---
_id: '5428'
abstract:
- lang: eng
text: "Simulation is an attractive alternative for language inclusion for automata
as it is an under-approximation of language inclusion, but usually has much lower
complexity. For non-deterministic automata, while language inclusion is PSPACE-complete,
simulation can be computed in polynomial time. Simulation has also been extended
in two orthogonal directions, namely, (1) fair simulation, for simulation over
specified set of infinite runs; and (2) quantitative simulation, for simulation
between weighted automata. Again, while fair trace inclusion is PSPACE-complete,
fair simulation can be computed in polynomial time. For weighted automata, the
(quantitative) language inclusion problem is undecidable for mean-payoff automata
and the decidability is open for discounted-sum automata, whereas the (quantitative)
simulation reduce to mean-payoff games and discounted-sum games, which admit pseudo-polynomial
time algorithms.\r\n\r\nIn this work, we study (quantitative) simulation for weighted
automata with Büchi acceptance conditions, i.e., we generalize fair simulation
from non-weighted automata to weighted automata. We show that imposing Büchi acceptance
conditions on weighted automata changes many fundamental properties of the simulation
games. For example, whereas for mean-payoff and discounted-sum games, the players
do not need memory to play optimally; we show in contrast that for simulation
games with Büchi acceptance conditions, (i) for mean-payoff objectives, optimal
strategies for both players require infinite memory in general, and (ii) for discounted-sum
objectives, optimal strategies need not exist for both players. While the simulation
games with Büchi acceptance conditions are more complicated (e.g., due to infinite-memory
requirements for mean-payoff objectives) as compared to their counterpart without
Büchi acceptance conditions, we still present pseudo-polynomial time algorithms
to solve simulation games with Büchi acceptance conditions for both weighted mean-payoff
and weighted discounted-sum automata."
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
- first_name: Yaron
full_name: Velner, Yaron
last_name: Velner
citation:
ama: Chatterjee K, Henzinger TA, Otop J, Velner Y. Quantitative Fair Simulation
Games. IST Austria; 2014. doi:10.15479/AT:IST-2014-315-v1-1
apa: Chatterjee, K., Henzinger, T. A., Otop, J., & Velner, Y. (2014). Quantitative
fair simulation games. IST Austria. https://doi.org/10.15479/AT:IST-2014-315-v1-1
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner.
Quantitative Fair Simulation Games. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-315-v1-1.
ieee: K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, Quantitative fair
simulation games. IST Austria, 2014.
ista: Chatterjee K, Henzinger TA, Otop J, Velner Y. 2014. Quantitative fair simulation
games, IST Austria, 26p.
mla: Chatterjee, Krishnendu, et al. Quantitative Fair Simulation Games. IST
Austria, 2014, doi:10.15479/AT:IST-2014-315-v1-1.
short: K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Quantitative Fair Simulation
Games, IST Austria, 2014.
date_created: 2018-12-12T11:39:16Z
date_published: 2014-12-05T00:00:00Z
date_updated: 2026-06-18T08:47:00Z
day: '05'
ddc:
- '004'
department:
- _id: ToHe
- _id: KrCh
doi: 10.15479/AT:IST-2014-315-v1-1
file:
- access_level: open_access
checksum: b1d573bc04365625ff9974880c0aa807
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:59Z
date_updated: 2020-07-14T12:46:52Z
file_id: '5521'
file_name: IST-2014-315-v1+1_report.pdf
file_size: 531046
relation: main_file
file_date_updated: 2020-07-14T12:46:52Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '26'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '315'
related_material:
record:
- id: '1066'
relation: later_version
status: public
status: public
title: Quantitative fair simulation games
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '5810'
abstract:
- lang: eng
text: A discrete spherical geodesic path between two voxels s and t lying on a discrete
sphere is a/the 1-connected shortest path from s to t, comprising voxels of the
discrete sphere intersected by the real plane passing through s, t, and the center
of the sphere. We show that the set of sphere voxels intersected by the aforesaid
real plane always contains a 1-connected cycle passing through s and t, and each
voxel in this set lies within an isothetic distance of 32 from the concerned plane.
Hence, to compute the path, the algorithm starts from s, and iteratively computes
each voxel p of the path from the predecessor of p. A novel number-theoretic property
and the 48-symmetry of discrete sphere are used for searching the 1-connected
voxels comprising the path. The algorithm is output-sensitive, having its time
and space complexities both linear in the length of the path. It can be extended
for constructing 1-connected discrete 3D circles of arbitrary orientations, specified
by a few appropriate input parameters. Experimental results and related analysis
demonstrate its efficiency and versatility.
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: Biswas R, Bhowmick P. On Finding Spherical Geodesic Paths and Circles in ℤ3.
2014;8668:396-409. doi:10.1007/978-3-319-09955-2_33
apa: 'Biswas, R., & Bhowmick, P. (2014). On Finding Spherical Geodesic Paths
and Circles in ℤ3. Presented at the DGCI: International Conference on Discrete
Geometry for Computer Imagery, Berlin, Heidelberg: Springer. https://doi.org/10.1007/978-3-319-09955-2_33'
chicago: 'Biswas, Ranita, and Partha Bhowmick. “On Finding Spherical Geodesic Paths
and Circles in ℤ3.” Lecture Notes in Computer Science. Berlin, Heidelberg: Springer,
2014. https://doi.org/10.1007/978-3-319-09955-2_33.'
ieee: R. Biswas and P. Bhowmick, “On Finding Spherical Geodesic Paths and Circles
in ℤ3,” vol. 8668. Springer, Berlin, Heidelberg, pp. 396–409, 2014.
ista: Biswas R, Bhowmick P. 2014. On Finding Spherical Geodesic Paths and Circles
in ℤ3. 8668, 396–409.
mla: Biswas, Ranita, and Partha Bhowmick. On Finding Spherical Geodesic Paths
and Circles in ℤ3. Vol. 8668, Springer, 2014, pp. 396–409, doi:10.1007/978-3-319-09955-2_33.
short: R. Biswas, P. Bhowmick, 8668 (2014) 396–409.
conference:
end_date: 2014-09-12
location: Siena, Italy
name: 'DGCI: International Conference on Discrete Geometry for Computer Imagery'
start_date: 2014-09-10
date_created: 2019-01-08T20:45:32Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2019-01-24T13:22:49Z
doi: 10.1007/978-3-319-09955-2_33
extern: '1'
intvolume: ' 8668'
language:
- iso: eng
oa_version: None
page: 396-409
place: Berlin, Heidelberg
publication_identifier:
isbn:
- '9783642387081'
- '9783642387098'
issn:
- 0302-9743
- 1611-3349
publication_status: published
publisher: Springer
quality_controlled: '1'
series_title: Lecture Notes in Computer Science
status: public
title: On Finding Spherical Geodesic Paths and Circles in ℤ3
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8668
year: '2014'
...
---
_id: '5813'
abstract:
- lang: eng
text: We consider homogeneous Bose gas in a large cubic box with periodic boundary
conditions, at zero temperature. We analyze its excitation spectrum in a certain
kind of a mean-field infinite-volume limit. We prove that under appropriate conditions
the excitation spectrum has the form predicted by the Bogoliubov approximation.
Our result can be viewed as an extension of the result of Seiringer (Commun. Math.
Phys.306:565–578, 2011) to large volumes.
article_processing_charge: No
author:
- first_name: Jan
full_name: Dereziński, Jan
last_name: Dereziński
- first_name: Marcin M
full_name: Napiórkowski, Marcin M
id: 4197AD04-F248-11E8-B48F-1D18A9856A87
last_name: Napiórkowski
citation:
ama: Dereziński J, Napiórkowski MM. Excitation spectrum of interacting bosons in
the Mean-Field Infinite-Volume limit. Annales Henri Poincaré. 2014;15(12):2409-2439.
doi:10.1007/s00023-013-0302-4
apa: Dereziński, J., & Napiórkowski, M. M. (2014). Excitation spectrum of interacting
bosons in the Mean-Field Infinite-Volume limit. Annales Henri Poincaré.
Springer Nature. https://doi.org/10.1007/s00023-013-0302-4
chicago: Dereziński, Jan, and Marcin M Napiórkowski. “Excitation Spectrum of Interacting
Bosons in the Mean-Field Infinite-Volume Limit.” Annales Henri Poincaré.
Springer Nature, 2014. https://doi.org/10.1007/s00023-013-0302-4.
ieee: J. Dereziński and M. M. Napiórkowski, “Excitation spectrum of interacting
bosons in the Mean-Field Infinite-Volume limit,” Annales Henri Poincaré,
vol. 15, no. 12. Springer Nature, pp. 2409–2439, 2014.
ista: Dereziński J, Napiórkowski MM. 2014. Excitation spectrum of interacting bosons
in the Mean-Field Infinite-Volume limit. Annales Henri Poincaré. 15(12), 2409–2439.
mla: Dereziński, Jan, and Marcin M. Napiórkowski. “Excitation Spectrum of Interacting
Bosons in the Mean-Field Infinite-Volume Limit.” Annales Henri Poincaré,
vol. 15, no. 12, Springer Nature, 2014, pp. 2409–39, doi:10.1007/s00023-013-0302-4.
short: J. Dereziński, M.M. Napiórkowski, Annales Henri Poincaré 15 (2014) 2409–2439.
date_created: 2019-01-10T09:02:58Z
date_published: 2014-01-10T00:00:00Z
date_updated: 2021-11-16T08:13:24Z
day: '10'
ddc:
- '530'
doi: 10.1007/s00023-013-0302-4
extern: '1'
file:
- access_level: open_access
checksum: 1f6c32c5d6ec90cdb0718c7f0103342e
content_type: application/pdf
creator: dernst
date_created: 2019-01-10T09:04:45Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5814'
file_name: 2014_Annales_Derezinski.pdf
file_size: 865230
relation: main_file
file_date_updated: 2020-07-14T12:47:11Z
has_accepted_license: '1'
intvolume: ' 15'
issue: '12'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 2409-2439
publication: Annales Henri Poincaré
publication_identifier:
issn:
- 1424-0637
- 1424-0661
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1007/s00023-014-0390-9
status: public
title: Excitation spectrum of interacting bosons in the Mean-Field Infinite-Volume
limit
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 15
year: '2014'
...
---
_id: '589'
abstract:
- lang: eng
text: We demonstrate a many-atom-cavity system with a high-finesse dual-wavelength
standing wave cavity in which all participating rubidium atoms are nearly identically
coupled to a 780-nm cavity mode. This homogeneous coupling is enforced by a one-dimensional
optical lattice formed by the field of a 1560-nm cavity mode.
author:
- first_name: Jongmin
full_name: Lee, Jongmin
last_name: Lee
- first_name: Geert
full_name: Vrijsen, Geert
last_name: Vrijsen
- first_name: Igor
full_name: Teper, Igor
last_name: Teper
- first_name: Onur
full_name: Onur Hosten
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Mark
full_name: Kasevich, Mark A
last_name: Kasevich
citation:
ama: Lee J, Vrijsen G, Teper I, Hosten O, Kasevich M. Many-atom-cavity QED system
with homogeneous atom-cavity coupling. Optics Letters. 2014;39(13):4005-4008.
doi:10.1364/OL.39.004005
apa: Lee, J., Vrijsen, G., Teper, I., Hosten, O., & Kasevich, M. (2014). Many-atom-cavity
QED system with homogeneous atom-cavity coupling. Optics Letters. OSA.
https://doi.org/10.1364/OL.39.004005
chicago: Lee, Jongmin, Geert Vrijsen, Igor Teper, Onur Hosten, and Mark Kasevich.
“Many-Atom-Cavity QED System with Homogeneous Atom-Cavity Coupling.” Optics
Letters. OSA, 2014. https://doi.org/10.1364/OL.39.004005.
ieee: J. Lee, G. Vrijsen, I. Teper, O. Hosten, and M. Kasevich, “Many-atom-cavity
QED system with homogeneous atom-cavity coupling,” Optics Letters, vol.
39, no. 13. OSA, pp. 4005–4008, 2014.
ista: Lee J, Vrijsen G, Teper I, Hosten O, Kasevich M. 2014. Many-atom-cavity QED
system with homogeneous atom-cavity coupling. Optics Letters. 39(13), 4005–4008.
mla: Lee, Jongmin, et al. “Many-Atom-Cavity QED System with Homogeneous Atom-Cavity
Coupling.” Optics Letters, vol. 39, no. 13, OSA, 2014, pp. 4005–08, doi:10.1364/OL.39.004005.
short: J. Lee, G. Vrijsen, I. Teper, O. Hosten, M. Kasevich, Optics Letters 39 (2014)
4005–4008.
date_created: 2018-12-11T11:47:21Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2021-01-12T08:05:09Z
day: '01'
doi: 10.1364/OL.39.004005
extern: 1
intvolume: ' 39'
issue: '13'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1311.1805
month: '07'
oa: 1
page: 4005 - 4008
publication: Optics Letters
publication_status: published
publisher: OSA
publist_id: '7216'
quality_controlled: 0
status: public
title: Many-atom-cavity QED system with homogeneous atom-cavity coupling
type: journal_article
volume: 39
year: '2014'
...
---
_id: '6122'
author:
- first_name: Gerit A.
full_name: Linneweber, Gerit A.
last_name: Linneweber
- first_name: Jake
full_name: Jacobson, Jake
last_name: Jacobson
- first_name: Karl Emanuel
full_name: Busch, Karl Emanuel
last_name: Busch
- first_name: Bruno
full_name: Hudry, Bruno
last_name: Hudry
- first_name: Christo P.
full_name: Christov, Christo P.
last_name: Christov
- first_name: Dirk
full_name: Dormann, Dirk
last_name: Dormann
- first_name: Michaela
full_name: Yuan, Michaela
last_name: Yuan
- first_name: Tomoki
full_name: Otani, Tomoki
last_name: Otani
- first_name: Elisabeth
full_name: Knust, Elisabeth
last_name: Knust
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
- first_name: Irene
full_name: Miguel-Aliaga, Irene
last_name: Miguel-Aliaga
citation:
ama: Linneweber GA, Jacobson J, Busch KE, et al. Neuronal control of metabolism
through nutrient-dependent modulation of tracheal branching. Cell. 2014;156(1-2):69-83.
doi:10.1016/j.cell.2013.12.008
apa: Linneweber, G. A., Jacobson, J., Busch, K. E., Hudry, B., Christov, C. P.,
Dormann, D., … Miguel-Aliaga, I. (2014). Neuronal control of metabolism through
nutrient-dependent modulation of tracheal branching. Cell. Elsevier. https://doi.org/10.1016/j.cell.2013.12.008
chicago: Linneweber, Gerit A., Jake Jacobson, Karl Emanuel Busch, Bruno Hudry, Christo P.
Christov, Dirk Dormann, Michaela Yuan, et al. “Neuronal Control of Metabolism
through Nutrient-Dependent Modulation of Tracheal Branching.” Cell. Elsevier,
2014. https://doi.org/10.1016/j.cell.2013.12.008.
ieee: G. A. Linneweber et al., “Neuronal control of metabolism through nutrient-dependent
modulation of tracheal branching,” Cell, vol. 156, no. 1–2. Elsevier, pp.
69–83, 2014.
ista: Linneweber GA, Jacobson J, Busch KE, Hudry B, Christov CP, Dormann D, Yuan
M, Otani T, Knust E, de Bono M, Miguel-Aliaga I. 2014. Neuronal control of metabolism
through nutrient-dependent modulation of tracheal branching. Cell. 156(1–2), 69–83.
mla: Linneweber, Gerit A., et al. “Neuronal Control of Metabolism through Nutrient-Dependent
Modulation of Tracheal Branching.” Cell, vol. 156, no. 1–2, Elsevier, 2014,
pp. 69–83, doi:10.1016/j.cell.2013.12.008.
short: G.A. Linneweber, J. Jacobson, K.E. Busch, B. Hudry, C.P. Christov, D. Dormann,
M. Yuan, T. Otani, E. Knust, M. de Bono, I. Miguel-Aliaga, Cell 156 (2014) 69–83.
date_created: 2019-03-19T14:35:30Z
date_published: 2014-01-16T00:00:00Z
date_updated: 2021-01-12T08:06:13Z
day: '16'
ddc:
- '570'
doi: 10.1016/j.cell.2013.12.008
extern: '1'
external_id:
pmid:
- '24439370'
file:
- access_level: open_access
checksum: ad6ef68f37fb711d9abcd97fc06ad316
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T14:40:38Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6123'
file_name: 2014_Elsevier_Linneweber.pdf
file_size: 5020084
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 156'
issue: 1-2
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 69-83
pmid: 1
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Neuronal control of metabolism through nutrient-dependent modulation of tracheal
branching
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 156
year: '2014'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '6124'
abstract:
- lang: eng
text: Despite the importance of G-protein coupled receptors (GPCRs) their biogenesis
is poorly understood. Like vertebrates, C. elegans uses a large family of GPCRs
as chemoreceptors. A subset of these receptors, such as ODR-10, requires the odr-4
and odr-8 genes to be appropriately localized to sensory cilia. The odr-4 gene
encodes a conserved tail-anchored transmembrane protein; the molecular identity
of odr-8 is unknown. Here, we show that odr-8 encodes the C. elegans ortholog
of Ufm1-specific protease 2 (UfSP2). UfSPs are cysteine proteases identified biochemically
by their ability to liberate the ubiquitin-like modifier Ufm1 from its pro-form
and protein conjugates. ODR-8/UfSP2 and ODR-4 are expressed in the same set of
twelve chemosensory neurons, and physically interact at the ER membrane. ODR-4
also binds ODR-10, suggesting that an ODR-4/ODR-8 complex promotes GPCR folding,
maturation, or export from the ER. The physical interaction between human ODR4
and UfSP2 suggests that this complex's role in GPCR biogenesis may be evolutionarily
conserved. Unexpectedly, mutant versions of ODR-8/UfSP2 lacking catalytic residues
required for protease activity can rescue all odr-8 mutant phenotypes tested.
Moreover, deleting C. elegans ufm-1 does not alter chemoreceptor traffic to cilia,
either in wild type or in odr-8 mutants. Thus, UfSP2 proteins have protease- and
Ufm1-independent functions in GPCR biogenesis.
article_number: e1004082
article_processing_charge: No
author:
- first_name: Changchun
full_name: Chen, Changchun
last_name: Chen
- first_name: Eisuke
full_name: Itakura, Eisuke
last_name: Itakura
- first_name: Katherine P.
full_name: Weber, Katherine P.
last_name: Weber
- first_name: Ramanujan S.
full_name: Hegde, Ramanujan S.
last_name: Hegde
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Chen C, Itakura E, Weber KP, Hegde RS, de Bono M. An ER complex of ODR-4 and
ODR-8/Ufm1 specific protease 2 promotes GPCR maturation by a Ufm1-independent
mechanism. PLoS Genetics. 2014;10(3). doi:10.1371/journal.pgen.1004082
apa: Chen, C., Itakura, E., Weber, K. P., Hegde, R. S., & de Bono, M. (2014).
An ER complex of ODR-4 and ODR-8/Ufm1 specific protease 2 promotes GPCR maturation
by a Ufm1-independent mechanism. PLoS Genetics. Public Library of Science
(PLoS). https://doi.org/10.1371/journal.pgen.1004082
chicago: Chen, Changchun, Eisuke Itakura, Katherine P. Weber, Ramanujan S. Hegde,
and Mario de Bono. “An ER Complex of ODR-4 and ODR-8/Ufm1 Specific Protease 2
Promotes GPCR Maturation by a Ufm1-Independent Mechanism.” PLoS Genetics.
Public Library of Science (PLoS), 2014. https://doi.org/10.1371/journal.pgen.1004082.
ieee: C. Chen, E. Itakura, K. P. Weber, R. S. Hegde, and M. de Bono, “An ER complex
of ODR-4 and ODR-8/Ufm1 specific protease 2 promotes GPCR maturation by a Ufm1-independent
mechanism,” PLoS Genetics, vol. 10, no. 3. Public Library of Science (PLoS),
2014.
ista: Chen C, Itakura E, Weber KP, Hegde RS, de Bono M. 2014. An ER complex of ODR-4
and ODR-8/Ufm1 specific protease 2 promotes GPCR maturation by a Ufm1-independent
mechanism. PLoS Genetics. 10(3), e1004082.
mla: Chen, Changchun, et al. “An ER Complex of ODR-4 and ODR-8/Ufm1 Specific Protease
2 Promotes GPCR Maturation by a Ufm1-Independent Mechanism.” PLoS Genetics,
vol. 10, no. 3, e1004082, Public Library of Science (PLoS), 2014, doi:10.1371/journal.pgen.1004082.
short: C. Chen, E. Itakura, K.P. Weber, R.S. Hegde, M. de Bono, PLoS Genetics 10
(2014).
date_created: 2019-03-19T14:45:56Z
date_published: 2014-03-06T00:00:00Z
date_updated: 2024-10-30T14:45:33Z
day: '06'
ddc:
- '570'
doi: 10.1371/journal.pgen.1004082
extern: '1'
external_id:
pmid:
- '24603482'
file:
- access_level: open_access
checksum: ac19941089a4262bb5bd74434a08b003
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T14:50:07Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6125'
file_name: 2014_PLOS_Chen.PDF
file_size: 8286819
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Genetics
publication_identifier:
issn:
- 1553-7404
publication_status: published
publisher: Public Library of Science (PLoS)
quality_controlled: '1'
status: public
title: An ER complex of ODR-4 and ODR-8/Ufm1 specific protease 2 promotes GPCR maturation
by a Ufm1-independent mechanism
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: 0043cee0-e5fc-11ee-9736-f83bc23afbf0
volume: 10
year: '2014'
...
---
_id: '6126'
abstract:
- lang: eng
text: Aerobic animals constantly monitor and adapt to changes in O2 levels. The
molecular mechanisms involved in sensing O2 are, however, incompletely understood.
Previous studies showed that a hexacoordinated globin called GLB-5 tunes the dynamic
range of O2-sensing neurons in natural C. elegans isolates, but is defective in
the N2 lab reference strain (McGrath et al., 2009; Persson et al., 2009). GLB-5
enables a sharp behavioral switch when O2 changes between 21 and 17%. Here, we
show that GLB-5 also confers rapid behavioral and cellular recovery from exposure
to hypoxia. Hypoxia reconfigures O2-evoked Ca2+ responses in the URX O2 sensors,
and GLB-5 enables rapid recovery of these responses upon re-oxygenation. Forward
genetic screens indicate that GLB-5's effects on O2 sensing require PDL-1, the
C. elegans ortholog of mammalian PrBP/PDE6δ protein. In mammals, PDE6δ regulates
the traffic and activity of prenylated proteins (Zhang et al., 2004; Norton et
al., 2005). PDL-1 promotes localization of GCY-33 and GCY-35, atypical soluble
guanylate cyclases that act as O2 sensors, to the dendritic endings of URX and
BAG neurons, where they colocalize with GLB-5. Both GCY-33 and GCY-35 are predicted
to be prenylated. Dendritic localization is not essential for GCY-35 to function
as an O2 sensor, but disrupting pdl-1 alters the URX neuron's O2 response properties.
Functional GLB-5 can restore dendritic localization of GCY-33 in pdl-1 mutants,
suggesting GCY-33 and GLB-5 are in a complex. Our data suggest GLB-5 and the soluble
guanylate cyclases operate in close proximity to sculpt O2 responses.
author:
- first_name: E.
full_name: Gross, E.
last_name: Gross
- first_name: Z.
full_name: Soltesz, Z.
last_name: Soltesz
- first_name: S.
full_name: Oda, S.
last_name: Oda
- first_name: V.
full_name: Zelmanovich, V.
last_name: Zelmanovich
- first_name: Z.
full_name: Abergel, Z.
last_name: Abergel
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Gross E, Soltesz Z, Oda S, Zelmanovich V, Abergel Z, de Bono M. GLOBIN-5-dependent
O2 responses are regulated by PDL-1/PrBP that targets prenylated soluble guanylate
cyclases to dendritic endings. Journal of Neuroscience. 2014;34(50):16726-16738.
doi:10.1523/jneurosci.5368-13.2014
apa: Gross, E., Soltesz, Z., Oda, S., Zelmanovich, V., Abergel, Z., & de Bono,
M. (2014). GLOBIN-5-dependent O2 responses are regulated by PDL-1/PrBP that targets
prenylated soluble guanylate cyclases to dendritic endings. Journal of Neuroscience.
Society for Neuroscience. https://doi.org/10.1523/jneurosci.5368-13.2014
chicago: Gross, E., Z. Soltesz, S. Oda, V. Zelmanovich, Z. Abergel, and Mario de
Bono. “GLOBIN-5-Dependent O2 Responses Are Regulated by PDL-1/PrBP That Targets
Prenylated Soluble Guanylate Cyclases to Dendritic Endings.” Journal of Neuroscience.
Society for Neuroscience, 2014. https://doi.org/10.1523/jneurosci.5368-13.2014.
ieee: E. Gross, Z. Soltesz, S. Oda, V. Zelmanovich, Z. Abergel, and M. de Bono,
“GLOBIN-5-dependent O2 responses are regulated by PDL-1/PrBP that targets prenylated
soluble guanylate cyclases to dendritic endings,” Journal of Neuroscience,
vol. 34, no. 50. Society for Neuroscience, pp. 16726–16738, 2014.
ista: Gross E, Soltesz Z, Oda S, Zelmanovich V, Abergel Z, de Bono M. 2014. GLOBIN-5-dependent
O2 responses are regulated by PDL-1/PrBP that targets prenylated soluble guanylate
cyclases to dendritic endings. Journal of Neuroscience. 34(50), 16726–16738.
mla: Gross, E., et al. “GLOBIN-5-Dependent O2 Responses Are Regulated by PDL-1/PrBP
That Targets Prenylated Soluble Guanylate Cyclases to Dendritic Endings.” Journal
of Neuroscience, vol. 34, no. 50, Society for Neuroscience, 2014, pp. 16726–38,
doi:10.1523/jneurosci.5368-13.2014.
short: E. Gross, Z. Soltesz, S. Oda, V. Zelmanovich, Z. Abergel, M. de Bono, Journal
of Neuroscience 34 (2014) 16726–16738.
date_created: 2019-03-19T14:52:26Z
date_published: 2014-12-10T00:00:00Z
date_updated: 2021-01-12T08:06:14Z
day: '10'
ddc:
- '570'
doi: 10.1523/jneurosci.5368-13.2014
extern: '1'
external_id:
pmid:
- '25505325'
file:
- access_level: open_access
checksum: a3dd71969f94c43909327cd083283d4b
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T14:55:58Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6127'
file_name: 2014_SFN_Gross.pdf
file_size: 3263422
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 34'
issue: '50'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 16726-16738
pmid: 1
publication: Journal of Neuroscience
publication_identifier:
issn:
- 0270-6474
- 1529-2401
publication_status: published
publisher: Society for Neuroscience
quality_controlled: '1'
status: public
title: GLOBIN-5-dependent O2 responses are regulated by PDL-1/PrBP that targets prenylated
soluble guanylate cyclases to dendritic endings
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: 34
year: '2014'
...
---
_id: '6178'
abstract:
- lang: eng
text: Mechanically coupled cells can generate forces driving cell and tissue morphogenesis
during development. Visualization and measuring of these forces is of major importance
to better understand the complexity of the biomechanic processes that shape cells
and tissues. Here, we describe how UV laser ablation can be utilized to quantitatively
assess mechanical tension in different tissues of the developing zebrafish and
in cultures of primary germ layer progenitor cells ex vivo.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Michael
full_name: Smutny, Michael
id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87
last_name: Smutny
orcid: 0000-0002-5920-9090
- first_name: Martin
full_name: Behrndt, Martin
id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87
last_name: Behrndt
- first_name: Pedro
full_name: Campinho, Pedro
id: 3AFBBC42-F248-11E8-B48F-1D18A9856A87
last_name: Campinho
orcid: 0000-0002-8526-5416
- first_name: Verena
full_name: Ruprecht, Verena
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: 'Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. UV laser ablation
to measure cell and tissue-generated forces in the zebrafish embryo in vivo and
ex vivo. In: Nelson C, ed. Tissue Morphogenesis. Vol 1189. MIMB. New York:
Springer; 2014:219-235. doi:10.1007/978-1-4939-1164-6_15'
apa: 'Smutny, M., Behrndt, M., Campinho, P., Ruprecht, V., & Heisenberg, C.-P.
J. (2014). UV laser ablation to measure cell and tissue-generated forces in the
zebrafish embryo in vivo and ex vivo. In C. Nelson (Ed.), Tissue Morphogenesis
(Vol. 1189, pp. 219–235). New York: Springer. https://doi.org/10.1007/978-1-4939-1164-6_15'
chicago: 'Smutny, Michael, Martin Behrndt, Pedro Campinho, Verena Ruprecht, and
Carl-Philipp J Heisenberg. “UV Laser Ablation to Measure Cell and Tissue-Generated
Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” In Tissue Morphogenesis,
edited by Celeste Nelson, 1189:219–35. MIMB. New York: Springer, 2014. https://doi.org/10.1007/978-1-4939-1164-6_15.'
ieee: 'M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, and C.-P. J. Heisenberg,
“UV laser ablation to measure cell and tissue-generated forces in the zebrafish
embryo in vivo and ex vivo,” in Tissue Morphogenesis, vol. 1189, C. Nelson,
Ed. New York: Springer, 2014, pp. 219–235.'
ista: 'Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. 2014.UV laser
ablation to measure cell and tissue-generated forces in the zebrafish embryo in
vivo and ex vivo. In: Tissue Morphogenesis. Methods in Molecular Biology, vol.
1189, 219–235.'
mla: Smutny, Michael, et al. “UV Laser Ablation to Measure Cell and Tissue-Generated
Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” Tissue Morphogenesis,
edited by Celeste Nelson, vol. 1189, Springer, 2014, pp. 219–35, doi:10.1007/978-1-4939-1164-6_15.
short: M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, C.-P.J. Heisenberg, in:,
C. Nelson (Ed.), Tissue Morphogenesis, Springer, New York, 2014, pp. 219–235.
corr_author: '1'
date_created: 2019-03-26T08:55:59Z
date_published: 2014-08-22T00:00:00Z
date_updated: 2026-04-16T10:31:19Z
day: '22'
department:
- _id: CaHe
doi: 10.1007/978-1-4939-1164-6_15
editor:
- first_name: Celeste
full_name: Nelson, Celeste
last_name: Nelson
external_id:
pmid:
- '25245697'
intvolume: ' 1189'
language:
- iso: eng
month: '08'
oa_version: None
page: 219-235
place: New York
pmid: 1
publication: Tissue Morphogenesis
publication_identifier:
eisbn:
- '9781493911646'
eissn:
- 1940-6029
isbn:
- '9781493911639'
issn:
- 1064-3745
publication_status: published
publisher: Springer
quality_controlled: '1'
series_title: MIMB
status: public
title: UV laser ablation to measure cell and tissue-generated forces in the zebrafish
embryo in vivo and ex vivo
type: book_chapter
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 1189
year: '2014'
...
---
_id: '6319'
abstract:
- lang: fre
text: Nous étudions le comportement asymptotique du nombre de variétés dans une
certaine classe ne satisfaisant pas le principe de Hasse. Cette étude repose sur
des résultats récemmentobtenus par Colliot-Thélène.
arxiv: 1
author:
- first_name: Régis de la
full_name: Bretèche, Régis de la
last_name: Bretèche
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
citation:
ama: Bretèche R de la, Browning TD. Contre-exemples au principe de Hasse pour certains
tores coflasques. Journal de Théorie des Nombres de Bordeaux. 2014;26(1):25-44.
doi:10.5802/jtnb.857
apa: Bretèche, R. de la, & Browning, T. D. (2014). Contre-exemples au principe
de Hasse pour certains tores coflasques. Journal de Théorie Des Nombres de
Bordeaux. Cellule MathDoc/CEDRAM. https://doi.org/10.5802/jtnb.857
chicago: Bretèche, Régis de la, and Timothy D Browning. “Contre-Exemples Au Principe
de Hasse Pour Certains Tores Coflasques.” Journal de Théorie Des Nombres de
Bordeaux. Cellule MathDoc/CEDRAM, 2014. https://doi.org/10.5802/jtnb.857.
ieee: R. de la Bretèche and T. D. Browning, “Contre-exemples au principe de Hasse
pour certains tores coflasques,” Journal de Théorie des Nombres de Bordeaux,
vol. 26, no. 1. Cellule MathDoc/CEDRAM, pp. 25–44, 2014.
ista: Bretèche R de la, Browning TD. 2014. Contre-exemples au principe de Hasse
pour certains tores coflasques. Journal de Théorie des Nombres de Bordeaux. 26(1),
25–44.
mla: Bretèche, Régis de la, and Timothy D. Browning. “Contre-Exemples Au Principe
de Hasse Pour Certains Tores Coflasques.” Journal de Théorie Des Nombres de
Bordeaux, vol. 26, no. 1, Cellule MathDoc/CEDRAM, 2014, pp. 25–44, doi:10.5802/jtnb.857.
short: R. de la Bretèche, T.D. Browning, Journal de Théorie Des Nombres de Bordeaux
26 (2014) 25–44.
date_created: 2019-04-16T13:40:13Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T08:07:03Z
doi: 10.5802/jtnb.857
extern: '1'
external_id:
arxiv:
- '1210.4236'
intvolume: ' 26'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1210.4236
oa: 1
oa_version: Preprint
page: 25-44
publication: Journal de Théorie des Nombres de Bordeaux
publication_identifier:
issn:
- 1246-7405
- 2118-8572
publication_status: published
publisher: Cellule MathDoc/CEDRAM
quality_controlled: '1'
status: public
title: Contre-exemples au principe de Hasse pour certains tores coflasques
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2014'
...
---
_id: '1979'
abstract:
- lang: eng
text: NADH-ubiquinone oxidoreductase (complex I) is the first and largest enzyme
in the respiratory chain of mitochondria and many bacteria. It couples the transfer
of two electrons between NADH and ubiquinone to the translocation of four protons
across the membrane. Complex I is an L-shaped assembly formed by the hydrophilic
(peripheral) arm, containing all the redox centres performing electron transfer
and the membrane arm, containing proton-translocating machinery. Mitochondrial
complex I consists of 44 subunits of about 1 MDa in total, whilst the prokaryotic
enzyme is simpler and generally consists of 14 conserved “core” subunits. Recently
we have determined the first atomic structure of the entire complex I, using the
enzyme from Thermus thermophilus (536 kDa, 16 subunits, 9 Fe-S clusters, 64 TM
helices). Structure suggests a unique coupling mechanism, with redox energy of
electron transfer driving proton translocation via long-range (up to ~200 Å) conformational
changes. It resembles a steam engine, with coupling elements (akin to coupling
rods) linking parts of this molecular machine.
author:
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Sazanov LA. The mechanism of coupling between electron transfer and proton
translocation in respiratory complex I. Journal of Bioenergetics and Biomembranes.
2014;46(4):247-253. doi:10.1007/s10863-014-9554-z
apa: Sazanov, L. A. (2014). The mechanism of coupling between electron transfer
and proton translocation in respiratory complex I. Journal of Bioenergetics
and Biomembranes. Springer. https://doi.org/10.1007/s10863-014-9554-z
chicago: Sazanov, Leonid A. “The Mechanism of Coupling between Electron Transfer
and Proton Translocation in Respiratory Complex I.” Journal of Bioenergetics
and Biomembranes. Springer, 2014. https://doi.org/10.1007/s10863-014-9554-z.
ieee: L. A. Sazanov, “The mechanism of coupling between electron transfer and proton
translocation in respiratory complex I,” Journal of Bioenergetics and Biomembranes,
vol. 46, no. 4. Springer, pp. 247–253, 2014.
ista: Sazanov LA. 2014. The mechanism of coupling between electron transfer and
proton translocation in respiratory complex I. Journal of Bioenergetics and Biomembranes.
46(4), 247–253.
mla: Sazanov, Leonid A. “The Mechanism of Coupling between Electron Transfer and
Proton Translocation in Respiratory Complex I.” Journal of Bioenergetics and
Biomembranes, vol. 46, no. 4, Springer, 2014, pp. 247–53, doi:10.1007/s10863-014-9554-z.
short: L.A. Sazanov, Journal of Bioenergetics and Biomembranes 46 (2014) 247–253.
date_created: 2018-12-11T11:55:01Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2021-01-12T06:54:28Z
day: '01'
doi: 10.1007/s10863-014-9554-z
extern: 1
intvolume: ' 46'
issue: '4'
month: '08'
page: 247 - 253
publication: Journal of Bioenergetics and Biomembranes
publication_status: published
publisher: Springer
publist_id: '5104'
quality_controlled: 0
status: public
title: The mechanism of coupling between electron transfer and proton translocation
in respiratory complex I
type: journal_article
volume: 46
year: '2014'
...
---
_id: '1980'
abstract:
- lang: eng
text: Non-proton pumping type II NADH dehydrogenase (NDH-2) plays a central role
in the respiratory metabolism of bacteria, and in the mitochondria of fungi, plants
and protists. The lack of NDH-2 in mammalian mitochondria and its essentiality
in important bacterial pathogens suggests these enzymes may represent a potential
new drug target to combat microbial pathogens. Here, we report the first crystal
structure of a bacterial NDH-2 enzyme at 2.5Å resolution from Caldalkalibacillus
thermarum. The NDH-2 structure reveals a homodimeric organization that has a unique
dimer interface. NDH-2 is localized to the cytoplasmic membrane by two separated
C-terminal membrane-anchoring regions that are essential for membrane localization
and FAD binding, but not NDH-2 dimerization. Comparison of bacterial NDH-2 with
the yeast NADH dehydrogenase (Ndi1) structure revealed non-overlapping binding
sites for quinone and NADH in the bacterial enzyme. The bacterial NDH-2 structure
establishes a framework for the structure-based design of small-molecule inhibitors.
acknowledgement: Funded by Health Research Council of New Zealand Royal Society
of New Zealand University of Otago New Zealand Synchrotron Group
author:
- first_name: Adam
full_name: 'Heikal, Adam '
last_name: Heikal
- first_name: Yoshio
full_name: Nakatani, Yoshio
last_name: Nakatani
- first_name: Elyse
full_name: Dunn, Elyse A
last_name: Dunn
- first_name: Marion
full_name: Weimar, Marion R
last_name: Weimar
- first_name: Catherine
full_name: Day, Catherine
last_name: Day
- first_name: Edward
full_name: Baker, Edward N
last_name: Baker
- first_name: Shaun
full_name: Lott, Shaun J
last_name: Lott
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
- first_name: Gregory
full_name: Cook, Gregory
last_name: Cook
citation:
ama: 'Heikal A, Nakatani Y, Dunn E, et al. Structure of the bacterial type II NADH
dehydrogenase: a monotopic membrane protein with an essential role in energy generation.
Molecular Microbiology. 2014;91(5):950-964. doi:10.1111/mmi.12507'
apa: 'Heikal, A., Nakatani, Y., Dunn, E., Weimar, M., Day, C., Baker, E., … Cook,
G. (2014). Structure of the bacterial type II NADH dehydrogenase: a monotopic
membrane protein with an essential role in energy generation. Molecular Microbiology.
Wiley-Blackwell. https://doi.org/10.1111/mmi.12507'
chicago: 'Heikal, Adam, Yoshio Nakatani, Elyse Dunn, Marion Weimar, Catherine Day,
Edward Baker, Shaun Lott, Leonid A Sazanov, and Gregory Cook. “Structure of the
Bacterial Type II NADH Dehydrogenase: A Monotopic Membrane Protein with an Essential
Role in Energy Generation.” Molecular Microbiology. Wiley-Blackwell, 2014.
https://doi.org/10.1111/mmi.12507.'
ieee: 'A. Heikal et al., “Structure of the bacterial type II NADH dehydrogenase:
a monotopic membrane protein with an essential role in energy generation,” Molecular
Microbiology, vol. 91, no. 5. Wiley-Blackwell, pp. 950–964, 2014.'
ista: 'Heikal A, Nakatani Y, Dunn E, Weimar M, Day C, Baker E, Lott S, Sazanov LA,
Cook G. 2014. Structure of the bacterial type II NADH dehydrogenase: a monotopic
membrane protein with an essential role in energy generation. Molecular Microbiology.
91(5), 950–964.'
mla: 'Heikal, Adam, et al. “Structure of the Bacterial Type II NADH Dehydrogenase:
A Monotopic Membrane Protein with an Essential Role in Energy Generation.” Molecular
Microbiology, vol. 91, no. 5, Wiley-Blackwell, 2014, pp. 950–64, doi:10.1111/mmi.12507.'
short: A. Heikal, Y. Nakatani, E. Dunn, M. Weimar, C. Day, E. Baker, S. Lott, L.A.
Sazanov, G. Cook, Molecular Microbiology 91 (2014) 950–964.
date_created: 2018-12-11T11:55:01Z
date_published: 2014-03-01T00:00:00Z
date_updated: 2021-01-12T06:54:29Z
day: '01'
doi: 10.1111/mmi.12507
extern: 1
intvolume: ' 91'
issue: '5'
month: '03'
page: 950 - 964
publication: Molecular Microbiology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5103'
quality_controlled: 0
status: public
title: 'Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane
protein with an essential role in energy generation'
type: journal_article
volume: 91
year: '2014'
...
---
_id: '1989'
abstract:
- lang: eng
text: During animal cell division, the cleavage furrow is positioned by microtubules
that signal to the actin cortex at the cell midplane. We developed a cell-free
system to recapitulate cytokinesis signaling using cytoplasmic extract from Xenopus
eggs. Microtubules grew out as asters from artificial centrosomes and met to organize
antiparallel overlap zones. These zones blocked the interpenetration of neighboring
asters and recruited cytokinesis midzone proteins, including the chromosomal passenger
complex (CPC) and centralspindlin. The CPC was transported to overlap zones, which
required two motor proteins, Kif4A and a Kif20A paralog. Using supported lipid
bilayers to mimic the plasma membrane, we observed the recruitment of cleavage
furrow markers, including an active RhoA reporter, at microtubule overlaps. This
system opens further approaches to understanding the biophysics of cytokinesis
signaling.
acknowledgement: 'This work was supported by NIH grant GM39565 (T.J.M.); MBL fellowships
from the Evans Foundation, MBL Associates, and the Colwin Fund (T.J.M. and C.M.F.);
HFSP fellowship LT000466/2012-L (M.L.); and NIH grant GM103785 (M.W.). '
article_processing_charge: No
author:
- first_name: Phuong
full_name: Nguyen, Phuong
last_name: Nguyen
- first_name: Aaron
full_name: Groen, Aaron
last_name: Groen
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Keisuke
full_name: Ishihara, Keisuke
last_name: Ishihara
- first_name: Martin
full_name: Wühr, Martin
last_name: Wühr
- first_name: Christine
full_name: Field, Christine
last_name: Field
- first_name: Timothy
full_name: Mitchison, Timothy
last_name: Mitchison
citation:
ama: Nguyen P, Groen A, Loose M, et al. Spatial organization of cytokinesis signaling
reconstituted in a cell-free system. Science. 2014;346(6206):244-247. doi:10.1126/science.1256773
apa: Nguyen, P., Groen, A., Loose, M., Ishihara, K., Wühr, M., Field, C., &
Mitchison, T. (2014). Spatial organization of cytokinesis signaling reconstituted
in a cell-free system. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.1256773
chicago: Nguyen, Phuong, Aaron Groen, Martin Loose, Keisuke Ishihara, Martin Wühr,
Christine Field, and Timothy Mitchison. “Spatial Organization of Cytokinesis Signaling
Reconstituted in a Cell-Free System.” Science. American Association for
the Advancement of Science, 2014. https://doi.org/10.1126/science.1256773.
ieee: P. Nguyen et al., “Spatial organization of cytokinesis signaling reconstituted
in a cell-free system,” Science, vol. 346, no. 6206. American Association
for the Advancement of Science, pp. 244–247, 2014.
ista: Nguyen P, Groen A, Loose M, Ishihara K, Wühr M, Field C, Mitchison T. 2014.
Spatial organization of cytokinesis signaling reconstituted in a cell-free system.
Science. 346(6206), 244–247.
mla: Nguyen, Phuong, et al. “Spatial Organization of Cytokinesis Signaling Reconstituted
in a Cell-Free System.” Science, vol. 346, no. 6206, American Association
for the Advancement of Science, 2014, pp. 244–47, doi:10.1126/science.1256773.
short: P. Nguyen, A. Groen, M. Loose, K. Ishihara, M. Wühr, C. Field, T. Mitchison,
Science 346 (2014) 244–247.
date_created: 2018-12-11T11:55:04Z
date_published: 2014-10-10T00:00:00Z
date_updated: 2025-08-05T14:39:34Z
day: '10'
doi: 10.1126/science.1256773
extern: '1'
intvolume: ' 346'
issue: '6206'
language:
- iso: eng
month: '10'
oa_version: None
page: 244 - 247
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '5093'
status: public
title: Spatial organization of cytokinesis signaling reconstituted in a cell-free
system
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 346
year: '2014'
...
---
_id: '1990'
abstract:
- lang: eng
text: 'Bacterial cytokinesis is commonly initiated by the Z-ring, a cytoskeletal
structure that assembles at the site of division. Its primary component is FtsZ,
a tubulin superfamily GTPase, which is recruited to the membrane by the actin-related
protein FtsA. Both proteins are required for the formation of the Z-ring, but
if and how they influence each other''s assembly dynamics is not known. Here,
we reconstituted FtsA-dependent recruitment of FtsZ polymers to supported membranes,
where both proteins self-organize into complex patterns, such as fast-moving filament
bundles and chirally rotating rings. Using fluorescence microscopy and biochemical
perturbations, we found that these large-scale rearrangements of FtsZ emerge from
its polymerization dynamics and a dual, antagonistic role of FtsA: recruitment
of FtsZ filaments to the membrane and negative regulation of FtsZ organization.
Our findings provide a model for the initial steps of bacterial cell division
and illustrate how dynamic polymers can self-organize into large-scale structures.'
acknowledgement: M.L. is supported by fellowships from EMBO (ALTF 394-2011) and HFSP
(LT000466/2012). Cytoskeleton dynamics research in the T.J.M. group is supported
by NIH-GM39565.
article_processing_charge: No
author:
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Timothy
full_name: Mitchison, Timothy
last_name: Mitchison
citation:
ama: Loose M, Mitchison T. The bacterial cell division proteins ftsA and ftsZ self-organize
into dynamic cytoskeletal patterns. Nature Cell Biology. 2014;16:38-46.
doi:10.1038/ncb2885
apa: Loose, M., & Mitchison, T. (2014). The bacterial cell division proteins
ftsA and ftsZ self-organize into dynamic cytoskeletal patterns. Nature Cell
Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2885
chicago: Loose, Martin, and Timothy Mitchison. “The Bacterial Cell Division Proteins
FtsA and FtsZ Self-Organize into Dynamic Cytoskeletal Patterns.” Nature Cell
Biology. Nature Publishing Group, 2014. https://doi.org/10.1038/ncb2885.
ieee: M. Loose and T. Mitchison, “The bacterial cell division proteins ftsA and
ftsZ self-organize into dynamic cytoskeletal patterns,” Nature Cell Biology,
vol. 16. Nature Publishing Group, pp. 38–46, 2014.
ista: Loose M, Mitchison T. 2014. The bacterial cell division proteins ftsA and
ftsZ self-organize into dynamic cytoskeletal patterns. Nature Cell Biology. 16,
38–46.
mla: Loose, Martin, and Timothy Mitchison. “The Bacterial Cell Division Proteins
FtsA and FtsZ Self-Organize into Dynamic Cytoskeletal Patterns.” Nature Cell
Biology, vol. 16, Nature Publishing Group, 2014, pp. 38–46, doi:10.1038/ncb2885.
short: M. Loose, T. Mitchison, Nature Cell Biology 16 (2014) 38–46.
date_created: 2018-12-11T11:55:05Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2025-08-05T14:41:58Z
day: '01'
doi: 10.1038/ncb2885
extern: '1'
external_id:
pmid:
- '24316672'
intvolume: ' 16'
language:
- iso: eng
month: '01'
oa_version: None
page: 38 - 46
pmid: 1
publication: Nature Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '5094'
status: public
title: The bacterial cell division proteins ftsA and ftsZ self-organize into dynamic
cytoskeletal patterns
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2014'
...
---
_id: '1994'
abstract:
- lang: eng
text: The emergence and radiation of multicellular land plants was driven by crucial
innovations to their body plans [1]. The directional transport of the phytohormone
auxin represents a key, plant-specific mechanism for polarization and patterning
in complex seed plants [2-5]. Here, we show that already in the early diverging
land plant lineage, as exemplified by the moss Physcomitrella patens, auxin transport
by PIN transporters is operational and diversified into ER-localized and plasma
membrane-localized PIN proteins. Gain-of-function and loss-of-function analyses
revealed that PIN-dependent intercellular auxin transport in Physcomitrella mediates
crucial developmental transitions in tip-growing filaments and waves of polarization
and differentiation in leaf-like structures. Plasma membrane PIN proteins localize
in a polar manner to the tips of moss filaments, revealing an unexpected relation
between polarization mechanisms in moss tip-growing cells and multicellular tissues
of seed plants. Our results trace the origins of polarization and auxin-mediated
patterning mechanisms and highlight the crucial role of polarized auxin transport
during the evolution of multicellular land plants.
article_processing_charge: No
author:
- first_name: Tom
full_name: Viaene, Tom
last_name: Viaene
- first_name: Katarina
full_name: Landberg, Katarina
last_name: Landberg
- first_name: Mattias
full_name: Thelander, Mattias
last_name: Thelander
- first_name: Eva
full_name: Medvecka, Eva
last_name: Medvecka
- first_name: Eric
full_name: Pederson, Eric
last_name: Pederson
- first_name: Elena
full_name: Feraru, Elena
last_name: Feraru
- first_name: Endymion
full_name: Cooper, Endymion
last_name: Cooper
- first_name: Mansour
full_name: Karimi, Mansour
last_name: Karimi
- first_name: Charles
full_name: Delwiche, Charles
last_name: Delwiche
- first_name: Karin
full_name: Ljung, Karin
last_name: Ljung
- first_name: Markus
full_name: Geisler, Markus
last_name: Geisler
- first_name: Eva
full_name: Sundberg, Eva
last_name: Sundberg
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Viaene T, Landberg K, Thelander M, et al. Directional auxin transport mechanisms
in early diverging land plants. Current Biology. 2014;24(23):2786-2791.
doi:10.1016/j.cub.2014.09.056
apa: Viaene, T., Landberg, K., Thelander, M., Medvecka, E., Pederson, E., Feraru,
E., … Friml, J. (2014). Directional auxin transport mechanisms in early diverging
land plants. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2014.09.056
chicago: Viaene, Tom, Katarina Landberg, Mattias Thelander, Eva Medvecka, Eric Pederson,
Elena Feraru, Endymion Cooper, et al. “Directional Auxin Transport Mechanisms
in Early Diverging Land Plants.” Current Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2014.09.056.
ieee: T. Viaene et al., “Directional auxin transport mechanisms in early
diverging land plants,” Current Biology, vol. 24, no. 23. Cell Press, pp.
2786–2791, 2014.
ista: Viaene T, Landberg K, Thelander M, Medvecka E, Pederson E, Feraru E, Cooper
E, Karimi M, Delwiche C, Ljung K, Geisler M, Sundberg E, Friml J. 2014. Directional
auxin transport mechanisms in early diverging land plants. Current Biology. 24(23),
2786–2791.
mla: Viaene, Tom, et al. “Directional Auxin Transport Mechanisms in Early Diverging
Land Plants.” Current Biology, vol. 24, no. 23, Cell Press, 2014, pp. 2786–91,
doi:10.1016/j.cub.2014.09.056.
short: T. Viaene, K. Landberg, M. Thelander, E. Medvecka, E. Pederson, E. Feraru,
E. Cooper, M. Karimi, C. Delwiche, K. Ljung, M. Geisler, E. Sundberg, J. Friml,
Current Biology 24 (2014) 2786–2791.
corr_author: '1'
date_created: 2018-12-11T11:55:06Z
date_published: 2014-12-01T00:00:00Z
date_updated: 2025-09-29T12:07:20Z
day: '01'
department:
- _id: JiFr
doi: 10.1016/j.cub.2014.09.056
ec_funded: 1
external_id:
isi:
- '000345808700019'
intvolume: ' 24'
isi: 1
issue: '23'
language:
- iso: eng
month: '12'
oa_version: None
page: 2786 - 2791
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '5088'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Directional auxin transport mechanisms in early diverging land plants
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 24
year: '2014'
...
---
_id: '1995'
abstract:
- lang: eng
text: 'Optical transport represents a natural route towards fast communications,
and it is currently used in large scale data transfer. The progressive miniaturization
of devices for information processing calls for the microscopic tailoring of light
transport and confinement at length scales appropriate for upcoming technologies.
With this goal in mind, we present a theoretical analysis of a one-dimensional
Fabry-Perot interferometer built with two highly saturable nonlinear mirrors:
a pair of two-level systems. Our approach captures nonlinear and nonreciprocal
effects of light transport that were not reported previously. Remarkably, we show
that such an elementary device can operate as a microscopic integrated optical
rectifier.'
article_number: '243601'
article_processing_charge: No
arxiv: 1
author:
- first_name: Filippo
full_name: Fratini, Filippo
last_name: Fratini
- first_name: Eduardo
full_name: Mascarenhas, Eduardo
last_name: Mascarenhas
- first_name: Laleh
full_name: Safari, Laleh
id: 3C325E5E-F248-11E8-B48F-1D18A9856A87
last_name: Safari
- first_name: Jean
full_name: Poizat, Jean
last_name: Poizat
- first_name: Daniel
full_name: Valente, Daniel
last_name: Valente
- first_name: Alexia
full_name: Auffèves, Alexia
last_name: Auffèves
- first_name: Dario
full_name: Gerace, Dario
last_name: Gerace
- first_name: Marcelo
full_name: Santos, Marcelo
last_name: Santos
citation:
ama: 'Fratini F, Mascarenhas E, Safari L, et al. Fabry-Perot interferometer with
quantum mirrors: Nonlinear light transport and rectification. Physical Review
Letters. 2014;113(24). doi:10.1103/PhysRevLett.113.243601'
apa: 'Fratini, F., Mascarenhas, E., Safari, L., Poizat, J., Valente, D., Auffèves,
A., … Santos, M. (2014). Fabry-Perot interferometer with quantum mirrors: Nonlinear
light transport and rectification. Physical Review Letters. American Physical
Society. https://doi.org/10.1103/PhysRevLett.113.243601'
chicago: 'Fratini, Filippo, Eduardo Mascarenhas, Laleh Safari, Jean Poizat, Daniel
Valente, Alexia Auffèves, Dario Gerace, and Marcelo Santos. “Fabry-Perot Interferometer
with Quantum Mirrors: Nonlinear Light Transport and Rectification.” Physical
Review Letters. American Physical Society, 2014. https://doi.org/10.1103/PhysRevLett.113.243601.'
ieee: 'F. Fratini et al., “Fabry-Perot interferometer with quantum mirrors:
Nonlinear light transport and rectification,” Physical Review Letters,
vol. 113, no. 24. American Physical Society, 2014.'
ista: 'Fratini F, Mascarenhas E, Safari L, Poizat J, Valente D, Auffèves A, Gerace
D, Santos M. 2014. Fabry-Perot interferometer with quantum mirrors: Nonlinear
light transport and rectification. Physical Review Letters. 113(24), 243601.'
mla: 'Fratini, Filippo, et al. “Fabry-Perot Interferometer with Quantum Mirrors:
Nonlinear Light Transport and Rectification.” Physical Review Letters,
vol. 113, no. 24, 243601, American Physical Society, 2014, doi:10.1103/PhysRevLett.113.243601.'
short: F. Fratini, E. Mascarenhas, L. Safari, J. Poizat, D. Valente, A. Auffèves,
D. Gerace, M. Santos, Physical Review Letters 113 (2014).
date_created: 2018-12-11T11:55:06Z
date_published: 2014-12-08T00:00:00Z
date_updated: 2025-09-29T12:06:45Z
day: '08'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.113.243601
ec_funded: 1
external_id:
arxiv:
- '1410.5972'
isi:
- '000346049700005'
intvolume: ' 113'
isi: 1
issue: '24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1410.5972
month: '12'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5085'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Fabry-Perot interferometer with quantum mirrors: Nonlinear light transport
and rectification'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 113
year: '2014'
...
---
_id: '1996'
abstract:
- lang: eng
text: Auxin polar transport, local maxima, and gradients have become an importantmodel
system for studying self-organization. Auxin distribution is regulated by auxin-dependent
positive feedback loops that are not well-understood at the molecular level. Previously,
we showed the involvement of the RHO of Plants (ROP) effector INTERACTOR of CONSTITUTIVELY
active ROP 1 (ICR1) in regulation of auxin transport and that ICR1 levels are
posttranscriptionally repressed at the site of maximum auxin accumulation at the
root tip. Here, we show that bimodal regulation of ICR1 levels by auxin is essential
for regulating formation of auxin local maxima and gradients. ICR1 levels increase
concomitant with increase in auxin response in lateral root primordia, cotyledon
tips, and provascular tissues. However, in the embryo hypophysis and root meristem,
when auxin exceeds critical levels, ICR1 is rapidly destabilized by an SCF(TIR1/AFB)
[SKP, Cullin, F-box (transport inhibitor response 1/auxin signaling F-box protein)]-dependent
auxin signaling mechanism. Furthermore, ectopic expression of ICR1 in the embryo
hypophysis resulted in reduction of auxin accumulation and concomitant root growth
arrest. ICR1 disappeared during root regeneration and lateral root initiation
concomitantly with the formation of a local auxin maximum in response to external
auxin treatments and transiently after gravitropic stimulation. Destabilization
of ICR1 was impaired after inhibition of auxin transport and signaling, proteasome
function, and protein synthesis. A mathematical model based on these findings
shows that an in vivo-like auxin distribution, rootward auxin flux, and shootward
reflux can be simulated without assuming preexisting tissue polarity. Our experimental
results and mathematical modeling indicate that regulation of auxin distribution
is tightly associated with auxin-dependent ICR1 levels.
article_processing_charge: No
author:
- first_name: Ora
full_name: Hazak, Ora
last_name: Hazak
- first_name: Uri
full_name: Obolski, Uri
last_name: Obolski
- first_name: Tomas
full_name: Prat, Tomas
id: 3DA3BFEE-F248-11E8-B48F-1D18A9856A87
last_name: Prat
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Lilach
full_name: Hadany, Lilach
last_name: Hadany
- first_name: Shaul
full_name: Yalovsky, Shaul
last_name: Yalovsky
citation:
ama: Hazak O, Obolski U, Prat T, Friml J, Hadany L, Yalovsky S. Bimodal regulation
of ICR1 levels generates self-organizing auxin distribution. PNAS. 2014;111(50):E5471-E5479.
doi:10.1073/pnas.1413918111
apa: Hazak, O., Obolski, U., Prat, T., Friml, J., Hadany, L., & Yalovsky, S.
(2014). Bimodal regulation of ICR1 levels generates self-organizing auxin distribution.
PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1413918111
chicago: Hazak, Ora, Uri Obolski, Tomas Prat, Jiří Friml, Lilach Hadany, and Shaul
Yalovsky. “Bimodal Regulation of ICR1 Levels Generates Self-Organizing Auxin Distribution.”
PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1413918111.
ieee: O. Hazak, U. Obolski, T. Prat, J. Friml, L. Hadany, and S. Yalovsky, “Bimodal
regulation of ICR1 levels generates self-organizing auxin distribution,” PNAS,
vol. 111, no. 50. National Academy of Sciences, pp. E5471–E5479, 2014.
ista: Hazak O, Obolski U, Prat T, Friml J, Hadany L, Yalovsky S. 2014. Bimodal regulation
of ICR1 levels generates self-organizing auxin distribution. PNAS. 111(50), E5471–E5479.
mla: Hazak, Ora, et al. “Bimodal Regulation of ICR1 Levels Generates Self-Organizing
Auxin Distribution.” PNAS, vol. 111, no. 50, National Academy of Sciences,
2014, pp. E5471–79, doi:10.1073/pnas.1413918111.
short: O. Hazak, U. Obolski, T. Prat, J. Friml, L. Hadany, S. Yalovsky, PNAS 111
(2014) E5471–E5479.
date_created: 2018-12-11T11:55:07Z
date_published: 2014-12-16T00:00:00Z
date_updated: 2025-09-29T12:06:13Z
day: '16'
department:
- _id: JiFr
doi: 10.1073/pnas.1413918111
external_id:
isi:
- '000346366500020'
intvolume: ' 111'
isi: 1
issue: '50'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4273421/
month: '12'
oa: 1
oa_version: Submitted Version
page: E5471 - E5479
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5083'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bimodal regulation of ICR1 levels generates self-organizing auxin distribution
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 111
year: '2014'
...
---
_id: '1998'
abstract:
- lang: eng
text: Immune systems are able to protect the body against secondary infection with
the same parasite. In insect colonies, this protection is not restricted to the
level of the individual organism, but also occurs at the societal level. Here,
we review recent evidence for and insights into the mechanisms underlying individual
and social immunisation in insects. We disentangle general immune-protective effects
from specific immune memory (priming), and examine immunisation in the context
of the lifetime of an individual and that of a colony, and of transgenerational
immunisation that benefits offspring. When appropriate, we discuss parallels with
disease defence strategies in human societies. We propose that recurrent parasitic
threats have shaped the evolution of both the individual immune systems and colony-level
social immunity in insects.
acknowledgement: "This work was funded by an ERC Starting Grant by the European Research
Council (to S.C.) and the ISTFELLOW program (Co-fund Marie Curie Actions of the
European Commission; to L.M.).\r\nWe thank Christopher D. Pull, Sophie A.O. Armitage,
Hinrich Schulenburg, Line V. Ugelvig, Matthias Konrad, Matthias Fürst, Miriam Stock,
Barbara Casillas-Perez and three anonymous referees for comments on the manuscript. "
article_processing_charge: No
author:
- first_name: Leila
full_name: El Masri, Leila
id: 349A6E66-F248-11E8-B48F-1D18A9856A87
last_name: El Masri
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: El Masri L, Cremer S. Individual and social immunisation in insects. Trends
in Immunology. 2014;35(10):471-482. doi:10.1016/j.it.2014.08.005
apa: El Masri, L., & Cremer, S. (2014). Individual and social immunisation in
insects. Trends in Immunology. Elsevier. https://doi.org/10.1016/j.it.2014.08.005
chicago: El Masri, Leila, and Sylvia Cremer. “Individual and Social Immunisation
in Insects.” Trends in Immunology. Elsevier, 2014. https://doi.org/10.1016/j.it.2014.08.005.
ieee: L. El Masri and S. Cremer, “Individual and social immunisation in insects,”
Trends in Immunology, vol. 35, no. 10. Elsevier, pp. 471–482, 2014.
ista: El Masri L, Cremer S. 2014. Individual and social immunisation in insects.
Trends in Immunology. 35(10), 471–482.
mla: El Masri, Leila, and Sylvia Cremer. “Individual and Social Immunisation in
Insects.” Trends in Immunology, vol. 35, no. 10, Elsevier, 2014, pp. 471–82,
doi:10.1016/j.it.2014.08.005.
short: L. El Masri, S. Cremer, Trends in Immunology 35 (2014) 471–482.
corr_author: '1'
date_created: 2018-12-11T11:55:07Z
date_published: 2014-10-01T00:00:00Z
date_updated: 2025-09-29T12:05:29Z
day: '01'
department:
- _id: SyCr
doi: 10.1016/j.it.2014.08.005
external_id:
isi:
- '000343632600006'
intvolume: ' 35'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa_version: None
page: 471 - 482
publication: Trends in Immunology
publication_status: published
publisher: Elsevier
publist_id: '5081'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Individual and social immunisation in insects
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 35
year: '2014'
...
---
OA_type: closed access
_id: '19994'
abstract:
- lang: eng
text: Firing patterns of hippocampal principal cells are thought to participate
in the formation of mnemonic representations of place, which ultimately can be
used to guide the behavior of animals in space. Past studies have suggested that
place-selective activity in the hippocampus can emphasize the representation of
discrete locations associated with a strong behavioral salience. In the first
part of this book chapter, we review work that has described how that hippocampal
neuronal activity patterns reorganize during spatial learning. These studies revealed
that new hippocampal maps emerge during spatial learning to represent the location
of goal locations and demonstrated that, during recall, the reinstatement of these
maps predicts successful memory performance. In the second part of this chapter,
we discuss the role of sleep in memory consolidation in the context of goal-oriented
spatial learning. We summarize work that has demonstrated the replay of goal-oriented
neuronal assembly patterns that predict subsequent memory recall. Moreover, we
argue that the initial strengthening of new maps may in fact take place during
learning, triggered by waking sharp-wave/ripple patterns occurring at goal locations.
These reviewed studies highlight that the reorganization and replay of place cell
firing patterns might constitute a circuit signature for the expression of newly
acquired hippocampal engrams.
alternative_title:
- Springer Series in Computational Neuroscience
article_processing_charge: No
author:
- first_name: David
full_name: Dupret, David
last_name: Dupret
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: 'Dupret D, Csicsvari JL. Reorganization of Hippocampal Place-Selective Patterns
During Goal-Directed Learning and Their Reactivation During Sleep. In: Analysis
and Modeling of Coordinated Multi-Neuronal Activity. Vol 12. NEUROSCI. Springer
Nature; 2014. doi:10.1007/978-1-4939-1969-7_6'
apa: Dupret, D., & Csicsvari, J. L. (2014). Reorganization of Hippocampal Place-Selective
Patterns During Goal-Directed Learning and Their Reactivation During Sleep. In
Analysis and Modeling of Coordinated Multi-neuronal Activity (Vol. 12).
Springer Nature. https://doi.org/10.1007/978-1-4939-1969-7_6
chicago: Dupret, David, and Jozsef L Csicsvari. “Reorganization of Hippocampal Place-Selective
Patterns During Goal-Directed Learning and Their Reactivation During Sleep.” In
Analysis and Modeling of Coordinated Multi-Neuronal Activity, Vol. 12.
NEUROSCI. Springer Nature, 2014. https://doi.org/10.1007/978-1-4939-1969-7_6.
ieee: D. Dupret and J. L. Csicsvari, “Reorganization of Hippocampal Place-Selective
Patterns During Goal-Directed Learning and Their Reactivation During Sleep,” in
Analysis and Modeling of Coordinated Multi-neuronal Activity, vol. 12,
Springer Nature, 2014.
ista: 'Dupret D, Csicsvari JL. 2014.Reorganization of Hippocampal Place-Selective
Patterns During Goal-Directed Learning and Their Reactivation During Sleep. In:
Analysis and Modeling of Coordinated Multi-neuronal Activity. Springer Series
in Computational Neuroscience, vol. 12.'
mla: Dupret, David, and Jozsef L. Csicsvari. “Reorganization of Hippocampal Place-Selective
Patterns During Goal-Directed Learning and Their Reactivation During Sleep.” Analysis
and Modeling of Coordinated Multi-Neuronal Activity, vol. 12, Springer Nature,
2014, doi:10.1007/978-1-4939-1969-7_6.
short: D. Dupret, J.L. Csicsvari, in:, Analysis and Modeling of Coordinated Multi-Neuronal
Activity, Springer Nature, 2014.
date_created: 2025-07-10T14:06:05Z
date_published: 2014-10-30T00:00:00Z
date_updated: 2025-09-23T09:36:44Z
day: '30'
department:
- _id: JoCs
doi: 10.1007/978-1-4939-1969-7_6
intvolume: ' 12'
language:
- iso: eng
month: '10'
oa_version: None
publication: Analysis and Modeling of Coordinated Multi-neuronal Activity
publication_identifier:
eisbn:
- '9781493919697'
eissn:
- 2197-1919
isbn:
- '9781493919680'
issn:
- 2197-1900
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: NEUROSCI
status: public
title: Reorganization of Hippocampal Place-Selective Patterns During Goal-Directed
Learning and Their Reactivation During Sleep
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2014'
...
---
_id: '2001'
abstract:
- lang: eng
text: Antibiotics affect bacterial cell physiology at many levels. Rather than just
compensating for the direct cellular defects caused by the drug, bacteria respond
to antibiotics by changing their morphology, macromolecular composition, metabolism,
gene expression and possibly even their mutation rate. Inevitably, these processes
affect each other, resulting in a complex response with changes in the expression
of numerous genes. Genome‐wide approaches can thus help in gaining a comprehensive
understanding of bacterial responses to antibiotics. In addition, a combination
of experimental and theoretical approaches is needed for identifying general principles
that underlie these responses. Here, we review recent progress in our understanding
of bacterial responses to antibiotics and their combinations, focusing on effects
at the levels of growth rate and gene expression. We concentrate on studies performed
in controlled laboratory conditions, which combine promising experimental techniques
with quantitative data analysis and mathematical modeling. While these basic research
approaches are not immediately applicable in the clinic, uncovering the principles
and mechanisms underlying bacterial responses to antibiotics may, in the long
term, contribute to the development of new treatment strategies to cope with and
prevent the rise of resistant pathogenic bacteria.
article_processing_charge: No
author:
- first_name: Karin
full_name: Mitosch, Karin
id: 39B66846-F248-11E8-B48F-1D18A9856A87
last_name: Mitosch
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Mitosch K, Bollenbach MT. Bacterial responses to antibiotics and their combinations.
Environmental Microbiology Reports. 2014;6(6):545-557. doi:10.1111/1758-2229.12190
apa: Mitosch, K., & Bollenbach, M. T. (2014). Bacterial responses to antibiotics
and their combinations. Environmental Microbiology Reports. Wiley. https://doi.org/10.1111/1758-2229.12190
chicago: Mitosch, Karin, and Mark Tobias Bollenbach. “Bacterial Responses to Antibiotics
and Their Combinations.” Environmental Microbiology Reports. Wiley, 2014.
https://doi.org/10.1111/1758-2229.12190.
ieee: K. Mitosch and M. T. Bollenbach, “Bacterial responses to antibiotics and their
combinations,” Environmental Microbiology Reports, vol. 6, no. 6. Wiley,
pp. 545–557, 2014.
ista: Mitosch K, Bollenbach MT. 2014. Bacterial responses to antibiotics and their
combinations. Environmental Microbiology Reports. 6(6), 545–557.
mla: Mitosch, Karin, and Mark Tobias Bollenbach. “Bacterial Responses to Antibiotics
and Their Combinations.” Environmental Microbiology Reports, vol. 6, no.
6, Wiley, 2014, pp. 545–57, doi:10.1111/1758-2229.12190.
short: K. Mitosch, M.T. Bollenbach, Environmental Microbiology Reports 6 (2014)
545–557.
corr_author: '1'
date_created: 2018-12-11T11:55:08Z
date_published: 2014-06-22T00:00:00Z
date_updated: 2026-04-08T14:21:56Z
day: '22'
department:
- _id: ToBo
doi: 10.1111/1758-2229.12190
ec_funded: 1
external_id:
isi:
- '000345702700002'
intvolume: ' 6'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 545 - 557
project:
- _id: 25EB3A80-B435-11E9-9278-68D0E5697425
grant_number: RGP0042/2013
name: Revealing the fundamental limits of cell growth
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303507'
name: Optimality principles in responses to antibiotics
publication: Environmental Microbiology Reports
publication_status: published
publisher: Wiley
publist_id: '5076'
quality_controlled: '1'
related_material:
record:
- id: '818'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Bacterial responses to antibiotics and their combinations
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 6
year: '2014'
...
---
_id: '2002'
abstract:
- lang: eng
text: Oriens-lacunosum moleculare (O-LM) interneurons in the CA1 region of the hippocampus
play a key role in feedback inhibition and in the control of network activity.
However, how these cells are efficiently activated in the network remains unclear.
To address this question, I performed recordings from CA1 pyramidal neuron axons,
the presynaptic fibers that provide feedback innervation of these interneurons.
Two forms of axonal action potential (AP) modulation were identified. First, repetitive
stimulation resulted in activity-dependent AP broadening. Broadening showed fast
onset, with marked changes in AP shape following a single AP. Second, tonic depolarization
in CA1 pyramidal neuron somata induced AP broadening in the axon, and depolarization-induced
broadening summated with activity-dependent broadening. Outsideout patch recordings
from CA1 pyramidal neuron axons revealed a high density of a-dendrotoxin (α-DTX)-sensitive,
inactivating K+ channels, suggesting that K+ channel inactivation mechanistically
contributes to AP broadening. To examine the functional consequences of axonal
AP modulation for synaptic transmission, I performed paired recordings between
synaptically connected CA1 pyramidal neurons and O-LM interneurons. CA1 pyramidal
neuron-O-LM interneuron excitatory postsynaptic currents (EPSCs) showed facilitation
during both repetitive stimulation and tonic depolarization of the presynaptic
neuron. Both effects were mimicked and occluded by α-DTX, suggesting that they
were mediated by K+ channel inactivation. Therefore, axonal AP modulation can
greatly facilitate the activation of O-LM interneurons. In conclusion, modulation
of AP shape in CA1 pyramidal neuron axons substantially enhances the efficacy
of principal neuron-interneuron synapses, promoting the activation of O-LM interneurons
in recurrent inhibitory microcircuits.
article_number: '0113124'
article_processing_charge: No
author:
- first_name: Sooyun
full_name: Kim, Sooyun
id: 394AB1C8-F248-11E8-B48F-1D18A9856A87
last_name: Kim
citation:
ama: Kim S. Action potential modulation in CA1 pyramidal neuron axons facilitates
OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus.
PLoS One. 2014;9(11). doi:10.1371/journal.pone.0113124
apa: Kim, S. (2014). Action potential modulation in CA1 pyramidal neuron axons facilitates
OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus.
PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0113124
chicago: Kim, Sooyun. “Action Potential Modulation in CA1 Pyramidal Neuron Axons
Facilitates OLM Interneuron Activation in Recurrent Inhibitory Microcircuits of
Rat Hippocampus.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0113124.
ieee: S. Kim, “Action potential modulation in CA1 pyramidal neuron axons facilitates
OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus,”
PLoS One, vol. 9, no. 11. Public Library of Science, 2014.
ista: Kim S. 2014. Action potential modulation in CA1 pyramidal neuron axons facilitates
OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus.
PLoS One. 9(11), 0113124.
mla: Kim, Sooyun. “Action Potential Modulation in CA1 Pyramidal Neuron Axons Facilitates
OLM Interneuron Activation in Recurrent Inhibitory Microcircuits of Rat Hippocampus.”
PLoS One, vol. 9, no. 11, 0113124, Public Library of Science, 2014, doi:10.1371/journal.pone.0113124.
short: S. Kim, PLoS One 9 (2014).
corr_author: '1'
date_created: 2018-12-11T11:55:09Z
date_published: 2014-11-19T00:00:00Z
date_updated: 2025-09-29T12:03:47Z
day: '19'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1371/journal.pone.0113124
ec_funded: 1
external_id:
isi:
- '000345533200070'
file:
- access_level: open_access
checksum: 85e4f4ea144f827272aaf376b2830564
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:52Z
date_updated: 2020-07-14T12:45:24Z
file_id: '5107'
file_name: IST-2016-434-v1+1_journal.pone.0113124.pdf
file_size: 5179993
relation: main_file
file_date_updated: 2020-07-14T12:45:24Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '11'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-sa/4.0/
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '5074'
pubrep_id: '434'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Action potential modulation in CA1 pyramidal neuron axons facilitates OLM interneuron
activation in recurrent inhibitory microcircuits of rat hippocampus
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 9
year: '2014'
...