---
_id: '12224'
abstract:
- lang: eng
text: Muskelin (Mkln1) is implicated in neuronal function, regulating plasma membrane
receptor trafficking. However, its influence on intrinsic brain activity and corresponding
behavioral processes remains unclear. Here we show that murine Mkln1
knockout causes non-habituating locomotor activity, increased exploratory drive,
and decreased locomotor response to amphetamine. Muskelin deficiency impairs social
novelty detection while promoting the retention of spatial reference memory and
fear extinction recall. This is strongly mirrored in either weaker or stronger
resting-state functional connectivity between critical circuits mediating locomotor
exploration and cognition. We show that Mkln1 deletion
alters dendrite branching and spine structure, coinciding with enhanced AMPAR-mediated
synaptic transmission but selective impairment in synaptic potentiation maintenance.
We identify muskelin at excitatory synapses and highlight its role in regulating
dendritic spine actin stability. Our findings point to aberrant spine actin modulation
and changes in glutamatergic synaptic function as critical mechanisms that contribute
to the neurobehavioral phenotype arising from Mkln1
ablation.
acknowledgement: "The authors are grateful to the UKE Animal Facilities (Hamburg)
for animal husbandry and Dr. Bastian Tiemann for his veterinary expertise and supervision
of animal care. We thank Dr. Franco Lombino for critically reading the manuscript
and for helpful discussion. This work was supported by grants from the Deutsche
Forschungsgemeinschaft (DFG) (FOR2419-KN556/11-1, FOR2419-KN556/11-2, KN556/12-1)
and the Landesforschungsförderung Hamburg (LFF-FV76) to M.K.\r\nOpen Access funding
enabled and organized by Projekt DEAL."
article_number: '589'
article_processing_charge: No
article_type: original
author:
- first_name: Mary W
full_name: Muhia, Mary W
id: ab7ed20f-09f7-11eb-909c-d5d0b443ee9d
last_name: Muhia
- first_name: PingAn
full_name: YuanXiang, PingAn
last_name: YuanXiang
- first_name: Jan
full_name: Sedlacik, Jan
last_name: Sedlacik
- first_name: Jürgen R.
full_name: Schwarz, Jürgen R.
last_name: Schwarz
- first_name: Frank F.
full_name: Heisler, Frank F.
last_name: Heisler
- first_name: Kira V.
full_name: Gromova, Kira V.
last_name: Gromova
- first_name: Edda
full_name: Thies, Edda
last_name: Thies
- first_name: Petra
full_name: Breiden, Petra
last_name: Breiden
- first_name: Yvonne
full_name: Pechmann, Yvonne
last_name: Pechmann
- first_name: Michael R.
full_name: Kreutz, Michael R.
last_name: Kreutz
- first_name: Matthias
full_name: Kneussel, Matthias
last_name: Kneussel
citation:
ama: Muhia MW, YuanXiang P, Sedlacik J, et al. Muskelin regulates actin-dependent
synaptic changes and intrinsic brain activity relevant to behavioral and cognitive
processes. Communications Biology. 2022;5. doi:10.1038/s42003-022-03446-1
apa: Muhia, M. W., YuanXiang, P., Sedlacik, J., Schwarz, J. R., Heisler, F. F.,
Gromova, K. V., … Kneussel, M. (2022). Muskelin regulates actin-dependent synaptic
changes and intrinsic brain activity relevant to behavioral and cognitive processes.
Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-022-03446-1
chicago: Muhia, Mary W, PingAn YuanXiang, Jan Sedlacik, Jürgen R. Schwarz, Frank
F. Heisler, Kira V. Gromova, Edda Thies, et al. “Muskelin Regulates Actin-Dependent
Synaptic Changes and Intrinsic Brain Activity Relevant to Behavioral and Cognitive
Processes.” Communications Biology. Springer Nature, 2022. https://doi.org/10.1038/s42003-022-03446-1.
ieee: M. W. Muhia et al., “Muskelin regulates actin-dependent synaptic changes
and intrinsic brain activity relevant to behavioral and cognitive processes,”
Communications Biology, vol. 5. Springer Nature, 2022.
ista: Muhia MW, YuanXiang P, Sedlacik J, Schwarz JR, Heisler FF, Gromova KV, Thies
E, Breiden P, Pechmann Y, Kreutz MR, Kneussel M. 2022. Muskelin regulates actin-dependent
synaptic changes and intrinsic brain activity relevant to behavioral and cognitive
processes. Communications Biology. 5, 589.
mla: Muhia, Mary W., et al. “Muskelin Regulates Actin-Dependent Synaptic Changes
and Intrinsic Brain Activity Relevant to Behavioral and Cognitive Processes.”
Communications Biology, vol. 5, 589, Springer Nature, 2022, doi:10.1038/s42003-022-03446-1.
short: M.W. Muhia, P. YuanXiang, J. Sedlacik, J.R. Schwarz, F.F. Heisler, K.V. Gromova,
E. Thies, P. Breiden, Y. Pechmann, M.R. Kreutz, M. Kneussel, Communications Biology
5 (2022).
corr_author: '1'
date_created: 2023-01-16T09:48:19Z
date_published: 2022-06-15T00:00:00Z
date_updated: 2024-10-09T21:03:48Z
day: '15'
ddc:
- '570'
department:
- _id: PreCl
doi: 10.1038/s42003-022-03446-1
external_id:
isi:
- '000811777900003'
file:
- access_level: open_access
checksum: bd95be1e77090208b79bc45ea8785d0b
content_type: application/pdf
creator: dernst
date_created: 2023-01-27T08:23:46Z
date_updated: 2023-01-27T08:23:46Z
file_id: '12417'
file_name: 2022_CommBiology_Muhia.pdf
file_size: 3968356
relation: main_file
success: 1
file_date_updated: 2023-01-27T08:23:46Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
keyword:
- General Agricultural and Biological Sciences
- General Biochemistry
- Genetics and Molecular Biology
- Medicine (miscellaneous)
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '06'
oa: 1
oa_version: Published Version
publication: Communications Biology
publication_identifier:
issn:
- 2399-3642
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity
relevant to behavioral and cognitive processes
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: 5
year: '2022'
...
---
_id: '12225'
abstract:
- lang: eng
text: In social networks, users often engage with like-minded peers. This selective
exposure to opinions might result in echo chambers, i.e., political fragmentation
and social polarization of user interactions. When echo chambers form, opinions
have a bimodal distribution with two peaks on opposite sides. In certain issues,
where either extreme positions contain a degree of misinformation, neutral consensus
is preferable for promoting discourse. In this paper, we use an opinion dynamics
model that naturally forms echo chambers in order to find a feedback mechanism
that bridges these communities and leads to a neutral consensus. We introduce the
random dynamical nudge (RDN), which presents each agent
with input from a random selection of other agents’ opinions and does not require
surveillance of every person’s opinions. Our computational results in two different
models suggest that the RDN leads to a unimodal distribution of opinions centered
around the neutral consensus. Furthermore, the RDN is effective both for preventing
the formation of echo chambers and also for depolarizing existing echo chambers.
Due to the simple and robust nature of the RDN, social media networks might be
able to implement a version of this self-feedback mechanism, when appropriate,
to prevent the segregation of online communities on complex social issues.
acknowledgement: CBC and AKN would like to thank Neuromatch Academy https://www.neuromatchacademy.org
for introducing the authors to each other. We thank Dr. Krešimir Josic (University
of Houston) , Fabian Baumann (Humboldt University) and Dr. Igor M. Sokolov (Humboldt
University) for carefully reading the early versions of the manuscript and providing
constructive feedback. CBC is supported by the German Deutscher Akademischer Austauschdienst
(DAAD, https://daad.de), the South African National Research Foundation (NRF, https://nrf.ac.za),
the University of Cape Town (UCT, https://uct.ac.za), and the NOMIS Foundation through
the NOMIS Fellowships at IST Austria program (https://nomisfoundation.ch). SVV appreciate
the generosity of Tecnológico de Monterrey for covering the publication fee.
article_number: '9234'
article_processing_charge: No
article_type: original
author:
- first_name: Christopher
full_name: Currin, Christopher
id: e8321fc5-3091-11eb-8a53-83f309a11ac9
last_name: Currin
orcid: 0000-0002-4809-5059
- first_name: Sebastián Vallejo
full_name: Vera, Sebastián Vallejo
last_name: Vera
- first_name: Ali
full_name: Khaledi-Nasab, Ali
last_name: Khaledi-Nasab
citation:
ama: Currin C, Vera SV, Khaledi-Nasab A. Depolarization of echo chambers by random
dynamical nudge. Scientific Reports. 2022;12. doi:10.1038/s41598-022-12494-w
apa: Currin, C., Vera, S. V., & Khaledi-Nasab, A. (2022). Depolarization of
echo chambers by random dynamical nudge. Scientific Reports. Springer Nature.
https://doi.org/10.1038/s41598-022-12494-w
chicago: Currin, Christopher, Sebastián Vallejo Vera, and Ali Khaledi-Nasab. “Depolarization
of Echo Chambers by Random Dynamical Nudge.” Scientific Reports. Springer
Nature, 2022. https://doi.org/10.1038/s41598-022-12494-w.
ieee: C. Currin, S. V. Vera, and A. Khaledi-Nasab, “Depolarization of echo chambers
by random dynamical nudge,” Scientific Reports, vol. 12. Springer Nature,
2022.
ista: Currin C, Vera SV, Khaledi-Nasab A. 2022. Depolarization of echo chambers
by random dynamical nudge. Scientific Reports. 12, 9234.
mla: Currin, Christopher, et al. “Depolarization of Echo Chambers by Random Dynamical
Nudge.” Scientific Reports, vol. 12, 9234, Springer Nature, 2022, doi:10.1038/s41598-022-12494-w.
short: C. Currin, S.V. Vera, A. Khaledi-Nasab, Scientific Reports 12 (2022).
date_created: 2023-01-16T09:48:30Z
date_published: 2022-06-02T00:00:00Z
date_updated: 2023-08-04T09:26:30Z
day: '02'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.1038/s41598-022-12494-w
external_id:
isi:
- '000805561200024'
pmid:
- '35654942'
file:
- access_level: open_access
checksum: e024a75f14ce5667795a31e44a259c52
content_type: application/pdf
creator: dernst
date_created: 2023-01-27T08:56:18Z
date_updated: 2023-01-27T08:56:18Z
file_id: '12418'
file_name: 2022_ScientificReports_Currin.pdf
file_size: 3625627
relation: main_file
success: 1
file_date_updated: 2023-01-27T08:56:18Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
keyword:
- Multidisciplinary
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific Reports
publication_identifier:
issn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Depolarization of echo chambers by random dynamical nudge
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: 12
year: '2022'
...
---
_id: '12226'
abstract:
- lang: eng
text: "Background: Biases of DNA repair can shape the nucleotide landscape of genomes
at evolutionary timescales. The molecular mechanisms of those biases are still
poorly understood because it is difficult to isolate the contributions of DNA
repair from those of DNA damage.\r\n\r\nResults: Here, we develop a genome-wide
assay whereby the same DNA lesion is repaired in different genomic contexts. We
insert thousands of barcoded transposons carrying a reporter of DNA mismatch repair
in the genome of mouse embryonic stem cells. Upon inducing a double-strand break
between tandem repeats, a mismatch is generated if the break is repaired through
single-strand annealing. The resolution of the mismatch showed a 60–80% bias in
favor of the strand with the longest 3′ flap. The location of the lesion in the
genome and the type of mismatch had little influence on the bias. Instead, we
observe a complete reversal of the bias when the longest 3′ flap is moved to the
opposite strand by changing the position of the double-strand break in the reporter.\r\n\r\nConclusions:
These results suggest that the processing of the double-strand break has a major
influence on the repair of mismatches during single-strand annealing."
acknowledgement: We acknowledge the financial support of the Natural Sciences and
Engineering Research Council of Canada (NSERC RGPIN-2020-06377), the Spanish Ministry
of Economy, Industry and Competitiveness (“Centro de Excelencia Severo Ochoa 2013-2017”,
Plan Estatal PGC2018-099807-B-I00), of the CERCA Programme/Generalitat de Catalunya,
and of the European Research Council (Synergy Grant 609989). VOP was supported by
the European Union’s Horizon 2020 research and innovation program under the Marie
Skłodowska-Curie programme (665385). We also acknowledge the support of the Spanish
Ministry of Economy and Competitiveness (MEIC) to the EMBL partnership.
article_number: '93'
article_processing_charge: No
article_type: original
author:
- first_name: Victoria
full_name: Pokusaeva, Victoria
id: 3184041C-F248-11E8-B48F-1D18A9856A87
last_name: Pokusaeva
orcid: 0000-0001-7660-444X
- first_name: Aránzazu Rosado
full_name: Diez, Aránzazu Rosado
last_name: Diez
- first_name: Lorena
full_name: Espinar, Lorena
last_name: Espinar
- first_name: Albert Torelló
full_name: Pérez, Albert Torelló
last_name: Pérez
- first_name: Guillaume J.
full_name: Filion, Guillaume J.
last_name: Filion
citation:
ama: Pokusaeva V, Diez AR, Espinar L, Pérez AT, Filion GJ. Strand asymmetry influences
mismatch resolution during single-strand annealing. Genome Biology. 2022;23.
doi:10.1186/s13059-022-02665-3
apa: Pokusaeva, V., Diez, A. R., Espinar, L., Pérez, A. T., & Filion, G. J.
(2022). Strand asymmetry influences mismatch resolution during single-strand annealing.
Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-022-02665-3
chicago: Pokusaeva, Victoria, Aránzazu Rosado Diez, Lorena Espinar, Albert Torelló
Pérez, and Guillaume J. Filion. “Strand Asymmetry Influences Mismatch Resolution
during Single-Strand Annealing.” Genome Biology. Springer Nature, 2022.
https://doi.org/10.1186/s13059-022-02665-3.
ieee: V. Pokusaeva, A. R. Diez, L. Espinar, A. T. Pérez, and G. J. Filion, “Strand
asymmetry influences mismatch resolution during single-strand annealing,” Genome
Biology, vol. 23. Springer Nature, 2022.
ista: Pokusaeva V, Diez AR, Espinar L, Pérez AT, Filion GJ. 2022. Strand asymmetry
influences mismatch resolution during single-strand annealing. Genome Biology.
23, 93.
mla: Pokusaeva, Victoria, et al. “Strand Asymmetry Influences Mismatch Resolution
during Single-Strand Annealing.” Genome Biology, vol. 23, 93, Springer
Nature, 2022, doi:10.1186/s13059-022-02665-3.
short: V. Pokusaeva, A.R. Diez, L. Espinar, A.T. Pérez, G.J. Filion, Genome Biology
23 (2022).
date_created: 2023-01-16T09:48:44Z
date_published: 2022-04-12T00:00:00Z
date_updated: 2025-03-31T16:01:11Z
day: '12'
ddc:
- '570'
department:
- _id: MaJö
doi: 10.1186/s13059-022-02665-3
ec_funded: 1
external_id:
isi:
- '000781953800001'
pmid:
- '35414014'
file:
- access_level: open_access
checksum: 17bb091fec04d82ba20a3458c4cfd2bd
content_type: application/pdf
creator: dernst
date_created: 2023-01-27T09:01:40Z
date_updated: 2023-01-27T09:01:40Z
file_id: '12419'
file_name: 2022_GenomeBiology_Pokusaeva.pdf
file_size: 4939342
relation: main_file
success: 1
file_date_updated: 2023-01-27T09:01:40Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
language:
- iso: eng
month: '04'
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
publication: Genome Biology
publication_identifier:
issn:
- 1474-760X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: software
url: 'https://github.com/cellcomplexitylab/strand_asymmetry '
- relation: software
url: https://hub.docker.com/r/gui11aume/strand_asymmetry
scopus_import: '1'
status: public
title: Strand asymmetry influences mismatch resolution during single-strand annealing
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: 23
year: '2022'
...
---
_id: '12227'
abstract:
- lang: eng
text: Polydicyclopentadiene (pDCPD), a thermoset with excellent mechanical properties,
has enormous potential as a lightweight, tough, and stable matrix material owing
to its highly cross-linked macromolecular network. This work describes generating
pDCPD-based foams and hierarchically porous carbons derived therefrom by combining
ring-opening metathesis polymerization (ROMP) of DCPD, high internal phase emulsions
(HIPEs) as structural templates, and subsequent carbonization. The structure and
function of the carbon foams were characterized and discussed in detail using
scanning electron, transmission electron, or atomic force microscopy (SEM, TEM,
AFM), electron energy-loss spectroscopy (TEM-EELS), N2 sorption, and analyses
of electrical conductivity as well as mechanical properties. The resulting materials
exhibited uniform, shape-retaining shrinkage of only ∼1/3 after carbonization.
No structural failure was observed even when the pDCPD precursor foams were heated
to 1400 °C. Instead, the high porosity, void size, and 3D interconnectivity were
fully preserved, and the void diameters could be adjusted between 87 and 2.5 μm.
Moreover, foams have a carbon content >97%, an electronic conductivity of up to
2800 S·m–1, a Young’s modulus of up to 2.1 GPa, and a specific surface area of
up to 1200 m2·g–1. Surprisingly, the pDCPD foams were carbonized into shapes other
than monoliths, such as 10’s of micron thick membranes or foamy coatings adhered
to a metal foil or grid substrate. The latter coatings even adhere upon bending.
Finally, as a use case, carbonized foams were applied as porous cathodes for Li–O2
batteries where the foams show a favorable combination of porosity, active surface
area, and pore size for outstanding capacity.
acknowledgement: S.K. acknowledges the financial support from the Slovenian Research
Agency (grants P1-0021, P2-0150). Support by Graz University of Technology (LP-03
– Porous Materials@Work) and from VARTA Innovation GmbH is kindly acknowledged.
We thank Umicore for providing the initiator and Matjaž Mazaj (National Institute
of Chemistry, Ljubljana) and Karel Jerabek (Czech Academy of Sciences) for measurements
and fruitful discussions. S.A.F. is indebted to the Austrian Federal Ministry of
Science, Research and Economy; the Austrian Research Promotion Agency (Grant No.
845364); and ISTA for support.
article_processing_charge: No
article_type: original
author:
- first_name: Sebastijan
full_name: Kovačič, Sebastijan
last_name: Kovačič
- first_name: Bettina
full_name: Schafzahl, Bettina
last_name: Schafzahl
- first_name: Nadejda B.
full_name: Matsko, Nadejda B.
last_name: Matsko
- first_name: Katharina
full_name: Gruber, Katharina
last_name: Gruber
- first_name: Martin
full_name: Schmuck, Martin
last_name: Schmuck
- first_name: Stefan
full_name: Koller, Stefan
last_name: Koller
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Christian
full_name: Slugovc, Christian
last_name: Slugovc
citation:
ama: 'Kovačič S, Schafzahl B, Matsko NB, et al. Carbon foams via ring-opening metathesis
polymerization of emulsion templates: A facile method to make carbon current collectors
for battery applications. ACS Applied Energy Materials. 2022;5(11):14381-14390.
doi:10.1021/acsaem.2c02787'
apa: 'Kovačič, S., Schafzahl, B., Matsko, N. B., Gruber, K., Schmuck, M., Koller,
S., … Slugovc, C. (2022). Carbon foams via ring-opening metathesis polymerization
of emulsion templates: A facile method to make carbon current collectors for battery
applications. ACS Applied Energy Materials. American Chemical Society.
https://doi.org/10.1021/acsaem.2c02787'
chicago: 'Kovačič, Sebastijan, Bettina Schafzahl, Nadejda B. Matsko, Katharina Gruber,
Martin Schmuck, Stefan Koller, Stefan Alexander Freunberger, and Christian Slugovc.
“Carbon Foams via Ring-Opening Metathesis Polymerization of Emulsion Templates:
A Facile Method to Make Carbon Current Collectors for Battery Applications.” ACS
Applied Energy Materials. American Chemical Society, 2022. https://doi.org/10.1021/acsaem.2c02787.'
ieee: 'S. Kovačič et al., “Carbon foams via ring-opening metathesis polymerization
of emulsion templates: A facile method to make carbon current collectors for battery
applications,” ACS Applied Energy Materials, vol. 5, no. 11. American Chemical
Society, pp. 14381–14390, 2022.'
ista: 'Kovačič S, Schafzahl B, Matsko NB, Gruber K, Schmuck M, Koller S, Freunberger
SA, Slugovc C. 2022. Carbon foams via ring-opening metathesis polymerization of
emulsion templates: A facile method to make carbon current collectors for battery
applications. ACS Applied Energy Materials. 5(11), 14381–14390.'
mla: 'Kovačič, Sebastijan, et al. “Carbon Foams via Ring-Opening Metathesis Polymerization
of Emulsion Templates: A Facile Method to Make Carbon Current Collectors for Battery
Applications.” ACS Applied Energy Materials, vol. 5, no. 11, American Chemical
Society, 2022, pp. 14381–90, doi:10.1021/acsaem.2c02787.'
short: S. Kovačič, B. Schafzahl, N.B. Matsko, K. Gruber, M. Schmuck, S. Koller,
S.A. Freunberger, C. Slugovc, ACS Applied Energy Materials 5 (2022) 14381–14390.
corr_author: '1'
date_created: 2023-01-16T09:48:53Z
date_published: 2022-10-16T00:00:00Z
date_updated: 2024-10-09T21:03:48Z
day: '16'
ddc:
- '540'
department:
- _id: StFr
doi: 10.1021/acsaem.2c02787
external_id:
isi:
- '000875635900001'
file:
- access_level: open_access
checksum: 572d15c250ab83d44f4e2c3aeb5f7388
content_type: application/pdf
creator: dernst
date_created: 2023-01-27T09:09:15Z
date_updated: 2023-01-27T09:09:15Z
file_id: '12420'
file_name: 2022_AppliedEnergyMaterials_Kovacic.pdf
file_size: 13105589
relation: main_file
success: 1
file_date_updated: 2023-01-27T09:09:15Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '11'
keyword:
- Electrical and Electronic Engineering
- Materials Chemistry
- Electrochemistry
- Energy Engineering and Power Technology
- Chemical Engineering (miscellaneous)
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 14381-14390
publication: ACS Applied Energy Materials
publication_identifier:
issn:
- 2574-0962
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Carbon foams via ring-opening metathesis polymerization of emulsion templates:
A facile method to make carbon current collectors for battery applications'
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: 5
year: '2022'
...
---
_id: '12228'
abstract:
- lang: eng
text: The question of how RNA, as the principal carrier of genetic information evolved
is fundamentally important for our understanding of the origin of life. The RNA
molecule is far too complex to have formed in one evolutionary step, suggesting
that ancestral proto-RNAs (first ancestor of RNA) may have existed, which evolved
over time into the RNA of today. Here we show that isoxazole nucleosides, which
are quickly formed from hydroxylamine, cyanoacetylene, urea and ribose, are plausible
precursors for RNA. The isoxazole nucleoside can rearrange within an RNA-strand
to give cytidine, which leads to an increase of pairing stability. If the proto-RNA
contains a canonical seed-nucleoside with defined stereochemistry, the seed-nucleoside
can control the configuration of the anomeric center that forms during the in-RNA
transformation. The results demonstrate that RNA could have emerged from evolutionarily
primitive precursor isoxazole ribosides after strand formation.
acknowledgement: We thank Stefan Wiedemann for the synthesis of reference compounds
and Pia Heinrichs for assistance in the NMR measurements of the oligonucleotides.
We also thank Dr. Luis Escobar and Jonas Feldmann for valued discussions. This work
was supported by the German Research Foundation (DFG) for financial support via
CRC1309 (Project ID 325871075, A04), CRC1361 (Project ID 893547839, P02) and CRC1032
(Project ID 201269156, A5). This project has received funding from the European
Research Council (ERC) under the European Union's Horizon 2020 research and innovation
program under grant agreement No 741912 (EpiR). We are grateful for additional funding
from the Volkswagen Foundation (EvoRib). Open Access funding enabled and organized
by Projekt DEAL.
article_number: e202211945
article_processing_charge: No
article_type: original
author:
- first_name: Felix
full_name: Xu, Felix
last_name: Xu
- first_name: Antony
full_name: Crisp, Antony
last_name: Crisp
- first_name: Thea
full_name: Schinkel, Thea
last_name: Schinkel
- first_name: Romeo C. A.
full_name: Dubini, Romeo C. A.
last_name: Dubini
- first_name: Sarah
full_name: Hübner, Sarah
last_name: Hübner
- first_name: Sidney
full_name: Becker, Sidney
last_name: Becker
- first_name: Florian
full_name: Schelter, Florian
last_name: Schelter
- first_name: Petra
full_name: Rovo, Petra
id: c316e53f-b965-11eb-b128-bb26acc59c00
last_name: Rovo
orcid: 0000-0001-8729-7326
- first_name: Thomas
full_name: Carell, Thomas
last_name: Carell
citation:
ama: Xu F, Crisp A, Schinkel T, et al. Isoxazole nucleosides as building blocks
for a plausible proto‐RNA. Angewandte Chemie International Edition. 2022;61(45).
doi:10.1002/anie.202211945
apa: Xu, F., Crisp, A., Schinkel, T., Dubini, R. C. A., Hübner, S., Becker, S.,
… Carell, T. (2022). Isoxazole nucleosides as building blocks for a plausible
proto‐RNA. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202211945
chicago: Xu, Felix, Antony Crisp, Thea Schinkel, Romeo C. A. Dubini, Sarah Hübner,
Sidney Becker, Florian Schelter, Petra Rovo, and Thomas Carell. “Isoxazole Nucleosides
as Building Blocks for a Plausible Proto‐RNA.” Angewandte Chemie International
Edition. Wiley, 2022. https://doi.org/10.1002/anie.202211945.
ieee: F. Xu et al., “Isoxazole nucleosides as building blocks for a plausible
proto‐RNA,” Angewandte Chemie International Edition, vol. 61, no. 45. Wiley,
2022.
ista: Xu F, Crisp A, Schinkel T, Dubini RCA, Hübner S, Becker S, Schelter F, Rovo
P, Carell T. 2022. Isoxazole nucleosides as building blocks for a plausible proto‐RNA.
Angewandte Chemie International Edition. 61(45), e202211945.
mla: Xu, Felix, et al. “Isoxazole Nucleosides as Building Blocks for a Plausible
Proto‐RNA.” Angewandte Chemie International Edition, vol. 61, no. 45, e202211945,
Wiley, 2022, doi:10.1002/anie.202211945.
short: F. Xu, A. Crisp, T. Schinkel, R.C.A. Dubini, S. Hübner, S. Becker, F. Schelter,
P. Rovo, T. Carell, Angewandte Chemie International Edition 61 (2022).
date_created: 2023-01-16T09:49:05Z
date_published: 2022-11-07T00:00:00Z
date_updated: 2025-06-11T13:40:23Z
day: '07'
ddc:
- '540'
department:
- _id: NMR
doi: 10.1002/anie.202211945
external_id:
isi:
- '000866428500001'
pmid:
- '36063071'
file:
- access_level: open_access
checksum: 4e8152454d12025d13f6e6e9ca06b5d0
content_type: application/pdf
creator: dernst
date_created: 2023-01-27T10:28:45Z
date_updated: 2023-01-27T10:28:45Z
file_id: '12422'
file_name: 2022_AngewandteChemieInternat_Xu.pdf
file_size: 1076715
relation: main_file
success: 1
file_date_updated: 2023-01-27T10:28:45Z
has_accepted_license: '1'
intvolume: ' 61'
isi: 1
issue: '45'
keyword:
- General Chemistry
- Catalysis
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Angewandte Chemie International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Isoxazole nucleosides as building blocks for a plausible proto‐RNA
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: 61
year: '2022'
...
---
_id: '12229'
abstract:
- lang: eng
text: "We present Bullshark, the first directed acyclic graph (DAG) based asynchronous
Byzantine Atomic Broadcast protocol that is optimized for the common synchronous
case. Like previous DAG-based BFT protocols [19, 25], Bullshark requires no extra
communication to achieve consensus on top of building the DAG. That is, parties
can totally order the vertices of the DAG by interpreting their local view of
the DAG edges. Unlike other asynchronous DAG-based protocols, Bullshark provides
a practical low latency fast-path that exploits synchronous periods and deprecates
the need for notoriously complex view-change and view-synchronization mechanisms.
Bullshark achieves this while maintaining all the desired properties of its predecessor
DAG-Rider [25]. Namely, it has optimal amortized communication complexity, it
provides fairness and asynchronous liveness, and safety is guaranteed even under
a quantum adversary.\r\n\r\nIn order to show the practicality and simplicity of
our approach, we also introduce a standalone partially synchronous version of
Bullshark, which we evaluate against the state of the art. The implemented protocol
is embarrassingly simple (200 LOC on top of an existing DAG-based mempool implementation).
It is highly efficient, achieving for example, 125,000 transactions per second
with a 2 seconds latency for a deployment of 50 parties. In the same setting,
the state of the art pays a steep 50% latency increase as it optimizes for asynchrony."
article_processing_charge: No
arxiv: 1
author:
- first_name: Alexander
full_name: Spiegelman, Alexander
last_name: Spiegelman
- first_name: Neil
full_name: Giridharan, Neil
last_name: Giridharan
- first_name: Alberto
full_name: Sonnino, Alberto
last_name: Sonnino
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
citation:
ama: 'Spiegelman A, Giridharan N, Sonnino A, Kokoris Kogias E. Bullshark: DAG BFT
protocols made practical. In: Proceedings of the 2022 ACM SIGSAC Conference
on Computer and Communications Security. Association for Computing Machinery;
2022:2705–2718. doi:10.1145/3548606.3559361'
apa: 'Spiegelman, A., Giridharan, N., Sonnino, A., & Kokoris Kogias, E. (2022).
Bullshark: DAG BFT protocols made practical. In Proceedings of the 2022 ACM
SIGSAC Conference on Computer and Communications Security (pp. 2705–2718).
Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3548606.3559361'
chicago: 'Spiegelman, Alexander, Neil Giridharan, Alberto Sonnino, and Eleftherios
Kokoris Kogias. “Bullshark: DAG BFT Protocols Made Practical.” In Proceedings
of the 2022 ACM SIGSAC Conference on Computer and Communications Security,
2705–2718. Association for Computing Machinery, 2022. https://doi.org/10.1145/3548606.3559361.'
ieee: 'A. Spiegelman, N. Giridharan, A. Sonnino, and E. Kokoris Kogias, “Bullshark:
DAG BFT protocols made practical,” in Proceedings of the 2022 ACM SIGSAC Conference
on Computer and Communications Security, Los Angeles, CA, United States, 2022,
pp. 2705–2718.'
ista: 'Spiegelman A, Giridharan N, Sonnino A, Kokoris Kogias E. 2022. Bullshark:
DAG BFT protocols made practical. Proceedings of the 2022 ACM SIGSAC Conference
on Computer and Communications Security. CCS: Conference on Computer and Communications
Security, 2705–2718.'
mla: 'Spiegelman, Alexander, et al. “Bullshark: DAG BFT Protocols Made Practical.”
Proceedings of the 2022 ACM SIGSAC Conference on Computer and Communications
Security, Association for Computing Machinery, 2022, pp. 2705–2718, doi:10.1145/3548606.3559361.'
short: A. Spiegelman, N. Giridharan, A. Sonnino, E. Kokoris Kogias, in:, Proceedings
of the 2022 ACM SIGSAC Conference on Computer and Communications Security, Association
for Computing Machinery, 2022, pp. 2705–2718.
conference:
end_date: 2022-11-11
location: Los Angeles, CA, United States
name: 'CCS: Conference on Computer and Communications Security'
start_date: 2022-11-07
date_created: 2023-01-16T09:49:48Z
date_published: 2022-11-01T00:00:00Z
date_updated: 2025-07-10T11:50:26Z
day: '01'
department:
- _id: ElKo
doi: 10.1145/3548606.3559361
external_id:
arxiv:
- '2201.05677'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2201.05677
month: '11'
oa: 1
oa_version: Preprint
page: 2705–2718
publication: Proceedings of the 2022 ACM SIGSAC Conference on Computer and Communications
Security
publication_identifier:
isbn:
- '9781450394505'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Bullshark: DAG BFT protocols made practical'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '12232'
abstract:
- lang: eng
text: We derive a precise asymptotic formula for the density of the small singular
values of the real Ginibre matrix ensemble shifted by a complex parameter z as
the dimension tends to infinity. For z away from the real axis the formula coincides
with that for the complex Ginibre ensemble we derived earlier in Cipolloni et
al. (Prob Math Phys 1:101–146, 2020). On the level of the one-point function of
the low lying singular values we thus confirm the transition from real to complex
Ginibre ensembles as the shift parameter z becomes genuinely complex; the analogous
phenomenon has been well known for eigenvalues. We use the superbosonization formula
(Littelmann et al. in Comm Math Phys 283:343–395, 2008) in a regime where the
main contribution comes from a three dimensional saddle manifold.
acknowledgement: Open access funding provided by Swiss Federal Institute of Technology
Zurich. Supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH
Zürich Foundation.
article_processing_charge: No
article_type: original
author:
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: Cipolloni G, Erdös L, Schröder DJ. Density of small singular values of the
shifted real Ginibre ensemble. Annales Henri Poincaré. 2022;23(11):3981-4002.
doi:10.1007/s00023-022-01188-8
apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2022). Density of small singular
values of the shifted real Ginibre ensemble. Annales Henri Poincaré. Springer
Nature. https://doi.org/10.1007/s00023-022-01188-8
chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Density of Small
Singular Values of the Shifted Real Ginibre Ensemble.” Annales Henri Poincaré.
Springer Nature, 2022. https://doi.org/10.1007/s00023-022-01188-8.
ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Density of small singular values
of the shifted real Ginibre ensemble,” Annales Henri Poincaré, vol. 23,
no. 11. Springer Nature, pp. 3981–4002, 2022.
ista: Cipolloni G, Erdös L, Schröder DJ. 2022. Density of small singular values
of the shifted real Ginibre ensemble. Annales Henri Poincaré. 23(11), 3981–4002.
mla: Cipolloni, Giorgio, et al. “Density of Small Singular Values of the Shifted
Real Ginibre Ensemble.” Annales Henri Poincaré, vol. 23, no. 11, Springer
Nature, 2022, pp. 3981–4002, doi:10.1007/s00023-022-01188-8.
short: G. Cipolloni, L. Erdös, D.J. Schröder, Annales Henri Poincaré 23 (2022) 3981–4002.
date_created: 2023-01-16T09:50:26Z
date_published: 2022-11-01T00:00:00Z
date_updated: 2023-08-04T09:33:52Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1007/s00023-022-01188-8
external_id:
isi:
- '000796323500001'
file:
- access_level: open_access
checksum: 5582f059feeb2f63e2eb68197a34d7dc
content_type: application/pdf
creator: dernst
date_created: 2023-01-27T11:06:47Z
date_updated: 2023-01-27T11:06:47Z
file_id: '12424'
file_name: 2022_AnnalesHenriP_Cipolloni.pdf
file_size: 1333638
relation: main_file
success: 1
file_date_updated: 2023-01-27T11:06:47Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
issue: '11'
keyword:
- Mathematical Physics
- Nuclear and High Energy Physics
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 3981-4002
publication: Annales Henri Poincaré
publication_identifier:
eissn:
- 1424-0661
issn:
- 1424-0637
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Density of small singular values of the shifted real Ginibre ensemble
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: 23
year: '2022'
...
---
_id: '12234'
abstract:
- lang: eng
text: Hybrid speciation—the origin of new species resulting from the hybridization
of genetically divergent lineages—was once considered rare, but genomic data suggest
that it may occur more often than once thought. In this study, Noguerales and
Ortego found genomic evidence supporting the hybrid origin of a grasshopper that
is able to exploit a broader range of host plants than either of its putative
parents.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
citation:
ama: 'Stankowski S. Digest: On the origin of a possible hybrid species. Evolution.
2022;76(11):2784-2785. doi:10.1111/evo.14632'
apa: 'Stankowski, S. (2022). Digest: On the origin of a possible hybrid species.
Evolution. Wiley. https://doi.org/10.1111/evo.14632'
chicago: 'Stankowski, Sean. “Digest: On the Origin of a Possible Hybrid Species.”
Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14632.'
ieee: 'S. Stankowski, “Digest: On the origin of a possible hybrid species,” Evolution,
vol. 76, no. 11. Wiley, pp. 2784–2785, 2022.'
ista: 'Stankowski S. 2022. Digest: On the origin of a possible hybrid species. Evolution.
76(11), 2784–2785.'
mla: 'Stankowski, Sean. “Digest: On the Origin of a Possible Hybrid Species.” Evolution,
vol. 76, no. 11, Wiley, 2022, pp. 2784–85, doi:10.1111/evo.14632.'
short: S. Stankowski, Evolution 76 (2022) 2784–2785.
corr_author: '1'
date_created: 2023-01-16T09:50:48Z
date_published: 2022-11-01T00:00:00Z
date_updated: 2025-06-11T13:40:40Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/evo.14632
external_id:
isi:
- '000855751600001'
pmid:
- '36112597'
file:
- access_level: open_access
checksum: 4c0f05083b414ac0323a1b9ee1abc275
content_type: application/pdf
creator: dernst
date_created: 2023-01-27T11:28:38Z
date_updated: 2023-01-27T11:28:38Z
file_id: '12425'
file_name: 2022_Evolution_Stankowski.pdf
file_size: 287282
relation: main_file
success: 1
file_date_updated: 2023-01-27T11:28:38Z
has_accepted_license: '1'
intvolume: ' 76'
isi: 1
issue: '11'
keyword:
- General Agricultural and Biological Sciences
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '11'
oa: 1
oa_version: Published Version
page: 2784-2785
pmid: 1
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Digest: On the origin of a possible hybrid species'
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: 76
year: '2022'
...
---
_id: '12235'
abstract:
- lang: eng
text: "Background: About 800 women die every day worldwide from pregnancy-related
complications, including excessive blood loss, infections and high-blood pressure
(World Health Organization, 2019). To improve screening for high-risk pregnancies,
we set out to identify patterns of maternal hematological changes associated with
future pregnancy complications.\r\n\r\nMethods: Using mixed effects models, we
established changes in 14 complete blood count (CBC) parameters for 1710 healthy
pregnancies and compared them to measurements from 98 pregnancy-induced hypertension,
106 gestational diabetes and 339 postpartum hemorrhage cases.\r\n\r\nResults:
Results show interindividual variations, but good individual repeatability in
CBC values during physiological pregnancies, allowing the identification of specific
alterations in women with obstetric complications. For example, in women with
uncomplicated pregnancies, haemoglobin count decreases of 0.12 g/L (95% CI −0.16,
−0.09) significantly per gestation week (p value <.001). Interestingly, this decrease
is three times more pronounced in women who will develop pregnancy-induced hypertension,
with an additional decrease of 0.39 g/L (95% CI −0.51, −0.26). We also confirm
that obstetric complications and white CBC predict the likelihood of giving birth
earlier during pregnancy.\r\n\r\nConclusion: We provide a comprehensive description
of the associations between haematological changes through pregnancy and three
major obstetric complications to support strategies for prevention, early-diagnosis
and maternal care."
acknowledgement: This project was funded by an SNSF Eccellenza Grant to MRR (PCEGP3-181181),
and by core funding from the Institute of Science and Technology Austria. We would
like to thank the participants of the study and all the midwives and doctors involved
for the computerized obstetrical data from the CHUV Maternity Hospital. Open access
funding provided by Universite de Lausanne.
article_processing_charge: No
article_type: original
author:
- first_name: Marion
full_name: Patxot, Marion
last_name: Patxot
- first_name: Miloš
full_name: Stojanov, Miloš
last_name: Stojanov
- first_name: Sven Erik
full_name: Ojavee, Sven Erik
last_name: Ojavee
- first_name: Rosanna Pescini
full_name: Gobert, Rosanna Pescini
last_name: Gobert
- first_name: Zoltán
full_name: Kutalik, Zoltán
last_name: Kutalik
- first_name: Mathilde
full_name: Gavillet, Mathilde
last_name: Gavillet
- first_name: David
full_name: Baud, David
last_name: Baud
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
citation:
ama: 'Patxot M, Stojanov M, Ojavee SE, et al. Haematological changes from conception
to childbirth: An indicator of major pregnancy complications. European Journal
of Haematology. 2022;109(5):566-575. doi:10.1111/ejh.13844'
apa: 'Patxot, M., Stojanov, M., Ojavee, S. E., Gobert, R. P., Kutalik, Z., Gavillet,
M., … Robinson, M. R. (2022). Haematological changes from conception to childbirth:
An indicator of major pregnancy complications. European Journal of Haematology.
Wiley. https://doi.org/10.1111/ejh.13844'
chicago: 'Patxot, Marion, Miloš Stojanov, Sven Erik Ojavee, Rosanna Pescini Gobert,
Zoltán Kutalik, Mathilde Gavillet, David Baud, and Matthew Richard Robinson. “Haematological
Changes from Conception to Childbirth: An Indicator of Major Pregnancy Complications.”
European Journal of Haematology. Wiley, 2022. https://doi.org/10.1111/ejh.13844.'
ieee: 'M. Patxot et al., “Haematological changes from conception to childbirth:
An indicator of major pregnancy complications,” European Journal of Haematology,
vol. 109, no. 5. Wiley, pp. 566–575, 2022.'
ista: 'Patxot M, Stojanov M, Ojavee SE, Gobert RP, Kutalik Z, Gavillet M, Baud D,
Robinson MR. 2022. Haematological changes from conception to childbirth: An indicator
of major pregnancy complications. European Journal of Haematology. 109(5), 566–575.'
mla: 'Patxot, Marion, et al. “Haematological Changes from Conception to Childbirth:
An Indicator of Major Pregnancy Complications.” European Journal of Haematology,
vol. 109, no. 5, Wiley, 2022, pp. 566–75, doi:10.1111/ejh.13844.'
short: M. Patxot, M. Stojanov, S.E. Ojavee, R.P. Gobert, Z. Kutalik, M. Gavillet,
D. Baud, M.R. Robinson, European Journal of Haematology 109 (2022) 566–575.
corr_author: '1'
date_created: 2023-01-16T09:50:58Z
date_published: 2022-11-01T00:00:00Z
date_updated: 2024-10-09T21:03:49Z
day: '01'
ddc:
- '570'
- '610'
department:
- _id: MaRo
doi: 10.1111/ejh.13844
external_id:
isi:
- '000849690500001'
pmid:
- '36059200'
file:
- access_level: open_access
checksum: a676d732f67c2990197e34f96b219370
content_type: application/pdf
creator: dernst
date_created: 2023-01-27T11:42:43Z
date_updated: 2023-01-27T11:42:43Z
file_id: '12426'
file_name: 2022_EuropJourHaematology_Patxot.pdf
file_size: 1225073
relation: main_file
success: 1
file_date_updated: 2023-01-27T11:42:43Z
has_accepted_license: '1'
intvolume: ' 109'
isi: 1
issue: '5'
keyword:
- Hematology
- General Medicine
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 566-575
pmid: 1
publication: European Journal of Haematology
publication_identifier:
eissn:
- 1600-0609
issn:
- 0902-4441
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Haematological changes from conception to childbirth: An indicator of major
pregnancy complications'
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 109
year: '2022'
...
---
OA_place: publisher
OA_type: free access
_id: '12238'
abstract:
- lang: eng
text: Upon the initiation of collective cell migration, the cells at the free edge
are specified as leader cells; however, the mechanism underlying the leader cell
specification remains elusive. Here, we show that lamellipodial extension after
the release from mechanical confinement causes sustained extracellular signal-regulated
kinase (ERK) activation and underlies the leader cell specification. Live-imaging
of Madin-Darby canine kidney (MDCK) cells and mouse epidermis through the use
of Förster resonance energy transfer (FRET)-based biosensors showed that leader
cells exhibit sustained ERK activation in a hepatocyte growth factor (HGF)-dependent
manner. Meanwhile, follower cells exhibit oscillatory ERK activation waves in
an epidermal growth factor (EGF) signaling-dependent manner. Lamellipodial extension
at the free edge increases the cellular sensitivity to HGF. The HGF-dependent
ERK activation, in turn, promotes lamellipodial extension, thereby forming a positive
feedback loop between cell extension and ERK activation and specifying the cells
at the free edge as the leader cells. Our findings show that the integration of
physical and biochemical cues underlies the leader cell specification during collective
cell migration.
acknowledgement: We thank the members of the Matsuda Laboratory for their helpful
discussion and encouragement, and we thank K. Hirano and K. Takakura for their technical
assistance. This work was supported by the Kyoto University Live Imaging Center.
Financial support was provided in the form of JSPS KAKENHI grants (nos. 17J02107
and 20K22653 to N.H., and 20H05898 and 19H00993 to M.M.), a JST CREST grant (no.
JPMJCR1654 to M.M.), a Moonshot R&D grant (no. JPMJPS2022-11 to M.M.), Generalitat
de Catalunya and the CERCA Programme (no. SGR-2017-01602 to X.T.), MICCINN/FEDER
(no. PGC2018-099645-B-I00 to X.T.), and European Research Council (no. Adv-883739
to X.T.). IBEC is a recipient of a Severo Ochoa Award of Excellence from the MINECO.
This work was partly supported by an Extramural Collaborative Research Grant of
Cancer Research Institute, Kanazawa University.
article_processing_charge: No
article_type: original
author:
- first_name: Naoya
full_name: Hino, Naoya
id: 5299a9ce-7679-11eb-a7bc-d1e62b936307
last_name: Hino
- first_name: Kimiya
full_name: Matsuda, Kimiya
last_name: Matsuda
- first_name: Yuya
full_name: Jikko, Yuya
last_name: Jikko
- first_name: Gembu
full_name: Maryu, Gembu
last_name: Maryu
- first_name: Katsuya
full_name: Sakai, Katsuya
last_name: Sakai
- first_name: Ryu
full_name: Imamura, Ryu
last_name: Imamura
- first_name: Shinya
full_name: Tsukiji, Shinya
last_name: Tsukiji
- first_name: Kazuhiro
full_name: Aoki, Kazuhiro
last_name: Aoki
- first_name: Kenta
full_name: Terai, Kenta
last_name: Terai
- first_name: Tsuyoshi
full_name: Hirashima, Tsuyoshi
last_name: Hirashima
- first_name: Xavier
full_name: Trepat, Xavier
last_name: Trepat
- first_name: Michiyuki
full_name: Matsuda, Michiyuki
last_name: Matsuda
citation:
ama: Hino N, Matsuda K, Jikko Y, et al. A feedback loop between lamellipodial extension
and HGF-ERK signaling specifies leader cells during collective cell migration.
Developmental Cell. 2022;57(19):2290-2304.e7. doi:10.1016/j.devcel.2022.09.003
apa: Hino, N., Matsuda, K., Jikko, Y., Maryu, G., Sakai, K., Imamura, R., … Matsuda,
M. (2022). A feedback loop between lamellipodial extension and HGF-ERK signaling
specifies leader cells during collective cell migration. Developmental Cell.
Elsevier. https://doi.org/10.1016/j.devcel.2022.09.003
chicago: Hino, Naoya, Kimiya Matsuda, Yuya Jikko, Gembu Maryu, Katsuya Sakai, Ryu
Imamura, Shinya Tsukiji, et al. “A Feedback Loop between Lamellipodial Extension
and HGF-ERK Signaling Specifies Leader Cells during Collective Cell Migration.”
Developmental Cell. Elsevier, 2022. https://doi.org/10.1016/j.devcel.2022.09.003.
ieee: N. Hino et al., “A feedback loop between lamellipodial extension and
HGF-ERK signaling specifies leader cells during collective cell migration,” Developmental
Cell, vol. 57, no. 19. Elsevier, p. 2290–2304.e7, 2022.
ista: Hino N, Matsuda K, Jikko Y, Maryu G, Sakai K, Imamura R, Tsukiji S, Aoki K,
Terai K, Hirashima T, Trepat X, Matsuda M. 2022. A feedback loop between lamellipodial
extension and HGF-ERK signaling specifies leader cells during collective cell
migration. Developmental Cell. 57(19), 2290–2304.e7.
mla: Hino, Naoya, et al. “A Feedback Loop between Lamellipodial Extension and HGF-ERK
Signaling Specifies Leader Cells during Collective Cell Migration.” Developmental
Cell, vol. 57, no. 19, Elsevier, 2022, p. 2290–2304.e7, doi:10.1016/j.devcel.2022.09.003.
short: N. Hino, K. Matsuda, Y. Jikko, G. Maryu, K. Sakai, R. Imamura, S. Tsukiji,
K. Aoki, K. Terai, T. Hirashima, X. Trepat, M. Matsuda, Developmental Cell 57
(2022) 2290–2304.e7.
corr_author: '1'
date_created: 2023-01-16T09:51:39Z
date_published: 2022-10-01T00:00:00Z
date_updated: 2026-06-18T17:25:21Z
day: '01'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2022.09.003
external_id:
isi:
- '000898428700006'
pmid:
- '36174555'
intvolume: ' 57'
isi: 1
issue: '19'
keyword:
- Developmental Biology
- Cell Biology
- General Biochemistry
- Genetics and Molecular Biology
- Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.devcel.2022.09.003
month: '10'
oa: 1
oa_version: Published Version
page: 2290-2304.e7
pmid: 1
publication: Developmental Cell
publication_identifier:
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: A feedback loop between lamellipodial extension and HGF-ERK signaling specifies
leader cells during collective cell migration
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2022'
...
---
_id: '12239'
abstract:
- lang: eng
text: Biological systems are the sum of their dynamic three-dimensional (3D) parts.
Therefore, it is critical to study biological structures in 3D and at high resolution
to gain insights into their physiological functions. Electron microscopy of metal
replicas of unroofed cells and isolated organelles has been a key technique to
visualize intracellular structures at nanometer resolution. However, many of these
methods require specialized equipment and personnel to complete them. Here, we
present novel accessible methods to analyze biological structures in unroofed
cells and biochemically isolated organelles in 3D and at nanometer resolution,
focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential
trafficking organelles, their detailed structural information is lacking due to
their poor preservation when observed via classical electron microscopy protocols
experiments. First, we establish a method to visualize CCVs in unroofed cells
using scanning transmission electron microscopy tomography, providing sufficient
resolution to define the clathrin coat arrangements. Critically, the samples are
prepared directly on electron microscopy grids, removing the requirement to use
extremely corrosive acids, thereby enabling the use of this method in any electron
microscopy lab. Secondly, we demonstrate that this standardized sample preparation
allows the direct comparison of isolated CCV samples with those visualized in
cells. Finally, to facilitate the high-throughput and robust screening of metal
replicated samples, we provide a deep learning analysis method to screen the “pseudo
3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes
accessible ways to examine the 3D structure of biological samples and provide
novel insights into the structure of plant CCVs.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: Bio
acknowledgement: A.J. is supported by funding from the Austrian Science Fund I3630B25
(to J.F.). This research was supported by the Scientific Service Units of Institute
of Science and Technology Austria (ISTA) through resources provided by the Electron
Microscopy Facility, Lab Support Facility, and the Imaging and Optics Facility.
We acknowledge Prof. David Robinson (Heidelberg) and Prof. Jan Traas (Lyon) for
making us aware of previously published classical on-grid preparation methods. No
conflict of interest declared.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Dana A.
full_name: Dahhan, Dana A.
last_name: Dahhan
- first_name: Sebastian Y.
full_name: Bednarek, Sebastian Y.
last_name: Bednarek
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Johnson AJ, Kaufmann W, Sommer CM, et al. Three-dimensional visualization of
planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant.
2022;15(10):1533-1542. doi:10.1016/j.molp.2022.09.003
apa: Johnson, A. J., Kaufmann, W., Sommer, C. M., Costanzo, T., Dahhan, D. A., Bednarek,
S. Y., & Friml, J. (2022). Three-dimensional visualization of planta clathrin-coated
vesicles at ultrastructural resolution. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2022.09.003
chicago: Johnson, Alexander J, Walter Kaufmann, Christoph M Sommer, Tommaso Costanzo,
Dana A. Dahhan, Sebastian Y. Bednarek, and Jiří Friml. “Three-Dimensional Visualization
of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” Molecular
Plant. Elsevier, 2022. https://doi.org/10.1016/j.molp.2022.09.003.
ieee: A. J. Johnson et al., “Three-dimensional visualization of planta clathrin-coated
vesicles at ultrastructural resolution,” Molecular Plant, vol. 15, no.
10. Elsevier, pp. 1533–1542, 2022.
ista: Johnson AJ, Kaufmann W, Sommer CM, Costanzo T, Dahhan DA, Bednarek SY, Friml
J. 2022. Three-dimensional visualization of planta clathrin-coated vesicles at
ultrastructural resolution. Molecular Plant. 15(10), 1533–1542.
mla: Johnson, Alexander J., et al. “Three-Dimensional Visualization of Planta Clathrin-Coated
Vesicles at Ultrastructural Resolution.” Molecular Plant, vol. 15, no.
10, Elsevier, 2022, pp. 1533–42, doi:10.1016/j.molp.2022.09.003.
short: A.J. Johnson, W. Kaufmann, C.M. Sommer, T. Costanzo, D.A. Dahhan, S.Y. Bednarek,
J. Friml, Molecular Plant 15 (2022) 1533–1542.
corr_author: '1'
date_created: 2023-01-16T09:51:49Z
date_published: 2022-10-03T00:00:00Z
date_updated: 2025-04-15T07:32:09Z
day: '03'
ddc:
- '580'
department:
- _id: JiFr
- _id: EM-Fac
- _id: Bio
doi: 10.1016/j.molp.2022.09.003
external_id:
isi:
- '000882769800009'
pmid:
- '36081349'
file:
- access_level: open_access
checksum: 04d5c12490052d03e4dc4412338a43dd
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T07:46:51Z
date_updated: 2023-01-30T07:46:51Z
file_id: '12435'
file_name: 2022_MolecularPlant_Johnson.pdf
file_size: 2307251
relation: main_file
success: 1
file_date_updated: 2023-01-30T07:46:51Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '10'
keyword:
- Plant Science
- Molecular Biology
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 1533-1542
pmid: 1
project:
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: Molecular Plant
publication_identifier:
issn:
- 1674-2052
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural
resolution
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2022'
...
---
_id: '12243'
abstract:
- lang: eng
text: 'We consider the eigenvalues of a large dimensional real or complex Ginibre
matrix in the region of the complex plane where their real parts reach their maximum
value. This maximum follows the Gumbel distribution and that these extreme eigenvalues
form a Poisson point process as the dimension asymptotically tends to infinity.
In the complex case, these facts have already been established by Bender [Probab.
Theory Relat. Fields 147, 241 (2010)] and in the real case by Akemann and Phillips
[J. Stat. Phys. 155, 421 (2014)] even for the more general elliptic ensemble with
a sophisticated saddle point analysis. The purpose of this article is to give
a very short direct proof in the Ginibre case with an effective error term. Moreover,
our estimates on the correlation kernel in this regime serve as a key input for
accurately locating [Formula: see text] for any large matrix X with i.i.d. entries
in the companion paper [G. Cipolloni et al., arXiv:2206.04448 (2022)]. '
acknowledgement: "The authors are grateful to G. Akemann for bringing Refs. 19 and
24–26 to their attention. Discussions with Guillaume Dubach on a preliminary version
of this project are acknowledged.\r\nL.E. and Y.X. were supported by the ERC Advanced
Grant “RMTBeyond” under Grant No. 101020331. D.S. was supported by Dr. Max Rössler,
the Walter Haefner Foundation, and the ETH Zürich Foundation."
article_number: '103303'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
- first_name: Yuanyuan
full_name: Xu, Yuanyuan
id: 7902bdb1-a2a4-11eb-a164-c9216f71aea3
last_name: Xu
orcid: 0000-0003-1559-1205
citation:
ama: Cipolloni G, Erdös L, Schröder DJ, Xu Y. Directional extremal statistics for
Ginibre eigenvalues. Journal of Mathematical Physics. 2022;63(10). doi:10.1063/5.0104290
apa: Cipolloni, G., Erdös, L., Schröder, D. J., & Xu, Y. (2022). Directional
extremal statistics for Ginibre eigenvalues. Journal of Mathematical Physics.
AIP Publishing. https://doi.org/10.1063/5.0104290
chicago: Cipolloni, Giorgio, László Erdös, Dominik J Schröder, and Yuanyuan Xu.
“Directional Extremal Statistics for Ginibre Eigenvalues.” Journal of Mathematical
Physics. AIP Publishing, 2022. https://doi.org/10.1063/5.0104290.
ieee: G. Cipolloni, L. Erdös, D. J. Schröder, and Y. Xu, “Directional extremal statistics
for Ginibre eigenvalues,” Journal of Mathematical Physics, vol. 63, no.
10. AIP Publishing, 2022.
ista: Cipolloni G, Erdös L, Schröder DJ, Xu Y. 2022. Directional extremal statistics
for Ginibre eigenvalues. Journal of Mathematical Physics. 63(10), 103303.
mla: Cipolloni, Giorgio, et al. “Directional Extremal Statistics for Ginibre Eigenvalues.”
Journal of Mathematical Physics, vol. 63, no. 10, 103303, AIP Publishing,
2022, doi:10.1063/5.0104290.
short: G. Cipolloni, L. Erdös, D.J. Schröder, Y. Xu, Journal of Mathematical Physics
63 (2022).
date_created: 2023-01-16T09:52:58Z
date_published: 2022-10-14T00:00:00Z
date_updated: 2025-04-14T07:57:18Z
day: '14'
ddc:
- '510'
- '530'
department:
- _id: LaEr
doi: 10.1063/5.0104290
ec_funded: 1
external_id:
arxiv:
- '2206.04443'
isi:
- '000869715800001'
file:
- access_level: open_access
checksum: 2db278ae5b07f345a7e3fec1f92b5c33
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T08:01:10Z
date_updated: 2023-01-30T08:01:10Z
file_id: '12436'
file_name: 2022_JourMathPhysics_Cipolloni2.pdf
file_size: 7356807
relation: main_file
success: 1
file_date_updated: 2023-01-30T08:01:10Z
has_accepted_license: '1'
intvolume: ' 63'
isi: 1
issue: '10'
keyword:
- Mathematical Physics
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: Journal of Mathematical Physics
publication_identifier:
eissn:
- 1089-7658
issn:
- 0022-2488
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Directional extremal statistics for Ginibre eigenvalues
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: 63
year: '2022'
...
---
_id: '12246'
abstract:
- lang: eng
text: The Lieb–Oxford inequality provides a lower bound on the Coulomb energy of
a classical system of N identical charges only in terms of their one-particle
density. We prove here a new estimate on the best constant in this inequality.
Numerical evaluation provides the value 1.58, which is a significant improvement
to the previously known value 1.64. The best constant has recently been shown
to be larger than 1.44. In a second part, we prove that the constant can be reduced
to 1.25 when the inequality is restricted to Hartree–Fock states. This is the
first proof that the exchange term is always much lower than the full indirect
Coulomb energy.
acknowledgement: We would like to thank David Gontier for useful advice on the numerical
simulations. This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation program (Grant
Agreements MDFT No. 725528 of M.L. and AQUAMS No. 694227 of R.S.). We are thankful
for the hospitality of the Institut Henri Poincaré in Paris, where part of this
work was done.
article_number: '92'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Mathieu
full_name: Lewin, Mathieu
last_name: Lewin
- first_name: Elliott H.
full_name: Lieb, Elliott H.
last_name: Lieb
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Lewin M, Lieb EH, Seiringer R. Improved Lieb–Oxford bound on the indirect and
exchange energies. Letters in Mathematical Physics. 2022;112(5). doi:10.1007/s11005-022-01584-5
apa: Lewin, M., Lieb, E. H., & Seiringer, R. (2022). Improved Lieb–Oxford bound
on the indirect and exchange energies. Letters in Mathematical Physics.
Springer Nature. https://doi.org/10.1007/s11005-022-01584-5
chicago: Lewin, Mathieu, Elliott H. Lieb, and Robert Seiringer. “Improved Lieb–Oxford
Bound on the Indirect and Exchange Energies.” Letters in Mathematical Physics.
Springer Nature, 2022. https://doi.org/10.1007/s11005-022-01584-5.
ieee: M. Lewin, E. H. Lieb, and R. Seiringer, “Improved Lieb–Oxford bound on the
indirect and exchange energies,” Letters in Mathematical Physics, vol.
112, no. 5. Springer Nature, 2022.
ista: Lewin M, Lieb EH, Seiringer R. 2022. Improved Lieb–Oxford bound on the indirect
and exchange energies. Letters in Mathematical Physics. 112(5), 92.
mla: Lewin, Mathieu, et al. “Improved Lieb–Oxford Bound on the Indirect and Exchange
Energies.” Letters in Mathematical Physics, vol. 112, no. 5, 92, Springer
Nature, 2022, doi:10.1007/s11005-022-01584-5.
short: M. Lewin, E.H. Lieb, R. Seiringer, Letters in Mathematical Physics 112 (2022).
date_created: 2023-01-16T09:53:54Z
date_published: 2022-09-15T00:00:00Z
date_updated: 2025-04-14T07:26:59Z
day: '15'
department:
- _id: RoSe
doi: 10.1007/s11005-022-01584-5
ec_funded: 1
external_id:
arxiv:
- '2203.12473'
isi:
- '000854762600001'
intvolume: ' 112'
isi: 1
issue: '5'
keyword:
- Mathematical Physics
- Statistical and Nonlinear Physics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2203.12473
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Letters in Mathematical Physics
publication_identifier:
eissn:
- 1573-0530
issn:
- 0377-9017
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Improved Lieb–Oxford bound on the indirect and exchange energies
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 112
year: '2022'
...
---
_id: '12247'
abstract:
- lang: eng
text: Chromosomal inversions have been shown to play a major role in a local adaptation
by suppressing recombination between alternative arrangements and maintaining
beneficial allele combinations. However, so far, their importance relative to
the remaining genome remains largely unknown. Understanding the genetic architecture
of adaptation requires better estimates of how loci of different effect sizes
contribute to phenotypic variation. Here, we used three Swedish islands where
the marine snail Littorina saxatilis has repeatedly evolved into two distinct
ecotypes along a habitat transition. We estimated the contribution of inversion
polymorphisms to phenotypic divergence while controlling for polygenic effects
in the remaining genome using a quantitative genetics framework. We confirmed
the importance of inversions but showed that contributions of loci outside inversions
are of similar magnitude, with variable proportions dependent on the trait and
the population. Some inversions showed consistent effects across all sites, whereas
others exhibited site-specific effects, indicating that the genomic basis for
replicated phenotypic divergence is only partly shared. The contributions of sexual
dimorphism as well as environmental factors to phenotypic variation were significant
but minor compared to inversions and polygenic background. Overall, this integrated
approach provides insight into the multiple mechanisms contributing to parallel
phenotypic divergence.
acknowledgement: We thank everyone who helped with fieldwork, snail processing, and
DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise
Liabot, Irena Senčić, and Zuzanna Zagrodzka. We also thank Rui Faria and Jenny Larsson
for their contributions, with inversions and shell shape respectively. KJ was funded
by the Swedish research council Vetenskapsrådet, grant number 2017-03798. R.K.B.
and E.K. were funded by the European Research Council (ERC-2015-AdG-693030-BARRIERS).
R.K.B. was also funded by the Natural Environment Research Council and the Swedish
Research Council Vetenskapsrådet.
article_processing_charge: No
article_type: original
author:
- first_name: Eva L.
full_name: Koch, Eva L.
last_name: Koch
- first_name: Mark
full_name: Ravinet, Mark
last_name: Ravinet
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. Genetic architecture
of repeated phenotypic divergence in Littorina saxatilis evolution. Evolution.
2022;76(10):2332-2346. doi:10.1111/evo.14602
apa: Koch, E. L., Ravinet, M., Westram, A. M., Johannesson, K., & Butlin, R.
K. (2022). Genetic architecture of repeated phenotypic divergence in Littorina
saxatilis evolution. Evolution. Wiley. https://doi.org/10.1111/evo.14602
chicago: Koch, Eva L., Mark Ravinet, Anja M Westram, Kerstin Johannesson, and Roger
K. Butlin. “Genetic Architecture of Repeated Phenotypic Divergence in Littorina
Saxatilis Evolution.” Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14602.
ieee: E. L. Koch, M. Ravinet, A. M. Westram, K. Johannesson, and R. K. Butlin, “Genetic
architecture of repeated phenotypic divergence in Littorina saxatilis evolution,”
Evolution, vol. 76, no. 10. Wiley, pp. 2332–2346, 2022.
ista: Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. 2022. Genetic architecture
of repeated phenotypic divergence in Littorina saxatilis evolution. Evolution.
76(10), 2332–2346.
mla: Koch, Eva L., et al. “Genetic Architecture of Repeated Phenotypic Divergence
in Littorina Saxatilis Evolution.” Evolution, vol. 76, no. 10, Wiley, 2022,
pp. 2332–46, doi:10.1111/evo.14602.
short: E.L. Koch, M. Ravinet, A.M. Westram, K. Johannesson, R.K. Butlin, Evolution
76 (2022) 2332–2346.
date_created: 2023-01-16T09:54:15Z
date_published: 2022-10-01T00:00:00Z
date_updated: 2023-08-04T09:42:11Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/evo.14602
external_id:
isi:
- '000848449100001'
pmid:
- '35994296'
file:
- access_level: open_access
checksum: defd8a4bea61cf00a3c88d4a30e2728c
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T08:45:35Z
date_updated: 2023-01-30T08:45:35Z
file_id: '12439'
file_name: 2022_Evolution_Koch.pdf
file_size: 2990581
relation: main_file
success: 1
file_date_updated: 2023-01-30T08:45:35Z
has_accepted_license: '1'
intvolume: ' 76'
isi: 1
issue: '10'
keyword:
- General Agricultural and Biological Sciences
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 2332-2346
pmid: 1
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '13066'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis
evolution
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: 76
year: '2022'
...
---
_id: '12251'
abstract:
- lang: eng
text: Amyloid formation is linked to devastating neurodegenerative diseases, motivating
detailed studies of the mechanisms of amyloid formation. For Aβ, the peptide associated
with Alzheimer’s disease, the mechanism and rate of aggregation have been established
for a range of variants and conditions in vitro and
in bodily fluids. A key outstanding question is how the relative stabilities of
monomers, fibrils and intermediates affect each step in the fibril formation process.
By monitoring the kinetics of aggregation of Aβ42, in the presence of urea or
guanidinium hydrochloride (GuHCl), we here determine the rates of the underlying
microscopic steps and establish the importance of changes in relative stability
induced by the presence of denaturant for each individual step. Denaturants shift
the equilibrium towards the unfolded state of each species. We find that a non-ionic
denaturant, urea, reduces the overall aggregation rate, and that the effect on
nucleation is stronger than the effect on elongation. Urea reduces the rate of
secondary nucleation by decreasing the coverage of fibril surfaces and the rate
of nucleus formation. It also reduces the rate of primary nucleation, increasing
its reaction order. The ionic denaturant, GuHCl, accelerates the aggregation at
low denaturant concentrations and decelerates the aggregation at high denaturant
concentrations. Below approximately 0.25 M GuHCl, the screening of repulsive electrostatic
interactions between peptides by the charged denaturant dominates, leading to
an increased aggregation rate. At higher GuHCl concentrations, the electrostatic
repulsion is completely screened, and the denaturing effect dominates. The results
illustrate how the differential effects of denaturants on stability of monomer,
oligomer and fibril translate to differential effects on microscopic steps, with
the rate of nucleation being most strongly reduced.
acknowledgement: This work was supported by grants from the Swedish Research Council
(grant no. 2015-00143) and the European Research Council (grant no. 340890).
article_number: '943355'
article_processing_charge: No
article_type: original
author:
- first_name: Tanja
full_name: Weiffert, Tanja
last_name: Weiffert
- first_name: Georg
full_name: Meisl, Georg
last_name: Meisl
- first_name: Samo
full_name: Curk, Samo
last_name: Curk
- first_name: Risto
full_name: Cukalevski, Risto
last_name: Cukalevski
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
- first_name: Sara
full_name: Linse, Sara
last_name: Linse
citation:
ama: Weiffert T, Meisl G, Curk S, et al. Influence of denaturants on amyloid β42
aggregation kinetics. Frontiers in Neuroscience. 2022;16. doi:10.3389/fnins.2022.943355
apa: Weiffert, T., Meisl, G., Curk, S., Cukalevski, R., Šarić, A., Knowles, T. P.
J., & Linse, S. (2022). Influence of denaturants on amyloid β42 aggregation
kinetics. Frontiers in Neuroscience. Frontiers Media. https://doi.org/10.3389/fnins.2022.943355
chicago: Weiffert, Tanja, Georg Meisl, Samo Curk, Risto Cukalevski, Anđela Šarić,
Tuomas P. J. Knowles, and Sara Linse. “Influence of Denaturants on Amyloid Β42
Aggregation Kinetics.” Frontiers in Neuroscience. Frontiers Media, 2022.
https://doi.org/10.3389/fnins.2022.943355.
ieee: T. Weiffert et al., “Influence of denaturants on amyloid β42 aggregation
kinetics,” Frontiers in Neuroscience, vol. 16. Frontiers Media, 2022.
ista: Weiffert T, Meisl G, Curk S, Cukalevski R, Šarić A, Knowles TPJ, Linse S.
2022. Influence of denaturants on amyloid β42 aggregation kinetics. Frontiers
in Neuroscience. 16, 943355.
mla: Weiffert, Tanja, et al. “Influence of Denaturants on Amyloid Β42 Aggregation
Kinetics.” Frontiers in Neuroscience, vol. 16, 943355, Frontiers Media,
2022, doi:10.3389/fnins.2022.943355.
short: T. Weiffert, G. Meisl, S. Curk, R. Cukalevski, A. Šarić, T.P.J. Knowles,
S. Linse, Frontiers in Neuroscience 16 (2022).
date_created: 2023-01-16T09:56:43Z
date_published: 2022-09-20T00:00:00Z
date_updated: 2023-08-04T09:48:56Z
day: '20'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.3389/fnins.2022.943355
external_id:
isi:
- '000866287100001'
file:
- access_level: open_access
checksum: e67d16113ffb4fb4fa38a183d169f210
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T09:15:13Z
date_updated: 2023-01-30T09:15:13Z
file_id: '12442'
file_name: 2022_FrontiersNeuroscience_Weiffert2.pdf
file_size: 19798610
relation: main_file
success: 1
file_date_updated: 2023-01-30T09:15:13Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
keyword:
- General Neuroscience
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Frontiers in Neuroscience
publication_identifier:
issn:
- 1662-453X
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
scopus_import: '1'
status: public
title: Influence of denaturants on amyloid β42 aggregation kinetics
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: 16
year: '2022'
...
---
_id: '12252'
abstract:
- lang: eng
text: The COVID−19 pandemic not only resulted in a global crisis, but also accelerated
vaccine development and antibody discovery. Herein we report a synthetic humanized
VHH library development pipeline for nanomolar-range affinity VHH binders to SARS-CoV-2
variants of concern (VoC) receptor binding domains (RBD) isolation. Trinucleotide-based
randomization of CDRs by Kunkel mutagenesis with the subsequent rolling-cycle
amplification resulted in more than 1011 diverse phage display
library in a manageable for a single person number of electroporation reactions.
We identified a number of nanomolar-range affinity VHH binders to SARS-CoV-2 variants
of concern (VoC) receptor binding domains (RBD) by screening a novel synthetic
humanized antibody library. In order to explore the most robust and fast method
for affinity improvement, we performed affinity maturation by CDR1 and CDR2 shuffling
and avidity engineering by multivalent trimeric VHH fusion protein construction.
As a result, H7-Fc and G12x3-Fc binders were developed with the affinities in
nM and pM range respectively. Importantly, these affinities are weakly influenced
by most of SARS-CoV-2 VoC mutations and they retain moderate binding to BA.4\5.
The plaque reduction neutralization test (PRNT) resulted in IC50 = 100 ng\ml and
9.6 ng\ml for H7-Fc and G12x3-Fc antibodies, respectively, for the emerging Omicron
BA.1 variant. Therefore, these VHH could expand the present landscape of SARS-CoV-2
neutralization binders with the therapeutic potential for present and future SARS-CoV-2
variants.
acknowledgement: The authors declare that this study received funding from Immunofusion.
The funder was not involved in the study design, collection, analysis, interpretation
of data, the writing of this article or the decision to submit it for publication.
article_number: '965446'
article_processing_charge: No
article_type: original
author:
- first_name: Dmitri
full_name: Dormeshkin, Dmitri
last_name: Dormeshkin
- first_name: Michail
full_name: Shapira, Michail
last_name: Shapira
- first_name: Simon
full_name: Dubovik, Simon
last_name: Dubovik
- first_name: Anton
full_name: Kavaleuski, Anton
id: 4968f7ad-eb97-11eb-a6c2-8ed382e8912c
last_name: Kavaleuski
orcid: 0000-0003-2091-526X
- first_name: Mikalai
full_name: Katsin, Mikalai
last_name: Katsin
- first_name: Alexandr
full_name: Migas, Alexandr
last_name: Migas
- first_name: Alexander
full_name: Meleshko, Alexander
last_name: Meleshko
- first_name: Sergei
full_name: Semyonov, Sergei
last_name: Semyonov
citation:
ama: Dormeshkin D, Shapira M, Dubovik S, et al. Isolation of an escape-resistant
SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library. Frontiers
in Immunology. 2022;13. doi:10.3389/fimmu.2022.965446
apa: Dormeshkin, D., Shapira, M., Dubovik, S., Kavaleuski, A., Katsin, M., Migas,
A., … Semyonov, S. (2022). Isolation of an escape-resistant SARS-CoV-2 neutralizing
nanobody from a novel synthetic nanobody library. Frontiers in Immunology.
Frontiers Media. https://doi.org/10.3389/fimmu.2022.965446
chicago: Dormeshkin, Dmitri, Michail Shapira, Simon Dubovik, Anton Kavaleuski, Mikalai
Katsin, Alexandr Migas, Alexander Meleshko, and Sergei Semyonov. “Isolation of
an Escape-Resistant SARS-CoV-2 Neutralizing Nanobody from a Novel Synthetic Nanobody
Library.” Frontiers in Immunology. Frontiers Media, 2022. https://doi.org/10.3389/fimmu.2022.965446.
ieee: D. Dormeshkin et al., “Isolation of an escape-resistant SARS-CoV-2
neutralizing nanobody from a novel synthetic nanobody library,” Frontiers in
Immunology, vol. 13. Frontiers Media, 2022.
ista: Dormeshkin D, Shapira M, Dubovik S, Kavaleuski A, Katsin M, Migas A, Meleshko
A, Semyonov S. 2022. Isolation of an escape-resistant SARS-CoV-2 neutralizing
nanobody from a novel synthetic nanobody library. Frontiers in Immunology. 13,
965446.
mla: Dormeshkin, Dmitri, et al. “Isolation of an Escape-Resistant SARS-CoV-2 Neutralizing
Nanobody from a Novel Synthetic Nanobody Library.” Frontiers in Immunology,
vol. 13, 965446, Frontiers Media, 2022, doi:10.3389/fimmu.2022.965446.
short: D. Dormeshkin, M. Shapira, S. Dubovik, A. Kavaleuski, M. Katsin, A. Migas,
A. Meleshko, S. Semyonov, Frontiers in Immunology 13 (2022).
date_created: 2023-01-16T09:56:57Z
date_published: 2022-09-16T00:00:00Z
date_updated: 2025-06-11T13:42:26Z
day: '16'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.3389/fimmu.2022.965446
external_id:
isi:
- '000862479100001'
pmid:
- '36189235'
file:
- access_level: open_access
checksum: f8f5d8110710033d0532e7e08bf9dad4
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T09:22:26Z
date_updated: 2023-01-30T09:22:26Z
file_id: '12443'
file_name: 2022_FrontiersImmunology_Dormeshkin.pdf
file_size: 5695892
relation: main_file
success: 1
file_date_updated: 2023-01-30T09:22:26Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
keyword:
- Immunology
- Immunology and Allergy
- COVID-19
- SARS-CoV-2
- synthetic library
- RBD
- neutralization nanobody
- VHH
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Immunology
publication_identifier:
issn:
- 1664-3224
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
scopus_import: '1'
status: public
title: Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel
synthetic nanobody library
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2022'
...
---
_id: '12253'
abstract:
- lang: eng
text: The sculpting of germ layers during gastrulation relies on the coordinated
migration of progenitor cells, yet the cues controlling these long-range directed
movements remain largely unknown. While directional migration often relies on
a chemokine gradient generated from a localized source, we find that zebrafish
ventrolateral mesoderm is guided by a self-generated gradient of the initially
uniformly expressed and secreted protein Toddler/ELABELA/Apela. We show that the
Apelin receptor, which is specifically expressed in mesodermal cells, has a dual
role during gastrulation, acting as a scavenger receptor to generate a Toddler
gradient, and as a chemokine receptor to sense this guidance cue. Thus, we uncover
a single receptor–based self-generated gradient as the enigmatic guidance cue
that can robustly steer the directional migration of mesoderm through the complex
and continuously changing environment of the gastrulating embryo.
acknowledgement: 'We thank K. Aumayer and the team of the biooptics facility at the
Vienna Biocenter, particularly P. Pasierbek and T. Müller, for support with microscopy;
K. Panser, C. Pribitzer, and the animal facility personnel for taking care of zebrafish;
M. Binner and A. Bandura for help with genotyping; M. Codina Tobias for help with
establishing the conditions for the Toddler overexpression compensation experiment;
T. Lubiana Alves for sharing the code for scRNA-Seq analyses; the Heisenberg laboratory,
particularly D. Pinheiro, for joint laboratory meetings, discussions on the project,
and providing the tg(gsc:CAAX-GFP) fish line; the Raz laboratory for providing the
Lifeact-GFP plasmid; A. Andersen, A. Schier, C.-P. Heisenberg, and E. Tanaka for
comments on the manuscript; and the entire Pauli laboratory, particularly K. Gert
and V. Deneke, for valuable discussions and feedback on the manuscript. Funding:
Work in A.P.’s laboratory has been supported by the IMP, which receives institutional
funding from Boehringer Ingelheim and the Austrian Research Promotion Agency (Headquarter
grant FFG-852936), as well as the FWF START program (Y 1031-B28 to A.P.), the Human
Frontier Science Program (HFSP) Career Development Award (CDA00066/2015 to A.P.)
and Young Investigator Grant (RGY0079/2020 to A.P.), the SFB RNA-Deco (project number
F 80 to A.P.), a Whitman Center Fellowship from the Marine Biological Laboratory
(to A.P.), and EMBO-YIP funds (to A.P.). This work was supported by the European
Union (European Research Council Starting Grant 851288 to E.H.). For the purpose
of Open Access, the authors have applied a CC BY public copyright license to any
Author Accepted Manuscript (AAM) version arising from this submission.'
article_number: eadd2488
article_processing_charge: No
article_type: original
author:
- first_name: Jessica
full_name: Stock, Jessica
last_name: Stock
- first_name: Tomas
full_name: Kazmar, Tomas
last_name: Kazmar
- first_name: Friederike
full_name: Schlumm, Friederike
last_name: Schlumm
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Andrea
full_name: Pauli, Andrea
last_name: Pauli
citation:
ama: Stock J, Kazmar T, Schlumm F, Hannezo EB, Pauli A. A self-generated Toddler
gradient guides mesodermal cell migration. Science Advances. 2022;8(37).
doi:10.1126/sciadv.add2488
apa: Stock, J., Kazmar, T., Schlumm, F., Hannezo, E. B., & Pauli, A. (2022).
A self-generated Toddler gradient guides mesodermal cell migration. Science
Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.add2488
chicago: Stock, Jessica, Tomas Kazmar, Friederike Schlumm, Edouard B Hannezo, and
Andrea Pauli. “A Self-Generated Toddler Gradient Guides Mesodermal Cell Migration.”
Science Advances. American Association for the Advancement of Science,
2022. https://doi.org/10.1126/sciadv.add2488.
ieee: J. Stock, T. Kazmar, F. Schlumm, E. B. Hannezo, and A. Pauli, “A self-generated
Toddler gradient guides mesodermal cell migration,” Science Advances, vol.
8, no. 37. American Association for the Advancement of Science, 2022.
ista: Stock J, Kazmar T, Schlumm F, Hannezo EB, Pauli A. 2022. A self-generated
Toddler gradient guides mesodermal cell migration. Science Advances. 8(37), eadd2488.
mla: Stock, Jessica, et al. “A Self-Generated Toddler Gradient Guides Mesodermal
Cell Migration.” Science Advances, vol. 8, no. 37, eadd2488, American Association
for the Advancement of Science, 2022, doi:10.1126/sciadv.add2488.
short: J. Stock, T. Kazmar, F. Schlumm, E.B. Hannezo, A. Pauli, Science Advances
8 (2022).
date_created: 2023-01-16T09:57:10Z
date_published: 2022-09-14T00:00:00Z
date_updated: 2025-04-14T07:52:27Z
day: '14'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1126/sciadv.add2488
ec_funded: 1
external_id:
isi:
- '000888875000009'
pmid:
- '36103529'
file:
- access_level: open_access
checksum: f59cdb824e5d4221045def81f46f6c65
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T09:27:49Z
date_updated: 2023-01-30T09:27:49Z
file_id: '12444'
file_name: 2022_ScienceAdvances_Stock.pdf
file_size: 1636732
relation: main_file
success: 1
file_date_updated: 2023-01-30T09:27:49Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '37'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: A self-generated Toddler gradient guides mesodermal cell migration
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 8
year: '2022'
...
---
_id: '12259'
abstract:
- lang: eng
text: 'Theoretical foundations of chaos have been predominantly laid out for finite-dimensional
dynamical systems, such as the three-body problem in classical mechanics and the
Lorenz model in dissipative systems. In contrast, many real-world chaotic phenomena,
e.g., weather, arise in systems with many (formally infinite) degrees of freedom,
which limits direct quantitative analysis of such systems using chaos theory.
In the present work, we demonstrate that the hydrodynamic pilot-wave systems offer
a bridge between low- and high-dimensional chaotic phenomena by allowing for a
systematic study of how the former connects to the latter. Specifically, we present
experimental results, which show the formation of low-dimensional chaotic attractors
upon destabilization of regular dynamics and a final transition to high-dimensional
chaos via the merging of distinct chaotic regions through a crisis bifurcation.
Moreover, we show that the post-crisis dynamics of the system can be rationalized
as consecutive scatterings from the nonattracting chaotic sets with lifetimes
following exponential distributions. '
acknowledgement: 'This work was partially funded by the Institute of Science and Technology
Austria Interdisciplinary Project Committee Grant “Pilot-Wave Hydrodynamics: Chaos
and Quantum Analogies.”'
article_number: '093138'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: George H
full_name: Choueiri, George H
id: 448BD5BC-F248-11E8-B48F-1D18A9856A87
last_name: Choueiri
- first_name: Balachandra
full_name: Suri, Balachandra
id: 47A5E706-F248-11E8-B48F-1D18A9856A87
last_name: Suri
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
citation:
ama: 'Choueiri GH, Suri B, Merrin J, Serbyn M, Hof B, Budanur NB. Crises and chaotic
scattering in hydrodynamic pilot-wave experiments. Chaos: An Interdisciplinary
Journal of Nonlinear Science. 2022;32(9). doi:10.1063/5.0102904'
apa: 'Choueiri, G. H., Suri, B., Merrin, J., Serbyn, M., Hof, B., & Budanur,
N. B. (2022). Crises and chaotic scattering in hydrodynamic pilot-wave experiments.
Chaos: An Interdisciplinary Journal of Nonlinear Science. AIP Publishing.
https://doi.org/10.1063/5.0102904'
chicago: 'Choueiri, George H, Balachandra Suri, Jack Merrin, Maksym Serbyn, Björn
Hof, and Nazmi B Budanur. “Crises and Chaotic Scattering in Hydrodynamic Pilot-Wave
Experiments.” Chaos: An Interdisciplinary Journal of Nonlinear Science.
AIP Publishing, 2022. https://doi.org/10.1063/5.0102904.'
ieee: 'G. H. Choueiri, B. Suri, J. Merrin, M. Serbyn, B. Hof, and N. B. Budanur,
“Crises and chaotic scattering in hydrodynamic pilot-wave experiments,” Chaos:
An Interdisciplinary Journal of Nonlinear Science, vol. 32, no. 9. AIP Publishing,
2022.'
ista: 'Choueiri GH, Suri B, Merrin J, Serbyn M, Hof B, Budanur NB. 2022. Crises
and chaotic scattering in hydrodynamic pilot-wave experiments. Chaos: An Interdisciplinary
Journal of Nonlinear Science. 32(9), 093138.'
mla: 'Choueiri, George H., et al. “Crises and Chaotic Scattering in Hydrodynamic
Pilot-Wave Experiments.” Chaos: An Interdisciplinary Journal of Nonlinear Science,
vol. 32, no. 9, 093138, AIP Publishing, 2022, doi:10.1063/5.0102904.'
short: 'G.H. Choueiri, B. Suri, J. Merrin, M. Serbyn, B. Hof, N.B. Budanur, Chaos:
An Interdisciplinary Journal of Nonlinear Science 32 (2022).'
date_created: 2023-01-16T09:58:16Z
date_published: 2022-09-26T00:00:00Z
date_updated: 2025-06-11T13:41:34Z
day: '26'
ddc:
- '530'
department:
- _id: MaSe
- _id: BjHo
- _id: NanoFab
doi: 10.1063/5.0102904
external_id:
arxiv:
- '2206.01531'
isi:
- '000861009600005'
pmid:
- '36182399'
file:
- access_level: open_access
checksum: 17881eff8b21969359a2dd64620120ba
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T09:41:12Z
date_updated: 2023-01-30T09:41:12Z
file_id: '12445'
file_name: 2022_Chaos_Choueiri.pdf
file_size: 3209644
relation: main_file
success: 1
file_date_updated: 2023-01-30T09:41:12Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
issue: '9'
keyword:
- Applied Mathematics
- General Physics and Astronomy
- Mathematical Physics
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: 'Chaos: An Interdisciplinary Journal of Nonlinear Science'
publication_identifier:
eissn:
- 1089-7682
issn:
- 1054-1500
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Crises and chaotic scattering in hydrodynamic pilot-wave experiments
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: 32
year: '2022'
...
---
_id: '12261'
abstract:
- lang: eng
text: 'Dose–response relationships are a general concept for quantitatively describing
biological systems across multiple scales, from the molecular to the whole-cell
level. A clinically relevant example is the bacterial growth response to antibiotics,
which is routinely characterized by dose–response curves. The shape of the dose–response
curve varies drastically between antibiotics and plays a key role in treatment,
drug interactions, and resistance evolution. However, the mechanisms shaping the
dose–response curve remain largely unclear. Here, we show in Escherichia coli
that the distinctively shallow dose–response curve of the antibiotic trimethoprim
is caused by a negative growth-mediated feedback loop: Trimethoprim slows growth,
which in turn weakens the effect of this antibiotic. At the molecular level, this
feedback is caused by the upregulation of the drug target dihydrofolate reductase
(FolA/DHFR). We show that this upregulation is not a specific response to trimethoprim
but follows a universal trend line that depends primarily on the growth rate,
irrespective of its cause. Rewiring the feedback loop alters the dose–response
curve in a predictable manner, which we corroborate using a mathematical model
of cellular resource allocation and growth. Our results indicate that growth-mediated
feedback loops may shape drug responses more generally and could be exploited
to design evolutionary traps that enable selection against drug resistance.'
acknowledged_ssus:
- _id: M-Shop
acknowledgement: This work was in part supported by Human Frontier Science Program
GrantRGP0042/2013, Marie Curie Career Integration Grant303507, AustrianScience Fund
(FWF) Grant P27201-B22, and German Research Foundation(DFG) Collaborative Research
Center (SFB)1310to TB. SAA was supportedby the European Union’s Horizon2020Research
and Innovation Programunder the Marie Skłodowska-Curie Grant agreement No707352.
We wouldlike to thank the Bollenbach group for regular fruitful discussions. We
areparticularly thankful for the technical assistance of Booshini Fernando andfor
discussions of the theoretical aspects with Gerrit Ansmann. We areindebted to Bor
Kavˇciˇc for invaluable advice, help with setting up theluciferase-based growth
monitoring system, and for sharing plasmids. Weacknowledge the IST Austria Miba
Machine Shop for their support inbuilding a housing for the stacker of the plate
reader, which enabled thehigh-throughput luciferase-based experiments. We are grateful
to RosalindAllen, Bor Kavˇciˇc and Dor Russ for feedback on the manuscript. Open
Accessfunding enabled and organized by Projekt DEAL.
article_number: e10490
article_processing_charge: No
article_type: original
author:
- first_name: Andreas
full_name: Angermayr, Andreas
id: 4677C796-F248-11E8-B48F-1D18A9856A87
last_name: Angermayr
orcid: 0000-0001-8619-2223
- first_name: Tin Yau
full_name: Pang, Tin Yau
last_name: Pang
- first_name: Guillaume
full_name: Chevereau, Guillaume
last_name: Chevereau
- first_name: Karin
full_name: Mitosch, Karin
id: 39B66846-F248-11E8-B48F-1D18A9856A87
last_name: Mitosch
- first_name: Martin J
full_name: Lercher, Martin J
last_name: Lercher
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. Growth‐mediated
negative feedback shapes quantitative antibiotic response. Molecular Systems
Biology. 2022;18(9). doi:10.15252/msb.202110490
apa: Angermayr, A., Pang, T. Y., Chevereau, G., Mitosch, K., Lercher, M. J., &
Bollenbach, M. T. (2022). Growth‐mediated negative feedback shapes quantitative
antibiotic response. Molecular Systems Biology. Embo Press. https://doi.org/10.15252/msb.202110490
chicago: Angermayr, Andreas, Tin Yau Pang, Guillaume Chevereau, Karin Mitosch, Martin
J Lercher, and Mark Tobias Bollenbach. “Growth‐mediated Negative Feedback Shapes
Quantitative Antibiotic Response.” Molecular Systems Biology. Embo Press,
2022. https://doi.org/10.15252/msb.202110490.
ieee: A. Angermayr, T. Y. Pang, G. Chevereau, K. Mitosch, M. J. Lercher, and M.
T. Bollenbach, “Growth‐mediated negative feedback shapes quantitative antibiotic
response,” Molecular Systems Biology, vol. 18, no. 9. Embo Press, 2022.
ista: Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. 2022.
Growth‐mediated negative feedback shapes quantitative antibiotic response. Molecular
Systems Biology. 18(9), e10490.
mla: Angermayr, Andreas, et al. “Growth‐mediated Negative Feedback Shapes Quantitative
Antibiotic Response.” Molecular Systems Biology, vol. 18, no. 9, e10490,
Embo Press, 2022, doi:10.15252/msb.202110490.
short: A. Angermayr, T.Y. Pang, G. Chevereau, K. Mitosch, M.J. Lercher, M.T. Bollenbach,
Molecular Systems Biology 18 (2022).
date_created: 2023-01-16T09:58:34Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2025-06-11T14:10:18Z
day: '01'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.15252/msb.202110490
external_id:
isi:
- '000856482800001'
pmid:
- '36124745'
file:
- access_level: open_access
checksum: 8b1d8f5ea20c8408acf466435fb6ae01
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T09:49:55Z
date_updated: 2023-01-30T09:49:55Z
file_id: '12446'
file_name: 2022_MolecularSystemsBio_Angermayr.pdf
file_size: 1098812
relation: main_file
success: 1
file_date_updated: 2023-01-30T09:49:55Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '9'
keyword:
- Applied Mathematics
- Computational Theory and Mathematics
- General Agricultural and Biological Sciences
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- Information Systems
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Molecular Systems Biology
publication_identifier:
eissn:
- 1744-4292
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Growth‐mediated negative feedback shapes quantitative antibiotic response
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: 18
year: '2022'
...
---
_id: '12262'
abstract:
- lang: eng
text: The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that
initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases
the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear
export, a strict requirement for downstream maturation. The molecular mechanism
of release remained elusive. Here, we report a series of cryo-EM structures that
captured the extraction of Rlp24 from pre-60S particles by Saccharomyces cerevisiae
Drg1. These structures reveal that Arx1 and the eukaryote-specific rRNA expansion
segment ES27 form a joint docking platform that positions Drg1 for efficient extraction
of Rlp24 from the pre-ribosome. The tips of the Drg1 N domains thereby guide the
Rlp24 C terminus into the central pore of the Drg1 hexamer, enabling extraction
by a hand-over-hand translocation mechanism. Our results uncover substrate recognition
and processing by Drg1 step by step and provide a comprehensive mechanistic picture
of the conserved modus operandi of AAA-ATPases.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: "We thank M. Fromont-Racine, A. Johnson, J. Woolford, S. Rospert,
J. P. G. Ballesta and\r\nE. Hurt for supplying antibodies. The work was supported
by Boehringer Ingelheim (to\r\nD. H.), the Austrian Science Foundation FWF (grants
32536 and 32977 to H. B.), the\r\nUK Medical Research Council (MR/T012412/1 to A.
J. W.) and the German Research\r\nFoundation (Emmy Noether Programme STE 2517/1-1
and STE 2517/5-1 to F.S.). We\r\nthank Norberto Escudero-Urquijo, Pablo Castro-Hartmann
and K. Dent, Cambridge\r\nInstitute for Medical Research, for their help in cryo-EM
during early phases of this\r\nproject. This research was supported by the Scientific
Service Units of IST Austria through\r\nresources provided by the Electron Microscopy
Facility. We thank S. Keller, Institute of\r\nMolecular Biosciences (Biophysics),
University Graz for support with the quantification of\r\nthe SPR particle release
assay. We thank I. Schaffner, University of Natural Resources and\r\nLife Sciences,
Vienna for her help in early stages of the SPR experiments."
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Prattes, Michael
last_name: Prattes
- first_name: Irina
full_name: Grishkovskaya, Irina
last_name: Grishkovskaya
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: Christina
full_name: Hetzmannseder, Christina
last_name: Hetzmannseder
- first_name: Gertrude
full_name: Zisser, Gertrude
last_name: Zisser
- first_name: Carolin
full_name: Sailer, Carolin
last_name: Sailer
- first_name: Vasileios
full_name: Kargas, Vasileios
last_name: Kargas
- first_name: Mathias
full_name: Loibl, Mathias
last_name: Loibl
- first_name: Magdalena
full_name: Gerhalter, Magdalena
last_name: Gerhalter
- first_name: Lisa
full_name: Kofler, Lisa
last_name: Kofler
- first_name: Alan J.
full_name: Warren, Alan J.
last_name: Warren
- first_name: Florian
full_name: Stengel, Florian
last_name: Stengel
- first_name: David
full_name: Haselbach, David
last_name: Haselbach
- first_name: Helmut
full_name: Bergler, Helmut
last_name: Bergler
citation:
ama: Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Visualizing maturation factor
extraction from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural
& Molecular Biology. 2022;29(9):942-953. doi:10.1038/s41594-022-00832-5
apa: Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Hetzmannseder, C., Zisser,
G., Sailer, C., … Bergler, H. (2022). Visualizing maturation factor extraction
from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural & Molecular
Biology. Springer Nature. https://doi.org/10.1038/s41594-022-00832-5
chicago: Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Christina
Hetzmannseder, Gertrude Zisser, Carolin Sailer, Vasileios Kargas, et al. “Visualizing
Maturation Factor Extraction from the Nascent Ribosome by the AAA-ATPase Drg1.”
Nature Structural & Molecular Biology. Springer Nature, 2022. https://doi.org/10.1038/s41594-022-00832-5.
ieee: M. Prattes et al., “Visualizing maturation factor extraction from the
nascent ribosome by the AAA-ATPase Drg1,” Nature Structural & Molecular
Biology, vol. 29, no. 9. Springer Nature, pp. 942–953, 2022.
ista: Prattes M, Grishkovskaya I, Hodirnau V-V, Hetzmannseder C, Zisser G, Sailer
C, Kargas V, Loibl M, Gerhalter M, Kofler L, Warren AJ, Stengel F, Haselbach D,
Bergler H. 2022. Visualizing maturation factor extraction from the nascent ribosome
by the AAA-ATPase Drg1. Nature Structural & Molecular Biology. 29(9), 942–953.
mla: Prattes, Michael, et al. “Visualizing Maturation Factor Extraction from the
Nascent Ribosome by the AAA-ATPase Drg1.” Nature Structural & Molecular
Biology, vol. 29, no. 9, Springer Nature, 2022, pp. 942–53, doi:10.1038/s41594-022-00832-5.
short: M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, C. Hetzmannseder, G. Zisser,
C. Sailer, V. Kargas, M. Loibl, M. Gerhalter, L. Kofler, A.J. Warren, F. Stengel,
D. Haselbach, H. Bergler, Nature Structural & Molecular Biology 29 (2022)
942–953.
date_created: 2023-01-16T09:59:06Z
date_published: 2022-09-12T00:00:00Z
date_updated: 2023-08-04T09:52:20Z
day: '12'
ddc:
- '570'
department:
- _id: EM-Fac
doi: 10.1038/s41594-022-00832-5
external_id:
isi:
- '000852942100004'
pmid:
- '36097293'
file:
- access_level: open_access
checksum: 2d5c3ec01718fefd7553052b0b8a0793
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T10:00:04Z
date_updated: 2023-01-30T10:00:04Z
file_id: '12447'
file_name: 2022_NatureStrucMolecBio_Prattes.pdf
file_size: 9935057
relation: main_file
success: 1
file_date_updated: 2023-01-30T10:00:04Z
has_accepted_license: '1'
intvolume: ' 29'
isi: 1
issue: '9'
keyword:
- Molecular Biology
- Structural Biology
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 942-953
pmid: 1
publication: Nature Structural & Molecular Biology
publication_identifier:
eissn:
- 1545-9985
issn:
- 1545-9993
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase
Drg1
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: 29
year: '2022'
...