---
_id: '8458'
abstract:
- lang: eng
text: The maintenance of bacterial cell shape and integrity is largely attributed
to peptidoglycan, a highly cross-linked biopolymer. The transpeptidases that perform
this cross-linking are important targets for antibiotics. Despite this biomedical
importance, to date no structure of a protein in complex with an intact bacterial
peptidoglycan has been resolved, primarily due to the large size and flexibility
of peptidoglycan sacculi. Here we use solid-state NMR spectroscopy to derive for
the first time an atomic model of an l,d-transpeptidase from Bacillus subtilis
bound to its natural substrate, the intact B. subtilis peptidoglycan. Importantly,
the model obtained from protein chemical shift perturbation data shows that both
domains—the catalytic domain as well as the proposed peptidoglycan recognition
domain—are important for the interaction and reveals a novel binding motif that
involves residues outside of the classical enzymatic pocket. Experiments on mutants
and truncated protein constructs independently confirm the binding site and the
implication of both domains. Through measurements of dipolar-coupling derived
order parameters of bond motion we show that protein binding reduces the flexibility
of peptidoglycan. This first report of an atomic model of a protein–peptidoglycan
complex paves the way for the design of new antibiotic drugs targeting l,d-transpeptidases.
The strategy developed here can be extended to the study of a large variety of
enzymes involved in peptidoglycan morphogenesis.
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: Sébastien
full_name: Triboulet, Sébastien
last_name: Triboulet
- first_name: Cédric
full_name: Laguri, Cédric
last_name: Laguri
- first_name: Catherine M.
full_name: Bougault, Catherine M.
last_name: Bougault
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Morgane
full_name: Callon, Morgane
last_name: Callon
- first_name: Michel
full_name: Arthur, Michel
last_name: Arthur
- first_name: Jean-Pierre
full_name: Simorre, Jean-Pierre
last_name: Simorre
citation:
ama: Schanda P, Triboulet S, Laguri C, et al. Atomic model of a cell-wall cross-linking
enzyme in complex with an intact bacterial peptidoglycan. Journal of the American
Chemical Society. 2014;136(51):17852-17860. doi:10.1021/ja5105987
apa: Schanda, P., Triboulet, S., Laguri, C., Bougault, C. M., Ayala, I., Callon,
M., … Simorre, J.-P. (2014). Atomic model of a cell-wall cross-linking enzyme
in complex with an intact bacterial peptidoglycan. Journal of the American
Chemical Society. American Chemical Society. https://doi.org/10.1021/ja5105987
chicago: Schanda, Paul, Sébastien Triboulet, Cédric Laguri, Catherine M. Bougault,
Isabel Ayala, Morgane Callon, Michel Arthur, and Jean-Pierre Simorre. “Atomic
Model of a Cell-Wall Cross-Linking Enzyme in Complex with an Intact Bacterial
Peptidoglycan.” Journal of the American Chemical Society. American Chemical
Society, 2014. https://doi.org/10.1021/ja5105987.
ieee: P. Schanda et al., “Atomic model of a cell-wall cross-linking enzyme
in complex with an intact bacterial peptidoglycan,” Journal of the American
Chemical Society, vol. 136, no. 51. American Chemical Society, pp. 17852–17860,
2014.
ista: Schanda P, Triboulet S, Laguri C, Bougault CM, Ayala I, Callon M, Arthur M,
Simorre J-P. 2014. Atomic model of a cell-wall cross-linking enzyme in complex
with an intact bacterial peptidoglycan. Journal of the American Chemical Society.
136(51), 17852–17860.
mla: Schanda, Paul, et al. “Atomic Model of a Cell-Wall Cross-Linking Enzyme in
Complex with an Intact Bacterial Peptidoglycan.” Journal of the American Chemical
Society, vol. 136, no. 51, American Chemical Society, 2014, pp. 17852–60,
doi:10.1021/ja5105987.
short: P. Schanda, S. Triboulet, C. Laguri, C.M. Bougault, I. Ayala, M. Callon,
M. Arthur, J.-P. Simorre, Journal of the American Chemical Society 136 (2014)
17852–17860.
date_created: 2020-09-18T10:07:52Z
date_published: 2014-11-27T00:00:00Z
date_updated: 2021-01-12T08:19:24Z
day: '27'
doi: 10.1021/ja5105987
extern: '1'
intvolume: ' 136'
issue: '51'
language:
- iso: eng
month: '11'
oa_version: None
page: 17852-17860
publication: Journal of the American Chemical Society
publication_identifier:
issn:
- 0002-7863
- 1520-5126
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Atomic model of a cell-wall cross-linking enzyme in complex with an intact
bacterial peptidoglycan
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 136
year: '2014'
...
---
_id: '8459'
abstract:
- lang: eng
text: Nuclear magnetic resonance (NMR) is a powerful tool for observing the motion
of biomolecules at the atomic level. One technique, the analysis of relaxation
dispersion phenomenon, is highly suited for studying the kinetics and thermodynamics
of biological processes. Built on top of the relax computational environment for
NMR dynamics is a new dispersion analysis designed to be comprehensive, accurate
and easy-to-use. The software supports more models, both numeric and analytic,
than current solutions. An automated protocol, available for scripting and driving
the graphical user interface (GUI), is designed to simplify the analysis of dispersion
data for NMR spectroscopists. Decreases in optimization time are granted by parallelization
for running on computer clusters and by skipping an initial grid search by using
parameters from one solution as the starting point for another —using analytic
model results for the numeric models, taking advantage of model nesting, and using
averaged non-clustered results for the clustered analysis.
article_processing_charge: No
article_type: original
author:
- first_name: Sébastien
full_name: Morin, Sébastien
last_name: Morin
- first_name: Troels E
full_name: Linnet, Troels E
last_name: Linnet
- first_name: Mathilde
full_name: Lescanne, Mathilde
last_name: Lescanne
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Gary S
full_name: Thompson, Gary S
last_name: Thompson
- first_name: Martin
full_name: Tollinger, Martin
last_name: Tollinger
- first_name: Kaare
full_name: Teilum, Kaare
last_name: Teilum
- first_name: Stéphane
full_name: Gagné, Stéphane
last_name: Gagné
- first_name: Dominique
full_name: Marion, Dominique
last_name: Marion
- first_name: Christian
full_name: Griesinger, Christian
last_name: Griesinger
- first_name: Martin
full_name: Blackledge, Martin
last_name: Blackledge
- first_name: Edward J
full_name: d’Auvergne, Edward J
last_name: d’Auvergne
citation:
ama: 'Morin S, Linnet TE, Lescanne M, et al. Relax: The analysis of biomolecular
kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics.
2014;30(15):2219-2220. doi:10.1093/bioinformatics/btu166'
apa: 'Morin, S., Linnet, T. E., Lescanne, M., Schanda, P., Thompson, G. S., Tollinger,
M., … d’Auvergne, E. J. (2014). Relax: The analysis of biomolecular kinetics and
thermodynamics using NMR relaxation dispersion data. Bioinformatics. Oxford
University Press. https://doi.org/10.1093/bioinformatics/btu166'
chicago: 'Morin, Sébastien, Troels E Linnet, Mathilde Lescanne, Paul Schanda, Gary
S Thompson, Martin Tollinger, Kaare Teilum, et al. “Relax: The Analysis of Biomolecular
Kinetics and Thermodynamics Using NMR Relaxation Dispersion Data.” Bioinformatics.
Oxford University Press, 2014. https://doi.org/10.1093/bioinformatics/btu166.'
ieee: 'S. Morin et al., “Relax: The analysis of biomolecular kinetics and
thermodynamics using NMR relaxation dispersion data,” Bioinformatics, vol.
30, no. 15. Oxford University Press, pp. 2219–2220, 2014.'
ista: 'Morin S, Linnet TE, Lescanne M, Schanda P, Thompson GS, Tollinger M, Teilum
K, Gagné S, Marion D, Griesinger C, Blackledge M, d’Auvergne EJ. 2014. Relax:
The analysis of biomolecular kinetics and thermodynamics using NMR relaxation
dispersion data. Bioinformatics. 30(15), 2219–2220.'
mla: 'Morin, Sébastien, et al. “Relax: The Analysis of Biomolecular Kinetics and
Thermodynamics Using NMR Relaxation Dispersion Data.” Bioinformatics, vol.
30, no. 15, Oxford University Press, 2014, pp. 2219–20, doi:10.1093/bioinformatics/btu166.'
short: S. Morin, T.E. Linnet, M. Lescanne, P. Schanda, G.S. Thompson, M. Tollinger,
K. Teilum, S. Gagné, D. Marion, C. Griesinger, M. Blackledge, E.J. d’Auvergne,
Bioinformatics 30 (2014) 2219–2220.
date_created: 2020-09-18T10:08:07Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2021-01-12T08:19:25Z
day: '01'
doi: 10.1093/bioinformatics/btu166
extern: '1'
intvolume: ' 30'
issue: '15'
keyword:
- Statistics and Probability
- Computational Theory and Mathematics
- Biochemistry
- Molecular Biology
- Computational Mathematics
- Computer Science Applications
language:
- iso: eng
month: '08'
oa_version: None
page: 2219-2220
publication: Bioinformatics
publication_identifier:
issn:
- 1367-4803
- 1460-2059
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1093/bioinformatics/btz397
status: public
title: 'Relax: The analysis of biomolecular kinetics and thermodynamics using NMR
relaxation dispersion data'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2014'
...
---
_id: '8460'
abstract:
- lang: eng
text: The function of proteins depends on their ability to sample a variety of states
differing in structure and free energy. Deciphering how the various thermally
accessible conformations are connected, and understanding their structures and
relative energies is crucial in rationalizing protein function. Many biomolecular
reactions take place within microseconds to milliseconds, and this timescale is
therefore of central functional importance. Here we show that R1ρ relaxation dispersion
experiments in magic‐angle‐spinning solid‐state NMR spectroscopy make it possible
to investigate the thermodynamics and kinetics of such exchange process, and gain
insight into structural features of short‐lived states.
article_processing_charge: No
article_type: original
author:
- first_name: Peixiang
full_name: Ma, Peixiang
last_name: Ma
- first_name: Jens D.
full_name: Haller, Jens D.
last_name: Haller
- first_name: Jérémy
full_name: Zajakala, Jérémy
last_name: Zajakala
- first_name: Pavel
full_name: Macek, Pavel
last_name: Macek
- first_name: Astrid C.
full_name: Sivertsen, Astrid C.
last_name: Sivertsen
- first_name: Dieter
full_name: Willbold, Dieter
last_name: Willbold
- first_name: Jérôme
full_name: Boisbouvier, Jérôme
last_name: Boisbouvier
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Ma P, Haller JD, Zajakala J, et al. Probing transient conformational states
of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte
Chemie International Edition. 2014;53(17):4312-4317. doi:10.1002/anie.201311275
apa: Ma, P., Haller, J. D., Zajakala, J., Macek, P., Sivertsen, A. C., Willbold,
D., … Schanda, P. (2014). Probing transient conformational states of proteins
by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie
International Edition. Wiley. https://doi.org/10.1002/anie.201311275
chicago: Ma, Peixiang, Jens D. Haller, Jérémy Zajakala, Pavel Macek, Astrid C. Sivertsen,
Dieter Willbold, Jérôme Boisbouvier, and Paul Schanda. “Probing Transient Conformational
States of Proteins by Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.”
Angewandte Chemie International Edition. Wiley, 2014. https://doi.org/10.1002/anie.201311275.
ieee: P. Ma et al., “Probing transient conformational states of proteins
by solid-state R1ρ relaxation-dispersion NMR spectroscopy,” Angewandte Chemie
International Edition, vol. 53, no. 17. Wiley, pp. 4312–4317, 2014.
ista: Ma P, Haller JD, Zajakala J, Macek P, Sivertsen AC, Willbold D, Boisbouvier
J, Schanda P. 2014. Probing transient conformational states of proteins by solid-state
R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie International Edition.
53(17), 4312–4317.
mla: Ma, Peixiang, et al. “Probing Transient Conformational States of Proteins by
Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.” Angewandte Chemie
International Edition, vol. 53, no. 17, Wiley, 2014, pp. 4312–17, doi:10.1002/anie.201311275.
short: P. Ma, J.D. Haller, J. Zajakala, P. Macek, A.C. Sivertsen, D. Willbold, J.
Boisbouvier, P. Schanda, Angewandte Chemie International Edition 53 (2014) 4312–4317.
date_created: 2020-09-18T10:08:53Z
date_published: 2014-03-18T00:00:00Z
date_updated: 2021-01-12T08:19:25Z
day: '18'
doi: 10.1002/anie.201311275
extern: '1'
intvolume: ' 53'
issue: '17'
language:
- iso: eng
month: '03'
oa_version: None
page: 4312-4317
publication: Angewandte Chemie International Edition
publication_identifier:
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion
NMR spectroscopy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 53
year: '2014'
...
---
_id: '8500'
abstract:
- lang: eng
text: The main model studied in this paper is a lattice of pendula with a nearest‐neighbor
coupling. If the coupling is weak, then the system is near‐integrable and KAM
tori fill most of the phase space. For all KAM trajectories the energy of each
pendulum stays within a narrow band for all time. Still, we show that for an arbitrarily
weak coupling of a certain localized type, the neighboring pendula can exchange
energy. In fact, the energy can be transferred between the pendula in any prescribed
way.
article_processing_charge: No
article_type: original
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Mark
full_name: Levi, Mark
last_name: Levi
- first_name: Maria
full_name: Saprykina, Maria
last_name: Saprykina
citation:
ama: Kaloshin V, Levi M, Saprykina M. Arnol′d diffusion in a pendulum lattice. Communications
on Pure and Applied Mathematics. 2014;67(5):748-775. doi:10.1002/cpa.21509
apa: Kaloshin, V., Levi, M., & Saprykina, M. (2014). Arnol′d diffusion in a
pendulum lattice. Communications on Pure and Applied Mathematics. Wiley.
https://doi.org/10.1002/cpa.21509
chicago: Kaloshin, Vadim, Mark Levi, and Maria Saprykina. “Arnol′d Diffusion in
a Pendulum Lattice.” Communications on Pure and Applied Mathematics. Wiley,
2014. https://doi.org/10.1002/cpa.21509.
ieee: V. Kaloshin, M. Levi, and M. Saprykina, “Arnol′d diffusion in a pendulum lattice,”
Communications on Pure and Applied Mathematics, vol. 67, no. 5. Wiley,
pp. 748–775, 2014.
ista: Kaloshin V, Levi M, Saprykina M. 2014. Arnol′d diffusion in a pendulum lattice.
Communications on Pure and Applied Mathematics. 67(5), 748–775.
mla: Kaloshin, Vadim, et al. “Arnol′d Diffusion in a Pendulum Lattice.” Communications
on Pure and Applied Mathematics, vol. 67, no. 5, Wiley, 2014, pp. 748–75,
doi:10.1002/cpa.21509.
short: V. Kaloshin, M. Levi, M. Saprykina, Communications on Pure and Applied Mathematics
67 (2014) 748–775.
date_created: 2020-09-18T10:47:01Z
date_published: 2014-05-01T00:00:00Z
date_updated: 2022-08-25T13:58:13Z
day: '01'
doi: 10.1002/cpa.21509
extern: '1'
intvolume: ' 67'
issue: '5'
keyword:
- Applied Mathematics
- General Mathematics
language:
- iso: eng
month: '05'
oa_version: None
page: 748-775
publication: Communications on Pure and Applied Mathematics
publication_identifier:
issn:
- 0010-3640
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Arnol′d diffusion in a pendulum lattice
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 67
year: '2014'
...
---
_id: '8501'
abstract:
- lang: eng
text: In this paper, we study small perturbations of a class of non-convex integrable
Hamiltonians with two degrees of freedom, and we prove a result of diffusion for
an open and dense set of perturbations, with an optimal time of diffusion which
grows linearly with respect to the inverse of the size of the perturbation.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Abed
full_name: Bounemoura, Abed
last_name: Bounemoura
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: Bounemoura A, Kaloshin V. Generic fast diffusion for a class of non-convex
Hamiltonians with two degrees of freedom. Moscow Mathematical Journal.
2014;14(2):181-203. doi:10.17323/1609-4514-2014-14-2-181-203
apa: Bounemoura, A., & Kaloshin, V. (2014). Generic fast diffusion for a class
of non-convex Hamiltonians with two degrees of freedom. Moscow Mathematical
Journal. Independent University of Moscow. https://doi.org/10.17323/1609-4514-2014-14-2-181-203
chicago: Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class
of Non-Convex Hamiltonians with Two Degrees of Freedom.” Moscow Mathematical
Journal. Independent University of Moscow, 2014. https://doi.org/10.17323/1609-4514-2014-14-2-181-203.
ieee: A. Bounemoura and V. Kaloshin, “Generic fast diffusion for a class of non-convex
Hamiltonians with two degrees of freedom,” Moscow Mathematical Journal,
vol. 14, no. 2. Independent University of Moscow, pp. 181–203, 2014.
ista: Bounemoura A, Kaloshin V. 2014. Generic fast diffusion for a class of non-convex
Hamiltonians with two degrees of freedom. Moscow Mathematical Journal. 14(2),
181–203.
mla: Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class of
Non-Convex Hamiltonians with Two Degrees of Freedom.” Moscow Mathematical Journal,
vol. 14, no. 2, Independent University of Moscow, 2014, pp. 181–203, doi:10.17323/1609-4514-2014-14-2-181-203.
short: A. Bounemoura, V. Kaloshin, Moscow Mathematical Journal 14 (2014) 181–203.
date_created: 2020-09-18T10:47:09Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T08:19:43Z
day: '01'
doi: 10.17323/1609-4514-2014-14-2-181-203
extern: '1'
external_id:
arxiv:
- '1304.3050'
intvolume: ' 14'
issue: '2'
keyword:
- General Mathematics
language:
- iso: eng
month: '04'
oa_version: Preprint
page: 181-203
publication: Moscow Mathematical Journal
publication_identifier:
issn:
- 1609-3321
- 1609-4514
publication_status: published
publisher: Independent University of Moscow
quality_controlled: '1'
status: public
title: Generic fast diffusion for a class of non-convex Hamiltonians with two degrees
of freedom
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2014'
...
---
_id: '852'
abstract:
- lang: eng
text: 'Rapid divergence of gene copies after duplication is thought to determine
the fate of the copies and evolution of novel protein functions. However, data
on howlong the gene copies continue to experience an elevated rate of evolution
remain scarce. Standard theory of gene duplications based on some level of genetic
redundancy of gene copies predicts that the period of accelerated evolutionmust
end relatively quickly. Using a maximum-likelihood approach we estimate preduplication,
initial postduplication, and recent postduplication rates of evolution that occurred
in themammalian lineage.Wefind that both gene copies experience a similar in magnitude
acceleration in their rate of evolution. The copy located in the original genomic
position typically returns to the preduplication rates of evolution in a short
period of time. The burst of faster evolution of the copy that is located in a
new genomic position typically lasts longer. Furthermore, the fast-evolving copies
on average continue to evolve faster than the preduplication rates far longer
than predicted by standard theory of gene duplications.We hypothesize that the
prolonged elevated rates of evolution are determined by functional properties
that were acquired during, or soon after, the gene duplication event. '
author:
- first_name: Oriol
full_name: Rosello, Oriol P
last_name: Rosello
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Rosello O, Kondrashov F. Long-Term asymmetrical acceleration of protein evolution
after gene duplication. Genome Biology and Evolution. 2014;6(8):1949-1955.
doi:10.1093/gbe/evu159
apa: Rosello, O., & Kondrashov, F. (2014). Long-Term asymmetrical acceleration
of protein evolution after gene duplication. Genome Biology and Evolution.
Oxford University Press. https://doi.org/10.1093/gbe/evu159
chicago: Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration
of Protein Evolution after Gene Duplication.” Genome Biology and Evolution.
Oxford University Press, 2014. https://doi.org/10.1093/gbe/evu159.
ieee: O. Rosello and F. Kondrashov, “Long-Term asymmetrical acceleration of protein
evolution after gene duplication,” Genome Biology and Evolution, vol. 6,
no. 8. Oxford University Press, pp. 1949–1955, 2014.
ista: Rosello O, Kondrashov F. 2014. Long-Term asymmetrical acceleration of protein
evolution after gene duplication. Genome Biology and Evolution. 6(8), 1949–1955.
mla: Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration
of Protein Evolution after Gene Duplication.” Genome Biology and Evolution,
vol. 6, no. 8, Oxford University Press, 2014, pp. 1949–55, doi:10.1093/gbe/evu159.
short: O. Rosello, F. Kondrashov, Genome Biology and Evolution 6 (2014) 1949–1955.
date_created: 2018-12-11T11:48:51Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2021-01-12T08:19:51Z
day: '01'
doi: 10.1093/gbe/evu159
extern: 1
intvolume: ' 6'
issue: '8'
month: '08'
page: 1949 - 1955
publication: Genome Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6797'
quality_controlled: 0
status: public
title: Long-Term asymmetrical acceleration of protein evolution after gene duplication
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
volume: 6
year: '2014'
...
---
_id: '856'
abstract:
- lang: eng
text: The emergence of new genes throughout evolution requires rewiring and extension
of regulatory networks. However, the molecular details of how the transcriptional
regulation of new gene copies evolves remain largely unexplored. Here we show
how duplication of a transcription factor gene allowed the emergence of two independent
regulatory circuits. Interestingly, the ancestral transcription factor was promiscuous
and could bind different motifs in its target promoters. After duplication, one
paralogue evolved increased binding specificity so that it only binds one type
of motif, whereas the other copy evolved a decreased activity so that it only
activates promoters that contain multiple binding sites. Interestingly, only a
few mutations in both the DNA-binding domains and in the promoter binding sites
were required to gradually disentangle the two networks. These results reveal
how duplication of a promiscuous transcription factor followed by concerted cis
and trans mutations allows expansion of a regulatory network.
acknowledgement: 'K.P. acknowledges financial support from TRIPLE I and a Belspo mobility
grant from the Belgian Federal Science Policy Office co-funded by the Marie Curie
Actions from the European Commission. Research in the lab of K.J.V. is supported
by ERC Starting Grant 241426, HFSP programme grant RGP0050/2013, VIB, EMBO YIP programme,
KU Leuven Programme Financing, FWO, and IWT. A.V. acknowledges RIKEN for the FPR
grant. The work of F.A.K. was supported by a grant of the HHMI International Early
Career Scientist Programme (grant #55007424), the Spanish Ministry of Economy and
Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP programme, two grants
from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia
Severo Ochoa 2013–2017 (grant #Sev-2012-0208)’ and (grant #BES-2013-064004) funded
by the European Regional Development Fund (ERDF), the European Union and the European
Research Council (grant #335980_EinME). K.V. is supported by an FWO postdoctoral
fellowship. Funders had no role in study design, data collection and analysis, decision
to publish or preparation of the manuscript.'
author:
- first_name: Ksenia
full_name: Pougach, Ksenia S
last_name: Pougach
- first_name: Arnout
full_name: Voet, Arnout R
last_name: Voet
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Karin
full_name: Voordeckers, Karin
last_name: Voordeckers
- first_name: Joaquin
full_name: Christiaens, Joaquin F
last_name: Christiaens
- first_name: Bianka
full_name: Baying, Bianka
last_name: Baying
- first_name: Vladimı́R
full_name: Bénès, Vladimı́r
last_name: Bénès
- first_name: Ryo
full_name: Sakai, Ryo
last_name: Sakai
- first_name: Jan
full_name: Aerts, Jan A
last_name: Aerts
- first_name: Bo
full_name: Zhu, Bo
last_name: Zhu
- first_name: Patrick
full_name: Van Dijck, Patrick
last_name: Van Dijck
- first_name: Kevin
full_name: Verstrepen, Kevin J
last_name: Verstrepen
citation:
ama: Pougach K, Voet A, Kondrashov F, et al. Duplication of a promiscuous transcription
factor drives the emergence of a new regulatory network. Nature Communications.
2014;5. doi:10.1038/ncomms5868
apa: Pougach, K., Voet, A., Kondrashov, F., Voordeckers, K., Christiaens, J., Baying,
B., … Verstrepen, K. (2014). Duplication of a promiscuous transcription factor
drives the emergence of a new regulatory network. Nature Communications.
Nature Publishing Group. https://doi.org/10.1038/ncomms5868
chicago: Pougach, Ksenia, Arnout Voet, Fyodor Kondrashov, Karin Voordeckers, Joaquin
Christiaens, Bianka Baying, Vladimı́R Bénès, et al. “Duplication of a Promiscuous
Transcription Factor Drives the Emergence of a New Regulatory Network.” Nature
Communications. Nature Publishing Group, 2014. https://doi.org/10.1038/ncomms5868.
ieee: K. Pougach et al., “Duplication of a promiscuous transcription factor
drives the emergence of a new regulatory network,” Nature Communications,
vol. 5. Nature Publishing Group, 2014.
ista: Pougach K, Voet A, Kondrashov F, Voordeckers K, Christiaens J, Baying B, Bénès
V, Sakai R, Aerts J, Zhu B, Van Dijck P, Verstrepen K. 2014. Duplication of a
promiscuous transcription factor drives the emergence of a new regulatory network.
Nature Communications. 5.
mla: Pougach, Ksenia, et al. “Duplication of a Promiscuous Transcription Factor
Drives the Emergence of a New Regulatory Network.” Nature Communications,
vol. 5, Nature Publishing Group, 2014, doi:10.1038/ncomms5868.
short: K. Pougach, A. Voet, F. Kondrashov, K. Voordeckers, J. Christiaens, B. Baying,
V. Bénès, R. Sakai, J. Aerts, B. Zhu, P. Van Dijck, K. Verstrepen, Nature Communications
5 (2014).
date_created: 2018-12-11T11:48:52Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T08:20:01Z
day: '01'
doi: 10.1038/ncomms5868
extern: 1
intvolume: ' 5'
month: '01'
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '6790'
quality_controlled: 0
status: public
title: Duplication of a promiscuous transcription factor drives the emergence of a
new regulatory network
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
volume: 5
year: '2014'
...
---
_id: '863'
abstract:
- lang: eng
text: The origins of neural systems remain unresolved. In contrast to other basal
metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived
muscular systems. These holoplanktonic predators also have sophisticated ciliated
locomotion, behaviour and distinct development. Here we present the draft genome
of Pleurobrachia bachei, Pacific sea gooseberry, together with ten other ctenophore
transcriptomes, and show that they are remarkably distinct from other animal genomes
in their content of neurogenic, immune and developmental genes. Our integrative
analyses place Ctenophora as the earliest lineage within Metazoa. This hypothesis
is supported by comparative analysis of multiple gene families, including the
apparent absence of HOX genes, canonical microRNA machinery, and reduced immune
complement in ctenophores. Although two distinct nervous systems are well recognized
in ctenophores, many bilaterian neuron-specific genes and genes of 'classical'
neurotransmitter pathways either are absent or, if present, are not expressed
in neurons. Our metabolomic and physiological data are consistent with the hypothesis
that ctenophore neural systems, and possibly muscle specification, evolved independently
from those in other animals.
acknowledgement: We thank Friday Harbor Laboratories for facilities during animal
collection and Marine Genomics apprenticeships (L.L.M., B.J.S.); E. Dabe, G. Winters,
J. Netherton, N. Churches and C. Bostwick for help with animal, tissue, in situ,
RNA and DNA assays; and X.-X. Tan, F. Lu and T. Tyazelova for sequencing. We thank
F. Nivens for videos and P. L. Williams for database support. This work was supported
by NSF (NSF-0744649 and NSF CNS-0821622 to L.L.M.; NSF CHE-1111705 to J.V.S.), NIH
(1R01GM097502, R01MH097062, R21RR025699 and 5R21DA030118 to L.L.M.; P30 DA018310
to J.V.S.; R01 AG029360 and 1S10RR027052 to E.I.R.), NASA NNX13AJ31G (to K.M.H.,
L.L.M. and K.M.K.), NSERC 458115 and 211598 (J.P.R.), University of Florida Opportunity
Funds/McKnight Brain Research and Florida Biodiversity Institute (L.L.M.), Rostock
Inc./A.V. Chikunov (E.I.R.), grant from Russian Federation Government 14.B25.31.0033
(Resolution No.220) (E.I.R.). F.A.K., I.S.P. and R.D. were supported by HHMI (55007424),
EMBO and MINECO (BFU2012-31329 and Sev-2012-0208). Contributions of AU Marine Biology
Program 117 and Molette laboratory 22.
author:
- first_name: Leonid
full_name: Moroz, Leonid L
last_name: Moroz
- first_name: Kevin
full_name: Kocot, Kevin M
last_name: Kocot
- first_name: Mathew
full_name: Citarella, Mathew R
last_name: Citarella
- first_name: Sohn
full_name: Dosung, Sohn
last_name: Dosung
- first_name: Tigran
full_name: Norekian, Tigran P
last_name: Norekian
- first_name: Inna
full_name: Povolotskaya, Inna
last_name: Povolotskaya
- first_name: Anastasia
full_name: Grigorenko, Anastasia P
last_name: Grigorenko
- first_name: Christopher
full_name: Dailey, Christopher A
last_name: Dailey
- first_name: Eugene
full_name: Berezikov, Eugene
last_name: Berezikov
- first_name: Katherine
full_name: Buckley, Katherine M
last_name: Buckley
- first_name: Andrey
full_name: Ptitsyn, Andrey A
last_name: Ptitsyn
- first_name: Denis
full_name: Reshetov, Denis A
last_name: Reshetov
- first_name: Krishanu
full_name: Mukherjee, Krishanu
last_name: Mukherjee
- first_name: Tatiana
full_name: Moroz, Tatiana P
last_name: Moroz
- first_name: Yelena
full_name: Bobkova, Yelena V
last_name: Bobkova
- first_name: Fahong
full_name: Yu, Fahong
last_name: Yu
- first_name: Vladimir
full_name: Kapitonov, Vladimir V
last_name: Kapitonov
- first_name: Jerzy
full_name: Jurka, Jerzy W
last_name: Jurka
- first_name: Yuriy
full_name: Bobkov, Yuriy V
last_name: Bobkov
- first_name: Joshua
full_name: Swore, Joshua J
last_name: Swore
- first_name: David
full_name: Girardo, David O
last_name: Girardo
- first_name: Alexander
full_name: Fodor, Alexander
last_name: Fodor
- first_name: Fedor
full_name: Gusev, Fedor E
last_name: Gusev
- first_name: Rachel
full_name: Sanford, Rachel S
last_name: Sanford
- first_name: Rebecca
full_name: Bruders, Rebecca
last_name: Bruders
- first_name: Ellen
full_name: Kittler, Ellen L
last_name: Kittler
- first_name: Claudia
full_name: Mills, Claudia E
last_name: Mills
- first_name: Jonathan
full_name: Rast, Jonathan P
last_name: Rast
- first_name: Romain
full_name: Derelle, Romain
last_name: Derelle
- first_name: Victor
full_name: Solovyev, Victor
last_name: Solovyev
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Billie
full_name: Swalla, Billie J
last_name: Swalla
- first_name: Jonathan
full_name: Sweedler, Jonathan V
last_name: Sweedler
- first_name: Evgeny
full_name: Rogaev, Evgeny I
last_name: Rogaev
- first_name: Kenneth
full_name: Halanych, Kenneth M
last_name: Halanych
- first_name: Andrea
full_name: Kohn, Andrea B
last_name: Kohn
citation:
ama: Moroz L, Kocot K, Citarella M, et al. The ctenophore genome and the evolutionary
origins of neural systems. Nature. 2014;510(7503):109-114. doi:10.1038/nature13400
apa: Moroz, L., Kocot, K., Citarella, M., Dosung, S., Norekian, T., Povolotskaya,
I., … Kohn, A. (2014). The ctenophore genome and the evolutionary origins of neural
systems. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13400
chicago: Moroz, Leonid, Kevin Kocot, Mathew Citarella, Sohn Dosung, Tigran Norekian,
Inna Povolotskaya, Anastasia Grigorenko, et al. “The Ctenophore Genome and the
Evolutionary Origins of Neural Systems.” Nature. Nature Publishing Group,
2014. https://doi.org/10.1038/nature13400.
ieee: L. Moroz et al., “The ctenophore genome and the evolutionary origins
of neural systems,” Nature, vol. 510, no. 7503. Nature Publishing Group,
pp. 109–114, 2014.
ista: Moroz L, Kocot K, Citarella M, Dosung S, Norekian T, Povolotskaya I, Grigorenko
A, Dailey C, Berezikov E, Buckley K, Ptitsyn A, Reshetov D, Mukherjee K, Moroz
T, Bobkova Y, Yu F, Kapitonov V, Jurka J, Bobkov Y, Swore J, Girardo D, Fodor
A, Gusev F, Sanford R, Bruders R, Kittler E, Mills C, Rast J, Derelle R, Solovyev
V, Kondrashov F, Swalla B, Sweedler J, Rogaev E, Halanych K, Kohn A. 2014. The
ctenophore genome and the evolutionary origins of neural systems. Nature. 510(7503),
109–114.
mla: Moroz, Leonid, et al. “The Ctenophore Genome and the Evolutionary Origins of
Neural Systems.” Nature, vol. 510, no. 7503, Nature Publishing Group, 2014,
pp. 109–14, doi:10.1038/nature13400.
short: L. Moroz, K. Kocot, M. Citarella, S. Dosung, T. Norekian, I. Povolotskaya,
A. Grigorenko, C. Dailey, E. Berezikov, K. Buckley, A. Ptitsyn, D. Reshetov, K.
Mukherjee, T. Moroz, Y. Bobkova, F. Yu, V. Kapitonov, J. Jurka, Y. Bobkov, J.
Swore, D. Girardo, A. Fodor, F. Gusev, R. Sanford, R. Bruders, E. Kittler, C.
Mills, J. Rast, R. Derelle, V. Solovyev, F. Kondrashov, B. Swalla, J. Sweedler,
E. Rogaev, K. Halanych, A. Kohn, Nature 510 (2014) 109–114.
date_created: 2018-12-11T11:48:54Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T08:20:21Z
day: '01'
doi: 10.1038/nature13400
extern: 1
intvolume: ' 510'
issue: '7503'
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '01'
page: 109 - 114
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6785'
quality_controlled: 0
status: public
title: The ctenophore genome and the evolutionary origins of neural systems
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
volume: 510
year: '2014'
...
---
_id: '865'
abstract:
- lang: eng
text: Research on existing drugs often discovers novel mechanisms of their action
and leads to the expansion of their therapeutic scope and subsequent remarketing.
The Wnt signaling pathway is of the immediate therapeutic relevance, as it plays
critical roles in cancer development and progression. However, drugs which disrupt
this pathway are unavailable despite the high demand. Here we report an attempt
to identify antagonists of the Wnt-FZD interaction among the library of the FDA-approved
drugs. We performed an in silico screening which brought up several potential
antagonists of the ligand-receptor interaction. 14 of these substances were tested
using the TopFlash luciferase reporter assay and four of them identified as active
and specific inhibitors of the Wnt3a-induced signaling. However, further analysis
through GTP-binding and β-catenin stabilization assays showed that the compounds
do not target the Wnt-FZD pair, but inhibit the signaling at downstream levels.
We further describe the previously unknown inhibitory activity of an anti-leprosy
drug clofazimine in the Wnt pathway and provide data demonstrating its efficiency
in suppressing growth of Wnt-dependent triple-negative breast cancer cells. These
data provide a basis for further investigations of the efficiency of clofazimine
in treatment of Wnt-dependent cancers.
author:
- first_name: Alexey
full_name: Koval, Alexey V
last_name: Koval
- first_name: Peter
full_name: Vlasov, Peter K
last_name: Vlasov
- first_name: Polina
full_name: Shichkova, Polina
last_name: Shichkova
- first_name: S
full_name: Khunderyakova, S
last_name: Khunderyakova
- first_name: Yury
full_name: Markov, Yury
last_name: Markov
- first_name: J
full_name: Panchenko, J
last_name: Panchenko
- first_name: A
full_name: Volodina, A
last_name: Volodina
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Vladimir
full_name: Katanaev, Vladimir L
last_name: Katanaev
citation:
ama: Koval A, Vlasov P, Shichkova P, et al. Anti leprosy drug clofazimine inhibits
growth of triple-negative breast cancer cells via inhibition of canonical Wnt
signaling. Biochemical Pharmacology. 2014;87(4):571-578. doi:10.1016/j.bcp.2013.12.007
apa: Koval, A., Vlasov, P., Shichkova, P., Khunderyakova, S., Markov, Y., Panchenko,
J., … Katanaev, V. (2014). Anti leprosy drug clofazimine inhibits growth of triple-negative
breast cancer cells via inhibition of canonical Wnt signaling. Biochemical
Pharmacology. Elsevier. https://doi.org/10.1016/j.bcp.2013.12.007
chicago: Koval, Alexey, Peter Vlasov, Polina Shichkova, S Khunderyakova, Yury Markov,
J Panchenko, A Volodina, Fyodor Kondrashov, and Vladimir Katanaev. “Anti Leprosy
Drug Clofazimine Inhibits Growth of Triple-Negative Breast Cancer Cells via Inhibition
of Canonical Wnt Signaling.” Biochemical Pharmacology. Elsevier, 2014.
https://doi.org/10.1016/j.bcp.2013.12.007.
ieee: A. Koval et al., “Anti leprosy drug clofazimine inhibits growth of
triple-negative breast cancer cells via inhibition of canonical Wnt signaling,”
Biochemical Pharmacology, vol. 87, no. 4. Elsevier, pp. 571–578, 2014.
ista: Koval A, Vlasov P, Shichkova P, Khunderyakova S, Markov Y, Panchenko J, Volodina
A, Kondrashov F, Katanaev V. 2014. Anti leprosy drug clofazimine inhibits growth
of triple-negative breast cancer cells via inhibition of canonical Wnt signaling.
Biochemical Pharmacology. 87(4), 571–578.
mla: Koval, Alexey, et al. “Anti Leprosy Drug Clofazimine Inhibits Growth of Triple-Negative
Breast Cancer Cells via Inhibition of Canonical Wnt Signaling.” Biochemical
Pharmacology, vol. 87, no. 4, Elsevier, 2014, pp. 571–78, doi:10.1016/j.bcp.2013.12.007.
short: A. Koval, P. Vlasov, P. Shichkova, S. Khunderyakova, Y. Markov, J. Panchenko,
A. Volodina, F. Kondrashov, V. Katanaev, Biochemical Pharmacology 87 (2014) 571–578.
date_created: 2018-12-11T11:48:55Z
date_published: 2014-02-15T00:00:00Z
date_updated: 2021-01-12T08:20:24Z
day: '15'
doi: 10.1016/j.bcp.2013.12.007
extern: 1
intvolume: ' 87'
issue: '4'
month: '02'
page: 571 - 578
publication: Biochemical Pharmacology
publication_status: published
publisher: Elsevier
publist_id: '6782'
quality_controlled: 0
status: public
title: Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer
cells via inhibition of canonical Wnt signaling
type: journal_article
volume: 87
year: '2014'
...
---
_id: '892'
abstract:
- lang: eng
text: The study of molecular evolution is important because it reveals how protein
functions emerge and evolve. Recently, several types of studies indicated that
substitutions in molecular evolution occur in a compensatory manner, whereby the
occurrence of a substitution depends on the amino acid residues at other sites.
However, a molecular or structural basis behind the compensation often remains
obscure. Here, we review studies on the interface of structural biology and molecular
evolution that revealed novel aspects of compensatory evolution. In many cases
structural studies benefit from evolutionary data while structural data often
add a functional dimension to the study of molecular evolution.
acknowledgement: |
The work has been supported by a grant of the HHMI International Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness (EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017 (Sev-2012-0208)’ and (BFU2012-31329), the European Union and the European Research Council grant (335980_EinME), RFBR (13-04-00253a), MCB RAS (01201358029) and MES RK Grants.
author:
- first_name: Dmitry
full_name: Ivankov, Dmitry N
last_name: Ivankov
- first_name: Alexei
full_name: Finkelstein, Alexei V
last_name: Finkelstein
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Ivankov D, Finkelstein A, Kondrashov F. A structural perspective of compensatory
evolution. Current Opinion in Structural Biology. 2014;26(1):104-112. doi:10.1016/j.sbi.2014.05.004
apa: Ivankov, D., Finkelstein, A., & Kondrashov, F. (2014). A structural perspective
of compensatory evolution. Current Opinion in Structural Biology. Elsevier.
https://doi.org/10.1016/j.sbi.2014.05.004
chicago: Ivankov, Dmitry, Alexei Finkelstein, and Fyodor Kondrashov. “A Structural
Perspective of Compensatory Evolution.” Current Opinion in Structural Biology.
Elsevier, 2014. https://doi.org/10.1016/j.sbi.2014.05.004.
ieee: D. Ivankov, A. Finkelstein, and F. Kondrashov, “A structural perspective of
compensatory evolution,” Current Opinion in Structural Biology, vol. 26,
no. 1. Elsevier, pp. 104–112, 2014.
ista: Ivankov D, Finkelstein A, Kondrashov F. 2014. A structural perspective of
compensatory evolution. Current Opinion in Structural Biology. 26(1), 104–112.
mla: Ivankov, Dmitry, et al. “A Structural Perspective of Compensatory Evolution.”
Current Opinion in Structural Biology, vol. 26, no. 1, Elsevier, 2014,
pp. 104–12, doi:10.1016/j.sbi.2014.05.004.
short: D. Ivankov, A. Finkelstein, F. Kondrashov, Current Opinion in Structural
Biology 26 (2014) 104–112.
date_created: 2018-12-11T11:49:03Z
date_published: 2014-06-01T00:00:00Z
date_updated: 2021-01-12T08:21:21Z
day: '01'
doi: 10.1016/j.sbi.2014.05.004
extern: 1
intvolume: ' 26'
issue: '1'
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '06'
page: 104 - 112
publication: Current Opinion in Structural Biology
publication_status: published
publisher: Elsevier
publist_id: '6756'
quality_controlled: 0
status: public
title: A structural perspective of compensatory evolution
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
volume: 26
year: '2014'
...
---
_id: '9050'
abstract:
- lang: eng
text: Self-propelled particles can exhibit surprising non-equilibrium behaviors,
and how they interact with obstacles or boundaries remains an important open problem.
Here we show that chemically propelled micro-rods can be captured, with little
change in their speed, into close orbits around solid spheres resting on or near
a horizontal plane. We show that this interaction between sphere and particle
is short-range, occurring even for spheres smaller than the particle length, and
for a variety of sphere materials. We consider a simple model, based on lubrication
theory, of a force- and torque-free swimmer driven by a surface slip (the phoretic
propulsion mechanism) and moving near a solid surface. The model demonstrates
capture, or movement towards the surface, and yields speeds independent of distance.
This study reveals the crucial aspects of activity–driven interactions of self-propelled
particles with passive objects, and brings into question the use of colloidal
tracers as probes of active matter.
article_number: '1784'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Daisuke
full_name: Takagi, Daisuke
last_name: Takagi
- 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: Adam B.
full_name: Braunschweig, Adam B.
last_name: Braunschweig
- first_name: Michael J.
full_name: Shelley, Michael J.
last_name: Shelley
- first_name: Jun
full_name: Zhang, Jun
last_name: Zhang
citation:
ama: Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. Hydrodynamic capture
of microswimmers into sphere-bound orbits. Soft Matter. 2014;10(11). doi:10.1039/c3sm52815d
apa: Takagi, D., Palacci, J. A., Braunschweig, A. B., Shelley, M. J., & Zhang,
J. (2014). Hydrodynamic capture of microswimmers into sphere-bound orbits. Soft
Matter. Royal Society of Chemistry . https://doi.org/10.1039/c3sm52815d
chicago: Takagi, Daisuke, Jérémie A Palacci, Adam B. Braunschweig, Michael J. Shelley,
and Jun Zhang. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.”
Soft Matter. Royal Society of Chemistry , 2014. https://doi.org/10.1039/c3sm52815d.
ieee: D. Takagi, J. A. Palacci, A. B. Braunschweig, M. J. Shelley, and J. Zhang,
“Hydrodynamic capture of microswimmers into sphere-bound orbits,” Soft Matter,
vol. 10, no. 11. Royal Society of Chemistry , 2014.
ista: Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. 2014. Hydrodynamic
capture of microswimmers into sphere-bound orbits. Soft Matter. 10(11), 1784.
mla: Takagi, Daisuke, et al. “Hydrodynamic Capture of Microswimmers into Sphere-Bound
Orbits.” Soft Matter, vol. 10, no. 11, 1784, Royal Society of Chemistry
, 2014, doi:10.1039/c3sm52815d.
short: D. Takagi, J.A. Palacci, A.B. Braunschweig, M.J. Shelley, J. Zhang, Soft
Matter 10 (2014).
date_created: 2021-02-01T13:43:31Z
date_published: 2014-03-21T00:00:00Z
date_updated: 2023-02-23T13:47:35Z
day: '21'
doi: 10.1039/c3sm52815d
extern: '1'
external_id:
arxiv:
- '1309.5662'
pmid:
- '24800268'
intvolume: ' 10'
issue: '11'
keyword:
- General Chemistry
- Condensed Matter Physics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1309.5662
month: '03'
oa: 1
oa_version: Preprint
pmid: 1
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: 'Royal Society of Chemistry '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Hydrodynamic capture of microswimmers into sphere-bound orbits
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 10
year: '2014'
...
---
_id: '9166'
abstract:
- lang: eng
text: Light-activated self-propelled colloids are synthesized and their active motion
is studied using optical microscopy. We propose a versatile route using different
photoactive materials, and demonstrate a multiwavelength activation and propulsion.
Thanks to the photoelectrochemical properties of two semiconductor materials (α-Fe2O3
and TiO2), a light with an energy higher than the bandgap triggers the reaction
of decomposition of hydrogen peroxide and produces a chemical cloud around the
particle. It induces a phoretic attraction with neighbouring colloids as well
as an osmotic self-propulsion of the particle on the substrate. We use these mechanisms
to form colloidal cargos as well as self-propelled particles where the light-activated
component is embedded into a dielectric sphere. The particles are self-propelled
along a direction otherwise randomized by thermal fluctuations, and exhibit a
persistent random walk. For sufficient surface density, the particles spontaneously
form ‘living crystals’ which are mobile, break apart and reform. Steering the
particle with an external magnetic field, we show that the formation of the dense
phase results from the collisions heads-on of the particles. This effect is intrinsically
non-equilibrium and a novel principle of organization for systems without detailed
balance. Engineering families of particles self-propelled by different wavelength
demonstrate a good understanding of both the physics and the chemistry behind
the system and points to a general route for designing new families of self-propelled
particles.
article_number: '20130372'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- 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: S.
full_name: Sacanna, S.
last_name: Sacanna
- first_name: S.-H.
full_name: Kim, S.-H.
last_name: Kim
- first_name: G.-R.
full_name: Yi, G.-R.
last_name: Yi
- first_name: D. J.
full_name: Pine, D. J.
last_name: Pine
- first_name: P. M.
full_name: Chaikin, P. M.
last_name: Chaikin
citation:
ama: 'Palacci JA, Sacanna S, Kim S-H, Yi G-R, Pine DJ, Chaikin PM. Light-activated
self-propelled colloids. Philosophical Transactions of the Royal Society A:
Mathematical, Physical and Engineering Sciences. 2014;372(2029). doi:10.1098/rsta.2013.0372'
apa: 'Palacci, J. A., Sacanna, S., Kim, S.-H., Yi, G.-R., Pine, D. J., & Chaikin,
P. M. (2014). Light-activated self-propelled colloids. Philosophical Transactions
of the Royal Society A: Mathematical, Physical and Engineering Sciences. The
Royal Society. https://doi.org/10.1098/rsta.2013.0372'
chicago: 'Palacci, Jérémie A, S. Sacanna, S.-H. Kim, G.-R. Yi, D. J. Pine, and P.
M. Chaikin. “Light-Activated Self-Propelled Colloids.” Philosophical Transactions
of the Royal Society A: Mathematical, Physical and Engineering Sciences. The
Royal Society, 2014. https://doi.org/10.1098/rsta.2013.0372.'
ieee: 'J. A. Palacci, S. Sacanna, S.-H. Kim, G.-R. Yi, D. J. Pine, and P. M. Chaikin,
“Light-activated self-propelled colloids,” Philosophical Transactions of the
Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 372,
no. 2029. The Royal Society, 2014.'
ista: 'Palacci JA, Sacanna S, Kim S-H, Yi G-R, Pine DJ, Chaikin PM. 2014. Light-activated
self-propelled colloids. Philosophical Transactions of the Royal Society A: Mathematical,
Physical and Engineering Sciences. 372(2029), 20130372.'
mla: 'Palacci, Jérémie A., et al. “Light-Activated Self-Propelled Colloids.” Philosophical
Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences,
vol. 372, no. 2029, 20130372, The Royal Society, 2014, doi:10.1098/rsta.2013.0372.'
short: 'J.A. Palacci, S. Sacanna, S.-H. Kim, G.-R. Yi, D.J. Pine, P.M. Chaikin,
Philosophical Transactions of the Royal Society A: Mathematical, Physical and
Engineering Sciences 372 (2014).'
date_created: 2021-02-18T14:31:11Z
date_published: 2014-11-28T00:00:00Z
date_updated: 2021-02-22T10:44:16Z
day: '28'
doi: 10.1098/rsta.2013.0372
extern: '1'
external_id:
arxiv:
- '1410.7278'
pmid:
- '25332383'
intvolume: ' 372'
issue: '2029'
keyword:
- General Engineering
- General Physics and Astronomy
- General Mathematics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1098/rsta.2013.0372
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: 'Philosophical Transactions of the Royal Society A: Mathematical, Physical
and Engineering Sciences'
publication_identifier:
eissn:
- 1471-2962
issn:
- 1364-503X
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Light-activated self-propelled colloids
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 372
year: '2014'
...
---
_id: '925'
abstract:
- lang: eng
text: The morphological stability of biological tubes is crucial for the efficient
circulation of fluids and gases. Failure of this stability causes irregularly
shaped tubes found in multiple pathological conditions. Here, we report that Drosophila
mutants of the ESCRT III component Shrub/Vps32 exhibit a strikingly elongated
sinusoidal tube phenotype. This is caused by excessive apical membrane synthesis
accompanied by the ectopic accumulation and overactivation of Crumbs in swollen
endosomes. Furthermore, we demonstrate that the apical extracellular matrix (aECM)
of the tracheal tube is a viscoelastic material coupled with the apical membrane.
We present a simple mechanical model in which aECM elasticity, apical membrane
growth, and their interaction are three vital parameters determining the stability
of biological tubes. Our findings demonstrate a mechanical role for the extracellular
matrix and suggest that the interaction of the apical membrane and an elastic
aECM determines the final morphology of biological tubes independent of cell shape.
acknowledgement: We thank F. Gao, R.E. Ward, S. Luschnig, T. Okajima, M. Affolter,
D. Bilder, E. Knust, T. Tanaka, A. Nakamura, C. Samakovlis, K. Saigo, M. Furuse,
the Bloomington Stock Center, Drosophila Genetic Resource Center in Kyoto, Japan,
and the Developmental Studies Hybridoma Bank for generously providing antibodies
and fly stocks; H. Wada for UAS-3×TagRFP fly and dye injection; Y.H. Zhang for plasmid
and protocol for CBP preparation; and J. Prost and J.F. Joanny for their support
for the project and discussion. We also thank T. Shibata, Y. Morishita, T. Kondo,
and G. Sheng for critically reading the manuscript. This work was supported by a
Grant-in-Aid for Scientific Research on Innovative Areas from MEXT Japan to S.H.
and the RIKEN Foreign Postdoctoral Researcher Program to B.D.
article_processing_charge: No
author:
- first_name: Bo
full_name: Dong, Bo
last_name: Dong
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Shigeo
full_name: Hayashi, Shigeo
last_name: Hayashi
citation:
ama: Dong B, Hannezo EB, Hayashi S. Balance between apical membrane growth and luminal
matrix resistance determines epithelial tubule shape. Cell Reports. 2014;7(4):941-950.
doi:10.1016/j.celrep.2014.03.066
apa: Dong, B., Hannezo, E. B., & Hayashi, S. (2014). Balance between apical
membrane growth and luminal matrix resistance determines epithelial tubule shape.
Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2014.03.066
chicago: Dong, Bo, Edouard B Hannezo, and Shigeo Hayashi. “Balance between Apical
Membrane Growth and Luminal Matrix Resistance Determines Epithelial Tubule Shape.”
Cell Reports. Cell Press, 2014. https://doi.org/10.1016/j.celrep.2014.03.066.
ieee: B. Dong, E. B. Hannezo, and S. Hayashi, “Balance between apical membrane growth
and luminal matrix resistance determines epithelial tubule shape,” Cell Reports,
vol. 7, no. 4. Cell Press, pp. 941–950, 2014.
ista: Dong B, Hannezo EB, Hayashi S. 2014. Balance between apical membrane growth
and luminal matrix resistance determines epithelial tubule shape. Cell Reports.
7(4), 941–950.
mla: Dong, Bo, et al. “Balance between Apical Membrane Growth and Luminal Matrix
Resistance Determines Epithelial Tubule Shape.” Cell Reports, vol. 7, no.
4, Cell Press, 2014, pp. 941–50, doi:10.1016/j.celrep.2014.03.066.
short: B. Dong, E.B. Hannezo, S. Hayashi, Cell Reports 7 (2014) 941–950.
date_created: 2018-12-11T11:49:14Z
date_published: 2014-05-22T00:00:00Z
date_updated: 2021-01-12T08:21:57Z
day: '22'
doi: 10.1016/j.celrep.2014.03.066
extern: '1'
intvolume: ' 7'
issue: '4'
language:
- iso: eng
month: '05'
oa_version: None
page: 941 - 950
publication: Cell Reports
publication_status: published
publisher: Cell Press
publist_id: '6515'
status: public
title: Balance between apical membrane growth and luminal matrix resistance determines
epithelial tubule shape
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2014'
...
---
_id: '926'
abstract:
- lang: eng
text: 'The regulation of cell growth in animal tissues is a question of critical
importance: most tissues contain different types of cells in interconversion and
the fraction of each type has to be controlled in a precise way, by mechanisms
that remain unclear. Here, we provide a theoretical framework for the homeostasis
of stem-cell-containing epithelial tissues using mechanical equations, which describe
the size of the tissue and kinetic equations, which describe the interconversions
of the cell populations. We show that several features, such as the evolution
of stem cell fractions during intestinal development, the shape of a developing
intestinal wall, as well as the increase in the proliferative compartment in cancer
initiation, can be studied and understood from generic modelling which does not
rely on a particular regulatory mechanism. Finally, inspired by recent experiments,
we propose a model where cell division rates are regulated by the mechanical stresses
in the epithelial sheet. We show that pressure-controlled growth can, in addition
to the previous features, also explain with few parameters the formation of stem
cell compartments as well as the morphologies observed when a colonic crypt becomes
cancerous. We also discuss optimal strategies of wound healing, in connection
with experiments on the cornea.'
acknowledgement: We thank Jens Elgeti and Silvia Fre for fruitful discussions.
article_processing_charge: No
author:
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Jacques
full_name: Prost, Jacques
last_name: Prost
- first_name: Jean
full_name: Joanny, Jean
last_name: Joanny
citation:
ama: Hannezo EB, Prost J, Joanny J. Growth homeostatic regulation and stem cell
dynamics in tissues. Journal of the Royal Society Interface. 2014;11(93).
doi:10.1098/rsif.2013.0895
apa: Hannezo, E. B., Prost, J., & Joanny, J. (2014). Growth homeostatic regulation
and stem cell dynamics in tissues. Journal of the Royal Society Interface.
Royal Society of London. https://doi.org/10.1098/rsif.2013.0895
chicago: Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Growth Homeostatic
Regulation and Stem Cell Dynamics in Tissues.” Journal of the Royal Society
Interface. Royal Society of London, 2014. https://doi.org/10.1098/rsif.2013.0895.
ieee: E. B. Hannezo, J. Prost, and J. Joanny, “Growth homeostatic regulation and
stem cell dynamics in tissues,” Journal of the Royal Society Interface,
vol. 11, no. 93. Royal Society of London, 2014.
ista: Hannezo EB, Prost J, Joanny J. 2014. Growth homeostatic regulation and stem
cell dynamics in tissues. Journal of the Royal Society Interface. 11(93).
mla: Hannezo, Edouard B., et al. “Growth Homeostatic Regulation and Stem Cell Dynamics
in Tissues.” Journal of the Royal Society Interface, vol. 11, no. 93, Royal
Society of London, 2014, doi:10.1098/rsif.2013.0895.
short: E.B. Hannezo, J. Prost, J. Joanny, Journal of the Royal Society Interface
11 (2014).
date_created: 2018-12-11T11:49:14Z
date_published: 2014-04-06T00:00:00Z
date_updated: 2021-01-12T08:21:57Z
day: '06'
doi: 10.1098/rsif.2013.0895
extern: '1'
intvolume: ' 11'
issue: '93'
language:
- iso: eng
month: '04'
oa_version: None
publication: Journal of the Royal Society Interface
publication_status: published
publisher: Royal Society of London
publist_id: '6516'
status: public
title: Growth homeostatic regulation and stem cell dynamics in tissues
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2014'
...
---
_id: '927'
abstract:
- lang: eng
text: Morphogenesis during embryo development requires the coordination of mechanical
forces to generate the macroscopic shapes of organs. We propose a minimal theoretical
model, based on cell adhesion and actomyosin contractility, which describes the
various shapes of epithelial cells and the bending and buckling of epithelial
sheets, as well as the relative stability of cellular tubes and spheres. We show
that, to understand these processes, a full 3D description of the cells is needed,
but that simple scaling laws can still be derived. The morphologies observed in
vivo can be understood as stable points of mechanical equations and the transitions
between them are either continuous or discontinuous. We then focus on epithelial
sheet bending, a ubiquitous morphogenetic process. We calculate the curvature
of an epithelium as a function of actin belt tension as well as of cell-cell and
and cell-substrate tension. The model allows for a comparison of the relative
stabilities of spherical or cylindrical cellular structures (acini or tubes).
Finally, we propose a unique type of buckling instability of epithelia, driven
by a flattening of individual cell shapes, and discuss experimental tests to verify
our predictions.
article_processing_charge: No
author:
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Jacques
full_name: Prost, Jacques
last_name: Prost
- first_name: Jean
full_name: Joanny, Jean
last_name: Joanny
citation:
ama: Hannezo EB, Prost J, Joanny J. Theory of epithelial sheet morphology in three
dimensions. PNAS. 2014;111(1):27-32. doi:10.1073/pnas.1312076111
apa: Hannezo, E. B., Prost, J., & Joanny, J. (2014). Theory of epithelial sheet
morphology in three dimensions. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1312076111
chicago: Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Theory of Epithelial
Sheet Morphology in Three Dimensions.” PNAS. National Academy of Sciences,
2014. https://doi.org/10.1073/pnas.1312076111.
ieee: E. B. Hannezo, J. Prost, and J. Joanny, “Theory of epithelial sheet morphology
in three dimensions,” PNAS, vol. 111, no. 1. National Academy of Sciences,
pp. 27–32, 2014.
ista: Hannezo EB, Prost J, Joanny J. 2014. Theory of epithelial sheet morphology
in three dimensions. PNAS. 111(1), 27–32.
mla: Hannezo, Edouard B., et al. “Theory of Epithelial Sheet Morphology in Three
Dimensions.” PNAS, vol. 111, no. 1, National Academy of Sciences, 2014,
pp. 27–32, doi:10.1073/pnas.1312076111.
short: E.B. Hannezo, J. Prost, J. Joanny, PNAS 111 (2014) 27–32.
date_created: 2018-12-11T11:49:14Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T08:21:58Z
day: '01'
doi: 10.1073/pnas.1312076111
extern: '1'
intvolume: ' 111'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 27 - 32
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6517'
status: public
title: Theory of epithelial sheet morphology in three dimensions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 111
year: '2014'
...
---
_id: '7038'
article_processing_charge: No
author:
- first_name: Kristóf
full_name: Huszár, Kristóf
id: 33C26278-F248-11E8-B48F-1D18A9856A87
last_name: Huszár
orcid: 0000-0002-5445-5057
- first_name: Michal
full_name: Rolinek, Michal
id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87
last_name: Rolinek
citation:
ama: Huszár K, Rolinek M. Playful Math - An Introduction to Mathematical Games.
IST Austria
apa: Huszár, K., & Rolinek, M. (n.d.). Playful Math - An introduction to
mathematical games. IST Austria.
chicago: Huszár, Kristóf, and Michal Rolinek. Playful Math - An Introduction
to Mathematical Games. IST Austria, n.d.
ieee: K. Huszár and M. Rolinek, Playful Math - An introduction to mathematical
games. IST Austria.
ista: Huszár K, Rolinek M. Playful Math - An introduction to mathematical games,
IST Austria, 5p.
mla: Huszár, Kristóf, and Michal Rolinek. Playful Math - An Introduction to Mathematical
Games. IST Austria.
short: K. Huszár, M. Rolinek, Playful Math - An Introduction to Mathematical Games,
IST Austria, n.d.
date_created: 2019-11-18T15:57:05Z
date_published: 2014-06-30T00:00:00Z
date_updated: 2020-07-14T23:11:45Z
day: '30'
ddc:
- '510'
department:
- _id: VlKo
- _id: UlWa
file:
- access_level: open_access
checksum: 2b94e5e1f4c3fe8ab89b12806276fb09
content_type: application/pdf
creator: dernst
date_created: 2019-11-18T15:57:51Z
date_updated: 2020-07-14T12:47:48Z
file_id: '7039'
file_name: 2014_Playful_Math_Huszar.pdf
file_size: 511233
relation: main_file
file_date_updated: 2020-07-14T12:47:48Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '5'
publication_status: draft
publisher: IST Austria
status: public
title: Playful Math - An introduction to mathematical games
type: working_paper
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '7071'
abstract:
- lang: eng
text: Spin and orbital quantum numbers play a key role in the physics of Mott insulators,
but in most systems they are connected only indirectly—via the Pauli exclusion
principle and the Coulomb interaction. Iridium-based oxides (iridates) introduce
strong spin–orbit coupling directly, such that these numbers become entwined together
and the Mott physics attains a strong orbital character. In the layered honeycomb
iridates this is thought to generate highly spin–anisotropic magnetic interactions,
coupling the spin to a given spatial direction of exchange and leading to strongly
frustrated magnetism. Here we report a new iridate structure that has the same
local connectivity as the layered honeycomb and exhibits striking evidence for
highly spin–anisotropic exchange. The basic structural units of this material
suggest that a new family of three-dimensional structures could exist, the ‘harmonic
honeycomb’ iridates, of which the present compound is the first example.
article_number: '4203'
article_processing_charge: No
article_type: original
author:
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
- first_name: Tess E.
full_name: Smidt, Tess E.
last_name: Smidt
- first_name: Itamar
full_name: Kimchi, Itamar
last_name: Kimchi
- first_name: Nicholas P.
full_name: Breznay, Nicholas P.
last_name: Breznay
- first_name: Alun
full_name: Biffin, Alun
last_name: Biffin
- first_name: Sungkyun
full_name: Choi, Sungkyun
last_name: Choi
- first_name: Roger D.
full_name: Johnson, Roger D.
last_name: Johnson
- first_name: Radu
full_name: Coldea, Radu
last_name: Coldea
- first_name: Pilanda
full_name: Watkins-Curry, Pilanda
last_name: Watkins-Curry
- first_name: Gregory T.
full_name: McCandless, Gregory T.
last_name: McCandless
- first_name: Julia Y.
full_name: Chan, Julia Y.
last_name: Chan
- first_name: Felipe
full_name: Gandara, Felipe
last_name: Gandara
- first_name: Z.
full_name: Islam, Z.
last_name: Islam
- first_name: Ashvin
full_name: Vishwanath, Ashvin
last_name: Vishwanath
- first_name: Arkady
full_name: Shekhter, Arkady
last_name: Shekhter
- first_name: Ross D.
full_name: McDonald, Ross D.
last_name: McDonald
- first_name: James G.
full_name: Analytis, James G.
last_name: Analytis
citation:
ama: Modic KA, Smidt TE, Kimchi I, et al. Realization of a three-dimensional spin–anisotropic
harmonic honeycomb iridate. Nature Communications. 2014;5. doi:10.1038/ncomms5203
apa: Modic, K. A., Smidt, T. E., Kimchi, I., Breznay, N. P., Biffin, A., Choi, S.,
… Analytis, J. G. (2014). Realization of a three-dimensional spin–anisotropic
harmonic honeycomb iridate. Nature Communications. Springer Science and
Business Media LLC. https://doi.org/10.1038/ncomms5203
chicago: Modic, Kimberly A, Tess E. Smidt, Itamar Kimchi, Nicholas P. Breznay, Alun
Biffin, Sungkyun Choi, Roger D. Johnson, et al. “Realization of a Three-Dimensional
Spin–Anisotropic Harmonic Honeycomb Iridate.” Nature Communications. Springer
Science and Business Media LLC, 2014. https://doi.org/10.1038/ncomms5203.
ieee: K. A. Modic et al., “Realization of a three-dimensional spin–anisotropic
harmonic honeycomb iridate,” Nature Communications, vol. 5. Springer Science
and Business Media LLC, 2014.
ista: Modic KA, Smidt TE, Kimchi I, Breznay NP, Biffin A, Choi S, Johnson RD, Coldea
R, Watkins-Curry P, McCandless GT, Chan JY, Gandara F, Islam Z, Vishwanath A,
Shekhter A, McDonald RD, Analytis JG. 2014. Realization of a three-dimensional
spin–anisotropic harmonic honeycomb iridate. Nature Communications. 5, 4203.
mla: Modic, Kimberly A., et al. “Realization of a Three-Dimensional Spin–Anisotropic
Harmonic Honeycomb Iridate.” Nature Communications, vol. 5, 4203, Springer
Science and Business Media LLC, 2014, doi:10.1038/ncomms5203.
short: K.A. Modic, T.E. Smidt, I. Kimchi, N.P. Breznay, A. Biffin, S. Choi, R.D.
Johnson, R. Coldea, P. Watkins-Curry, G.T. McCandless, J.Y. Chan, F. Gandara,
Z. Islam, A. Vishwanath, A. Shekhter, R.D. McDonald, J.G. Analytis, Nature Communications
5 (2014).
date_created: 2019-11-19T13:22:39Z
date_published: 2014-06-27T00:00:00Z
date_updated: 2021-01-12T08:11:42Z
day: '27'
ddc:
- '530'
doi: 10.1038/ncomms5203
extern: '1'
file:
- access_level: open_access
checksum: d290f0bfa93c5169cc6c8086874c5a78
content_type: application/pdf
creator: dernst
date_created: 2019-11-26T12:44:23Z
date_updated: 2020-07-14T12:47:48Z
file_id: '7113'
file_name: 2014_NatureComm_Modic.pdf
file_size: 4832820
relation: main_file
file_date_updated: 2020-07-14T12:47:48Z
has_accepted_license: '1'
intvolume: ' 5'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Science and Business Media LLC
quality_controlled: '1'
status: public
title: Realization of a three-dimensional spin–anisotropic harmonic honeycomb iridate
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2014'
...
---
_id: '7072'
abstract:
- lang: eng
text: We investigate the structural and magnetic properties of two molecule-based
magnets synthesized from the same starting components. Their different structural
motifs promote contrasting exchange pathways and consequently lead to markedly
different magnetic ground states. Through examination of their structural and
magnetic properties we show that [Cu(pyz)(H2O)(gly)2](ClO4)2 may be considered
a quasi-one-dimensional quantum Heisenberg antiferromagnet whereas the related
compound [Cu(pyz)(gly)](ClO4), which is formed from dimers of antiferromagnetically
interacting Cu2+ spins, remains disordered down to at least 0.03 K in zero field
but shows a field-temperature phase diagram reminiscent of that seen in materials
showing a Bose-Einstein condensation of magnons.
article_number: '207201'
article_processing_charge: No
article_type: original
author:
- first_name: T.
full_name: Lancaster, T.
last_name: Lancaster
- first_name: P. A.
full_name: Goddard, P. A.
last_name: Goddard
- first_name: S. J.
full_name: Blundell, S. J.
last_name: Blundell
- first_name: F. R.
full_name: Foronda, F. R.
last_name: Foronda
- first_name: S.
full_name: Ghannadzadeh, S.
last_name: Ghannadzadeh
- first_name: J. S.
full_name: Möller, J. S.
last_name: Möller
- first_name: P. J.
full_name: Baker, P. J.
last_name: Baker
- first_name: F. L.
full_name: Pratt, F. L.
last_name: Pratt
- first_name: C.
full_name: Baines, C.
last_name: Baines
- first_name: L.
full_name: Huang, L.
last_name: Huang
- first_name: J.
full_name: Wosnitza, J.
last_name: Wosnitza
- first_name: R. D.
full_name: McDonald, R. D.
last_name: McDonald
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
- first_name: J.
full_name: Singleton, J.
last_name: Singleton
- first_name: C. V.
full_name: Topping, C. V.
last_name: Topping
- first_name: T. A. W.
full_name: Beale, T. A. W.
last_name: Beale
- first_name: F.
full_name: Xiao, F.
last_name: Xiao
- first_name: J. A.
full_name: Schlueter, J. A.
last_name: Schlueter
- first_name: A. M.
full_name: Barton, A. M.
last_name: Barton
- first_name: R. D.
full_name: Cabrera, R. D.
last_name: Cabrera
- first_name: K. E.
full_name: Carreiro, K. E.
last_name: Carreiro
- first_name: H. E.
full_name: Tran, H. E.
last_name: Tran
- first_name: J. L.
full_name: Manson, J. L.
last_name: Manson
citation:
ama: Lancaster T, Goddard PA, Blundell SJ, et al. Controlling magnetic order and
quantum disorder in molecule-based magnets. Physical Review Letters. 2014;112(20).
doi:10.1103/physrevlett.112.207201
apa: Lancaster, T., Goddard, P. A., Blundell, S. J., Foronda, F. R., Ghannadzadeh,
S., Möller, J. S., … Manson, J. L. (2014). Controlling magnetic order and quantum
disorder in molecule-based magnets. Physical Review Letters. APS. https://doi.org/10.1103/physrevlett.112.207201
chicago: Lancaster, T., P. A. Goddard, S. J. Blundell, F. R. Foronda, S. Ghannadzadeh,
J. S. Möller, P. J. Baker, et al. “Controlling Magnetic Order and Quantum Disorder
in Molecule-Based Magnets.” Physical Review Letters. APS, 2014. https://doi.org/10.1103/physrevlett.112.207201.
ieee: T. Lancaster et al., “Controlling magnetic order and quantum disorder
in molecule-based magnets,” Physical Review Letters, vol. 112, no. 20.
APS, 2014.
ista: Lancaster T, Goddard PA, Blundell SJ, Foronda FR, Ghannadzadeh S, Möller JS,
Baker PJ, Pratt FL, Baines C, Huang L, Wosnitza J, McDonald RD, Modic KA, Singleton
J, Topping CV, Beale TAW, Xiao F, Schlueter JA, Barton AM, Cabrera RD, Carreiro
KE, Tran HE, Manson JL. 2014. Controlling magnetic order and quantum disorder
in molecule-based magnets. Physical Review Letters. 112(20), 207201.
mla: Lancaster, T., et al. “Controlling Magnetic Order and Quantum Disorder in Molecule-Based
Magnets.” Physical Review Letters, vol. 112, no. 20, 207201, APS, 2014,
doi:10.1103/physrevlett.112.207201.
short: T. Lancaster, P.A. Goddard, S.J. Blundell, F.R. Foronda, S. Ghannadzadeh,
J.S. Möller, P.J. Baker, F.L. Pratt, C. Baines, L. Huang, J. Wosnitza, R.D. McDonald,
K.A. Modic, J. Singleton, C.V. Topping, T.A.W. Beale, F. Xiao, J.A. Schlueter,
A.M. Barton, R.D. Cabrera, K.E. Carreiro, H.E. Tran, J.L. Manson, Physical Review
Letters 112 (2014).
date_created: 2019-11-19T13:23:13Z
date_published: 2014-05-19T00:00:00Z
date_updated: 2021-01-12T08:11:42Z
day: '19'
doi: 10.1103/physrevlett.112.207201
extern: '1'
intvolume: ' 112'
issue: '20'
language:
- iso: eng
month: '05'
oa_version: None
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: APS
quality_controlled: '1'
status: public
title: Controlling magnetic order and quantum disorder in molecule-based magnets
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2014'
...
---
_id: '7300'
abstract:
- lang: eng
text: Photoinduced electron transfer (PET), which causes pH-dependent quenching
of fluorescent dyes, is more effectively introduced by phenolic groups than by
amino groups which have been much more commonly used so far. That is demonstrated
by fluorescence measurements involving several classes of fluorophores. Electrochemical
measurements show that PET in several amino-modified dyes is thermodynamically
favorable, even though it was not experimentally found, underlining the importance
of kinetic aspects to the process. Consequently, the attachment of phenolic groups
allows for fast and simple preparation of a wide selection of fluorescent pH-probes
with tailor-made spectral properties, sensitive ranges, and individual advantages,
so that a large number of applications can be realized. Fluorophores carrying
phenolic groups may also be used for sensing analytes other than pH or molecular
switching and signaling.
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
full_name: Aigner, Daniel
last_name: Aigner
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Martin
full_name: Wilkening, Martin
last_name: Wilkening
- first_name: Robert
full_name: Saf, Robert
last_name: Saf
- first_name: Sergey M.
full_name: Borisov, Sergey M.
last_name: Borisov
- first_name: Ingo
full_name: Klimant, Ingo
last_name: Klimant
citation:
ama: Aigner D, Freunberger SA, Wilkening M, Saf R, Borisov SM, Klimant I. Enhancing
photoinduced electron transfer efficiency of fluorescent pH-probes with halogenated
phenols. Analytical Chemistry. 2014;86(18):9293-9300. doi:10.1021/ac502513g
apa: Aigner, D., Freunberger, S. A., Wilkening, M., Saf, R., Borisov, S. M., &
Klimant, I. (2014). Enhancing photoinduced electron transfer efficiency of fluorescent
pH-probes with halogenated phenols. Analytical Chemistry. ACS. https://doi.org/10.1021/ac502513g
chicago: Aigner, Daniel, Stefan Alexander Freunberger, Martin Wilkening, Robert
Saf, Sergey M. Borisov, and Ingo Klimant. “Enhancing Photoinduced Electron Transfer
Efficiency of Fluorescent PH-Probes with Halogenated Phenols.” Analytical Chemistry.
ACS, 2014. https://doi.org/10.1021/ac502513g.
ieee: D. Aigner, S. A. Freunberger, M. Wilkening, R. Saf, S. M. Borisov, and I.
Klimant, “Enhancing photoinduced electron transfer efficiency of fluorescent pH-probes
with halogenated phenols,” Analytical Chemistry, vol. 86, no. 18. ACS,
pp. 9293–9300, 2014.
ista: Aigner D, Freunberger SA, Wilkening M, Saf R, Borisov SM, Klimant I. 2014.
Enhancing photoinduced electron transfer efficiency of fluorescent pH-probes with
halogenated phenols. Analytical Chemistry. 86(18), 9293–9300.
mla: Aigner, Daniel, et al. “Enhancing Photoinduced Electron Transfer Efficiency
of Fluorescent PH-Probes with Halogenated Phenols.” Analytical Chemistry,
vol. 86, no. 18, ACS, 2014, pp. 9293–300, doi:10.1021/ac502513g.
short: D. Aigner, S.A. Freunberger, M. Wilkening, R. Saf, S.M. Borisov, I. Klimant,
Analytical Chemistry 86 (2014) 9293–9300.
date_created: 2020-01-15T12:17:17Z
date_published: 2014-08-14T00:00:00Z
date_updated: 2021-01-12T08:12:53Z
day: '14'
doi: 10.1021/ac502513g
extern: '1'
intvolume: ' 86'
issue: '18'
language:
- iso: eng
month: '08'
oa_version: None
page: 9293-9300
publication: Analytical Chemistry
publication_identifier:
issn:
- 0003-2700
- 1520-6882
publication_status: published
publisher: ACS
quality_controlled: '1'
status: public
title: Enhancing photoinduced electron transfer efficiency of fluorescent pH-probes
with halogenated phenols
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 86
year: '2014'
...
---
_id: '7301'
abstract:
- lang: eng
text: Several problems arise at the O2 (positive) electrode in the Li-air battery,
including solvent/electrode decomposition and electrode passivation by insulating
Li2O2. Progress partially depends on exploring the basic electrochemistry of O2
reduction. Here we describe the effect of complexing-cations on the electrochemical
reduction of O2 in DMSO in the presence and absence of a Li salt. The solubility
of alkaline peroxides in DMSO is enhanced by the complexing-cations, consistent
with their strong interaction with reduced O2. The complexing-cations also increase
the rate of the 1-electron O2 reduction to O2•– by up to six-fold (k° = 2.4 ×10–3
to 1.5 × 10–2 cm s–1) whether or not Li+ ions are present. In the absence of Li+,
the complexing-cations also promote the reduction of O2•– to O22–. In the presence
of Li+ and complexing-cations, and despite the interaction of the reduced O2 with
the latter, SERS confirms that the product is still Li2O2.
article_processing_charge: No
article_type: original
author:
- first_name: Chunmei
full_name: Li, Chunmei
last_name: Li
- first_name: Olivier
full_name: Fontaine, Olivier
last_name: Fontaine
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Lee
full_name: Johnson, Lee
last_name: Johnson
- first_name: Sylvie
full_name: Grugeon, Sylvie
last_name: Grugeon
- first_name: Stéphane
full_name: Laruelle, Stéphane
last_name: Laruelle
- first_name: Peter G.
full_name: Bruce, Peter G.
last_name: Bruce
- first_name: Michel
full_name: Armand, Michel
last_name: Armand
citation:
ama: 'Li C, Fontaine O, Freunberger SA, et al. Aprotic Li–O2 battery: Influence
of complexing agents on oxygen reduction in an aprotic solvent. The Journal
of Physical Chemistry C. 2014;118(7):3393-3401. doi:10.1021/jp4093805'
apa: 'Li, C., Fontaine, O., Freunberger, S. A., Johnson, L., Grugeon, S., Laruelle,
S., … Armand, M. (2014). Aprotic Li–O2 battery: Influence of complexing agents
on oxygen reduction in an aprotic solvent. The Journal of Physical Chemistry
C. ACS. https://doi.org/10.1021/jp4093805'
chicago: 'Li, Chunmei, Olivier Fontaine, Stefan Alexander Freunberger, Lee Johnson,
Sylvie Grugeon, Stéphane Laruelle, Peter G. Bruce, and Michel Armand. “Aprotic
Li–O2 Battery: Influence of Complexing Agents on Oxygen Reduction in an Aprotic
Solvent.” The Journal of Physical Chemistry C. ACS, 2014. https://doi.org/10.1021/jp4093805.'
ieee: 'C. Li et al., “Aprotic Li–O2 battery: Influence of complexing agents
on oxygen reduction in an aprotic solvent,” The Journal of Physical Chemistry
C, vol. 118, no. 7. ACS, pp. 3393–3401, 2014.'
ista: 'Li C, Fontaine O, Freunberger SA, Johnson L, Grugeon S, Laruelle S, Bruce
PG, Armand M. 2014. Aprotic Li–O2 battery: Influence of complexing agents on oxygen
reduction in an aprotic solvent. The Journal of Physical Chemistry C. 118(7),
3393–3401.'
mla: 'Li, Chunmei, et al. “Aprotic Li–O2 Battery: Influence of Complexing Agents
on Oxygen Reduction in an Aprotic Solvent.” The Journal of Physical Chemistry
C, vol. 118, no. 7, ACS, 2014, pp. 3393–401, doi:10.1021/jp4093805.'
short: C. Li, O. Fontaine, S.A. Freunberger, L. Johnson, S. Grugeon, S. Laruelle,
P.G. Bruce, M. Armand, The Journal of Physical Chemistry C 118 (2014) 3393–3401.
date_created: 2020-01-15T12:17:28Z
date_published: 2014-01-29T00:00:00Z
date_updated: 2021-01-12T08:12:53Z
day: '29'
doi: 10.1021/jp4093805
extern: '1'
intvolume: ' 118'
issue: '7'
language:
- iso: eng
month: '01'
oa_version: None
page: 3393-3401
publication: The Journal of Physical Chemistry C
publication_identifier:
issn:
- 1932-7447
- 1932-7455
publication_status: published
publisher: ACS
quality_controlled: '1'
status: public
title: 'Aprotic Li–O2 battery: Influence of complexing agents on oxygen reduction
in an aprotic solvent'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2014'
...