---
_id: '18216'
abstract:
- lang: eng
text: Protein structure, both at the global and local level, dictates function.
Proteins fold from chains of amino acids, forming secondary structures, α-helices
and β-strands, that, at least for globular proteins, subsequently fold into a
three-dimensional structure. Here, we show that a Ramachandran-type plot focusing
on the two dihedral angles separated by the peptide bond, and entirely contained
within an amino acid pair, defines a local structural unit. We further demonstrate
the usefulness of this cross-peptide-bond Ramachandran plot by showing that it
captures β-turn conformations in coil regions, that traditional Ramachandran plot
outliers fall into occupied regions of our plot, and that thermophilic proteins
prefer specific amino acid pair conformations. Further, we demonstrate experimentally
that the effect of a point mutation on backbone conformation and protein stability
depends on the amino acid pair context, i.e., the identity of the adjacent amino
acid, in a manner predictable by our method.
article_number: e2301064120
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Aviv A.
full_name: Rosenberg, Aviv A.
last_name: Rosenberg
- first_name: Nitsan
full_name: Yehishalom, Nitsan
last_name: Yehishalom
- first_name: Ailie
full_name: Marx, Ailie
last_name: Marx
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
citation:
ama: Rosenberg AA, Yehishalom N, Marx A, Bronstein AM. An amino-domino model described
by a cross-peptide-bond Ramachandran plot defines amino acid pairs as local structural
units. Proceedings of the National Academy of Sciences. 2023;120(44). doi:10.1073/pnas.2301064120
apa: Rosenberg, A. A., Yehishalom, N., Marx, A., & Bronstein, A. M. (2023).
An amino-domino model described by a cross-peptide-bond Ramachandran plot defines
amino acid pairs as local structural units. Proceedings of the National Academy
of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2301064120
chicago: Rosenberg, Aviv A., Nitsan Yehishalom, Ailie Marx, and Alex M. Bronstein.
“An Amino-Domino Model Described by a Cross-Peptide-Bond Ramachandran Plot Defines
Amino Acid Pairs as Local Structural Units.” Proceedings of the National Academy
of Sciences. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2301064120.
ieee: A. A. Rosenberg, N. Yehishalom, A. Marx, and A. M. Bronstein, “An amino-domino
model described by a cross-peptide-bond Ramachandran plot defines amino acid pairs
as local structural units,” Proceedings of the National Academy of Sciences,
vol. 120, no. 44. National Academy of Sciences, 2023.
ista: Rosenberg AA, Yehishalom N, Marx A, Bronstein AM. 2023. An amino-domino model
described by a cross-peptide-bond Ramachandran plot defines amino acid pairs as
local structural units. Proceedings of the National Academy of Sciences. 120(44),
e2301064120.
mla: Rosenberg, Aviv A., et al. “An Amino-Domino Model Described by a Cross-Peptide-Bond
Ramachandran Plot Defines Amino Acid Pairs as Local Structural Units.” Proceedings
of the National Academy of Sciences, vol. 120, no. 44, e2301064120, National
Academy of Sciences, 2023, doi:10.1073/pnas.2301064120.
short: A.A. Rosenberg, N. Yehishalom, A. Marx, A.M. Bronstein, Proceedings of the
National Academy of Sciences 120 (2023).
date_created: 2024-10-08T12:50:36Z
date_published: 2023-10-25T00:00:00Z
date_updated: 2024-10-09T11:55:12Z
day: '25'
doi: 10.1073/pnas.2301064120
extern: '1'
external_id:
pmid:
- '37878722'
intvolume: ' 120'
issue: '44'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.2301064120
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: An amino-domino model described by a cross-peptide-bond Ramachandran plot defines
amino acid pairs as local structural units
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 120
year: '2023'
...
---
_id: '13201'
abstract:
- lang: eng
text: As a crucial nitrogen source, nitrate (NO3−) is a key nutrient for plants.
Accordingly, root systems adapt to maximize NO3− availability, a developmental
regulation also involving the phytohormone auxin. Nonetheless, the molecular mechanisms
underlying this regulation remain poorly understood. Here, we identify low-nitrate-resistant
mutant (lonr) in Arabidopsis (Arabidopsis thaliana), whose root growth fails to
adapt to low-NO3− conditions. lonr2 is defective in the high-affinity NO3− transporter
NRT2.1. lonr2 (nrt2.1) mutants exhibit defects in polar auxin transport, and their
low-NO3−-induced root phenotype depends on the PIN7 auxin exporter activity. NRT2.1
directly associates with PIN7 and antagonizes PIN7-mediated auxin efflux depending
on NO3− levels. These results reveal a mechanism by which NRT2.1 in response to
NO3− limitation directly regulates auxin transport activity and, thus, root growth.
This adaptive mechanism contributes to the root developmental plasticity to help
plants cope with changes in NO3− availability.
acknowledgement: We are grateful to Caifu Jiang for providing ethyl metha-nesulfonate-
mutagenized population, Yi Wang for providing Xenopus oocytes, Jun Fan and Zhaosheng
Kong for providing tobacco BY- 2 cells, and Claus Schwechheimer, Alain Gojon, and
Shutang Tan for helpful discussions. This work was supported by the National Key
Research and Development Program of China (2021YFF1000500), the National Natural Science Foundation of China (32170265 and 32022007), Hainan Provincial Natural Science Foundation of China (323CXTD379), Chinese Universities Scientific Fund (2023TC019), Beijing Municipal Natural Science Foundation (5192011), Beijing Outstanding University Discipline Program, and China
Postdoctoral Science Foundation (BH2020259460).
article_number: e2221313120
article_processing_charge: No
article_type: original
author:
- first_name: Yalu
full_name: Wang, Yalu
last_name: Wang
- first_name: Zhi
full_name: Yuan, Zhi
last_name: Yuan
- first_name: Jinyi
full_name: Wang, Jinyi
last_name: Wang
- first_name: Huixin
full_name: Xiao, Huixin
last_name: Xiao
- first_name: Lu
full_name: Wan, Lu
last_name: Wan
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Yan
full_name: Guo, Yan
last_name: Guo
- first_name: Zhizhong
full_name: Gong, Zhizhong
last_name: Gong
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jing
full_name: Zhang, Jing
last_name: Zhang
citation:
ama: Wang Y, Yuan Z, Wang J, et al. The nitrate transporter NRT2.1 directly antagonizes
PIN7-mediated auxin transport for root growth adaptation. Proceedings of the
National Academy of Sciences of the United States of America. 2023;120(25).
doi:10.1073/pnas.2221313120
apa: Wang, Y., Yuan, Z., Wang, J., Xiao, H., Wan, L., Li, L., … Zhang, J. (2023).
The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport
for root growth adaptation. Proceedings of the National Academy of Sciences
of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2221313120
chicago: Wang, Yalu, Zhi Yuan, Jinyi Wang, Huixin Xiao, Lu Wan, Lanxin Li, Yan Guo,
Zhizhong Gong, Jiří Friml, and Jing Zhang. “The Nitrate Transporter NRT2.1 Directly
Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2221313120.
ieee: Y. Wang et al., “The nitrate transporter NRT2.1 directly antagonizes
PIN7-mediated auxin transport for root growth adaptation,” Proceedings of the
National Academy of Sciences of the United States of America, vol. 120, no.
25. National Academy of Sciences, 2023.
ista: Wang Y, Yuan Z, Wang J, Xiao H, Wan L, Li L, Guo Y, Gong Z, Friml J, Zhang
J. 2023. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin
transport for root growth adaptation. Proceedings of the National Academy of Sciences
of the United States of America. 120(25), e2221313120.
mla: Wang, Yalu, et al. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated
Auxin Transport for Root Growth Adaptation.” Proceedings of the National Academy
of Sciences of the United States of America, vol. 120, no. 25, e2221313120,
National Academy of Sciences, 2023, doi:10.1073/pnas.2221313120.
short: Y. Wang, Z. Yuan, J. Wang, H. Xiao, L. Wan, L. Li, Y. Guo, Z. Gong, J. Friml,
J. Zhang, Proceedings of the National Academy of Sciences of the United States
of America 120 (2023).
date_created: 2023-07-09T22:01:12Z
date_published: 2023-06-12T00:00:00Z
date_updated: 2023-12-13T23:30:04Z
day: '12'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1073/pnas.2221313120
external_id:
isi:
- '001030689600003'
pmid:
- '37307446'
file:
- access_level: open_access
checksum: d800e06252eaefba28531fa9440f23f0
content_type: application/pdf
creator: alisjak
date_created: 2023-07-10T08:48:40Z
date_updated: 2023-12-13T23:30:03Z
embargo: 2023-12-12
file_id: '13204'
file_name: 2023_PNAS_Wang.pdf
file_size: 5244581
relation: main_file
file_date_updated: 2023-12-13T23:30:03Z
has_accepted_license: '1'
intvolume: ' 120'
isi: 1
issue: '25'
language:
- iso: eng
month: '06'
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'
scopus_import: '1'
status: public
title: The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport
for root growth adaptation
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 120
year: '2023'
...
---
_id: '10888'
abstract:
- lang: eng
text: Despite the growing interest in using chemical genetics in plant research,
small molecule target identification remains a major challenge. The cellular thermal
shift assay coupled with high-resolution mass spectrometry (CETSA MS) that monitors
changes in the thermal stability of proteins caused by their interactions with
small molecules, other proteins, or posttranslational modifications, allows the
discovery of drug targets or the study of protein–metabolite and protein–protein
interactions mainly in mammalian cells. To showcase the applicability of this
method in plants, we applied CETSA MS to intact Arabidopsis thaliana cells and
identified the thermal proteome of the plant-specific glycogen synthase kinase
3 (GSK3) inhibitor, bikinin. A comparison between the thermal and the phosphoproteomes
of bikinin revealed the auxin efflux carrier PIN-FORMED1 (PIN1) as a substrate
of the Arabidopsis GSK3s that negatively regulate the brassinosteroid signaling.
We established that PIN1 phosphorylation by the GSK3s is essential for maintaining
its intracellular polarity that is required for auxin-mediated regulation of vascular
patterning in the leaf, thus revealing cross-talk between brassinosteroid and
auxin signaling.
acknowledgement: "We thank Yanhai Yin for providing the anti-BES1 antibody, Johan
Winne and Brenda Callebaut for synthesizing bikinin, Yuki Kondo and Hiroo Fukuda
for published materials, Tomasz Nodzy\x03nski for useful advice, and Martine De
Cock for help in preparing the manuscript. This\r\nwork was supported by the China
Scholarship Council for predoctoral (Q.L. and X.X.) and postdoctoral (Y.Z.) fellowships;
the Agency for Innovation by Science and Technology for a predoctoral fellowship
(W.D.); the Research Foundation-Flanders, Projects G009018N and G002121N (E.R.);
and the VIB TechWatch Fund (E.R.)."
article_number: e2118220119
article_processing_charge: No
article_type: original
author:
- first_name: Qing
full_name: Lu, Qing
last_name: Lu
- first_name: Yonghong
full_name: Zhang, Yonghong
last_name: Zhang
- first_name: Joakim
full_name: Hellner, Joakim
last_name: Hellner
- first_name: Caterina
full_name: Giannini, Caterina
id: e3fdddd5-f6e0-11ea-865d-ca99ee6367f4
last_name: Giannini
- first_name: Xiangyu
full_name: Xu, Xiangyu
last_name: Xu
- first_name: Jarne
full_name: Pauwels, Jarne
last_name: Pauwels
- first_name: Qian
full_name: Ma, Qian
last_name: Ma
- first_name: Wim
full_name: Dejonghe, Wim
last_name: Dejonghe
- first_name: Huibin
full_name: Han, Huibin
id: 31435098-F248-11E8-B48F-1D18A9856A87
last_name: Han
- first_name: Brigitte
full_name: Van De Cotte, Brigitte
last_name: Van De Cotte
- first_name: Francis
full_name: Impens, Francis
last_name: Impens
- first_name: Kris
full_name: Gevaert, Kris
last_name: Gevaert
- first_name: Ive
full_name: De Smet, Ive
last_name: De Smet
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Daniel Martinez
full_name: Molina, Daniel Martinez
last_name: Molina
- first_name: Eugenia
full_name: Russinova, Eugenia
last_name: Russinova
citation:
ama: Lu Q, Zhang Y, Hellner J, et al. Proteome-wide cellular thermal shift assay
reveals unexpected cross-talk between brassinosteroid and auxin signaling. Proceedings
of the National Academy of Sciences of the United States of America. 2022;119(11).
doi:10.1073/pnas.2118220119
apa: Lu, Q., Zhang, Y., Hellner, J., Giannini, C., Xu, X., Pauwels, J., … Russinova,
E. (2022). Proteome-wide cellular thermal shift assay reveals unexpected cross-talk
between brassinosteroid and auxin signaling. Proceedings of the National Academy
of Sciences of the United States of America. National Academy of Sciences.
https://doi.org/10.1073/pnas.2118220119
chicago: Lu, Qing, Yonghong Zhang, Joakim Hellner, Caterina Giannini, Xiangyu Xu,
Jarne Pauwels, Qian Ma, et al. “Proteome-Wide Cellular Thermal Shift Assay Reveals Unexpected
Cross-Talk between Brassinosteroid and Auxin Signaling.” Proceedings of the
National Academy of Sciences of the United States of America. National Academy
of Sciences, 2022. https://doi.org/10.1073/pnas.2118220119.
ieee: Q. Lu et al., “Proteome-wide cellular thermal shift assay reveals unexpected
cross-talk between brassinosteroid and auxin signaling,” Proceedings of the
National Academy of Sciences of the United States of America, vol. 119, no.
11. National Academy of Sciences, 2022.
ista: Lu Q, Zhang Y, Hellner J, Giannini C, Xu X, Pauwels J, Ma Q, Dejonghe W, Han
H, Van De Cotte B, Impens F, Gevaert K, De Smet I, Friml J, Molina DM, Russinova
E. 2022. Proteome-wide cellular thermal shift assay reveals unexpected cross-talk
between brassinosteroid and auxin signaling. Proceedings of the National Academy
of Sciences of the United States of America. 119(11), e2118220119.
mla: Lu, Qing, et al. “Proteome-Wide Cellular Thermal Shift Assay Reveals Unexpected
Cross-Talk between Brassinosteroid and Auxin Signaling.” Proceedings of the
National Academy of Sciences of the United States of America, vol. 119, no.
11, e2118220119, National Academy of Sciences, 2022, doi:10.1073/pnas.2118220119.
short: Q. Lu, Y. Zhang, J. Hellner, C. Giannini, X. Xu, J. Pauwels, Q. Ma, W. Dejonghe,
H. Han, B. Van De Cotte, F. Impens, K. Gevaert, I. De Smet, J. Friml, D.M. Molina,
E. Russinova, Proceedings of the National Academy of Sciences of the United States
of America 119 (2022).
date_created: 2022-03-20T23:01:39Z
date_published: 2022-03-07T00:00:00Z
date_updated: 2025-05-14T11:01:45Z
day: '07'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1073/pnas.2118220119
external_id:
isi:
- '000771756300008'
pmid:
- '35254915'
file:
- access_level: open_access
checksum: 83e0fea7919570d0b519b41193342571
content_type: application/pdf
creator: dernst
date_created: 2022-03-21T09:19:47Z
date_updated: 2022-03-21T09:19:47Z
file_id: '10910'
file_name: 2022_PNAS_Lu.pdf
file_size: 2169534
relation: main_file
success: 1
file_date_updated: 2022-03-21T09:19:47Z
has_accepted_license: '1'
intvolume: ' 119'
isi: 1
issue: '11'
language:
- iso: eng
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
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between
brassinosteroid and auxin signaling
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2022'
...
---
_id: '11702'
abstract:
- lang: eng
text: When Mendel’s work was rediscovered in 1900, and extended to establish classical
genetics, it was initially seen in opposition to Darwin’s theory of evolution
by natural selection on continuous variation, as represented by the biometric
research program that was the foundation of quantitative genetics. As Fisher,
Haldane, and Wright established a century ago, Mendelian inheritance is exactly
what is needed for natural selection to work efficiently. Yet, the synthesis remains
unfinished. We do not understand why sexual reproduction and a fair meiosis predominate
in eukaryotes, or how far these are responsible for their diversity and complexity.
Moreover, although quantitative geneticists have long known that adaptive variation
is highly polygenic, and that this is essential for efficient selection, this
is only now becoming appreciated by molecular biologists—and we still do not have
a good framework for understanding polygenic variation or diffuse function.
acknowledgement: I thank Laura Hayward, Jitka Polechova, and Anja Westram for discussions
and comments.
article_number: e2122147119
article_processing_charge: No
article_type: original
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. The “New Synthesis.” Proceedings of the National Academy of Sciences
of the United States of America. 2022;119(30). doi:10.1073/pnas.2122147119
apa: Barton, N. H. (2022). The “New Synthesis.” Proceedings of the National Academy
of Sciences of the United States of America. National Academy of Sciences.
https://doi.org/10.1073/pnas.2122147119
chicago: Barton, Nicholas H. “The ‘New Synthesis.’” Proceedings of the National
Academy of Sciences of the United States of America. National Academy of Sciences,
2022. https://doi.org/10.1073/pnas.2122147119.
ieee: N. H. Barton, “The ‘New Synthesis,’” Proceedings of the National Academy
of Sciences of the United States of America, vol. 119, no. 30. National Academy
of Sciences, 2022.
ista: Barton NH. 2022. The ‘New Synthesis’. Proceedings of the National Academy
of Sciences of the United States of America. 119(30), e2122147119.
mla: Barton, Nicholas H. “The ‘New Synthesis.’” Proceedings of the National Academy
of Sciences of the United States of America, vol. 119, no. 30, e2122147119,
National Academy of Sciences, 2022, doi:10.1073/pnas.2122147119.
short: N.H. Barton, Proceedings of the National Academy of Sciences of the United
States of America 119 (2022).
corr_author: '1'
date_created: 2022-07-31T22:01:47Z
date_published: 2022-07-18T00:00:00Z
date_updated: 2025-05-14T11:01:10Z
day: '18'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1073/pnas.2122147119
external_id:
pmid:
- '35858408'
file:
- access_level: open_access
checksum: 06c866196a8957f0c37b8a121771c885
content_type: application/pdf
creator: dernst
date_created: 2022-08-01T10:58:28Z
date_updated: 2022-08-01T10:58:28Z
file_id: '11716'
file_name: 2022_PNAS_Barton.pdf
file_size: 848511
relation: main_file
success: 1
file_date_updated: 2022-08-01T10:58:28Z
has_accepted_license: '1'
intvolume: ' 119'
issue: '30'
language:
- iso: eng
month: '07'
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'
scopus_import: '1'
status: public
title: The "New Synthesis"
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: 119
year: '2022'
...
---
_id: '11723'
abstract:
- lang: eng
text: Plant cell growth responds rapidly to various stimuli, adapting architecture
to environmental changes. Two major endogenous signals regulating growth are the
phytohormone auxin and the secreted peptides rapid alkalinization factors (RALFs).
Both trigger very rapid cellular responses and also exert long-term effects [Du
et al., Annu. Rev. Plant Biol. 71, 379–402 (2020); Blackburn et al., Plant Physiol.
182, 1657–1666 (2020)]. However, the way, in which these distinct signaling pathways
converge to regulate growth, remains unknown. Here, using vertical confocal microscopy
combined with a microfluidic chip, we addressed the mechanism of RALF action on
growth. We observed correlation between RALF1-induced rapid Arabidopsis thaliana
root growth inhibition and apoplast alkalinization during the initial phase of
the response, and revealed that RALF1 reversibly inhibits primary root growth
through apoplast alkalinization faster than within 1 min. This rapid apoplast
alkalinization was the result of RALF1-induced net H+ influx and was mediated
by the receptor FERONIA (FER). Furthermore, we investigated the cross-talk between
RALF1 and the auxin signaling pathways during root growth regulation. The results
showed that RALF-FER signaling triggered auxin signaling with a delay of approximately
1 h by up-regulating auxin biosynthesis, thus contributing to sustained RALF1-induced
growth inhibition. This biphasic RALF1 action on growth allows plants to respond
rapidly to environmental stimuli and also reprogram growth and development in
the long term.
acknowledgement: We thank Sarah M. Assmann, Kris Vissenberg, and Nadine Paris for
kindly sharing seeds; Matyáš Fendrych for initiating this project and providing
constant support; Lukas Fiedler for revising the manuscript; and Huibin Han and
Arseny Savin for contributing to genotyping. This work was supported by the Austrian
Science Fund (FWF) I 3630-B25 (to J.F.) and the Doctoral Fellowship Progrmme of
the Austrian Academy of Sciences (to L.L.) We also acknowledge Taif University Researchers
Supporting Project TURSP-HC2021/02 and funding “Plants as a tool for sustainable
global development (no. CZ.02.1.01/0.0/0.0/16_019/0000827).”
article_number: e2121058119
article_processing_charge: No
article_type: original
author:
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Huihuang
full_name: Chen, Huihuang
id: 83c96512-15b2-11ec-abd3-b7eede36184f
last_name: Chen
- first_name: Saqer S.
full_name: Alotaibi, Saqer S.
last_name: Alotaibi
- first_name: Aleš
full_name: Pěnčík, Aleš
last_name: Pěnčík
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Ondřej
full_name: Novák, Ondřej
last_name: Novák
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Li L, Chen H, Alotaibi SS, et al. RALF1 peptide triggers biphasic root growth
inhibition upstream of auxin biosynthesis. Proceedings of the National Academy
of Sciences of the United States of America. 2022;119(31). doi:10.1073/pnas.2121058119
apa: Li, L., Chen, H., Alotaibi, S. S., Pěnčík, A., Adamowski, M., Novák, O., &
Friml, J. (2022). RALF1 peptide triggers biphasic root growth inhibition upstream
of auxin biosynthesis. Proceedings of the National Academy of Sciences of the
United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2121058119
chicago: Li, Lanxin, Huihuang Chen, Saqer S. Alotaibi, Aleš Pěnčík, Maciek Adamowski,
Ondřej Novák, and Jiří Friml. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition
Upstream of Auxin Biosynthesis.” Proceedings of the National Academy of Sciences
of the United States of America. National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2121058119.
ieee: L. Li et al., “RALF1 peptide triggers biphasic root growth inhibition
upstream of auxin biosynthesis,” Proceedings of the National Academy of Sciences
of the United States of America, vol. 119, no. 31. National Academy of Sciences,
2022.
ista: Li L, Chen H, Alotaibi SS, Pěnčík A, Adamowski M, Novák O, Friml J. 2022.
RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis.
Proceedings of the National Academy of Sciences of the United States of America.
119(31), e2121058119.
mla: Li, Lanxin, et al. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition
Upstream of Auxin Biosynthesis.” Proceedings of the National Academy of Sciences
of the United States of America, vol. 119, no. 31, e2121058119, National Academy
of Sciences, 2022, doi:10.1073/pnas.2121058119.
short: L. Li, H. Chen, S.S. Alotaibi, A. Pěnčík, M. Adamowski, O. Novák, J. Friml,
Proceedings of the National Academy of Sciences of the United States of America
119 (2022).
corr_author: '1'
date_created: 2022-08-04T20:06:49Z
date_published: 2022-07-25T00:00:00Z
date_updated: 2025-05-14T11:01:00Z
day: '25'
ddc:
- '580'
department:
- _id: GradSch
- _id: JiFr
doi: 10.1073/pnas.2121058119
external_id:
isi:
- '000881496900002'
pmid:
- '35878023'
file:
- access_level: open_access
checksum: ae6f19b0d9efba6687f9e4dc1bab1d6e
content_type: application/pdf
creator: dernst
date_created: 2022-08-08T07:42:09Z
date_updated: 2022-08-08T07:42:09Z
file_id: '11747'
file_name: 2022_PNAS_Li.pdf
file_size: 2506262
relation: main_file
success: 1
file_date_updated: 2022-08-08T07:42:09Z
has_accepted_license: '1'
intvolume: ' 119'
isi: 1
issue: '31'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
- _id: 26B4D67E-B435-11E9-9278-68D0E5697425
grant_number: '25351'
name: 'A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated
Rapid Growth Inhibition in Arabidopsis Root'
publication: 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'
scopus_import: '1'
status: public
title: RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2022'
...
---
_id: '11733'
abstract:
- lang: eng
text: Genetically informed, deep-phenotyped biobanks are an important research resource
and it is imperative that the most powerful, versatile, and efficient analysis
approaches are used. Here, we apply our recently developed Bayesian grouped mixture
of regressions model (GMRM) in the UK and Estonian Biobanks and obtain the highest
genomic prediction accuracy reported to date across 21 heritable traits. When
compared to other approaches, GMRM accuracy was greater than annotation prediction
models run in the LDAK or LDPred-funct software by 15% (SE 7%) and 14% (SE 2%),
respectively, and was 18% (SE 3%) greater than a baseline BayesR model without
single-nucleotide polymorphism (SNP) markers grouped into minor allele frequency–linkage
disequilibrium (MAF-LD) annotation categories. For height, the prediction accuracy
R2 was 47% in a UK Biobank holdout sample, which was 76% of the estimated h2SNP.
We then extend our GMRM prediction model to provide mixed-linear model association
(MLMA) SNP marker estimates for genome-wide association (GWAS) discovery, which
increased the independent loci detected to 16,162 in unrelated UK Biobank individuals,
compared to 10,550 from BoltLMM and 10,095 from Regenie, a 62 and 65% increase,
respectively. The average χ2 value of the leading markers increased by 15.24 (SE
0.41) for every 1% increase in prediction accuracy gained over a baseline BayesR
model across the traits. Thus, we show that modeling genetic associations accounting
for MAF and LD differences among SNP markers, and incorporating prior knowledge
of genomic function, is important for both genomic prediction and discovery in
large-scale individual-level studies.
acknowledgement: This project was funded by Swiss National Science Foundation Eccellenza
Grant PCEGP3-181181(toM.R.R.) and by core funding from the Institute of Science
and Technology Austria. P.M.V. acknowledges funding from the Australian National
Health and Medical Research Council (1113400) and the Australian Research Council
(FL180100072). K.L. and R.M. were supported by the Estonian Research Council Grant
PRG687. Estonian Biobank computations were performed in the High-Performance Computing
Centre, University of Tartu.
article_number: e2121279119
article_processing_charge: No
article_type: original
author:
- first_name: Etienne J.
full_name: Orliac, Etienne J.
last_name: Orliac
- first_name: Daniel
full_name: Trejo Banos, Daniel
last_name: Trejo Banos
- first_name: Sven E.
full_name: Ojavee, Sven E.
last_name: Ojavee
- first_name: Kristi
full_name: Läll, Kristi
last_name: Läll
- first_name: Reedik
full_name: Mägi, Reedik
last_name: Mägi
- first_name: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
citation:
ama: Orliac EJ, Trejo Banos D, Ojavee SE, et al. Improving GWAS discovery and genomic
prediction accuracy in biobank data. Proceedings of the National Academy of
Sciences of the United States of America. 2022;119(31). doi:10.1073/pnas.2121279119
apa: Orliac, E. J., Trejo Banos, D., Ojavee, S. E., Läll, K., Mägi, R., Visscher,
P. M., & Robinson, M. R. (2022). Improving GWAS discovery and genomic prediction
accuracy in biobank data. Proceedings of the National Academy of Sciences of
the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2121279119
chicago: Orliac, Etienne J., Daniel Trejo Banos, Sven E. Ojavee, Kristi Läll, Reedik
Mägi, Peter M. Visscher, and Matthew Richard Robinson. “Improving GWAS Discovery
and Genomic Prediction Accuracy in Biobank Data.” Proceedings of the National
Academy of Sciences of the United States of America. National Academy of Sciences,
2022. https://doi.org/10.1073/pnas.2121279119.
ieee: E. J. Orliac et al., “Improving GWAS discovery and genomic prediction
accuracy in biobank data,” Proceedings of the National Academy of Sciences
of the United States of America, vol. 119, no. 31. National Academy of Sciences,
2022.
ista: Orliac EJ, Trejo Banos D, Ojavee SE, Läll K, Mägi R, Visscher PM, Robinson
MR. 2022. Improving GWAS discovery and genomic prediction accuracy in biobank
data. Proceedings of the National Academy of Sciences of the United States of
America. 119(31), e2121279119.
mla: Orliac, Etienne J., et al. “Improving GWAS Discovery and Genomic Prediction
Accuracy in Biobank Data.” Proceedings of the National Academy of Sciences
of the United States of America, vol. 119, no. 31, e2121279119, National Academy
of Sciences, 2022, doi:10.1073/pnas.2121279119.
short: E.J. Orliac, D. Trejo Banos, S.E. Ojavee, K. Läll, R. Mägi, P.M. Visscher,
M.R. Robinson, Proceedings of the National Academy of Sciences of the United States
of America 119 (2022).
corr_author: '1'
date_created: 2022-08-07T22:01:56Z
date_published: 2022-07-29T00:00:00Z
date_updated: 2025-06-12T06:22:37Z
day: '29'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.1073/pnas.2121279119
external_id:
isi:
- '000881496900003'
pmid:
- '35905320'
file:
- access_level: open_access
checksum: b5d2024e19fbad6f85a5e384e44d0f3b
content_type: application/pdf
creator: dernst
date_created: 2022-08-08T07:31:19Z
date_updated: 2022-08-08T07:31:19Z
file_id: '11745'
file_name: 2022_PNAS_Orliac.pdf
file_size: 1001164
relation: main_file
success: 1
file_date_updated: 2022-08-08T07:31:19Z
has_accepted_license: '1'
intvolume: ' 119'
isi: 1
issue: '31'
language:
- iso: eng
month: '07'
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
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
record:
- id: '13064'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Improving GWAS discovery and genomic prediction accuracy in biobank data
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2022'
...
---
_id: '11734'
abstract:
- lang: eng
text: Mineral nutrition is one of the key environmental factors determining plant
development and growth. Nitrate is the major form of macronutrient nitrogen that
plants take up from the soil. Fluctuating availability or deficiency of this element
severely limits plant growth and negatively affects crop production in the agricultural
system. To cope with the heterogeneity of nitrate distribution in soil, plants
evolved a complex regulatory mechanism that allows rapid adjustment of physiological
and developmental processes to the status of this nutrient. The root, as a major
exploitation organ that controls the uptake of nitrate to the plant body, acts
as a regulatory hub that, according to nitrate availability, coordinates the growth
and development of other plant organs. Here, we identified a regulatory framework,
where cytokinin response factors (CRFs) play a central role as a molecular readout
of the nitrate status in roots to guide shoot adaptive developmental response.
We show that nitrate-driven activation of NLP7, a master regulator of nitrate
response in plants, fine tunes biosynthesis of cytokinin in roots and its translocation
to shoots where it enhances expression of CRFs. CRFs, through direct transcriptional
regulation of PIN auxin transporters, promote the flow of auxin and thereby stimulate
the development of shoot organs.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: "We acknowledge Hana Semeradova, Juan Carlos Montesinos, Nicola Cavallari,
Marc¸al Gallem\x03ı, Kaori Tabata, Andrej Hurn\x03y, and Sascha Waidmann for sharing
materials; and Marina Borges Osorio for critical reading of the manuscript. Work
in the E. Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S)
to K.O., R.A., and E. Benkova. We acknowledge the Bioimaging Facility and Life Science
Facilities of the Institute of Science\r\nand Technology Austria. We give sincere
thanks to Hana Martınkova and Petra Amakorova for their help with cytokinin analyses.
This work was funded by the Czech Science Foundation (Project No. 19-00973S)."
article_number: e2122460119
article_processing_charge: No
article_type: original
author:
- first_name: Rashed
full_name: Abualia, Rashed
id: 4827E134-F248-11E8-B48F-1D18A9856A87
last_name: Abualia
orcid: 0000-0002-9357-9415
- first_name: Krisztina
full_name: Ötvös, Krisztina
id: 29B901B0-F248-11E8-B48F-1D18A9856A87
last_name: Ötvös
orcid: 0000-0002-5503-4983
- first_name: Ondřej
full_name: Novák, Ondřej
last_name: Novák
- first_name: Eleonore
full_name: Bouguyon, Eleonore
last_name: Bouguyon
- first_name: Kevin
full_name: Domanegg, Kevin
id: a24c7829-16e8-11ed-8527-c4d36ffb7539
last_name: Domanegg
orcid: 0000-0002-1215-4264
- first_name: Anne
full_name: Krapp, Anne
last_name: Krapp
- first_name: Philip
full_name: Nacry, Philip
last_name: Nacry
- first_name: Alain
full_name: Gojon, Alain
last_name: Gojon
- first_name: Benoit
full_name: Lacombe, Benoit
last_name: Lacombe
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Abualia R, Ötvös K, Novák O, et al. Molecular framework integrating nitrate
sensing in root and auxin-guided shoot adaptive responses. Proceedings of the
National Academy of Sciences of the United States of America. 2022;119(31).
doi:10.1073/pnas.2122460119
apa: Abualia, R., Ötvös, K., Novák, O., Bouguyon, E., Domanegg, K., Krapp, A., …
Benková, E. (2022). Molecular framework integrating nitrate sensing in root and
auxin-guided shoot adaptive responses. Proceedings of the National Academy
of Sciences of the United States of America. National Academy of Sciences.
https://doi.org/10.1073/pnas.2122460119
chicago: Abualia, Rashed, Krisztina Ötvös, Ondřej Novák, Eleonore Bouguyon, Kevin
Domanegg, Anne Krapp, Philip Nacry, Alain Gojon, Benoit Lacombe, and Eva Benková.
“Molecular Framework Integrating Nitrate Sensing in Root and Auxin-Guided Shoot
Adaptive Responses.” Proceedings of the National Academy of Sciences of the
United States of America. National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2122460119.
ieee: R. Abualia et al., “Molecular framework integrating nitrate sensing
in root and auxin-guided shoot adaptive responses,” Proceedings of the National
Academy of Sciences of the United States of America, vol. 119, no. 31. National
Academy of Sciences, 2022.
ista: Abualia R, Ötvös K, Novák O, Bouguyon E, Domanegg K, Krapp A, Nacry P, Gojon
A, Lacombe B, Benková E. 2022. Molecular framework integrating nitrate sensing
in root and auxin-guided shoot adaptive responses. Proceedings of the National
Academy of Sciences of the United States of America. 119(31), e2122460119.
mla: Abualia, Rashed, et al. “Molecular Framework Integrating Nitrate Sensing in
Root and Auxin-Guided Shoot Adaptive Responses.” Proceedings of the National
Academy of Sciences of the United States of America, vol. 119, no. 31, e2122460119,
National Academy of Sciences, 2022, doi:10.1073/pnas.2122460119.
short: R. Abualia, K. Ötvös, O. Novák, E. Bouguyon, K. Domanegg, A. Krapp, P. Nacry,
A. Gojon, B. Lacombe, E. Benková, Proceedings of the National Academy of Sciences
of the United States of America 119 (2022).
corr_author: '1'
date_created: 2022-08-07T22:01:57Z
date_published: 2022-07-25T00:00:00Z
date_updated: 2025-05-14T11:00:29Z
day: '25'
ddc:
- '570'
department:
- _id: EvBe
doi: 10.1073/pnas.2122460119
external_id:
isi:
- '000881496900007'
pmid:
- '35878040'
file:
- access_level: open_access
checksum: 6e97dedc281247fc3fe238a209f14af0
content_type: application/pdf
creator: dernst
date_created: 2022-08-08T07:09:58Z
date_updated: 2022-08-08T07:09:58Z
file_id: '11744'
file_name: 2022_PNAS_Abualia.pdf
file_size: 3092330
relation: main_file
success: 1
file_date_updated: 2022-08-08T07:09:58Z
has_accepted_license: '1'
intvolume: ' 119'
isi: 1
issue: '31'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2542D156-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 1774-B16
name: Hormone cross-talk drives nutrient dependent plant development
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Molecular framework integrating nitrate sensing in root and auxin-guided shoot
adaptive responses
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2022'
...
---
_id: '11841'
abstract:
- lang: eng
text: Primary nucleation is the fundamental event that initiates the conversion
of proteins from their normal physiological forms into pathological amyloid aggregates
associated with the onset and development of disorders including systemic amyloidosis,
as well as the neurodegenerative conditions Alzheimer’s and Parkinson’s diseases.
It has become apparent that the presence of surfaces can dramatically modulate
nucleation. However, the underlying physicochemical parameters governing this
process have been challenging to elucidate, with interfaces in some cases having
been found to accelerate aggregation, while in others they can inhibit the kinetics
of this process. Here we show through kinetic analysis that for three different
fibril-forming proteins, interfaces affect the aggregation reaction mainly through
modulating the primary nucleation step. Moreover, we show through direct measurements
of the Gibbs free energy of adsorption, combined with theory and coarse-grained
computer simulations, that overall nucleation rates are suppressed at high and
at low surface interaction strengths but significantly enhanced at intermediate
strengths, and we verify these regimes experimentally. Taken together, these results
provide a quantitative description of the fundamental process which triggers amyloid
formation and shed light on the key factors that control this process.
acknowledgement: "The research leading to these results has received funding from
the European Research Council (ERC) under the European Union’s Seventh Framework
Programme (FP7/2007-2013) through the ERC grant PhysProt\r\n(agreement 337969).
We are grateful for financial support from the Biotechnology and Biological Sciences
Research Council (BBSRC) (T.P.J.K.), the Newman\r\nFoundation (T.P.J.K.), the Wellcome
Trust (T.P.J.K. and M.V.), Peterhouse College\r\nCambridge (T.C.T.M.), the ERC Starting
Grant (StG) Non-Equilibrium Protein Assembly (NEPA) (A.S.), the Royal Society (A.S.),
the Academy of Medical Sciences\r\n(A.S. and J.K.), and the Cambridge Centre for
Misfolding Diseases (CMD)."
article_number: e2109718119
article_processing_charge: No
article_type: original
author:
- first_name: Zenon
full_name: Toprakcioglu, Zenon
last_name: Toprakcioglu
- first_name: Ayaka
full_name: Kamada, Ayaka
last_name: Kamada
- first_name: Thomas C.T.
full_name: Michaels, Thomas C.T.
last_name: Michaels
- first_name: Mengqi
full_name: Xie, Mengqi
last_name: Xie
- first_name: Johannes
full_name: Krausser, Johannes
last_name: Krausser
- first_name: Jiapeng
full_name: Wei, Jiapeng
last_name: Wei
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Michele
full_name: Vendruscolo, Michele
last_name: Vendruscolo
- first_name: Tuomas P.J.
full_name: Knowles, Tuomas P.J.
last_name: Knowles
citation:
ama: Toprakcioglu Z, Kamada A, Michaels TCT, et al. Adsorption free energy predicts
amyloid protein nucleation rates. Proceedings of the National Academy of Sciences
of the United States of America. 2022;119(31). doi:10.1073/pnas.2109718119
apa: Toprakcioglu, Z., Kamada, A., Michaels, T. C. T., Xie, M., Krausser, J., Wei,
J., … Knowles, T. P. J. (2022). Adsorption free energy predicts amyloid protein
nucleation rates. Proceedings of the National Academy of Sciences of the United
States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2109718119
chicago: Toprakcioglu, Zenon, Ayaka Kamada, Thomas C.T. Michaels, Mengqi Xie, Johannes
Krausser, Jiapeng Wei, Anđela Šarić, Michele Vendruscolo, and Tuomas P.J. Knowles.
“Adsorption Free Energy Predicts Amyloid Protein Nucleation Rates.” Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2109718119.
ieee: Z. Toprakcioglu et al., “Adsorption free energy predicts amyloid protein
nucleation rates,” Proceedings of the National Academy of Sciences of the United
States of America, vol. 119, no. 31. National Academy of Sciences, 2022.
ista: Toprakcioglu Z, Kamada A, Michaels TCT, Xie M, Krausser J, Wei J, Šarić A,
Vendruscolo M, Knowles TPJ. 2022. Adsorption free energy predicts amyloid protein
nucleation rates. Proceedings of the National Academy of Sciences of the United
States of America. 119(31), e2109718119.
mla: Toprakcioglu, Zenon, et al. “Adsorption Free Energy Predicts Amyloid Protein
Nucleation Rates.” Proceedings of the National Academy of Sciences of the United
States of America, vol. 119, no. 31, e2109718119, National Academy of Sciences,
2022, doi:10.1073/pnas.2109718119.
short: Z. Toprakcioglu, A. Kamada, T.C.T. Michaels, M. Xie, J. Krausser, J. Wei,
A. Šarić, M. Vendruscolo, T.P.J. Knowles, Proceedings of the National Academy
of Sciences of the United States of America 119 (2022).
date_created: 2022-08-14T22:01:45Z
date_published: 2022-07-28T00:00:00Z
date_updated: 2025-06-12T06:21:34Z
day: '28'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1073/pnas.2109718119
ec_funded: 1
external_id:
isi:
- '000903753500002'
pmid:
- '35901206'
file:
- access_level: open_access
checksum: 0fe3878896cbeb6c44e29222ec2f336a
content_type: application/pdf
creator: dernst
date_created: 2023-10-04T09:05:44Z
date_updated: 2023-10-04T09:05:44Z
file_id: '14386'
file_name: 2022_PNAS_Toprakcioglu.pdf
file_size: 2476021
relation: main_file
success: 1
file_date_updated: 2023-10-04T09:05:44Z
has_accepted_license: '1'
intvolume: ' 119'
isi: 1
issue: '31'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 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'
scopus_import: '1'
status: public
title: Adsorption free energy predicts amyloid protein nucleation rates
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2022'
...
---
_id: '12081'
abstract:
- lang: eng
text: 'Selection accumulates information in the genome—it guides stochastically
evolving populations toward states (genotype frequencies) that would be unlikely
under neutrality. This can be quantified as the Kullback–Leibler (KL) divergence
between the actual distribution of genotype frequencies and the corresponding
neutral distribution. First, we show that this population-level information sets
an upper bound on the information at the level of genotype and phenotype, limiting
how precisely they can be specified by selection. Next, we study how the accumulation
and maintenance of information is limited by the cost of selection, measured as
the genetic load or the relative fitness variance, both of which we connect to
the control-theoretic KL cost of control. The information accumulation rate is
upper bounded by the population size times the cost of selection. This bound is
very general, and applies across models (Wright–Fisher, Moran, diffusion) and
to arbitrary forms of selection, mutation, and recombination. Finally, the cost
of maintaining information depends on how it is encoded: Specifying a single allele
out of two is expensive, but one bit encoded among many weakly specified loci
(as in a polygenic trait) is cheap.'
acknowledgement: We thank Ksenia Khudiakova, Wiktor Młynarski, Sean Stankowski, and
two anonymous reviewers for discussions and comments on the manuscript. G.T. and
M.H. acknowledge funding from the Human Frontier Science Program Grant RGP0032/2018.
N.B. acknowledges funding from ERC Grant 250152 “Information and Evolution.”
article_number: e2123152119
article_processing_charge: No
article_type: original
author:
- first_name: Michal
full_name: Hledik, Michal
id: 4171253A-F248-11E8-B48F-1D18A9856A87
last_name: Hledik
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: '1'
citation:
ama: Hledik M, Barton NH, Tkačik G. Accumulation and maintenance of information
in evolution. Proceedings of the National Academy of Sciences of the United
States of America. 2022;119(36). doi:10.1073/pnas.2123152119
apa: Hledik, M., Barton, N. H., & Tkačik, G. (2022). Accumulation and maintenance
of information in evolution. Proceedings of the National Academy of Sciences
of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2123152119
chicago: Hledik, Michal, Nicholas H Barton, and Gašper Tkačik. “Accumulation and
Maintenance of Information in Evolution.” Proceedings of the National Academy
of Sciences of the United States of America. National Academy of Sciences,
2022. https://doi.org/10.1073/pnas.2123152119.
ieee: M. Hledik, N. H. Barton, and G. Tkačik, “Accumulation and maintenance of information
in evolution,” Proceedings of the National Academy of Sciences of the United
States of America, vol. 119, no. 36. National Academy of Sciences, 2022.
ista: Hledik M, Barton NH, Tkačik G. 2022. Accumulation and maintenance of information
in evolution. Proceedings of the National Academy of Sciences of the United States
of America. 119(36), e2123152119.
mla: Hledik, Michal, et al. “Accumulation and Maintenance of Information in Evolution.”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 119, no. 36, e2123152119, National Academy of Sciences, 2022, doi:10.1073/pnas.2123152119.
short: M. Hledik, N.H. Barton, G. Tkačik, Proceedings of the National Academy of
Sciences of the United States of America 119 (2022).
corr_author: '1'
date_created: 2022-09-11T22:01:55Z
date_published: 2022-08-29T00:00:00Z
date_updated: 2026-04-07T12:59:24Z
day: '29'
ddc:
- '570'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1073/pnas.2123152119
ec_funded: 1
external_id:
isi:
- '000889278400014'
pmid:
- '36037343'
file:
- access_level: open_access
checksum: 6dec51f6567da9039982a571508a8e4d
content_type: application/pdf
creator: dernst
date_created: 2022-09-12T08:08:12Z
date_updated: 2022-09-12T08:08:12Z
file_id: '12091'
file_name: 2022_PNAS_Hledik.pdf
file_size: 2165752
relation: main_file
success: 1
file_date_updated: 2022-09-12T08:08:12Z
has_accepted_license: '1'
intvolume: ' 119'
isi: 1
issue: '36'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 2665AAFE-B435-11E9-9278-68D0E5697425
grant_number: RGP0034/2018
name: Can evolution minimize spurious signaling crosstalk to reach optimal performance?
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: '15020'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Accumulation and maintenance of information in evolution
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2022'
...
---
_id: '12577'
abstract:
- lang: eng
text: Glaciers are key components of the mountain water towers of Asia and are vital
for downstream domestic, agricultural, and industrial uses. The glacier mass loss
rate over the southeastern Tibetan Plateau is among the highest in Asia and has
accelerated in recent decades. This acceleration has been attributed to increased
warming, but the mechanisms behind these glaciers’ high sensitivity to warming
remain unclear, while the influence of changes in precipitation over the past
decades is poorly quantified. Here, we reconstruct glacier mass changes and catchment
runoff since 1975 at a benchmark glacier, Parlung No. 4, to shed light on the
drivers of recent mass losses for the monsoonal, spring-accumulation glaciers
of the Tibetan Plateau. Our modeling demonstrates how a temperature increase (mean
of 0.39∘C ⋅dec−1since 1990) has accelerated
mass loss rates by altering both the ablation and accumulation regimes in a complex
manner. The majority of the post-2000 mass loss occurred during the monsoon months,
caused by simultaneous decreases in the solid precipitation ratio (from 0.70 to
0.56) and precipitation amount (–10%), leading to reduced monsoon accumulation
(–26%). Higher solid precipitation in spring (+18%) during the last two decades
was increasingly important in mitigating glacier mass loss by providing mass to
the glacier and protecting it from melting in the early monsoon. With bare ice
exposed to warmer temperatures for longer periods, icemelt and catchment discharge
have unsustainably intensified since the start of the 21st century, raising concerns
for long-term water supply and hazard occurrence in the region.
article_number: e2109796119
article_processing_charge: No
article_type: original
author:
- first_name: Achille
full_name: Jouberton, Achille
last_name: Jouberton
- first_name: Thomas E.
full_name: Shaw, Thomas E.
last_name: Shaw
- first_name: Evan
full_name: Miles, Evan
last_name: Miles
- first_name: Michael
full_name: McCarthy, Michael
last_name: McCarthy
- first_name: Stefan
full_name: Fugger, Stefan
last_name: Fugger
- first_name: Shaoting
full_name: Ren, Shaoting
last_name: Ren
- first_name: Amaury
full_name: Dehecq, Amaury
last_name: Dehecq
- first_name: Wei
full_name: Yang, Wei
last_name: Yang
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
citation:
ama: Jouberton A, Shaw TE, Miles E, et al. Warming-induced monsoon precipitation
phase change intensifies glacier mass loss in the southeastern Tibetan Plateau.
PNAS. 2022;119(37). doi:10.1073/pnas.2109796119
apa: Jouberton, A., Shaw, T. E., Miles, E., McCarthy, M., Fugger, S., Ren, S., …
Pellicciotti, F. (2022). Warming-induced monsoon precipitation phase change intensifies
glacier mass loss in the southeastern Tibetan Plateau. PNAS. Proceedings
of the National Academy of Sciences. https://doi.org/10.1073/pnas.2109796119
chicago: Jouberton, Achille, Thomas E. Shaw, Evan Miles, Michael McCarthy, Stefan
Fugger, Shaoting Ren, Amaury Dehecq, Wei Yang, and Francesca Pellicciotti. “Warming-Induced
Monsoon Precipitation Phase Change Intensifies Glacier Mass Loss in the Southeastern
Tibetan Plateau.” PNAS. Proceedings of the National Academy of Sciences,
2022. https://doi.org/10.1073/pnas.2109796119.
ieee: A. Jouberton et al., “Warming-induced monsoon precipitation phase change
intensifies glacier mass loss in the southeastern Tibetan Plateau,” PNAS,
vol. 119, no. 37. Proceedings of the National Academy of Sciences, 2022.
ista: Jouberton A, Shaw TE, Miles E, McCarthy M, Fugger S, Ren S, Dehecq A, Yang
W, Pellicciotti F. 2022. Warming-induced monsoon precipitation phase change intensifies
glacier mass loss in the southeastern Tibetan Plateau. PNAS. 119(37), e2109796119.
mla: Jouberton, Achille, et al. “Warming-Induced Monsoon Precipitation Phase Change
Intensifies Glacier Mass Loss in the Southeastern Tibetan Plateau.” PNAS,
vol. 119, no. 37, e2109796119, Proceedings of the National Academy of Sciences,
2022, doi:10.1073/pnas.2109796119.
short: A. Jouberton, T.E. Shaw, E. Miles, M. McCarthy, S. Fugger, S. Ren, A. Dehecq,
W. Yang, F. Pellicciotti, PNAS 119 (2022).
date_created: 2023-02-20T08:10:02Z
date_published: 2022-09-06T00:00:00Z
date_updated: 2023-02-28T13:50:37Z
day: '06'
doi: 10.1073/pnas.2109796119
extern: '1'
intvolume: ' 119'
issue: '37'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '09'
oa_version: None
publication: PNAS
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Warming-induced monsoon precipitation phase change intensifies glacier mass
loss in the southeastern Tibetan Plateau
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2022'
...
---
_id: '10766'
abstract:
- lang: eng
text: Tension of the actomyosin cell cortex plays a key role in determining cell–cell
contact growth and size. The level of cortical tension outside of the cell–cell
contact, when pulling at the contact edge, scales with the total size to which
a cell–cell contact can grow [J.-L. Maître et al., Science 338, 253–256 (2012)].
Here, we show in zebrafish primary germ-layer progenitor cells that this monotonic
relationship only applies to a narrow range of cortical tension increase and that
above a critical threshold, contact size inversely scales with cortical tension.
This switch from cortical tension increasing to decreasing progenitor cell–cell
contact size is caused by cortical tension promoting E-cadherin anchoring to the
actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin
at the contact. After tension-mediated E-cadherin stabilization at the contact
exceeds a critical threshold level, the rate by which the contact expands in response
to pulling forces from the cortex sharply drops, leading to smaller contacts at
physiologically relevant timescales of contact formation. Thus, the activity of
cortical tension in expanding cell–cell contact size is limited by tension-stabilizing
E-cadherin–actin complexes at the contact.
acknowledged_ssus:
- _id: Bio
- _id: EM-Fac
- _id: PreCl
acknowledgement: 'We thank Guillaume Salbreaux, Silvia Grigolon, Edouard Hannezo,
and Vanessa Barone for discussions and comments on the manuscript and Shayan Shamipour
and Daniel Capek for help with data analysis. We also thank the Imaging & Optics,
Electron Microscopy, and Zebrafish Facility Scientific Service Units at the Institute
of Science and Technology Austria (ISTA)Nasser Darwish-Miranda for continuous support.
We acknowledge Hitoshi Morita for the gift of VinculinB-GFP plasmid. This research
was supported by an ISTA Fellow Marie-Curie Co-funding of regional, national, and
international programmes Grant P_IST_EU01 (to J.S.), European Molecular Biology
Organization Long-Term Fellowship Grant, ALTF reference number: 187-2013 (to M.S.),
Schroedinger Fellowship J4332-B28 (to M.S.), and European Research Council Advanced
Grant (MECSPEC; to C.-P.H.).'
article_number: e2122030119
article_processing_charge: No
article_type: original
author:
- first_name: Jana
full_name: Slovakova, Jana
id: 30F3F2F0-F248-11E8-B48F-1D18A9856A87
last_name: Slovakova
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Feyza N
full_name: Arslan, Feyza N
id: 49DA7910-F248-11E8-B48F-1D18A9856A87
last_name: Arslan
orcid: 0000-0001-5809-9566
- first_name: Silvia
full_name: Caballero Mancebo, Silvia
id: 2F1E1758-F248-11E8-B48F-1D18A9856A87
last_name: Caballero Mancebo
orcid: 0000-0002-5223-3346
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Slovakova J, Sikora MK, Arslan FN, et al. Tension-dependent stabilization of
E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor
cells. Proceedings of the National Academy of Sciences of the United States
of America. 2022;119(8). doi:10.1073/pnas.2122030119
apa: Slovakova, J., Sikora, M. K., Arslan, F. N., Caballero Mancebo, S., Krens,
G., Kaufmann, W., … Heisenberg, C.-P. J. (2022). Tension-dependent stabilization
of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor
cells. Proceedings of the National Academy of Sciences of the United States
of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2122030119
chicago: Slovakova, Jana, Mateusz K Sikora, Feyza N Arslan, Silvia Caballero Mancebo,
Gabriel Krens, Walter Kaufmann, Jack Merrin, and Carl-Philipp J Heisenberg. “Tension-Dependent
Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer
Progenitor Cells.” Proceedings of the National Academy of Sciences of the United
States of America. National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2122030119.
ieee: J. Slovakova et al., “Tension-dependent stabilization of E-cadherin
limits cell-cell contact expansion in zebrafish germ-layer progenitor cells,”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 119, no. 8. National Academy of Sciences, 2022.
ista: Slovakova J, Sikora MK, Arslan FN, Caballero Mancebo S, Krens G, Kaufmann
W, Merrin J, Heisenberg C-PJ. 2022. Tension-dependent stabilization of E-cadherin
limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings
of the National Academy of Sciences of the United States of America. 119(8), e2122030119.
mla: Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits
Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” Proceedings
of the National Academy of Sciences of the United States of America, vol.
119, no. 8, e2122030119, National Academy of Sciences, 2022, doi:10.1073/pnas.2122030119.
short: J. Slovakova, M.K. Sikora, F.N. Arslan, S. Caballero Mancebo, G. Krens, W.
Kaufmann, J. Merrin, C.-P.J. Heisenberg, Proceedings of the National Academy of
Sciences of the United States of America 119 (2022).
corr_author: '1'
date_created: 2022-02-20T23:01:31Z
date_published: 2022-02-14T00:00:00Z
date_updated: 2026-04-02T12:54:56Z
day: '14'
ddc:
- '570'
department:
- _id: CaHe
- _id: EM-Fac
- _id: Bio
doi: 10.1073/pnas.2122030119
ec_funded: 1
external_id:
isi:
- '000766926900009'
pmid:
- '35165179'
file:
- access_level: open_access
checksum: d49f83c3580613966f71768ddb9a55a5
content_type: application/pdf
creator: dernst
date_created: 2022-02-21T08:45:11Z
date_updated: 2022-02-21T08:45:11Z
file_id: '10780'
file_name: 2022_PNAS_Slovakova.pdf
file_size: 1609678
relation: main_file
success: 1
file_date_updated: 2022-02-21T08:45:11Z
has_accepted_license: '1'
intvolume: ' 119'
isi: 1
issue: '8'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
- _id: 2521E28E-B435-11E9-9278-68D0E5697425
grant_number: 187-2013
name: Modulation of adhesion function in cell-cell contact formation by cortical
tension
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
record:
- id: '9750'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion
in zebrafish germ-layer progenitor cells
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 119
year: '2022'
...
---
_id: '12667'
abstract:
- lang: eng
text: Unlike crystalline atomic and ionic solids, texture development due to crystallographically
preferred growth in colloidal crystals is less studied. Here we investigate the
underlying mechanisms of the texture evolution in an evaporation-induced colloidal
assembly process through experiments, modeling, and theoretical analysis. In this
widely used approach to obtain large-area colloidal crystals, the colloidal particles
are driven to the meniscus via the evaporation of a solvent or matrix precursor
solution where they close-pack to form a face-centered cubic colloidal assembly.
Via two-dimensional large-area crystallographic mapping, we show that the initial
crystal orientation is dominated by the interaction of particles with the meniscus,
resulting in the expected coalignment of the close-packed direction with the local
meniscus geometry. By combining with crystal structure analysis at a single-particle
level, we further reveal that, at the later stage of self-assembly, however, the
colloidal crystal undergoes a gradual rotation facilitated by geometrically necessary
dislocations (GNDs) and achieves a large-area uniform crystallographic orientation
with the close-packed direction perpendicular to the meniscus and parallel to
the growth direction. Classical slip analysis, finite element-based mechanical
simulation, computational colloidal assembly modeling, and continuum theory unequivocally
show that these GNDs result from the tensile stress field along the meniscus direction
due to the constrained shrinkage of the colloidal crystal during drying. The generation
of GNDs with specific slip systems within individual grains leads to crystallographic
rotation to accommodate the mechanical stress. The mechanistic understanding reported
here can be utilized to control crystallographic features of colloidal assemblies,
and may provide further insights into crystallographically preferred growth in
synthetic, biological, and geological crystals.
article_number: e2107588118
article_processing_charge: No
article_type: original
author:
- first_name: Ling
full_name: Li, Ling
last_name: Li
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Haizhao
full_name: Yang, Haizhao
last_name: Yang
- first_name: Katherine R.
full_name: Phillips, Katherine R.
last_name: Phillips
- first_name: Zian
full_name: Jia, Zian
last_name: Jia
- first_name: Hongshun
full_name: Chen, Hongshun
last_name: Chen
- first_name: Lifeng
full_name: Wang, Lifeng
last_name: Wang
- first_name: Jinjin
full_name: Zhong, Jinjin
last_name: Zhong
- first_name: Anhua
full_name: Liu, Anhua
last_name: Liu
- first_name: Jianfeng
full_name: Lu, Jianfeng
last_name: Lu
- first_name: Jianwei
full_name: Shuai, Jianwei
last_name: Shuai
- first_name: Michael P.
full_name: Brenner, Michael P.
last_name: Brenner
- first_name: Frans
full_name: Spaepen, Frans
last_name: Spaepen
- first_name: Joanna
full_name: Aizenberg, Joanna
last_name: Aizenberg
citation:
ama: Li L, Goodrich CP, Yang H, et al. Microscopic origins of the crystallographically
preferred growth in evaporation-induced colloidal crystals. PNAS. 2021;118(32).
doi:10.1073/pnas.2107588118
apa: Li, L., Goodrich, C. P., Yang, H., Phillips, K. R., Jia, Z., Chen, H., … Aizenberg,
J. (2021). Microscopic origins of the crystallographically preferred growth in
evaporation-induced colloidal crystals. PNAS. Proceedings of the National
Academy of Sciences. https://doi.org/10.1073/pnas.2107588118
chicago: Li, Ling, Carl Peter Goodrich, Haizhao Yang, Katherine R. Phillips, Zian
Jia, Hongshun Chen, Lifeng Wang, et al. “Microscopic Origins of the Crystallographically
Preferred Growth in Evaporation-Induced Colloidal Crystals.” PNAS. Proceedings
of the National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2107588118.
ieee: L. Li et al., “Microscopic origins of the crystallographically preferred
growth in evaporation-induced colloidal crystals,” PNAS, vol. 118, no.
32. Proceedings of the National Academy of Sciences, 2021.
ista: Li L, Goodrich CP, Yang H, Phillips KR, Jia Z, Chen H, Wang L, Zhong J, Liu
A, Lu J, Shuai J, Brenner MP, Spaepen F, Aizenberg J. 2021. Microscopic origins
of the crystallographically preferred growth in evaporation-induced colloidal
crystals. PNAS. 118(32), e2107588118.
mla: Li, Ling, et al. “Microscopic Origins of the Crystallographically Preferred
Growth in Evaporation-Induced Colloidal Crystals.” PNAS, vol. 118, no.
32, e2107588118, Proceedings of the National Academy of Sciences, 2021, doi:10.1073/pnas.2107588118.
short: L. Li, C.P. Goodrich, H. Yang, K.R. Phillips, Z. Jia, H. Chen, L. Wang, J.
Zhong, A. Liu, J. Lu, J. Shuai, M.P. Brenner, F. Spaepen, J. Aizenberg, PNAS 118
(2021).
date_created: 2023-02-21T08:51:04Z
date_published: 2021-08-10T00:00:00Z
date_updated: 2023-02-23T10:45:44Z
day: '10'
ddc:
- '570'
doi: 10.1073/pnas.2107588118
extern: '1'
external_id:
pmid:
- '34341109'
file:
- access_level: open_access
checksum: 702f7ec60ce6f2815104ab649dc661a4
content_type: application/pdf
creator: dernst
date_created: 2023-02-23T10:42:07Z
date_updated: 2023-02-23T10:42:07Z
file_id: '12674'
file_name: 2021_PNAS_Li.pdf
file_size: 3275944
relation: main_file
success: 1
file_date_updated: 2023-02-23T10:42:07Z
has_accepted_license: '1'
intvolume: ' 118'
issue: '32'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: PNAS
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Microscopic origins of the crystallographically preferred growth in evaporation-induced
colloidal crystals
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2021'
...
---
_id: '15139'
abstract:
- lang: eng
text: Rotavirus genomes are distributed between 11 distinct RNA molecules, all of
which must be selectively copackaged during virus assembly. This likely occurs
through sequence-specific RNA interactions facilitated by the RNA chaperone NSP2.
Here, we report that NSP2 autoregulates its chaperone activity through its C-terminal
region (CTR) that promotes RNA–RNA interactions by limiting its helix-unwinding
activity. Unexpectedly, structural proteomics data revealed that the CTR does
not directly interact with RNA, while accelerating RNA release from NSP2. Cryo–electron
microscopy reconstructions of an NSP2–RNA complex reveal a highly conserved acidic
patch on the CTR, which is poised toward the bound RNA. Virus replication was
abrogated by charge-disrupting mutations within the acidic patch but completely
restored by charge-preserving mutations. Mechanistic similarities between NSP2
and the unrelated bacterial RNA chaperone Hfq suggest that accelerating RNA dissociation
while promoting intermolecular RNA interactions may be a widespread strategy of
RNA chaperone recycling.
article_number: e2100198118
article_processing_charge: No
article_type: original
author:
- first_name: Jack Peter Kelly
full_name: Bravo, Jack Peter Kelly
id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e
last_name: Bravo
orcid: 0000-0003-0456-0753
- first_name: Kira
full_name: Bartnik, Kira
last_name: Bartnik
- first_name: Luca
full_name: Venditti, Luca
last_name: Venditti
- first_name: Julia
full_name: Acker, Julia
last_name: Acker
- first_name: Emma H.
full_name: Gail, Emma H.
last_name: Gail
- first_name: Alice
full_name: Colyer, Alice
last_name: Colyer
- first_name: Chen
full_name: Davidovich, Chen
last_name: Davidovich
- first_name: Don C.
full_name: Lamb, Don C.
last_name: Lamb
- first_name: Roman
full_name: Tuma, Roman
last_name: Tuma
- first_name: Antonio N.
full_name: Calabrese, Antonio N.
last_name: Calabrese
- first_name: Alexander
full_name: Borodavka, Alexander
last_name: Borodavka
citation:
ama: Bravo JPK, Bartnik K, Venditti L, et al. Structural basis of rotavirus RNA
chaperone displacement and RNA annealing. Proceedings of the National Academy
of Sciences. 2021;118(41). doi:10.1073/pnas.2100198118
apa: Bravo, J. P. K., Bartnik, K., Venditti, L., Acker, J., Gail, E. H., Colyer,
A., … Borodavka, A. (2021). Structural basis of rotavirus RNA chaperone displacement
and RNA annealing. Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences. https://doi.org/10.1073/pnas.2100198118
chicago: Bravo, Jack Peter Kelly, Kira Bartnik, Luca Venditti, Julia Acker, Emma
H. Gail, Alice Colyer, Chen Davidovich, et al. “Structural Basis of Rotavirus
RNA Chaperone Displacement and RNA Annealing.” Proceedings of the National
Academy of Sciences. Proceedings of the National Academy of Sciences, 2021.
https://doi.org/10.1073/pnas.2100198118.
ieee: J. P. K. Bravo et al., “Structural basis of rotavirus RNA chaperone
displacement and RNA annealing,” Proceedings of the National Academy of Sciences,
vol. 118, no. 41. Proceedings of the National Academy of Sciences, 2021.
ista: Bravo JPK, Bartnik K, Venditti L, Acker J, Gail EH, Colyer A, Davidovich C,
Lamb DC, Tuma R, Calabrese AN, Borodavka A. 2021. Structural basis of rotavirus
RNA chaperone displacement and RNA annealing. Proceedings of the National Academy
of Sciences. 118(41), e2100198118.
mla: Bravo, Jack Peter Kelly, et al. “Structural Basis of Rotavirus RNA Chaperone
Displacement and RNA Annealing.” Proceedings of the National Academy of Sciences,
vol. 118, no. 41, e2100198118, Proceedings of the National Academy of Sciences,
2021, doi:10.1073/pnas.2100198118.
short: J.P.K. Bravo, K. Bartnik, L. Venditti, J. Acker, E.H. Gail, A. Colyer, C.
Davidovich, D.C. Lamb, R. Tuma, A.N. Calabrese, A. Borodavka, Proceedings of the
National Academy of Sciences 118 (2021).
date_created: 2024-03-20T10:42:45Z
date_published: 2021-10-06T00:00:00Z
date_updated: 2024-06-04T06:04:07Z
day: '06'
doi: 10.1073/pnas.2100198118
extern: '1'
external_id:
pmid:
- '34615715'
intvolume: ' 118'
issue: '41'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.2100198118
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structural basis of rotavirus RNA chaperone displacement and RNA annealing
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2021'
...
---
OA_place: publisher
OA_type: free access
_id: '18236'
abstract:
- lang: eng
text: 'Despite their great promise, artificial intelligence (AI) systems have yet
to become ubiquitous in the daily practice of medicine largely due to several
crucial unmet needs of healthcare practitioners. These include lack of explanations
in clinically meaningful terms, handling the presence of unknown medical conditions,
and transparency regarding the system’s limitations, both in terms of statistical
performance as well as recognizing situations for which the system’s predictions
are irrelevant. We articulate these unmet clinical needs as machine-learning (ML)
problems and systematically address them with cutting-edge ML techniques. We focus
on electrocardiogram (ECG) analysis as an example domain in which AI has great
potential and tackle two challenging tasks: the detection of a heterogeneous mix
of known and unknown arrhythmias from ECG and the identification of underlying
cardio-pathology from segments annotated as normal sinus rhythm recorded in patients
with an intermittent arrhythmia. We validate our methods by simulating a screening
for arrhythmias in a large-scale population while adhering to statistical significance
requirements. Specifically, our system 1) visualizes the relative importance of
each part of an ECG segment for the final model decision; 2) upholds specified
statistical constraints on its out-of-sample performance and provides uncertainty
estimation for its predictions; 3) handles inputs containing unknown rhythm types;
and 4) handles data from unseen patients while also flagging cases in which the
model’s outputs are not usable for a specific patient. This work represents a
significant step toward overcoming the limitations currently impeding the integration
of AI into clinical practice in cardiology and medicine in general.'
article_number: e2020620118
article_processing_charge: No
article_type: original
author:
- first_name: Yonatan
full_name: Elul, Yonatan
last_name: Elul
- first_name: Aviv A.
full_name: Rosenberg, Aviv A.
last_name: Rosenberg
- first_name: Assaf
full_name: Schuster, Assaf
last_name: Schuster
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
- first_name: Yael
full_name: Yaniv, Yael
last_name: Yaniv
citation:
ama: Elul Y, Rosenberg AA, Schuster A, Bronstein AM, Yaniv Y. Meeting the unmet
needs of clinicians from AI systems showcased for cardiology with deep-learning–based
ECG analysis. Proceedings of the National Academy of Sciences. 2021;118(24).
doi:10.1073/pnas.2020620118
apa: Elul, Y., Rosenberg, A. A., Schuster, A., Bronstein, A. M., & Yaniv, Y.
(2021). Meeting the unmet needs of clinicians from AI systems showcased for cardiology
with deep-learning–based ECG analysis. Proceedings of the National Academy
of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2020620118
chicago: Elul, Yonatan, Aviv A. Rosenberg, Assaf Schuster, Alex M. Bronstein, and
Yael Yaniv. “Meeting the Unmet Needs of Clinicians from AI Systems Showcased for
Cardiology with Deep-Learning–Based ECG Analysis.” Proceedings of the National
Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2020620118.
ieee: Y. Elul, A. A. Rosenberg, A. Schuster, A. M. Bronstein, and Y. Yaniv, “Meeting
the unmet needs of clinicians from AI systems showcased for cardiology with deep-learning–based
ECG analysis,” Proceedings of the National Academy of Sciences, vol. 118,
no. 24. National Academy of Sciences, 2021.
ista: Elul Y, Rosenberg AA, Schuster A, Bronstein AM, Yaniv Y. 2021. Meeting the
unmet needs of clinicians from AI systems showcased for cardiology with deep-learning–based
ECG analysis. Proceedings of the National Academy of Sciences. 118(24), e2020620118.
mla: Elul, Yonatan, et al. “Meeting the Unmet Needs of Clinicians from AI Systems
Showcased for Cardiology with Deep-Learning–Based ECG Analysis.” Proceedings
of the National Academy of Sciences, vol. 118, no. 24, e2020620118, National
Academy of Sciences, 2021, doi:10.1073/pnas.2020620118.
short: Y. Elul, A.A. Rosenberg, A. Schuster, A.M. Bronstein, Y. Yaniv, Proceedings
of the National Academy of Sciences 118 (2021).
date_created: 2024-10-08T12:58:09Z
date_published: 2021-06-07T00:00:00Z
date_updated: 2024-10-15T07:43:01Z
day: '07'
doi: 10.1073/pnas.2020620118
extern: '1'
external_id:
pmid:
- '34099565'
intvolume: ' 118'
issue: '24'
language:
- iso: eng
month: '06'
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Meeting the unmet needs of clinicians from AI systems showcased for cardiology
with deep-learning–based ECG analysis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2021'
...
---
_id: '8988'
abstract:
- lang: eng
text: The differentiation of cells depends on a precise control of their internal
organization, which is the result of a complex dynamic interplay between the cytoskeleton,
molecular motors, signaling molecules, and membranes. For example, in the developing
neuron, the protein ADAP1 (ADP-ribosylation factor GTPase-activating protein [ArfGAP]
with dual pleckstrin homology [PH] domains 1) has been suggested to control dendrite
branching by regulating the small GTPase ARF6. Together with the motor protein
KIF13B, ADAP1 is also thought to mediate delivery of the second messenger phosphatidylinositol
(3,4,5)-trisphosphate (PIP3) to the axon tip, thus contributing to PIP3 polarity.
However, what defines the function of ADAP1 and how its different roles are coordinated
are still not clear. Here, we studied ADAP1’s functions using in vitro reconstitutions.
We found that KIF13B transports ADAP1 along microtubules, but that PIP3 as well
as PI(3,4)P2 act as stop signals for this transport instead of being transported.
We also demonstrate that these phosphoinositides activate ADAP1’s enzymatic activity
to catalyze GTP hydrolysis by ARF6. Together, our results support a model for
the cellular function of ADAP1, where KIF13B transports ADAP1 until it encounters
high PIP3/PI(3,4)P2 concentrations in the plasma membrane. Here, ADAP1 disassociates
from the motor to inactivate ARF6, promoting dendrite branching.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: EM-Fac
acknowledgement: "We thank Urban Bezeljak, Natalia Baranova, Mar Lopez-Pelegrin, Catarina
Alcarva, and Victoria Faas for sharing reagents and helpful discussions. We thank
Veronika Szentirmai for help with protein purifications. We thank Carrie Bernecky,
Sascha Martens, and the M.L. lab for comments on the manuscript. We thank the bioimaging
facility, the life science facility, and Armel Nicolas from the mass spec facility
at the Institute of Science and Technology (IST) Austria for technical support.
C.D. acknowledges funding from the IST fellowship program; this work was supported
by Human Frontier Science Program Young Investigator Grant\r\nRGY0083/2016. "
article_number: e2010054118
article_processing_charge: No
article_type: original
author:
- first_name: Christian F
full_name: Düllberg, Christian F
id: 459064DC-F248-11E8-B48F-1D18A9856A87
last_name: Düllberg
orcid: 0000-0001-6335-9748
- first_name: Albert
full_name: Auer, Albert
id: 3018E8C2-F248-11E8-B48F-1D18A9856A87
last_name: Auer
orcid: 0000-0002-3580-2906
- first_name: Nikola
full_name: Canigova, Nikola
id: 3795523E-F248-11E8-B48F-1D18A9856A87
last_name: Canigova
orcid: 0000-0002-8518-5926
- first_name: Katrin
full_name: Loibl, Katrin
id: 3760F32C-F248-11E8-B48F-1D18A9856A87
last_name: Loibl
orcid: 0000-0002-2429-7668
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. In vitro reconstitution
reveals phosphoinositides as cargo-release factors and activators of the ARF6
GAP ADAP1. Proceedings of the National Academy of Sciences of the United States
of America. 2021;118(1). doi:10.1073/pnas.2010054118
apa: Düllberg, C. F., Auer, A., Canigova, N., Loibl, K., & Loose, M. (2021).
In vitro reconstitution reveals phosphoinositides as cargo-release factors and
activators of the ARF6 GAP ADAP1. Proceedings of the National Academy of Sciences
of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2010054118
chicago: Düllberg, Christian F, Albert Auer, Nikola Canigova, Katrin Loibl, and
Martin Loose. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release
Factors and Activators of the ARF6 GAP ADAP1.” Proceedings of the National
Academy of Sciences of the United States of America. National Academy of Sciences,
2021. https://doi.org/10.1073/pnas.2010054118.
ieee: C. F. Düllberg, A. Auer, N. Canigova, K. Loibl, and M. Loose, “In vitro reconstitution
reveals phosphoinositides as cargo-release factors and activators of the ARF6
GAP ADAP1,” Proceedings of the National Academy of Sciences of the United States
of America, vol. 118, no. 1. National Academy of Sciences, 2021.
ista: Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. 2021. In vitro reconstitution
reveals phosphoinositides as cargo-release factors and activators of the ARF6
GAP ADAP1. Proceedings of the National Academy of Sciences of the United States
of America. 118(1), e2010054118.
mla: Düllberg, Christian F., et al. “In Vitro Reconstitution Reveals Phosphoinositides
as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” Proceedings
of the National Academy of Sciences of the United States of America, vol.
118, no. 1, e2010054118, National Academy of Sciences, 2021, doi:10.1073/pnas.2010054118.
short: C.F. Düllberg, A. Auer, N. Canigova, K. Loibl, M. Loose, Proceedings of the
National Academy of Sciences of the United States of America 118 (2021).
corr_author: '1'
date_created: 2021-01-03T23:01:23Z
date_published: 2021-01-05T00:00:00Z
date_updated: 2026-06-18T19:37:53Z
day: '05'
ddc:
- '570'
department:
- _id: MaLo
- _id: MiSi
doi: 10.1073/pnas.2010054118
external_id:
isi:
- '000607270100018'
pmid:
- '33443153'
intvolume: ' 118'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.2010054118
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2599F062-B435-11E9-9278-68D0E5697425
grant_number: RGY0083/2016
name: Reconstitution of cell polarity and axis determination in a cell-free system
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'
scopus_import: '1'
status: public
title: In vitro reconstitution reveals phosphoinositides as cargo-release factors
and activators of the ARF6 GAP ADAP1
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2021'
...
---
_id: '8993'
abstract:
- lang: eng
text: N-1-naphthylphthalamic acid (NPA) is a key inhibitor of directional (polar)
transport of the hormone auxin in plants. For decades, it has been a pivotal tool
in elucidating the unique polar auxin transport-based processes underlying plant
growth and development. Its exact mode of action has long been sought after and
is still being debated, with prevailing mechanistic schemes describing only indirect
connections between NPA and the main transporters responsible for directional
transport, namely PIN auxin exporters. Here we present data supporting a model
in which NPA associates with PINs in a more direct manner than hitherto postulated.
We show that NPA inhibits PIN activity in a heterologous oocyte system and that
expression of NPA-sensitive PINs in plant, yeast, and oocyte membranes leads to
specific saturable NPA binding. We thus propose that PINs are a bona fide NPA
target. This offers a straightforward molecular basis for NPA inhibition of PIN-dependent
auxin transport and a logical parsimonious explanation for the known physiological
effects of NPA on plant growth, as well as an alternative hypothesis to interpret
past and future results. We also introduce PIN dimerization and describe an effect
of NPA on this, suggesting that NPA binding could be exploited to gain insights
into structural aspects of PINs related to their transport mechanism.
acknowledgement: "This work was supported by Austrian Science Fund Grant FWF P21533-B20
(to L.A.); German Research Foundation Grant DFG HA3468/6-1 (to U.Z.H.); and European
Research Council Grant 742985 (to J.F.). We thank Herta Steinkellner and Alexandra
Castilho for N. benthamiana plants, Fabian Nagelreiter for statistical advice, Lanassa
Bassukas for help with [ɣ32P]-\r\nATP assays, and Josef Penninger for providing
access to mass spectrometry instruments at the Vienna BioCenter Core Facilities.
We thank PNAS reviewers for the many comments and suggestions that helped to improve
this manuscript."
article_number: e2020857118
article_processing_charge: No
article_type: original
author:
- first_name: Lindy
full_name: Abas, Lindy
last_name: Abas
- first_name: Martina
full_name: Kolb, Martina
last_name: Kolb
- first_name: Johannes
full_name: Stadlmann, Johannes
last_name: Stadlmann
- first_name: Dorina P.
full_name: Janacek, Dorina P.
last_name: Janacek
- first_name: Kristina
full_name: Lukic, Kristina
id: 2B04DB84-F248-11E8-B48F-1D18A9856A87
last_name: Lukic
orcid: 0000-0003-1581-881X
- first_name: Claus
full_name: Schwechheimer, Claus
last_name: Schwechheimer
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
- first_name: Lukas
full_name: Mach, Lukas
last_name: Mach
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Ulrich Z.
full_name: Hammes, Ulrich Z.
last_name: Hammes
citation:
ama: Abas L, Kolb M, Stadlmann J, et al. Naphthylphthalamic acid associates with
and inhibits PIN auxin transporters. Proceedings of the National Academy of
Sciences of the United States of America. 2021;118(1). doi:10.1073/pnas.2020857118
apa: Abas, L., Kolb, M., Stadlmann, J., Janacek, D. P., Lukic, K., Schwechheimer,
C., … Hammes, U. Z. (2021). Naphthylphthalamic acid associates with and inhibits
PIN auxin transporters. Proceedings of the National Academy of Sciences of
the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2020857118
chicago: Abas, Lindy, Martina Kolb, Johannes Stadlmann, Dorina P. Janacek, Kristina
Lukic, Claus Schwechheimer, Leonid A Sazanov, Lukas Mach, Jiří Friml, and Ulrich
Z. Hammes. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.”
Proceedings of the National Academy of Sciences of the United States of America.
National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2020857118.
ieee: L. Abas et al., “Naphthylphthalamic acid associates with and inhibits
PIN auxin transporters,” Proceedings of the National Academy of Sciences of
the United States of America, vol. 118, no. 1. National Academy of Sciences,
2021.
ista: Abas L, Kolb M, Stadlmann J, Janacek DP, Lukic K, Schwechheimer C, Sazanov
LA, Mach L, Friml J, Hammes UZ. 2021. Naphthylphthalamic acid associates with
and inhibits PIN auxin transporters. Proceedings of the National Academy of Sciences
of the United States of America. 118(1), e2020857118.
mla: Abas, Lindy, et al. “Naphthylphthalamic Acid Associates with and Inhibits PIN
Auxin Transporters.” Proceedings of the National Academy of Sciences of the
United States of America, vol. 118, no. 1, e2020857118, National Academy of
Sciences, 2021, doi:10.1073/pnas.2020857118.
short: L. Abas, M. Kolb, J. Stadlmann, D.P. Janacek, K. Lukic, C. Schwechheimer,
L.A. Sazanov, L. Mach, J. Friml, U.Z. Hammes, Proceedings of the National Academy
of Sciences of the United States of America 118 (2021).
date_created: 2021-01-03T23:01:23Z
date_published: 2021-01-05T00:00:00Z
date_updated: 2026-06-18T19:38:20Z
day: '05'
ddc:
- '580'
department:
- _id: JiFr
- _id: LeSa
doi: 10.1073/pnas.2020857118
ec_funded: 1
external_id:
isi:
- '000607270100073'
pmid:
- '33443187'
intvolume: ' 118'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.2020857118
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
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:
link:
- relation: erratum
url: https://doi.org/10.1073/pnas.2102232118
scopus_import: '1'
status: public
title: Naphthylphthalamic acid associates with and inhibits PIN auxin transporters
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2021'
...
---
_id: '9257'
abstract:
- lang: eng
text: 'The inverse problem of designing component interactions to target emergent
structure is fundamental to numerous applications in biotechnology, materials
science, and statistical physics. Equally important is the inverse problem of
designing emergent kinetics, but this has received considerably less attention.
Using recent advances in automatic differentiation, we show how kinetic pathways
can be precisely designed by directly differentiating through statistical physics
models, namely free energy calculations and molecular dynamics simulations. We
consider two systems that are crucial to our understanding of structural self-assembly:
bulk crystallization and small nanoclusters. In each case, we are able to assemble
precise dynamical features. Using gradient information, we manipulate interactions
among constituent particles to tune the rate at which these systems yield specific
structures of interest. Moreover, we use this approach to learn nontrivial features
about the high-dimensional design space, allowing us to accurately predict when
multiple kinetic features can be simultaneously and independently controlled.
These results provide a concrete and generalizable foundation for studying nonstructural
self-assembly, including kinetic properties as well as other complex emergent
properties, in a vast array of systems.'
acknowledgement: We thank Agnese Curatolo, Megan Engel, Ofer Kimchi, Seong Ho Pahng,
and Roy Frostig for helpful discussions. This material is based on work supported
by NSF Graduate Research Fellowship Grant DGE1745303. This research was funded by
NSF Grant DMS-1715477, Materials Research Science and Engineering Centers Grant
DMR-1420570, and Office of Naval Research Grant N00014-17-1-3029. M.P.B. is an investigator
of the Simons Foundation.
article_number: e2024083118
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Ella M.
full_name: King, Ella M.
last_name: King
- first_name: Samuel S.
full_name: Schoenholz, Samuel S.
last_name: Schoenholz
- first_name: Ekin D.
full_name: Cubuk, Ekin D.
last_name: Cubuk
- first_name: Michael P.
full_name: Brenner, Michael P.
last_name: Brenner
citation:
ama: Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. Designing self-assembling
kinetics with differentiable statistical physics models. Proceedings of the
National Academy of Sciences of the United States of America. 2021;118(10).
doi:10.1073/pnas.2024083118
apa: Goodrich, C. P., King, E. M., Schoenholz, S. S., Cubuk, E. D., & Brenner,
M. P. (2021). Designing self-assembling kinetics with differentiable statistical
physics models. Proceedings of the National Academy of Sciences of the United
States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2024083118
chicago: Goodrich, Carl Peter, Ella M. King, Samuel S. Schoenholz, Ekin D. Cubuk,
and Michael P. Brenner. “Designing Self-Assembling Kinetics with Differentiable
Statistical Physics Models.” Proceedings of the National Academy of Sciences
of the United States of America. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2024083118.
ieee: C. P. Goodrich, E. M. King, S. S. Schoenholz, E. D. Cubuk, and M. P. Brenner,
“Designing self-assembling kinetics with differentiable statistical physics models,”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 118, no. 10. National Academy of Sciences, 2021.
ista: Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. 2021. Designing
self-assembling kinetics with differentiable statistical physics models. Proceedings
of the National Academy of Sciences of the United States of America. 118(10),
e2024083118.
mla: Goodrich, Carl Peter, et al. “Designing Self-Assembling Kinetics with Differentiable
Statistical Physics Models.” Proceedings of the National Academy of Sciences
of the United States of America, vol. 118, no. 10, e2024083118, National Academy
of Sciences, 2021, doi:10.1073/pnas.2024083118.
short: C.P. Goodrich, E.M. King, S.S. Schoenholz, E.D. Cubuk, M.P. Brenner, Proceedings
of the National Academy of Sciences of the United States of America 118 (2021).
date_created: 2021-03-21T23:01:20Z
date_published: 2021-03-09T00:00:00Z
date_updated: 2025-05-14T10:58:42Z
day: '09'
ddc:
- '530'
department:
- _id: CaGo
doi: 10.1073/pnas.2024083118
external_id:
isi:
- '000627429100097'
pmid:
- '33653960'
file:
- access_level: open_access
checksum: 5be8da2b1c0757feb1057f1a515cf9e0
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T12:23:54Z
date_updated: 2021-03-22T12:23:54Z
file_id: '9278'
file_name: 2021_PNAS_Goodrich.pdf
file_size: 1047954
relation: main_file
success: 1
file_date_updated: 2021-03-22T12:23:54Z
has_accepted_license: '1'
intvolume: ' 118'
isi: 1
issue: '10'
language:
- iso: eng
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'
scopus_import: '1'
status: public
title: Designing self-assembling kinetics with differentiable statistical physics
models
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2021'
...
---
_id: '9301'
abstract:
- lang: eng
text: Electrodepositing insulating lithium peroxide (Li2O2) is the key process during
discharge of aprotic Li–O2 batteries and determines rate, capacity, and reversibility.
Current understanding states that the partition between surface adsorbed and dissolved
lithium superoxide governs whether Li2O2 grows as a conformal surface film or
larger particles, leading to low or high capacities, respectively. However, better
understanding governing factors for Li2O2 packing density and capacity requires
structural sensitive in situ metrologies. Here, we establish in situ small- and
wide-angle X-ray scattering (SAXS/WAXS) as a suitable method to record the Li2O2
phase evolution with atomic to submicrometer resolution during cycling a custom-built
in situ Li–O2 cell. Combined with sophisticated data analysis, SAXS allows retrieving
rich quantitative structural information from complex multiphase systems. Surprisingly,
we find that features are absent that would point at a Li2O2 surface film formed
via two consecutive electron transfers, even in poorly solvating electrolytes
thought to be prototypical for surface growth. All scattering data can be modeled
by stacks of thin Li2O2 platelets potentially forming large toroidal particles.
Li2O2 solution growth is further justified by rotating ring-disk electrode measurements
and electron microscopy. Higher discharge overpotentials lead to smaller Li2O2
particles, but there is no transition to an electronically passivating, conformal
Li2O2 coating. Hence, mass transport of reactive species rather than electronic
transport through a Li2O2 film limits the discharge capacity. Provided that species
mobilities and carbon surface areas are high, this allows for high discharge capacities
even in weakly solvating electrolytes. The currently accepted Li–O2 reaction mechanism
ought to be reconsidered.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: S.A.F. and C.P. are indebted to the European Research Council under
the European Union's Horizon 2020 research and innovation program (Grant Agreement
No. 636069), the Austrian Federal Ministry of Science, Research and Economy, and
the Austrian Research Promotion Agency (Grant No. 845364). We acknowledge A. Zankel
and H. Schroettner for support with SEM measurements. C.P. thanks N. Kostoglou,
C. Koczwara, M. Hartmann, and M. Burian for discussions on gas sorption analysis,
C++ programming, Monte Carlo modeling, and in situ SAXS experiments, respectively.
We thank S. Stadlbauer for help with Karl Fischer titration, R. Riccò for gas sorption
measurements, and acknowledge Graz University of Technology for support through
the Lead Project LP-03. Likewise, the use of SOMAPP Lab, a core facility supported
by the Austrian Federal Ministry of Education, Science and Research, the Graz University
of Technology, the University of Graz, and Anton Paar GmbH is acknowledged. S.A.F.
is indebted to Institute of Science and Technology Austria (IST Austria) for support.
This research was supported by the Scientific Service Units of IST Austria through
resources provided by the Electron Microscopy Facility.
article_number: e2021893118
article_processing_charge: No
article_type: original
author:
- first_name: Christian
full_name: Prehal, Christian
last_name: Prehal
- first_name: Aleksej
full_name: Samojlov, Aleksej
last_name: Samojlov
- first_name: Manfred
full_name: Nachtnebel, Manfred
last_name: Nachtnebel
- first_name: Ludek
full_name: Lovicar, Ludek
id: 36DB3A20-F248-11E8-B48F-1D18A9856A87
last_name: Lovicar
orcid: 0000-0001-6206-4200
- first_name: Manfred
full_name: Kriechbaum, Manfred
last_name: Kriechbaum
- first_name: Heinz
full_name: Amenitsch, Heinz
last_name: Amenitsch
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Prehal C, Samojlov A, Nachtnebel M, et al. In situ small-angle X-ray scattering
reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes.
Proceedings of the National Academy of Sciences of the United States of America.
2021;118(14). doi:10.1073/pnas.2021893118
apa: Prehal, C., Samojlov, A., Nachtnebel, M., Lovicar, L., Kriechbaum, M., Amenitsch,
H., & Freunberger, S. A. (2021). In situ small-angle X-ray scattering reveals
solution phase discharge of Li–O2 batteries with weakly solvating electrolytes.
Proceedings of the National Academy of Sciences of the United States of America.
National Academy of Sciences. https://doi.org/10.1073/pnas.2021893118
chicago: Prehal, Christian, Aleksej Samojlov, Manfred Nachtnebel, Ludek Lovicar,
Manfred Kriechbaum, Heinz Amenitsch, and Stefan Alexander Freunberger. “In Situ
Small-Angle X-Ray Scattering Reveals Solution Phase Discharge of Li–O2 Batteries
with Weakly Solvating Electrolytes.” Proceedings of the National Academy of
Sciences of the United States of America. National Academy of Sciences, 2021.
https://doi.org/10.1073/pnas.2021893118.
ieee: C. Prehal et al., “In situ small-angle X-ray scattering reveals solution
phase discharge of Li–O2 batteries with weakly solvating electrolytes,” Proceedings
of the National Academy of Sciences of the United States of America, vol.
118, no. 14. National Academy of Sciences, 2021.
ista: Prehal C, Samojlov A, Nachtnebel M, Lovicar L, Kriechbaum M, Amenitsch H,
Freunberger SA. 2021. In situ small-angle X-ray scattering reveals solution phase
discharge of Li–O2 batteries with weakly solvating electrolytes. Proceedings of
the National Academy of Sciences of the United States of America. 118(14), e2021893118.
mla: Prehal, Christian, et al. “In Situ Small-Angle X-Ray Scattering Reveals Solution
Phase Discharge of Li–O2 Batteries with Weakly Solvating Electrolytes.” Proceedings
of the National Academy of Sciences of the United States of America, vol.
118, no. 14, e2021893118, National Academy of Sciences, 2021, doi:10.1073/pnas.2021893118.
short: C. Prehal, A. Samojlov, M. Nachtnebel, L. Lovicar, M. Kriechbaum, H. Amenitsch,
S.A. Freunberger, Proceedings of the National Academy of Sciences of the United
States of America 118 (2021).
date_created: 2021-03-31T07:00:01Z
date_published: 2021-04-06T00:00:00Z
date_updated: 2025-06-12T06:56:39Z
day: '06'
department:
- _id: StFr
- _id: EM-Fac
doi: 10.1073/pnas.2021893118
external_id:
isi:
- '000637398300050'
pmid:
- '33785597'
intvolume: ' 118'
isi: 1
issue: '14'
keyword:
- small-angle X-ray scattering
- oxygen reduction
- disproportionation
- Li-air battery
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.26434/chemrxiv.11447775
month: '04'
oa: 1
oa_version: Preprint
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'
scopus_import: '1'
status: public
title: In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2
batteries with weakly solvating electrolytes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2021'
...
---
_id: '9330'
abstract:
- lang: eng
text: In nerve cells the genes encoding for α2δ subunits of voltage-gated calcium
channels have been linked to synaptic functions and neurological disease. Here
we show that α2δ subunits are essential for the formation and organization of
glutamatergic synapses. Using a cellular α2δ subunit triple-knockout/knockdown
model, we demonstrate a failure in presynaptic differentiation evidenced by defective
presynaptic calcium channel clustering and calcium influx, smaller presynaptic
active zones, and a strongly reduced accumulation of presynaptic vesicle-associated
proteins (synapsin and vGLUT). The presynaptic defect is associated with the downscaling
of postsynaptic AMPA receptors and the postsynaptic density. The role of α2δ isoforms
as synaptic organizers is highly redundant, as each individual α2δ isoform can
rescue presynaptic calcium channel trafficking and expression of synaptic proteins.
Moreover, α2δ-2 and α2δ-3 with mutated metal ion-dependent adhesion sites can
fully rescue presynaptic synapsin expression but only partially calcium channel
trafficking, suggesting that the regulatory role of α2δ subunits is independent
from its role as a calcium channel subunit. Our findings influence the current
view on excitatory synapse formation. First, our study suggests that postsynaptic
differentiation is secondary to presynaptic differentiation. Second, the dependence
of presynaptic differentiation on α2δ implicates α2δ subunits as potential nucleation
points for the organization of synapses. Finally, our results suggest that α2δ
subunits act as transsynaptic organizers of glutamatergic synapses, thereby aligning
the synaptic active zone with the postsynaptic density.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: "We thank Arnold Schwartz for providing α2δ-1 knockout mice; Ariane
Benedetti, Sabine Baumgartner, Sandra Demetz, and Irene Mahlknecht for technical
support; Nadine Ortner and Andreas Lieb for electrophysiological experiments; the
team of the Electron Microscopy Facility at the Institute of Science and Technology
Austria for technical support related to ultrastructural analysis; Hermann Dietrich
and Anja Beierfuß and her team for animal care; Jutta Engel and Jörg Striessnig
for critical discussions; and Bruno Benedetti and Bernhard Flucher for critical
discussions and reading the manuscript. This study was supported by Austrian Science
Fund Grants P24079, F44060, F44150, and DOC30-B30 (to G.J.O.) and T855 (to M.C.),
European Research Council Grant AdG 694539 (to R.S.), Deutsche Forschungsgemeinschaft\r\nGrant
SFB1348-TP A03 (to M.M.), and Interdisziplinäre Zentrum für Klinische Forschung
Münster Grant Mi3/004/19 (to M.M.). This work is part of the PhD theses of C.L.S.,
S.M.G., and C.A."
article_processing_charge: No
article_type: original
author:
- first_name: Clemens L.
full_name: Schöpf, Clemens L.
last_name: Schöpf
- first_name: Cornelia
full_name: Ablinger, Cornelia
last_name: Ablinger
- first_name: Stefanie M.
full_name: Geisler, Stefanie M.
last_name: Geisler
- first_name: Ruslan I.
full_name: Stanika, Ruslan I.
last_name: Stanika
- first_name: Marta
full_name: Campiglio, Marta
last_name: Campiglio
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Benedikt
full_name: Nimmervoll, Benedikt
last_name: Nimmervoll
- first_name: Bettina
full_name: Schlick, Bettina
last_name: Schlick
- first_name: Johannes
full_name: Brockhaus, Johannes
last_name: Brockhaus
- first_name: Markus
full_name: Missler, Markus
last_name: Missler
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Gerald J.
full_name: Obermair, Gerald J.
last_name: Obermair
citation:
ama: Schöpf CL, Ablinger C, Geisler SM, et al. Presynaptic α2δ subunits are key
organizers of glutamatergic synapses. Proceedings of the National Academy of
Sciences of the United States of America. 2021;118(14). doi:10.1073/pnas.1920827118
apa: Schöpf, C. L., Ablinger, C., Geisler, S. M., Stanika, R. I., Campiglio, M.,
Kaufmann, W., … Obermair, G. J. (2021). Presynaptic α2δ subunits are key organizers
of glutamatergic synapses. Proceedings of the National Academy of Sciences
of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1920827118
chicago: Schöpf, Clemens L., Cornelia Ablinger, Stefanie M. Geisler, Ruslan I. Stanika,
Marta Campiglio, Walter Kaufmann, Benedikt Nimmervoll, et al. “Presynaptic Α2δ
Subunits Are Key Organizers of Glutamatergic Synapses.” Proceedings of the
National Academy of Sciences of the United States of America. National Academy
of Sciences, 2021. https://doi.org/10.1073/pnas.1920827118.
ieee: C. L. Schöpf et al., “Presynaptic α2δ subunits are key organizers of
glutamatergic synapses,” Proceedings of the National Academy of Sciences of
the United States of America, vol. 118, no. 14. National Academy of Sciences,
2021.
ista: Schöpf CL, Ablinger C, Geisler SM, Stanika RI, Campiglio M, Kaufmann W, Nimmervoll
B, Schlick B, Brockhaus J, Missler M, Shigemoto R, Obermair GJ. 2021. Presynaptic
α2δ subunits are key organizers of glutamatergic synapses. Proceedings of the
National Academy of Sciences of the United States of America. 118(14).
mla: Schöpf, Clemens L., et al. “Presynaptic Α2δ Subunits Are Key Organizers of
Glutamatergic Synapses.” Proceedings of the National Academy of Sciences of
the United States of America, vol. 118, no. 14, National Academy of Sciences,
2021, doi:10.1073/pnas.1920827118.
short: C.L. Schöpf, C. Ablinger, S.M. Geisler, R.I. Stanika, M. Campiglio, W. Kaufmann,
B. Nimmervoll, B. Schlick, J. Brockhaus, M. Missler, R. Shigemoto, G.J. Obermair,
Proceedings of the National Academy of Sciences of the United States of America
118 (2021).
date_created: 2021-04-18T22:01:40Z
date_published: 2021-04-06T00:00:00Z
date_updated: 2025-06-12T06:56:21Z
day: '06'
ddc:
- '570'
department:
- _id: EM-Fac
- _id: RySh
doi: 10.1073/pnas.1920827118
ec_funded: 1
external_id:
isi:
- '000637398300002'
pmid:
- '33782113'
file:
- access_level: open_access
checksum: dd014f68ae9d7d8d8fc4139a24e04506
content_type: application/pdf
creator: dernst
date_created: 2021-04-19T10:10:56Z
date_updated: 2021-04-19T10:10:56Z
file_id: '9340'
file_name: 2021_PNAS_Schoepf.pdf
file_size: 2603911
relation: main_file
success: 1
file_date_updated: 2021-04-19T10:10:56Z
has_accepted_license: '1'
intvolume: ' 118'
isi: 1
issue: '14'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Presynaptic α2δ subunits are key organizers of glutamatergic synapses
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2021'
...
---
_id: '9877'
abstract:
- lang: eng
text: 'Parent-of-origin–dependent gene expression in mammals and flowering plants
results from differing chromatin imprints (genomic imprinting) between maternally
and paternally inherited alleles. Imprinted gene expression in the endosperm of
seeds is associated with localized hypomethylation of maternally but not paternally
inherited DNA, with certain small RNAs also displaying parent-of-origin–specific
expression. To understand the evolution of imprinting mechanisms in Oryza sativa
(rice), we analyzed imprinting divergence among four cultivars that span both
japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted
genes are imprinted across cultivars and enriched for functions in chromatin and
transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted
genes display divergent imprinting. Analyses of DNA methylation and small RNAs
revealed that endosperm-specific 24-nt small RNA–producing loci show weak RNA-directed
DNA methylation, frequently overlap genes, and are imprinted four times more often
than genes. However, imprinting divergence most often correlated with local DNA
methylation epimutations (9 of 17 assessable loci), which were largely stable
within subspecies. Small insertion/deletion events and transposable element insertions
accompanied 4 of the 9 locally epimutated loci and associated with imprinting
divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic
variation occurred at key regulatory regions—the promoter and transcription start
site of maternally biased genes, and the promoter and gene body of paternally
biased genes. Our results reinforce models for the role of maternal-specific DNA
hypomethylation in imprinting of both maternally and paternally biased genes,
and highlight the role of transposition and epimutation in rice imprinting evolution.'
acknowledgement: We thank W. Schackwitz, M. Joel, and the Joint Genome Institute sequencing
team for generating the IR64 genome sequence and initial analysis; L. Bartley and
E. Marvinney for genomic DNA preparation for IR64 resequencing; and the University
of California (UC), Berkeley Sanger sequencing team for technical advice and service.
This work was partially funded by NSF Grant IOS-1025890 (to R.L.F. and D.Z.), NIH
Grant GM69415 (to R.L.F. and D.Z.), NIH Grant GM122968 (to P.C.R.), a Young Investigator
Grant from the Arnold and Mabel Beckman Foundation (to D.Z.), an International Fulbright
Science and Technology Award (to J.A.R.), and a Taiwan Ministry of Education Studying
Abroad Scholarship (to P.-H.H.). This work used the Vincent J. Coates Genomics Sequencing
Laboratory at UC Berkeley, supported by NIH Instrumentation Grant S10 OD018174.
article_number: e2104445118
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Deling
full_name: Ruan, Deling
last_name: Ruan
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Manoj K.
full_name: Sharma, Manoj K.
last_name: Sharma
- first_name: Rita
full_name: Sharma, Rita
last_name: Sharma
- first_name: XinYi
full_name: Ye, XinYi
last_name: Ye
- first_name: Nicholas D.
full_name: Nguyen, Nicholas D.
last_name: Nguyen
- first_name: Sukhranjan
full_name: Nijjar, Sukhranjan
last_name: Nijjar
- first_name: Pamela C.
full_name: Ronald, Pamela C.
last_name: Ronald
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Rodrigues JA, Hsieh P-H, Ruan D, et al. Divergence among rice cultivars reveals
roles for transposition and epimutation in ongoing evolution of genomic imprinting.
Proceedings of the National Academy of Sciences of the United States of America.
2021;118(29). doi:10.1073/pnas.2104445118
apa: Rodrigues, J. A., Hsieh, P.-H., Ruan, D., Nishimura, T., Sharma, M. K., Sharma,
R., … Zilberman, D. (2021). Divergence among rice cultivars reveals roles for
transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences. https://doi.org/10.1073/pnas.2104445118
chicago: Rodrigues, Jessica A., Ping-Hung Hsieh, Deling Ruan, Toshiro Nishimura,
Manoj K. Sharma, Rita Sharma, XinYi Ye, et al. “Divergence among Rice Cultivars
Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic
Imprinting.” Proceedings of the National Academy of Sciences of the United
States of America. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2104445118.
ieee: J. A. Rodrigues et al., “Divergence among rice cultivars reveals roles
for transposition and epimutation in ongoing evolution of genomic imprinting,”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 118, no. 29. National Academy of Sciences, 2021.
ista: Rodrigues JA, Hsieh P-H, Ruan D, Nishimura T, Sharma MK, Sharma R, Ye X, Nguyen
ND, Nijjar S, Ronald PC, Fischer RL, Zilberman D. 2021. Divergence among rice
cultivars reveals roles for transposition and epimutation in ongoing evolution
of genomic imprinting. Proceedings of the National Academy of Sciences of the
United States of America. 118(29), e2104445118.
mla: Rodrigues, Jessica A., et al. “Divergence among Rice Cultivars Reveals Roles
for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 118, no. 29, e2104445118, National Academy of Sciences, 2021, doi:10.1073/pnas.2104445118.
short: J.A. Rodrigues, P.-H. Hsieh, D. Ruan, T. Nishimura, M.K. Sharma, R. Sharma,
X. Ye, N.D. Nguyen, S. Nijjar, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings
of the National Academy of Sciences of the United States of America 118 (2021).
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title: Divergence among rice cultivars reveals roles for transposition and epimutation
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