---
_id: '15116'
abstract:
- lang: eng
text: Water is known to play an important role in collagen self-assembly, but it
is still largely unclear how water–collagen interactions influence the assembly
process and determine the fibril network properties. Here, we use the H2O/D2O
isotope effect on the hydrogen-bond strength in water to investigate the role
of hydration in collagen self-assembly. We dissolve collagen in H2O and D2O and
compare the growth kinetics and the structure of the collagen assemblies formed
in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster
in D2O than in H2O, and collagen in D2O self-assembles into much thinner fibrils,
that form a more inhomogeneous and softer network, with a fourfold reduction in
elastic modulus when compared to H2O. Combining spectroscopic measurements with
atomistic simulations, we show that collagen in D2O is less hydrated than in H2O.
This partial dehydration lowers the enthalpic penalty for water removal and reorganization
at the collagen–water interface, increasing the self-assembly rate and the number
of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained
simulations show that the acceleration in the initial nucleation rate can be reproduced
by the enhancement of electrostatic interactions. These results show that water
acts as a mediator between collagen monomers, by modulating their interactions
so as to optimize the assembly process and, thus, the final network properties.
We believe that isotopically modulating the hydration of proteins can be a valuable
method to investigate the role of water in protein structural dynamics and protein
self-assembly.
acknowledgement: We thank Dr. Steven Roeters (Aarhus University), Dr. Federica Burla,
and Prof. Dr. Mischa Bonn (Institute for Polymer Research, Mainz, Germany) for the
useful discussions. We thank Dr. Wim Roeterdink and Michiel Hilberts for technical
support. G.H.K. acknowledges financial support by the “BaSyC Building a Synthetic
Cell” Gravitation grant (024.003.019) of The Netherlands Ministry of Education,
Culture and Science (OCW) and The Netherlands Organization for Scientific Research
and from NWO grant OCENW.GROOT.2019.022. This work has received support from the
National Research Foundation of Korea (NRF), funded by the Ministry of Science and
ICT, under Grant No. 2022K1A3A1A04062969. This publication is part of the project
(with Project Number VI.Veni.212.240) of the research programme NWO Talent Programme
Veni 2021, which is financed by the Dutch Research Council (NWO). I.M.I. acknowledges
support from the Sectorplan Bèta & Techniek of the Dutch Government and the Dementia
Research - Synapsis Foundation Switzerland. A.Š. and K.K. acknowledge support from
Royal Society and European Research Council Starting Grant. G. Giubertoni kindly
thanks to the Care4Bones community and the Collagen Café community for reminding
that we do not own the knowledge we create, but it is, rather, a collective resource
intended for the advancement of human progress.
article_number: e2313162121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Giulia
full_name: Giubertoni, Giulia
last_name: Giubertoni
- first_name: Liru
full_name: Feng, Liru
last_name: Feng
- first_name: Kevin
full_name: Klein, Kevin
last_name: Klein
- first_name: Guido
full_name: Giannetti, Guido
last_name: Giannetti
- first_name: Luco
full_name: Rutten, Luco
last_name: Rutten
- first_name: Yeji
full_name: Choi, Yeji
last_name: Choi
- first_name: Anouk
full_name: Van Der Net, Anouk
last_name: Van Der Net
- first_name: Gerard
full_name: Castro-Linares, Gerard
last_name: Castro-Linares
- first_name: Federico
full_name: Caporaletti, Federico
last_name: Caporaletti
- first_name: Dimitra
full_name: Micha, Dimitra
last_name: Micha
- first_name: Johannes
full_name: Hunger, Johannes
last_name: Hunger
- first_name: Antoine
full_name: Deblais, Antoine
last_name: Deblais
- first_name: Daniel
full_name: Bonn, Daniel
last_name: Bonn
- first_name: Nico
full_name: Sommerdijk, Nico
last_name: Sommerdijk
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Ioana M.
full_name: Ilie, Ioana M.
last_name: Ilie
- first_name: Gijsje H.
full_name: Koenderink, Gijsje H.
last_name: Koenderink
- first_name: Sander
full_name: Woutersen, Sander
last_name: Woutersen
citation:
ama: Giubertoni G, Feng L, Klein K, et al. Elucidating the role of water in collagen
self-assembly by isotopically modulating collagen hydration. Proceedings of
the National Academy of Sciences of the United States of America. 2024;121(11).
doi:10.1073/pnas.2313162121
apa: Giubertoni, G., Feng, L., Klein, K., Giannetti, G., Rutten, L., Choi, Y., …
Woutersen, S. (2024). Elucidating the role of water in collagen self-assembly
by isotopically modulating collagen hydration. Proceedings of the National
Academy of Sciences of the United States of America. National Academy of Sciences.
https://doi.org/10.1073/pnas.2313162121
chicago: Giubertoni, Giulia, Liru Feng, Kevin Klein, Guido Giannetti, Luco Rutten,
Yeji Choi, Anouk Van Der Net, et al. “Elucidating the Role of Water in Collagen
Self-Assembly by Isotopically Modulating Collagen Hydration.” Proceedings of
the National Academy of Sciences of the United States of America. National
Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2313162121.
ieee: G. Giubertoni et al., “Elucidating the role of water in collagen self-assembly
by isotopically modulating collagen hydration,” Proceedings of the National
Academy of Sciences of the United States of America, vol. 121, no. 11. National
Academy of Sciences, 2024.
ista: Giubertoni G, Feng L, Klein K, Giannetti G, Rutten L, Choi Y, Van Der Net
A, Castro-Linares G, Caporaletti F, Micha D, Hunger J, Deblais A, Bonn D, Sommerdijk
N, Šarić A, Ilie IM, Koenderink GH, Woutersen S. 2024. Elucidating the role of
water in collagen self-assembly by isotopically modulating collagen hydration.
Proceedings of the National Academy of Sciences of the United States of America.
121(11), e2313162121.
mla: Giubertoni, Giulia, et al. “Elucidating the Role of Water in Collagen Self-Assembly
by Isotopically Modulating Collagen Hydration.” Proceedings of the National
Academy of Sciences of the United States of America, vol. 121, no. 11, e2313162121,
National Academy of Sciences, 2024, doi:10.1073/pnas.2313162121.
short: G. Giubertoni, L. Feng, K. Klein, G. Giannetti, L. Rutten, Y. Choi, A. Van
Der Net, G. Castro-Linares, F. Caporaletti, D. Micha, J. Hunger, A. Deblais, D.
Bonn, N. Sommerdijk, A. Šarić, I.M. Ilie, G.H. Koenderink, S. Woutersen, Proceedings
of the National Academy of Sciences of the United States of America 121 (2024).
das_tickbox: '1'
dataavailabilitystatement: Turbidity data; IR and 2D-IR data; TEM images; cryo-TEM
images; CRM images; coarse grained simulations; molecular dynamics simulation data
have been deposited in UvAauas.figshare 10.21942/uva.24829896
date_created: 2024-03-17T23:00:57Z
date_published: 2024-03-12T00:00:00Z
date_updated: 2026-09-24T10:42:11Z
day: '12'
ddc:
- '550'
department:
- _id: AnSa
doi: 10.1073/pnas.2313162121
external_id:
isi:
- '001206387400001'
pmid:
- '38451946'
file:
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checksum: a3f7fdc29dd9f0a38952ab4e322b3a05
content_type: application/pdf
creator: dernst
date_created: 2024-03-19T10:22:42Z
date_updated: 2024-03-19T10:22:42Z
file_id: '15125'
file_name: 2024_PNAS_Giubertoni.pdf
file_size: 12952586
relation: main_file
success: 1
file_date_updated: 2024-03-19T10:22:42Z
fulldoi: https://doi.org/10.1073/pnas.2313162121
has_accepted_license: '1'
intvolume: ' 121'
isi: 1
issue: '11'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
record:
- id: '15126'
relation: research_data
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: no
title: Elucidating the role of water in collagen self-assembly by isotopically modulating
collagen hydration
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 121
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18526'
abstract:
- lang: eng
text: Multivesicular endosomes (MVEs) sequester membrane proteins destined for degradation
within intralumenal vesicles (ILVs), a process mediated by the membrane-remodeling
action of Endosomal Sorting Complex Required for Transport (ESCRT) proteins. In
Arabidopsis, endosomal membrane constriction and scission are uncoupled, resulting
in the formation of extensive concatenated ILV networks and enhancing cargo sequestration
efficiency. Here, we used a combination of electron tomography, computer simulations,
and mathematical modeling to address the questions of when concatenated ILV networks
evolved in plants and what drives their formation. Through morphometric analyses
of tomographic reconstructions of endosomes across yeast, algae, and various land
plants, we have found that ILV concatenation is widespread within plant species,
but only prevalent in seed plants, especially in flowering plants. Multiple budding
sites that require the formation of pores in the limiting membrane were only identified
in hornworts and seed plants, suggesting that this mechanism has evolved independently
in both plant lineages. To identify the conditions under which these multiple
budding sites can arise, we used particle-based molecular dynamics simulations
and found that changes in ESCRT filament properties, such as filament curvature
and membrane binding energy, can generate the membrane shapes observed in multiple
budding sites. To understand the relationship between membrane budding activity
and ILV network topology, we performed computational simulations and identified
a set of membrane remodeling parameters that can recapitulate our tomographic
datasets.
acknowledgement: We would like to thank Janice Pennington for her support with electron
tomography data collection, Dr. Ingrid Jordon-Thaden, director of the Botany Garden
and Greenhouse of University of Wisconsin Madison, for her invaluable assistance
collecting plant materials, Dr. Marie Trest for providing Chara specimens, and Dr.
Nicholas Keuler for his advice on statistical analyses. We thank Charlie Hamilton
for exploring the initial computational model. This work was supported by grant
NSF MCB 2114603 and NIH 1S10OD026769-01 to M.S.O. F.F acknowledges support as a
NOMIS Fellow from the NOMIS Foundation. A.Š. acknowledges ERC Starting Grant “NEPA”
802960.
article_number: e2409407121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Ethan
full_name: Weiner, Ethan
last_name: Weiner
- first_name: Elizabeth
full_name: Berryman, Elizabeth
last_name: Berryman
- first_name: Felix F
full_name: Frey, Felix F
id: a0270b37-8f1a-11ec-95c7-8e710c59a4f3
last_name: Frey
orcid: 0000-0001-8501-6017
- first_name: Ariadna González
full_name: Solís, Ariadna González
last_name: Solís
- first_name: André
full_name: Leier, André
last_name: Leier
- first_name: Tatiana Marquez
full_name: Lago, Tatiana Marquez
last_name: Lago
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Marisa S.
full_name: Otegui, Marisa S.
last_name: Otegui
citation:
ama: Weiner E, Berryman E, Frey FF, et al. Endosomal membrane budding patterns in
plants. Proceedings of the National Academy of Sciences of the United States
of America. 2024;121(44). doi:10.1073/pnas.2409407121
apa: Weiner, E., Berryman, E., Frey, F. F., Solís, A. G., Leier, A., Lago, T. M.,
… Otegui, M. S. (2024). Endosomal membrane budding patterns in plants. Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences. https://doi.org/10.1073/pnas.2409407121
chicago: Weiner, Ethan, Elizabeth Berryman, Felix F Frey, Ariadna González Solís,
André Leier, Tatiana Marquez Lago, Anđela Šarić, and Marisa S. Otegui. “Endosomal
Membrane Budding Patterns in Plants.” Proceedings of the National Academy of
Sciences of the United States of America. National Academy of Sciences, 2024.
https://doi.org/10.1073/pnas.2409407121.
ieee: E. Weiner et al., “Endosomal membrane budding patterns in plants,”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 121, no. 44. National Academy of Sciences, 2024.
ista: Weiner E, Berryman E, Frey FF, Solís AG, Leier A, Lago TM, Šarić A, Otegui
MS. 2024. Endosomal membrane budding patterns in plants. Proceedings of the National
Academy of Sciences of the United States of America. 121(44), e2409407121.
mla: Weiner, Ethan, et al. “Endosomal Membrane Budding Patterns in Plants.” Proceedings
of the National Academy of Sciences of the United States of America, vol.
121, no. 44, e2409407121, National Academy of Sciences, 2024, doi:10.1073/pnas.2409407121.
short: E. Weiner, E. Berryman, F.F. Frey, A.G. Solís, A. Leier, T.M. Lago, A. Šarić,
M.S. Otegui, Proceedings of the National Academy of Sciences of the United States
of America 121 (2024).
das_tickbox: '1'
dataavailabilitystatement: Electron tomogram files are deposited in EMPIAR under EMPIAR-12299
(54). All other data are included in the manuscript and/or supporting information
date_created: 2024-11-10T23:01:59Z
date_published: 2024-10-29T00:00:00Z
date_updated: 2026-09-24T10:41:24Z
day: '29'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1073/pnas.2409407121
ec_funded: 1
external_id:
isi:
- '001349500800007'
pmid:
- '39441629'
file:
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checksum: 21c82d2ab58ff99b2bd0489797be42e5
content_type: application/pdf
creator: dernst
date_created: 2024-11-11T09:35:15Z
date_updated: 2024-11-11T09:35:15Z
file_id: '18538'
file_name: 2024_PNAS_Weiner.pdf
file_size: 5268074
relation: main_file
success: 1
file_date_updated: 2024-11-11T09:35:15Z
fulldoi: https://doi.org/10.1073/pnas.2409407121
has_accepted_license: '1'
intvolume: ' 121'
isi: 1
issue: '44'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Endosomal membrane budding patterns in plants
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 121
year: '2024'
...
---
APC_amount: 1530 EUR
OA_place: publisher
OA_type: gold
_id: '15401'
abstract:
- lang: eng
text: Amide-proton-detected magic-angle-spinning NMR of deuterated proteins has
become a main technique in NMR-based structural biology. In standard deuteration
protocols that rely on D2O-based culture media, non-exchangeable amide sites remain
deuterated, making these sites unobservable. Here we demonstrate that proteins
produced with a H2O-based culture medium doped with deuterated cell lysate allow
scientists to overcome this “reprotonation bottleneck” while retaining a high
level of deuteration (ca. 80 %) and narrow linewidths. We quantified coherence
lifetimes of several proteins prepared with this labeling pattern over a range
of magic-angle-spinning (MAS) frequencies (40–100 kHz). We demonstrate that under
commonly used conditions (50–60 kHz MAS), the amide 1H linewidths with our labeling
approach are comparable to those of perdeuterated proteins and better than those
of protonated samples at 100 kHz. For three proteins in the 33–50 kDa size range,
many previously unobserved amides become visible. We report how to prepare the
deuterated cell lysate for our approach from fractions of perdeuterated cultures
which are usually discarded, and we show that such media can be used identically
to commercial media. The residual protonation of Hα sites allows for well-resolved
Hα-detected spectra and Hα resonance assignment, exemplified by the de novo assignment
of 168 Hα sites in a 39 kDa protein. The approach based on this H2O/cell-lysate
deuteration and MAS frequencies compatible with 1.3 or 1.9 mm rotors presents
a strong sensitivity benefit over 0.7 mm 100 kHz MAS experiments.
acknowledged_ssus:
- _id: NMR
acknowledgement: "We thank Dominique Madern (IBS Grenoble) for providing the plasmid
for MalDH and feedback on the article, Alicia Vallet for excellent support at the
Grenoble NMR facility, and Petra Rovo and Margarita Valhondo at the IST Austria
NMR Service Unit. We thank Dorothea Anrather in the mass spectrometry facility of
Max Perutz Labs for the mass spectrometry analysis using the instruments of the
Vienna BioCenter Core Facilities (VBCF). We are grateful to Jean-Pierre Andrieu
(Plateforme Seq3A, IBS Grenoble) for the analysis of the amino acid composition
of the in-house-prepared lysates. We are grateful to Rasmus Linser (Technical University
Dortmund) for sharing a paper draft describing a similar study. This work was supported
by the Austrian Science Fund (FWF; project number I5812-B). We thank Tobias Schubeis
(Lyon) and the reviewers for constructive input.\r\nThis research has been supported
by the Austrian Science Fund (grant no. I5812-B). Part of this work used the platforms
of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the
Grenoble Partnership for 40 Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02)
and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles
Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003). IBS acknowledges integration
into the Interdisciplinary Research Institute of Grenoble (IRIG, 45 CEA). Charles-Adrien
Arnaud was funded by GRAL."
article_processing_charge: Yes
article_type: original
author:
- first_name: Federico
full_name: Napoli, Federico
id: d42e08e7-f4fc-11eb-af0a-d71e26138f1b
last_name: Napoli
orcid: 0000-0002-9043-136X
- first_name: Jia-Ying
full_name: Guan, Jia-Ying
last_name: Guan
- first_name: Charles-Adrien
full_name: Arnaud, Charles-Adrien
last_name: Arnaud
- first_name: Pavel
full_name: Macek, Pavel
last_name: Macek
- first_name: Hugo
full_name: Fraga, Hugo
last_name: Fraga
- first_name: Cécile
full_name: Breyton, Cécile
last_name: Breyton
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Napoli F, Guan J-Y, Arnaud C-A, et al. Deuteration of proteins boosted by
cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without
the reprotonation bottleneck. Magnetic Resonance. 2024;5(1):33-49. doi:10.5194/mr-5-33-2024'
apa: 'Napoli, F., Guan, J.-Y., Arnaud, C.-A., Macek, P., Fraga, H., Breyton, C.,
& Schanda, P. (2024). Deuteration of proteins boosted by cell lysates: High-resolution
amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck.
Magnetic Resonance. Copernicus Publications. https://doi.org/10.5194/mr-5-33-2024'
chicago: 'Napoli, Federico, Jia-Ying Guan, Charles-Adrien Arnaud, Pavel Macek, Hugo
Fraga, Cécile Breyton, and Paul Schanda. “Deuteration of Proteins Boosted by Cell
Lysates: High-Resolution Amide and Ha Magic-Angle-Spinning (MAS) NMR without the
Reprotonation Bottleneck.” Magnetic Resonance. Copernicus Publications,
2024. https://doi.org/10.5194/mr-5-33-2024.'
ieee: 'F. Napoli et al., “Deuteration of proteins boosted by cell lysates:
High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation
bottleneck,” Magnetic Resonance, vol. 5, no. 1. Copernicus Publications,
pp. 33–49, 2024.'
ista: 'Napoli F, Guan J-Y, Arnaud C-A, Macek P, Fraga H, Breyton C, Schanda P. 2024.
Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha
magic-angle-spinning (MAS) NMR without the reprotonation bottleneck. Magnetic
Resonance. 5(1), 33–49.'
mla: 'Napoli, Federico, et al. “Deuteration of Proteins Boosted by Cell Lysates:
High-Resolution Amide and Ha Magic-Angle-Spinning (MAS) NMR without the Reprotonation
Bottleneck.” Magnetic Resonance, vol. 5, no. 1, Copernicus Publications,
2024, pp. 33–49, doi:10.5194/mr-5-33-2024.'
short: F. Napoli, J.-Y. Guan, C.-A. Arnaud, P. Macek, H. Fraga, C. Breyton, P. Schanda,
Magnetic Resonance 5 (2024) 33–49.
corr_author: '1'
date_created: 2024-05-16T15:02:43Z
date_published: 2024-04-19T00:00:00Z
date_updated: 2026-09-24T10:36:36Z
day: '19'
ddc:
- '530'
department:
- _id: PaSc
doi: 10.5194/mr-5-33-2024
external_id:
pmid:
- '40384771'
file:
- access_level: open_access
checksum: 80ea50114e428461ca9530d3bd5d89e4
content_type: application/pdf
creator: dernst
date_created: 2024-05-22T07:01:15Z
date_updated: 2024-05-22T07:01:15Z
file_id: '15413'
file_name: 2024_MagneticResonance_Napoli.pdf
file_size: 6657865
relation: main_file
success: 1
file_date_updated: 2024-05-22T07:01:15Z
fulldoi: https://doi.org/10.5194/mr-5-33-2024
has_accepted_license: '1'
intvolume: ' 5'
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 33-49
pmid: 1
project:
- _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf
grant_number: I05812
name: AlloSpace. The emergence and mechanisms of allostery
- _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1
call_identifier: FWF
name: FWF Open Access Fund
publication: Magnetic Resonance
publication_identifier:
issn:
- 2699-0016
publication_status: published
publisher: Copernicus Publications
quality_controlled: '1'
related_material:
record:
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relation: research_data
status: public
scopus_import: '1'
status: public
title: 'Deuteration of proteins boosted by cell lysates: High-resolution amide and
Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2024'
...
---
_id: '18072'
abstract:
- lang: eng
text: The individualization of chromosomes during early mitosis and their clustering
upon exit from cell division are two key transitions that ensure efficient segregation
of eukaryotic chromosomes. Both processes are regulated by the surfactant-like
protein Ki-67, but how Ki-67 achieves these diametric functions has remained unknown.
Here, we report that Ki-67 radically switches from a chromosome repellent to a
chromosome attractant during anaphase in human cells. We show that Ki-67 dephosphorylation
during mitotic exit and the simultaneous exposure of a conserved basic patch induce
the RNA-dependent formation of a liquid-like condensed phase on the chromosome
surface. Experiments and coarse-grained simulations support a model in which the
coalescence of chromosome surfaces, driven by co-condensation of Ki-67 and RNA,
promotes clustering of chromosomes. Our study reveals how the switch of Ki-67
from a surfactant to a liquid-like condensed phase can generate mechanical forces
during genome segregation that are required for re-establishing nuclear-cytoplasmic
compartmentalization after mitosis.
acknowledgement: We thank Daniel W. Gerlich for providing cell lines, the EMBL Advanced
Light Microscopy Facility (ALMF) for support, Christian H. Haering and Thomas Quail
for input on the manuscript, and Martina Dees for cloning several Ki-67 constructs.
This work was supported by the German Research Foundation (DFG project number 402723784)
and the Human Frontier Science Program (CDA00045/2019). A.H.-A. and A.B. have received
PhD fellowships from the Boehringer Ingelheim Fonds, V.S. and A.Š. were supported
by the European Research Council (ERC) under the European Union’s Horizon 2020 research
and innovation programme (grant no. 802960), and Y.H. was supported by a fellowship
from the EMBL interdisciplinary Postdoc (EIPOD) program (Marie Sklodowska-Curie
Actions, COFUND grant agreement 664726).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Alberto
full_name: Hernandez-Armendariz, Alberto
last_name: Hernandez-Armendariz
- first_name: Valerio
full_name: Sorichetti, Valerio
id: ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b
last_name: Sorichetti
orcid: 0000-0002-9645-6576
- first_name: Yuki
full_name: Hayashi, Yuki
last_name: Hayashi
- first_name: Zuzana
full_name: Koskova, Zuzana
last_name: Koskova
- first_name: Andreas
full_name: Brunner, Andreas
last_name: Brunner
- first_name: Jan
full_name: Ellenberg, Jan
last_name: Ellenberg
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Sara
full_name: Cuylen-Haering, Sara
last_name: Cuylen-Haering
citation:
ama: Hernandez-Armendariz A, Sorichetti V, Hayashi Y, et al. A liquid-like coat
mediates chromosome clustering during mitotic exit. Molecular Cell. 2024;84(17):P3254-3270.E9.
doi:10.1016/j.molcel.2024.07.022
apa: Hernandez-Armendariz, A., Sorichetti, V., Hayashi, Y., Koskova, Z., Brunner,
A., Ellenberg, J., … Cuylen-Haering, S. (2024). A liquid-like coat mediates chromosome
clustering during mitotic exit. Molecular Cell. Cell Press. https://doi.org/10.1016/j.molcel.2024.07.022
chicago: Hernandez-Armendariz, Alberto, Valerio Sorichetti, Yuki Hayashi, Zuzana
Koskova, Andreas Brunner, Jan Ellenberg, Anđela Šarić, and Sara Cuylen-Haering.
“A Liquid-like Coat Mediates Chromosome Clustering during Mitotic Exit.” Molecular
Cell. Cell Press, 2024. https://doi.org/10.1016/j.molcel.2024.07.022.
ieee: A. Hernandez-Armendariz et al., “A liquid-like coat mediates chromosome
clustering during mitotic exit,” Molecular Cell, vol. 84, no. 17. Cell
Press, p. P3254–3270.E9, 2024.
ista: Hernandez-Armendariz A, Sorichetti V, Hayashi Y, Koskova Z, Brunner A, Ellenberg
J, Šarić A, Cuylen-Haering S. 2024. A liquid-like coat mediates chromosome clustering
during mitotic exit. Molecular Cell. 84(17), P3254–3270.E9.
mla: Hernandez-Armendariz, Alberto, et al. “A Liquid-like Coat Mediates Chromosome
Clustering during Mitotic Exit.” Molecular Cell, vol. 84, no. 17, Cell
Press, 2024, p. P3254–3270.E9, doi:10.1016/j.molcel.2024.07.022.
short: A. Hernandez-Armendariz, V. Sorichetti, Y. Hayashi, Z. Koskova, A. Brunner,
J. Ellenberg, A. Šarić, S. Cuylen-Haering, Molecular Cell 84 (2024) P3254–3270.E9.
das_tickbox: '1'
dataavailabilitystatement: 'Raw image files of all figures have been deposited at
Mendeley Data and are publicly available as of the date of publication (Mendeley
data: https://doi.org/10.17632/dwcpnncsyd.1). All other data reported in this paper
will be shared by the lead contact upon request'
date_created: 2024-09-15T22:01:41Z
date_published: 2024-09-05T00:00:00Z
date_updated: 2026-09-24T10:43:18Z
day: '05'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1016/j.molcel.2024.07.022
ec_funded: 1
external_id:
isi:
- '001309051100001'
pmid:
- '39153474'
file:
- access_level: open_access
checksum: 3f360e0287b8ec79fb2b8b02b5070360
content_type: application/pdf
creator: dernst
date_created: 2024-09-16T07:38:38Z
date_updated: 2024-09-16T07:38:38Z
file_id: '18075'
file_name: 2024_MolecularCell_HernandezArmendariz.pdf
file_size: 11654644
relation: main_file
success: 1
file_date_updated: 2024-09-16T07:38:38Z
fulldoi: https://doi.org/10.1016/j.molcel.2024.07.022
has_accepted_license: '1'
intvolume: ' 84'
isi: 1
issue: '17'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: P3254-3270.E9
pmid: 1
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
publication: Molecular Cell
publication_identifier:
eissn:
- 1097-4164
issn:
- 1097-2765
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
record:
- id: '22987'
relation: research_data
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: A liquid-like coat mediates chromosome clustering during mitotic exit
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 84
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '17239'
abstract:
- lang: eng
text: Collagen is the most abundant protein in tissue scaffolds in live organisms.
Collagen can self-assemble in vitro, which has led to a number of biotechnological
and biomedical applications. To understand the dominant factors that participate
in the formation of collagen nanostructures, here we study in real time and with
nanoscale resolution the disassembly and reassembly of collagens. We implement
a high-speed force microscope, which provides in situ high spatiotemporal resolution
images of collagen nanostructures under changing pH conditions. The disassembly
and reassembly are dominated by the electrostatic interactions among amino-acid
residues of different molecules. Acidic conditions favor disassembly by neutralizing
negatively charged residues. The process sets a net repulsive force between collagen
molecules. A neutral pH favors the presence of negative and positively charged
residues along the collagen molecules, which promotes their electrostatic attraction.
Molecular dynamics simulations reproduce the experimental behavior and validate
the electrostatic-based model of the disassembly and reassembly processes.
acknowledgement: We are grateful to Nancy Forde (Simon Fraser University) for her
motivating comments. Financial support from the Ministerio de Ciencia, Innovación
y Universidades (PID2019-106801GB-I00 and PID2022-136851NB-I00) is acknowledged.
A.Š. and K.K. acknowledge support from the Royal Society University Research Fellowship
and ERC the European Union’s Horizon 2020584 Research and Innovation Programme (Grant
No. 585 80296).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Clara
full_name: Garcia-Sacristan, Clara
last_name: Garcia-Sacristan
- first_name: Victor G.
full_name: Gisbert, Victor G.
last_name: Gisbert
- first_name: Kevin
full_name: Klein, Kevin
id: 1e7ede04-9e54-11f0-9ec4-8d4d5563c398
last_name: Klein
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Ricardo
full_name: Garcia, Ricardo
last_name: Garcia
citation:
ama: Garcia-Sacristan C, Gisbert VG, Klein K, Šarić A, Garcia R. In operando imaging
electrostatic-driven disassembly and reassembly of collagen nanostructures. ACS
Nano. 2024;18(28):18485-18492. doi:10.1021/acsnano.4c03839
apa: Garcia-Sacristan, C., Gisbert, V. G., Klein, K., Šarić, A., & Garcia, R.
(2024). In operando imaging electrostatic-driven disassembly and reassembly of
collagen nanostructures. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.4c03839
chicago: Garcia-Sacristan, Clara, Victor G. Gisbert, Kevin Klein, Anđela Šarić,
and Ricardo Garcia. “In Operando Imaging Electrostatic-Driven Disassembly and
Reassembly of Collagen Nanostructures.” ACS Nano. American Chemical Society,
2024. https://doi.org/10.1021/acsnano.4c03839.
ieee: C. Garcia-Sacristan, V. G. Gisbert, K. Klein, A. Šarić, and R. Garcia, “In
operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures,”
ACS Nano, vol. 18, no. 28. American Chemical Society, pp. 18485–18492,
2024.
ista: Garcia-Sacristan C, Gisbert VG, Klein K, Šarić A, Garcia R. 2024. In operando
imaging electrostatic-driven disassembly and reassembly of collagen nanostructures.
ACS Nano. 18(28), 18485–18492.
mla: Garcia-Sacristan, Clara, et al. “In Operando Imaging Electrostatic-Driven Disassembly
and Reassembly of Collagen Nanostructures.” ACS Nano, vol. 18, no. 28,
American Chemical Society, 2024, pp. 18485–92, doi:10.1021/acsnano.4c03839.
short: C. Garcia-Sacristan, V.G. Gisbert, K. Klein, A. Šarić, R. Garcia, ACS Nano
18 (2024) 18485–18492.
das_tickbox: '0'
date_created: 2024-07-14T22:01:12Z
date_published: 2024-07-16T00:00:00Z
date_updated: 2026-09-24T10:43:56Z
day: '16'
ddc:
- '540'
department:
- _id: AnSa
doi: 10.1021/acsnano.4c03839
ec_funded: 1
external_id:
isi:
- '001263155500001'
pmid:
- '38958189'
file:
- access_level: open_access
checksum: b7e9ce718e92f568bcb3810e8e28e458
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T12:06:48Z
date_updated: 2025-01-09T12:06:48Z
file_id: '18808'
file_name: 2024_ACSNano_GarciaSacristan.pdf
file_size: 10036838
relation: main_file
success: 1
file_date_updated: 2025-01-09T12:06:48Z
fulldoi: https://doi.org/10.1021/acsnano.4c03839
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '28'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 18485-18492
pmid: 1
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
publication: ACS Nano
publication_identifier:
eissn:
- 1936-086X
issn:
- 1936-0851
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: In operando imaging electrostatic-driven disassembly and reassembly of collagen
nanostructures
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 18
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '18704'
abstract:
- lang: eng
text: Clathrin-mediated endocytosis is the main pathway used by eukaryotic cells
to take up extracellular material, but the dominant physical mechanisms driving
this process are still elusive. Recently, several high-resolution imaging techniques
have been used on different cell lines to measure the geometrical properties of
clathrin-coated pits over their whole lifetime. Here, we first show that the combination
of all datasets with the recently introduced cooperative curvature model defines
a consensus pathway, which is characterized by a flat-to-curved transition at
finite area, followed by linear growth and subsequent saturation of curvature.
We then apply an energetic model for the composite of the plasma membrane and
clathrin coat to this consensus pathway to show that the dominant mechanism for
invagination could be coat stiffening, which might originate from cooperative
interactions between the different clathrin molecules and progressively drives
the system toward its intrinsic curvature. Our theory predicts that two length
scales determine the invagination pathway, namely the patch size at which the
flat-to-curved transition occurs and the final pit radius.
acknowledgement: We thank Markus Mund, Aline Tschanz, and Jonas Ries for helpful discussions
and a critical reading of the manuscript. We also kindly acknowledge Simon Scheuring
for providing the HS-AFM data for the analysis of clathrin coat invagination. We
thank the reviewers of previous versions of this manuscript for useful feedback
that helped us to improve this work. F.F. acknowledges financial support by the
NOMIS foundation. U.S.S. was supported by the Deutsche Forschungsgemeinschaft (DFG,
German Research Foundation) under Project No. 240245660 (SFB 1129). Moreover, he
is a member of the Interdisciplinary Center for Scientific Computing (IWR) at Heidelberg
and of the Max Planck School Matter to Life supported by the German Federal Ministry
of Education and Research (BMBF) in collaboration with the Max Planck Society.
article_number: '064403'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Felix F
full_name: Frey, Felix F
id: a0270b37-8f1a-11ec-95c7-8e710c59a4f3
last_name: Frey
orcid: 0000-0001-8501-6017
- first_name: Ulrich S.
full_name: Schwarz, Ulrich S.
last_name: Schwarz
citation:
ama: Frey FF, Schwarz US. Coat stiffening can explain invagination of clathrin-coated
membranes. Physical Review E. 2024;110(6). doi:10.1103/PhysRevE.110.064403
apa: Frey, F. F., & Schwarz, U. S. (2024). Coat stiffening can explain invagination
of clathrin-coated membranes. Physical Review E. American Physical Society.
https://doi.org/10.1103/PhysRevE.110.064403
chicago: Frey, Felix F, and Ulrich S. Schwarz. “Coat Stiffening Can Explain Invagination
of Clathrin-Coated Membranes.” Physical Review E. American Physical Society,
2024. https://doi.org/10.1103/PhysRevE.110.064403.
ieee: F. F. Frey and U. S. Schwarz, “Coat stiffening can explain invagination of
clathrin-coated membranes,” Physical Review E, vol. 110, no. 6. American
Physical Society, 2024.
ista: Frey FF, Schwarz US. 2024. Coat stiffening can explain invagination of clathrin-coated
membranes. Physical Review E. 110(6), 064403.
mla: Frey, Felix F., and Ulrich S. Schwarz. “Coat Stiffening Can Explain Invagination
of Clathrin-Coated Membranes.” Physical Review E, vol. 110, no. 6, 064403,
American Physical Society, 2024, doi:10.1103/PhysRevE.110.064403.
short: F.F. Frey, U.S. Schwarz, Physical Review E 110 (2024).
das_tickbox: '0'
date_created: 2024-12-22T23:01:48Z
date_published: 2024-12-10T00:00:00Z
date_updated: 2026-09-24T10:43:36Z
day: '10'
department:
- _id: AnSa
doi: 10.1103/PhysRevE.110.064403
external_id:
arxiv:
- '2405.02820'
isi:
- '001379135100004'
pmid:
- '39916158'
fulldoi: https://doi.org/10.1103/PhysRevE.110.064403
intvolume: ' 110'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2405.02820
month: '12'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review E
publication_identifier:
eissn:
- 2470-0053
issn:
- 2470-0045
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Coat stiffening can explain invagination of clathrin-coated membranes
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 110
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '22987'
abstract:
- lang: eng
text: 'Imaging data of all main and supplementary figures. The files are the raw
microcopy files including all Z-slices and timepoints. '
article_processing_charge: No
author:
- first_name: Alberto
full_name: Hernandez-Armendariz, Alberto
last_name: Hernandez-Armendariz
- first_name: Sara
full_name: Cuylen-Haering, Sara
last_name: Cuylen-Haering
citation:
ama: Hernandez-Armendariz A, Cuylen-Haering S. A liquid-like coat mediates chromosome
clustering during mitotic exit. Hernandez-Armendariz et al. 2024. doi:10.17632/dwcpnncsyd.1
apa: Hernandez-Armendariz, A., & Cuylen-Haering, S. (2024). A liquid-like coat
mediates chromosome clustering during mitotic exit. Hernandez-Armendariz et al.
Repository. https://doi.org/10.17632/dwcpnncsyd.1
chicago: Hernandez-Armendariz, Alberto, and Sara Cuylen-Haering. “A Liquid-like
Coat Mediates Chromosome Clustering during Mitotic Exit. Hernandez-Armendariz
et Al.” Repository, 2024. https://doi.org/10.17632/dwcpnncsyd.1.
ieee: A. Hernandez-Armendariz and S. Cuylen-Haering, “A liquid-like coat mediates
chromosome clustering during mitotic exit. Hernandez-Armendariz et al.” Repository,
2024.
ista: Hernandez-Armendariz A, Cuylen-Haering S. 2024. A liquid-like coat mediates
chromosome clustering during mitotic exit. Hernandez-Armendariz et al., Repository,
10.17632/dwcpnncsyd.1.
mla: Hernandez-Armendariz, Alberto, and Sara Cuylen-Haering. A Liquid-like Coat
Mediates Chromosome Clustering during Mitotic Exit. Hernandez-Armendariz et Al.
Repository, 2024, doi:10.17632/dwcpnncsyd.1.
short: A. Hernandez-Armendariz, S. Cuylen-Haering, (2024).
date_created: 2026-09-24T10:38:23Z
date_published: 2024-08-22T00:00:00Z
date_updated: 2026-09-24T10:43:18Z
day: '22'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.17632/dwcpnncsyd.1
fulldoi: https://doi.org/10.17632/dwcpnncsyd.1
main_file_link:
- open_access: '1'
url: https://doi.org/10.17632/dwcpnncsyd.1
month: '08'
oa: 1
oa_version: None
publisher: Repository
related_material:
record:
- id: '18072'
relation: used_in_publication
status: public
status: public
title: A liquid-like coat mediates chromosome clustering during mitotic exit. Hernandez-Armendariz
et al.
type: research_data_reference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '22940'
article_processing_charge: No
author:
- first_name: Astrid
full_name: ' Sivertsen, Astrid'
last_name: ' Sivertsen'
- first_name: Federico
full_name: Napoli, Federico
last_name: Napoli
- first_name: Paul
full_name: Schanda, Paul
last_name: Schanda
citation:
ama: Sivertsen A, Napoli F, Schanda P. Amide and a-hydrogens extension to the Solid-state
NMR assignment of P. horikoshii TET2. 2024. doi:10.13018/BMR52400
apa: Sivertsen, A., Napoli, F., & Schanda, P. (2024). Amide and a-hydrogens
extension to the Solid-state NMR assignment of P. horikoshii TET2. Repository.
https://doi.org/10.13018/BMR52400
chicago: Sivertsen, Astrid, Federico Napoli, and Paul Schanda. “Amide and A-Hydrogens
Extension to the Solid-State NMR Assignment of P. Horikoshii TET2.” Repository,
2024. https://doi.org/10.13018/BMR52400.
ieee: A. Sivertsen, F. Napoli, and P. Schanda, “Amide and a-hydrogens extension
to the Solid-state NMR assignment of P. horikoshii TET2.” Repository, 2024.
ista: Sivertsen A, Napoli F, Schanda P. 2024. Amide and a-hydrogens extension to
the Solid-state NMR assignment of P. horikoshii TET2, Repository, 10.13018/BMR52400.
mla: Sivertsen, Astrid, et al. Amide and A-Hydrogens Extension to the Solid-State
NMR Assignment of P. Horikoshii TET2. Repository, 2024, doi:10.13018/BMR52400.
short: A. Sivertsen, F. Napoli, P. Schanda, (2024).
date_created: 2026-09-17T09:10:45Z
date_published: 2024-05-15T00:00:00Z
date_updated: 2026-09-24T10:36:36Z
day: '15'
ddc:
- '530'
department:
- _id: PaSc
doi: 10.13018/BMR52400
fulldoi: https://doi.org/10.13018/BMR52400
main_file_link:
- open_access: '1'
url: https://doi.org/10.13018/BMR52400
month: '05'
oa: 1
oa_version: None
publisher: Repository
related_material:
record:
- id: '15401'
relation: used_in_publication
status: public
status: public
title: Amide and a-hydrogens extension to the Solid-state NMR assignment of P. horikoshii
TET2
type: research_data_reference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
_id: '15126'
abstract:
- lang: eng
text: This zip file contains data, and analysis for the paper "Elucidating the role
of water in collagen self-assembly by isotopically modulating collagen hydration".
article_processing_charge: No
author:
- first_name: G.
full_name: Giubertoni, G.
last_name: Giubertoni
- first_name: S.
full_name: Woutersen, S.
last_name: Woutersen
citation:
ama: Giubertoni G, Woutersen S. Dataset Collagen Self Assembly in H2O and D2O. 2024.
doi:10.21942/UVA.24829896
apa: Giubertoni, G., & Woutersen, S. (2024). Dataset Collagen Self Assembly
in H2O and D2O. Figshare. https://doi.org/10.21942/UVA.24829896
chicago: Giubertoni, G., and S. Woutersen. “Dataset Collagen Self Assembly in H2O
and D2O.” Figshare, 2024. https://doi.org/10.21942/UVA.24829896.
ieee: G. Giubertoni and S. Woutersen, “Dataset Collagen Self Assembly in H2O and
D2O.” Figshare, 2024.
ista: Giubertoni G, Woutersen S. 2024. Dataset Collagen Self Assembly in H2O and
D2O, Figshare, 10.21942/UVA.24829896.
mla: Giubertoni, G., and S. Woutersen. Dataset Collagen Self Assembly in H2O
and D2O. Figshare, 2024, doi:10.21942/UVA.24829896.
short: G. Giubertoni, S. Woutersen, (2024).
date_created: 2024-03-19T10:47:16Z
date_published: 2024-02-14T00:00:00Z
date_updated: 2026-09-24T10:42:12Z
day: '14'
ddc:
- '550'
doi: 10.21942/UVA.24829896
extern: '1'
fulldoi: https://doi.org/10.21942/UVA.24829896
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.21942/UVA.24829896
month: '02'
oa: 1
oa_version: Published Version
publisher: Figshare
related_material:
record:
- id: '15116'
relation: used_in_publication
status: public
status: public
title: Dataset Collagen Self Assembly in H2O and D2O
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data_reference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
_id: '17374'
abstract:
- lang: eng
text: Achieving photorealistic 3D view synthesis and relighting of human portraits
is pivotal for advancing AR/VR applications. Existing methodologies in portrait
relighting demonstrate substantial limitations in terms of generalization and
3D consistency, coupled with inaccuracies in physically realistic lighting and
identity preservation. Furthermore, personalization from a single view is difficult
to achieve and often requires multiview images during the testing phase or involves
slow optimization processes. This paper introduces Lite2Relight , a novel technique
that can predict 3D consistent head poses of portraits while performing physically
plausible light editing at interactive speed. Our method uniquely extends the
generative capabilities and efficient volumetric representation of EG3D, leveraging
a lightstage dataset to implicitly disentangle face reflectance and perform relighting
under target HDRI environment maps. By utilizing a pre-trained geometry-aware
encoder and a feature alignment module, we map input images into a relightable
3D space, enhancing them with a strong face geometry and reflectance prior. Through
extensive quantitative and qualitative evaluations, we show that our method outperforms
the state-of-the-art methods in terms of efficacy, photorealism, and practical
application. This includes producing 3D-consistent results of the full head, including
hair, eyes, and expressions. Lite2Relight paves the way for large-scale adoption
of photorealistic portrait editing in various domains, offering a robust, interactive
solution to a previously constrained problem.
acknowledgement: This work was supported by the ERC Consolidator Grant 4DReply (770784).
We extend our gratitude to Shrisha Bharadwaj for providing feedback and constant
support.
article_number: '41'
article_processing_charge: Yes (in subscription journal)
arxiv: 1
author:
- first_name: Pramod
full_name: Rao, Pramod
last_name: Rao
- first_name: Gereon
full_name: Fox, Gereon
last_name: Fox
- first_name: Abhimitra
full_name: Meka, Abhimitra
last_name: Meka
- first_name: B. R.
full_name: Mallikarjun, B. R.
last_name: Mallikarjun
- first_name: Fangneng
full_name: Zhan, Fangneng
last_name: Zhan
- first_name: Tim
full_name: Weyrich, Tim
last_name: Weyrich
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Hanspeter
full_name: Pfister, Hanspeter
last_name: Pfister
- first_name: Wojciech
full_name: Matusik, Wojciech
last_name: Matusik
- first_name: Mohamed
full_name: Elgharib, Mohamed
last_name: Elgharib
- first_name: Christian
full_name: Theobalt, Christian
last_name: Theobalt
citation:
ama: 'Rao P, Fox G, Meka A, et al. Lite2Relight: 3D-aware single image portrait
relighting. In: Proceedings - SIGGRAPH 2024 Conference Papers. Association
for Computing Machinery; 2024. doi:10.1145/3641519.3657470'
apa: 'Rao, P., Fox, G., Meka, A., Mallikarjun, B. R., Zhan, F., Weyrich, T., … Theobalt,
C. (2024). Lite2Relight: 3D-aware single image portrait relighting. In Proceedings
- SIGGRAPH 2024 Conference Papers. Denver, CO, United States: Association
for Computing Machinery. https://doi.org/10.1145/3641519.3657470'
chicago: 'Rao, Pramod, Gereon Fox, Abhimitra Meka, B. R. Mallikarjun, Fangneng Zhan,
Tim Weyrich, Bernd Bickel, et al. “Lite2Relight: 3D-Aware Single Image Portrait
Relighting.” In Proceedings - SIGGRAPH 2024 Conference Papers. Association
for Computing Machinery, 2024. https://doi.org/10.1145/3641519.3657470.'
ieee: 'P. Rao et al., “Lite2Relight: 3D-aware single image portrait relighting,”
in Proceedings - SIGGRAPH 2024 Conference Papers, Denver, CO, United States,
2024.'
ista: 'Rao P, Fox G, Meka A, Mallikarjun BR, Zhan F, Weyrich T, Bickel B, Pfister
H, Matusik W, Elgharib M, Theobalt C. 2024. Lite2Relight: 3D-aware single image
portrait relighting. Proceedings - SIGGRAPH 2024 Conference Papers. SIGGRAPH:
Computer Graphics and Interactive Techniques Conference, 41.'
mla: 'Rao, Pramod, et al. “Lite2Relight: 3D-Aware Single Image Portrait Relighting.”
Proceedings - SIGGRAPH 2024 Conference Papers, 41, Association for Computing
Machinery, 2024, doi:10.1145/3641519.3657470.'
short: P. Rao, G. Fox, A. Meka, B.R. Mallikarjun, F. Zhan, T. Weyrich, B. Bickel,
H. Pfister, W. Matusik, M. Elgharib, C. Theobalt, in:, Proceedings - SIGGRAPH
2024 Conference Papers, Association for Computing Machinery, 2024.
conference:
end_date: 2024-08-01
location: Denver, CO, United States
name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference'
start_date: 2024-07-27
das_tickbox: '0'
date_created: 2024-08-04T22:01:21Z
date_published: 2024-07-13T00:00:00Z
date_updated: 2026-09-24T11:00:21Z
day: '13'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3641519.3657470
external_id:
arxiv:
- '2407.10487'
isi:
- '001282218200076'
file:
- access_level: open_access
checksum: 4650f6d1419e675929133e46a91ca177
content_type: application/pdf
creator: dernst
date_created: 2024-08-05T08:25:18Z
date_updated: 2024-08-05T08:25:18Z
file_id: '17387'
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file_size: 59683257
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isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Proceedings - SIGGRAPH 2024 Conference Papers
publication_identifier:
isbn:
- '9798400705250'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: 'Lite2Relight: 3D-aware single image portrait relighting'
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: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
APC_amount: 12348 EUR
OA_place: publisher
OA_type: hybrid
_id: '17460'
abstract:
- lang: eng
text: Filaments in the cell commonly treadmill. Driven by energy consumption, they
grow on one end while shrinking on the other, causing filaments to appear motile
even though individual proteins remain static. This process is characteristic
of cytoskeletal filaments and leads to collective filament self-organization.
Here we show that treadmilling drives filament nematic ordering by dissolving
misaligned filaments. Taking the bacterial FtsZ protein involved in cell division
as an example, we show that this mechanism aligns FtsZ filaments in vitro and
drives the organization of the division ring in living Bacillus subtilis cells.
We find that ordering via local dissolution also allows the system to quickly
respond to chemical and geometrical biases in the cell, enabling us to quantitatively
explain the ring formation dynamics in vivo. Beyond FtsZ and other cytoskeletal
filaments, our study identifies a mechanism for self-organization via constant
birth and death of energy-consuming filaments.
acknowledgement: We thank I. Palaia (ISTA) for useful discussions and K. Lim and R.
W. Wong (WPI-Nano Life Science Institute, Kanazawa University) for providing access
to HS-AFM. We would like to thank B. Prats Mateu (MSD Austria, Vienna) for providing
the HS-AFM data. This work was supported by the Royal Society (grant no. UF160266;
C.V.-C. and A.Š.), the European Union’s Horizon 2020 Research and Innovation Programme
(grant no. 802960; A.Š.), the Austrian Science Fund (FWF) Stand-Alone P34607 (M.L.)
and a Wellcome Trust and Royal Society Sir Henry Dale Fellowship (grant no. 206670/Z/17/Z;
S.H. and K.D.W.).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Christian Eduardo
full_name: Vanhille-Campos, Christian Eduardo
id: 3adeca52-9313-11ed-b1ac-c170b2505714
last_name: Vanhille-Campos
- first_name: Kevin D.
full_name: Whitley, Kevin D.
last_name: Whitley
- first_name: Philipp
full_name: Radler, Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Séamus
full_name: Holden, Séamus
last_name: Holden
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Vanhille-Campos CE, Whitley KD, Radler P, Loose M, Holden S, Šarić A. Self-organization
of mortal filaments and its role in bacterial division ring formation. Nature
Physics. 2024;20:1670-1678. doi:10.1038/s41567-024-02597-8
apa: Vanhille-Campos, C. E., Whitley, K. D., Radler, P., Loose, M., Holden, S.,
& Šarić, A. (2024). Self-organization of mortal filaments and its role in
bacterial division ring formation. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-024-02597-8
chicago: Vanhille-Campos, Christian Eduardo, Kevin D. Whitley, Philipp Radler, Martin
Loose, Séamus Holden, and Anđela Šarić. “Self-Organization of Mortal Filaments
and Its Role in Bacterial Division Ring Formation.” Nature Physics. Springer
Nature, 2024. https://doi.org/10.1038/s41567-024-02597-8.
ieee: C. E. Vanhille-Campos, K. D. Whitley, P. Radler, M. Loose, S. Holden, and
A. Šarić, “Self-organization of mortal filaments and its role in bacterial division
ring formation,” Nature Physics, vol. 20. Springer Nature, pp. 1670–1678,
2024.
ista: Vanhille-Campos CE, Whitley KD, Radler P, Loose M, Holden S, Šarić A. 2024.
Self-organization of mortal filaments and its role in bacterial division ring
formation. Nature Physics. 20, 1670–1678.
mla: Vanhille-Campos, Christian Eduardo, et al. “Self-Organization of Mortal Filaments
and Its Role in Bacterial Division Ring Formation.” Nature Physics, vol.
20, Springer Nature, 2024, pp. 1670–78, doi:10.1038/s41567-024-02597-8.
short: C.E. Vanhille-Campos, K.D. Whitley, P. Radler, M. Loose, S. Holden, A. Šarić,
Nature Physics 20 (2024) 1670–1678.
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: The simulation data presented in this work are available
from the University College London public data repository at https://doi.org/10.5522/04/24754527
(ref. 74). Live-cell imaging of FtsZ rings data presented in this work are from
ref. 23. High-speed atomic force microscopy data presented in this work are from
ref. 9. Total internal reflection fluorescence microscopy data presented in this
work are from refs. 37,75,76
date_created: 2024-08-25T22:01:08Z
date_published: 2024-10-01T00:00:00Z
date_updated: 2026-09-24T10:58:39Z
day: '01'
ddc:
- '570'
department:
- _id: AnSa
- _id: MaLo
doi: 10.1038/s41567-024-02597-8
ec_funded: 1
external_id:
isi:
- '001289394500005'
pmid:
- '39416851'
file:
- access_level: open_access
checksum: c4842152e2b90d67f48ea8c9ed7c473b
content_type: application/pdf
creator: dernst
date_created: 2025-04-14T06:06:35Z
date_updated: 2025-04-14T06:06:35Z
file_id: '19556'
file_name: 2024_NaturePhysics_VanhilleCampos.pdf
file_size: 8058249
relation: main_file
success: 1
file_date_updated: 2025-04-14T06:06:35Z
fulldoi: https://doi.org/10.1038/s41567-024-02597-8
has_accepted_license: '1'
intvolume: ' 20'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 1670-1678
pmid: 1
popular_science: '1'
project:
- _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d
grant_number: P34607
name: In vitro reconstitution of bacterial cell division
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '22988'
relation: research_data
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Self-organization of mortal filaments and its role in bacterial division ring
formation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 20
year: '2024'
...
---
_id: '14488'
abstract:
- lang: eng
text: 'Portrait viewpoint and illumination editing is an important problem with
several applications in VR/AR, movies, and photography. Comprehensive knowledge
of geometry and illumination is critical for obtaining photorealistic results.
Current methods are unable to explicitly model in 3D while handling both viewpoint
and illumination editing from a single image. In this paper, we propose VoRF,
a novel approach that can take even a single portrait image as input and relight
human heads under novel illuminations that can be viewed from arbitrary viewpoints.
VoRF represents a human head as a continuous volumetric field and learns a prior
model of human heads using a coordinate-based MLP with individual latent spaces
for identity and illumination. The prior model is learned in an auto-decoder manner
over a diverse class of head shapes and appearances, allowing VoRF to generalize
to novel test identities from a single input image. Additionally, VoRF has a reflectance
MLP that uses the intermediate features of the prior model for rendering One-Light-at-A-Time
(OLAT) images under novel views. We synthesize novel illuminations by combining
these OLAT images with target environment maps. Qualitative and quantitative evaluations
demonstrate the effectiveness of VoRF for relighting and novel view synthesis,
even when applied to unseen subjects under uncontrolled illumination. This work
is an extension of Rao et al. (VoRF: Volumetric Relightable Faces 2022). We provide
extensive evaluation and ablative studies of our model and also provide an application,
where any face can be relighted using textual input.'
acknowledgement: Open Access funding enabled and organized by Projekt DEAL.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Pramod
full_name: Rao, Pramod
last_name: Rao
- first_name: B. R.
full_name: Mallikarjun, B. R.
last_name: Mallikarjun
- first_name: Gereon
full_name: Fox, Gereon
last_name: Fox
- first_name: Tim
full_name: Weyrich, Tim
last_name: Weyrich
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Hanspeter
full_name: Pfister, Hanspeter
last_name: Pfister
- first_name: Wojciech
full_name: Matusik, Wojciech
last_name: Matusik
- first_name: Fangneng
full_name: Zhan, Fangneng
last_name: Zhan
- first_name: Ayush
full_name: Tewari, Ayush
last_name: Tewari
- first_name: Christian
full_name: Theobalt, Christian
last_name: Theobalt
- first_name: Mohamed
full_name: Elgharib, Mohamed
last_name: Elgharib
citation:
ama: Rao P, Mallikarjun BR, Fox G, et al. A deeper analysis of volumetric relightiable
faces. International Journal of Computer Vision. 2024;132:1148-1166. doi:10.1007/s11263-023-01899-3
apa: Rao, P., Mallikarjun, B. R., Fox, G., Weyrich, T., Bickel, B., Pfister, H.,
… Elgharib, M. (2024). A deeper analysis of volumetric relightiable faces. International
Journal of Computer Vision. Springer Nature. https://doi.org/10.1007/s11263-023-01899-3
chicago: Rao, Pramod, B. R. Mallikarjun, Gereon Fox, Tim Weyrich, Bernd Bickel,
Hanspeter Pfister, Wojciech Matusik, et al. “A Deeper Analysis of Volumetric Relightiable
Faces.” International Journal of Computer Vision. Springer Nature, 2024.
https://doi.org/10.1007/s11263-023-01899-3.
ieee: P. Rao et al., “A deeper analysis of volumetric relightiable faces,”
International Journal of Computer Vision, vol. 132. Springer Nature, pp.
1148–1166, 2024.
ista: Rao P, Mallikarjun BR, Fox G, Weyrich T, Bickel B, Pfister H, Matusik W, Zhan
F, Tewari A, Theobalt C, Elgharib M. 2024. A deeper analysis of volumetric relightiable
faces. International Journal of Computer Vision. 132, 1148–1166.
mla: Rao, Pramod, et al. “A Deeper Analysis of Volumetric Relightiable Faces.” International
Journal of Computer Vision, vol. 132, Springer Nature, 2024, pp. 1148–66,
doi:10.1007/s11263-023-01899-3.
short: P. Rao, B.R. Mallikarjun, G. Fox, T. Weyrich, B. Bickel, H. Pfister, W. Matusik,
F. Zhan, A. Tewari, C. Theobalt, M. Elgharib, International Journal of Computer
Vision 132 (2024) 1148–1166.
das_tickbox: '1'
dataavailabilitystatement: 'Due to privacy concerns, we cannot make the dataset used
in our project publicly available. However, to demonstrate the effectiveness of
our proposed method, we evaluate our approach using publicly available datasets
such as H3DS (Ramon et al., 2021): https://github.com/CrisalixSA/h3ds, FFHQ (Karras
et al., 2021): https://github.com/NVlabs/ffhq-dataset, and CelebA (Liu et al., 2015):
https://mmlab.ie.cuhk.edu.hk/projects/CelebA.html. Using these datasets allows us
to evaluate the generalization ability of our proposed method on unseen data. H3DS
provides high-quality 3D scans of human faces, FFHQ contains high-resolution facial
images, and CelebA is a large-scale dataset of celebrity faces. We use these datasets
to evaluate the performance of our proposed method in various scenarios, such as
face rotation and relighting, and compare them with state-of-the-art methods.'
date_created: 2023-11-05T23:00:54Z
date_published: 2024-04-01T00:00:00Z
date_updated: 2026-09-24T10:59:50Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1007/s11263-023-01899-3
external_id:
isi:
- '001091935600002'
pmid:
- '38549787'
file:
- access_level: open_access
checksum: 5eef1d920f6fe700d7856098000d05f1
content_type: application/pdf
creator: dernst
date_created: 2024-07-22T11:07:14Z
date_updated: 2024-07-22T11:07:14Z
file_id: '17304'
file_name: 2024_IJCV_Rao.pdf
file_size: 9942520
relation: main_file
success: 1
file_date_updated: 2024-07-22T11:07:14Z
fulldoi: https://doi.org/10.1007/s11263-023-01899-3
has_accepted_license: '1'
intvolume: ' 132'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1148-1166
pmid: 1
publication: International Journal of Computer Vision
publication_identifier:
eissn:
- 1573-1405
issn:
- 0920-5691
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
researchdata_availability: no (restricted access)
scopus_import: '1'
status: public
supplementarymaterial: no
title: A deeper analysis of volumetric relightiable faces
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 132
year: '2024'
...
---
OA_type: closed access
_id: '18912'
abstract:
- lang: eng
text: This paper presents a computational method for automatically creating fabricable
3D wire sculptures from various input modalities, including 3D models, images,
and even text. There are several challenges to wire art creation. For example,
artists must express the desired visual as a sparse wire representation. It is
also difficult to manually bend wires in the air without guidance to fabricate
the designed 3D curves. Our workflow solves these challenges by using two core
techniques. First, we present an algorithm that automatically generates a fabricable
3D curve representation of the target based on a loss function that measures the
semantic distance between the rendered curve and the target. The loss function
can be defined using different pre-trained vision-language neural networks to
generate wire art from different input types. The loss function is then optimized
using differentiable rendering specifically targeting 3D parametric curves. Our
method can incorporate various fabrication constraints on the wire as additional
regularization terms in the optimization process. Second, we present an algorithm
to generate a 3D printable jig structure that can be used to fabricate the generated
wire path. The major challenge in the jig generation stems from the design of
an intersection-free surface mesh for 3D printing, which we address with our inflation
algorithm. The experimental results indicate that our method can handle a wider
range of input types and can produce physically fabricable wire shapes compared
to previous wire generation methods. Various wire arts have been fabricated using
our 3D-printed jig to demonstrate its effectiveness in 3D wire bending.
acknowledgement: The authors thank the anonymous reviewers for their valuable comments
and suggestions for improving the paper. This work was supported by JSPS KAKENHI
Grant Numbers JP21K11910, 23KJ0699 and JST AdCORP, Grant Number JPMJKB2302, Japan.
This work was partially supported by Israel Science Foundation Grant number 1390/19
and Joint NSFC-ISF Research Grant no. 3077/23. We thank Riku Toyota for his useful
advice on wire selection and Takeo Igarashi for his assistance in arranging the
collaboration of the authors.
article_number: '134'
article_processing_charge: No
author:
- first_name: Kenji
full_name: Tojo, Kenji
last_name: Tojo
- first_name: Ariel
full_name: Shamir, Ariel
last_name: Shamir
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Nobuyuki
full_name: Umetani, Nobuyuki
last_name: Umetani
citation:
ama: 'Tojo K, Shamir A, Bickel B, Umetani N. Fabricable 3D wire art. In: SIGGRAPH
’24: ACM SIGGRAPH 2024 Conference Papers. ACM; 2024. doi:10.1145/3641519.3657453'
apa: 'Tojo, K., Shamir, A., Bickel, B., & Umetani, N. (2024). Fabricable 3D
wire art. In SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers. Denver,
CO, United States: ACM. https://doi.org/10.1145/3641519.3657453'
chicago: 'Tojo, Kenji, Ariel Shamir, Bernd Bickel, and Nobuyuki Umetani. “Fabricable
3D Wire Art.” In SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers. ACM,
2024. https://doi.org/10.1145/3641519.3657453.'
ieee: 'K. Tojo, A. Shamir, B. Bickel, and N. Umetani, “Fabricable 3D wire art,”
in SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers, Denver, CO, United
States, 2024.'
ista: 'Tojo K, Shamir A, Bickel B, Umetani N. 2024. Fabricable 3D wire art. SIGGRAPH
’24: ACM SIGGRAPH 2024 Conference Papers. SIGGRAPH: Computer Graphics and Interactive
Techniques Conference, 134.'
mla: 'Tojo, Kenji, et al. “Fabricable 3D Wire Art.” SIGGRAPH ’24: ACM SIGGRAPH
2024 Conference Papers, 134, ACM, 2024, doi:10.1145/3641519.3657453.'
short: 'K. Tojo, A. Shamir, B. Bickel, N. Umetani, in:, SIGGRAPH ’24: ACM SIGGRAPH
2024 Conference Papers, ACM, 2024.'
conference:
end_date: 2024-08-01
location: Denver, CO, United States
name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference'
start_date: 2024-07-28
corr_author: '1'
das_tickbox: '0'
date_created: 2025-01-27T13:47:35Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2026-09-24T11:00:48Z
day: '01'
department:
- _id: BeBi
doi: 10.1145/3641519.3657453
external_id:
isi:
- '001282218200059'
fulldoi: https://doi.org/10.1145/3641519.3657453
isi: 1
language:
- iso: eng
month: '07'
oa_version: None
publication: 'SIGGRAPH ''24: ACM SIGGRAPH 2024 Conference Papers'
publication_identifier:
isbn:
- '9798400705250'
publication_status: published
publisher: ACM
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Fabricable 3D wire art
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '22988'
abstract:
- lang: eng
text: "This repository contains all the necessary files to replicate the simulations
and analyse the data presented in the following publication: \"Self-organization
of mortal filaments and its role in bacterial division ring formation\" - C. Vanhille-Campos
et al. (DOI: https://doi.org/10.1038/s41567-024-02597-8) See README files for
details.\r\n\r\nABSTRACT:\r\n\r\nFilaments in the cell commonly treadmill. Driven
by energy consumption, they grow on one end while shrinking on the other, causing
filaments to appear motile even though individual proteins remain static. This
process is characteristic of cytoskeletal filaments and leads to collective filament
self-organization. Here we show that treadmilling drives filament nematic ordering
by dissolving misaligned filaments. Taking the bacterial FtsZ protein involved
in cell division as an example, we show that this mechanism aligns FtsZ filaments
in vitro and drives the formation of the division ring in living Bacillus subtilis
cells. We find that ordering via local dissolution also allows the system to quickly
respond to chemical and geometrical biases in the cell, enabling us to quantitatively
explain the ring formation dynamics in vivo. Beyond FtsZ and other cytoskeletal
filaments, our study identifies a mechanism for self-organization via constant
birth and death of energy-consuming filaments."
article_processing_charge: No
author:
- first_name: Christian
full_name: Vanhille Campos, Christian
last_name: Vanhille Campos
- first_name: Andela
full_name: Saric, Andela
last_name: Saric
citation:
ama: Vanhille Campos C, Saric A. Self-organization of mortal filaments and its role
in bacterial division ring formation. 2024. doi:10.5522/04/24754527
apa: Vanhille Campos, C., & Saric, A. (2024). Self-organization of mortal filaments
and its role in bacterial division ring formation. Repository. https://doi.org/10.5522/04/24754527
chicago: Vanhille Campos, Christian, and Andela Saric. “Self-Organization of Mortal
Filaments and Its Role in Bacterial Division Ring Formation.” Repository, 2024.
https://doi.org/10.5522/04/24754527.
ieee: C. Vanhille Campos and A. Saric, “Self-organization of mortal filaments and
its role in bacterial division ring formation.” Repository, 2024.
ista: Vanhille Campos C, Saric A. 2024. Self-organization of mortal filaments and
its role in bacterial division ring formation, Repository, 10.5522/04/24754527.
mla: Vanhille Campos, Christian, and Andela Saric. Self-Organization of Mortal
Filaments and Its Role in Bacterial Division Ring Formation. Repository, 2024,
doi:10.5522/04/24754527.
short: C. Vanhille Campos, A. Saric, (2024).
date_created: 2026-09-24T10:56:29Z
date_published: 2024-07-11T00:00:00Z
date_updated: 2026-09-24T10:58:40Z
day: '11'
ddc:
- '570'
department:
- _id: AnSa
- _id: MaLo
doi: 10.5522/04/24754527
fulldoi: https://doi.org/10.5522/04/24754527
main_file_link:
- open_access: '1'
url: https://doi.org/10.5522/04/24754527
month: '07'
oa: 1
oa_version: None
publisher: Repository
related_material:
record:
- id: '17460'
relation: used_in_publication
status: public
status: public
title: Self-organization of mortal filaments and its role in bacterial division ring
formation
type: research_data_reference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
_id: '17458'
abstract:
- lang: eng
text: Changes in gene dosage can have tremendous evolutionary potential (e.g. whole-genome
duplications), but without compensatory mechanisms, they can also lead to gene
dysregulation and pathologies. Sex chromosomes are a paradigmatic example of naturally
occurring gene dosage differences and their compensation. In species with chromosome-based
sex determination, individuals within the same population necessarily show ‘natural’
differences in gene dosage for the sex chromosomes. In this Review, we focus on
the mammalian X chromosome and discuss recent new insights into the dosage-compensation
mechanisms that evolved along with the emergence of sex chromosomes, namely X-inactivation
and X-upregulation. We also discuss the evolution of the genetic loci and molecular
players involved, as well as the regulatory diversity and potentially different
requirements for dosage compensation across mammalian species.
acknowledgement: We thank Estelle Nicolas for critical feedback on the manuscript
and Ikuhiro Okamoto for critical feedback on the figures. We apologise to authors
whose work we overlooked or did not discuss or cite due to limits in the number
of references. We thank the anonymous reviewers for pointing us to additional literature
and for their constructive feedback. Figures were prepared with BioRender.com. D.C.
is supported by a fellowship from Ligue Contre le Cancer (LNCC_TAJT25850) and R.G.
holds a tenured research position from the Centre National de la Recherche Scientifique
(France). Research in the Galupa lab is supported by a grant from the Fondation
pour la Recherche Médicale (AJE202305017142). Open Access funding provided by Fondation
pour la Recherche Médicale. Deposited in PMC for immediate release.
article_number: dev202891
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Daniela
full_name: Cecalev, Daniela
last_name: Cecalev
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Rafael
full_name: Galupa, Rafael
last_name: Galupa
citation:
ama: Cecalev D, Vicoso B, Galupa R. Compensation of gene dosage on the mammalian
X. Development. 2024;151(15). doi:10.1242/dev.202891
apa: Cecalev, D., Vicoso, B., & Galupa, R. (2024). Compensation of gene dosage
on the mammalian X. Development. Company of Biologists. https://doi.org/10.1242/dev.202891
chicago: Cecalev, Daniela, Beatriz Vicoso, and Rafael Galupa. “Compensation of Gene
Dosage on the Mammalian X.” Development. Company of Biologists, 2024. https://doi.org/10.1242/dev.202891.
ieee: D. Cecalev, B. Vicoso, and R. Galupa, “Compensation of gene dosage on the
mammalian X,” Development, vol. 151, no. 15. Company of Biologists, 2024.
ista: Cecalev D, Vicoso B, Galupa R. 2024. Compensation of gene dosage on the mammalian
X. Development. 151(15), dev202891.
mla: Cecalev, Daniela, et al. “Compensation of Gene Dosage on the Mammalian X.”
Development, vol. 151, no. 15, dev202891, Company of Biologists, 2024,
doi:10.1242/dev.202891.
short: D. Cecalev, B. Vicoso, R. Galupa, Development 151 (2024).
das_tickbox: '0'
date_created: 2024-08-25T22:01:07Z
date_published: 2024-08-14T00:00:00Z
date_updated: 2026-09-24T11:05:40Z
day: '14'
ddc:
- '599'
department:
- _id: BeVi
doi: 10.1242/dev.202891
external_id:
isi:
- '001292608800003'
pmid:
- '39140247'
file:
- access_level: open_access
checksum: 5e428bda0440d3f957c694b315a8f2a9
content_type: application/pdf
creator: cchlebak
date_created: 2024-08-28T10:32:16Z
date_updated: 2024-08-28T10:32:16Z
file_id: '17464'
file_name: 2024_Development_Cecalev.pdf
file_size: 2085135
relation: main_file
success: 1
file_date_updated: 2024-08-28T10:32:16Z
fulldoi: https://doi.org/10.1242/dev.202891
has_accepted_license: '1'
intvolume: ' 151'
isi: 1
issue: '15'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
popular_science: '1'
publication: Development
publication_identifier:
eissn:
- 1477-9129
issn:
- 0950-1991
publication_status: published
publisher: Company of Biologists
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Compensation of gene dosage on the mammalian X
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 151
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18479'
abstract:
- lang: eng
text: The dominance of beneficial mutations is a key evolutionary parameter affecting
the rate and genetic basis of adaptation, yet it is notoriously difficult to estimate.
A leading method to infer it is to compare the relative rates of adaptive substitution
for X-linked and autosomal genes, which—according to a classic model by Charlesworth
et al. (1987)—is a simple function of the dominance of new beneficial mutations.
Recent evidence that rates of adaptive substitution are faster for X-linked genes
implies, accordingly, that beneficial mutations are usually recessive. However,
this conclusion is incompatible with leading theories of dominance, which predict
that beneficial mutations tend to be dominant or overdominant with respect to
fitness. To address this incompatibility, we use Fisher’s geometric model to predict
the distribution of fitness effects of new mutations and the relative rates of
positively selected substitution on the X and autosomes. Previous predictions
of faster-X theory emerge as a special case of our model in which the phenotypic
effects of mutations are small relative to the distance to the phenotypic optimum.
But as mutational effects become large relative to the optimum, we observe an
elevated tempo of positively selected substitutions on the X relative to the autosomes
across a broader range of dominance conditions, including those predicted by theories
of dominance. Our results imply that, contrary to previous models, dominant and
overdominant beneficial mutations can plausibly generate patterns of faster-X
adaptation. We discuss resulting implications for genomic studies of adaptation
and inferences of dominance.
acknowledgement: This work was supported by funds from the Australian Research Council
and The School of Biological Sciences at Monash University. F.R. was funded by a
H2020 Marie Skłodowska-Curie COFUND Action (No. 101034413). We thank three anonymous
reviewers for suggestions that substantially improved the paper and breadth of the
analysis.
article_number: e2406335121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Yasmine
full_name: Mcdonough, Yasmine
last_name: Mcdonough
- first_name: Filip
full_name: Ruzicka, Filip
id: 347955dd-57b0-11ee-9095-c28bdd368f4b
last_name: Ruzicka
- first_name: Tim
full_name: Connallon, Tim
last_name: Connallon
citation:
ama: Mcdonough Y, Ruzicka F, Connallon T. Reconciling theories of dominance with
the relative rates of adaptive substitution on sex chromosomes and autosomes.
Proceedings of the National Academy of Sciences of the United States of America.
2024;121(44). doi:10.1073/pnas.2406335121
apa: Mcdonough, Y., Ruzicka, F., & Connallon, T. (2024). Reconciling theories
of dominance with the relative rates of adaptive substitution on sex chromosomes
and autosomes. Proceedings of the National Academy of Sciences of the United
States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2406335121
chicago: Mcdonough, Yasmine, Filip Ruzicka, and Tim Connallon. “Reconciling Theories
of Dominance with the Relative Rates of Adaptive Substitution on Sex Chromosomes
and Autosomes.” Proceedings of the National Academy of Sciences of the United
States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2406335121.
ieee: Y. Mcdonough, F. Ruzicka, and T. Connallon, “Reconciling theories of dominance
with the relative rates of adaptive substitution on sex chromosomes and autosomes,”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 121, no. 44. National Academy of Sciences, 2024.
ista: Mcdonough Y, Ruzicka F, Connallon T. 2024. Reconciling theories of dominance
with the relative rates of adaptive substitution on sex chromosomes and autosomes.
Proceedings of the National Academy of Sciences of the United States of America.
121(44), e2406335121.
mla: Mcdonough, Yasmine, et al. “Reconciling Theories of Dominance with the Relative
Rates of Adaptive Substitution on Sex Chromosomes and Autosomes.” Proceedings
of the National Academy of Sciences of the United States of America, vol.
121, no. 44, e2406335121, National Academy of Sciences, 2024, doi:10.1073/pnas.2406335121.
short: Y. Mcdonough, F. Ruzicka, T. Connallon, Proceedings of the National Academy
of Sciences of the United States of America 121 (2024).
das_tickbox: '1'
dataavailabilitystatement: All study data are included in the article and/or supporting
information.
date_created: 2024-10-27T23:01:44Z
date_published: 2024-10-29T00:00:00Z
date_updated: 2026-09-24T11:12:56Z
day: '29'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1073/pnas.2406335121
ec_funded: 1
external_id:
isi:
- '001359216400017'
pmid:
- '39436652'
file:
- access_level: open_access
checksum: 73db3c87b35753e0f4324417f164a35e
content_type: application/pdf
creator: dernst
date_created: 2024-11-04T10:29:43Z
date_updated: 2024-11-04T10:29:43Z
file_id: '18501'
file_name: 2024_PNAS_McDonough.pdf
file_size: 1299095
relation: main_file
success: 1
file_date_updated: 2024-11-04T10:29:43Z
fulldoi: https://doi.org/10.1073/pnas.2406335121
has_accepted_license: '1'
intvolume: ' 121'
isi: 1
issue: '44'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
researchdata_availability: yes (supplementary data)
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Reconciling theories of dominance with the relative rates of adaptive substitution
on sex chromosomes and autosomes
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 121
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18761'
abstract:
- lang: eng
text: Termites, together with cockroaches, belong to the Blattodea. They possess
an XX/XY sex determination system which has evolved from an XX/X0 system present
in other Blattodean species, such as cockroaches and wood roaches. Little is currently
known about the sex chromosomes of termites, their gene content, or their evolution.
We here investigate the X chromosome of multiple termite species and compare them
with the X chromosome of cockroaches using genomic and transcriptomic data. We
find that the X chromosome of the termite Macrotermes natalensis is large and
differentiated showing hall marks of sex chromosome evolution such as dosage compensation,
while this does not seem to be the case in the other two termite species investigated
here where sex chromosomes may be evolutionary younger. Furthermore, the X chromosome
in M. natalensis is different from the X chromosome found in the cockroach Blattella
germanica indicating that sex chromosome turn-over events may have happened during
termite evolution.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "urthermore, we thank all lab members and collaborators for feedback
on the project. Specifically, Dino McMahon provided R. flavipes males and females,
Judith Korb provided C. secundus males and females, gave feedback on the project
and discussed questions on termite reproduction, Mireille Vasseur-Cognet provided
M. natalensis males and females, Ariana Macon performed the lab work for sequencing
and the Vicoso group gave critical feedback on the project. We furthermore thank
the HPC group at IST Austria and Christian Meesters at JGU Mainz for their technical
support.\r\nThis work was supported by a Österreichischer Wissenschaftsfonds (FWF)
grant of the Meitner Programme to A.K.H. (project number M 2484), funding by the
Deutsche Forschungsgemeinschaft (DFG) of the Research Training Group GenEvo (project
number 407023052) to A.K.H., R.F., and A.D., and funding of the DFG within the Schwerpunktprogramm
Gevol to A.K.H. and R.M. (project number 503256468)."
article_number: evae265
article_processing_charge: Yes
article_type: original
author:
- first_name: Roxanne
full_name: Fraser, Roxanne
last_name: Fraser
- first_name: Ruth
full_name: Moraa, Ruth
last_name: Moraa
- first_name: Annika
full_name: Djolai, Annika
last_name: Djolai
- first_name: Nils
full_name: Meisenheimer, Nils
last_name: Meisenheimer
- first_name: Sophie
full_name: Laube, Sophie
last_name: Laube
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
citation:
ama: Fraser R, Moraa R, Djolai A, et al. Evidence for a novel X chromosome in termites.
Genome Biology and Evolution. 2024;16(12). doi:10.1093/gbe/evae265
apa: Fraser, R., Moraa, R., Djolai, A., Meisenheimer, N., Laube, S., Vicoso, B.,
& Huylmans, A. K. (2024). Evidence for a novel X chromosome in termites. Genome
Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evae265
chicago: Fraser, Roxanne, Ruth Moraa, Annika Djolai, Nils Meisenheimer, Sophie Laube,
Beatriz Vicoso, and Ann K Huylmans. “Evidence for a Novel X Chromosome in Termites.”
Genome Biology and Evolution. Oxford University Press, 2024. https://doi.org/10.1093/gbe/evae265.
ieee: R. Fraser et al., “Evidence for a novel X chromosome in termites,”
Genome Biology and Evolution, vol. 16, no. 12. Oxford University Press,
2024.
ista: Fraser R, Moraa R, Djolai A, Meisenheimer N, Laube S, Vicoso B, Huylmans AK.
2024. Evidence for a novel X chromosome in termites. Genome Biology and Evolution.
16(12), evae265.
mla: Fraser, Roxanne, et al. “Evidence for a Novel X Chromosome in Termites.” Genome
Biology and Evolution, vol. 16, no. 12, evae265, Oxford University Press,
2024, doi:10.1093/gbe/evae265.
short: R. Fraser, R. Moraa, A. Djolai, N. Meisenheimer, S. Laube, B. Vicoso, A.K.
Huylmans, Genome Biology and Evolution 16 (2024).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: Male and female DNAseq reads for the termites C. secundus,
M. natalensis, and R. flavipes can be found in the NCBI SRA under accession codes
SRR30467421-SRR30467422, SRR30467423-SRR30467424, and SRR30467425-SRR30467426, respectively
(all BioProject PRJNA1153745)
date_created: 2025-01-05T23:01:58Z
date_published: 2024-12-01T00:00:00Z
date_updated: 2026-09-24T11:16:00Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/gbe/evae265
external_id:
isi:
- '001380841100001'
pmid:
- '39658246'
file:
- access_level: open_access
checksum: 9cf8fd14580dd694dd810ccca808ad0e
content_type: application/pdf
creator: dernst
date_created: 2025-01-08T08:28:07Z
date_updated: 2025-01-08T08:28:07Z
file_id: '18772'
file_name: 2024_GBE_Fraser.pdf
file_size: 795106
relation: main_file
success: 1
file_date_updated: 2025-01-08T08:28:07Z
fulldoi: https://doi.org/10.1093/gbe/evae265
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '12'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26641CAC-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02484
name: Sex Determination in Termites
publication: Genome Biology and Evolution
publication_identifier:
eissn:
- 1759-6653
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Evidence for a novel X chromosome in termites
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 16
year: '2024'
...
---
_id: '17362'
abstract:
- lang: eng
text: This is the supplementary data for the paper titled "Single-nucleus atlas
of the Artemia female reproductive system suggests germline repression of the
Z chromosome", where we described the generation and analysis of single-nucleus
expression and chromatin-accessibility data from the female reproductive system
of Artemia franciscana. We compared our dataset to the published Drosophila single-nucleus
data (over 400 million years of divergence) and highlighted the extreme conservation
of several of the molecular pathways of oogenesis and meiosis. We found evidence
of global transcriptional quiescence and chromatin condensation in late germ cells,
highlighting the conserved role of this repressive stage in arthropod oogenesis.
Additionally, we explored the expression patterns of the ZW sex chromosomes during
oogenesis. Our data shows that the Z-chromosome is consistently downregulated
in germline cells. While this is partly driven by a lack of dosage compensation
in the germline, a subset of cells show stronger repression of the Z chromosome.
acknowledged_ssus:
- _id: ScienComp
article_processing_charge: No
author:
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: 'Elkrewi MN, Vicoso B. Data for: “Single-nucleus atlas of the Artemia female
reproductive system suggests germline repression of the Z chromosome.” 2024. doi:10.15479/AT:ISTA:17362'
apa: 'Elkrewi, M. N., & Vicoso, B. (2024). Data for: “Single-nucleus atlas of
the Artemia female reproductive system suggests germline repression of the Z chromosome.”
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:17362'
chicago: 'Elkrewi, Marwan N, and Beatriz Vicoso. “Data for: ‘Single-Nucleus Atlas
of the Artemia Female Reproductive System Suggests Germline Repression of the
Z Chromosome.’” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:17362.'
ieee: 'M. N. Elkrewi and B. Vicoso, “Data for: ‘Single-nucleus atlas of the Artemia
female reproductive system suggests germline repression of the Z chromosome.’”
Institute of Science and Technology Austria, 2024.'
ista: 'Elkrewi MN, Vicoso B. 2024. Data for: ‘Single-nucleus atlas of the Artemia
female reproductive system suggests germline repression of the Z chromosome’,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:17362.'
mla: 'Elkrewi, Marwan N., and Beatriz Vicoso. Data for: “Single-Nucleus Atlas
of the Artemia Female Reproductive System Suggests Germline Repression of the
Z Chromosome.” Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:17362.'
short: M.N. Elkrewi, B. Vicoso, (2024).
corr_author: '1'
date_created: 2024-08-02T07:27:45Z
date_published: 2024-08-05T00:00:00Z
date_updated: 2026-09-24T11:17:37Z
day: '05'
ddc:
- '576'
department:
- _id: GradSch
- _id: BeVi
doi: 10.15479/AT:ISTA:17362
file:
- access_level: open_access
checksum: 26b5d41b3103f4284dd97d56e370a5b6
content_type: text/plain
creator: melkrewi
date_created: 2024-08-05T22:24:18Z
date_updated: 2024-08-05T22:24:18Z
file_id: '17394'
file_name: README.txt
file_size: 2465
relation: main_file
success: 1
- access_level: open_access
checksum: 95adab5e36148015da313505e3910707
content_type: application/x-zip-compressed
creator: melkrewi
date_created: 2024-08-05T23:28:52Z
date_updated: 2024-08-05T23:28:52Z
file_id: '17395'
file_name: Data_artemia_single_nucleus_atlas.zip
file_size: 2526735400
relation: main_file
success: 1
file_date_updated: 2024-08-05T23:28:52Z
fulldoi: https://doi.org/10.15479/AT:ISTA:17362
has_accepted_license: '1'
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396
grant_number: F8810
name: The highjacking of meiosis for asexual reproduction
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '17890'
relation: used_in_publication
status: public
status: public
title: 'Data for: "Single-nucleus atlas of the Artemia female reproductive system
suggests germline repression of the Z chromosome"'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18952'
abstract:
- lang: eng
text: 'A seventh blind test of crystal structure prediction was organized by the
Cambridge Crystallographic Data Centre featuring seven target systems of varying
complexity: a silicon and iodine-containing molecule, a copper coordination complex,
a near-rigid molecule, a cocrystal, a polymorphic small agrochemical, a highly
flexible polymorphic drug candidate, and a polymorphic morpholine salt. In this
first of two parts focusing on structure generation methods, many crystal structure
prediction (CSP) methods performed well for the small but flexible agrochemical
compound, successfully reproducing the experimentally observed crystal structures,
while few groups were successful for the systems of higher complexity. A powder
X-ray diffraction (PXRD) assisted exercise demonstrated the use of CSP in successfully
determining a crystal structure from a low-quality PXRD pattern. The use of CSP
in the prediction of likely cocrystal stoichiometry was also explored, demonstrating
multiple possible approaches. Crystallographic disorder emerged as an important
theme throughout the test as both a challenge for analysis and a major achievement
where two groups blindly predicted the existence of disorder for the first time.
Additionally, large-scale comparisons of the sets of predicted crystal structures
also showed that some methods yield sets that largely contain the same crystal
structures.'
acknowledgement: "The CCDC Blind Test Team. The CCDC organizers (L. M. Hunnisett,
J. Nyman, N. Francia, I. Sugden, G. Sadiq, and J. C. Cole) gratefully acknowledge
numerous CCDC colleagues for\r\ntheir helpful feedback and suggestions on the manuscript
(P. McCabe, E. Pidcock, P. Martinez-Bulit, C. Kingsbury), providing useful python
knowledge (A. Moldovan), providing and maintaining internal compute resources (K.
Taylor, M. Burling, J. Swift, L. Wallis), monitoring and depositing structures in
the CSD (S. Ward, K. Orzechowska, V. Menon), support in organization of the blind
test meeting (E. Clarke),and improvements to the Crystal Packing Similarity tool
(M.\r\nRead). Data analysis was performed using resources provided by the Cambridge
Service for Data Driven Discovery (CSD3) operated by the University of Cambridge
Research Computing Service (www.csd3.cam.ac.uk), provided by Dell EMC and Intel
using Tier-2 funding from the Engineering and Physical Sciences Research Council
(capital grant EP/T022159/1), and DiRAC funding from the Science and Technology
Facilities Council (www.dirac.ac.uk). N. Francia thanks M. Salvalaglio for advice
on the metadynamics simulations and the University College London for providing
access to the Kathleen High Performance Computing Facility Kathleen@UCL) on which
simulations were performed. N. Francia also thanks V. Kurlin and D. E. Widdowson
for counselling on crystal structure similarity. I. Sugden and N. Francia participated
in the blind test as members of Groups 1 and 24, respectively. They were involved
in the analysis of the results.\r\nand in writing this paper only after all results
were made\r\navailable to participants."
article_processing_charge: Yes (in subscription journal)
article_type: original
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last_name: Nyman
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full_name: Francia, Nicholas
last_name: Francia
- first_name: Nathan S.
full_name: Abraham, Nathan S.
last_name: Abraham
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full_name: Adjiman, Claire S.
last_name: Adjiman
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last_name: Alkhidir
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last_name: Almehairbi
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last_name: Anelli
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full_name: Anstine, Dylan M.
last_name: Anstine
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last_name: Anthony
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last_name: Arnold
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last_name: Bellucci
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full_name: Bhardwaj, Rajni M.
last_name: Bhardwaj
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full_name: Bier, Imanuel
last_name: Bier
- first_name: Joanna A.
full_name: Bis, Joanna A.
last_name: Bis
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last_name: Bowskill
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last_name: Bramley
- first_name: Jan Gerit
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full_name: Cadden, Joseph
last_name: Cadden
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last_name: Carino
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last_name: Chang
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id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Sarah M.
full_name: Clarke, Sarah M.
last_name: Clarke
- first_name: Simon J.
full_name: Coles, Simon J.
last_name: Coles
- first_name: Richard I.
full_name: Cooper, Richard I.
last_name: Cooper
- first_name: Ricky
full_name: Couch, Ricky
last_name: Couch
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last_name: Cuadrado
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last_name: Darden
- first_name: Graeme M.
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last_name: Day
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last_name: Dhokale
- first_name: Bouke P.
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last_name: van Eijck
- first_name: Mark R. J.
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last_name: Elsegood
- first_name: Dzmitry
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last_name: Firaha
- first_name: Wenbo
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last_name: Fu
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last_name: Fukuzawa
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last_name: Glover
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last_name: Goto
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last_name: Hoja
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- first_name: He
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- first_name: Alexander
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- first_name: Congcong
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- first_name: Yifei Michelle
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- first_name: Zenghui
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last_name: Liu
- first_name: Zhi-Pan
full_name: Liu, Zhi-Pan
last_name: Liu
- first_name: Joseph W.
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- first_name: Zahrasadat
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- first_name: Hari S.
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last_name: Shi
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last_name: Skillman
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full_name: Song, Hongxing
last_name: Song
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last_name: Strasser
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full_name: van de Streek, Jacco
last_name: van de Streek
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full_name: Sugden, Isaac J.
last_name: Sugden
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full_name: Sun, Guangxu
last_name: Sun
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full_name: Szalewicz, Krzysztof
last_name: Szalewicz
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full_name: Tan, Benjamin I.
last_name: Tan
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full_name: Tan, Lu
last_name: Tan
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full_name: Tarczynski, Frank
last_name: Tarczynski
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full_name: Taylor, Christopher R.
last_name: Taylor
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full_name: Tkatchenko, Alexandre
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last_name: Tom
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full_name: Utsumi, Yohei
last_name: Utsumi
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full_name: Vogt-Maranto, Leslie
last_name: Vogt-Maranto
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full_name: Weatherston, Jake
last_name: Weatherston
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full_name: Wilkinson, Luke J.
last_name: Wilkinson
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full_name: Willacy, Robert D.
last_name: Willacy
- first_name: Lukasz
full_name: Wojtas, Lukasz
last_name: Wojtas
- first_name: Grahame R.
full_name: Woollam, Grahame R.
last_name: Woollam
- first_name: Zhuocen
full_name: Yang, Zhuocen
last_name: Yang
- first_name: Etsuo
full_name: Yonemochi, Etsuo
last_name: Yonemochi
- first_name: Xin
full_name: Yue, Xin
last_name: Yue
- first_name: Qun
full_name: Zeng, Qun
last_name: Zeng
- first_name: Yizu
full_name: Zhang, Yizu
last_name: Zhang
- first_name: Tian
full_name: Zhou, Tian
last_name: Zhou
- first_name: Yunfei
full_name: Zhou, Yunfei
last_name: Zhou
- first_name: Roman
full_name: Zubatyuk, Roman
last_name: Zubatyuk
- first_name: Jason C.
full_name: Cole, Jason C.
last_name: Cole
citation:
ama: 'Hunnisett LM, Nyman J, Francia N, et al. The seventh blind test of crystal
structure prediction: Structure generation methods. Acta Crystallographica
Section B. 2024;80(6):517-547. doi:10.1107/s2052520624007492'
apa: 'Hunnisett, L. M., Nyman, J., Francia, N., Abraham, N. S., Adjiman, C. S.,
Aitipamula, S., … Cole, J. C. (2024). The seventh blind test of crystal structure
prediction: Structure generation methods. Acta Crystallographica Section B.
International Union of Crystallography. https://doi.org/10.1107/s2052520624007492'
chicago: 'Hunnisett, Lily M., Jonas Nyman, Nicholas Francia, Nathan S. Abraham,
Claire S. Adjiman, Srinivasulu Aitipamula, Tamador Alkhidir, et al. “The Seventh
Blind Test of Crystal Structure Prediction: Structure Generation Methods.” Acta
Crystallographica Section B. International Union of Crystallography, 2024.
https://doi.org/10.1107/s2052520624007492.'
ieee: 'L. M. Hunnisett et al., “The seventh blind test of crystal structure
prediction: Structure generation methods,” Acta Crystallographica Section B,
vol. 80, no. 6. International Union of Crystallography, pp. 517–547, 2024.'
ista: 'Hunnisett LM et al. 2024. The seventh blind test of crystal structure prediction:
Structure generation methods. Acta Crystallographica Section B. 80(6), 517–547.'
mla: 'Hunnisett, Lily M., et al. “The Seventh Blind Test of Crystal Structure Prediction:
Structure Generation Methods.” Acta Crystallographica Section B, vol. 80,
no. 6, International Union of Crystallography, 2024, pp. 517–47, doi:10.1107/s2052520624007492.'
short: L.M. Hunnisett, J. Nyman, N. Francia, N.S. Abraham, C.S. Adjiman, S. Aitipamula,
T. Alkhidir, M. Almehairbi, A. Anelli, D.M. Anstine, J.E. Anthony, J.E. Arnold,
F. Bahrami, M.A. Bellucci, R.M. Bhardwaj, I. Bier, J.A. Bis, A.D. Boese, D.H.
Bowskill, J. Bramley, J.G. Brandenburg, D.E. Braun, P.W.V. Butler, J. Cadden,
S. Carino, E.J. Chan, C. Chang, B. Cheng, S.M. Clarke, S.J. Coles, R.I. Cooper,
R. Couch, R. Cuadrado, T. Darden, G.M. Day, H. Dietrich, Y. Ding, A. DiPasquale,
B. Dhokale, B.P. van Eijck, M.R.J. Elsegood, D. Firaha, W. Fu, K. Fukuzawa, J.
Glover, H. Goto, C. Greenwell, R. Guo, J. Harter, J. Helfferich, D.W.M. Hofmann,
J. Hoja, J. Hone, R. Hong, G. Hutchison, Y. Ikabata, O. Isayev, O. Ishaque, V.
Jain, Y. Jin, A. Jing, E.R. Johnson, I. Jones, K.V.J. Jose, E.A. Kabova, A. Keates,
P.F. Kelly, D. Khakimov, S. Konstantinopoulos, L.N. Kuleshova, H. Li, X. Lin,
A. List, C. Liu, Y.M. Liu, Z. Liu, Z.-P. Liu, J.W. Lubach, N. Marom, A.A. Maryewski,
H. Matsui, A. Mattei, R.A. Mayo, J.W. Melkumov, S. Mohamed, Z. Momenzadeh Abardeh,
H.S. Muddana, N. Nakayama, K.S. Nayal, M.A. Neumann, R. Nikhar, S. Obata, D. O’Connor,
A.R. Oganov, K. Okuwaki, A. Otero-de-la-Roza, C.C. Pantelides, S. Parkin, C.J.
Pickard, L. Pilia, T. Pivina, R. Podeszwa, A.J.A. Price, L.S. Price, S.L. Price,
M.R. Probert, A. Pulido, G.R. Ramteke, A.U. Rehman, S.M. Reutzel-Edens, J. Rogal,
M.J. Ross, A.F. Rumson, G. Sadiq, Z.M. Saeed, A. Salimi, M. Salvalaglio, L. Sanders
de Almada, K. Sasikumar, S. Sekharan, C. Shang, K. Shankland, K. Shinohara, B.
Shi, X. Shi, A.G. Skillman, H. Song, N. Strasser, J. van de Streek, I.J. Sugden,
G. Sun, K. Szalewicz, B.I. Tan, L. Tan, F. Tarczynski, C.R. Taylor, A. Tkatchenko,
R. Tom, M.E. Tuckerman, Y. Utsumi, L. Vogt-Maranto, J. Weatherston, L.J. Wilkinson,
R.D. Willacy, L. Wojtas, G.R. Woollam, Z. Yang, E. Yonemochi, X. Yue, Q. Zeng,
Y. Zhang, T. Zhou, Y. Zhou, R. Zubatyuk, J.C. Cole, Acta Crystallographica Section
B 80 (2024) 517–547.
das_tickbox: '0'
date_created: 2025-01-29T11:07:36Z
date_published: 2024-12-01T00:00:00Z
date_updated: 2026-09-24T11:31:46Z
day: '01'
ddc:
- '540'
department:
- _id: BiCh
doi: 10.1107/s2052520624007492
external_id:
isi:
- '001388840500003'
pmid:
- '39405196'
file:
- access_level: open_access
checksum: 33b8083e76564cc918182b0b0b2cc023
content_type: application/pdf
creator: dernst
date_created: 2025-01-29T11:09:48Z
date_updated: 2025-01-29T11:09:48Z
file_id: '18954'
file_name: 2024_ActaCrystallographicaB_Hunnisett.pdf
file_size: 10061037
relation: main_file
success: 1
file_date_updated: 2025-01-29T11:09:48Z
fulldoi: https://doi.org/10.1107/s2052520624007492
has_accepted_license: '1'
intvolume: ' 80'
isi: 1
issue: '6'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 517-547
pmid: 1
publication: Acta Crystallographica Section B
publication_identifier:
issn:
- 2052-5206
publication_status: published
publisher: International Union of Crystallography
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: 'The seventh blind test of crystal structure prediction: Structure generation
methods'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 80
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '15311'
abstract:
- lang: eng
text: Materials with low thermal conductivity usually have complex crystal structures.
Herein we experimentally find that a simple crystal structure material AgTlI2
(I4/mcm) owns an extremely low thermal conductivity of 0.25 W/mK at room temperature.
To understand this anomaly, we perform in-depth theoretical studies based on ab
initio molecular dynamics simulations and anharmonic lattice dynamics. We find
that the unique atomic arrangement and weak chemical bonding provide a permissive
environment for strong oscillations of Ag atoms, leading to a considerable rattling
behaviour and giant lattice anharmonicity. This feature is also verified by the
experimental probability density function refinement of single-crystal diffraction.
The particularly strong anharmonicity breaks down the conventional phonon gas
model, giving rise to non-negligible wavelike phonon behaviours in AgTlI2 at 300
K. Intriguingly, unlike many strongly anharmonic materials where a small propagative
thermal conductivity is often accompanied by a large diffusive thermal conductivity,
we find an unusual coexistence of ultralow propagative and diffusive thermal conductivities
in AgTlI2 based on the thermal transport unified theory. This study underscores
the potential of simple crystal structures in achieving low thermal conductivity
and encourages further experimental research to enrich the family of materials
with ultralow thermal conductivity.
acknowledgement: "We thank Bingqing Cheng (IST Austria) and Terumasa Tadano (NIMS\r\nJapan)
for reading the manuscript and providing insightful comments.\r\nThis work is supported
by the Research Grants Council of Hong Kong\r\n(C7002-22Y and 17318122). ZZ acknowledges
the European Union’s\r\nHorizon 2020 research and innovation programme under the
Marie\r\nSkłodowska-Curie grant agreement No. 101034413. XS acknowledges\r\nfunding
from the European Union’s Horizon 2020 research and innovation programme under the
Marie Sklodowska-Curie grant agreement\r\nNo. 101034329, and the WINNING Normandy
Programme supported by\r\nthe Normandy Region. The computations were performed using\r\nresearch
computing facilities offered by Information Technology Services, at the University
of Hong Kong."
article_number: '3007'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Zezhu
full_name: Zeng, Zezhu
id: 54a2c730-803f-11ed-ab7e-95b29d2680e7
last_name: Zeng
orcid: 0000-0001-5126-4928
- first_name: Xingchen
full_name: Shen, Xingchen
last_name: Shen
- first_name: Ruihuan
full_name: Cheng, Ruihuan
last_name: Cheng
- first_name: Olivier
full_name: Perez, Olivier
last_name: Perez
- first_name: Niuchang
full_name: Ouyang, Niuchang
last_name: Ouyang
- first_name: Zheyong
full_name: Fan, Zheyong
last_name: Fan
- first_name: Pierric
full_name: Lemoine, Pierric
last_name: Lemoine
- first_name: Bernard
full_name: Raveau, Bernard
last_name: Raveau
- first_name: Emmanuel
full_name: Guilmeau, Emmanuel
last_name: Guilmeau
- first_name: Yue
full_name: Chen, Yue
last_name: Chen
citation:
ama: Zeng Z, Shen X, Cheng R, et al. Pushing thermal conductivity to its lower limit
in crystals with simple structures. Nature Communications. 2024;15. doi:10.1038/s41467-024-46799-3
apa: Zeng, Z., Shen, X., Cheng, R., Perez, O., Ouyang, N., Fan, Z., … Chen, Y. (2024).
Pushing thermal conductivity to its lower limit in crystals with simple structures.
Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-46799-3
chicago: Zeng, Zezhu, Xingchen Shen, Ruihuan Cheng, Olivier Perez, Niuchang Ouyang,
Zheyong Fan, Pierric Lemoine, Bernard Raveau, Emmanuel Guilmeau, and Yue Chen.
“Pushing Thermal Conductivity to Its Lower Limit in Crystals with Simple Structures.”
Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-46799-3.
ieee: Z. Zeng et al., “Pushing thermal conductivity to its lower limit in
crystals with simple structures,” Nature Communications, vol. 15. Springer
Nature, 2024.
ista: Zeng Z, Shen X, Cheng R, Perez O, Ouyang N, Fan Z, Lemoine P, Raveau B, Guilmeau
E, Chen Y. 2024. Pushing thermal conductivity to its lower limit in crystals with
simple structures. Nature Communications. 15, 3007.
mla: Zeng, Zezhu, et al. “Pushing Thermal Conductivity to Its Lower Limit in Crystals
with Simple Structures.” Nature Communications, vol. 15, 3007, Springer
Nature, 2024, doi:10.1038/s41467-024-46799-3.
short: Z. Zeng, X. Shen, R. Cheng, O. Perez, N. Ouyang, Z. Fan, P. Lemoine, B. Raveau,
E. Guilmeau, Y. Chen, Nature Communications 15 (2024).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: "All necessary source data files generated for this study
are available in the SI repository https://github.com/ZengZezhu/Thermal-conductivity-AgTlI2
see ref 72.\r\n72. Zeng, Z. et al. Source data for pushing thermal conductivity
to its lower limit in crystals with simple structures. Zenodo (2024)."
date_created: 2024-04-14T22:01:00Z
date_published: 2024-04-08T00:00:00Z
date_updated: 2026-09-24T11:20:55Z
day: '08'
ddc:
- '530'
department:
- _id: BiCh
doi: 10.1038/s41467-024-46799-3
ec_funded: 1
external_id:
arxiv:
- '2310.01838'
isi:
- '001198902100029'
pmid:
- '38589376'
file:
- access_level: open_access
checksum: f81bd6ba42f740d060fb446eeebc1035
content_type: application/pdf
creator: cchlebak
date_created: 2024-04-26T10:34:07Z
date_updated: 2024-04-26T10:34:07Z
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file_name: 2024_NatComm_Zeng.pdf
file_size: 3049375
relation: main_file
success: 1
file_date_updated: 2024-04-26T10:34:07Z
fulldoi: https://doi.org/10.1038/s41467-024-46799-3
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Pushing thermal conductivity to its lower limit in crystals with simple structures
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 15
year: '2024'
...