---
_id: '8680'
abstract:
- lang: eng
text: Animal development entails the organization of specific cell types in space
and time, and spatial patterns must form in a robust manner. In the zebrafish
spinal cord, neural progenitors form stereotypic patterns despite noisy morphogen
signaling and large-scale cellular rearrangements during morphogenesis and growth.
By directly measuring adhesion forces and preferences for three types of endogenous
neural progenitors, we provide evidence for the differential adhesion model in
which differences in intercellular adhesion mediate cell sorting. Cell type–specific
combinatorial expression of different classes of cadherins (N-cadherin, cadherin
11, and protocadherin 19) results in homotypic preference ex vivo and patterning
robustness in vivo. Furthermore, the differential adhesion code is regulated by
the sonic hedgehog morphogen gradient. We propose that robust patterning during
tissue morphogenesis results from interplay between adhesion-based self-organization
and morphogen-directed patterning.
acknowledgement: "We thank the members of the Megason and Heisenberg labs for critical
discussions of and technical assistance during the work and B. Appel, S. Holley,
J. Jontes, and D. Gilmour for transgenic fish. This work is supported by the Damon
Runyon Cancer Foundation, a NICHD K99 fellowship (1K99HD092623), a Travelling Fellowship
of the Company of Biologists, a Collaborative Research grant from the Burroughs
Wellcome Foundation (T.Y.-C.T.), NIH grant 01GM107733 (T.Y.-C.T. and S.G.M.), NIH
grant R01NS102322 (T.C.-C. and H.K.), and an ERC advanced grant\r\n(MECSPEC) (C.-P.H.)."
article_processing_charge: No
article_type: original
author:
- first_name: Tony Y.-C.
full_name: Tsai, Tony Y.-C.
last_name: Tsai
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Peng
full_name: Xia, Peng
id: 4AB6C7D0-F248-11E8-B48F-1D18A9856A87
last_name: Xia
orcid: 0000-0002-5419-7756
- first_name: Tugba
full_name: Colak-Champollion, Tugba
last_name: Colak-Champollion
- first_name: Holger
full_name: Knaut, Holger
last_name: Knaut
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Sean G.
full_name: Megason, Sean G.
last_name: Megason
citation:
ama: Tsai TY-C, Sikora MK, Xia P, et al. An adhesion code ensures robust pattern
formation during tissue morphogenesis. Science. 2020;370(6512):113-116.
doi:10.1126/science.aba6637
apa: Tsai, T. Y.-C., Sikora, M. K., Xia, P., Colak-Champollion, T., Knaut, H., Heisenberg,
C.-P. J., & Megason, S. G. (2020). An adhesion code ensures robust pattern
formation during tissue morphogenesis. Science. American Association for
the Advancement of Science. https://doi.org/10.1126/science.aba6637
chicago: Tsai, Tony Y.-C., Mateusz K Sikora, Peng Xia, Tugba Colak-Champollion,
Holger Knaut, Carl-Philipp J Heisenberg, and Sean G. Megason. “An Adhesion Code
Ensures Robust Pattern Formation during Tissue Morphogenesis.” Science.
American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.aba6637.
ieee: T. Y.-C. Tsai et al., “An adhesion code ensures robust pattern formation
during tissue morphogenesis,” Science, vol. 370, no. 6512. American Association
for the Advancement of Science, pp. 113–116, 2020.
ista: Tsai TY-C, Sikora MK, Xia P, Colak-Champollion T, Knaut H, Heisenberg C-PJ,
Megason SG. 2020. An adhesion code ensures robust pattern formation during tissue
morphogenesis. Science. 370(6512), 113–116.
mla: Tsai, Tony Y. C., et al. “An Adhesion Code Ensures Robust Pattern Formation
during Tissue Morphogenesis.” Science, vol. 370, no. 6512, American Association
for the Advancement of Science, 2020, pp. 113–16, doi:10.1126/science.aba6637.
short: T.Y.-C. Tsai, M.K. Sikora, P. Xia, T. Colak-Champollion, H. Knaut, C.-P.J.
Heisenberg, S.G. Megason, Science 370 (2020) 113–116.
date_created: 2020-10-19T14:09:38Z
date_published: 2020-10-02T00:00:00Z
date_updated: 2025-06-12T07:00:41Z
day: '02'
department:
- _id: CaHe
doi: 10.1126/science.aba6637
ec_funded: 1
external_id:
isi:
- '000579169000053'
pmid:
- '33004519'
intvolume: ' 370'
isi: 1
issue: '6512'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/803635v1
month: '10'
oa: 1
oa_version: Preprint
page: 113-116
pmid: 1
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/sticking-together/
scopus_import: '1'
status: public
title: An adhesion code ensures robust pattern formation during tissue morphogenesis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 370
year: '2020'
...
---
_id: '9059'
abstract:
- lang: eng
text: 'From rock salt to nanoparticle superlattices, complex structure can emerge
from simple building blocks that attract each other through Coulombic forces1-4.
On the micrometre scale, however, colloids in water defy the intuitively simple
idea of forming crystals from oppositely charged partners, instead forming non-equilibrium
structures such as clusters and gels5-7. Although various systems have been engineered
to grow binary crystals8-11, native surface charge in aqueous conditions has not
been used to assemble crystalline materials. Here we form ionic colloidal crystals
in water through an approach that we refer to as polymer-attenuated Coulombic
self-assembly. The key to crystallization is the use of a neutral polymer to keep
particles separated by well defined distances, allowing us to tune the attractive
overlap of electrical double layers, directing particles to disperse, crystallize
or become permanently fixed on demand. The nucleation and growth of macroscopic
single crystals is demonstrated by using the Debye screening length to fine-tune
assembly. Using a variety of colloidal particles and commercial polymers, ionic
colloidal crystals isostructural to caesium chloride, sodium chloride, aluminium
diboride and K4C60 are selected according to particle size ratios. Once fixed
by simply diluting out solution salts, crystals are pulled out of the water for
further manipulation, demonstrating an accurate translation from solution-phase
assembly to dried solid structures. In contrast to other assembly approaches,
in which particles must be carefully engineered to encode binding information12-18,
polymer-attenuated Coulombic self-assembly enables conventional colloids to be
used as model colloidal ions, primed for crystallization. '
article_processing_charge: No
article_type: original
author:
- first_name: Theodore
full_name: Hueckel, Theodore
last_name: Hueckel
- first_name: Glen M.
full_name: Hocky, Glen M.
last_name: Hocky
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: Stefano
full_name: Sacanna, Stefano
last_name: Sacanna
citation:
ama: Hueckel T, Hocky GM, Palacci JA, Sacanna S. Ionic solids from common colloids.
Nature. 2020;580(7804):487-490. doi:10.1038/s41586-020-2205-0
apa: Hueckel, T., Hocky, G. M., Palacci, J. A., & Sacanna, S. (2020). Ionic
solids from common colloids. Nature. Springer Nature. https://doi.org/10.1038/s41586-020-2205-0
chicago: Hueckel, Theodore, Glen M. Hocky, Jérémie A Palacci, and Stefano Sacanna.
“Ionic Solids from Common Colloids.” Nature. Springer Nature, 2020. https://doi.org/10.1038/s41586-020-2205-0.
ieee: T. Hueckel, G. M. Hocky, J. A. Palacci, and S. Sacanna, “Ionic solids from
common colloids,” Nature, vol. 580, no. 7804. Springer Nature, pp. 487–490,
2020.
ista: Hueckel T, Hocky GM, Palacci JA, Sacanna S. 2020. Ionic solids from common
colloids. Nature. 580(7804), 487–490.
mla: Hueckel, Theodore, et al. “Ionic Solids from Common Colloids.” Nature,
vol. 580, no. 7804, Springer Nature, 2020, pp. 487–90, doi:10.1038/s41586-020-2205-0.
short: T. Hueckel, G.M. Hocky, J.A. Palacci, S. Sacanna, Nature 580 (2020) 487–490.
date_created: 2021-02-02T13:30:50Z
date_published: 2020-04-23T00:00:00Z
date_updated: 2023-02-23T13:47:55Z
day: '23'
doi: 10.1038/s41586-020-2205-0
extern: '1'
external_id:
pmid:
- '32322078'
intvolume: ' 580'
issue: '7804'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '04'
oa_version: None
page: 487-490
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ionic solids from common colloids
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 580
year: '2020'
...
---
_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
arxiv: 1
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: '10619'
abstract:
- lang: eng
text: The quantum anomalous Hall (QAH) effect combines topology and magnetism to
produce precisely quantized Hall resistance at zero magnetic field. We report
the observation of a QAH effect in twisted bilayer graphene aligned to hexagonal
boron nitride. The effect is driven by intrinsic strong interactions, which polarize
the electrons into a single spin- and valley-resolved moiré miniband with Chern
number C = 1. In contrast to magnetically doped systems, the measured transport
energy gap is larger than the Curie temperature for magnetic ordering, and quantization
to within 0.1% of the von Klitzing constant persists to temperatures of several
kelvin at zero magnetic field. Electrical currents as small as 1 nanoampere controllably
switch the magnetic order between states of opposite polarization, forming an
electrically rewritable magnetic memory.
acknowledgement: The authors acknowledge discussions with A. Macdonald, Y. Saito,
and M. Zaletel.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: M.
full_name: Serlin, M.
last_name: Serlin
- first_name: C. L.
full_name: Tschirhart, C. L.
last_name: Tschirhart
- first_name: Hryhoriy
full_name: Polshyn, Hryhoriy
id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
last_name: Polshyn
orcid: 0000-0001-8223-8896
- first_name: Y.
full_name: Zhang, Y.
last_name: Zhang
- first_name: J.
full_name: Zhu, J.
last_name: Zhu
- first_name: K.
full_name: Watanabe, K.
last_name: Watanabe
- first_name: T.
full_name: Taniguchi, T.
last_name: Taniguchi
- first_name: L.
full_name: Balents, L.
last_name: Balents
- first_name: A. F.
full_name: Young, A. F.
last_name: Young
citation:
ama: Serlin M, Tschirhart CL, Polshyn H, et al. Intrinsic quantized anomalous Hall
effect in a moiré heterostructure. Science. 2019;367(6480):900-903. doi:10.1126/science.aay5533
apa: Serlin, M., Tschirhart, C. L., Polshyn, H., Zhang, Y., Zhu, J., Watanabe, K.,
… Young, A. F. (2019). Intrinsic quantized anomalous Hall effect in a moiré heterostructure.
Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aay5533
chicago: Serlin, M., C. L. Tschirhart, Hryhoriy Polshyn, Y. Zhang, J. Zhu, K. Watanabe,
T. Taniguchi, L. Balents, and A. F. Young. “Intrinsic Quantized Anomalous Hall
Effect in a Moiré Heterostructure.” Science. American Association for the
Advancement of Science, 2019. https://doi.org/10.1126/science.aay5533.
ieee: M. Serlin et al., “Intrinsic quantized anomalous Hall effect in a moiré
heterostructure,” Science, vol. 367, no. 6480. American Association for
the Advancement of Science, pp. 900–903, 2019.
ista: Serlin M, Tschirhart CL, Polshyn H, Zhang Y, Zhu J, Watanabe K, Taniguchi
T, Balents L, Young AF. 2019. Intrinsic quantized anomalous Hall effect in a moiré
heterostructure. Science. 367(6480), 900–903.
mla: Serlin, M., et al. “Intrinsic Quantized Anomalous Hall Effect in a Moiré Heterostructure.”
Science, vol. 367, no. 6480, American Association for the Advancement of
Science, 2019, pp. 900–03, doi:10.1126/science.aay5533.
short: M. Serlin, C.L. Tschirhart, H. Polshyn, Y. Zhang, J. Zhu, K. Watanabe, T.
Taniguchi, L. Balents, A.F. Young, Science 367 (2019) 900–903.
date_created: 2022-01-13T14:21:32Z
date_published: 2019-12-19T00:00:00Z
date_updated: 2023-02-21T16:00:09Z
day: '19'
doi: 10.1126/science.aay5533
extern: '1'
external_id:
arxiv:
- '1907.00261'
pmid:
- '31857492'
intvolume: ' 367'
issue: '6480'
keyword:
- multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1907.00261
month: '12'
oa: 1
oa_version: Preprint
page: 900-903
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
record:
- id: '10697'
relation: other
status: public
- id: '10698'
relation: other
status: public
- id: '10699'
relation: other
status: public
scopus_import: '1'
status: public
title: Intrinsic quantized anomalous Hall effect in a moiré heterostructure
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 367
year: '2019'
...
---
_id: '10625'
abstract:
- lang: eng
text: The discovery of superconductivity and exotic insulating phases in twisted
bilayer graphene has established this material as a model system of strongly correlated
electrons. To achieve superconductivity, the two layers of graphene need to be
at a very precise angle with respect to each other. Yankowitz et al. now show
that another experimental knob, hydrostatic pressure, can be used to tune the
phase diagram of twisted bilayer graphene (see the Perspective by Feldman). Applying
pressure increased the coupling between the layers, which shifted the superconducting
transition to higher angles and somewhat higher temperatures.
acknowledgement: We thank J. Zhu and H. Zhou for experimental assistance and D. Shahar,
A. Millis, O. Vafek, M. Zaletel, L. Balents, C. Xu, A. Bernevig, L. Fu, M. Koshino,
and P. Moon for helpful discussions.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Matthew
full_name: Yankowitz, Matthew
last_name: Yankowitz
- first_name: Shaowen
full_name: Chen, Shaowen
last_name: Chen
- first_name: Hryhoriy
full_name: Polshyn, Hryhoriy
id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
last_name: Polshyn
orcid: 0000-0001-8223-8896
- first_name: Yuxuan
full_name: Zhang, Yuxuan
last_name: Zhang
- first_name: K.
full_name: Watanabe, K.
last_name: Watanabe
- first_name: T.
full_name: Taniguchi, T.
last_name: Taniguchi
- first_name: David
full_name: Graf, David
last_name: Graf
- first_name: Andrea F.
full_name: Young, Andrea F.
last_name: Young
- first_name: Cory R.
full_name: Dean, Cory R.
last_name: Dean
citation:
ama: Yankowitz M, Chen S, Polshyn H, et al. Tuning superconductivity in twisted
bilayer graphene. Science. 2019;363(6431):1059-1064. doi:10.1126/science.aav1910
apa: Yankowitz, M., Chen, S., Polshyn, H., Zhang, Y., Watanabe, K., Taniguchi, T.,
… Dean, C. R. (2019). Tuning superconductivity in twisted bilayer graphene. Science.
American Association for the Advancement of Science (AAAS). https://doi.org/10.1126/science.aav1910
chicago: Yankowitz, Matthew, Shaowen Chen, Hryhoriy Polshyn, Yuxuan Zhang, K. Watanabe,
T. Taniguchi, David Graf, Andrea F. Young, and Cory R. Dean. “Tuning Superconductivity
in Twisted Bilayer Graphene.” Science. American Association for the Advancement
of Science (AAAS), 2019. https://doi.org/10.1126/science.aav1910.
ieee: M. Yankowitz et al., “Tuning superconductivity in twisted bilayer graphene,”
Science, vol. 363, no. 6431. American Association for the Advancement of
Science (AAAS), pp. 1059–1064, 2019.
ista: Yankowitz M, Chen S, Polshyn H, Zhang Y, Watanabe K, Taniguchi T, Graf D,
Young AF, Dean CR. 2019. Tuning superconductivity in twisted bilayer graphene.
Science. 363(6431), 1059–1064.
mla: Yankowitz, Matthew, et al. “Tuning Superconductivity in Twisted Bilayer Graphene.”
Science, vol. 363, no. 6431, American Association for the Advancement of
Science (AAAS), 2019, pp. 1059–64, doi:10.1126/science.aav1910.
short: M. Yankowitz, S. Chen, H. Polshyn, Y. Zhang, K. Watanabe, T. Taniguchi, D.
Graf, A.F. Young, C.R. Dean, Science 363 (2019) 1059–1064.
date_created: 2022-01-14T12:14:58Z
date_published: 2019-01-24T00:00:00Z
date_updated: 2022-01-14T13:48:32Z
day: '24'
doi: 10.1126/science.aav1910
extern: '1'
external_id:
arxiv:
- '1808.07865'
pmid:
- '30679385 '
intvolume: ' 363'
issue: '6431'
keyword:
- multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1808.07865
month: '01'
oa: 1
oa_version: Preprint
page: 1059-1064
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science (AAAS)
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tuning superconductivity in twisted bilayer graphene
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 363
year: '2019'
...
---
_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
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
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: '13374'
abstract:
- lang: eng
text: Confining molecules to volumes only slightly larger than the molecules themselves
can profoundly alter their properties. Molecular switches—entities that can be
toggled between two or more forms upon exposure to an external stimulus—often
require conformational freedom to isomerize. Therefore, placing these switches
in confined spaces can render them non-operational. To preserve the switchability
of these species under confinement, we work with a water-soluble coordination
cage that is flexible enough to adapt its shape to the conformation of the encapsulated
guest. We show that owing to its flexibility, the cage is not only capable of
accommodating—and solubilizing in water—several light-responsive spiropyran-based
molecular switches, but, more importantly, it also provides an environment suitable
for the efficient, reversible photoisomerization of the bound guests. Our findings
pave the way towards studying various molecular switching processes in confined
environments.
article_number: '641'
article_processing_charge: No
article_type: original
author:
- first_name: Dipak
full_name: Samanta, Dipak
last_name: Samanta
- first_name: Daria
full_name: Galaktionova, Daria
last_name: Galaktionova
- first_name: Julius
full_name: Gemen, Julius
last_name: Gemen
- first_name: Linda J. W.
full_name: Shimon, Linda J. W.
last_name: Shimon
- first_name: Yael
full_name: Diskin-Posner, Yael
last_name: Diskin-Posner
- first_name: Liat
full_name: Avram, Liat
last_name: Avram
- first_name: Petr
full_name: Král, Petr
last_name: Král
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Samanta D, Galaktionova D, Gemen J, et al. Reversible chromism of spiropyran
in the cavity of a flexible coordination cage. Nature Communications. 2018;9.
doi:10.1038/s41467-017-02715-6
apa: Samanta, D., Galaktionova, D., Gemen, J., Shimon, L. J. W., Diskin-Posner,
Y., Avram, L., … Klajn, R. (2018). Reversible chromism of spiropyran in the cavity
of a flexible coordination cage. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-017-02715-6
chicago: Samanta, Dipak, Daria Galaktionova, Julius Gemen, Linda J. W. Shimon, Yael
Diskin-Posner, Liat Avram, Petr Král, and Rafal Klajn. “Reversible Chromism of
Spiropyran in the Cavity of a Flexible Coordination Cage.” Nature Communications.
Springer Nature, 2018. https://doi.org/10.1038/s41467-017-02715-6.
ieee: D. Samanta et al., “Reversible chromism of spiropyran in the cavity
of a flexible coordination cage,” Nature Communications, vol. 9. Springer
Nature, 2018.
ista: Samanta D, Galaktionova D, Gemen J, Shimon LJW, Diskin-Posner Y, Avram L,
Král P, Klajn R. 2018. Reversible chromism of spiropyran in the cavity of a flexible
coordination cage. Nature Communications. 9, 641.
mla: Samanta, Dipak, et al. “Reversible Chromism of Spiropyran in the Cavity of
a Flexible Coordination Cage.” Nature Communications, vol. 9, 641, Springer
Nature, 2018, doi:10.1038/s41467-017-02715-6.
short: D. Samanta, D. Galaktionova, J. Gemen, L.J.W. Shimon, Y. Diskin-Posner, L.
Avram, P. Král, R. Klajn, Nature Communications 9 (2018).
date_created: 2023-08-01T09:39:32Z
date_published: 2018-02-13T00:00:00Z
date_updated: 2024-10-14T12:14:34Z
day: '13'
doi: 10.1038/s41467-017-02715-6
extern: '1'
external_id:
pmid:
- '29440687'
intvolume: ' 9'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-017-02715-6
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41467-018-03701-2
scopus_import: '1'
status: public
title: Reversible chromism of spiropyran in the cavity of a flexible coordination
cage
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
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: 2024-10-14T12:14:53Z
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: '14284'
abstract:
- lang: eng
text: Pore-forming toxins (PFT) are virulence factors that transform from soluble
to membrane-bound states. The Yersinia YaxAB system represents a family of binary
α-PFTs with orthologues in human, insect, and plant pathogens, with unknown structures.
YaxAB was shown to be cytotoxic and likely involved in pathogenesis, though the
molecular basis for its two-component lytic mechanism remains elusive. Here, we
present crystal structures of YaxA and YaxB, together with a cryo-electron microscopy
map of the YaxAB complex. Our structures reveal a pore predominantly composed
of decamers of YaxA–YaxB heterodimers. Both subunits bear membrane-active moieties,
but only YaxA is capable of binding to membranes by itself. YaxB can subsequently
be recruited to membrane-associated YaxA and induced to present its lytic transmembrane
helices. Pore formation can progress by further oligomerization of YaxA–YaxB dimers.
Our results allow for a comparison between pore assemblies belonging to the wider
ClyA-like family of α-PFTs, highlighting diverse pore architectures.
article_number: '1806'
article_processing_charge: No
article_type: original
author:
- first_name: Bastian
full_name: Bräuning, Bastian
last_name: Bräuning
- first_name: Eva
full_name: Bertosin, Eva
last_name: Bertosin
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Christian
full_name: Ihling, Christian
last_name: Ihling
- first_name: Alexandra
full_name: Schatt, Alexandra
last_name: Schatt
- first_name: Agnes
full_name: Adler, Agnes
last_name: Adler
- first_name: Klaus
full_name: Richter, Klaus
last_name: Richter
- first_name: Andrea
full_name: Sinz, Andrea
last_name: Sinz
- first_name: Hendrik
full_name: Dietz, Hendrik
last_name: Dietz
- first_name: Michael
full_name: Groll, Michael
last_name: Groll
citation:
ama: Bräuning B, Bertosin E, Praetorius FM, et al. Structure and mechanism of the
two-component α-helical pore-forming toxin YaxAB. Nature Communications.
2018;9. doi:10.1038/s41467-018-04139-2
apa: Bräuning, B., Bertosin, E., Praetorius, F. M., Ihling, C., Schatt, A., Adler,
A., … Groll, M. (2018). Structure and mechanism of the two-component α-helical
pore-forming toxin YaxAB. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-04139-2
chicago: Bräuning, Bastian, Eva Bertosin, Florian M Praetorius, Christian Ihling,
Alexandra Schatt, Agnes Adler, Klaus Richter, Andrea Sinz, Hendrik Dietz, and
Michael Groll. “Structure and Mechanism of the Two-Component α-Helical Pore-Forming
Toxin YaxAB.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-04139-2.
ieee: B. Bräuning et al., “Structure and mechanism of the two-component α-helical
pore-forming toxin YaxAB,” Nature Communications, vol. 9. Springer Nature,
2018.
ista: Bräuning B, Bertosin E, Praetorius FM, Ihling C, Schatt A, Adler A, Richter
K, Sinz A, Dietz H, Groll M. 2018. Structure and mechanism of the two-component
α-helical pore-forming toxin YaxAB. Nature Communications. 9, 1806.
mla: Bräuning, Bastian, et al. “Structure and Mechanism of the Two-Component α-Helical
Pore-Forming Toxin YaxAB.” Nature Communications, vol. 9, 1806, Springer
Nature, 2018, doi:10.1038/s41467-018-04139-2.
short: B. Bräuning, E. Bertosin, F.M. Praetorius, C. Ihling, A. Schatt, A. Adler,
K. Richter, A. Sinz, H. Dietz, M. Groll, Nature Communications 9 (2018).
date_created: 2023-09-06T12:07:33Z
date_published: 2018-05-04T00:00:00Z
date_updated: 2023-11-07T11:46:12Z
day: '04'
doi: 10.1038/s41467-018-04139-2
extern: '1'
external_id:
pmid:
- '29728606'
intvolume: ' 9'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-018-04139-2
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2018'
...
---
_id: '8618'
abstract:
- lang: eng
text: The reversibly switchable fluorescent proteins (RSFPs) commonly used for RESOLFT
nanoscopy have been developed from fluorescent proteins of the GFP superfamily.
These proteins are bright, but exhibit several drawbacks such as relatively large
size, oxygen-dependence, sensitivity to low pH, and limited switching speed. Therefore,
RSFPs from other origins with improved properties need to be explored. Here, we
report the development of two RSFPs based on the LOV domain of the photoreceptor
protein YtvA from Bacillus subtilis. LOV domains obtain their fluorescence by
association with the abundant cellular cofactor flavin mononucleotide (FMN). Under
illumination with blue and ultraviolet light, they undergo a photocycle, making
these proteins inherently photoswitchable. Our first improved variant, rsLOV1,
can be used for RESOLFT imaging, whereas rsLOV2 proved useful for STED nanoscopy
of living cells with a resolution of down to 50 nm. In addition to their smaller
size compared to GFP-related proteins (17 kDa instead of 27 kDa) and their usability
at low pH, rsLOV1 and rsLOV2 exhibit faster switching kinetics, switching on and
off 3 times faster than rsEGFP2, the fastest-switching RSFP reported to date.
Therefore, LOV-domain-based RSFPs have potential for applications where the switching
speed of GFP-based proteins is limiting.
article_number: '2724'
article_processing_charge: No
article_type: original
author:
- first_name: Carola
full_name: Gregor, Carola
last_name: Gregor
- first_name: Sven C.
full_name: Sidenstein, Sven C.
last_name: Sidenstein
- first_name: Martin
full_name: Andresen, Martin
last_name: Andresen
- first_name: Steffen J.
full_name: Sahl, Steffen J.
last_name: Sahl
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Stefan W.
full_name: Hell, Stefan W.
last_name: Hell
citation:
ama: Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. Novel reversibly
switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from
the bacterial photoreceptor YtvA. Scientific Reports. 2018;8. doi:10.1038/s41598-018-19947-1
apa: Gregor, C., Sidenstein, S. C., Andresen, M., Sahl, S. J., Danzl, J. G., &
Hell, S. W. (2018). Novel reversibly switchable fluorescent proteins for RESOLFT
and STED nanoscopy engineered from the bacterial photoreceptor YtvA. Scientific
Reports. Springer Nature. https://doi.org/10.1038/s41598-018-19947-1
chicago: Gregor, Carola, Sven C. Sidenstein, Martin Andresen, Steffen J. Sahl, Johann
G Danzl, and Stefan W. Hell. “Novel Reversibly Switchable Fluorescent Proteins
for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.”
Scientific Reports. Springer Nature, 2018. https://doi.org/10.1038/s41598-018-19947-1.
ieee: C. Gregor, S. C. Sidenstein, M. Andresen, S. J. Sahl, J. G. Danzl, and S.
W. Hell, “Novel reversibly switchable fluorescent proteins for RESOLFT and STED
nanoscopy engineered from the bacterial photoreceptor YtvA,” Scientific Reports,
vol. 8. Springer Nature, 2018.
ista: Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. 2018. Novel
reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered
from the bacterial photoreceptor YtvA. Scientific Reports. 8, 2724.
mla: Gregor, Carola, et al. “Novel Reversibly Switchable Fluorescent Proteins for
RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.”
Scientific Reports, vol. 8, 2724, Springer Nature, 2018, doi:10.1038/s41598-018-19947-1.
short: C. Gregor, S.C. Sidenstein, M. Andresen, S.J. Sahl, J.G. Danzl, S.W. Hell,
Scientific Reports 8 (2018).
date_created: 2020-10-06T16:33:37Z
date_published: 2018-02-09T00:00:00Z
date_updated: 2024-10-21T06:02:43Z
day: '09'
ddc:
- '570'
department:
- _id: JoDa
doi: 10.1038/s41598-018-19947-1
external_id:
isi:
- '000424630400037'
pmid:
- '29426833'
file:
- access_level: open_access
checksum: e642080fcbde9584c63544f587c74f03
content_type: application/pdf
creator: dernst
date_created: 2020-10-06T16:35:16Z
date_updated: 2020-10-06T16:35:16Z
file_id: '8619'
file_name: 2018_ScientificReports_Gregor.pdf
file_size: 2818077
relation: main_file
success: 1
file_date_updated: 2020-10-06T16:35:16Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
keyword:
- Multidisciplinary
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific Reports
publication_identifier:
issn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy
engineered from the bacterial photoreceptor YtvA
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2018'
...
---
_id: '9135'
abstract:
- lang: eng
text: Idealized simulations of tropical moist convection have revealed that clouds
can spontaneously clump together in a process called self-aggregation. This results
in a state where a moist cloudy region with intense deep convection is surrounded
by extremely dry subsiding air devoid of deep convection. Because of the idealized
settings of the simulations where it was discovered, the relevance of self-aggregation
to the real world is still debated. Here, we show that self-aggregation feedbacks
play a leading-order role in the spontaneous genesis of tropical cyclones in cloud-resolving
simulations. Those feedbacks accelerate the cyclogenesis process by a factor of
2, and the feedbacks contributing to the cyclone formation show qualitative and
quantitative agreement with the self-aggregation process. Once the cyclone is
formed, wind-induced surface heat exchange (WISHE) effects dominate, although
we find that self-aggregation feedbacks have a small but nonnegligible contribution
to the maintenance of the mature cyclone. Our results suggest that self-aggregation,
and the framework developed for its study, can help shed more light into the physical
processes leading to cyclogenesis and cyclone intensification. In particular,
our results point out the importance of the longwave radiative cooling outside
the cyclone.
article_processing_charge: No
article_type: original
author:
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: David M.
full_name: Romps, David M.
last_name: Romps
citation:
ama: Muller CJ, Romps DM. Acceleration of tropical cyclogenesis by self-aggregation
feedbacks. Proceedings of the National Academy of Sciences. 2018;115(12):2930-2935.
doi:10.1073/pnas.1719967115
apa: Muller, C. J., & Romps, D. M. (2018). Acceleration of tropical cyclogenesis
by self-aggregation feedbacks. Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1719967115
chicago: Muller, Caroline J, and David M. Romps. “Acceleration of Tropical Cyclogenesis
by Self-Aggregation Feedbacks.” Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1719967115.
ieee: C. J. Muller and D. M. Romps, “Acceleration of tropical cyclogenesis by self-aggregation
feedbacks,” Proceedings of the National Academy of Sciences, vol. 115,
no. 12. Proceedings of the National Academy of Sciences, pp. 2930–2935, 2018.
ista: Muller CJ, Romps DM. 2018. Acceleration of tropical cyclogenesis by self-aggregation
feedbacks. Proceedings of the National Academy of Sciences. 115(12), 2930–2935.
mla: Muller, Caroline J., and David M. Romps. “Acceleration of Tropical Cyclogenesis
by Self-Aggregation Feedbacks.” Proceedings of the National Academy of Sciences,
vol. 115, no. 12, Proceedings of the National Academy of Sciences, 2018, pp. 2930–35,
doi:10.1073/pnas.1719967115.
short: C.J. Muller, D.M. Romps, Proceedings of the National Academy of Sciences
115 (2018) 2930–2935.
date_created: 2021-02-15T14:18:16Z
date_published: 2018-03-20T00:00:00Z
date_updated: 2022-01-24T12:39:49Z
day: '20'
doi: 10.1073/pnas.1719967115
extern: '1'
intvolume: ' 115'
issue: '12'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1719967115
month: '03'
oa: 1
oa_version: Published Version
page: 2930-2935
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: Acceleration of tropical cyclogenesis by self-aggregation feedbacks
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 115
year: '2018'
...
---
_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: '13381'
abstract:
- lang: eng
text: Self-assembly of inorganic nanoparticles has been used to prepare hundreds
of different colloidal crystals, but almost invariably with the restriction that
the particles must be densely packed. Here, we show that non–close-packed nanoparticle
arrays can be fabricated through the selective removal of one of two components
comprising binary nanoparticle superlattices. First, a variety of binary nanoparticle
superlattices were prepared at the liquid-air interface, including several arrangements
that were previously unknown. Molecular dynamics simulations revealed the particular
role of the liquid in templating the formation of superlattices not achievable
through self-assembly in bulk solution. Second, upon stabilization, all of these
binary superlattices could be transformed into distinct “nanoallotropes”—nanoporous
materials having the same chemical composition but differing in their nanoscale
architectures.
article_processing_charge: No
article_type: original
author:
- first_name: Thumu
full_name: Udayabhaskararao, Thumu
last_name: Udayabhaskararao
- first_name: Thomas
full_name: Altantzis, Thomas
last_name: Altantzis
- first_name: Lothar
full_name: Houben, Lothar
last_name: Houben
- first_name: Marc
full_name: Coronado-Puchau, Marc
last_name: Coronado-Puchau
- first_name: Judith
full_name: Langer, Judith
last_name: Langer
- first_name: Ronit
full_name: Popovitz-Biro, Ronit
last_name: Popovitz-Biro
- first_name: Luis M.
full_name: Liz-Marzán, Luis M.
last_name: Liz-Marzán
- first_name: Lela
full_name: Vuković, Lela
last_name: Vuković
- first_name: Petr
full_name: Král, Petr
last_name: Král
- first_name: Sara
full_name: Bals, Sara
last_name: Bals
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Udayabhaskararao T, Altantzis T, Houben L, et al. Tunable porous nanoallotropes
prepared by post-assembly etching of binary nanoparticle superlattices. Science.
2017;358(6362):514-518. doi:10.1126/science.aan6046
apa: Udayabhaskararao, T., Altantzis, T., Houben, L., Coronado-Puchau, M., Langer,
J., Popovitz-Biro, R., … Klajn, R. (2017). Tunable porous nanoallotropes prepared
by post-assembly etching of binary nanoparticle superlattices. Science.
American Association for the Advancement of Science. https://doi.org/10.1126/science.aan6046
chicago: Udayabhaskararao, Thumu, Thomas Altantzis, Lothar Houben, Marc Coronado-Puchau,
Judith Langer, Ronit Popovitz-Biro, Luis M. Liz-Marzán, et al. “Tunable Porous
Nanoallotropes Prepared by Post-Assembly Etching of Binary Nanoparticle Superlattices.”
Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aan6046.
ieee: T. Udayabhaskararao et al., “Tunable porous nanoallotropes prepared
by post-assembly etching of binary nanoparticle superlattices,” Science,
vol. 358, no. 6362. American Association for the Advancement of Science, pp. 514–518,
2017.
ista: Udayabhaskararao T, Altantzis T, Houben L, Coronado-Puchau M, Langer J, Popovitz-Biro
R, Liz-Marzán LM, Vuković L, Král P, Bals S, Klajn R. 2017. Tunable porous nanoallotropes
prepared by post-assembly etching of binary nanoparticle superlattices. Science.
358(6362), 514–518.
mla: Udayabhaskararao, Thumu, et al. “Tunable Porous Nanoallotropes Prepared by
Post-Assembly Etching of Binary Nanoparticle Superlattices.” Science, vol.
358, no. 6362, American Association for the Advancement of Science, 2017, pp.
514–18, doi:10.1126/science.aan6046.
short: T. Udayabhaskararao, T. Altantzis, L. Houben, M. Coronado-Puchau, J. Langer,
R. Popovitz-Biro, L.M. Liz-Marzán, L. Vuković, P. Král, S. Bals, R. Klajn, Science
358 (2017) 514–518.
date_created: 2023-08-01T09:41:16Z
date_published: 2017-10-27T00:00:00Z
date_updated: 2024-10-14T12:15:38Z
day: '27'
doi: 10.1126/science.aan6046
extern: '1'
external_id:
pmid:
- '29074773'
intvolume: ' 358'
issue: '6362'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://repository.uantwerpen.be/docman/irua/8d722e/147242_2018_06_07.pdf
month: '10'
oa: 1
oa_version: Submitted Version
page: 514-518
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tunable porous nanoallotropes prepared by post-assembly etching of binary nanoparticle
superlattices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 358
year: '2017'
...
---
_id: '13384'
abstract:
- lang: eng
text: Although methane is a volatile gas, it can be efficiently trapped in ice,
which can then be readily set on fire. Beyond the curiosity of this “burning ice,”
caged methane is of great importance as one of the world's largest natural gas
resources. In these materials, known as clathrates, methane molecules are tightly
bound in nanometer-sized, regularly interspaced cages. Other inorganic materials,
such as the silica mineral chibaite, can similarly encapsulate methane and higher
hydrocarbons. Simple organic compounds have also been found to trap various organic
molecules upon crystallization.
article_processing_charge: No
article_type: original
author:
- first_name: Dipak
full_name: Samanta, Dipak
last_name: Samanta
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Samanta D, Klajn R. Clathrates grow up. Science. 2017;355(6328):912-912.
doi:10.1126/science.aam7927
apa: Samanta, D., & Klajn, R. (2017). Clathrates grow up. Science. American
Association for the Advancement of Science. https://doi.org/10.1126/science.aam7927
chicago: Samanta, Dipak, and Rafal Klajn. “Clathrates Grow Up.” Science.
American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aam7927.
ieee: D. Samanta and R. Klajn, “Clathrates grow up,” Science, vol. 355, no.
6328. American Association for the Advancement of Science, pp. 912–912, 2017.
ista: Samanta D, Klajn R. 2017. Clathrates grow up. Science. 355(6328), 912–912.
mla: Samanta, Dipak, and Rafal Klajn. “Clathrates Grow Up.” Science, vol.
355, no. 6328, American Association for the Advancement of Science, 2017, pp.
912–912, doi:10.1126/science.aam7927.
short: D. Samanta, R. Klajn, Science 355 (2017) 912–912.
date_created: 2023-08-01T09:41:55Z
date_published: 2017-03-03T00:00:00Z
date_updated: 2024-10-14T12:16:09Z
day: '03'
doi: 10.1126/science.aam7927
extern: '1'
external_id:
pmid:
- '28254902'
intvolume: ' 355'
issue: '6328'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '03'
oa_version: None
page: 912-912
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Clathrates grow up
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 355
year: '2017'
...
---
_id: '14005'
abstract:
- lang: eng
text: Strong-field photoelectron holography and laser-induced electron diffraction
(LIED) are two powerful emerging methods for probing the ultrafast dynamics of
molecules. However, both of them have remained restricted to static systems and
to nuclear dynamics induced by strong-field ionization. Here we extend these promising
methods to image purely electronic valence-shell dynamics in molecules using photoelectron
holography. In the same experiment, we use LIED and photoelectron holography simultaneously,
to observe coupled electronic-rotational dynamics taking place on similar timescales.
These results offer perspectives for imaging ultrafast dynamics of molecules on
femtosecond to attosecond timescales.
article_number: '15651'
article_processing_charge: No
article_type: original
author:
- first_name: Samuel G.
full_name: Walt, Samuel G.
last_name: Walt
- first_name: Niraghatam
full_name: Bhargava Ram, Niraghatam
last_name: Bhargava Ram
- first_name: Marcos
full_name: Atala, Marcos
last_name: Atala
- first_name: Nikolay I
full_name: Shvetsov-Shilovski, Nikolay I
last_name: Shvetsov-Shilovski
- first_name: Aaron
full_name: von Conta, Aaron
last_name: von Conta
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Manfred
full_name: Lein, Manfred
last_name: Lein
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
citation:
ama: Walt SG, Bhargava Ram N, Atala M, et al. Dynamics of valence-shell electrons
and nuclei probed by strong-field holography and rescattering. Nature Communications.
2017;8. doi:10.1038/ncomms15651
apa: Walt, S. G., Bhargava Ram, N., Atala, M., Shvetsov-Shilovski, N. I., von Conta,
A., Baykusheva, D. R., … Wörner, H. J. (2017). Dynamics of valence-shell electrons
and nuclei probed by strong-field holography and rescattering. Nature Communications.
Springer Nature. https://doi.org/10.1038/ncomms15651
chicago: Walt, Samuel G., Niraghatam Bhargava Ram, Marcos Atala, Nikolay I Shvetsov-Shilovski,
Aaron von Conta, Denitsa Rangelova Baykusheva, Manfred Lein, and Hans Jakob Wörner.
“Dynamics of Valence-Shell Electrons and Nuclei Probed by Strong-Field Holography
and Rescattering.” Nature Communications. Springer Nature, 2017. https://doi.org/10.1038/ncomms15651.
ieee: S. G. Walt et al., “Dynamics of valence-shell electrons and nuclei
probed by strong-field holography and rescattering,” Nature Communications,
vol. 8. Springer Nature, 2017.
ista: Walt SG, Bhargava Ram N, Atala M, Shvetsov-Shilovski NI, von Conta A, Baykusheva
DR, Lein M, Wörner HJ. 2017. Dynamics of valence-shell electrons and nuclei probed
by strong-field holography and rescattering. Nature Communications. 8, 15651.
mla: Walt, Samuel G., et al. “Dynamics of Valence-Shell Electrons and Nuclei Probed
by Strong-Field Holography and Rescattering.” Nature Communications, vol.
8, 15651, Springer Nature, 2017, doi:10.1038/ncomms15651.
short: S.G. Walt, N. Bhargava Ram, M. Atala, N.I. Shvetsov-Shilovski, A. von Conta,
D.R. Baykusheva, M. Lein, H.J. Wörner, Nature Communications 8 (2017).
date_created: 2023-08-10T06:36:09Z
date_published: 2017-06-15T00:00:00Z
date_updated: 2023-08-22T08:26:06Z
day: '15'
doi: 10.1038/ncomms15651
extern: '1'
external_id:
pmid:
- '28643771'
intvolume: ' 8'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/ncomms15651
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamics of valence-shell electrons and nuclei probed by strong-field holography
and rescattering
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '14008'
abstract:
- lang: eng
text: Time-resolved x-ray absorption spectroscopy (TR-XAS) has so far practically
been limited to large-scale facilities, to subpicosecond temporal resolution,
and to the condensed phase. We report the realization of TR-XAS with a temporal
resolution in the low femtosecond range by developing a tabletop high-harmonic
source reaching up to 350 electron volts, thus partially covering the spectral
region of 280 to 530 electron volts, where water is transmissive. We used this
source to follow previously unexamined light-induced chemical reactions in the
lowest electronic states of isolated CF4+ and SF6+ molecules in the gas phase.
By probing element-specific core-to-valence transitions at the carbon K-edge or
the sulfur L-edges, we characterized their reaction paths and observed the effect
of symmetry breaking through the splitting of absorption bands and Rydberg-valence
mixing induced by the geometry changes.
article_processing_charge: No
article_type: original
author:
- first_name: Yoann
full_name: Pertot, Yoann
last_name: Pertot
- first_name: Cédric
full_name: Schmidt, Cédric
last_name: Schmidt
- first_name: Mary
full_name: Matthews, Mary
last_name: Matthews
- first_name: Adrien
full_name: Chauvet, Adrien
last_name: Chauvet
- first_name: Martin
full_name: Huppert, Martin
last_name: Huppert
- first_name: Vit
full_name: Svoboda, Vit
last_name: Svoboda
- first_name: Aaron
full_name: von Conta, Aaron
last_name: von Conta
- first_name: Andres
full_name: Tehlar, Andres
last_name: Tehlar
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Jean-Pierre
full_name: Wolf, Jean-Pierre
last_name: Wolf
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
citation:
ama: Pertot Y, Schmidt C, Matthews M, et al. Time-resolved x-ray absorption spectroscopy
with a water window high-harmonic source. Science. 2017;355(6322):264-267.
doi:10.1126/science.aah6114
apa: Pertot, Y., Schmidt, C., Matthews, M., Chauvet, A., Huppert, M., Svoboda, V.,
… Wörner, H. J. (2017). Time-resolved x-ray absorption spectroscopy with a water
window high-harmonic source. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.aah6114
chicago: Pertot, Yoann, Cédric Schmidt, Mary Matthews, Adrien Chauvet, Martin Huppert,
Vit Svoboda, Aaron von Conta, et al. “Time-Resolved x-Ray Absorption Spectroscopy
with a Water Window High-Harmonic Source.” Science. American Association
for the Advancement of Science, 2017. https://doi.org/10.1126/science.aah6114.
ieee: Y. Pertot et al., “Time-resolved x-ray absorption spectroscopy with
a water window high-harmonic source,” Science, vol. 355, no. 6322. American
Association for the Advancement of Science, pp. 264–267, 2017.
ista: Pertot Y, Schmidt C, Matthews M, Chauvet A, Huppert M, Svoboda V, von Conta
A, Tehlar A, Baykusheva DR, Wolf J-P, Wörner HJ. 2017. Time-resolved x-ray absorption
spectroscopy with a water window high-harmonic source. Science. 355(6322), 264–267.
mla: Pertot, Yoann, et al. “Time-Resolved x-Ray Absorption Spectroscopy with a Water
Window High-Harmonic Source.” Science, vol. 355, no. 6322, American Association
for the Advancement of Science, 2017, pp. 264–67, doi:10.1126/science.aah6114.
short: Y. Pertot, C. Schmidt, M. Matthews, A. Chauvet, M. Huppert, V. Svoboda, A.
von Conta, A. Tehlar, D.R. Baykusheva, J.-P. Wolf, H.J. Wörner, Science 355 (2017)
264–267.
date_created: 2023-08-10T06:36:39Z
date_published: 2017-01-05T00:00:00Z
date_updated: 2023-08-22T08:34:38Z
day: '05'
doi: 10.1126/science.aah6114
extern: '1'
external_id:
pmid:
- '28059713'
intvolume: ' 355'
issue: '6322'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '01'
oa_version: None
page: 264-267
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Time-resolved x-ray absorption spectroscopy with a water window high-harmonic
source
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 355
year: '2017'
...
---
_id: '15156'
abstract:
- lang: eng
text: Circadian clocks are ubiquitous timing systems that induce rhythms of biological
activities in synchrony with night and day. In cyanobacteria, timing is generated
by a posttranslational clock consisting of KaiA, KaiB, and KaiC proteins and a
set of output signaling proteins, SasA and CikA, which transduce this rhythm to
control gene expression. Here, we describe crystal and nuclear magnetic resonance
structures of KaiB-KaiC,KaiA-KaiB-KaiC, and CikA-KaiB complexes. They reveal how
the metamorphic properties of KaiB, a protein that adopts two distinct folds,
and the post–adenosine triphosphate hydrolysis state of KaiC create a hub around
which nighttime signaling events revolve, including inactivation of KaiA and reciprocal
regulation of the mutually antagonistic signaling proteins, SasA and CikA.
article_processing_charge: No
article_type: original
author:
- first_name: Roger
full_name: Tseng, Roger
last_name: Tseng
- first_name: Nicolette F.
full_name: Goularte, Nicolette F.
last_name: Goularte
- first_name: Archana
full_name: Chavan, Archana
last_name: Chavan
- first_name: Jansen
full_name: Luu, Jansen
last_name: Luu
- first_name: Susan E.
full_name: Cohen, Susan E.
last_name: Cohen
- first_name: Yong-Gang
full_name: Chang, Yong-Gang
last_name: Chang
- first_name: Joel
full_name: Heisler, Joel
last_name: Heisler
- first_name: Sheng
full_name: Li, Sheng
last_name: Li
- first_name: Alicia Kathleen
full_name: Michael, Alicia Kathleen
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
- first_name: Sarvind
full_name: Tripathi, Sarvind
last_name: Tripathi
- first_name: Susan S.
full_name: Golden, Susan S.
last_name: Golden
- first_name: Andy
full_name: LiWang, Andy
last_name: LiWang
- first_name: Carrie L.
full_name: Partch, Carrie L.
last_name: Partch
citation:
ama: Tseng R, Goularte NF, Chavan A, et al. Structural basis of the day-night transition
in a bacterial circadian clock. Science. 2017;355(6330):1174-1180. doi:10.1126/science.aag2516
apa: Tseng, R., Goularte, N. F., Chavan, A., Luu, J., Cohen, S. E., Chang, Y.-G.,
… Partch, C. L. (2017). Structural basis of the day-night transition in a bacterial
circadian clock. Science. American Association for the Advancement of Science.
https://doi.org/10.1126/science.aag2516
chicago: Tseng, Roger, Nicolette F. Goularte, Archana Chavan, Jansen Luu, Susan
E. Cohen, Yong-Gang Chang, Joel Heisler, et al. “Structural Basis of the Day-Night
Transition in a Bacterial Circadian Clock.” Science. American Association
for the Advancement of Science, 2017. https://doi.org/10.1126/science.aag2516.
ieee: R. Tseng et al., “Structural basis of the day-night transition in a
bacterial circadian clock,” Science, vol. 355, no. 6330. American Association
for the Advancement of Science, pp. 1174–1180, 2017.
ista: Tseng R, Goularte NF, Chavan A, Luu J, Cohen SE, Chang Y-G, Heisler J, Li
S, Michael AK, Tripathi S, Golden SS, LiWang A, Partch CL. 2017. Structural basis
of the day-night transition in a bacterial circadian clock. Science. 355(6330),
1174–1180.
mla: Tseng, Roger, et al. “Structural Basis of the Day-Night Transition in a Bacterial
Circadian Clock.” Science, vol. 355, no. 6330, American Association for
the Advancement of Science, 2017, pp. 1174–80, doi:10.1126/science.aag2516.
short: R. Tseng, N.F. Goularte, A. Chavan, J. Luu, S.E. Cohen, Y.-G. Chang, J. Heisler,
S. Li, A.K. Michael, S. Tripathi, S.S. Golden, A. LiWang, C.L. Partch, Science
355 (2017) 1174–1180.
date_created: 2024-03-21T07:56:24Z
date_published: 2017-03-17T00:00:00Z
date_updated: 2024-03-25T12:16:44Z
day: '17'
doi: 10.1126/science.aag2516
extern: '1'
intvolume: ' 355'
issue: '6330'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '03'
oa_version: None
page: 1174-1180
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structural basis of the day-night transition in a bacterial circadian clock
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 355
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: '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
arxiv: 1
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: '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'
...