---
_id: '14841'
abstract:
- lang: eng
text: De novo heterozygous variants in KCNC2 encoding the voltage-gated potassium
(K+) channel subunit Kv3.2 are a recently described cause of developmental and
epileptic encephalopathy (DEE). A de novo variant in KCNC2 c.374G > A (p.Cys125Tyr)
was identified via exome sequencing in a patient with DEE. Relative to wild-type
Kv3.2, Kv3.2-p.Cys125Tyr induces K+ currents exhibiting a large hyperpolarizing
shift in the voltage dependence of activation, accelerated activation, and delayed
deactivation consistent with a relative stabilization of the open conformation,
along with increased current density. Leveraging the cryogenic electron microscopy
(cryo-EM) structure of Kv3.1, molecular dynamic simulations suggest that a strong
π-π stacking interaction between the variant Tyr125 and Tyr156 in the α-6 helix
of the T1 domain promotes a relative stabilization of the open conformation of
the channel, which underlies the observed gain of function. A multicompartment
computational model of a Kv3-expressing parvalbumin-positive cerebral cortex fast-spiking
γ-aminobutyric acidergic (GABAergic) interneuron (PV-IN) demonstrates how the
Kv3.2-Cys125Tyr variant impairs neuronal excitability and dysregulates inhibition
in cerebral cortex circuits to explain the resulting epilepsy.
acknowledgement: This work was supported by an ERC Consolidator Grant (SYNAPSEEK)
to T.P.V., the NOMIS Foundation through the NOMIS Fellowships program at IST Austria
to C.B.C., a Jefferson Synaptic Biology Center Pilot Project Grant to M.C., NIH
NINDS U54 NS108874 (PI, Alfred L. George), and NIH NINDS R01 NS122887 to E.M.G.
The computations were enabled by resources provided by the Swedish National Infrastructure
for Computing (SNIC) at the PDC Center for High-Performance Computing, KTH Royal
Institute of Technology, partially funded by the Swedish Research Council through
grant agreement no. 2018-05973. We thank Akshay Sridhar for the fruitful discussion
of the project.
article_number: e2307776121
article_processing_charge: No
article_type: original
author:
- first_name: Jerome
full_name: Clatot, Jerome
last_name: Clatot
- first_name: Christopher
full_name: Currin, Christopher
id: e8321fc5-3091-11eb-8a53-83f309a11ac9
last_name: Currin
orcid: 0000-0002-4809-5059
- first_name: Qiansheng
full_name: Liang, Qiansheng
last_name: Liang
- first_name: Tanadet
full_name: Pipatpolkai, Tanadet
last_name: Pipatpolkai
- first_name: Shavonne L.
full_name: Massey, Shavonne L.
last_name: Massey
- first_name: Ingo
full_name: Helbig, Ingo
last_name: Helbig
- first_name: Lucie
full_name: Delemotte, Lucie
last_name: Delemotte
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Manuel
full_name: Covarrubias, Manuel
last_name: Covarrubias
- first_name: Ethan M.
full_name: Goldberg, Ethan M.
last_name: Goldberg
citation:
ama: Clatot J, Currin C, Liang Q, et al. A structurally precise mechanism links
an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction.
Proceedings of the National Academy of Sciences of the United States of America.
2024;121(3). doi:10.1073/pnas.2307776121
apa: Clatot, J., Currin, C., Liang, Q., Pipatpolkai, T., Massey, S. L., Helbig,
I., … Goldberg, E. M. (2024). A structurally precise mechanism links an epilepsy-associated
KCNC2 potassium channel mutation to interneuron dysfunction. Proceedings of
the National Academy of Sciences of the United States of America. Proceedings
of the National Academy of Sciences. https://doi.org/10.1073/pnas.2307776121
chicago: Clatot, Jerome, Christopher Currin, Qiansheng Liang, Tanadet Pipatpolkai,
Shavonne L. Massey, Ingo Helbig, Lucie Delemotte, Tim P Vogels, Manuel Covarrubias,
and Ethan M. Goldberg. “A Structurally Precise Mechanism Links an Epilepsy-Associated
KCNC2 Potassium Channel Mutation to Interneuron Dysfunction.” Proceedings of
the National Academy of Sciences of the United States of America. Proceedings
of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2307776121.
ieee: J. Clatot et al., “A structurally precise mechanism links an epilepsy-associated
KCNC2 potassium channel mutation to interneuron dysfunction,” Proceedings of
the National Academy of Sciences of the United States of America, vol. 121,
no. 3. Proceedings of the National Academy of Sciences, 2024.
ista: Clatot J, Currin C, Liang Q, Pipatpolkai T, Massey SL, Helbig I, Delemotte
L, Vogels TP, Covarrubias M, Goldberg EM. 2024. A structurally precise mechanism
links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction.
Proceedings of the National Academy of Sciences of the United States of America.
121(3), e2307776121.
mla: Clatot, Jerome, et al. “A Structurally Precise Mechanism Links an Epilepsy-Associated
KCNC2 Potassium Channel Mutation to Interneuron Dysfunction.” Proceedings of
the National Academy of Sciences of the United States of America, vol. 121,
no. 3, e2307776121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2307776121.
short: J. Clatot, C. Currin, Q. Liang, T. Pipatpolkai, S.L. Massey, I. Helbig, L.
Delemotte, T.P. Vogels, M. Covarrubias, E.M. Goldberg, Proceedings of the National
Academy of Sciences of the United States of America 121 (2024).
date_created: 2024-01-21T23:00:56Z
date_published: 2024-01-16T00:00:00Z
date_updated: 2024-01-23T10:20:40Z
day: '16'
department:
- _id: TiVo
doi: 10.1073/pnas.2307776121
ec_funded: 1
external_id:
pmid:
- '38194456'
intvolume: ' 121'
issue: '3'
language:
- iso: eng
month: '01'
oa_version: None
pmid: 1
project:
- _id: 0aacfa84-070f-11eb-9043-d7eb2c709234
call_identifier: H2020
grant_number: '819603'
name: Learning the shape of synaptic plasticity rules for neuronal architectures
and function through machine learning.
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: software
url: 'https://github.com/ChrisCurrin/pv-kcnc2 '
scopus_import: '1'
status: public
title: A structurally precise mechanism links an epilepsy-associated KCNC2 potassium
channel mutation to interneuron dysfunction
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 121
year: '2024'
...
---
_id: '15001'
abstract:
- lang: eng
text: "Self-replication of amyloid fibrils via secondary nucleation is an intriguing
physicochemical phenomenon in which existing fibrils catalyze the formation of
their own copies. The molecular events behind this fibril surface-mediated process
remain largely inaccessible to current structural and imaging techniques. Using
statistical mechanics, computer modeling, and chemical kinetics, we show that
the catalytic structure of the fibril surface can be inferred from the aggregation
behavior in the presence and absence of a fibril-binding inhibitor. We apply our
approach to the case of Alzheimer’s A\r\n amyloid fibrils formed in the presence
of proSP-C Brichos inhibitors. We find that self-replication of A\r\n fibrils
occurs on small catalytic sites on the fibril surface, which are far apart from
each other, and each of which can be covered by a single Brichos inhibitor."
acknowledgement: We acknowledge support from the Erasmus programme and the University
College London Institute for the Physics of Living Systems (S.C., T.C.T.M., A.Š.),
the Biotechnology and Biological Sciences Research Council (T.P.J.K.), the Engineering
and Physical Sciences Research Council (D.F.), the European Research Council (T.P.J.K.,
S.L., D.F., and A.Š.), the Frances and Augustus Newman Foundation (T.P.J.K.), the
Academy of Medical Sciences and Wellcome Trust (A.Š.), and the Royal Society (S.C.
and A.Š.).
article_number: e2220075121
article_processing_charge: Yes
article_type: original
author:
- first_name: Samo
full_name: Curk, Samo
id: 031eff0d-d481-11ee-8508-cd12a7a86e5b
last_name: Curk
orcid: 0000-0001-6160-9766
- first_name: Johannes
full_name: Krausser, Johannes
last_name: Krausser
- first_name: Georg
full_name: Meisl, Georg
last_name: Meisl
- first_name: Daan
full_name: Frenkel, Daan
last_name: Frenkel
- first_name: Sara
full_name: Linse, Sara
last_name: Linse
- first_name: Thomas C.T.
full_name: Michaels, Thomas C.T.
last_name: Michaels
- first_name: Tuomas P.J.
full_name: Knowles, Tuomas P.J.
last_name: Knowles
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Curk S, Krausser J, Meisl G, et al. Self-replication of Aβ42 aggregates occurs
on small and isolated fibril sites. Proceedings of the National Academy of
Sciences of the United States of America. 2024;121(7). doi:10.1073/pnas.2220075121
apa: Curk, S., Krausser, J., Meisl, G., Frenkel, D., Linse, S., Michaels, T. C.
T., … Šarić, A. (2024). Self-replication of Aβ42 aggregates occurs on small and
isolated fibril sites. Proceedings of the National Academy of Sciences of the
United States of America. Proceedings of the National Academy of Sciences.
https://doi.org/10.1073/pnas.2220075121
chicago: Curk, Samo, Johannes Krausser, Georg Meisl, Daan Frenkel, Sara Linse, Thomas
C.T. Michaels, Tuomas P.J. Knowles, and Anđela Šarić. “Self-Replication of Aβ42
Aggregates Occurs on Small and Isolated Fibril Sites.” Proceedings of the National
Academy of Sciences of the United States of America. Proceedings of the National
Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2220075121.
ieee: S. Curk et al., “Self-replication of Aβ42 aggregates occurs on small
and isolated fibril sites,” Proceedings of the National Academy of Sciences
of the United States of America, vol. 121, no. 7. Proceedings of the National
Academy of Sciences, 2024.
ista: Curk S, Krausser J, Meisl G, Frenkel D, Linse S, Michaels TCT, Knowles TPJ,
Šarić A. 2024. Self-replication of Aβ42 aggregates occurs on small and isolated
fibril sites. Proceedings of the National Academy of Sciences of the United States
of America. 121(7), e2220075121.
mla: Curk, Samo, et al. “Self-Replication of Aβ42 Aggregates Occurs on Small and
Isolated Fibril Sites.” Proceedings of the National Academy of Sciences of
the United States of America, vol. 121, no. 7, e2220075121, Proceedings of
the National Academy of Sciences, 2024, doi:10.1073/pnas.2220075121.
short: S. Curk, J. Krausser, G. Meisl, D. Frenkel, S. Linse, T.C.T. Michaels, T.P.J.
Knowles, A. Šarić, Proceedings of the National Academy of Sciences of the United
States of America 121 (2024).
date_created: 2024-02-18T23:01:00Z
date_published: 2024-02-13T00:00:00Z
date_updated: 2024-02-26T08:45:56Z
day: '13'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1073/pnas.2220075121
ec_funded: 1
external_id:
pmid:
- '38335256'
file:
- access_level: open_access
checksum: 5aeb65bcc0dd829b1f9ab307c5031d4b
content_type: application/pdf
creator: dernst
date_created: 2024-02-26T08:20:00Z
date_updated: 2024-02-26T08:20:00Z
file_id: '15026'
file_name: 2024_PNAS_Curk.pdf
file_size: 7699487
relation: main_file
success: 1
file_date_updated: 2024-02-26T08:20:00Z
has_accepted_license: '1'
intvolume: ' 121'
issue: '7'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '02'
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
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
related_material:
record:
- id: '15027'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites
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: 121
year: '2024'
...
---
_id: '15084'
abstract:
- lang: eng
text: "GABAB receptor (GBR) activation inhibits neurotransmitter release in axon
terminals in the brain, except in medial habenula (MHb) terminals, which show
robust potentiation. However, mechanisms underlying this enigmatic potentiation
remain elusive. Here, we report that GBR activation on MHb terminals induces an
activity-dependent transition from a facilitating, tonic to a depressing, phasic
neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase
in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked
synaptic vesicles (SVs) at the presynaptic active zone (AZ). Strikingly, the depressing
phasic release exhibits looser coupling distance than the tonic release. Furthermore,
the tonic and phasic release are selectively affected by deletion of synaptoporin
(SPO) and Ca\r\n 2+\r\n -dependent
activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation,
the short-term plasticity associated with tonic release, and CAPS2 retains the
increased RRP for initial responses in phasic response trains. The cytosolic protein
CAPS2 showed a SV-associated distribution similar to the vesicular transmembrane
protein SPO, and they were colocalized in the same terminals. We developed the
“Flash and Freeze-fracture” method, and revealed the release of SPO-associated
vesicles in both tonic and phasic modes and activity-dependent recruitment of
CAPS2 to the AZ during phasic release, which lasted several minutes. Overall,
these results indicate that GBR activation translocates CAPS2 to the AZ along
with the fusion of CAPS2-associated SVs, contributing to persistency of the RRP
increase. Thus, we identified structural and molecular mechanisms underlying tonic
and phasic neurotransmitter release and their transition by GBR activation in
MHb terminals."
acknowledged_ssus:
- _id: M-Shop
- _id: PreCl
- _id: EM-Fac
acknowledgement: We thank Erwin Neher and Ipe Ninan for critical comments on the manuscript.
This project has received funding from the European Research Council (ERC) and European
Commission, under the European Union’s Horizon 2020 research and innovation program
(ERC grant agreement no. 694539 to R.S. and the Marie Skłodowska-Curie grant agreement
no. 665385 to C.Ö.). This study was supported by the Cooperative Study Program of
Center for Animal Resources and Collaborative Study of NINS. We thank Kohgaku Eguchi
for statistical analysis, Yu Kasugai for additional EM imaging, Robert Beattie for
the design of the slice recovery chamber for Flash and Freeze experiments, Todor
Asenov from the ISTA machine shop for custom part preparations for high-pressure
freezing, the ISTA preclinical facility for animal caretaking, and the ISTA EM facilities
for technical support.
article_number: e2301449121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Peter
full_name: Koppensteiner, Peter
id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87
last_name: Koppensteiner
orcid: 0000-0002-3509-1948
- first_name: Pradeep
full_name: Bhandari, Pradeep
id: 45EDD1BC-F248-11E8-B48F-1D18A9856A87
last_name: Bhandari
orcid: 0000-0003-0863-4481
- first_name: Hüseyin C
full_name: Önal, Hüseyin C
id: 4659D740-F248-11E8-B48F-1D18A9856A87
last_name: Önal
orcid: 0000-0002-2771-2011
- first_name: Carolina
full_name: Borges Merjane, Carolina
id: 4305C450-F248-11E8-B48F-1D18A9856A87
last_name: Borges Merjane
orcid: 0000-0003-0005-401X
- first_name: Elodie
full_name: Le Monnier, Elodie
id: 3B59276A-F248-11E8-B48F-1D18A9856A87
last_name: Le Monnier
- first_name: Utsa
full_name: Roy, Utsa
id: 4d26cf11-5355-11ee-ae5a-eb05e255b9b2
last_name: Roy
- first_name: Yukihiro
full_name: Nakamura, Yukihiro
last_name: Nakamura
- first_name: Tetsushi
full_name: Sadakata, Tetsushi
last_name: Sadakata
- first_name: Makoto
full_name: Sanbo, Makoto
last_name: Sanbo
- first_name: Masumi
full_name: Hirabayashi, Masumi
last_name: Hirabayashi
- first_name: JeongSeop
full_name: Rhee, JeongSeop
last_name: Rhee
- first_name: Nils
full_name: Brose, Nils
last_name: Brose
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Koppensteiner P, Bhandari P, Önal C, et al. GABAB receptors induce phasic release
from medial habenula terminals through activity-dependent recruitment of release-ready
vesicles. Proceedings of the National Academy of Sciences. 2024;121(8).
doi:10.1073/pnas.2301449121
apa: Koppensteiner, P., Bhandari, P., Önal, C., Borges Merjane, C., Le Monnier,
E., Roy, U., … Shigemoto, R. (2024). GABAB receptors induce phasic release from
medial habenula terminals through activity-dependent recruitment of release-ready
vesicles. Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences. https://doi.org/10.1073/pnas.2301449121
chicago: Koppensteiner, Peter, Pradeep Bhandari, Cihan Önal, Carolina Borges Merjane,
Elodie Le Monnier, Utsa Roy, Yukihiro Nakamura, et al. “GABAB Receptors Induce
Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment
of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2301449121.
ieee: P. Koppensteiner et al., “GABAB receptors induce phasic release from
medial habenula terminals through activity-dependent recruitment of release-ready
vesicles,” Proceedings of the National Academy of Sciences, vol. 121, no.
8. Proceedings of the National Academy of Sciences, 2024.
ista: Koppensteiner P, Bhandari P, Önal C, Borges Merjane C, Le Monnier E, Roy U,
Nakamura Y, Sadakata T, Sanbo M, Hirabayashi M, Rhee J, Brose N, Jonas PM, Shigemoto
R. 2024. GABAB receptors induce phasic release from medial habenula terminals
through activity-dependent recruitment of release-ready vesicles. Proceedings
of the National Academy of Sciences. 121(8), e2301449121.
mla: Koppensteiner, Peter, et al. “GABAB Receptors Induce Phasic Release from Medial
Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.”
Proceedings of the National Academy of Sciences, vol. 121, no. 8, e2301449121,
Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2301449121.
short: P. Koppensteiner, P. Bhandari, C. Önal, C. Borges Merjane, E. Le Monnier,
U. Roy, Y. Nakamura, T. Sadakata, M. Sanbo, M. Hirabayashi, J. Rhee, N. Brose,
P.M. Jonas, R. Shigemoto, Proceedings of the National Academy of Sciences 121
(2024).
date_created: 2024-03-05T09:23:55Z
date_published: 2024-02-20T00:00:00Z
date_updated: 2024-03-12T13:44:18Z
day: '20'
ddc:
- '570'
department:
- _id: RySh
- _id: PeJo
doi: 10.1073/pnas.2301449121
ec_funded: 1
external_id:
pmid:
- '38346189'
file:
- access_level: open_access
checksum: b25b2a057c266ff317a48b0d54d6fc8a
content_type: application/pdf
creator: dernst
date_created: 2024-03-12T13:42:42Z
date_updated: 2024-03-12T13:42:42Z
file_id: '15110'
file_name: 2024_PNAS_Koppensteiner.pdf
file_size: 13648221
relation: main_file
success: 1
file_date_updated: 2024-03-12T13:42:42Z
has_accepted_license: '1'
intvolume: ' 121'
issue: '8'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
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'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/neuronal-insights-flash-and-freeze-fracture/
record:
- id: '13173'
relation: research_data
status: public
status: public
title: GABAB receptors induce phasic release from medial habenula terminals through
activity-dependent recruitment of release-ready vesicles
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: 121
year: '2024'
...
---
_id: '15083'
abstract:
- lang: eng
text: 'Direct reciprocity is a powerful mechanism for cooperation in social
dilemmas. The very logic of reciprocity, however, seems to require that individuals
are symmetric, and that everyone has the same means to influence each others’
payoffs. Yet in many applications, individuals are asymmetric. Herein, we study
the effect of asymmetry in linear public good games. Individuals may differ in
their endowments (their ability to contribute to a public good) and in their productivities
(how effective their contributions are). Given the individuals’ productivities,
we ask which allocation of endowments is optimal for cooperation. To this end,
we consider two notions of optimality. The first notion focuses on the resilience
of cooperation. The respective endowment distribution ensures that full cooperation
is feasible even under the most adverse conditions. The second notion focuses
on efficiency. The corresponding endowment distribution maximizes group welfare.
Using analytical methods, we fully characterize these two endowment distributions.
This analysis reveals that both optimality notions favor some endowment inequality:
More productive players ought to get higher endowments. Yet the two notions disagree
on how unequal endowments are supposed to be. A focus on resilience results in
less inequality. With additional simulations, we show that the optimal endowment
allocation needs to account for both the resilience and the efficiency of cooperation.'
acknowledgement: 'This work was supported by the European Research Council CoG 863818
(ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529:
E-DIRECT (to C.H.), the European Union’s Horizon 2020 research and innovation program
under the Marie Skłodowska-Curie Grant Agreement #754411 and the French Agence Nationale
de la Recherche (under the Investissement d’Avenir Programme, ANR-17-EURE-0010)
(to M.K.).'
article_number: e2315558121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Valentin
full_name: Hübner, Valentin
id: 2c8aa207-dc7d-11ea-9b2f-f22972ecd910
last_name: Hübner
- first_name: Manuel
full_name: Staab, Manuel
last_name: Staab
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Maria
full_name: Kleshnina, Maria
last_name: Kleshnina
citation:
ama: Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. Efficiency and resilience
of cooperation in asymmetric social dilemmas. Proceedings of the National Academy
of Sciences. 2024;121(10). doi:10.1073/pnas.2315558121
apa: Hübner, V., Staab, M., Hilbe, C., Chatterjee, K., & Kleshnina, M. (2024).
Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings
of the National Academy of Sciences. Proceedings of the National Academy of
Sciences. https://doi.org/10.1073/pnas.2315558121
chicago: Hübner, Valentin, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee,
and Maria Kleshnina. “Efficiency and Resilience of Cooperation in Asymmetric Social
Dilemmas.” Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2315558121.
ieee: V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, and M. Kleshnina, “Efficiency
and resilience of cooperation in asymmetric social dilemmas,” Proceedings of
the National Academy of Sciences, vol. 121, no. 10. Proceedings of the National
Academy of Sciences, 2024.
ista: Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. 2024. Efficiency and
resilience of cooperation in asymmetric social dilemmas. Proceedings of the National
Academy of Sciences. 121(10), e2315558121.
mla: Hübner, Valentin, et al. “Efficiency and Resilience of Cooperation in Asymmetric
Social Dilemmas.” Proceedings of the National Academy of Sciences, vol.
121, no. 10, e2315558121, Proceedings of the National Academy of Sciences, 2024,
doi:10.1073/pnas.2315558121.
short: V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, M. Kleshnina, Proceedings of
the National Academy of Sciences 121 (2024).
date_created: 2024-03-05T09:18:49Z
date_published: 2024-03-05T00:00:00Z
date_updated: 2024-03-12T13:29:25Z
day: '05'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1073/pnas.2315558121
ec_funded: 1
external_id:
pmid:
- '38408249'
file:
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checksum: 068520e3efd4d008bb9177e8aedb7d22
content_type: application/pdf
creator: dernst
date_created: 2024-03-12T13:12:22Z
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file_name: 2024_PNAS_Huebner.pdf
file_size: 2203220
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file_date_updated: 2024-03-12T13:12:22Z
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month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
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'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/what-math-tells-us-about-social-dilemmas/
record:
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relation: research_data
status: public
status: public
title: Efficiency and resilience of cooperation in asymmetric social dilemmas
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: 121
year: '2024'
...
---
_id: '14478'
abstract:
- lang: eng
text: Entire chromosomes are typically only transmitted vertically from one generation
to the next. The horizontal transfer of such chromosomes has long been considered
improbable, yet gained recent support in several pathogenic fungi where it may
affect the fitness or host specificity. To date, it is unknown how these transfers
occur, how common they are and whether they can occur between different species.
In this study, we show multiple independent instances of horizontal transfers
of the same accessory chromosome between two distinct strains of the asexual entomopathogenic
fungusMetarhizium robertsiiduring experimental co-infection
of its insect host, the Argentine ant. Notably, only the one chromosome – but
no other – was transferred from the donor to the recipient strain. The recipient
strain, now harboring the accessory chromosome, exhibited a competitive advantage
under certain host conditions. By phylogenetic analysis we further demonstrate
that the same accessory chromosome was horizontally transferred in a natural environment
betweenM. robertsiiand another congeneric insect pathogen,M.
guizhouense. Hence horizontal chromosome transfer is not limited
to the observed frequent events within species during experimental infections
but also occurs naturally across species. The transferred accessory chromosome
contains genes that might be involved in its preferential horizontal transfer,
encoding putative histones and histone-modifying enzymes, but also putative virulence
factors that may support its establishment. Our study reveals that both intra-
and interspecies horizontal transfer of entire chromosomes is more frequent than
previously assumed, likely representing a not uncommon mechanism for gene exchange.Significance
StatementThe enormous success of bacterial pathogens has
been attributed to their ability to exchange genetic material between one another.
Similarly, in eukaryotes, horizontal transfer of genetic material allowed the
spread of virulence factors across species. The horizontal transfer of whole chromosomes
could be an important pathway for such exchange of genetic material, but little
is known about the origin of transferable chromosomes and how frequently they
are exchanged. Here, we show that the transfer of accessory chromosomes - chromosomes
that are non-essential but may provide fitness benefits - is common during fungal
co-infections and is even possible between distant pathogenic species, highlighting
the importance of horizontal gene transfer via chromosome transfer also for the
evolution and function of eukaryotic pathogens.
acknowledgement: We thank Bernhardt Steinwender, Jorgen Eilenberg, and Nicolai V.
Meyling for the fungal strains. We further thank Chengshu Wang for providing the
short sequencing reads for M. guizhouense ARESF977 he used for his published genome
assembly, and Kristian Ullrich for help in the bioinformatics analysis for methylation
pattern in Nanopore reads, and the VBC and the Max Planck Society for the use of
their sequencing centers. We thank Barbara Milutinović and Hinrich Schulenburg for
discussion, and Tal Dagan and Jens Rolff for comments on a previous version of the
manuscript. Fig. 1A was created with BioRender.com. This study received funding
by the European Research Council under the European Union’s Horizon 2020 Research
and Innovation Programme (No. 771402; EPIDEMICSonCHIP) to S.C. and by the German
Research Foundation (DFG grant HA9263/1-1) to M.H.
article_number: e2316284121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Michael
full_name: Habig, Michael
last_name: Habig
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Judith
full_name: Müller, Judith
last_name: Müller
- first_name: Eva H.
full_name: Stukenbrock, Eva H.
last_name: Stukenbrock
- first_name: Hanna
full_name: Leitner, Hanna
id: 8fc5c6f6-5903-11ec-abad-c83f046253e7
last_name: Leitner
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Habig M, Grasse AV, Müller J, Stukenbrock EH, Leitner H, Cremer S. Frequent
horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings
of the National Academy of Sciences of the United States of America. 2024;121(11).
doi:10.1073/pnas.2316284121
apa: Habig, M., Grasse, A. V., Müller, J., Stukenbrock, E. H., Leitner, H., &
Cremer, S. (2024). Frequent horizontal chromosome transfer between asexual fungal
insect pathogens. Proceedings of the National Academy of Sciences of the United
States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2316284121
chicago: Habig, Michael, Anna V Grasse, Judith Müller, Eva H. Stukenbrock, Hanna
Leitner, and Sylvia Cremer. “Frequent Horizontal Chromosome Transfer between Asexual
Fungal Insect Pathogens.” Proceedings of the National Academy of Sciences of
the United States of America. Proceedings of the National Academy of Sciences,
2024. https://doi.org/10.1073/pnas.2316284121.
ieee: M. Habig, A. V. Grasse, J. Müller, E. H. Stukenbrock, H. Leitner, and S. Cremer,
“Frequent horizontal chromosome transfer between asexual fungal insect pathogens,”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 121, no. 11. Proceedings of the National Academy of Sciences, 2024.
ista: Habig M, Grasse AV, Müller J, Stukenbrock EH, Leitner H, Cremer S. 2024. Frequent
horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings
of the National Academy of Sciences of the United States of America. 121(11),
e2316284121.
mla: Habig, Michael, et al. “Frequent Horizontal Chromosome Transfer between Asexual
Fungal Insect Pathogens.” Proceedings of the National Academy of Sciences of
the United States of America, vol. 121, no. 11, e2316284121, Proceedings of
the National Academy of Sciences, 2024, doi:10.1073/pnas.2316284121.
short: M. Habig, A.V. Grasse, J. Müller, E.H. Stukenbrock, H. Leitner, S. Cremer,
Proceedings of the National Academy of Sciences of the United States of America
121 (2024).
date_created: 2023-10-31T13:30:00Z
date_published: 2024-03-12T00:00:00Z
date_updated: 2024-03-19T09:07:20Z
day: '12'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.1073/pnas.2316284121
ec_funded: 1
external_id:
pmid:
- '38442176'
file:
- access_level: open_access
checksum: f5e871db617b682edc71fcd08670dc81
content_type: application/pdf
creator: dernst
date_created: 2024-03-19T09:02:57Z
date_updated: 2024-03-19T09:02:57Z
file_id: '15124'
file_name: 2024_PNAS_Habig.pdf
file_size: 5750361
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success: 1
file_date_updated: 2024-03-19T09:02:57Z
has_accepted_license: '1'
intvolume: ' 121'
issue: '11'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2649B4DE-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771402'
name: Epidemics in ant societies on a chip
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: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Frequent horizontal chromosome transfer between asexual fungal insect pathogens
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: 121
year: '2024'
...
---
_id: '15116'
abstract:
- lang: eng
text: Water is known to play an important role in collagen self-assembly, but it
is still largely unclear how water–collagen interactions influence the assembly
process and determine the fibril network properties. Here, we use the H2O/D2O
isotope effect on the hydrogen-bond strength in water to investigate the role
of hydration in collagen self-assembly. We dissolve collagen in H2O and D2O and
compare the growth kinetics and the structure of the collagen assemblies formed
in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster
in D2O than in H2O, and collagen in D2O self-assembles into much thinner fibrils,
that form a more inhomogeneous and softer network, with a fourfold reduction in
elastic modulus when compared to H2O. Combining spectroscopic measurements with
atomistic simulations, we show that collagen in D2O is less hydrated than in H2O.
This partial dehydration lowers the enthalpic penalty for water removal and reorganization
at the collagen–water interface, increasing the self-assembly rate and the number
of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained
simulations show that the acceleration in the initial nucleation rate can be reproduced
by the enhancement of electrostatic interactions. These results show that water
acts as a mediator between collagen monomers, by modulating their interactions
so as to optimize the assembly process and, thus, the final network properties.
We believe that isotopically modulating the hydration of proteins can be a valuable
method to investigate the role of water in protein structural dynamics and protein
self-assembly.
acknowledgement: We thank Dr. Steven Roeters (Aarhus University), Dr. Federica Burla,
and Prof. Dr. Mischa Bonn (Institute for Polymer Research, Mainz, Germany) for the
useful discussions. We thank Dr. Wim Roeterdink and Michiel Hilberts for technical
support. G.H.K. acknowledges financial support by the “BaSyC Building a Synthetic
Cell” Gravitation grant (024.003.019) of The Netherlands Ministry of Education,
Culture and Science (OCW) and The Netherlands Organization for Scientific Research
and from NWO grant OCENW.GROOT.2019.022. This work has received support from the
National Research Foundation of Korea (NRF), funded by the Ministry of Science and
ICT, under Grant No. 2022K1A3A1A04062969. This publication is part of the project
(with Project Number VI.Veni.212.240) of the research programme NWO Talent Programme
Veni 2021, which is financed by the Dutch Research Council (NWO). I.M.I. acknowledges
support from the Sectorplan Bèta & Techniek of the Dutch Government and the Dementia
Research - Synapsis Foundation Switzerland. A.Š. and K.K. acknowledge support from
Royal Society and European Research Council Starting Grant. G. Giubertoni kindly
thanks to the Care4Bones community and the Collagen Café community for reminding
that we do not own the knowledge we create, but it is, rather, a collective resource
intended for the advancement of human progress.
article_number: e2313162121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Giulia
full_name: Giubertoni, Giulia
last_name: Giubertoni
- first_name: Liru
full_name: Feng, Liru
last_name: Feng
- first_name: Kevin
full_name: Klein, Kevin
last_name: Klein
- first_name: Guido
full_name: Giannetti, Guido
last_name: Giannetti
- first_name: Luco
full_name: Rutten, Luco
last_name: Rutten
- first_name: Yeji
full_name: Choi, Yeji
last_name: Choi
- first_name: Anouk
full_name: Van Der Net, Anouk
last_name: Van Der Net
- first_name: Gerard
full_name: Castro-Linares, Gerard
last_name: Castro-Linares
- first_name: Federico
full_name: Caporaletti, Federico
last_name: Caporaletti
- first_name: Dimitra
full_name: Micha, Dimitra
last_name: Micha
- first_name: Johannes
full_name: Hunger, Johannes
last_name: Hunger
- first_name: Antoine
full_name: Deblais, Antoine
last_name: Deblais
- first_name: Daniel
full_name: Bonn, Daniel
last_name: Bonn
- first_name: Nico
full_name: Sommerdijk, Nico
last_name: Sommerdijk
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Ioana M.
full_name: Ilie, Ioana M.
last_name: Ilie
- first_name: Gijsje H.
full_name: Koenderink, Gijsje H.
last_name: Koenderink
- first_name: Sander
full_name: Woutersen, Sander
last_name: Woutersen
citation:
ama: Giubertoni G, Feng L, Klein K, et al. Elucidating the role of water in collagen
self-assembly by isotopically modulating collagen hydration. Proceedings of
the National Academy of Sciences of the United States of America. 2024;121(11).
doi:10.1073/pnas.2313162121
apa: Giubertoni, G., Feng, L., Klein, K., Giannetti, G., Rutten, L., Choi, Y., …
Woutersen, S. (2024). Elucidating the role of water in collagen self-assembly
by isotopically modulating collagen hydration. Proceedings of the National
Academy of Sciences of the United States of America. Proceedings of the National
Academy of Sciences. https://doi.org/10.1073/pnas.2313162121
chicago: Giubertoni, Giulia, Liru Feng, Kevin Klein, Guido Giannetti, Luco Rutten,
Yeji Choi, Anouk Van Der Net, et al. “Elucidating the Role of Water in Collagen
Self-Assembly by Isotopically Modulating Collagen Hydration.” Proceedings of
the National Academy of Sciences of the United States of America. Proceedings
of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2313162121.
ieee: G. Giubertoni et al., “Elucidating the role of water in collagen self-assembly
by isotopically modulating collagen hydration,” Proceedings of the National
Academy of Sciences of the United States of America, vol. 121, no. 11. Proceedings
of the National Academy of Sciences, 2024.
ista: Giubertoni G, Feng L, Klein K, Giannetti G, Rutten L, Choi Y, Van Der Net
A, Castro-Linares G, Caporaletti F, Micha D, Hunger J, Deblais A, Bonn D, Sommerdijk
N, Šarić A, Ilie IM, Koenderink GH, Woutersen S. 2024. Elucidating the role of
water in collagen self-assembly by isotopically modulating collagen hydration.
Proceedings of the National Academy of Sciences of the United States of America.
121(11), e2313162121.
mla: Giubertoni, Giulia, et al. “Elucidating the Role of Water in Collagen Self-Assembly
by Isotopically Modulating Collagen Hydration.” Proceedings of the National
Academy of Sciences of the United States of America, vol. 121, no. 11, e2313162121,
Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2313162121.
short: G. Giubertoni, L. Feng, K. Klein, G. Giannetti, L. Rutten, Y. Choi, A. Van
Der Net, G. Castro-Linares, F. Caporaletti, D. Micha, J. Hunger, A. Deblais, D.
Bonn, N. Sommerdijk, A. Šarić, I.M. Ilie, G.H. Koenderink, S. Woutersen, Proceedings
of the National Academy of Sciences of the United States of America 121 (2024).
date_created: 2024-03-17T23:00:57Z
date_published: 2024-03-12T00:00:00Z
date_updated: 2024-03-19T11:41:32Z
day: '12'
ddc:
- '550'
department:
- _id: AnSa
doi: 10.1073/pnas.2313162121
external_id:
pmid:
- '38451946'
file:
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checksum: a3f7fdc29dd9f0a38952ab4e322b3a05
content_type: application/pdf
creator: dernst
date_created: 2024-03-19T10:22:42Z
date_updated: 2024-03-19T10:22:42Z
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intvolume: ' 121'
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language:
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license: https://creativecommons.org/licenses/by/4.0/
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
related_material:
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relation: research_data
status: public
scopus_import: '1'
status: public
title: Elucidating the role of water in collagen self-assembly by isotopically modulating
collagen hydration
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 121
year: '2024'
...
---
_id: '13315'
abstract:
- lang: eng
text: How do statistical dependencies in measurement noise influence high-dimensional
inference? To answer this, we study the paradigmatic spiked matrix model of principal
components analysis (PCA), where a rank-one matrix is corrupted by additive noise.
We go beyond the usual independence assumption on the noise entries, by drawing
the noise from a low-order polynomial orthogonal matrix ensemble. The resulting
noise correlations make the setting relevant for applications but analytically
challenging. We provide characterization of the Bayes optimal limits of inference
in this model. If the spike is rotation invariant, we show that standard spectral
PCA is optimal. However, for more general priors, both PCA and the existing approximate
message-passing algorithm (AMP) fall short of achieving the information-theoretic
limits, which we compute using the replica method from statistical physics. We
thus propose an AMP, inspired by the theory of adaptive Thouless–Anderson–Palmer
equations, which is empirically observed to saturate the conjectured theoretical
limit. This AMP comes with a rigorous state evolution analysis tracking its performance.
Although we focus on specific noise distributions, our methodology can be generalized
to a wide class of trace matrix ensembles at the cost of more involved expressions.
Finally, despite the seemingly strong assumption of rotation-invariant noise,
our theory empirically predicts algorithmic performance on real data, pointing
at strong universality properties.
acknowledgement: J.B. was funded by the European Union (ERC, CHORAL, project number
101039794). Views and opinions expressed are however those of the author(s) only
and do not necessarily reflect those of the European Union or the European Research
Council. Neither the European Union nor the granting authority can be held responsible
for them. M.M. was supported by the 2019 Lopez-Loreta Prize. We would like to thank
the reviewers for the insightful comments and, in particular, for suggesting the
BAMP-inspired denoisers leading to AMP-AP.
article_number: e2302028120
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jean
full_name: Barbier, Jean
last_name: Barbier
- first_name: Francesco
full_name: Camilli, Francesco
last_name: Camilli
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Manuel
full_name: Sáenz, Manuel
last_name: Sáenz
citation:
ama: Barbier J, Camilli F, Mondelli M, Sáenz M. Fundamental limits in structured
principal component analysis and how to reach them. Proceedings of the National
Academy of Sciences of the United States of America. 2023;120(30). doi:10.1073/pnas.2302028120
apa: Barbier, J., Camilli, F., Mondelli, M., & Sáenz, M. (2023). Fundamental
limits in structured principal component analysis and how to reach them. Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences. https://doi.org/10.1073/pnas.2302028120
chicago: Barbier, Jean, Francesco Camilli, Marco Mondelli, and Manuel Sáenz. “Fundamental
Limits in Structured Principal Component Analysis and How to Reach Them.” Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2302028120.
ieee: J. Barbier, F. Camilli, M. Mondelli, and M. Sáenz, “Fundamental limits in
structured principal component analysis and how to reach them,” Proceedings
of the National Academy of Sciences of the United States of America, vol.
120, no. 30. National Academy of Sciences, 2023.
ista: Barbier J, Camilli F, Mondelli M, Sáenz M. 2023. Fundamental limits in structured
principal component analysis and how to reach them. Proceedings of the National
Academy of Sciences of the United States of America. 120(30), e2302028120.
mla: Barbier, Jean, et al. “Fundamental Limits in Structured Principal Component
Analysis and How to Reach Them.” Proceedings of the National Academy of Sciences
of the United States of America, vol. 120, no. 30, e2302028120, National Academy
of Sciences, 2023, doi:10.1073/pnas.2302028120.
short: J. Barbier, F. Camilli, M. Mondelli, M. Sáenz, Proceedings of the National
Academy of Sciences of the United States of America 120 (2023).
date_created: 2023-07-30T22:01:02Z
date_published: 2023-07-25T00:00:00Z
date_updated: 2023-10-17T11:44:55Z
day: '25'
ddc:
- '000'
department:
- _id: MaMo
doi: 10.1073/pnas.2302028120
external_id:
pmid:
- '37463204'
file:
- access_level: open_access
checksum: 1fc06228afdb3aa80cf8e7766bcf9dc5
content_type: application/pdf
creator: dernst
date_created: 2023-07-31T07:30:48Z
date_updated: 2023-07-31T07:30:48Z
file_id: '13323'
file_name: 2023_PNAS_Barbier.pdf
file_size: 995933
relation: main_file
success: 1
file_date_updated: 2023-07-31T07:30:48Z
has_accepted_license: '1'
intvolume: ' 120'
issue: '30'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/fcamilli95/Structured-PCA-
scopus_import: '1'
status: public
title: Fundamental limits in structured principal component analysis and how to reach
them
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: 120
year: '2023'
...
---
_id: '14037'
abstract:
- lang: eng
text: 'Traditionally, nuclear spin is not considered to affect biological processes.
Recently, this has changed as isotopic fractionation that deviates from classical
mass dependence was reported both in vitro and in vivo. In these cases, the isotopic
effect correlates with the nuclear magnetic spin. Here, we show nuclear spin effects
using stable oxygen isotopes (16O, 17O, and 18O) in two separate setups: an artificial
dioxygen production system and biological aquaporin channels in cells. We observe
that oxygen dynamics in chiral environments (in particular its transport) depend
on nuclear spin, suggesting future applications for controlled isotope separation
to be used, for instance, in NMR. To demonstrate the mechanism behind our findings,
we formulate theoretical models based on a nuclear-spin-enhanced switch between
electronic spin states. Accounting for the role of nuclear spin in biology can
provide insights into the role of quantum effects in living systems and help inspire
the development of future biotechnology solutions.'
acknowledgement: N.M.-S. acknowledges the support of the Ministry of Energy, Israel,
as part of the scholarship program for graduate students in the fields of energy.
M.L. acknowledges support by the European Research Council (ERC) Starting Grant
No. 801770 (ANGULON). Y.P. acknowledges the support of the Ministry of Innovation,
Science and Technology, Israel Grant No. 1001593872. Y.P acknowledges the support
of the BSF-NSF 094 Grant No. 2022503.
article_number: e2300828120
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Ofek
full_name: Vardi, Ofek
last_name: Vardi
- first_name: Naama
full_name: Maroudas-Sklare, Naama
last_name: Maroudas-Sklare
- first_name: Yuval
full_name: Kolodny, Yuval
last_name: Kolodny
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: Amijai
full_name: Saragovi, Amijai
last_name: Saragovi
- first_name: Nir
full_name: Galili, Nir
last_name: Galili
- first_name: Stav
full_name: Ferrera, Stav
last_name: Ferrera
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Nir
full_name: Yuran, Nir
last_name: Yuran
- first_name: Hagit P.
full_name: Affek, Hagit P.
last_name: Affek
- first_name: Boaz
full_name: Luz, Boaz
last_name: Luz
- first_name: Yonaton
full_name: Goldsmith, Yonaton
last_name: Goldsmith
- first_name: Nir
full_name: Keren, Nir
last_name: Keren
- first_name: Shira
full_name: Yochelis, Shira
last_name: Yochelis
- first_name: Itay
full_name: Halevy, Itay
last_name: Halevy
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Yossi
full_name: Paltiel, Yossi
last_name: Paltiel
citation:
ama: Vardi O, Maroudas-Sklare N, Kolodny Y, et al. Nuclear spin effects in biological
processes. Proceedings of the National Academy of Sciences of the United States
of America. 2023;120(32). doi:10.1073/pnas.2300828120
apa: Vardi, O., Maroudas-Sklare, N., Kolodny, Y., Volosniev, A., Saragovi, A., Galili,
N., … Paltiel, Y. (2023). Nuclear spin effects in biological processes. Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences. https://doi.org/10.1073/pnas.2300828120
chicago: Vardi, Ofek, Naama Maroudas-Sklare, Yuval Kolodny, Artem Volosniev, Amijai
Saragovi, Nir Galili, Stav Ferrera, et al. “Nuclear Spin Effects in Biological
Processes.” Proceedings of the National Academy of Sciences of the United States
of America. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2300828120.
ieee: O. Vardi et al., “Nuclear spin effects in biological processes,” Proceedings
of the National Academy of Sciences of the United States of America, vol.
120, no. 32. National Academy of Sciences, 2023.
ista: Vardi O, Maroudas-Sklare N, Kolodny Y, Volosniev A, Saragovi A, Galili N,
Ferrera S, Ghazaryan A, Yuran N, Affek HP, Luz B, Goldsmith Y, Keren N, Yochelis
S, Halevy I, Lemeshko M, Paltiel Y. 2023. Nuclear spin effects in biological processes.
Proceedings of the National Academy of Sciences of the United States of America.
120(32), e2300828120.
mla: Vardi, Ofek, et al. “Nuclear Spin Effects in Biological Processes.” Proceedings
of the National Academy of Sciences of the United States of America, vol.
120, no. 32, e2300828120, National Academy of Sciences, 2023, doi:10.1073/pnas.2300828120.
short: O. Vardi, N. Maroudas-Sklare, Y. Kolodny, A. Volosniev, A. Saragovi, N. Galili,
S. Ferrera, A. Ghazaryan, N. Yuran, H.P. Affek, B. Luz, Y. Goldsmith, N. Keren,
S. Yochelis, I. Halevy, M. Lemeshko, Y. Paltiel, Proceedings of the National Academy
of Sciences of the United States of America 120 (2023).
date_created: 2023-08-13T22:01:12Z
date_published: 2023-07-31T00:00:00Z
date_updated: 2023-10-17T11:45:25Z
day: '31'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1073/pnas.2300828120
ec_funded: 1
external_id:
pmid:
- '37523549'
file:
- access_level: open_access
checksum: a5ed64788a5acef9b9a300a26fa5a177
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T07:43:45Z
date_updated: 2023-08-14T07:43:45Z
file_id: '14047'
file_name: 2023_PNAS_Vardi.pdf
file_size: 1003092
relation: main_file
success: 1
file_date_updated: 2023-08-14T07:43:45Z
has_accepted_license: '1'
intvolume: ' 120'
issue: '32'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
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: Nuclear spin effects in biological processes
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: 120
year: '2023'
...
---
_id: '14666'
abstract:
- lang: eng
text: So-called spontaneous activity is a central hallmark of most nervous systems.
Such non-causal firing is contrary to the tenet of spikes as a means of communication,
and its purpose remains unclear. We propose that self-initiated firing can serve
as a release valve to protect neurons from the toxic conditions arising in mitochondria
from lower-than-baseline energy consumption. To demonstrate the viability of our
hypothesis, we built a set of models that incorporate recent experimental results
indicating homeostatic control of metabolic products—Adenosine triphosphate (ATP),
adenosine diphosphate (ADP), and reactive oxygen species (ROS)—by changes in firing.
We explore the relationship of metabolic cost of spiking with its effect on the
temporal patterning of spikes and reproduce experimentally observed changes in
intrinsic firing in the fruitfly dorsal fan-shaped body neuron in a model with
ROS-modulated potassium channels. We also show that metabolic spiking homeostasis
can produce indefinitely sustained avalanche dynamics in cortical circuits. Our
theory can account for key features of neuronal activity observed in many studies
ranging from ion channel function all the way to resting state dynamics. We finish
with a set of experimental predictions that would confirm an integrated, crucial
role for metabolically regulated spiking and firmly link metabolic homeostasis
and neuronal function.
acknowledgement: We thank Prof. C. Nazaret and Prof. J.-P. Mazat for sharing the code
of their mitochondrial model. We also thank G. Miesenböck, E. Marder, L. Abbott,
A. Kempf, P. Hasenhuetl, W. Podlaski, F. Zenke, E. Agnes, P. Bozelos, J. Watson,
B. Confavreux, and G. Christodoulou, and the rest of the Vogels Lab for their feedback.
This work was funded by Wellcome Trust and Royal Society Sir Henry Dale Research
Fellowship (WT100000), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z),
and a UK Research and Innovation, Biotechnology and Biological Sciences Research
Council grant (UKRI-BBSRC BB/N019512/1).
article_number: e2306525120
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Chaitanya
full_name: Chintaluri, Chaitanya
id: E4EDB536-3485-11EA-98D2-20AF3DDC885E
last_name: Chintaluri
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: Chintaluri C, Vogels TP. Metabolically regulated spiking could serve neuronal
energy homeostasis and protect from reactive oxygen species. Proceedings of
the National Academy of Sciences of the United States of America. 2023;120(48).
doi:10.1073/pnas.2306525120
apa: Chintaluri, C., & Vogels, T. P. (2023). Metabolically regulated spiking
could serve neuronal energy homeostasis and protect from reactive oxygen species.
Proceedings of the National Academy of Sciences of the United States of America.
National Academy of Sciences. https://doi.org/10.1073/pnas.2306525120
chicago: Chintaluri, Chaitanya, and Tim P Vogels. “Metabolically Regulated Spiking
Could Serve Neuronal Energy Homeostasis and Protect from Reactive Oxygen Species.”
Proceedings of the National Academy of Sciences of the United States of America.
National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2306525120.
ieee: C. Chintaluri and T. P. Vogels, “Metabolically regulated spiking could serve
neuronal energy homeostasis and protect from reactive oxygen species,” Proceedings
of the National Academy of Sciences of the United States of America, vol.
120, no. 48. National Academy of Sciences, 2023.
ista: Chintaluri C, Vogels TP. 2023. Metabolically regulated spiking could serve
neuronal energy homeostasis and protect from reactive oxygen species. Proceedings
of the National Academy of Sciences of the United States of America. 120(48),
e2306525120.
mla: Chintaluri, Chaitanya, and Tim P. Vogels. “Metabolically Regulated Spiking
Could Serve Neuronal Energy Homeostasis and Protect from Reactive Oxygen Species.”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 120, no. 48, e2306525120, National Academy of Sciences, 2023, doi:10.1073/pnas.2306525120.
short: C. Chintaluri, T.P. Vogels, Proceedings of the National Academy of Sciences
of the United States of America 120 (2023).
date_created: 2023-12-10T23:01:00Z
date_published: 2023-11-21T00:00:00Z
date_updated: 2023-12-11T12:47:41Z
day: '21'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.1073/pnas.2306525120
external_id:
pmid:
- '37988463'
file:
- access_level: open_access
checksum: bf4ec38602a70dae4338077a5a4d497f
content_type: application/pdf
creator: dernst
date_created: 2023-12-11T12:45:12Z
date_updated: 2023-12-11T12:45:12Z
file_id: '14678'
file_name: 2023_PNAS_Chintaluri.pdf
file_size: 16891602
relation: main_file
success: 1
file_date_updated: 2023-12-11T12:45:12Z
has_accepted_license: '1'
intvolume: ' 120'
issue: '48'
language:
- iso: eng
month: '11'
oa: 1
oa_version: None
pmid: 1
project:
- _id: c084a126-5a5b-11eb-8a69-d75314a70a87
grant_number: 214316/Z/18/Z
name: What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent
neuronal networks.
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: software
url: https://github.com/ccluri/metabolic_spiking
scopus_import: '1'
status: public
title: Metabolically regulated spiking could serve neuronal energy homeostasis and
protect from reactive oxygen species
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: 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: '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. Proceedings of the 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. Proceedings of the 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. Proceedings
of the 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,
Proceedings of the 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).
date_created: 2022-07-31T22:01:47Z
date_published: 2022-07-18T00:00:00Z
date_updated: 2022-08-01T11:00:25Z
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: Proceedings of the 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: '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: '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. Proceedings of the 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. Proceedings
of the 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. Proceedings of the 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, Proceedings of the 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: 2023-08-03T06:06:27Z
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: Proceedings of the 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
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. Proceedings of the 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. Proceedings of the 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. Proceedings
of the 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,
Proceedings of the 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).
date_created: 2022-08-07T22:01:57Z
date_published: 2022-07-25T00:00:00Z
date_updated: 2023-08-03T12:39:29Z
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: Proceedings of the 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
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. Proceedings of the 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. Proceedings of the 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. Proceedings of the 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, Proceedings
of the 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).
date_created: 2022-08-07T22:01:56Z
date_published: 2022-07-29T00:00:00Z
date_updated: 2023-08-03T12:40:38Z
day: '29'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.1073/pnas.2121279119
external_id:
isi:
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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
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file_date_updated: 2022-08-08T07:31:19Z
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intvolume: ' 119'
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issue: '31'
language:
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month: '07'
oa: 1
oa_version: Published Version
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
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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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
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. 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.
Proceedings of the 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.
Proceedings of the 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,
vol. 119, no. 31. Proceedings of the 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. 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,
vol. 119, no. 31, e2121058119, Proceedings of the 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 119 (2022).
date_created: 2022-08-04T20:06:49Z
date_published: 2022-07-25T00:00:00Z
date_updated: 2023-08-03T12:43:53Z
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
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: 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
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. Proceedings of the 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. Proceedings
of the 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. Proceedings of the 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, Proceedings of the 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: 2023-10-04T09:06:52Z
day: '28'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1073/pnas.2109718119
ec_funded: 1
external_id:
isi:
- '000903753500002'
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
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: Proceedings of the 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. 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.
Proceedings of the 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. Proceedings of the 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, vol. 119,
no. 36. Proceedings of the 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. 119(36), e2123152119.
mla: Hledik, Michal, et al. “Accumulation and Maintenance of Information in Evolution.”
Proceedings of the National Academy of Sciences, vol. 119, no. 36, e2123152119,
Proceedings of the 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 119 (2022).
date_created: 2022-09-11T22:01:55Z
date_published: 2022-08-29T00:00:00Z
date_updated: 2024-03-06T14:22:51Z
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
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
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: '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. 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. 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.
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, 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. 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,
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 118 (2021).
date_created: 2021-03-21T23:01:20Z
date_published: 2021-03-09T00:00:00Z
date_updated: 2023-08-07T14:19:34Z
day: '09'
ddc:
- '530'
department:
- _id: CaGo
doi: 10.1073/pnas.2024083118
external_id:
isi:
- '000627429100097'
pmid:
- '33653960'
file:
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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
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
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. PNAS. 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. PNAS. 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.” PNAS. 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,” PNAS, 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. PNAS. 118(14).
mla: Schöpf, Clemens L., et al. “Presynaptic Α2δ Subunits Are Key Organizers of
Glutamatergic Synapses.” PNAS, 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,
PNAS 118 (2021).
date_created: 2021-04-18T22:01:40Z
date_published: 2021-04-06T00:00:00Z
date_updated: 2023-08-08T13:08:47Z
day: '06'
ddc:
- '570'
department:
- _id: EM-Fac
- _id: RySh
doi: 10.1073/pnas.1920827118
ec_funded: 1
external_id:
isi:
- '000637398300002'
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
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: PNAS
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
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. 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. 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. 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, 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. 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, 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 118 (2021).
date_created: 2021-08-10T19:30:41Z
date_published: 2021-07-16T00:00:00Z
date_updated: 2023-08-11T10:28:10Z
day: '16'
ddc:
- '580'
- '570'
department:
- _id: DaZi
doi: 10.1073/pnas.2104445118
external_id:
isi:
- '000685037700012'
pmid:
- '34272287'
file:
- access_level: open_access
checksum: 19e84ad8c03c60222744ee8e16cd6998
content_type: application/pdf
creator: asandaue
date_created: 2021-08-11T09:31:41Z
date_updated: 2021-08-11T09:31:41Z
file_id: '9879'
file_name: 2021_ProceedingsOfTheNationalAcademyOfSciences_Rodrigues.pdf
file_size: 1898360
relation: main_file
success: 1
file_date_updated: 2021-08-11T09:31:41Z
has_accepted_license: '1'
intvolume: ' 118'
isi: 1
issue: '29'
language:
- iso: eng
month: '07'
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: Divergence among rice cultivars reveals roles for transposition and epimutation
in ongoing evolution of genomic imprinting
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: 118
year: '2021'
...
---
_id: '10299'
abstract:
- lang: eng
text: Turbulence generally arises in shear flows if velocities and hence, inertial
forces are sufficiently large. In striking contrast, viscoelastic fluids can exhibit
disordered motion even at vanishing inertia. Intermediate between these cases,
a state of chaotic motion, “elastoinertial turbulence” (EIT), has been observed
in a narrow Reynolds number interval. We here determine the origin of EIT in experiments
and show that characteristic EIT structures can be detected across an unexpectedly
wide range of parameters. Close to onset, a pattern of chevron-shaped streaks
emerges in qualitative agreement with linear and weakly nonlinear theory. However,
in experiments, the dynamics remain weakly chaotic, and the instability can be
traced to far lower Reynolds numbers than permitted by theory. For increasing
inertia, the flow undergoes a transformation to a wall mode composed of inclined
near-wall streaks and shear layers. This mode persists to what is known as the
“maximum drag reduction limit,” and overall EIT is found to dominate viscoelastic
flows across more than three orders of magnitude in Reynolds number.
acknowledgement: We thank Y. Dubief, R. Kerswell, E. Marensi, V. Shankar, V. Steinberg,
and V. Terrapon for discussions and helpful comments. A.V. and B.H. acknowledge
funding from the Austrian Science Fund, grant I4188-N30, within the Deutsche Forschungsgemeinschaft
research unit FOR 2688.
article_number: e2102350118
article_processing_charge: No
article_type: original
author:
- first_name: George H
full_name: Choueiri, George H
id: 448BD5BC-F248-11E8-B48F-1D18A9856A87
last_name: Choueiri
- first_name: Jose M
full_name: Lopez Alonso, Jose M
id: 40770848-F248-11E8-B48F-1D18A9856A87
last_name: Lopez Alonso
orcid: 0000-0002-0384-2022
- first_name: Atul
full_name: Varshney, Atul
id: 2A2006B2-F248-11E8-B48F-1D18A9856A87
last_name: Varshney
orcid: 0000-0002-3072-5999
- first_name: Sarath
full_name: Sankar, Sarath
last_name: Sankar
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. Experimental observation
of the origin and structure of elastoinertial turbulence. Proceedings of the
National Academy of Sciences. 2021;118(45). doi:10.1073/pnas.2102350118
apa: Choueiri, G. H., Lopez Alonso, J. M., Varshney, A., Sankar, S., & Hof,
B. (2021). Experimental observation of the origin and structure of elastoinertial
turbulence. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.2102350118
chicago: Choueiri, George H, Jose M Lopez Alonso, Atul Varshney, Sarath Sankar,
and Björn Hof. “Experimental Observation of the Origin and Structure of Elastoinertial
Turbulence.” Proceedings of the National Academy of Sciences. National
Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2102350118.
ieee: G. H. Choueiri, J. M. Lopez Alonso, A. Varshney, S. Sankar, and B. Hof, “Experimental
observation of the origin and structure of elastoinertial turbulence,” Proceedings
of the National Academy of Sciences, vol. 118, no. 45. National Academy of
Sciences, 2021.
ista: Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. 2021. Experimental
observation of the origin and structure of elastoinertial turbulence. Proceedings
of the National Academy of Sciences. 118(45), e2102350118.
mla: Choueiri, George H., et al. “Experimental Observation of the Origin and Structure
of Elastoinertial Turbulence.” Proceedings of the National Academy of Sciences,
vol. 118, no. 45, e2102350118, National Academy of Sciences, 2021, doi:10.1073/pnas.2102350118.
short: G.H. Choueiri, J.M. Lopez Alonso, A. Varshney, S. Sankar, B. Hof, Proceedings
of the National Academy of Sciences 118 (2021).
date_created: 2021-11-17T13:24:24Z
date_published: 2021-11-03T00:00:00Z
date_updated: 2023-08-14T11:50:10Z
day: '03'
department:
- _id: BjHo
doi: 10.1073/pnas.2102350118
external_id:
arxiv:
- '2103.00023'
isi:
- '000720926900019'
pmid:
- ' 34732570'
intvolume: ' 118'
isi: 1
issue: '45'
keyword:
- multidisciplinary
- elastoinertial turbulence
- viscoelastic flows
- elastic instability
- drag reduction
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2103.00023
month: '11'
oa: 1
oa_version: Preprint
pmid: 1
project:
- _id: 238B8092-32DE-11EA-91FC-C7463DDC885E
call_identifier: FWF
grant_number: I04188
name: Instabilities in pulsating pipe flow of Newtonian and complex fluids
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: Experimental observation of the origin and structure of elastoinertial turbulence
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
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. 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. 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. 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, 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. 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, 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 118 (2021).
date_created: 2021-03-31T07:00:01Z
date_published: 2021-04-06T00:00:00Z
date_updated: 2023-09-05T13:27:18Z
day: '06'
department:
- _id: StFr
- _id: EM-Fac
doi: 10.1073/pnas.2021893118
external_id:
isi:
- '000637398300050'
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
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'
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 118
year: '2021'
...
---
_id: '9887'
abstract:
- lang: eng
text: Clathrin-mediated endocytosis is the major route of entry of cargos into cells
and thus underpins many physiological processes. During endocytosis, an area of
flat membrane is remodeled by proteins to create a spherical vesicle against intracellular
forces. The protein machinery which mediates this membrane bending in plants is
unknown. However, it is known that plant endocytosis is actin independent, thus
indicating that plants utilize a unique mechanism to mediate membrane bending
against high-turgor pressure compared to other model systems. Here, we investigate
the TPLATE complex, a plant-specific endocytosis protein complex. It has been
thought to function as a classical adaptor functioning underneath the clathrin
coat. However, by using biochemical and advanced live microscopy approaches, we
found that TPLATE is peripherally associated with clathrin-coated vesicles and
localizes at the rim of endocytosis events. As this localization is more fitting
to the protein machinery involved in membrane bending during endocytosis, we examined
cells in which the TPLATE complex was disrupted and found that the clathrin structures
present as flat patches. This suggests a requirement of the TPLATE complex for
membrane bending during plant clathrin–mediated endocytosis. Next, we used in
vitro biophysical assays to confirm that the TPLATE complex possesses protein
domains with intrinsic membrane remodeling activity. These results redefine the
role of the TPLATE complex and implicate it as a key component of the evolutionarily
distinct plant endocytosis mechanism, which mediates endocytic membrane bending
against the high-turgor pressure in plant cells.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: Bio
acknowledgement: 'We gratefully thank Julie Neveu and Dr. Amanda Barranco of the Grégory
Vert laboratory for help preparing plants in France, Dr. Zuzana Gelova for help
and advice with protoplast generation, Dr. Stéphane Vassilopoulos and Dr. Florian
Schur for advice regarding EM tomography, Alejandro Marquiegui Alvaro for help with
material generation, and Dr. Lukasz Kowalski for generously gifting us the mWasabi
protein. This research was supported by the Scientific Service Units of Institute
of Science and Technology Austria (IST Austria) through resources provided by the
Electron Microscopy Facility, Lab Support Facility (particularly Dorota Jaworska),
and the Bioimaging Facility. We acknowledge the Advanced Microscopy Facility of
the Vienna BioCenter Core Facilities for use of the 3D SIM. For the mass spectrometry
analysis of proteins, we acknowledge the University of Natural Resources and Life
Sciences (BOKU) Core Facility Mass Spectrometry. This work was supported by the
following funds: A.J. is supported by funding from the Austrian Science Fund I3630B25
to J.F. P.M. and E.B. are supported by Agence Nationale de la Recherche ANR-11-EQPX-0029
Morphoscope2 and ANR-10-INBS-04 France BioImaging. S.Y.B. is supported by the NSF
No. 1121998 and 1614915. J.W. and D.V.D. are supported by the European Research
Council Grant 682436 (to D.V.D.), a China Scholarship Council Grant 201508440249
(to J.W.), and by a Ghent University Special Research Co-funding Grant ST01511051
(to J.W.).'
article_number: e2113046118
article_processing_charge: No
article_type: original
author:
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Dana A
full_name: Dahhan, Dana A
last_name: Dahhan
- first_name: Nataliia
full_name: Gnyliukh, Nataliia
id: 390C1120-F248-11E8-B48F-1D18A9856A87
last_name: Gnyliukh
orcid: 0000-0002-2198-0509
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Vanessa
full_name: Zheden, Vanessa
id: 39C5A68A-F248-11E8-B48F-1D18A9856A87
last_name: Zheden
orcid: 0000-0002-9438-4783
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Pierre
full_name: Mahou, Pierre
last_name: Mahou
- first_name: Mónika
full_name: Hrtyan, Mónika
id: 45A71A74-F248-11E8-B48F-1D18A9856A87
last_name: Hrtyan
- first_name: Jie
full_name: Wang, Jie
last_name: Wang
- first_name: Juan L
full_name: Aguilera Servin, Juan L
id: 2A67C376-F248-11E8-B48F-1D18A9856A87
last_name: Aguilera Servin
orcid: 0000-0002-2862-8372
- first_name: Daniël
full_name: van Damme, Daniël
last_name: van Damme
- first_name: Emmanuel
full_name: Beaurepaire, Emmanuel
last_name: Beaurepaire
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Sebastian Y
full_name: Bednarek, Sebastian Y
last_name: Bednarek
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Johnson AJ, Dahhan DA, Gnyliukh N, et al. The TPLATE complex mediates membrane
bending during plant clathrin-mediated endocytosis. Proceedings of the National
Academy of Sciences. 2021;118(51). doi:10.1073/pnas.2113046118
apa: Johnson, A. J., Dahhan, D. A., Gnyliukh, N., Kaufmann, W., Zheden, V., Costanzo,
T., … Friml, J. (2021). The TPLATE complex mediates membrane bending during plant
clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences.
National Academy of Sciences. https://doi.org/10.1073/pnas.2113046118
chicago: Johnson, Alexander J, Dana A Dahhan, Nataliia Gnyliukh, Walter Kaufmann,
Vanessa Zheden, Tommaso Costanzo, Pierre Mahou, et al. “The TPLATE Complex Mediates
Membrane Bending during Plant Clathrin-Mediated Endocytosis.” Proceedings of
the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2113046118.
ieee: A. J. Johnson et al., “The TPLATE complex mediates membrane bending
during plant clathrin-mediated endocytosis,” Proceedings of the National Academy
of Sciences, vol. 118, no. 51. National Academy of Sciences, 2021.
ista: Johnson AJ, Dahhan DA, Gnyliukh N, Kaufmann W, Zheden V, Costanzo T, Mahou
P, Hrtyan M, Wang J, Aguilera Servin JL, van Damme D, Beaurepaire E, Loose M,
Bednarek SY, Friml J. 2021. The TPLATE complex mediates membrane bending during
plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences.
118(51), e2113046118.
mla: Johnson, Alexander J., et al. “The TPLATE Complex Mediates Membrane Bending
during Plant Clathrin-Mediated Endocytosis.” Proceedings of the National Academy
of Sciences, vol. 118, no. 51, e2113046118, National Academy of Sciences,
2021, doi:10.1073/pnas.2113046118.
short: A.J. Johnson, D.A. Dahhan, N. Gnyliukh, W. Kaufmann, V. Zheden, T. Costanzo,
P. Mahou, M. Hrtyan, J. Wang, J.L. Aguilera Servin, D. van Damme, E. Beaurepaire,
M. Loose, S.Y. Bednarek, J. Friml, Proceedings of the National Academy of Sciences
118 (2021).
date_created: 2021-08-11T14:11:43Z
date_published: 2021-12-14T00:00:00Z
date_updated: 2024-02-19T11:06:09Z
day: '14'
ddc:
- '580'
department:
- _id: JiFr
- _id: MaLo
- _id: EvBe
- _id: EM-Fac
- _id: NanoFab
doi: 10.1073/pnas.2113046118
external_id:
isi:
- '000736417600043'
pmid:
- '34907016'
file:
- access_level: open_access
checksum: 8d01e72e22c4fb1584e72d8601947069
content_type: application/pdf
creator: cchlebak
date_created: 2021-12-15T08:59:40Z
date_updated: 2021-12-15T08:59:40Z
file_id: '10546'
file_name: 2021_PNAS_Johnson.pdf
file_size: 2757340
relation: main_file
success: 1
file_date_updated: 2021-12-15T08:59:40Z
has_accepted_license: '1'
intvolume: ' 118'
isi: 1
issue: '51'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: earlier_version
url: https://doi.org/10.1101/2021.04.26.441441
record:
- id: '14510'
relation: dissertation_contains
status: public
- id: '14988'
relation: research_data
status: public
status: public
title: The TPLATE complex mediates membrane bending during plant clathrin-mediated
endocytosis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 118
year: '2021'
...
---
_id: '10336'
abstract:
- lang: eng
text: Biological membranes can dramatically accelerate the aggregation of normally
soluble protein molecules into amyloid fibrils and alter the fibril morphologies,
yet the molecular mechanisms through which this accelerated nucleation takes place
are not yet understood. Here, we develop a coarse-grained model to systematically
explore the effect that the structural properties of the lipid membrane and the
nature of protein–membrane interactions have on the nucleation rates of amyloid
fibrils. We identify two physically distinct nucleation pathways—protein-rich
and lipid-rich—and quantify how the membrane fluidity and protein–membrane affinity
control the relative importance of those molecular pathways. We find that the
membrane’s susceptibility to reshaping and being incorporated into the fibrillar
aggregates is a key determinant of its ability to promote protein aggregation.
We then characterize the rates and the free-energy profile associated with this
heterogeneous nucleation process, in which the surface itself participates in
the aggregate structure. Finally, we compare quantitatively our data to experiments
on membrane-catalyzed amyloid aggregation of α-synuclein, a protein implicated
in Parkinson’s disease that predominately nucleates on membranes. More generally,
our results provide a framework for understanding macromolecular aggregation on
lipid membranes in a broad biological and biotechnological context.
acknowledgement: We thank T. C. T. Michaels for reading the manuscript. This work
was supported by the Academy of Medical Science (J.K. and A.Š.), the Cambridge Center
for Misfolding Diseases (T.P.J.K.), the Biotechnology and Biological Sciences Research
Council (T.P.J.K.), the Frances and Augustus Newman Foundation (T.P.J.K.), the European
Research Council Grant PhysProt Agreement 337969, the Wellcome Trust (A.Š. and T.P.J.K.),
the Royal Society (A.Š.), the Medical Research Council (J.K. and A.Š.), and the
UK Materials and Molecular Modeling Hub for computational resources, which is partially
funded by Engineering and Physical Sciences Research Council Grant EP/P020194/1.
article_processing_charge: No
article_type: original
author:
- first_name: Johannes
full_name: Krausser, Johannes
last_name: Krausser
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Krausser J, Knowles TPJ, Šarić A. Physical mechanisms of amyloid nucleation
on fluid membranes. Proceedings of the National Academy of Sciences. 2020;117(52):33090-33098.
doi:10.1073/pnas.2007694117
apa: Krausser, J., Knowles, T. P. J., & Šarić, A. (2020). Physical mechanisms
of amyloid nucleation on fluid membranes. Proceedings of the National Academy
of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2007694117
chicago: Krausser, Johannes, Tuomas P. J. Knowles, and Anđela Šarić. “Physical Mechanisms
of Amyloid Nucleation on Fluid Membranes.” Proceedings of the National Academy
of Sciences. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2007694117.
ieee: J. Krausser, T. P. J. Knowles, and A. Šarić, “Physical mechanisms of amyloid
nucleation on fluid membranes,” Proceedings of the National Academy of Sciences,
vol. 117, no. 52. National Academy of Sciences, pp. 33090–33098, 2020.
ista: Krausser J, Knowles TPJ, Šarić A. 2020. Physical mechanisms of amyloid nucleation
on fluid membranes. Proceedings of the National Academy of Sciences. 117(52),
33090–33098.
mla: Krausser, Johannes, et al. “Physical Mechanisms of Amyloid Nucleation on Fluid
Membranes.” Proceedings of the National Academy of Sciences, vol. 117,
no. 52, National Academy of Sciences, 2020, pp. 33090–98, doi:10.1073/pnas.2007694117.
short: J. Krausser, T.P.J. Knowles, A. Šarić, Proceedings of the National Academy
of Sciences 117 (2020) 33090–33098.
date_created: 2021-11-25T15:07:09Z
date_published: 2020-12-16T00:00:00Z
date_updated: 2021-11-25T15:35:58Z
day: '16'
doi: 10.1073/pnas.2007694117
extern: '1'
external_id:
pmid:
- '33328273'
intvolume: ' 117'
issue: '52'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2019.12.22.886267v2
month: '12'
oa: 1
oa_version: Published Version
page: 33090-33098
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: Physical mechanisms of amyloid nucleation on fluid membranes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 117
year: '2020'
...
---
_id: '10347'
abstract:
- lang: eng
text: Understanding the mechanism of action of compounds capable of inhibiting amyloid-fibril
formation is critical to the development of potential therapeutics against protein-misfolding
diseases. A fundamental challenge for progress is the range of possible target
species and the disparate timescales involved, since the aggregating proteins
are simultaneously the reactants, products, intermediates, and catalysts of the
reaction. It is a complex problem, therefore, to choose the states of the aggregating
proteins that should be bound by the compounds to achieve the most potent inhibition.
We present here a comprehensive kinetic theory of amyloid-aggregation inhibition
that reveals the fundamental thermodynamic and kinetic signatures characterizing
effective inhibitors by identifying quantitative relationships between the aggregation
and binding rate constants. These results provide general physical laws to guide
the design and optimization of inhibitors of amyloid-fibril formation, revealing
in particular the important role of on-rates in the binding of the inhibitors.
acknowledgement: We acknowledge support from Peterhouse, Cambridge (T.C.T.M.); the
Swiss National Science Foundation (T.C.T.M.); the Royal Society (A.S. and S.C.);
the Academy of Medical Sciences (A.S.); Sidney Sussex College, Cambridge (G.M.);
Newnham College, Cambridge (G.T.H.); the Wellcome Trust (T.P.J.K.); the Cambridge
Center for Misfolding Diseases (T.P.J.K. and M.V.); the Biotechnology and Biological
Sciences Research Council (T.P.J.K.); the Frances and Augustus Newman Foundation
(T.P.J.K.); and the Synapsis Foundation for Alzheimer’s disease (P.A.). The research
leading to these results has received funding from the European Research Council
(ERC) under the European Union’s Seventh Framework Program (FP7/2007-2013) through
the ERC Grant PhysProt (Agreement 337969).
article_processing_charge: No
article_type: original
author:
- first_name: Thomas C. T.
full_name: Michaels, Thomas C. T.
last_name: Michaels
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Georg
full_name: Meisl, Georg
last_name: Meisl
- first_name: Gabriella T.
full_name: Heller, Gabriella T.
last_name: Heller
- first_name: Samo
full_name: Curk, Samo
last_name: Curk
- first_name: Paolo
full_name: Arosio, Paolo
last_name: Arosio
- first_name: Sara
full_name: Linse, Sara
last_name: Linse
- first_name: Christopher M.
full_name: Dobson, Christopher M.
last_name: Dobson
- 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: Michaels TCT, Šarić A, Meisl G, et al. Thermodynamic and kinetic design principles
for amyloid-aggregation inhibitors. Proceedings of the National Academy of
Sciences. 2020;117(39):24251-24257. doi:10.1073/pnas.2006684117
apa: Michaels, T. C. T., Šarić, A., Meisl, G., Heller, G. T., Curk, S., Arosio,
P., … Knowles, T. P. J. (2020). Thermodynamic and kinetic design principles for
amyloid-aggregation inhibitors. Proceedings of the National Academy of Sciences.
National Academy of Sciences. https://doi.org/10.1073/pnas.2006684117
chicago: Michaels, Thomas C. T., Anđela Šarić, Georg Meisl, Gabriella T. Heller,
Samo Curk, Paolo Arosio, Sara Linse, Christopher M. Dobson, Michele Vendruscolo,
and Tuomas P. J. Knowles. “Thermodynamic and Kinetic Design Principles for Amyloid-Aggregation
Inhibitors.” Proceedings of the National Academy of Sciences. National
Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2006684117.
ieee: T. C. T. Michaels et al., “Thermodynamic and kinetic design principles
for amyloid-aggregation inhibitors,” Proceedings of the National Academy of
Sciences, vol. 117, no. 39. National Academy of Sciences, pp. 24251–24257,
2020.
ista: Michaels TCT, Šarić A, Meisl G, Heller GT, Curk S, Arosio P, Linse S, Dobson
CM, Vendruscolo M, Knowles TPJ. 2020. Thermodynamic and kinetic design principles
for amyloid-aggregation inhibitors. Proceedings of the National Academy of Sciences.
117(39), 24251–24257.
mla: Michaels, Thomas C. T., et al. “Thermodynamic and Kinetic Design Principles
for Amyloid-Aggregation Inhibitors.” Proceedings of the National Academy of
Sciences, vol. 117, no. 39, National Academy of Sciences, 2020, pp. 24251–57,
doi:10.1073/pnas.2006684117.
short: T.C.T. Michaels, A. Šarić, G. Meisl, G.T. Heller, S. Curk, P. Arosio, S.
Linse, C.M. Dobson, M. Vendruscolo, T.P.J. Knowles, Proceedings of the National
Academy of Sciences 117 (2020) 24251–24257.
date_created: 2021-11-26T07:48:27Z
date_published: 2020-09-14T00:00:00Z
date_updated: 2021-11-26T08:59:06Z
day: '14'
doi: 10.1073/pnas.2006684117
extern: '1'
external_id:
pmid:
- '32929030'
intvolume: ' 117'
issue: '39'
keyword:
- multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2020.02.22.960716
month: '09'
oa: 1
oa_version: Published Version
page: 24251-24257
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: Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 117
year: '2020'
...
---
_id: '7580'
abstract:
- lang: eng
text: The eukaryotic endomembrane system is controlled by small GTPases of the Rab
family, which are activated at defined times and locations in a switch-like manner.
While this switch is well understood for an individual protein, how regulatory
networks produce intracellular activity patterns is currently not known. Here,
we combine in vitro reconstitution experiments with computational modeling to
study a minimal Rab5 activation network. We find that the molecular interactions
in this system give rise to a positive feedback and bistable collective switching
of Rab5. Furthermore, we find that switching near the critical point is intrinsically
stochastic and provide evidence that controlling the inactive population of Rab5
on the membrane can shape the network response. Notably, we demonstrate that collective
switching can spread on the membrane surface as a traveling wave of Rab5 activation.
Together, our findings reveal how biochemical signaling networks control vesicle
trafficking pathways and how their nonequilibrium properties define the spatiotemporal
organization of the cell.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
article_processing_charge: No
article_type: original
author:
- first_name: Urban
full_name: Bezeljak, Urban
id: 2A58201A-F248-11E8-B48F-1D18A9856A87
last_name: Bezeljak
orcid: 0000-0003-1365-5631
- first_name: Hrushikesh
full_name: Loya, Hrushikesh
last_name: Loya
- first_name: Beata M
full_name: Kaczmarek, Beata M
id: 36FA4AFA-F248-11E8-B48F-1D18A9856A87
last_name: Kaczmarek
- first_name: Timothy E.
full_name: Saunders, Timothy E.
last_name: Saunders
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. Stochastic activation
and bistability in a Rab GTPase regulatory network. Proceedings of the National
Academy of Sciences. 2020;117(12):6504-6549. doi:10.1073/pnas.1921027117
apa: Bezeljak, U., Loya, H., Kaczmarek, B. M., Saunders, T. E., & Loose, M.
(2020). Stochastic activation and bistability in a Rab GTPase regulatory network.
Proceedings of the National Academy of Sciences. Proceedings of the National
Academy of Sciences. https://doi.org/10.1073/pnas.1921027117
chicago: Bezeljak, Urban, Hrushikesh Loya, Beata M Kaczmarek, Timothy E. Saunders,
and Martin Loose. “Stochastic Activation and Bistability in a Rab GTPase Regulatory
Network.” Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1921027117.
ieee: U. Bezeljak, H. Loya, B. M. Kaczmarek, T. E. Saunders, and M. Loose, “Stochastic
activation and bistability in a Rab GTPase regulatory network,” Proceedings
of the National Academy of Sciences, vol. 117, no. 12. Proceedings of the
National Academy of Sciences, pp. 6504–6549, 2020.
ista: Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. 2020. Stochastic activation
and bistability in a Rab GTPase regulatory network. Proceedings of the National
Academy of Sciences. 117(12), 6504–6549.
mla: Bezeljak, Urban, et al. “Stochastic Activation and Bistability in a Rab GTPase
Regulatory Network.” Proceedings of the National Academy of Sciences, vol.
117, no. 12, Proceedings of the National Academy of Sciences, 2020, pp. 6504–49,
doi:10.1073/pnas.1921027117.
short: U. Bezeljak, H. Loya, B.M. Kaczmarek, T.E. Saunders, M. Loose, Proceedings
of the National Academy of Sciences 117 (2020) 6504–6549.
date_created: 2020-03-12T05:32:26Z
date_published: 2020-03-24T00:00:00Z
date_updated: 2023-09-07T13:17:06Z
day: '24'
department:
- _id: MaLo
- _id: CaBe
doi: 10.1073/pnas.1921027117
external_id:
isi:
- '000521821800040'
intvolume: ' 117'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/776567
month: '03'
oa: 1
oa_version: Preprint
page: 6504-6549
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
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/proteins-as-molecular-switches/
record:
- id: '8341'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Stochastic activation and bistability in a Rab GTPase regulatory network
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 117
year: '2020'
...
---
_id: '15061'
abstract:
- lang: eng
text: The actin cytoskeleton, a dynamic network of actin filaments and associated
F-actin–binding proteins, is fundamentally important in eukaryotes. α-Actinins
are major F-actin bundlers that are inhibited by Ca2+ in nonmuscle cells. Here
we report the mechanism of Ca2+-mediated regulation of Entamoeba histolytica α-actinin-2
(EhActn2) with features expected for the common ancestor of Entamoeba and higher
eukaryotic α-actinins. Crystal structures of Ca2+-free and Ca2+-bound EhActn2
reveal a calmodulin-like domain (CaMD) uniquely inserted within the rod domain.
Integrative studies reveal an exceptionally high affinity of the EhActn2 CaMD
for Ca2+, binding of which can only be regulated in the presence of physiological
concentrations of Mg2+. Ca2+ binding triggers an increase in protein multidomain
rigidity, reducing conformational flexibility of F-actin–binding domains via interdomain
cross-talk and consequently inhibiting F-actin bundling. In vivo studies uncover
that EhActn2 plays an important role in phagocytic cup formation and might constitute
a new drug target for amoebic dysentery.
acknowledged_ssus:
- _id: LifeSc
acknowledgement: "We thank the staff of the macromolecular crystallography (MX) and
SAXS beamlines at the European Synchrotron Radiation facility, Diamond, and Swiss
Light Source for excellent support, and the Life Sciences Facility of the Institute
of Science and Technology Austria for usage of the rheometer. We thank Life Sciences
editors for editing assistance. EM data were\r\nrecorded at the EM Facility of the
Vienna BioCenter Core Facilities (Austria). Confocal microscopy was carried out
at the Advanced Instrument Research Facility, Jawaharlal Nehru University. K.D.-C.’s
research was supported by the Initial Training Network MUZIC (ITN-MUZIC) (N°238423),
Austrian Science Fund (FWF) Projects I525, I1593, P22276, P19060, and W1221, Laura
Bassi Centre of Optimized Structural Studies (N°253275), a Wellcome Trust Collaborative
Award (201543/Z/16/Z), COST Action BM1405, Vienna Science and Technology Fund (WWTF)
Chemical Biology Project LS17-008, and Christian Doppler Laboratory for High-Content
Structural Biology and Biotechnology. K.Z., J.L.A., C.S., E.A.G., and A.S. were
supported by the University of Vienna, J.K. by a Wellcome Trust Collaborative Award
and by the Centre of Optimized Structural Studies, M.P. by FWF Project I1593, E.d.A.R.
ITN-MUZIC, and FWF Projects I525 and I1593, and T.C.M. and L.C. by FWF Project I
2408-B22. E.A.G. acknowledges the PhD program Structure and Interaction of Biological
Macromolecules. M.B. acknowledges the University Grant Commission, India, for a
senior research fellowship. A.B. acknowledges a JC Bose Fellowship from the Science
Engineering Research Council. "
article_processing_charge: No
article_type: original
author:
- first_name: Nikos
full_name: Pinotsis, Nikos
last_name: Pinotsis
- first_name: Karolina
full_name: Zielinska, Karolina
last_name: Zielinska
- first_name: Mrigya
full_name: Babuta, Mrigya
last_name: Babuta
- first_name: Joan L.
full_name: Arolas, Joan L.
last_name: Arolas
- first_name: Julius
full_name: Kostan, Julius
last_name: Kostan
- first_name: Muhammad Bashir
full_name: Khan, Muhammad Bashir
last_name: Khan
- first_name: Claudia
full_name: Schreiner, Claudia
last_name: Schreiner
- first_name: Anita P
full_name: Testa Salmazo, Anita P
id: 41F1F098-F248-11E8-B48F-1D18A9856A87
last_name: Testa Salmazo
- first_name: Luciano
full_name: Ciccarelli, Luciano
last_name: Ciccarelli
- first_name: Martin
full_name: Puchinger, Martin
last_name: Puchinger
- first_name: Eirini A.
full_name: Gkougkoulia, Eirini A.
last_name: Gkougkoulia
- first_name: Euripedes de Almeida
full_name: Ribeiro, Euripedes de Almeida
last_name: Ribeiro
- first_name: Thomas C.
full_name: Marlovits, Thomas C.
last_name: Marlovits
- first_name: Alok
full_name: Bhattacharya, Alok
last_name: Bhattacharya
- first_name: Kristina
full_name: Djinovic-Carugo, Kristina
last_name: Djinovic-Carugo
citation:
ama: Pinotsis N, Zielinska K, Babuta M, et al. Calcium modulates the domain flexibility
and function of an α-actinin similar to the ancestral α-actinin. Proceedings
of the National Academy of Sciences. 2020;117(36):22101-22112. doi:10.1073/pnas.1917269117
apa: Pinotsis, N., Zielinska, K., Babuta, M., Arolas, J. L., Kostan, J., Khan, M.
B., … Djinovic-Carugo, K. (2020). Calcium modulates the domain flexibility and
function of an α-actinin similar to the ancestral α-actinin. Proceedings of
the National Academy of Sciences. Proceedings of the National Academy of Sciences.
https://doi.org/10.1073/pnas.1917269117
chicago: Pinotsis, Nikos, Karolina Zielinska, Mrigya Babuta, Joan L. Arolas, Julius
Kostan, Muhammad Bashir Khan, Claudia Schreiner, et al. “Calcium Modulates the
Domain Flexibility and Function of an α-Actinin Similar to the Ancestral α-Actinin.”
Proceedings of the National Academy of Sciences. Proceedings of the National
Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1917269117.
ieee: N. Pinotsis et al., “Calcium modulates the domain flexibility and function
of an α-actinin similar to the ancestral α-actinin,” Proceedings of the National
Academy of Sciences, vol. 117, no. 36. Proceedings of the National Academy
of Sciences, pp. 22101–22112, 2020.
ista: Pinotsis N, Zielinska K, Babuta M, Arolas JL, Kostan J, Khan MB, Schreiner
C, Testa Salmazo AP, Ciccarelli L, Puchinger M, Gkougkoulia EA, Ribeiro E de A,
Marlovits TC, Bhattacharya A, Djinovic-Carugo K. 2020. Calcium modulates the domain
flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings
of the National Academy of Sciences. 117(36), 22101–22112.
mla: Pinotsis, Nikos, et al. “Calcium Modulates the Domain Flexibility and Function
of an α-Actinin Similar to the Ancestral α-Actinin.” Proceedings of the National
Academy of Sciences, vol. 117, no. 36, Proceedings of the National Academy
of Sciences, 2020, pp. 22101–12, doi:10.1073/pnas.1917269117.
short: N. Pinotsis, K. Zielinska, M. Babuta, J.L. Arolas, J. Kostan, M.B. Khan,
C. Schreiner, A.P. Testa Salmazo, L. Ciccarelli, M. Puchinger, E.A. Gkougkoulia,
E. de A. Ribeiro, T.C. Marlovits, A. Bhattacharya, K. Djinovic-Carugo, Proceedings
of the National Academy of Sciences 117 (2020) 22101–22112.
date_created: 2024-03-04T10:03:52Z
date_published: 2020-09-08T00:00:00Z
date_updated: 2024-03-04T10:14:44Z
day: '08'
department:
- _id: CaBe
doi: 10.1073/pnas.1917269117
external_id:
pmid:
- '32848067'
intvolume: ' 117'
issue: '36'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.191726911
month: '09'
oa: 1
oa_version: Published Version
page: 22101-22112
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'
status: public
title: Calcium modulates the domain flexibility and function of an α-actinin similar
to the ancestral α-actinin
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 117
year: '2020'
...
---
_id: '8002'
abstract:
- lang: eng
text: Wound healing in plant tissues, consisting of rigid cell wall-encapsulated
cells, represents a considerable challenge and occurs through largely unknown
mechanisms distinct from those in animals. Owing to their inability to migrate,
plant cells rely on targeted cell division and expansion to regenerate wounds.
Strict coordination of these wound-induced responses is essential to ensure efficient,
spatially restricted wound healing. Single-cell tracking by live imaging allowed
us to gain mechanistic insight into the wound perception and coordination of wound
responses after laser-based wounding in Arabidopsis root. We revealed a crucial
contribution of the collapse of damaged cells in wound perception and detected
an auxin increase specific to cells immediately adjacent to the wound. This localized
auxin increase balances wound-induced cell expansion and restorative division
rates in a dose-dependent manner, leading to tumorous overproliferation when the
canonical TIR1 auxin signaling is disrupted. Auxin and wound-induced turgor pressure
changes together also spatially define the activation of key components of regeneration,
such as the transcription regulator ERF115. Our observations suggest that the
wound signaling involves the sensing of collapse of damaged cells and a local
auxin signaling activation to coordinate the downstream transcriptional responses
in the immediate wound vicinity.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
article_number: '202003346'
article_processing_charge: No
article_type: original
author:
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
orcid: 0000-0001-8295-2926
- first_name: Juan C
full_name: Montesinos López, Juan C
id: 310A8E3E-F248-11E8-B48F-1D18A9856A87
last_name: Montesinos López
orcid: 0000-0001-9179-6099
- first_name: Petra
full_name: Marhavá, Petra
id: 44E59624-F248-11E8-B48F-1D18A9856A87
last_name: Marhavá
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Saiko
full_name: Yoshida, Saiko
id: 2E46069C-F248-11E8-B48F-1D18A9856A87
last_name: Yoshida
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Hörmayer L, Montesinos López JC, Marhavá P, Benková E, Yoshida S, Friml J.
Wounding-induced changes in cellular pressure and localized auxin signalling spatially
coordinate restorative divisions in roots. Proceedings of the National Academy
of Sciences. 2020;117(26). doi:10.1073/pnas.2003346117
apa: Hörmayer, L., Montesinos López, J. C., Marhavá, P., Benková, E., Yoshida, S.,
& Friml, J. (2020). Wounding-induced changes in cellular pressure and localized
auxin signalling spatially coordinate restorative divisions in roots. Proceedings
of the National Academy of Sciences. Proceedings of the National Academy of
Sciences. https://doi.org/10.1073/pnas.2003346117
chicago: Hörmayer, Lukas, Juan C Montesinos López, Petra Marhavá, Eva Benková, Saiko
Yoshida, and Jiří Friml. “Wounding-Induced Changes in Cellular Pressure and Localized
Auxin Signalling Spatially Coordinate Restorative Divisions in Roots.” Proceedings
of the National Academy of Sciences. Proceedings of the National Academy of
Sciences, 2020. https://doi.org/10.1073/pnas.2003346117.
ieee: L. Hörmayer, J. C. Montesinos López, P. Marhavá, E. Benková, S. Yoshida, and
J. Friml, “Wounding-induced changes in cellular pressure and localized auxin signalling
spatially coordinate restorative divisions in roots,” Proceedings of the National
Academy of Sciences, vol. 117, no. 26. Proceedings of the National Academy
of Sciences, 2020.
ista: Hörmayer L, Montesinos López JC, Marhavá P, Benková E, Yoshida S, Friml J.
2020. Wounding-induced changes in cellular pressure and localized auxin signalling
spatially coordinate restorative divisions in roots. Proceedings of the National
Academy of Sciences. 117(26), 202003346.
mla: Hörmayer, Lukas, et al. “Wounding-Induced Changes in Cellular Pressure and
Localized Auxin Signalling Spatially Coordinate Restorative Divisions in Roots.”
Proceedings of the National Academy of Sciences, vol. 117, no. 26, 202003346,
Proceedings of the National Academy of Sciences, 2020, doi:10.1073/pnas.2003346117.
short: L. Hörmayer, J.C. Montesinos López, P. Marhavá, E. Benková, S. Yoshida, J.
Friml, Proceedings of the National Academy of Sciences 117 (2020).
date_created: 2020-06-22T13:33:52Z
date_published: 2020-06-30T00:00:00Z
date_updated: 2024-03-28T23:30:10Z
day: '30'
ddc:
- '580'
department:
- _id: JiFr
- _id: EvBe
doi: 10.1073/pnas.2003346117
ec_funded: 1
external_id:
isi:
- '000565729700033'
pmid:
- '32541049'
file:
- access_level: open_access
checksum: 908b09437680181de9990915f2113aca
content_type: application/pdf
creator: dernst
date_created: 2020-06-23T11:30:53Z
date_updated: 2020-07-14T12:48:07Z
file_id: '8009'
file_name: 2020_PNAS_Hoermayer.pdf
file_size: 2407102
relation: main_file
file_date_updated: 2020-07-14T12:48:07Z
has_accepted_license: '1'
intvolume: ' 117'
isi: 1
issue: '26'
language:
- iso: eng
month: '06'
oa: 1
oa_version: None
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 262EF96E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29988
name: RNA-directed DNA methylation in plant development
publication: 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'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/how-wounded-plants-coordinate-their-healing/
record:
- id: '9992'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Wounding-induced changes in cellular pressure and localized auxin signalling
spatially coordinate restorative divisions in roots
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 117
year: '2020'
...
---
_id: '9460'
abstract:
- lang: eng
text: Epigenetic reprogramming is required for proper regulation of gene expression
in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for
seed viability, pollen function, and successful reproduction. The DEMETER (DME)
DNA glycosylase initiates localized DNA demethylation in vegetative and central
cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively.
In rice, the central cell genome displays local DNA hypomethylation, suggesting
that active DNA demethylation also occurs in rice; however, the enzyme responsible
for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING
1a (ROS1a) gene, which is related to DME and is essential for rice seed viability
and pollen function. Here, we report genome-wide analyses of DNA methylation in
wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative
cell genome is locally hypomethylated compared with sperm by a process that requires
ROS1a activity. We show that many ROS1a target sequences in the vegetative cell
are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates
the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation
is indirectly promoted by DNA demethylation in the vegetative cell. These results
reveal that DNA glycosylase-mediated DNA demethylation processes are conserved
in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally,
although global non-CG methylation levels of sperm and egg differ, the maternal
and paternal embryo genomes show similar non-CG methylation levels, suggesting
that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell
fusion.
article_processing_charge: No
article_type: original
author:
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Akemi
full_name: Ono, Akemi
last_name: Ono
- first_name: Stefan
full_name: Scholten, Stefan
last_name: Scholten
- first_name: Tetsu
full_name: Kinoshita, Tetsu
last_name: Kinoshita
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Takashi
full_name: Okamoto, Takashi
last_name: Okamoto
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
citation:
ama: Kim MY, Ono A, Scholten S, et al. DNA demethylation by ROS1a in rice vegetative
cells promotes methylation in sperm. Proceedings of the National Academy of
Sciences. 2019;116(19):9652-9657. doi:10.1073/pnas.1821435116
apa: Kim, M. Y., Ono, A., Scholten, S., Kinoshita, T., Zilberman, D., Okamoto, T.,
& Fischer, R. L. (2019). DNA demethylation by ROS1a in rice vegetative cells
promotes methylation in sperm. Proceedings of the National Academy of Sciences.
National Academy of Sciences. https://doi.org/10.1073/pnas.1821435116
chicago: Kim, M. Yvonne, Akemi Ono, Stefan Scholten, Tetsu Kinoshita, Daniel Zilberman,
Takashi Okamoto, and Robert L. Fischer. “DNA Demethylation by ROS1a in Rice Vegetative
Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of
Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1821435116.
ieee: M. Y. Kim et al., “DNA demethylation by ROS1a in rice vegetative cells
promotes methylation in sperm,” Proceedings of the National Academy of Sciences,
vol. 116, no. 19. National Academy of Sciences, pp. 9652–9657, 2019.
ista: Kim MY, Ono A, Scholten S, Kinoshita T, Zilberman D, Okamoto T, Fischer RL.
2019. DNA demethylation by ROS1a in rice vegetative cells promotes methylation
in sperm. Proceedings of the National Academy of Sciences. 116(19), 9652–9657.
mla: Kim, M. Yvonne, et al. “DNA Demethylation by ROS1a in Rice Vegetative Cells
Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences,
vol. 116, no. 19, National Academy of Sciences, 2019, pp. 9652–57, doi:10.1073/pnas.1821435116.
short: M.Y. Kim, A. Ono, S. Scholten, T. Kinoshita, D. Zilberman, T. Okamoto, R.L.
Fischer, Proceedings of the National Academy of Sciences 116 (2019) 9652–9657.
date_created: 2021-06-04T12:38:20Z
date_published: 2019-05-07T00:00:00Z
date_updated: 2021-12-14T07:52:30Z
day: '07'
ddc:
- '580'
department:
- _id: DaZi
doi: 10.1073/pnas.1821435116
extern: '1'
external_id:
pmid:
- '31000601'
file:
- access_level: open_access
checksum: 5b0ae3779b8b21b5223bd2d3cceede3a
content_type: application/pdf
creator: asandaue
date_created: 2021-06-04T12:50:47Z
date_updated: 2021-06-04T12:50:47Z
file_id: '9461'
file_name: 2019_PNAS_Kim.pdf
file_size: 1142540
relation: main_file
success: 1
file_date_updated: 2021-06-04T12:50:47Z
has_accepted_license: '1'
intvolume: ' 116'
issue: '19'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 9652-9657
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: DNA demethylation by ROS1a in rice vegetative cells promotes methylation in
sperm
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 116
year: '2019'
...
---
_id: '9689'
abstract:
- lang: eng
text: A central goal of computational physics and chemistry is to predict material
properties by using first-principles methods based on the fundamental laws of
quantum mechanics. However, the high computational costs of these methods typically
prevent rigorous predictions of macroscopic quantities at finite temperatures,
such as heat capacity, density, and chemical potential. Here, we enable such predictions
by marrying advanced free-energy methods with data-driven machine-learning interatomic
potentials. We show that, for the ubiquitous and technologically essential system
of water, a first-principles thermodynamic description not only leads to excellent
agreement with experiments, but also reveals the crucial role of nuclear quantum
fluctuations in modulating the thermodynamic stabilities of different phases of
water.
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Edgar A.
full_name: Engel, Edgar A.
last_name: Engel
- first_name: Jörg
full_name: Behler, Jörg
last_name: Behler
- first_name: Christoph
full_name: Dellago, Christoph
last_name: Dellago
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. Ab initio thermodynamics
of liquid and solid water. Proceedings of the National Academy of Sciences.
2019;116(4):1110-1115. doi:10.1073/pnas.1815117116
apa: Cheng, B., Engel, E. A., Behler, J., Dellago, C., & Ceriotti, M. (2019).
Ab initio thermodynamics of liquid and solid water. Proceedings of the National
Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1815117116
chicago: Cheng, Bingqing, Edgar A. Engel, Jörg Behler, Christoph Dellago, and Michele
Ceriotti. “Ab Initio Thermodynamics of Liquid and Solid Water.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1815117116.
ieee: B. Cheng, E. A. Engel, J. Behler, C. Dellago, and M. Ceriotti, “Ab initio
thermodynamics of liquid and solid water,” Proceedings of the National Academy
of Sciences, vol. 116, no. 4. National Academy of Sciences, pp. 1110–1115,
2019.
ista: Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. 2019. Ab initio thermodynamics
of liquid and solid water. Proceedings of the National Academy of Sciences. 116(4),
1110–1115.
mla: Cheng, Bingqing, et al. “Ab Initio Thermodynamics of Liquid and Solid Water.”
Proceedings of the National Academy of Sciences, vol. 116, no. 4, National
Academy of Sciences, 2019, pp. 1110–15, doi:10.1073/pnas.1815117116.
short: B. Cheng, E.A. Engel, J. Behler, C. Dellago, M. Ceriotti, Proceedings of
the National Academy of Sciences 116 (2019) 1110–1115.
date_created: 2021-07-19T10:17:09Z
date_published: 2019-01-22T00:00:00Z
date_updated: 2023-02-23T14:05:08Z
day: '22'
doi: 10.1073/pnas.1815117116
extern: '1'
external_id:
arxiv:
- '1811.08630'
pmid:
- '30610171'
intvolume: ' 116'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1815117116
month: '01'
oa: 1
oa_version: Published Version
page: 1110-1115
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: Ab initio thermodynamics of liquid and solid water
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 116
year: '2019'
...
---
_id: '14001'
abstract:
- lang: eng
text: Chiral molecules interact and react differently with other chiral objects,
depending on their handedness. Therefore, it is essential to understand and ultimately
control the evolution of molecular chirality during chemical reactions. Although
highly sophisticated techniques for the controlled synthesis of chiral molecules
have been developed, the observation of chirality on the natural femtosecond time
scale of a chemical reaction has so far remained out of reach in the gas phase.
Here, we demonstrate a general experimental technique, based on high-harmonic
generation in tailored laser fields, and apply it to probe the time evolution
of molecular chirality during the photodissociation of 2-iodobutane. These measurements
show a change in sign and a pronounced increase in the magnitude of the chiral
response over the first 100 fs, followed by its decay within less than 500 fs,
revealing the photodissociation to achiral products. The observed time evolution
is explained in terms of the variation of the electric and magnetic transition-dipole
moments between the lowest electronic states of the cation as a function of the
reaction coordinate. These results open the path to investigations of the chirality
of molecular-reaction pathways, light-induced chirality in chemical processes,
and the control of molecular chirality through tailored laser pulses.
article_processing_charge: No
article_type: original
author:
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Daniel
full_name: Zindel, Daniel
last_name: Zindel
- first_name: Vít
full_name: Svoboda, Vít
last_name: Svoboda
- first_name: Elias
full_name: Bommeli, Elias
last_name: Bommeli
- first_name: Manuel
full_name: Ochsner, Manuel
last_name: Ochsner
- first_name: Andres
full_name: Tehlar, Andres
last_name: Tehlar
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
citation:
ama: Baykusheva DR, Zindel D, Svoboda V, et al. Real-time probing of chirality during
a chemical reaction. Proceedings of the National Academy of Sciences. 2019;116(48):23923-23929.
doi:10.1073/pnas.1907189116
apa: Baykusheva, D. R., Zindel, D., Svoboda, V., Bommeli, E., Ochsner, M., Tehlar,
A., & Wörner, H. J. (2019). Real-time probing of chirality during a chemical
reaction. Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences. https://doi.org/10.1073/pnas.1907189116
chicago: Baykusheva, Denitsa Rangelova, Daniel Zindel, Vít Svoboda, Elias Bommeli,
Manuel Ochsner, Andres Tehlar, and Hans Jakob Wörner. “Real-Time Probing of Chirality
during a Chemical Reaction.” Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1907189116.
ieee: D. R. Baykusheva et al., “Real-time probing of chirality during a chemical
reaction,” Proceedings of the National Academy of Sciences, vol. 116, no.
48. Proceedings of the National Academy of Sciences, pp. 23923–23929, 2019.
ista: Baykusheva DR, Zindel D, Svoboda V, Bommeli E, Ochsner M, Tehlar A, Wörner
HJ. 2019. Real-time probing of chirality during a chemical reaction. Proceedings
of the National Academy of Sciences. 116(48), 23923–23929.
mla: Baykusheva, Denitsa Rangelova, et al. “Real-Time Probing of Chirality during
a Chemical Reaction.” Proceedings of the National Academy of Sciences,
vol. 116, no. 48, Proceedings of the National Academy of Sciences, 2019, pp. 23923–29,
doi:10.1073/pnas.1907189116.
short: D.R. Baykusheva, D. Zindel, V. Svoboda, E. Bommeli, M. Ochsner, A. Tehlar,
H.J. Wörner, Proceedings of the National Academy of Sciences 116 (2019) 23923–23929.
date_created: 2023-08-09T13:10:36Z
date_published: 2019-11-13T00:00:00Z
date_updated: 2023-08-22T07:40:05Z
day: '13'
doi: 10.1073/pnas.1907189116
extern: '1'
external_id:
arxiv:
- '1906.10818'
pmid:
- '31723044'
intvolume: ' 116'
issue: '48'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1907189116
month: '11'
oa: 1
oa_version: Published Version
page: 23923-23929
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: Real-time probing of chirality during a chemical reaction
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 116
year: '2019'
...
---
_id: '196'
abstract:
- lang: eng
text: 'The abelian sandpile serves as a model to study self-organized criticality,
a phenomenon occurring in biological, physical and social processes. The identity
of the abelian group is a fractal composed of self-similar patches, and its limit
is subject of extensive collaborative research. Here, we analyze the evolution
of the sandpile identity under harmonic fields of different orders. We show that
this evolution corresponds to periodic cycles through the abelian group characterized
by the smooth transformation and apparent conservation of the patches constituting
the identity. The dynamics induced by second and third order harmonics resemble
smooth stretchings, respectively translations, of the identity, while the ones
induced by fourth order harmonics resemble magnifications and rotations. Starting
with order three, the dynamics pass through extended regions of seemingly random
configurations which spontaneously reassemble into accentuated patterns. We show
that the space of harmonic functions projects to the extended analogue of the
sandpile group, thus providing a set of universal coordinates identifying configurations
between different domains. Since the original sandpile group is a subgroup of
the extended one, this directly implies that it admits a natural renormalization.
Furthermore, we show that the harmonic fields can be induced by simple Markov
processes, and that the corresponding stochastic dynamics show remarkable robustness
over hundreds of periods. Finally, we encode information into seemingly random
configurations, and decode this information with an algorithm requiring minimal
prior knowledge. Our results suggest that harmonic fields might split the sandpile
group into sub-sets showing different critical coefficients, and that it might
be possible to extend the fractal structure of the identity beyond the boundaries
of its domain. '
acknowledgement: "M.L. is grateful to the members of the C Guet and G Tkacik groups
for valuable comments and support. M.S. is grateful to Nikita Kalinin for inspiring
communications.\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Moritz
full_name: Lang, Moritz
id: 29E0800A-F248-11E8-B48F-1D18A9856A87
last_name: Lang
- first_name: Mikhail
full_name: Shkolnikov, Mikhail
id: 35084A62-F248-11E8-B48F-1D18A9856A87
last_name: Shkolnikov
orcid: 0000-0002-4310-178X
citation:
ama: Lang M, Shkolnikov M. Harmonic dynamics of the Abelian sandpile. Proceedings
of the National Academy of Sciences. 2019;116(8):2821-2830. doi:10.1073/pnas.1812015116
apa: Lang, M., & Shkolnikov, M. (2019). Harmonic dynamics of the Abelian sandpile.
Proceedings of the National Academy of Sciences. National Academy of Sciences.
https://doi.org/10.1073/pnas.1812015116
chicago: Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian
Sandpile.” Proceedings of the National Academy of Sciences. National Academy
of Sciences, 2019. https://doi.org/10.1073/pnas.1812015116.
ieee: M. Lang and M. Shkolnikov, “Harmonic dynamics of the Abelian sandpile,” Proceedings
of the National Academy of Sciences, vol. 116, no. 8. National Academy of
Sciences, pp. 2821–2830, 2019.
ista: Lang M, Shkolnikov M. 2019. Harmonic dynamics of the Abelian sandpile. Proceedings
of the National Academy of Sciences. 116(8), 2821–2830.
mla: Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian Sandpile.”
Proceedings of the National Academy of Sciences, vol. 116, no. 8, National
Academy of Sciences, 2019, pp. 2821–30, doi:10.1073/pnas.1812015116.
short: M. Lang, M. Shkolnikov, Proceedings of the National Academy of Sciences 116
(2019) 2821–2830.
date_created: 2018-12-11T11:45:08Z
date_published: 2019-02-19T00:00:00Z
date_updated: 2023-09-11T14:09:34Z
day: '19'
department:
- _id: CaGu
- _id: GaTk
- _id: TaHa
doi: 10.1073/pnas.1812015116
external_id:
arxiv:
- '1806.10823'
isi:
- '000459074400013'
pmid:
- ' 30728300'
intvolume: ' 116'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1812015116
month: '02'
oa: 1
oa_version: Published Version
page: 2821-2830
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- description: News on IST Webpage
relation: press_release
url: https://ist.ac.at/en/news/famous-sandpile-model-shown-to-move-like-a-traveling-sand-dune/
scopus_import: '1'
status: public
title: Harmonic dynamics of the Abelian sandpile
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 116
year: '2019'
...
---
_id: '6999'
abstract:
- lang: eng
text: Plasmodesmata (PD) are plant-specific membrane-lined channels that create
cytoplasmic and membrane continuities between adjacent cells, thereby facilitating
cell–cell communication and virus movement. Plant cells have evolved diverse mechanisms
to regulate PD plasticity in response to numerous environmental stimuli. In particular,
during defense against plant pathogens, the defense hormone, salicylic acid (SA),
plays a crucial role in the regulation of PD permeability in a callose-dependent
manner. Here, we uncover a mechanism by which plants restrict the spreading of
virus and PD cargoes using SA signaling by increasing lipid order and closure
of PD. We showed that exogenous SA application triggered the compartmentalization
of lipid raft nanodomains through a modulation of the lipid raft-regulatory protein,
Remorin (REM). Genetic studies, superresolution imaging, and transmission electron
microscopy observation together demonstrated that Arabidopsis REM1.2 and REM1.3
are crucial for plasma membrane nanodomain assembly to control PD aperture and
functionality. In addition, we also found that a 14-3-3 epsilon protein modulates
REM clustering and membrane nanodomain compartmentalization through its direct
interaction with REM proteins. This study unveils a molecular mechanism by which
the key plant defense hormone, SA, triggers membrane lipid nanodomain reorganization,
thereby regulating PD closure to impede virus spreading.
article_processing_charge: No
article_type: original
author:
- first_name: D
full_name: Huang, D
last_name: Huang
- first_name: Y
full_name: Sun, Y
last_name: Sun
- first_name: Z
full_name: Ma, Z
last_name: Ma
- first_name: M
full_name: Ke, M
last_name: Ke
- first_name: Y
full_name: Cui, Y
last_name: Cui
- first_name: Z
full_name: Chen, Z
last_name: Chen
- first_name: C
full_name: Chen, C
last_name: Chen
- first_name: C
full_name: Ji, C
last_name: Ji
- first_name: TM
full_name: Tran, TM
last_name: Tran
- first_name: L
full_name: Yang, L
last_name: Yang
- first_name: SM
full_name: Lam, SM
last_name: Lam
- first_name: Y
full_name: Han, Y
last_name: Han
- first_name: G
full_name: Shu, G
last_name: Shu
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Y
full_name: Miao, Y
last_name: Miao
- first_name: L
full_name: Jiang, L
last_name: Jiang
- first_name: X
full_name: Chen, X
last_name: Chen
citation:
ama: Huang D, Sun Y, Ma Z, et al. Salicylic acid-mediated plasmodesmal closure via
Remorin-dependent lipid organization. Proceedings of the National Academy of
Sciences of the United States of America. 2019;116(42):21274-21284. doi:10.1073/pnas.1911892116
apa: Huang, D., Sun, Y., Ma, Z., Ke, M., Cui, Y., Chen, Z., … Chen, X. (2019). Salicylic
acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. Proceedings
of the National Academy of Sciences of the United States of America. Proceedings
of the National Academy of Sciences. https://doi.org/10.1073/pnas.1911892116
chicago: Huang, D, Y Sun, Z Ma, M Ke, Y Cui, Z Chen, C Chen, et al. “Salicylic Acid-Mediated
Plasmodesmal Closure via Remorin-Dependent Lipid Organization.” Proceedings
of the National Academy of Sciences of the United States of America. Proceedings
of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1911892116.
ieee: D. Huang et al., “Salicylic acid-mediated plasmodesmal closure via
Remorin-dependent lipid organization,” Proceedings of the National Academy
of Sciences of the United States of America, vol. 116, no. 42. Proceedings
of the National Academy of Sciences, pp. 21274–21284, 2019.
ista: Huang D, Sun Y, Ma Z, Ke M, Cui Y, Chen Z, Chen C, Ji C, Tran T, Yang L, Lam
S, Han Y, Shu G, Friml J, Miao Y, Jiang L, Chen X. 2019. Salicylic acid-mediated
plasmodesmal closure via Remorin-dependent lipid organization. Proceedings of
the National Academy of Sciences of the United States of America. 116(42), 21274–21284.
mla: Huang, D., et al. “Salicylic Acid-Mediated Plasmodesmal Closure via Remorin-Dependent
Lipid Organization.” Proceedings of the National Academy of Sciences of the
United States of America, vol. 116, no. 42, Proceedings of the National Academy
of Sciences, 2019, pp. 21274–84, doi:10.1073/pnas.1911892116.
short: D. Huang, Y. Sun, Z. Ma, M. Ke, Y. Cui, Z. Chen, C. Chen, C. Ji, T. Tran,
L. Yang, S. Lam, Y. Han, G. Shu, J. Friml, Y. Miao, L. Jiang, X. Chen, Proceedings
of the National Academy of Sciences of the United States of America 116 (2019)
21274–21284.
date_created: 2019-11-12T11:42:05Z
date_published: 2019-10-15T00:00:00Z
date_updated: 2023-10-17T12:32:37Z
day: '15'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1073/pnas.1911892116
external_id:
isi:
- '000490183000068'
pmid:
- '31575745'
file:
- access_level: open_access
checksum: 258c666bc6253eab81961f61169eefae
content_type: application/pdf
creator: dernst
date_created: 2019-11-13T08:22:28Z
date_updated: 2020-07-14T12:47:46Z
file_id: '7012'
file_name: 2019_PNAS_Huang.pdf
file_size: 3287466
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
intvolume: ' 116'
isi: 1
issue: '42'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 21274-21284
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: Proceedings of the National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1073/pnas.2004738117
scopus_import: '1'
status: public
title: Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization
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: 116
year: '2019'
...
---
_id: '9471'
abstract:
- lang: eng
text: The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation
and is required for endosperm genomic imprinting and embryo viability. Targets
of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons
and at the boundaries of large transposons, but how DME interacts with these diverse
chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1)
subunit of the chromatin remodeler FACT (facilitates chromatin transactions),
was previously shown to be involved in the DME-dependent regulation of genomic
imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction
between DME and chromatin, we focused on the activity of the two FACT subunits,
SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found
that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of
target sites, the first being euchromatic and accessible to DME, but the second,
representing over half of DME targets, requiring the action of FACT for DME-mediated
DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets
are GC-rich heterochromatin domains with high nucleosome occupancy enriched with
H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated
linker histone H1 specifically mediates the requirement for FACT at a subset of
DME-target loci. Overall, our results demonstrate that FACT is required for DME
targeting by facilitating its access to heterochromatin.
article_processing_charge: No
article_type: original
author:
- first_name: Jennifer M.
full_name: Frost, Jennifer M.
last_name: Frost
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Guen Tae
full_name: Park, Guen Tae
last_name: Park
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Miyuki
full_name: Nakamura, Miyuki
last_name: Nakamura
- first_name: Samuel J. H.
full_name: Lin, Samuel J. H.
last_name: Lin
- first_name: Hyunjin
full_name: Yoo, Hyunjin
last_name: Yoo
- first_name: Jaemyung
full_name: Choi, Jaemyung
last_name: Choi
- first_name: Yoko
full_name: Ikeda, Yoko
last_name: Ikeda
- first_name: Tetsu
full_name: Kinoshita, Tetsu
last_name: Kinoshita
- first_name: Yeonhee
full_name: Choi, Yeonhee
last_name: Choi
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
citation:
ama: Frost JM, Kim MY, Park GT, et al. FACT complex is required for DNA demethylation
at heterochromatin during reproduction in Arabidopsis. Proceedings of the National
Academy of Sciences. 2018;115(20):E4720-E4729. doi:10.1073/pnas.1713333115
apa: Frost, J. M., Kim, M. Y., Park, G. T., Hsieh, P.-H., Nakamura, M., Lin, S.
J. H., … Fischer, R. L. (2018). FACT complex is required for DNA demethylation
at heterochromatin during reproduction in Arabidopsis. Proceedings of the National
Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1713333115
chicago: Frost, Jennifer M., M. Yvonne Kim, Guen Tae Park, Ping-Hung Hsieh, Miyuki
Nakamura, Samuel J. H. Lin, Hyunjin Yoo, et al. “FACT Complex Is Required for
DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1713333115.
ieee: J. M. Frost et al., “FACT complex is required for DNA demethylation
at heterochromatin during reproduction in Arabidopsis,” Proceedings of the
National Academy of Sciences, vol. 115, no. 20. National Academy of Sciences,
pp. E4720–E4729, 2018.
ista: Frost JM, Kim MY, Park GT, Hsieh P-H, Nakamura M, Lin SJH, Yoo H, Choi J,
Ikeda Y, Kinoshita T, Choi Y, Zilberman D, Fischer RL. 2018. FACT complex is required
for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings
of the National Academy of Sciences. 115(20), E4720–E4729.
mla: Frost, Jennifer M., et al. “FACT Complex Is Required for DNA Demethylation
at Heterochromatin during Reproduction in Arabidopsis.” Proceedings of the
National Academy of Sciences, vol. 115, no. 20, National Academy of Sciences,
2018, pp. E4720–29, doi:10.1073/pnas.1713333115.
short: J.M. Frost, M.Y. Kim, G.T. Park, P.-H. Hsieh, M. Nakamura, S.J.H. Lin, H.
Yoo, J. Choi, Y. Ikeda, T. Kinoshita, Y. Choi, D. Zilberman, R.L. Fischer, Proceedings
of the National Academy of Sciences 115 (2018) E4720–E4729.
date_created: 2021-06-07T06:11:28Z
date_published: 2018-05-15T00:00:00Z
date_updated: 2021-12-14T07:53:40Z
day: '15'
ddc:
- '580'
department:
- _id: DaZi
doi: 10.1073/pnas.1713333115
extern: '1'
external_id:
pmid:
- '29712855'
file:
- access_level: open_access
checksum: 810260dc0e3cc3033e15c19ad0dc123e
content_type: application/pdf
creator: asandaue
date_created: 2021-06-07T06:16:38Z
date_updated: 2021-06-07T06:16:38Z
file_id: '9472'
file_name: 2018_PNAS_Frost.pdf
file_size: 3045260
relation: main_file
success: 1
file_date_updated: 2021-06-07T06:16:38Z
has_accepted_license: '1'
intvolume: ' 115'
issue: '20'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: E4720-E4729
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'
related_material:
link:
- relation: earlier_version
url: 'https://doi.org/10.1101/187674 '
scopus_import: '1'
status: public
title: FACT complex is required for DNA demethylation at heterochromatin during reproduction
in Arabidopsis
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 115
year: '2018'
...
---
_id: '12607'
abstract:
- lang: eng
text: Supraglacial ice cliffs exist on debris-covered glaciers worldwide, but despite
their importance as melt hot spots, their life cycle is little understood. Early
field observations had advanced a hypothesis of survival of north-facing and disappearance
of south-facing cliffs, which is central for predicting the contribution of cliffs
to total glacier mass losses. Their role as windows of energy transfer suggests
they may explain the anomalously high mass losses of debris-covered glaciers in
High Mountain Asia (HMA) despite the insulating debris, currently at the center
of a debated controversy. We use a 3D model of cliff evolution coupled to very
high-resolution topographic data to demonstrate that ice cliffs facing south (in
the Northern Hemisphere) disappear within a few months due to enhanced solar radiation
receipts and that aspect is the key control on cliffs evolution. We reproduce
continuous flattening of south-facing cliffs, a result of their vertical gradient
of incoming solar radiation and sky view factor. Our results establish that only
north-facing cliffs are recurrent features and thus stable contributors to the
melting of debris-covered glaciers. Satellite observations and mass balance modeling
confirms that few south-facing cliffs of small size exist on the glaciers of Langtang,
and their contribution to the glacier volume losses is very small (∼1%). This
has major implications for the mass balance of HMA debris-covered glaciers as
it provides the basis for new parameterizations of cliff evolution and distribution
to constrain volume losses in a region where glaciers are highly relevant as water
sources for millions of people.
article_processing_charge: No
article_type: original
author:
- first_name: Pascal
full_name: Buri, Pascal
last_name: Buri
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
citation:
ama: Buri P, Pellicciotti F. Aspect controls the survival of ice cliffs on debris-covered
glaciers. PNAS. 2018;115(17):4369-4374. doi:10.1073/pnas.1713892115
apa: Buri, P., & Pellicciotti, F. (2018). Aspect controls the survival of ice
cliffs on debris-covered glaciers. PNAS. Proceedings of the National Academy
of Sciences. https://doi.org/10.1073/pnas.1713892115
chicago: Buri, Pascal, and Francesca Pellicciotti. “Aspect Controls the Survival
of Ice Cliffs on Debris-Covered Glaciers.” PNAS. Proceedings of the National
Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1713892115.
ieee: P. Buri and F. Pellicciotti, “Aspect controls the survival of ice cliffs on
debris-covered glaciers,” PNAS, vol. 115, no. 17. Proceedings of the National
Academy of Sciences, pp. 4369–4374, 2018.
ista: Buri P, Pellicciotti F. 2018. Aspect controls the survival of ice cliffs on
debris-covered glaciers. PNAS. 115(17), 4369–4374.
mla: Buri, Pascal, and Francesca Pellicciotti. “Aspect Controls the Survival of
Ice Cliffs on Debris-Covered Glaciers.” PNAS, vol. 115, no. 17, Proceedings
of the National Academy of Sciences, 2018, pp. 4369–74, doi:10.1073/pnas.1713892115.
short: P. Buri, F. Pellicciotti, PNAS 115 (2018) 4369–4374.
date_created: 2023-02-20T08:13:41Z
date_published: 2018-04-09T00:00:00Z
date_updated: 2023-02-28T11:35:18Z
day: '09'
doi: 10.1073/pnas.1713892115
extern: '1'
intvolume: ' 115'
issue: '17'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1713892115
month: '04'
oa: 1
oa_version: Published Version
page: 4369-4374
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: Aspect controls the survival of ice cliffs on debris-covered glaciers
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 115
year: '2018'
...
---
_id: '13376'
abstract:
- lang: eng
text: Efficient molecular switching in confined spaces is critical for the successful
development of artificial molecular machines. However, molecular switching events
often entail large structural changes and therefore require conformational freedom,
which is typically limited under confinement conditions. Here, we investigated
the behavior of azobenzene—the key building block of light-controlled molecular
machines—in a confined environment that is flexible and can adapt its shape to
that of the bound guest. To this end, we encapsulated several structurally diverse
azobenzenes within the cavity of a flexible, water-soluble coordination cage,
and investigated their light-responsive behavior. Using UV/Vis absorption spectroscopy
and a combination of NMR methods, we showed that each of the encapsulated azobenzenes
exhibited distinct switching properties. An azobenzene forming a 1:1 host–guest
inclusion complex could be efficiently photoisomerized in a reversible fashion.
In contrast, successful switching in inclusion complexes incorporating two azobenzene
guests was dependent on the availability of free cages in the system, and it involved
reversible trafficking of azobenzene between the cages. In the absence of extra
cages, photoswitching was either suppressed or it involved expulsion of azobenzene
from the cage and consequently its precipitation from the solution. This finding
was utilized to develop an information storage medium in which messages could
be written and erased in a reversible fashion using light.
article_processing_charge: No
article_type: original
author:
- first_name: Dipak
full_name: Samanta, Dipak
last_name: Samanta
- first_name: Julius
full_name: Gemen, Julius
last_name: Gemen
- first_name: Zonglin
full_name: Chu, Zonglin
last_name: Chu
- first_name: Yael
full_name: Diskin-Posner, Yael
last_name: Diskin-Posner
- first_name: Linda J. W.
full_name: Shimon, Linda J. W.
last_name: Shimon
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Samanta D, Gemen J, Chu Z, Diskin-Posner Y, Shimon LJW, Klajn R. Reversible
photoswitching of encapsulated azobenzenes in water. Proceedings of the National
Academy of Sciences. 2018;115(38):9379-9384. doi:10.1073/pnas.1712787115
apa: Samanta, D., Gemen, J., Chu, Z., Diskin-Posner, Y., Shimon, L. J. W., &
Klajn, R. (2018). Reversible photoswitching of encapsulated azobenzenes in water.
Proceedings of the National Academy of Sciences. Proceedings of the National
Academy of Sciences. https://doi.org/10.1073/pnas.1712787115
chicago: Samanta, Dipak, Julius Gemen, Zonglin Chu, Yael Diskin-Posner, Linda J.
W. Shimon, and Rafal Klajn. “Reversible Photoswitching of Encapsulated Azobenzenes
in Water.” Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1712787115.
ieee: D. Samanta, J. Gemen, Z. Chu, Y. Diskin-Posner, L. J. W. Shimon, and R. Klajn,
“Reversible photoswitching of encapsulated azobenzenes in water,” Proceedings
of the National Academy of Sciences, vol. 115, no. 38. Proceedings of the
National Academy of Sciences, pp. 9379–9384, 2018.
ista: Samanta D, Gemen J, Chu Z, Diskin-Posner Y, Shimon LJW, Klajn R. 2018. Reversible
photoswitching of encapsulated azobenzenes in water. Proceedings of the National
Academy of Sciences. 115(38), 9379–9384.
mla: Samanta, Dipak, et al. “Reversible Photoswitching of Encapsulated Azobenzenes
in Water.” Proceedings of the National Academy of Sciences, vol. 115, no.
38, Proceedings of the National Academy of Sciences, 2018, pp. 9379–84, doi:10.1073/pnas.1712787115.
short: D. Samanta, J. Gemen, Z. Chu, Y. Diskin-Posner, L.J.W. Shimon, R. Klajn,
Proceedings of the National Academy of Sciences 115 (2018) 9379–9384.
date_created: 2023-08-01T09:40:00Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-08-07T10:58:11Z
day: '01'
doi: 10.1073/pnas.1712787115
extern: '1'
external_id:
pmid:
- '29717041'
intvolume: ' 115'
issue: '38'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1712787115
month: '05'
oa: 1
oa_version: Published Version
page: 9379-9384
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: Reversible photoswitching of encapsulated azobenzenes in water
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 115
year: '2018'
...
---
_id: '6010'
abstract:
- lang: eng
text: The optic tectum (TeO), or superior colliculus, is a multisensory midbrain
center that organizes spatially orienting responses to relevant stimuli. To define
the stimulus with the highest priority at each moment, a network of reciprocal
connections between the TeO and the isthmi promotes competition between concurrent
tectal inputs. In the avian midbrain, the neurons mediating enhancement and suppression
of tectal inputs are located in separate isthmic nuclei, facilitating the analysis
of the neural processes that mediate competition. A specific subset of radial
neurons in the intermediate tectal layers relay retinal inputs to the isthmi,
but at present it is unclear whether separate neurons innervate individual nuclei
or a single neural type sends a common input to several of them. In this study,
we used in vitro neural tracing and cell-filling experiments in chickens to show
that single neurons innervate, via axon collaterals, the three nuclei that comprise
the isthmotectal network. This demonstrates that the input signals representing
the strength of the incoming stimuli are simultaneously relayed to the mechanisms
promoting both enhancement and suppression of the input signals. By performing
in vivo recordings in anesthetized chicks, we also show that this common input
generates synchrony between both antagonistic mechanisms, demonstrating that activity
enhancement and suppression are closely coordinated. From a computational point
of view, these results suggest that these tectal neurons constitute integrative
nodes that combine inputs from different sources to drive in parallel several
concurrent neural processes, each performing complementary functions within the
network through different firing patterns and connectivity.
article_processing_charge: No
author:
- first_name: Florencia
full_name: Garrido-Charad, Florencia
last_name: Garrido-Charad
- first_name: Tomas A
full_name: Vega Zuniga, Tomas A
id: 2E7C4E78-F248-11E8-B48F-1D18A9856A87
last_name: Vega Zuniga
- first_name: Cristián
full_name: Gutiérrez-Ibáñez, Cristián
last_name: Gutiérrez-Ibáñez
- first_name: Pedro
full_name: Fernandez, Pedro
last_name: Fernandez
- first_name: Luciana
full_name: López-Jury, Luciana
last_name: López-Jury
- first_name: Cristian
full_name: González-Cabrera, Cristian
last_name: González-Cabrera
- first_name: Harvey J.
full_name: Karten, Harvey J.
last_name: Karten
- first_name: Harald
full_name: Luksch, Harald
last_name: Luksch
- first_name: Gonzalo J.
full_name: Marín, Gonzalo J.
last_name: Marín
citation:
ama: Garrido-Charad F, Vega Zuniga TA, Gutiérrez-Ibáñez C, et al. “Shepherd’s crook”
neurons drive and synchronize the enhancing and suppressive mechanisms of the
midbrain stimulus selection network. Proceedings of the National Academy of
Sciences. 2018;115(32):E7615-E7623. doi:10.1073/pnas.1804517115
apa: Garrido-Charad, F., Vega Zuniga, T. A., Gutiérrez-Ibáñez, C., Fernandez, P.,
López-Jury, L., González-Cabrera, C., … Marín, G. J. (2018). “Shepherd’s crook”
neurons drive and synchronize the enhancing and suppressive mechanisms of the
midbrain stimulus selection network. Proceedings of the National Academy of
Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1804517115
chicago: Garrido-Charad, Florencia, Tomas A Vega Zuniga, Cristián Gutiérrez-Ibáñez,
Pedro Fernandez, Luciana López-Jury, Cristian González-Cabrera, Harvey J. Karten,
Harald Luksch, and Gonzalo J. Marín. ““Shepherd’s Crook” Neurons Drive and Synchronize
the Enhancing and Suppressive Mechanisms of the Midbrain Stimulus Selection Network.”
Proceedings of the National Academy of Sciences. National Academy of Sciences,
2018. https://doi.org/10.1073/pnas.1804517115.
ieee: F. Garrido-Charad et al., ““Shepherd’s crook” neurons drive and synchronize
the enhancing and suppressive mechanisms of the midbrain stimulus selection network,”
Proceedings of the National Academy of Sciences, vol. 115, no. 32. National
Academy of Sciences, pp. E7615–E7623, 2018.
ista: Garrido-Charad F, Vega Zuniga TA, Gutiérrez-Ibáñez C, Fernandez P, López-Jury
L, González-Cabrera C, Karten HJ, Luksch H, Marín GJ. 2018. “Shepherd’s crook”
neurons drive and synchronize the enhancing and suppressive mechanisms of the
midbrain stimulus selection network. Proceedings of the National Academy of Sciences.
115(32), E7615–E7623.
mla: Garrido-Charad, Florencia, et al. ““Shepherd’s Crook” Neurons Drive and Synchronize
the Enhancing and Suppressive Mechanisms of the Midbrain Stimulus Selection Network.”
Proceedings of the National Academy of Sciences, vol. 115, no. 32, National
Academy of Sciences, 2018, pp. E7615–23, doi:10.1073/pnas.1804517115.
short: F. Garrido-Charad, T.A. Vega Zuniga, C. Gutiérrez-Ibáñez, P. Fernandez, L.
López-Jury, C. González-Cabrera, H.J. Karten, H. Luksch, G.J. Marín, Proceedings
of the National Academy of Sciences 115 (2018) E7615–E7623.
date_created: 2019-02-14T14:33:34Z
date_published: 2018-08-07T00:00:00Z
date_updated: 2023-09-19T14:35:36Z
day: '07'
department:
- _id: MaJö
doi: 10.1073/pnas.1804517115
external_id:
isi:
- '000440982000020'
pmid:
- '30026198'
intvolume: ' 115'
isi: 1
issue: '32'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30026198
month: '08'
oa: 1
oa_version: Submitted Version
page: E7615-E7623
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: “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive
mechanisms of the midbrain stimulus selection network
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '10373'
abstract:
- lang: eng
text: 'Electric charges are conserved. The same would be expected to hold for magnetic
charges, yet magnetic monopoles have never been observed. It is therefore surprising
that the laws of nonequilibrium thermodynamics, combined with Maxwell’s equations,
suggest that colloidal particles heated or cooled in certain polar or paramagnetic
solvents may behave as if they carry an electric/magnetic charge. Here, we present
numerical simulations that show that the field distribution around a pair of such
heated/cooled colloidal particles agrees quantitatively with the theoretical predictions
for a pair of oppositely charged electric or magnetic monopoles. However, in other
respects, the nonequilibrium colloidal particles do not behave as monopoles: They
cannot be moved by a homogeneous applied field. The numerical evidence for the
monopole-like fields around heated/cooled colloidal particles is crucial because
the experimental and numerical determination of forces between such colloidal
particles would be complicated by the presence of other effects, such as thermophoresis.'
acknowledgement: P.W. acknowledges many invaluable discussions with Martin Neumann,
Chao Zhang, Michiel Sprik, Aleks Reinhardt, Carl Pölking, and Tine Curk. We acknowledge
financial support from the Austrian Academy of Sciences through a doctoral (DOC)
fellowship (to P.W.), the Austrian Science Fund (FWF) within the Spezialforschungsbereich
Vienna Computational Materials Laboratory (Project F41) (C.D.), and the European
Union Early Training Network NANOTRANS (Grant 674979 to D. Frenkel). The results
presented here have been achieved in part using the Vienna Scientific Cluster.
article_processing_charge: No
article_type: original
author:
- first_name: Peter
full_name: Wirnsberger, Peter
last_name: Wirnsberger
- first_name: Domagoj
full_name: Fijan, Domagoj
last_name: Fijan
- first_name: Roger A.
full_name: Lightwood, Roger A.
last_name: Lightwood
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Christoph
full_name: Dellago, Christoph
last_name: Dellago
- first_name: Daan
full_name: Frenkel, Daan
last_name: Frenkel
citation:
ama: Wirnsberger P, Fijan D, Lightwood RA, Šarić A, Dellago C, Frenkel D. Numerical
evidence for thermally induced monopoles. Proceedings of the National Academy
of Sciences. 2017;114(19):4911-4914. doi:10.1073/pnas.1621494114
apa: Wirnsberger, P., Fijan, D., Lightwood, R. A., Šarić, A., Dellago, C., &
Frenkel, D. (2017). Numerical evidence for thermally induced monopoles. Proceedings
of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1621494114
chicago: Wirnsberger, Peter, Domagoj Fijan, Roger A. Lightwood, Anđela Šarić, Christoph
Dellago, and Daan Frenkel. “Numerical Evidence for Thermally Induced Monopoles.”
Proceedings of the National Academy of Sciences. National Academy of Sciences,
2017. https://doi.org/10.1073/pnas.1621494114.
ieee: P. Wirnsberger, D. Fijan, R. A. Lightwood, A. Šarić, C. Dellago, and D. Frenkel,
“Numerical evidence for thermally induced monopoles,” Proceedings of the National
Academy of Sciences, vol. 114, no. 19. National Academy of Sciences, pp. 4911–4914,
2017.
ista: Wirnsberger P, Fijan D, Lightwood RA, Šarić A, Dellago C, Frenkel D. 2017.
Numerical evidence for thermally induced monopoles. Proceedings of the National
Academy of Sciences. 114(19), 4911–4914.
mla: Wirnsberger, Peter, et al. “Numerical Evidence for Thermally Induced Monopoles.”
Proceedings of the National Academy of Sciences, vol. 114, no. 19, National
Academy of Sciences, 2017, pp. 4911–14, doi:10.1073/pnas.1621494114.
short: P. Wirnsberger, D. Fijan, R.A. Lightwood, A. Šarić, C. Dellago, D. Frenkel,
Proceedings of the National Academy of Sciences 114 (2017) 4911–4914.
date_created: 2021-11-29T09:28:24Z
date_published: 2017-04-24T00:00:00Z
date_updated: 2021-11-29T09:59:12Z
day: '24'
doi: 10.1073/pnas.1621494114
extern: '1'
external_id:
arxiv:
- '1610.06840'
pmid:
- '28439003'
intvolume: ' 114'
issue: '19'
keyword:
- multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.pnas.org/content/114/19/4911
month: '04'
oa: 1
oa_version: Published Version
page: 4911-4914
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: Numerical evidence for thermally induced monopoles
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 114
year: '2017'
...
---
_id: '8018'
abstract:
- lang: eng
text: 'Nervous systems use excitatory cell assemblies to encode and represent sensory
percepts. Similarly, synaptically connected cell assemblies or "engrams" are thought
to represent memories of past experience. Multiple lines of recent evidence indicate
that brain systems create and use inhibitory replicas of excitatory representations
for important cognitive functions. Such matched "inhibitory engrams" can form
through homeostatic potentiation of inhibition onto postsynaptic cells that show
increased levels of excitation. Inhibitory engrams can reduce behavioral responses
to familiar stimuli, thereby resulting in behavioral habituation. In addition,
by preventing inappropriate activation of excitatory memory engrams, inhibitory
engrams can make memories quiescent, stored in a latent form that is available
for context-relevant activation. In neural networks with balanced excitatory and
inhibitory engrams, the release of innate responses and recall of associative
memories can occur through focused disinhibition. Understanding mechanisms that
regulate the formation and expression of inhibitory engrams in vivo may help not
only to explain key features of cognition but also to provide insight into transdiagnostic
traits associated with psychiatric conditions such as autism, schizophrenia, and
posttraumatic stress disorder. '
article_processing_charge: No
article_type: original
author:
- first_name: Helen C.
full_name: Barron, Helen C.
last_name: Barron
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Timothy E.
full_name: Behrens, Timothy E.
last_name: Behrens
- first_name: Mani
full_name: Ramaswami, Mani
last_name: Ramaswami
citation:
ama: Barron HC, Vogels TP, Behrens TE, Ramaswami M. Inhibitory engrams in perception
and memory. Proceedings of the National Academy of Sciences. 2017;114(26):6666-6674.
doi:10.1073/pnas.1701812114
apa: Barron, H. C., Vogels, T. P., Behrens, T. E., & Ramaswami, M. (2017). Inhibitory
engrams in perception and memory. Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1701812114
chicago: Barron, Helen C., Tim P Vogels, Timothy E. Behrens, and Mani Ramaswami.
“Inhibitory Engrams in Perception and Memory.” Proceedings of the National
Academy of Sciences. Proceedings of the National Academy of Sciences, 2017.
https://doi.org/10.1073/pnas.1701812114.
ieee: H. C. Barron, T. P. Vogels, T. E. Behrens, and M. Ramaswami, “Inhibitory engrams
in perception and memory,” Proceedings of the National Academy of Sciences,
vol. 114, no. 26. Proceedings of the National Academy of Sciences, pp. 6666–6674,
2017.
ista: Barron HC, Vogels TP, Behrens TE, Ramaswami M. 2017. Inhibitory engrams in
perception and memory. Proceedings of the National Academy of Sciences. 114(26),
6666–6674.
mla: Barron, Helen C., et al. “Inhibitory Engrams in Perception and Memory.” Proceedings
of the National Academy of Sciences, vol. 114, no. 26, Proceedings of the
National Academy of Sciences, 2017, pp. 6666–74, doi:10.1073/pnas.1701812114.
short: H.C. Barron, T.P. Vogels, T.E. Behrens, M. Ramaswami, Proceedings of the
National Academy of Sciences 114 (2017) 6666–6674.
date_created: 2020-06-25T12:56:58Z
date_published: 2017-06-27T00:00:00Z
date_updated: 2021-01-12T08:16:33Z
day: '27'
doi: 10.1073/pnas.1701812114
extern: '1'
external_id:
pmid:
- '28611219'
intvolume: ' 114'
issue: '26'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5495250/
month: '06'
oa: 1
oa_version: Published Version
page: 6666-6674
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'
status: public
title: Inhibitory engrams in perception and memory
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 114
year: '2017'
...
---
_id: '15157'
abstract:
- lang: eng
text: The basic helix–loop–helix PAS domain (bHLH-PAS) transcription factor CLOCK:BMAL1
(brain and muscle Arnt-like protein 1) sits at the core of the mammalian circadian
transcription/translation feedback loop. Precise control of CLOCK:BMAL1 activity
by coactivators and repressors establishes the ∼24-h periodicity of gene expression.
Formation of a repressive complex, defined by the core clock proteins cryptochrome
1 (CRY1):CLOCK:BMAL1, plays an important role controlling the switch from repression
to activation each day. Here we show that CRY1 binds directly to the PAS domain
core of CLOCK:BMAL1, driven primarily by interaction with the CLOCK PAS-B domain.
Integrative modeling and solution X-ray scattering studies unambiguously position
a key loop of the CLOCK PAS-B domain in the secondary pocket of CRY1, analogous
to the antenna chromophore-binding pocket of photolyase. CRY1 docks onto the transcription
factor alongside the PAS domains, extending above the DNA-binding bHLH domain.
Single point mutations at the interface on either CRY1 or CLOCK disrupt formation
of the ternary complex, highlighting the importance of this interface for direct
regulation of CLOCK:BMAL1 activity by CRY1.
article_processing_charge: No
article_type: original
author:
- first_name: Alicia Kathleen
full_name: Michael, Alicia Kathleen
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
- first_name: Jennifer L.
full_name: Fribourgh, Jennifer L.
last_name: Fribourgh
- first_name: Yogarany
full_name: Chelliah, Yogarany
last_name: Chelliah
- first_name: Colby R.
full_name: Sandate, Colby R.
last_name: Sandate
- first_name: Greg L.
full_name: Hura, Greg L.
last_name: Hura
- first_name: Dina
full_name: Schneidman-Duhovny, Dina
last_name: Schneidman-Duhovny
- first_name: Sarvind M.
full_name: Tripathi, Sarvind M.
last_name: Tripathi
- first_name: Joseph S.
full_name: Takahashi, Joseph S.
last_name: Takahashi
- first_name: Carrie L.
full_name: Partch, Carrie L.
last_name: Partch
citation:
ama: Michael AK, Fribourgh JL, Chelliah Y, et al. Formation of a repressive complex
in the mammalian circadian clock is mediated by the secondary pocket of CRY1.
Proceedings of the National Academy of Sciences. 2017;114(7):1560-1565.
doi:10.1073/pnas.1615310114
apa: Michael, A. K., Fribourgh, J. L., Chelliah, Y., Sandate, C. R., Hura, G. L.,
Schneidman-Duhovny, D., … Partch, C. L. (2017). Formation of a repressive complex
in the mammalian circadian clock is mediated by the secondary pocket of CRY1.
Proceedings of the National Academy of Sciences. Proceedings of the National
Academy of Sciences. https://doi.org/10.1073/pnas.1615310114
chicago: Michael, Alicia K., Jennifer L. Fribourgh, Yogarany Chelliah, Colby R.
Sandate, Greg L. Hura, Dina Schneidman-Duhovny, Sarvind M. Tripathi, Joseph S.
Takahashi, and Carrie L. Partch. “Formation of a Repressive Complex in the Mammalian
Circadian Clock Is Mediated by the Secondary Pocket of CRY1.” Proceedings of
the National Academy of Sciences. Proceedings of the National Academy of Sciences,
2017. https://doi.org/10.1073/pnas.1615310114.
ieee: A. K. Michael et al., “Formation of a repressive complex in the mammalian
circadian clock is mediated by the secondary pocket of CRY1,” Proceedings of
the National Academy of Sciences, vol. 114, no. 7. Proceedings of the National
Academy of Sciences, pp. 1560–1565, 2017.
ista: Michael AK, Fribourgh JL, Chelliah Y, Sandate CR, Hura GL, Schneidman-Duhovny
D, Tripathi SM, Takahashi JS, Partch CL. 2017. Formation of a repressive complex
in the mammalian circadian clock is mediated by the secondary pocket of CRY1.
Proceedings of the National Academy of Sciences. 114(7), 1560–1565.
mla: Michael, Alicia K., et al. “Formation of a Repressive Complex in the Mammalian
Circadian Clock Is Mediated by the Secondary Pocket of CRY1.” Proceedings of
the National Academy of Sciences, vol. 114, no. 7, Proceedings of the National
Academy of Sciences, 2017, pp. 1560–65, doi:10.1073/pnas.1615310114.
short: A.K. Michael, J.L. Fribourgh, Y. Chelliah, C.R. Sandate, G.L. Hura, D. Schneidman-Duhovny,
S.M. Tripathi, J.S. Takahashi, C.L. Partch, Proceedings of the National Academy
of Sciences 114 (2017) 1560–1565.
date_created: 2024-03-21T07:56:50Z
date_published: 2017-01-31T00:00:00Z
date_updated: 2024-03-25T12:12:23Z
day: '31'
doi: 10.1073/pnas.1615310114
extern: '1'
external_id:
pmid:
- '28143926'
intvolume: ' 114'
issue: '7'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1615310114
month: '01'
oa: 1
oa_version: Published Version
page: 1560-1565
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: Formation of a repressive complex in the mammalian circadian clock is mediated
by the secondary pocket of CRY1
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '12618'
abstract:
- lang: eng
text: Mountain ranges are the world’s natural water towers and provide water resources
for millions of people. However, their hydrological balance and possible future
changes in river flow remain poorly understood because of high meteorological
variability, physical inaccessibility, and the complex interplay between climate,
cryosphere, and hydrological processes. Here, we use a state-of-the art glacio-hydrological
model informed by data from high-altitude observations and the latest climate
change scenarios to quantify the climate change impact on water resources of two
contrasting catchments vulnerable to changes in the cryosphere. The two study
catchments are located in the Central Andes of Chile and in the Nepalese Himalaya
in close vicinity of densely populated areas. Although both sites reveal a strong
decrease in glacier area, they show a remarkably different hydrological response
to projected climate change. In the Juncal catchment in Chile, runoff is likely
to sharply decrease in the future and the runoff seasonality is sensitive to projected
climatic changes. In the Langtang catchment in Nepal, future water availability
is on the rise for decades to come with limited shifts between seasons. Owing
to the high spatiotemporal resolution of the simulations and process complexity
included in the modeling, the response times and the mechanisms underlying the
variations in glacier area and river flow can be well constrained. The projections
indicate that climate change adaptation in Central Chile should focus on dealing
with a reduction in water availability, whereas in Nepal preparedness for flood
extremes should be the policy priority.
article_processing_charge: No
article_type: original
author:
- first_name: Silvan
full_name: Ragettli, Silvan
last_name: Ragettli
- first_name: Walter W.
full_name: Immerzeel, Walter W.
last_name: Immerzeel
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
citation:
ama: Ragettli S, Immerzeel WW, Pellicciotti F. Contrasting climate change impact
on river flows from high-altitude catchments in the Himalayan and Andes Mountains.
PNAS. 2016;113(33):9222-9227. doi:10.1073/pnas.1606526113
apa: Ragettli, S., Immerzeel, W. W., & Pellicciotti, F. (2016). Contrasting
climate change impact on river flows from high-altitude catchments in the Himalayan
and Andes Mountains. PNAS. Proceedings of the National Academy of Sciences.
https://doi.org/10.1073/pnas.1606526113
chicago: Ragettli, Silvan, Walter W. Immerzeel, and Francesca Pellicciotti. “Contrasting
Climate Change Impact on River Flows from High-Altitude Catchments in the Himalayan
and Andes Mountains.” PNAS. Proceedings of the National Academy of Sciences,
2016. https://doi.org/10.1073/pnas.1606526113.
ieee: S. Ragettli, W. W. Immerzeel, and F. Pellicciotti, “Contrasting climate change
impact on river flows from high-altitude catchments in the Himalayan and Andes
Mountains,” PNAS, vol. 113, no. 33. Proceedings of the National Academy
of Sciences, pp. 9222–9227, 2016.
ista: Ragettli S, Immerzeel WW, Pellicciotti F. 2016. Contrasting climate change
impact on river flows from high-altitude catchments in the Himalayan and Andes
Mountains. PNAS. 113(33), 9222–9227.
mla: Ragettli, Silvan, et al. “Contrasting Climate Change Impact on River Flows
from High-Altitude Catchments in the Himalayan and Andes Mountains.” PNAS,
vol. 113, no. 33, Proceedings of the National Academy of Sciences, 2016, pp. 9222–27,
doi:10.1073/pnas.1606526113.
short: S. Ragettli, W.W. Immerzeel, F. Pellicciotti, PNAS 113 (2016) 9222–9227.
date_created: 2023-02-20T08:14:58Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2023-02-24T10:48:43Z
day: '01'
doi: 10.1073/pnas.1606526113
extern: '1'
external_id:
pmid:
- '27482082'
intvolume: ' 113'
issue: '33'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1606526113
month: '08'
oa: 1
oa_version: Published Version
page: 9222-9227
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: Contrasting climate change impact on river flows from high-altitude catchments
in the Himalayan and Andes Mountains
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '9477'
abstract:
- lang: eng
text: Cytosine methylation is a DNA modification with important regulatory functions
in eukaryotes. In flowering plants, sexual reproduction is accompanied by extensive
DNA demethylation, which is required for proper gene expression in the endosperm,
a nutritive extraembryonic seed tissue. Endosperm arises from a fusion of a sperm
cell carried in the pollen and a female central cell. Endosperm DNA demethylation
is observed specifically on the chromosomes inherited from the central cell in
Arabidopsis thaliana, rice, and maize, and requires the DEMETER DNA demethylase
in Arabidopsis. DEMETER is expressed in the central cell before fertilization,
suggesting that endosperm demethylation patterns are inherited from the central
cell. Down-regulation of the MET1 DNA methyltransferase has also been proposed
to contribute to central cell demethylation. However, with the exception of three
maize genes, central cell DNA methylation has not been directly measured, leaving
the origin and mechanism of endosperm demethylation uncertain. Here, we report
genome-wide analysis of DNA methylation in the central cells of Arabidopsis and
rice—species that diverged 150 million years ago—as well as in rice egg cells.
We find that DNA demethylation in both species is initiated in central cells,
which requires DEMETER in Arabidopsis. However, we do not observe a global reduction
of CG methylation that would be indicative of lowered MET1 activity; on the contrary,
CG methylation efficiency is elevated in female gametes compared with nonsexual
tissues. Our results demonstrate that locus-specific, active DNA demethylation
in the central cell is the origin of maternal chromosome hypomethylation in the
endosperm.
article_processing_charge: No
article_type: original
author:
- first_name: Kyunghyuk
full_name: Park, Kyunghyuk
last_name: Park
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: Jin-Sup
full_name: Park, Jin-Sup
last_name: Park
- first_name: Youbong
full_name: Hyun, Youbong
last_name: Hyun
- first_name: Takashi
full_name: Okamoto, Takashi
last_name: Okamoto
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Yeonhee
full_name: Choi, Yeonhee
last_name: Choi
- first_name: Stefan
full_name: Scholten, Stefan
last_name: Scholten
citation:
ama: Park K, Kim MY, Vickers M, et al. DNA demethylation is initiated in the central
cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences.
2016;113(52):15138-15143. doi:10.1073/pnas.1619047114
apa: Park, K., Kim, M. Y., Vickers, M., Park, J.-S., Hyun, Y., Okamoto, T., … Scholten,
S. (2016). DNA demethylation is initiated in the central cells of Arabidopsis
and rice. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.1619047114
chicago: Park, Kyunghyuk, M. Yvonne Kim, Martin Vickers, Jin-Sup Park, Youbong Hyun,
Takashi Okamoto, Daniel Zilberman, et al. “DNA Demethylation Is Initiated in the
Central Cells of Arabidopsis and Rice.” Proceedings of the National Academy
of Sciences. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1619047114.
ieee: K. Park et al., “DNA demethylation is initiated in the central cells
of Arabidopsis and rice,” Proceedings of the National Academy of Sciences,
vol. 113, no. 52. National Academy of Sciences, pp. 15138–15143, 2016.
ista: Park K, Kim MY, Vickers M, Park J-S, Hyun Y, Okamoto T, Zilberman D, Fischer
RL, Feng X, Choi Y, Scholten S. 2016. DNA demethylation is initiated in the central
cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences.
113(52), 15138–15143.
mla: Park, Kyunghyuk, et al. “DNA Demethylation Is Initiated in the Central Cells
of Arabidopsis and Rice.” Proceedings of the National Academy of Sciences,
vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15138–43, doi:10.1073/pnas.1619047114.
short: K. Park, M.Y. Kim, M. Vickers, J.-S. Park, Y. Hyun, T. Okamoto, D. Zilberman,
R.L. Fischer, X. Feng, Y. Choi, S. Scholten, Proceedings of the National Academy
of Sciences 113 (2016) 15138–15143.
date_created: 2021-06-07T07:10:59Z
date_published: 2016-12-27T00:00:00Z
date_updated: 2023-05-08T11:00:07Z
day: '27'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1073/pnas.1619047114
extern: '1'
external_id:
pmid:
- '27956642'
intvolume: ' 113'
issue: '52'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1619047114
month: '12'
oa: 1
oa_version: Published Version
page: 15138-15143
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: DNA demethylation is initiated in the central cells of Arabidopsis and rice
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '9473'
abstract:
- lang: eng
text: Cytosine DNA methylation regulates the expression of eukaryotic genes and
transposons. Methylation is copied by methyltransferases after DNA replication,
which results in faithful transmission of methylation patterns during cell division
and, at least in flowering plants, across generations. Transgenerational inheritance
is mediated by a small group of cells that includes gametes and their progenitors.
However, methylation is usually analyzed in somatic tissues that do not contribute
to the next generation, and the mechanisms of transgenerational inheritance are
inferred from such studies. To gain a better understanding of how DNA methylation
is inherited, we analyzed purified Arabidopsis thaliana sperm and vegetative cells-the
cell types that comprise pollen-with mutations in the DRM, CMT2, and CMT3 methyltransferases.
We find that DNA methylation dependency on these enzymes is similar in sperm,
vegetative cells, and somatic tissues, although DRM activity extends into heterochromatin
in vegetative cells, likely reflecting transcription of heterochromatic transposons
in this cell type. We also show that lack of histone H1, which elevates heterochromatic
DNA methylation in somatic tissues, does not have this effect in pollen. Instead,
levels of CG methylation in wild-type sperm and vegetative cells, as well as in
wild-type microspores from which both pollen cell types originate, are substantially
higher than in wild-type somatic tissues and similar to those of H1-depleted roots.
Our results demonstrate that the mechanisms of methylation maintenance are similar
between pollen and somatic cells, but the efficiency of CG methylation is higher
in pollen, allowing methylation patterns to be accurately inherited across generations.
article_processing_charge: No
article_type: original
author:
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Toby
full_name: Buttress, Toby
last_name: Buttress
- first_name: Hongbo
full_name: Gao, Hongbo
last_name: Gao
- first_name: Matthew
full_name: Couchman, Matthew
last_name: Couchman
- 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
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: Hsieh P-H, He S, Buttress T, et al. Arabidopsis male sexual lineage exhibits
more robust maintenance of CG methylation than somatic tissues. Proceedings
of the National Academy of Sciences. 2016;113(52):15132-15137. doi:10.1073/pnas.1619074114
apa: Hsieh, P.-H., He, S., Buttress, T., Gao, H., Couchman, M., Fischer, R. L.,
… Feng, X. (2016). Arabidopsis male sexual lineage exhibits more robust maintenance
of CG methylation than somatic tissues. Proceedings of the National Academy
of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1619074114
chicago: Hsieh, Ping-Hung, Shengbo He, Toby Buttress, Hongbo Gao, Matthew Couchman,
Robert L. Fischer, Daniel Zilberman, and Xiaoqi Feng. “Arabidopsis Male Sexual
Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.”
Proceedings of the National Academy of Sciences. National Academy of Sciences,
2016. https://doi.org/10.1073/pnas.1619074114.
ieee: P.-H. Hsieh et al., “Arabidopsis male sexual lineage exhibits more
robust maintenance of CG methylation than somatic tissues,” Proceedings of
the National Academy of Sciences, vol. 113, no. 52. National Academy of Sciences,
pp. 15132–15137, 2016.
ista: Hsieh P-H, He S, Buttress T, Gao H, Couchman M, Fischer RL, Zilberman D, Feng
X. 2016. Arabidopsis male sexual lineage exhibits more robust maintenance of CG
methylation than somatic tissues. Proceedings of the National Academy of Sciences.
113(52), 15132–15137.
mla: Hsieh, Ping-Hung, et al. “Arabidopsis Male Sexual Lineage Exhibits More Robust
Maintenance of CG Methylation than Somatic Tissues.” Proceedings of the National
Academy of Sciences, vol. 113, no. 52, National Academy of Sciences, 2016,
pp. 15132–37, doi:10.1073/pnas.1619074114.
short: P.-H. Hsieh, S. He, T. Buttress, H. Gao, M. Couchman, R.L. Fischer, D. Zilberman,
X. Feng, Proceedings of the National Academy of Sciences 113 (2016) 15132–15137.
date_created: 2021-06-07T06:21:39Z
date_published: 2016-12-27T00:00:00Z
date_updated: 2023-05-08T11:00:40Z
day: '27'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1073/pnas.1619074114
extern: '1'
external_id:
pmid:
- '27956643'
intvolume: ' 113'
issue: '52'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1619074114
month: '12'
oa: 1
oa_version: Published Version
page: 15132-15137
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: Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation
than somatic tissues
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '14304'
abstract:
- lang: eng
text: Despite the recent rapid progress in cryo-electron microscopy (cryo-EM), there
still exist ample opportunities for improvement in sample preparation. Macromolecular
complexes may disassociate or adopt nonrandom orientations against the extended
air–water interface that exists for a short time before the sample is frozen.
We designed a hollow support structure using 3D DNA origami to protect complexes
from the detrimental effects of cryo-EM sample preparation. For a first proof-of-principle,
we concentrated on the transcription factor p53, which binds to specific DNA sequences
on double-stranded DNA. The support structures spontaneously form monolayers of
preoriented particles in a thin film of water, and offer advantages in particle
picking and sorting. By controlling the position of the binding sequence on a
single helix that spans the hollow support structure, we also sought to control
the orientation of individual p53 complexes. Although the latter did not yet yield
the desired results, the support structures did provide partial information about
the relative orientations of individual p53 complexes. We used this information
to calculate a tomographic 3D reconstruction, and refined this structure to a
final resolution of ∼15 Å. This structure settles an ongoing debate about the
symmetry of the p53 tetramer bound to DNA.
article_processing_charge: No
article_type: original
author:
- first_name: Thomas G.
full_name: Martin, Thomas G.
last_name: Martin
- first_name: Tanmay A. M.
full_name: Bharat, Tanmay A. M.
last_name: Bharat
- first_name: Andreas C.
full_name: Joerger, Andreas C.
last_name: Joerger
- first_name: Xiao-chen
full_name: Bai, Xiao-chen
last_name: Bai
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Alan R.
full_name: Fersht, Alan R.
last_name: Fersht
- first_name: Hendrik
full_name: Dietz, Hendrik
last_name: Dietz
- first_name: Sjors H. W.
full_name: Scheres, Sjors H. W.
last_name: Scheres
citation:
ama: Martin TG, Bharat TAM, Joerger AC, et al. Design of a molecular support for
cryo-EM structure determination. PNAS. 2016;113(47):E7456-E7463. doi:10.1073/pnas.1612720113
apa: Martin, T. G., Bharat, T. A. M., Joerger, A. C., Bai, X., Praetorius, F. M.,
Fersht, A. R., … Scheres, S. H. W. (2016). Design of a molecular support for cryo-EM
structure determination. PNAS. Proceedings of the National Academy of Sciences.
https://doi.org/10.1073/pnas.1612720113
chicago: Martin, Thomas G., Tanmay A. M. Bharat, Andreas C. Joerger, Xiao-chen Bai,
Florian M Praetorius, Alan R. Fersht, Hendrik Dietz, and Sjors H. W. Scheres.
“Design of a Molecular Support for Cryo-EM Structure Determination.” PNAS.
Proceedings of the National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1612720113.
ieee: T. G. Martin et al., “Design of a molecular support for cryo-EM structure
determination,” PNAS, vol. 113, no. 47. Proceedings of the National Academy
of Sciences, pp. E7456–E7463, 2016.
ista: Martin TG, Bharat TAM, Joerger AC, Bai X, Praetorius FM, Fersht AR, Dietz
H, Scheres SHW. 2016. Design of a molecular support for cryo-EM structure determination.
PNAS. 113(47), E7456–E7463.
mla: Martin, Thomas G., et al. “Design of a Molecular Support for Cryo-EM Structure
Determination.” PNAS, vol. 113, no. 47, Proceedings of the National Academy
of Sciences, 2016, pp. E7456–63, doi:10.1073/pnas.1612720113.
short: T.G. Martin, T.A.M. Bharat, A.C. Joerger, X. Bai, F.M. Praetorius, A.R. Fersht,
H. Dietz, S.H.W. Scheres, PNAS 113 (2016) E7456–E7463.
date_created: 2023-09-06T12:53:48Z
date_published: 2016-10-13T00:00:00Z
date_updated: 2023-11-07T11:53:06Z
day: '13'
doi: 10.1073/pnas.1612720113
extern: '1'
external_id:
pmid:
- '27821763'
intvolume: ' 113'
issue: '47'
language:
- iso: eng
month: '10'
oa_version: Published Version
page: E7456-E7463
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: Design of a molecular support for cryo-EM structure determination
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '10382'
abstract:
- lang: eng
text: 'Protein oligomers have been implicated as toxic agents in a wide range of
amyloid-related diseases. However, it has remained unsolved whether the oligomers
are a necessary step in the formation of amyloid fibrils or just a dangerous byproduct.
Analogously, it has not been resolved if the amyloid nucleation process is a classical
one-step nucleation process or a two-step process involving prenucleation clusters.
We use coarse-grained computer simulations to study the effect of nonspecific
attractions between peptides on the primary nucleation process underlying amyloid
fibrillization. We find that, for peptides that do not attract, the classical
one-step nucleation mechanism is possible but only at nonphysiologically high
peptide concentrations. At low peptide concentrations, which mimic the physiologically
relevant regime, attractive interpeptide interactions are essential for fibril
formation. Nucleation then inevitably takes place through a two-step mechanism
involving prefibrillar oligomers. We show that oligomers not only help peptides
meet each other but also, create an environment that facilitates the conversion
of monomers into the β-sheet–rich form characteristic of fibrils. Nucleation typically
does not proceed through the most prevalent oligomers but through an oligomer
size that is only observed in rare fluctuations, which is why such aggregates
might be hard to capture experimentally. Finally, we find that the nucleation
of amyloid fibrils cannot be described by classical nucleation theory: in the
two-step mechanism, the critical nucleus size increases with increases in both
concentration and interpeptide interactions, which is in direct contrast with
predictions from classical nucleation theory.'
acknowledgement: We thank Michele Vendruscolo, Iskra Staneva, and William M. Jacobs,
for helpful discussions. A.Š. acknowledges support from the Human Frontier Science
Program and Emmanuel College. Y.C.C. and D.F. are supported by Engineering and Physical
Sciences Research Council Programme Grant EP/I001352/1. T.P.J.K. acknowledges the
Frances and Augustus Newman Foundation, the European Research Council, and the Biotechnology
and Biological Sciences Research Council. D.F. acknowledges European Research Council
Advanced Grant 227758.
article_processing_charge: No
article_type: original
author:
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Yassmine C.
full_name: Chebaro, Yassmine C.
last_name: Chebaro
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
- first_name: Daan
full_name: Frenkel, Daan
last_name: Frenkel
citation:
ama: Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. Crucial role of nonspecific interactions
in amyloid nucleation. Proceedings of the National Academy of Sciences.
2014;111(50):17869-17874. doi:10.1073/pnas.1410159111
apa: Šarić, A., Chebaro, Y. C., Knowles, T. P. J., & Frenkel, D. (2014). Crucial
role of nonspecific interactions in amyloid nucleation. Proceedings of the
National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1410159111
chicago: Šarić, Anđela, Yassmine C. Chebaro, Tuomas P. J. Knowles, and Daan Frenkel.
“Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1410159111.
ieee: A. Šarić, Y. C. Chebaro, T. P. J. Knowles, and D. Frenkel, “Crucial role of
nonspecific interactions in amyloid nucleation,” Proceedings of the National
Academy of Sciences, vol. 111, no. 50. National Academy of Sciences, pp. 17869–17874,
2014.
ista: Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. 2014. Crucial role of nonspecific
interactions in amyloid nucleation. Proceedings of the National Academy of Sciences.
111(50), 17869–17874.
mla: Šarić, Anđela, et al. “Crucial Role of Nonspecific Interactions in Amyloid
Nucleation.” Proceedings of the National Academy of Sciences, vol. 111,
no. 50, National Academy of Sciences, 2014, pp. 17869–74, doi:10.1073/pnas.1410159111.
short: A. Šarić, Y.C. Chebaro, T.P.J. Knowles, D. Frenkel, Proceedings of the National
Academy of Sciences 111 (2014) 17869–17874.
date_created: 2021-11-29T13:09:53Z
date_published: 2014-12-01T00:00:00Z
date_updated: 2021-11-29T13:29:05Z
day: '01'
doi: 10.1073/pnas.1410159111
extern: '1'
external_id:
arxiv:
- '1412.0897'
pmid:
- '25453085'
intvolume: ' 111'
issue: '50'
keyword:
- multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.pnas.org/content/111/50/17869
month: '12'
oa: 1
oa_version: Published Version
page: 17869-17874
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: Crucial role of nonspecific interactions in amyloid nucleation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 111
year: '2014'
...
---
_id: '8021'
abstract:
- lang: eng
text: 'Most excitatory inputs in the mammalian brain are made on dendritic spines,
rather than on dendritic shafts. Spines compartmentalize calcium, and this biochemical
isolation can underlie input-specific synaptic plasticity, providing a raison
d''etre for spines. However, recent results indicate that the spine can experience
a membrane potential different from that in the parent dendrite, as though the
spine neck electrically isolated the spine. Here we use two-photon calcium imaging
of mouse neocortical pyramidal neurons to analyze the correlation between the
morphologies of spines activated under minimal synaptic stimulation and the excitatory
postsynaptic potentials they generate. We find that excitatory postsynaptic potential
amplitudes are inversely correlated with spine neck lengths. Furthermore, a spike
timing-dependent plasticity protocol, in which two-photon glutamate uncaging over
a spine is paired with postsynaptic spikes, produces rapid shrinkage of the spine
neck and concomitant increases in the amplitude of the evoked spine potentials.
Using numerical simulations, we explore the parameter regimes for the spine neck
resistance and synaptic conductance changes necessary to explain our observations.
Our data, directly correlating synaptic and morphological plasticity, imply that
long-necked spines have small or negligible somatic voltage contributions, but
that, upon synaptic stimulation paired with postsynaptic activity, they can shorten
their necks and increase synaptic efficacy, thus changing the input/output gain
of pyramidal neurons. '
article_processing_charge: No
article_type: original
author:
- first_name: R.
full_name: Araya, R.
last_name: Araya
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: R.
full_name: Yuste, R.
last_name: Yuste
citation:
ama: Araya R, Vogels TP, Yuste R. Activity-dependent dendritic spine neck changes
are correlated with synaptic strength. Proceedings of the National Academy
of Sciences. 2014;111(28):E2895-E2904. doi:10.1073/pnas.1321869111
apa: Araya, R., Vogels, T. P., & Yuste, R. (2014). Activity-dependent dendritic
spine neck changes are correlated with synaptic strength. Proceedings of the
National Academy of Sciences. Proceedings of the National Academy of Sciences.
https://doi.org/10.1073/pnas.1321869111
chicago: Araya, R., Tim P Vogels, and R. Yuste. “Activity-Dependent Dendritic Spine
Neck Changes Are Correlated with Synaptic Strength.” Proceedings of the National
Academy of Sciences. Proceedings of the National Academy of Sciences, 2014.
https://doi.org/10.1073/pnas.1321869111.
ieee: R. Araya, T. P. Vogels, and R. Yuste, “Activity-dependent dendritic spine
neck changes are correlated with synaptic strength,” Proceedings of the National
Academy of Sciences, vol. 111, no. 28. Proceedings of the National Academy
of Sciences, pp. E2895–E2904, 2014.
ista: Araya R, Vogels TP, Yuste R. 2014. Activity-dependent dendritic spine neck
changes are correlated with synaptic strength. Proceedings of the National Academy
of Sciences. 111(28), E2895–E2904.
mla: Araya, R., et al. “Activity-Dependent Dendritic Spine Neck Changes Are Correlated
with Synaptic Strength.” Proceedings of the National Academy of Sciences,
vol. 111, no. 28, Proceedings of the National Academy of Sciences, 2014, pp. E2895–904,
doi:10.1073/pnas.1321869111.
short: R. Araya, T.P. Vogels, R. Yuste, Proceedings of the National Academy of Sciences
111 (2014) E2895–E2904.
date_created: 2020-06-25T13:06:24Z
date_published: 2014-07-15T00:00:00Z
date_updated: 2021-01-12T08:16:34Z
day: '15'
doi: 10.1073/pnas.1321869111
extern: '1'
external_id:
pmid:
- '24982196'
intvolume: ' 111'
issue: '28'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104910/
month: '07'
oa: 1
oa_version: Published Version
page: E2895-E2904
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'
status: public
title: Activity-dependent dendritic spine neck changes are correlated with synaptic
strength
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 111
year: '2014'
...
---
_id: '9479'
abstract:
- lang: eng
text: Centromeres mediate chromosome segregation and are defined by the centromere-specific
histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from
centromeres is a general property of terminally differentiated cells, and the
persistence of CenH3 increases the risk of diseases such as cancer. However, active
mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen
vegetative cells, which transport engulfed sperm by extended tip growth, undergo
loss of CenH3; centromeric heterochromatin decondensation; and bulk activation
of silent rRNA genes, accompanied by their translocation into the nucleolus. Here,
we show that these processes are blocked by mutations in the evolutionarily conserved
AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97
proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier
(SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates
with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as
well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations.
In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are
uniquely clustered together within the nucleolus and all major rRNA gene variants,
including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant
vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed
centromeric heterochromatin at the external periphery of the nucleolus. Our results
indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres
and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus
for ribosome production, which fuels single nucleus-driven pollen tube growth
and is essential for plant reproduction.
article_processing_charge: No
article_type: original
author:
- first_name: Zsuzsanna
full_name: Mérai, Zsuzsanna
last_name: Mérai
- first_name: Nina
full_name: Chumak, Nina
last_name: Chumak
- first_name: Marcelina
full_name: García-Aguilar, Marcelina
last_name: García-Aguilar
- first_name: Tzung-Fu
full_name: Hsieh, Tzung-Fu
last_name: Hsieh
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Vera K.
full_name: Schoft, Vera K.
last_name: Schoft
- first_name: János
full_name: Bindics, János
last_name: Bindics
- first_name: Lucyna
full_name: Ślusarz, Lucyna
last_name: Ślusarz
- first_name: Stéphanie
full_name: Arnoux, Stéphanie
last_name: Arnoux
- first_name: Susanne
full_name: Opravil, Susanne
last_name: Opravil
- first_name: Karl
full_name: Mechtler, Karl
last_name: Mechtler
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Hisashi
full_name: Tamaru, Hisashi
last_name: Tamaru
citation:
ama: Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone
Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and
activates ribosomal RNA genes. Proceedings of the National Academy of Sciences.
2014;111(45):16166-16171. doi:10.1073/pnas.1418564111
apa: Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft,
V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles
sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA
genes. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.1418564111
chicago: Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh,
Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular
Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin,
and Activates Ribosomal RNA Genes.” Proceedings of the National Academy of
Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1418564111.
ieee: Z. Mérai et al., “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles
sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA
genes,” Proceedings of the National Academy of Sciences, vol. 111, no.
45. National Academy of Sciences, pp. 16166–16171, 2014.
ista: Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics
J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru
H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated
centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings
of the National Academy of Sciences. 111(45), 16166–16171.
mla: Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles
Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA
Genes.” Proceedings of the National Academy of Sciences, vol. 111, no.
45, National Academy of Sciences, 2014, pp. 16166–71, doi:10.1073/pnas.1418564111.
short: Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft,
J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L.
Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014)
16166–16171.
date_created: 2021-06-07T07:23:43Z
date_published: 2014-11-11T00:00:00Z
date_updated: 2021-12-14T08:23:26Z
day: '11'
department:
- _id: DaZi
doi: 10.1073/pnas.1418564111
extern: '1'
external_id:
pmid:
- '25344531'
intvolume: ' 111'
issue: '45'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1418564111
month: '11'
oa: 1
oa_version: Published Version
page: 16166-16171
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: The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres,
decondenses heterochromatin, and activates ribosomal RNA genes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 111
year: '2014'
...
---
_id: '9481'
abstract:
- lang: eng
text: Arabidopsis thaliana endosperm, a transient tissue that nourishes the embryo,
exhibits extensive localized DNA demethylation on maternally inherited chromosomes.
Demethylation mediates parent-of-origin–specific (imprinted) gene expression but
is apparently unnecessary for the extensive accumulation of maternally biased
small RNA (sRNA) molecules detected in seeds. Endosperm DNA in the distantly related
monocots rice and maize is likewise locally hypomethylated, but whether this hypomethylation
is generally parent-of-origin specific is unknown. Imprinted expression of sRNA
also remains uninvestigated in monocot seeds. Here, we report high-coverage sequencing
of the Kitaake rice cultivar that enabled us to show that localized hypomethylation
in rice endosperm occurs solely on the maternal genome, preferring regions of
high DNA accessibility. Maternally expressed imprinted genes are enriched for
hypomethylation at putative promoter regions and transcriptional termini and paternally
expressed genes at promoters and gene bodies, mirroring our recent results in
A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are
dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are
expressed from both parental genomes and correlate with hypomethylation. Overlaps
between imprinted sRNA loci and imprinted genes expressed from opposite alleles
suggest that sRNAs may regulate genomic imprinting. Whereas sRNAs in seedling
tissues primarily originate from small class II (cut-and-paste) transposable elements,
those in endosperm are more uniformly derived, including sequences from other
transposon classes, as well as genic and intergenic regions. Our data indicate
that the endosperm exhibits a unique pattern of sRNA expression and suggest that
localized hypomethylation of maternal endosperm DNA is conserved in flowering
plants.
article_processing_charge: No
article_type: original
author:
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Randy
full_name: Ruan, Randy
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: 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, Ruan R, Nishimura T, et al. Imprinted expression of genes and
small RNA is associated with localized hypomethylation of the maternal genome
in rice endosperm. Proceedings of the National Academy of Sciences. 2013;110(19):7934-7939.
doi:10.1073/pnas.1306164110
apa: Rodrigues, J. A., Ruan, R., Nishimura, T., Sharma, M. K., Sharma, R., Ronald,
P. C., … Zilberman, D. (2013). Imprinted expression of genes and small RNA is
associated with localized hypomethylation of the maternal genome in rice endosperm.
Proceedings of the National Academy of Sciences. National Academy of Sciences.
https://doi.org/10.1073/pnas.1306164110
chicago: Rodrigues, Jessica A., Randy Ruan, Toshiro Nishimura, Manoj K. Sharma,
Rita Sharma, Pamela C Ronald, Robert L. Fischer, and Daniel Zilberman. “Imprinted
Expression of Genes and Small RNA Is Associated with Localized Hypomethylation
of the Maternal Genome in Rice Endosperm.” Proceedings of the National Academy
of Sciences. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1306164110.
ieee: J. A. Rodrigues et al., “Imprinted expression of genes and small RNA
is associated with localized hypomethylation of the maternal genome in rice endosperm,”
Proceedings of the National Academy of Sciences, vol. 110, no. 19. National
Academy of Sciences, pp. 7934–7939, 2013.
ista: Rodrigues JA, Ruan R, Nishimura T, Sharma MK, Sharma R, Ronald PC, Fischer
RL, Zilberman D. 2013. Imprinted expression of genes and small RNA is associated
with localized hypomethylation of the maternal genome in rice endosperm. Proceedings
of the National Academy of Sciences. 110(19), 7934–7939.
mla: Rodrigues, Jessica A., et al. “Imprinted Expression of Genes and Small RNA
Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.”
Proceedings of the National Academy of Sciences, vol. 110, no. 19, National
Academy of Sciences, 2013, pp. 7934–39, doi:10.1073/pnas.1306164110.
short: J.A. Rodrigues, R. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, P.C. Ronald,
R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 110
(2013) 7934–7939.
date_created: 2021-06-07T07:31:02Z
date_published: 2013-05-07T00:00:00Z
date_updated: 2021-12-14T08:26:44Z
day: '07'
department:
- _id: DaZi
doi: 10.1073/pnas.1306164110
extern: '1'
external_id:
pmid:
- '23613580'
intvolume: ' 110'
issue: '19'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1306164110
month: '05'
oa: 1
oa_version: Published Version
page: 7934-7939
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: Imprinted expression of genes and small RNA is associated with localized hypomethylation
of the maternal genome in rice endosperm
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 110
year: '2013'
...
---
_id: '9483'
abstract:
- lang: eng
text: Imprinted genes are expressed primarily or exclusively from either the maternal
or paternal allele, a phenomenon that occurs in flowering plants and mammals.
Flowering plant imprinted gene expression has been described primarily in endosperm,
a terminal nutritive tissue consumed by the embryo during seed development or
after germination. Imprinted expression in Arabidopsis thaliana endosperm is orchestrated
by differences in cytosine DNA methylation between the paternal and maternal genomes
as well as by Polycomb group proteins. Currently, only 11 imprinted A. thaliana
genes are known. Here, we use extensive sequencing of cDNA libraries to identify
9 paternally expressed and 34 maternally expressed imprinted genes in A. thaliana
endosperm that are regulated by the DNA-demethylating glycosylase DEMETER, the
DNA methyltransferase MET1, and/or the core Polycomb group protein FIE. These
genes encode transcription factors, proteins involved in hormone signaling, components
of the ubiquitin protein degradation pathway, regulators of histone and DNA methylation,
and small RNA pathway proteins. We also identify maternally expressed genes that
may be regulated by unknown mechanisms or deposited from maternal tissues. We
did not detect any imprinted genes in the embryo. Our results show that imprinted
gene expression is an extensive mechanistically complex phenomenon that likely
affects multiple aspects of seed development.
article_processing_charge: No
article_type: original
author:
- first_name: Tzung-Fu
full_name: Hsieh, Tzung-Fu
last_name: Hsieh
- first_name: Juhyun
full_name: Shin, Juhyun
last_name: Shin
- first_name: Rie
full_name: Uzawa, Rie
last_name: Uzawa
- first_name: Pedro
full_name: Silva, Pedro
last_name: Silva
- first_name: Stephanie
full_name: Cohen, Stephanie
last_name: Cohen
- first_name: Matthew J.
full_name: Bauer, Matthew J.
last_name: Bauer
- first_name: Meryl
full_name: Hashimoto, Meryl
last_name: Hashimoto
- first_name: Ryan C.
full_name: Kirkbride, Ryan C.
last_name: Kirkbride
- first_name: John J.
full_name: Harada, John J.
last_name: Harada
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
citation:
ama: Hsieh T-F, Shin J, Uzawa R, et al. Regulation of imprinted gene expression
in Arabidopsis endosperm. Proceedings of the National Academy of Sciences.
2011;108(5):1755-1762. doi:10.1073/pnas.1019273108
apa: Hsieh, T.-F., Shin, J., Uzawa, R., Silva, P., Cohen, S., Bauer, M. J., … Fischer,
R. L. (2011). Regulation of imprinted gene expression in Arabidopsis endosperm.
Proceedings of the National Academy of Sciences. National Academy of Sciences.
https://doi.org/10.1073/pnas.1019273108
chicago: Hsieh, Tzung-Fu, Juhyun Shin, Rie Uzawa, Pedro Silva, Stephanie Cohen,
Matthew J. Bauer, Meryl Hashimoto, et al. “Regulation of Imprinted Gene Expression
in Arabidopsis Endosperm.” Proceedings of the National Academy of Sciences.
National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1019273108.
ieee: T.-F. Hsieh et al., “Regulation of imprinted gene expression in Arabidopsis
endosperm,” Proceedings of the National Academy of Sciences, vol. 108,
no. 5. National Academy of Sciences, pp. 1755–1762, 2011.
ista: Hsieh T-F, Shin J, Uzawa R, Silva P, Cohen S, Bauer MJ, Hashimoto M, Kirkbride
RC, Harada JJ, Zilberman D, Fischer RL. 2011. Regulation of imprinted gene expression
in Arabidopsis endosperm. Proceedings of the National Academy of Sciences. 108(5),
1755–1762.
mla: Hsieh, Tzung-Fu, et al. “Regulation of Imprinted Gene Expression in Arabidopsis
Endosperm.” Proceedings of the National Academy of Sciences, vol. 108,
no. 5, National Academy of Sciences, 2011, pp. 1755–62, doi:10.1073/pnas.1019273108.
short: T.-F. Hsieh, J. Shin, R. Uzawa, P. Silva, S. Cohen, M.J. Bauer, M. Hashimoto,
R.C. Kirkbride, J.J. Harada, D. Zilberman, R.L. Fischer, Proceedings of the National
Academy of Sciences 108 (2011) 1755–1762.
date_created: 2021-06-07T07:40:38Z
date_published: 2011-02-01T00:00:00Z
date_updated: 2021-12-14T08:33:49Z
day: '01'
department:
- _id: DaZi
doi: 10.1073/pnas.1019273108
extern: '1'
external_id:
pmid:
- '21257907'
intvolume: ' 108'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1019273108
month: '02'
oa: 1
oa_version: Published Version
page: 1755-1762
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: Regulation of imprinted gene expression in Arabidopsis endosperm
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 108
year: '2011'
...
---
_id: '14305'
abstract:
- lang: eng
text: Understanding the mechanism of protein folding requires a detailed knowledge
of the structural properties of the barriers separating unfolded from native conformations.
The S-peptide from ribonuclease S forms its α-helical structure only upon binding
to the folded S-protein. We characterized the transition state for this binding-induced
folding reaction at high resolution by determining the effect of site-specific
backbone thioxylation and side-chain modifications on the kinetics and thermodynamics
of the reaction, which allows us to monitor formation of backbone hydrogen bonds
and side-chain interactions in the transition state. The experiments reveal that
α-helical structure in the S-peptide is absent in the transition state of binding.
Recognition between the unfolded S-peptide and the S-protein is mediated by loosely
packed hydrophobic side-chain interactions in two well defined regions on the
S-peptide. Close packing and helix formation occurs rapidly after binding. Introducing
hydrophobic residues at positions outside the recognition region can drastically
slow down association.
article_processing_charge: No
article_type: original
author:
- first_name: Annett
full_name: Bachmann, Annett
last_name: Bachmann
- first_name: Dirk
full_name: Wildemann, Dirk
last_name: Wildemann
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Gunter
full_name: Fischer, Gunter
last_name: Fischer
- first_name: Thomas
full_name: Kiefhaber, Thomas
last_name: Kiefhaber
citation:
ama: Bachmann A, Wildemann D, Praetorius FM, Fischer G, Kiefhaber T. Mapping backbone
and side-chain interactions in the transition state of a coupled protein folding
and binding reaction. PNAS. 2011;108(10):3952-3957. doi:10.1073/pnas.1012668108
apa: Bachmann, A., Wildemann, D., Praetorius, F. M., Fischer, G., & Kiefhaber,
T. (2011). Mapping backbone and side-chain interactions in the transition state
of a coupled protein folding and binding reaction. PNAS. Proceedings of
the National Academy of Sciences. https://doi.org/10.1073/pnas.1012668108
chicago: Bachmann, Annett, Dirk Wildemann, Florian M Praetorius, Gunter Fischer,
and Thomas Kiefhaber. “Mapping Backbone and Side-Chain Interactions in the Transition
State of a Coupled Protein Folding and Binding Reaction.” PNAS. Proceedings
of the National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1012668108.
ieee: A. Bachmann, D. Wildemann, F. M. Praetorius, G. Fischer, and T. Kiefhaber,
“Mapping backbone and side-chain interactions in the transition state of a coupled
protein folding and binding reaction,” PNAS, vol. 108, no. 10. Proceedings
of the National Academy of Sciences, pp. 3952–3957, 2011.
ista: Bachmann A, Wildemann D, Praetorius FM, Fischer G, Kiefhaber T. 2011. Mapping
backbone and side-chain interactions in the transition state of a coupled protein
folding and binding reaction. PNAS. 108(10), 3952–3957.
mla: Bachmann, Annett, et al. “Mapping Backbone and Side-Chain Interactions in the
Transition State of a Coupled Protein Folding and Binding Reaction.” PNAS,
vol. 108, no. 10, Proceedings of the National Academy of Sciences, 2011, pp. 3952–57,
doi:10.1073/pnas.1012668108.
short: A. Bachmann, D. Wildemann, F.M. Praetorius, G. Fischer, T. Kiefhaber, PNAS
108 (2011) 3952–3957.
date_created: 2023-09-06T12:54:36Z
date_published: 2011-01-12T00:00:00Z
date_updated: 2023-11-07T11:50:29Z
day: '12'
doi: 10.1073/pnas.1012668108
extern: '1'
external_id:
pmid:
- '21325613'
intvolume: ' 108'
issue: '10'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1012668108
month: '01'
oa: 1
oa_version: Published Version
page: 3952-3957
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: Mapping backbone and side-chain interactions in the transition state of a coupled
protein folding and binding reaction
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2011'
...
---
_id: '9485'
abstract:
- lang: eng
text: 'Cytosine methylation silences transposable elements in plants, vertebrates,
and fungi but also regulates gene expression. Plant methylation is catalyzed by
three families of enzymes, each with a preferred sequence context: CG, CHG (H
= A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis
thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally
hypomethylated in the CG context while retaining high non-CG methylation. Global
methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition
remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all
sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas
CG hypomethylation is localized. CHH methylation of small transposable elements
is increased in embryos, suggesting that endosperm demethylation enhances transposon
silencing. Genes preferentially expressed in endosperm, including those coding
for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated
in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm
biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is
conserved among angiosperms and has a profound effect on gene expression in cereal
crops.'
article_processing_charge: No
article_type: original
author:
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Pedro
full_name: Silva, Pedro
last_name: Silva
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Bradley
full_name: Dotson, Bradley
last_name: Dotson
- first_name: Matthew D.
full_name: Brooks, Matthew D.
last_name: Brooks
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zemach A, Kim MY, Silva P, et al. Local DNA hypomethylation activates genes
in rice endosperm. Proceedings of the National Academy of Sciences. 2010;107(43):18729-18734.
doi:10.1073/pnas.1009695107
apa: Zemach, A., Kim, M. Y., Silva, P., Rodrigues, J. A., Dotson, B., Brooks, M.
D., & Zilberman, D. (2010). Local DNA hypomethylation activates genes in rice
endosperm. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.1009695107
chicago: Zemach, Assaf, M. Yvonne Kim, Pedro Silva, Jessica A. Rodrigues, Bradley
Dotson, Matthew D. Brooks, and Daniel Zilberman. “Local DNA Hypomethylation Activates
Genes in Rice Endosperm.” Proceedings of the National Academy of Sciences.
National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.1009695107.
ieee: A. Zemach et al., “Local DNA hypomethylation activates genes in rice
endosperm,” Proceedings of the National Academy of Sciences, vol. 107,
no. 43. National Academy of Sciences, pp. 18729–18734, 2010.
ista: Zemach A, Kim MY, Silva P, Rodrigues JA, Dotson B, Brooks MD, Zilberman D.
2010. Local DNA hypomethylation activates genes in rice endosperm. Proceedings
of the National Academy of Sciences. 107(43), 18729–18734.
mla: Zemach, Assaf, et al. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.”
Proceedings of the National Academy of Sciences, vol. 107, no. 43, National
Academy of Sciences, 2010, pp. 18729–34, doi:10.1073/pnas.1009695107.
short: A. Zemach, M.Y. Kim, P. Silva, J.A. Rodrigues, B. Dotson, M.D. Brooks, D.
Zilberman, Proceedings of the National Academy of Sciences 107 (2010) 18729–18734.
date_created: 2021-06-07T09:31:01Z
date_published: 2010-10-26T00:00:00Z
date_updated: 2021-12-14T08:40:02Z
day: '26'
department:
- _id: DaZi
doi: 10.1073/pnas.1009695107
extern: '1'
external_id:
pmid:
- '20937895'
intvolume: ' 107'
issue: '43'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1009695107
month: '10'
oa: 1
oa_version: Published Version
page: 18729-18734
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: Local DNA hypomethylation activates genes in rice endosperm
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 107
year: '2010'
...
---
_id: '8483'
abstract:
- lang: eng
text: Atom-resolved real-time studies of kinetic processes in proteins have been
hampered in the past by the lack of experimental techniques that yield sufficient
temporal and atomic resolution. Here we present band-selective optimized flip-angle
short transient (SOFAST) real-time 2D NMR spectroscopy, a method that allows simultaneous
observation of reaction kinetics for a large number of nuclear sites along the
polypeptide chain of a protein with an unprecedented time resolution of a few
seconds. SOFAST real-time 2D NMR spectroscopy combines fast NMR data acquisition
techniques with rapid sample mixing inside the NMR magnet to initiate the kinetic
event. We demonstrate the use of SOFAST real-time 2D NMR to monitor the conformational
transition of α-lactalbumin from a molten globular to the native state for a large
number of amide sites along the polypeptide chain. The kinetic behavior observed
for the disappearance of the molten globule and the appearance of the native state
is monoexponential and uniform along the polypeptide chain. This observation confirms
previous findings that a single transition state ensemble controls folding of
α-lactalbumin from the molten globule to the native state. In a second application,
the spontaneous unfolding of native ubiquitin under nondenaturing conditions is
characterized by amide hydrogen exchange rate constants measured at high pH by
using SOFAST real-time 2D NMR. Our data reveal that ubiquitin unfolds in a gradual
manner with distinct unfolding regimes.
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: V.
full_name: Forge, V.
last_name: Forge
- first_name: B.
full_name: Brutscher, B.
last_name: Brutscher
citation:
ama: Schanda P, Forge V, Brutscher B. Protein folding and unfolding studied at atomic
resolution by fast two-dimensional NMR spectroscopy. Proceedings of the National
Academy of Sciences. 2007;104(27):11257-11262. doi:10.1073/pnas.0702069104
apa: Schanda, P., Forge, V., & Brutscher, B. (2007). Protein folding and unfolding
studied at atomic resolution by fast two-dimensional NMR spectroscopy. Proceedings
of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.0702069104
chicago: Schanda, Paul, V. Forge, and B. Brutscher. “Protein Folding and Unfolding
Studied at Atomic Resolution by Fast Two-Dimensional NMR Spectroscopy.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2007. https://doi.org/10.1073/pnas.0702069104.
ieee: P. Schanda, V. Forge, and B. Brutscher, “Protein folding and unfolding studied
at atomic resolution by fast two-dimensional NMR spectroscopy,” Proceedings
of the National Academy of Sciences, vol. 104, no. 27. National Academy of
Sciences, pp. 11257–11262, 2007.
ista: Schanda P, Forge V, Brutscher B. 2007. Protein folding and unfolding studied
at atomic resolution by fast two-dimensional NMR spectroscopy. Proceedings of
the National Academy of Sciences. 104(27), 11257–11262.
mla: Schanda, Paul, et al. “Protein Folding and Unfolding Studied at Atomic Resolution
by Fast Two-Dimensional NMR Spectroscopy.” Proceedings of the National Academy
of Sciences, vol. 104, no. 27, National Academy of Sciences, 2007, pp. 11257–62,
doi:10.1073/pnas.0702069104.
short: P. Schanda, V. Forge, B. Brutscher, Proceedings of the National Academy of
Sciences 104 (2007) 11257–11262.
date_created: 2020-09-18T10:12:54Z
date_published: 2007-07-03T00:00:00Z
date_updated: 2021-01-12T08:19:35Z
day: '03'
doi: 10.1073/pnas.0702069104
extern: '1'
intvolume: ' 104'
issue: '27'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '07'
oa_version: None
page: 11257-11262
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'
status: public
title: Protein folding and unfolding studied at atomic resolution by fast two-dimensional
NMR spectroscopy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 104
year: '2007'
...
---
_id: '9487'
abstract:
- lang: eng
text: Cytosine DNA methylation is considered to be a stable epigenetic mark, but
active demethylation has been observed in both plants and animals. In Arabidopsis
thaliana, DNA glycosylases of the DEMETER (DME) family remove methylcytosines
from DNA. Demethylation by DME is necessary for genomic imprinting, and demethylation
by a related protein, REPRESSOR OF SILENCING1, prevents gene silencing in a transgenic
background. However, the extent and function of demethylation by DEMETER-LIKE
(DML) proteins in WT plants is not known. Using genome-tiling microarrays, we
mapped DNA methylation in mutant and WT plants and identified 179 loci actively
demethylated by DML enzymes. Mutations in DML genes lead to locus-specific DNA
hypermethylation. Reintroducing WT DML genes restores most loci to the normal
pattern of methylation, although at some loci, hypermethylated epialleles persist.
Of loci demethylated by DML enzymes, >80% are near or overlap genes. Genic demethylation
by DML enzymes primarily occurs at the 5′ and 3′ ends, a pattern opposite to the
overall distribution of WT DNA methylation. Our results show that demethylation
by DML DNA glycosylases edits the patterns of DNA methylation within the Arabidopsis
genome to protect genes from potentially deleterious methylation.
article_processing_charge: No
article_type: original
author:
- first_name: Jon
full_name: Penterman, Jon
last_name: Penterman
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Jin Hoe
full_name: Huh, Jin Hoe
last_name: Huh
- first_name: Tracy
full_name: Ballinger, Tracy
last_name: Ballinger
- first_name: Steven
full_name: Henikoff, Steven
last_name: Henikoff
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
citation:
ama: Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL. DNA
demethylation in the Arabidopsis genome. Proceedings of the National Academy
of Sciences. 2007;104(16):6752-6757. doi:10.1073/pnas.0701861104
apa: Penterman, J., Zilberman, D., Huh, J. H., Ballinger, T., Henikoff, S., &
Fischer, R. L. (2007). DNA demethylation in the Arabidopsis genome. Proceedings
of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.0701861104
chicago: Penterman, Jon, Daniel Zilberman, Jin Hoe Huh, Tracy Ballinger, Steven
Henikoff, and Robert L. Fischer. “DNA Demethylation in the Arabidopsis Genome.”
Proceedings of the National Academy of Sciences. National Academy of Sciences,
2007. https://doi.org/10.1073/pnas.0701861104.
ieee: J. Penterman, D. Zilberman, J. H. Huh, T. Ballinger, S. Henikoff, and R. L.
Fischer, “DNA demethylation in the Arabidopsis genome,” Proceedings of the
National Academy of Sciences, vol. 104, no. 16. National Academy of Sciences,
pp. 6752–6757, 2007.
ista: Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL. 2007.
DNA demethylation in the Arabidopsis genome. Proceedings of the National Academy
of Sciences. 104(16), 6752–6757.
mla: Penterman, Jon, et al. “DNA Demethylation in the Arabidopsis Genome.” Proceedings
of the National Academy of Sciences, vol. 104, no. 16, National Academy of
Sciences, 2007, pp. 6752–57, doi:10.1073/pnas.0701861104.
short: J. Penterman, D. Zilberman, J.H. Huh, T. Ballinger, S. Henikoff, R.L. Fischer,
Proceedings of the National Academy of Sciences 104 (2007) 6752–6757.
date_created: 2021-06-07T09:38:21Z
date_published: 2007-04-17T00:00:00Z
date_updated: 2021-12-14T08:55:12Z
day: '17'
department:
- _id: DaZi
doi: 10.1073/pnas.0701861104
extern: '1'
external_id:
pmid:
- '17409185'
intvolume: ' 104'
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.0701861104
month: '04'
oa: 1
oa_version: Published Version
page: 6752-6757
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: DNA demethylation in the Arabidopsis genome
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 104
year: '2007'
...
---
_id: '13425'
abstract:
- lang: eng
text: Nanoparticles (NPs) decorated with ligands combining photoswitchable dipoles
and covalent cross-linkers can be assembled by light into organized, three-dimensional
suprastructures of various types and sizes. NPs covered with only few photoactive
ligands form metastable crystals that can be assembled and disassembled “on demand”
by using light of different wavelengths. For higher surface concentrations, self-assembly
is irreversible, and the NPs organize into permanently cross-linked structures
including robust supracrystals and plastic spherical aggregates.
article_processing_charge: No
article_type: original
author:
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Kyle J. M.
full_name: Bishop, Kyle J. M.
last_name: Bishop
- first_name: Bartosz A.
full_name: Grzybowski, Bartosz A.
last_name: Grzybowski
citation:
ama: Klajn R, Bishop KJM, Grzybowski BA. Light-controlled self-assembly of reversible
and irreversible nanoparticle suprastructures. Proceedings of the National
Academy of Sciences. 2007;104(25):10305-10309. doi:10.1073/pnas.0611371104
apa: Klajn, R., Bishop, K. J. M., & Grzybowski, B. A. (2007). Light-controlled
self-assembly of reversible and irreversible nanoparticle suprastructures. Proceedings
of the National Academy of Sciences. Proceedings of the National Academy of
Sciences. https://doi.org/10.1073/pnas.0611371104
chicago: Klajn, Rafal, Kyle J. M. Bishop, and Bartosz A. Grzybowski. “Light-Controlled
Self-Assembly of Reversible and Irreversible Nanoparticle Suprastructures.” Proceedings
of the National Academy of Sciences. Proceedings of the National Academy of
Sciences, 2007. https://doi.org/10.1073/pnas.0611371104.
ieee: R. Klajn, K. J. M. Bishop, and B. A. Grzybowski, “Light-controlled self-assembly
of reversible and irreversible nanoparticle suprastructures,” Proceedings of
the National Academy of Sciences, vol. 104, no. 25. Proceedings of the National
Academy of Sciences, pp. 10305–10309, 2007.
ista: Klajn R, Bishop KJM, Grzybowski BA. 2007. Light-controlled self-assembly of
reversible and irreversible nanoparticle suprastructures. Proceedings of the National
Academy of Sciences. 104(25), 10305–10309.
mla: Klajn, Rafal, et al. “Light-Controlled Self-Assembly of Reversible and Irreversible
Nanoparticle Suprastructures.” Proceedings of the National Academy of Sciences,
vol. 104, no. 25, Proceedings of the National Academy of Sciences, 2007, pp. 10305–09,
doi:10.1073/pnas.0611371104.
short: R. Klajn, K.J.M. Bishop, B.A. Grzybowski, Proceedings of the National Academy
of Sciences 104 (2007) 10305–10309.
date_created: 2023-08-01T10:31:19Z
date_published: 2007-06-19T00:00:00Z
date_updated: 2023-08-08T11:24:51Z
day: '19'
doi: 10.1073/pnas.0611371104
extern: '1'
external_id:
pmid:
- '17563381'
intvolume: ' 104'
issue: '25'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.0611371104
month: '06'
oa: 1
oa_version: Published Version
page: 10305-10309
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: Light-controlled self-assembly of reversible and irreversible nanoparticle
suprastructures
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 104
year: '2007'
...
---
_id: '11877'
abstract:
- lang: eng
text: The World Wide Web provides a unprecedented opportunity to automatically analyze
a large sample of interests and activity in the world. We discuss methods for
extracting knowledge from the web by randomly sampling and analyzing hosts and
pages, and by analyzing the link structure of the web and how links accumulate
over time. A variety of interesting and valuable information can be extracted,
such as the distribution of web pages over domains, the distribution of interest
in different areas, communities related to different topics, the nature of competition
in different categories of sites, and the degree of communication between different
communities or countries.
article_processing_charge: No
article_type: original
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Steve
full_name: Lawrence, Steve
last_name: Lawrence
citation:
ama: Henzinger MH, Lawrence S. Extracting knowledge from the World Wide Web. Proceedings
of the National Academy of Sciences. 2004;101(suppl_1):5186-5191. doi:10.1073/pnas.0307528100
apa: Henzinger, M. H., & Lawrence, S. (2004). Extracting knowledge from the
World Wide Web. Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences. https://doi.org/10.1073/pnas.0307528100
chicago: Henzinger, Monika H, and Steve Lawrence. “Extracting Knowledge from the
World Wide Web.” Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences, 2004. https://doi.org/10.1073/pnas.0307528100.
ieee: M. H. Henzinger and S. Lawrence, “Extracting knowledge from the World Wide
Web,” Proceedings of the National Academy of Sciences, vol. 101, no. suppl_1.
Proceedings of the National Academy of Sciences, pp. 5186–5191, 2004.
ista: Henzinger MH, Lawrence S. 2004. Extracting knowledge from the World Wide Web.
Proceedings of the National Academy of Sciences. 101(suppl_1), 5186–5191.
mla: Henzinger, Monika H., and Steve Lawrence. “Extracting Knowledge from the World
Wide Web.” Proceedings of the National Academy of Sciences, vol. 101, no.
suppl_1, Proceedings of the National Academy of Sciences, 2004, pp. 5186–91, doi:10.1073/pnas.0307528100.
short: M.H. Henzinger, S. Lawrence, Proceedings of the National Academy of Sciences
101 (2004) 5186–5191.
date_created: 2022-08-16T13:06:10Z
date_published: 2004-04-06T00:00:00Z
date_updated: 2023-02-17T12:21:43Z
day: '06'
doi: 10.1073/pnas.0307528100
extern: '1'
external_id:
pmid:
- '14745041'
intvolume: ' 101'
issue: suppl_1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC387294/
month: '04'
oa: 1
oa_version: Published Version
page: 5186-5191
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: Extracting knowledge from the World Wide Web
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 101
year: '2004'
...
---
_id: '3466'
abstract:
- lang: eng
text: Amphibian myelinated nerve fibers were treated with collagenase and protease.
Axons with retraction of the myelin sheath were patch-clamped in the nodal and
paranodal region. One type of Na channel was found. It has a single-channel conductance
of 11 pS (15 degrees C) and is blocked by tetrodotoxin. Averaged events show the
typical activation and inactivation kinetics of macroscopic Na current. Three
potential-dependent K channels were identified (I, F, and S channel). The I channel,
being the most frequent type, has a single-channel conductance of 23 pS (inward
current, 105 mM K on both sides of the membrane), activates between -60 and -30
mV, deactivates with intermediate kinetics, and is sensitive to dendrotoxin. The
F channel has a conductance of 30 pS, activates between -40 and 60 mV, and deactivates
with fast kinetics. The former inactivates within tens of seconds; the latter
inactivates within seconds. The third type, the S channel, has a conductance of
7 pS and deactivates slowly. All three channels can be blocked by external tetraethylammonium
chloride. We suggest that these distinct K channel types form the basis for the
different components of macroscopic K current described previously.
acknowledgement: We thank Drs. C. Baumann, D. Siemen, and W. Stuhmer for reading the
manuscript and Dr. F. Dreyer for the generous gift of DTX. The study was supported
by the Deutsche Forschungsgemeinschaft.
article_processing_charge: No
article_type: original
author:
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Michael
full_name: Bräu, Michael
last_name: Bräu
- first_name: Markus
full_name: Hermsteiner, Markus
last_name: Hermsteiner
- first_name: Werner
full_name: Vogel, Werner
last_name: Vogel
citation:
ama: Jonas PM, Bräu M, Hermsteiner M, Vogel W. Single-channel recording in myelinated
nerve fibers reveals one type of Na channel but different K channels. PNAS.
1989;86(18):7238-7242. doi:10.1073/pnas.86.18.7238
apa: Jonas, P. M., Bräu, M., Hermsteiner, M., & Vogel, W. (1989). Single-channel
recording in myelinated nerve fibers reveals one type of Na channel but different
K channels. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.86.18.7238
chicago: Jonas, Peter M, Michael Bräu, Markus Hermsteiner, and Werner Vogel. “Single-Channel
Recording in Myelinated Nerve Fibers Reveals One Type of Na Channel but Different
K Channels.” PNAS. National Academy of Sciences, 1989. https://doi.org/10.1073/pnas.86.18.7238.
ieee: P. M. Jonas, M. Bräu, M. Hermsteiner, and W. Vogel, “Single-channel recording
in myelinated nerve fibers reveals one type of Na channel but different K channels,”
PNAS, vol. 86, no. 18. National Academy of Sciences, pp. 7238–7242, 1989.
ista: Jonas PM, Bräu M, Hermsteiner M, Vogel W. 1989. Single-channel recording in
myelinated nerve fibers reveals one type of Na channel but different K channels.
PNAS. 86(18), 7238–7242.
mla: Jonas, Peter M., et al. “Single-Channel Recording in Myelinated Nerve Fibers
Reveals One Type of Na Channel but Different K Channels.” PNAS, vol. 86,
no. 18, National Academy of Sciences, 1989, pp. 7238–42, doi:10.1073/pnas.86.18.7238.
short: P.M. Jonas, M. Bräu, M. Hermsteiner, W. Vogel, PNAS 86 (1989) 7238–7242.
date_created: 2018-12-11T12:03:28Z
date_published: 1989-09-01T00:00:00Z
date_updated: 2022-02-14T16:12:33Z
day: '01'
doi: 10.1073/pnas.86.18.7238
extern: '1'
external_id:
pmid:
- '2550937 '
intvolume: ' 86'
issue: '18'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC298032/?tool=pubmed
month: '09'
oa: 1
oa_version: Published Version
page: 7238 - 7242
pmid: 1
publication: PNAS
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
publist_id: '2921'
quality_controlled: '1'
status: public
title: Single-channel recording in myelinated nerve fibers reveals one type of Na
channel but different K channels
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 86
year: '1989'
...