonore Mourad, Christian Prehal, Christian Leypold, Andreas
Windischbacher, Daniel Mijailovic, Christian Slugovc, et al. “Mechanism of Mediated
Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” Nature
Chemistry. Springer Nature, 2021. https://doi.org/10.1038/s41557-021-00643-z.
ieee: Y. K. Petit et al., “Mechanism of mediated alkali peroxide oxidation
and triplet versus singlet oxygen formation,” Nature Chemistry, vol. 13,
no. 5. Springer Nature, pp. 465–471, 2021.
ista: Petit YK, Mourad E, Prehal C, Leypold C, Windischbacher A, Mijailovic D, Slugovc
C, Borisov SM, Zojer E, Brutti S, Fontaine O, Freunberger SA. 2021. Mechanism
of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation.
Nature Chemistry. 13(5), 465–471.
mla: Petit, Yann K., et al. “Mechanism of Mediated Alkali Peroxide Oxidation and
Triplet versus Singlet Oxygen Formation.” Nature Chemistry, vol. 13, no.
5, Springer Nature, 2021, pp. 465–71, doi:10.1038/s41557-021-00643-z.
short: Y.K. Petit, E. Mourad, C. Prehal, C. Leypold, A. Windischbacher, D. Mijailovic,
C. Slugovc, S.M. Borisov, E. Zojer, S. Brutti, O. Fontaine, S.A. Freunberger,
Nature Chemistry 13 (2021) 465–471.
corr_author: '1'
date_created: 2021-03-16T11:12:20Z
date_published: 2021-03-15T00:00:00Z
date_updated: 2024-10-09T21:00:28Z
day: '15'
ddc:
- '540'
department:
- _id: StFr
doi: 10.1038/s41557-021-00643-z
external_id:
isi:
- '000629296400001'
pmid:
- '33723377'
file:
- access_level: open_access
checksum: 3ee3f8dd79ed1b7bb0929fce184c8012
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T11:46:00Z
date_updated: 2021-09-16T22:30:03Z
embargo: 2021-09-15
file_id: '9276'
file_name: 2021_NatureChem_Petit_acceptedVersion.pdf
file_size: 1811448
relation: main_file
file_date_updated: 2021-09-16T22:30:03Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '5'
keyword:
- General Chemistry
- General Chemical Engineering
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 465-471
pmid: 1
publication: Nature Chemistry
publication_identifier:
eissn:
- 1755-4349
issn:
- 1755-4330
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanism of mediated alkali peroxide oxidation and triplet versus singlet
oxygen formation
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 13
year: '2021'
...
---
_id: '9438'
abstract:
- lang: eng
text: Rigorous investigation of synaptic transmission requires analysis of unitary
synaptic events by simultaneous recording from presynaptic terminals and postsynaptic
target neurons. However, this has been achieved at only a limited number of model
synapses, including the squid giant synapse and the mammalian calyx of Held. Cortical
presynaptic terminals have been largely inaccessible to direct presynaptic recording,
due to their small size. Here, we describe a protocol for improved subcellular
patch-clamp recording in rat and mouse brain slices, with the synapse in a largely
intact environment. Slice preparation takes ~2 h, recording ~3 h and post hoc
morphological analysis 2 d. Single presynaptic hippocampal mossy fiber terminals
are stimulated minimally invasively in the bouton-attached configuration, in which
the cytoplasmic content remains unperturbed, or in the whole-bouton configuration,
in which the cytoplasmic composition can be precisely controlled. Paired pre–postsynaptic
recordings can be integrated with biocytin labeling and morphological analysis,
allowing correlative investigation of synapse structure and function. Paired recordings
can be obtained from mossy fiber terminals in slices from both rats and mice,
implying applicability to genetically modified synapses. Paired recordings can
also be performed together with axon tract stimulation or optogenetic activation,
allowing comparison of unitary and compound synaptic events in the same target
cell. Finally, paired recordings can be combined with spontaneous event analysis,
permitting collection of miniature events generated at a single identified synapse.
In conclusion, the subcellular patch-clamp techniques detailed here should facilitate
analysis of biophysics, plasticity and circuit function of cortical synapses in
the mammalian central nervous system.
acknowledged_ssus:
- _id: M-Shop
acknowledgement: This project received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement no. 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen
Forschung (Z 312-B27, Wittgenstein award to P.J., V 739-B27 to C.B.M.). We are grateful
to F. Marr and C. Altmutter for excellent technical assistance and cell reconstruction,
E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST
Austria, especially T. Asenov and Miba machine shop, for maximally efficient support.
article_processing_charge: No
article_type: original
author:
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Yuji
full_name: Okamoto, Yuji
id: 3337E116-F248-11E8-B48F-1D18A9856A87
last_name: Okamoto
orcid: 0000-0003-0408-6094
- first_name: Carolina
full_name: Borges Merjane, Carolina
id: 4305C450-F248-11E8-B48F-1D18A9856A87
last_name: Borges Merjane
orcid: 0000-0003-0005-401X
- first_name: Victor M
full_name: Vargas Barroso, Victor M
id: 2F55A9DE-F248-11E8-B48F-1D18A9856A87
last_name: Vargas Barroso
- first_name: Benjamin
full_name: Suter, Benjamin
id: 4952F31E-F248-11E8-B48F-1D18A9856A87
last_name: Suter
orcid: 0000-0002-9885-6936
- 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: Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas
PM. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous
pre- and postsynaptic recording at cortical synapses. Nature Protocols.
2021;16(6):2947–2967. doi:10.1038/s41596-021-00526-0
apa: Vandael, D. H., Okamoto, Y., Borges Merjane, C., Vargas Barroso, V. M., Suter,
B., & Jonas, P. M. (2021). Subcellular patch-clamp techniques for single-bouton
stimulation and simultaneous pre- and postsynaptic recording at cortical synapses.
Nature Protocols. Springer Nature. https://doi.org/10.1038/s41596-021-00526-0
chicago: Vandael, David H, Yuji Okamoto, Carolina Borges Merjane, Victor M Vargas
Barroso, Benjamin Suter, and Peter M Jonas. “Subcellular Patch-Clamp Techniques
for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording
at Cortical Synapses.” Nature Protocols. Springer Nature, 2021. https://doi.org/10.1038/s41596-021-00526-0.
ieee: D. H. Vandael, Y. Okamoto, C. Borges Merjane, V. M. Vargas Barroso, B. Suter,
and P. M. Jonas, “Subcellular patch-clamp techniques for single-bouton stimulation
and simultaneous pre- and postsynaptic recording at cortical synapses,” Nature
Protocols, vol. 16, no. 6. Springer Nature, pp. 2947–2967, 2021.
ista: Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas
PM. 2021. Subcellular patch-clamp techniques for single-bouton stimulation and
simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols.
16(6), 2947–2967.
mla: Vandael, David H., et al. “Subcellular Patch-Clamp Techniques for Single-Bouton
Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.”
Nature Protocols, vol. 16, no. 6, Springer Nature, 2021, pp. 2947–2967,
doi:10.1038/s41596-021-00526-0.
short: D.H. Vandael, Y. Okamoto, C. Borges Merjane, V.M. Vargas Barroso, B. Suter,
P.M. Jonas, Nature Protocols 16 (2021) 2947–2967.
corr_author: '1'
date_created: 2021-05-30T22:01:24Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2025-04-22T22:30:43Z
day: '01'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1038/s41596-021-00526-0
ec_funded: 1
external_id:
isi:
- '000650528700003'
pmid:
- '33990799'
file:
- access_level: open_access
checksum: 7eb580abd8893cdb0b410cf41bc8c263
content_type: application/pdf
creator: cziletti
date_created: 2021-07-08T12:27:55Z
date_updated: 2021-12-02T23:30:05Z
embargo: 2021-12-01
file_id: '9639'
file_name: VandaeletalAuthorVersion2021.pdf
file_size: 38574802
relation: main_file
file_date_updated: 2021-12-02T23:30:05Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 2947–2967
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
- _id: 2696E7FE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: V00739
name: Structural plasticity at mossy fiber-CA3 synapses
publication: Nature Protocols
publication_identifier:
eissn:
- 1750-2799
issn:
- 1754-2189
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous
pre- and postsynaptic recording at cortical synapses
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2021'
...
---
_id: '9437'
abstract:
- lang: eng
text: The synaptic connection from medial habenula (MHb) to interpeduncular nucleus
(IPN) is critical for emotion-related behaviors and uniquely expresses R-type
Ca2+ channels (Cav2.3) and auxiliary GABAB receptor (GBR) subunits, the K+-channel
tetramerization domain-containing proteins (KCTDs). Activation of GBRs facilitates
or inhibits transmitter release from MHb terminals depending on the IPN subnucleus,
but the role of KCTDs is unknown. We therefore examined the localization and function
of Cav2.3, GBRs, and KCTDs in this pathway in mice. We show in heterologous cells
that KCTD8 and KCTD12b directly bind to Cav2.3 and that KCTD8 potentiates Cav2.3
currents in the absence of GBRs. In the rostral IPN, KCTD8, KCTD12b, and Cav2.3
co-localize at the presynaptic active zone. Genetic deletion indicated a bidirectional
modulation of Cav2.3-mediated release by these KCTDs with a compensatory increase
of KCTD8 in the active zone in KCTD12b-deficient mice. The interaction of Cav2.3
with KCTDs therefore scales synaptic strength independent of GBR activation.
acknowledgement: We are grateful to Akari Hagiwara and Toshihisa Ohtsuka for CAST
antibody, and Masahiko Watanabe for neurexin antibody. We thank David Adams for
kindly providing the stable Cav2.3 cell line. Cav2.3 KO mice were kindly provided
by Tsutomu Tanabe. This project has received funding from the European Research
Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020
research and innovation programme (ERC grant agreement no. 694539 to Ryuichi Shigemoto,
no. 692692 to Peter Jonas, and the Marie Skłodowska-Curie grant agreement no. 665385
to Cihan Önal), the Swiss National Science Foundation Grant 31003A-172881 to Bernhard
Bettler and Deutsche Forschungsgemeinschaft (For 2143) and BIOSS-2 to Akos Kulik.
article_number: e68274
article_processing_charge: No
article_type: original
author:
- first_name: Pradeep
full_name: Bhandari, Pradeep
id: 45EDD1BC-F248-11E8-B48F-1D18A9856A87
last_name: Bhandari
orcid: 0000-0003-0863-4481
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Diego
full_name: Fernández-Fernández, Diego
last_name: Fernández-Fernández
- first_name: Thorsten
full_name: Fritzius, Thorsten
last_name: Fritzius
- first_name: David
full_name: Kleindienst, David
id: 42E121A4-F248-11E8-B48F-1D18A9856A87
last_name: Kleindienst
- first_name: Hüseyin C
full_name: Önal, Hüseyin C
id: 4659D740-F248-11E8-B48F-1D18A9856A87
last_name: Önal
orcid: 0000-0002-2771-2011
- first_name: Jacqueline-Claire
full_name: Montanaro-Punzengruber, Jacqueline-Claire
id: 3786AB44-F248-11E8-B48F-1D18A9856A87
last_name: Montanaro-Punzengruber
- first_name: Martin
full_name: Gassmann, Martin
last_name: Gassmann
- 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: Akos
full_name: Kulik, Akos
last_name: Kulik
- first_name: Bernhard
full_name: Bettler, Bernhard
last_name: Bettler
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Peter
full_name: Koppensteiner, Peter
id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87
last_name: Koppensteiner
orcid: 0000-0002-3509-1948
citation:
ama: Bhandari P, Vandael DH, Fernández-Fernández D, et al. GABAB receptor auxiliary
subunits modulate Cav2.3-mediated release from medial habenula terminals. eLife.
2021;10. doi:10.7554/ELIFE.68274
apa: Bhandari, P., Vandael, D. H., Fernández-Fernández, D., Fritzius, T., Kleindienst,
D., Önal, C., … Koppensteiner, P. (2021). GABAB receptor auxiliary subunits modulate
Cav2.3-mediated release from medial habenula terminals. ELife. eLife Sciences
Publications. https://doi.org/10.7554/ELIFE.68274
chicago: Bhandari, Pradeep, David H Vandael, Diego Fernández-Fernández, Thorsten
Fritzius, David Kleindienst, Cihan Önal, Jacqueline-Claire Montanaro-Punzengruber,
et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from
Medial Habenula Terminals.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/ELIFE.68274.
ieee: P. Bhandari et al., “GABAB receptor auxiliary subunits modulate Cav2.3-mediated
release from medial habenula terminals,” eLife, vol. 10. eLife Sciences
Publications, 2021.
ista: Bhandari P, Vandael DH, Fernández-Fernández D, Fritzius T, Kleindienst D,
Önal C, Montanaro-Punzengruber J-C, Gassmann M, Jonas PM, Kulik A, Bettler B,
Shigemoto R, Koppensteiner P. 2021. GABAB receptor auxiliary subunits modulate
Cav2.3-mediated release from medial habenula terminals. eLife. 10, e68274.
mla: Bhandari, Pradeep, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated
Release from Medial Habenula Terminals.” ELife, vol. 10, e68274, eLife
Sciences Publications, 2021, doi:10.7554/ELIFE.68274.
short: P. Bhandari, D.H. Vandael, D. Fernández-Fernández, T. Fritzius, D. Kleindienst,
C. Önal, J.-C. Montanaro-Punzengruber, M. Gassmann, P.M. Jonas, A. Kulik, B. Bettler,
R. Shigemoto, P. Koppensteiner, ELife 10 (2021).
date_created: 2021-05-30T22:01:23Z
date_published: 2021-04-29T00:00:00Z
date_updated: 2026-07-02T22:31:03Z
day: '29'
ddc:
- '570'
department:
- _id: RySh
- _id: PeJo
doi: 10.7554/ELIFE.68274
ec_funded: 1
external_id:
isi:
- '000651761700001'
pmid:
- '33913808'
file:
- access_level: open_access
checksum: 6ebcb79999f889766f7cd79ee134ad28
content_type: application/pdf
creator: cziletti
date_created: 2021-05-31T09:43:09Z
date_updated: 2021-05-31T09:43:09Z
file_id: '9440'
file_name: 2021_eLife_Bhandari.pdf
file_size: 8174719
relation: main_file
success: 1
file_date_updated: 2021-05-31T09:43:09Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
link:
- relation: earlier_version
url: https://doi.org/10.1101/2020.04.16.045112
record:
- id: '19271'
relation: dissertation_contains
status: public
- id: '9562'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial
habenula terminals
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: 10
year: '2021'
...
---
OA_place: publisher
_id: '9562'
abstract:
- lang: eng
text: Left-right asymmetries can be considered a fundamental organizational principle
of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell
synaptic connection shows an input-side dependent asymmetry where the hemispheric
location of the presynaptic CA3 neuron determines the synaptic properties. Left-input
synapses terminating on apical dendrites in stratum radiatum have a higher density
of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1
and smaller areas with less often perforated PSDs. On the other hand, left-input
synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities
than right-input ones. Apical and basal synapses further employ different signaling
pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize
synaptic membrane proteins with high sensitivity and resolution, and has been
used to reveal the asymmetry at the electron microscopic level. However, it requires
time-consuming manual demarcation of the synaptic surface for quantitative measurements.
To facilitate the analysis of replica labeling, I first developed a software named
Darea, which utilizes deep-learning to automatize this demarcation. With Darea
I characterized the synaptic distribution of NMDA and AMPA receptors as well as
the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I
explored the role of GluN2B and its carboxy-terminus in the establishment of input-side
dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B
expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged
to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were
detected. We further discovered a previously unknown functional asymmetry of GluN2A,
which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus
plays a critical role in normal formation of input-side dependent asymmetry.
acknowledged_ssus:
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: David
full_name: Kleindienst, David
id: 42E121A4-F248-11E8-B48F-1D18A9856A87
last_name: Kleindienst
citation:
ama: 'Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor
subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning.
2021. doi:10.15479/at:ista:9562'
apa: 'Kleindienst, D. (2021). 2B or not 2B: Hippocampal asymmetries mediated
by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis
by Deep-Learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9562'
chicago: 'Kleindienst, David. “2B or Not 2B: Hippocampal Asymmetries Mediated by
NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by
Deep-Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9562.'
ieee: 'D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor
subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,”
Institute of Science and Technology Austria, 2021.'
ista: 'Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA
receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning.
Institute of Science and Technology Austria.'
mla: 'Kleindienst, David. 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA
Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning.
Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9562.'
short: 'D. Kleindienst, 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor
Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning,
Institute of Science and Technology Austria, 2021.'
corr_author: '1'
date_created: 2021-06-17T14:10:47Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2026-04-08T07:12:31Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
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- _id: RySh
doi: 10.15479/at:ista:9562
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publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
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record:
- id: '9756'
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status: public
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status: public
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status: public
- id: '8532'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
title: '2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B
C-terminus and high-throughput image analysis by Deep-Learning'
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2021'
...
---
_id: '9428'
abstract:
- lang: eng
text: Thermalization is the inevitable fate of many complex quantum systems, whose
dynamics allow them to fully explore the vast configuration space regardless of
the initial state---the behaviour known as quantum ergodicity. In a quest for
experimental realizations of coherent long-time dynamics, efforts have focused
on ergodicity-breaking mechanisms, such as integrability and localization. The
recent discovery of persistent revivals in quantum simulators based on Rydberg
atoms have pointed to the existence of a new type of behaviour where the system
rapidly relaxes for most initial conditions, while certain initial states give
rise to non-ergodic dynamics. This collective effect has been named ”quantum many-body
scarring’by analogy with a related form of weak ergodicity breaking that occurs
for a single particle inside a stadium billiard potential. In this Review, we
provide a pedagogical introduction to quantum many-body scars and highlight the
emerging connections with the semiclassical quantization of many-body systems.
We discuss the relation between scars and more general routes towards weak violations
of ergodicity due to embedded algebras and non-thermal eigenstates, and highlight
possible applications of scars in quantum technology.
acknowledgement: We thank our collaborators K. Bull, S. Choi, J.-Y. Desaules, W. W.
Ho, A. Hudomal, M. Lukin, I. Martin, H. Pichler, N. Regnault, I. Vasić and in particular
A. Michailidis and C. Turner, without whom this work would not have been possible.
We also benefited from discussions with E. Altman, B. A. Bernevig, A. Chandran,
P. Fendley, V. Khemani and L. Motrunich. M.S. was supported by the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement no. 850899). D.A.A. was supported by the Swiss National Science
Foundation and by the ERC under the European Union’s Horizon 2020 research and innovation
programme (grant agreement no. 864597). Z.P. acknowledges support by the Leverhulme
Trust Research Leadership Award RL-2019-015.
article_processing_charge: No
article_type: review
arxiv: 1
author:
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Dmitry A.
full_name: Abanin, Dmitry A.
last_name: Abanin
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
citation:
ama: Serbyn M, Abanin DA, Papić Z. Quantum many-body scars and weak breaking of
ergodicity. Nature Physics. 2021;17(6):675–685. doi:10.1038/s41567-021-01230-2
apa: Serbyn, M., Abanin, D. A., & Papić, Z. (2021). Quantum many-body scars
and weak breaking of ergodicity. Nature Physics. Nature Research. https://doi.org/10.1038/s41567-021-01230-2
chicago: Serbyn, Maksym, Dmitry A. Abanin, and Zlatko Papić. “Quantum Many-Body
Scars and Weak Breaking of Ergodicity.” Nature Physics. Nature Research,
2021. https://doi.org/10.1038/s41567-021-01230-2.
ieee: M. Serbyn, D. A. Abanin, and Z. Papić, “Quantum many-body scars and weak breaking
of ergodicity,” Nature Physics, vol. 17, no. 6. Nature Research, pp. 675–685,
2021.
ista: Serbyn M, Abanin DA, Papić Z. 2021. Quantum many-body scars and weak breaking
of ergodicity. Nature Physics. 17(6), 675–685.
mla: Serbyn, Maksym, et al. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.”
Nature Physics, vol. 17, no. 6, Nature Research, 2021, pp. 675–685, doi:10.1038/s41567-021-01230-2.
short: M. Serbyn, D.A. Abanin, Z. Papić, Nature Physics 17 (2021) 675–685.
date_created: 2021-05-28T09:03:50Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2025-04-14T07:52:09Z
day: '01'
ddc:
- '539'
department:
- _id: MaSe
doi: 10.1038/s41567-021-01230-2
ec_funded: 1
external_id:
arxiv:
- '2011.09486'
isi:
- '000655563800002'
file:
- access_level: open_access
checksum: 316ed42ea1b42b0f1a3025bb476266fc
content_type: application/pdf
creator: patrickd
date_created: 2021-09-20T09:27:43Z
date_updated: 2021-12-02T23:30:03Z
embargo: 2021-12-01
file_id: '10026'
file_name: RevisedQMBSreview.pdf
file_size: 10028836
relation: main_file
file_date_updated: 2021-12-02T23:30:03Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Preprint
page: 675–685
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
publication_status: published
publisher: Nature Research
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantum many-body scars and weak breaking of ergodicity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2021'
...