---
_id: '2968'
abstract:
- lang: eng
text: Little is known about the stability of trophic relationships in complex natural
communities over evolutionary timescales. Here, we use sequence data from 18 nuclear
loci to reconstruct and compare the intraspecific histories of major Pleistocene
refugial populations in the Middle East, the Balkans and Iberia in a guild of
four Chalcid parasitoids (Cecidostiba fungosa, Cecidostiba semifascia, Hobbya
stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop
a likelihood method to numerically estimate models of divergence between three
populations from multilocus data. We investigate the power of this framework on
simulated data, and-using triplet alignments of intronic loci-quantify the support
for all possible divergence relationships between refugial populations in the
four parasitoids. Although an East to West order of population divergence has
highest support in all but one species, we cannot rule out alternative population
tree topologies. Comparing the estimated times of population splits between species,
we find that one species, M. amaenus, has a significantly older history than the
rest of the guild and must have arrived in central Europe at least one glacial
cycle prior to other guild members. This suggests that although all four species
may share a common origin in the East, they expanded westwards into Europe at
different times. © 2012 Blackwell Publishing Ltd.
acknowledgement: "This work was supported by funding from the UK Natural Environment
Research Council to KL (NE/I020288/1) and GS (NE/H000038/1, NE/E014453/1, NER/B/504406/1,
NER/B/S2003/00856) and a grant from the European Research Council (250152) to NB.\r\nWe
thank Majide Tavakoli, Juli Pujade-Villar and Pablo-Fuentes Utrilla for contributing
specimens. Mike Hickerson and three anonymous reviewers gave helpful comments on
earlier versions of the manuscript. "
author:
- first_name: Konrad
full_name: Lohse, Konrad
last_name: Lohse
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: George
full_name: Melika, George
last_name: Melika
- first_name: Graham
full_name: Stone, Graham
last_name: Stone
citation:
ama: Lohse K, Barton NH, Melika G, Stone G. A likelihood based comparison of population
histories in a parasitoid guild. Molecular Ecology. 2012;21(18):4605-4617.
doi:10.1111/j.1365-294X.2012.05700.x
apa: Lohse, K., Barton, N. H., Melika, G., & Stone, G. (2012). A likelihood
based comparison of population histories in a parasitoid guild. Molecular Ecology.
Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05700.x
chicago: Lohse, Konrad, Nicholas H Barton, George Melika, and Graham Stone. “A Likelihood
Based Comparison of Population Histories in a Parasitoid Guild.” Molecular
Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05700.x.
ieee: K. Lohse, N. H. Barton, G. Melika, and G. Stone, “A likelihood based comparison
of population histories in a parasitoid guild,” Molecular Ecology, vol.
21, no. 18. Wiley-Blackwell, pp. 4605–4617, 2012.
ista: Lohse K, Barton NH, Melika G, Stone G. 2012. A likelihood based comparison
of population histories in a parasitoid guild. Molecular Ecology. 21(18), 4605–4617.
mla: Lohse, Konrad, et al. “A Likelihood Based Comparison of Population Histories
in a Parasitoid Guild.” Molecular Ecology, vol. 21, no. 18, Wiley-Blackwell,
2012, pp. 4605–17, doi:10.1111/j.1365-294X.2012.05700.x.
short: K. Lohse, N.H. Barton, G. Melika, G. Stone, Molecular Ecology 21 (2012) 4605–4617.
date_created: 2018-12-11T12:00:36Z
date_published: 2012-09-01T00:00:00Z
date_updated: 2023-05-30T13:07:47Z
day: '01'
ddc:
- '570'
- '579'
department:
- _id: NiBa
doi: 10.1111/j.1365-294X.2012.05700.x
ec_funded: 1
file:
- access_level: open_access
checksum: c14ee4cb2a8ba9575bfd8a9bb7a883bb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:47Z
date_updated: 2020-07-14T12:45:57Z
file_id: '5304'
file_name: IST-2014-296-v1+1_4_wasps_revised3.pdf
file_size: 235820
relation: main_file
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checksum: f00afc5b887c8222014b57375b8caece
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:48Z
date_updated: 2020-07-14T12:45:57Z
file_id: '5305'
file_name: IST-2014-296-v1+2_4_wasps_Supporting2.pdf
file_size: 41975
relation: main_file
file_date_updated: 2020-07-14T12:45:57Z
has_accepted_license: '1'
intvolume: ' 21'
issue: '18'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 4605 - 4617
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Molecular Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3746'
pubrep_id: '296'
quality_controlled: '1'
related_material:
record:
- id: '13075'
relation: research_data
status: public
scopus_import: 1
status: public
title: A likelihood based comparison of population histories in a parasitoid guild
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2012'
...
---
_id: '2969'
abstract:
- lang: eng
text: "The coupling between presynaptic Ca^(2+) channels and Ca^(2+) sensors of
exocytosis is a key determinant of synaptic transmission. Evoked release from
parvalbumin (PV)-expressing interneurons is triggered by nanodomain coupling of
P/Q-type Ca^(2+) channels, whereas release from cholecystokinin (CCK)-containing
interneurons is generated by microdomain coupling of N-type channels. Nanodomain
coupling has several functional advantages, including speed and efficacy of transmission.
One potential disadvantage is that stochastic\r\nopening of presynaptic Ca^(2+)
channels may trigger spontaneous transmitter release. We addressed this possibility
in rat hippocampal\r\ngranule cells, which receive converging inputs from different
inhibitory sources. Both reduction of extracellular Ca^(2+) concentration and
the unselective Ca^(2+) channel blocker Cd^(2+) reduced the frequency of miniature
IPSCs (mIPSCs) in granule cells by ~50%, suggesting that the opening of presynaptic
Ca^(2+) channels contributes to spontaneous release. Application of the selective
P/Q-type Ca^(2+) channel blocker\r\nω-agatoxin IVa had no detectable effects,
whereas both the N-type blocker ω-conotoxin GVIa and the L-type blocker nimodipine
reduced\r\nmIPSC frequency. Furthermore, both the fast Ca^(2+) chelator BAPTA-AM
and the slow chelator EGTA-AM reduced the mIPSC frequency,\r\nsuggesting that
Ca^(2+)-dependent spontaneous release is triggered by microdomain rather than
nanodomain coupling. The CB_(1) receptor\r\nagonist WIN 55212-2 also decreased
spontaneous release; this effect was occluded by prior application of ω-conotoxin
GVIa, suggesting that a major fraction of Ca^(2+)-dependent spontaneous release
was generated at the terminals of CCK-expressing interneurons. Tonic inhibition
generated by spontaneous opening of presynaptic N- and L-type Ca^(2+) channels
may be important for hippocampal information processing.\r\n"
acknowledgement: This work was supported by grants from the Deutsche Forschungsgemeinschaft
(TR 3/B10, Leibniz program, GSC-4 Spemann Graduate School) and the European Union
(European Research Council Advanced Grant).
author:
- first_name: Sarit
full_name: Goswami, Sarit
id: 3A578F32-F248-11E8-B48F-1D18A9856A87
last_name: Goswami
- first_name: Iancu
full_name: Bucurenciu, Iancu
last_name: Bucurenciu
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Goswami S, Bucurenciu I, Jonas PM. Miniature IPSCs in hippocampal granule cells
are triggered by voltage-gated Ca^(2+) channels via microdomain coupling. Journal
of Neuroscience. 2012;32(41):14294-14304. doi:10.1523/JNEUROSCI.6104-11.2012
apa: Goswami, S., Bucurenciu, I., & Jonas, P. M. (2012). Miniature IPSCs in
hippocampal granule cells are triggered by voltage-gated Ca^(2+) channels via
microdomain coupling. Journal of Neuroscience. Society for Neuroscience.
https://doi.org/10.1523/JNEUROSCI.6104-11.2012
chicago: Goswami, Sarit, Iancu Bucurenciu, and Peter M Jonas. “Miniature IPSCs in
Hippocampal Granule Cells Are Triggered by Voltage-Gated Ca^(2+) Channels via
Microdomain Coupling.” Journal of Neuroscience. Society for Neuroscience,
2012. https://doi.org/10.1523/JNEUROSCI.6104-11.2012.
ieee: S. Goswami, I. Bucurenciu, and P. M. Jonas, “Miniature IPSCs in hippocampal
granule cells are triggered by voltage-gated Ca^(2+) channels via microdomain
coupling,” Journal of Neuroscience, vol. 32, no. 41. Society for Neuroscience,
pp. 14294–14304, 2012.
ista: Goswami S, Bucurenciu I, Jonas PM. 2012. Miniature IPSCs in hippocampal granule
cells are triggered by voltage-gated Ca^(2+) channels via microdomain coupling.
Journal of Neuroscience. 32(41), 14294–14304.
mla: Goswami, Sarit, et al. “Miniature IPSCs in Hippocampal Granule Cells Are Triggered
by Voltage-Gated Ca^(2+) Channels via Microdomain Coupling.” Journal of Neuroscience,
vol. 32, no. 41, Society for Neuroscience, 2012, pp. 14294–304, doi:10.1523/JNEUROSCI.6104-11.2012.
short: S. Goswami, I. Bucurenciu, P.M. Jonas, Journal of Neuroscience 32 (2012)
14294–14304.
date_created: 2018-12-11T12:00:36Z
date_published: 2012-10-10T00:00:00Z
date_updated: 2021-01-12T07:40:08Z
day: '10'
department:
- _id: PeJo
doi: 10.1523/JNEUROSCI.6104-11.2012
external_id:
pmid:
- '23055500'
intvolume: ' 32'
issue: '41'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3632771/
month: '10'
oa: 1
oa_version: Submitted Version
page: 14294 - 14304
pmid: 1
project:
- _id: 25BDE9A4-B435-11E9-9278-68D0E5697425
grant_number: SFB-TR3-TP10B
name: Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '3744'
quality_controlled: '1'
scopus_import: 1
status: public
title: Miniature IPSCs in hippocampal granule cells are triggered by voltage-gated
Ca^(2+) channels via microdomain coupling
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2012'
...
---
_id: '2970'
abstract:
- lang: eng
text: Morphogen gradients regulate the patterning and growth of many tissues, hence
a key question is how they are established and maintained during development.
Theoretical descriptions have helped to explain how gradient shape is controlled
by the rates of morphogen production, spreading and degradation. These effective
rates have been measured using fluorescence recovery after photobleaching (FRAP)
and photoactivation. To unravel which molecular events determine the effective
rates, such tissue-level assays have been combined with genetic analysis, high-resolution
assays, and models that take into account interactions with receptors, extracellular
components and trafficking. Nevertheless, because of the natural and experimental
data variability, and the underlying assumptions of transport models, it remains
challenging to conclusively distinguish between cellular mechanisms.
acknowledgement: AK is currently supported by an MRC CDF. MGG and OW were supported
by the Swiss National Science Foundation, grants from the Swiss SystemsX.ch initiative,
LipidX-2008/011, an ERC advanced investigator grant and the Polish-Swiss research
program.
author:
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
- first_name: Ortrud
full_name: Wartlick, Ortrud
last_name: Wartlick
- first_name: Frank
full_name: Julicher, Frank
last_name: Julicher
- first_name: Marcos
full_name: Gonzalez Gaitan, Marcos
last_name: Gonzalez Gaitan
citation:
ama: 'Kicheva A, Bollenbach MT, Wartlick O, Julicher F, Gonzalez Gaitan M. Investigating
the principles of morphogen gradient formation: from tissues to cells. Current
Opinion in Genetics & Development. 2012;22(6):527-532. doi:10.1016/j.gde.2012.08.004'
apa: 'Kicheva, A., Bollenbach, M. T., Wartlick, O., Julicher, F., & Gonzalez
Gaitan, M. (2012). Investigating the principles of morphogen gradient formation:
from tissues to cells. Current Opinion in Genetics & Development. Elsevier.
https://doi.org/10.1016/j.gde.2012.08.004'
chicago: 'Kicheva, Anna, Mark Tobias Bollenbach, Ortrud Wartlick, Frank Julicher,
and Marcos Gonzalez Gaitan. “Investigating the Principles of Morphogen Gradient
Formation: From Tissues to Cells.” Current Opinion in Genetics & Development.
Elsevier, 2012. https://doi.org/10.1016/j.gde.2012.08.004.'
ieee: 'A. Kicheva, M. T. Bollenbach, O. Wartlick, F. Julicher, and M. Gonzalez Gaitan,
“Investigating the principles of morphogen gradient formation: from tissues to
cells,” Current Opinion in Genetics & Development, vol. 22, no. 6.
Elsevier, pp. 527–532, 2012.'
ista: 'Kicheva A, Bollenbach MT, Wartlick O, Julicher F, Gonzalez Gaitan M. 2012.
Investigating the principles of morphogen gradient formation: from tissues to
cells. Current Opinion in Genetics & Development. 22(6), 527–532.'
mla: 'Kicheva, Anna, et al. “Investigating the Principles of Morphogen Gradient
Formation: From Tissues to Cells.” Current Opinion in Genetics & Development,
vol. 22, no. 6, Elsevier, 2012, pp. 527–32, doi:10.1016/j.gde.2012.08.004.'
short: A. Kicheva, M.T. Bollenbach, O. Wartlick, F. Julicher, M. Gonzalez Gaitan,
Current Opinion in Genetics & Development 22 (2012) 527–532.
date_created: 2018-12-11T12:00:37Z
date_published: 2012-12-01T00:00:00Z
date_updated: 2021-01-12T07:40:09Z
day: '01'
department:
- _id: ToBo
doi: 10.1016/j.gde.2012.08.004
intvolume: ' 22'
issue: '6'
language:
- iso: eng
month: '12'
oa_version: None
page: 527 - 532
publication: Current Opinion in Genetics & Development
publication_status: published
publisher: Elsevier
publist_id: '3739'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Investigating the principles of morphogen gradient formation: from tissues
to cells'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2012'
...
---
_id: '2971'
abstract:
- lang: eng
text: 'We study the task of interactive semantic labeling of a segmentation hierarchy.
To this end we propose a framework interleaving two components: an automatic labeling
step, based on a Conditional Random Field whose dependencies are defined by the
inclusion tree of the segmentation hierarchy, and an interaction step that integrates
incremental input from a human user. Evaluated on two distinct datasets, the proposed
interactive approach efficiently integrates human interventions and illustrates
the advantages of structured prediction in an interactive framework. '
author:
- first_name: Georg
full_name: Zankl, Georg
last_name: Zankl
- first_name: Yll
full_name: Haxhimusa, Yll
last_name: Haxhimusa
- first_name: Adrian
full_name: Ion, Adrian
id: 29F89302-F248-11E8-B48F-1D18A9856A87
last_name: Ion
citation:
ama: 'Zankl G, Haxhimusa Y, Ion A. Interactive labeling of image segmentation hierarchies.
In: Vol 7476. Springer; 2012:11-20. doi:10.1007/978-3-642-32717-9_2'
apa: 'Zankl, G., Haxhimusa, Y., & Ion, A. (2012). Interactive labeling of image
segmentation hierarchies (Vol. 7476, pp. 11–20). Presented at the Pattern Recognition,
Graz, Austria: Springer. https://doi.org/10.1007/978-3-642-32717-9_2'
chicago: Zankl, Georg, Yll Haxhimusa, and Adrian Ion. “Interactive Labeling of Image
Segmentation Hierarchies,” 7476:11–20. Springer, 2012. https://doi.org/10.1007/978-3-642-32717-9_2.
ieee: G. Zankl, Y. Haxhimusa, and A. Ion, “Interactive labeling of image segmentation
hierarchies,” presented at the Pattern Recognition, Graz, Austria, 2012, vol.
7476, pp. 11–20.
ista: Zankl G, Haxhimusa Y, Ion A. 2012. Interactive labeling of image segmentation
hierarchies. Pattern Recognition vol. 7476, 11–20.
mla: Zankl, Georg, et al. Interactive Labeling of Image Segmentation Hierarchies.
Vol. 7476, Springer, 2012, pp. 11–20, doi:10.1007/978-3-642-32717-9_2.
short: G. Zankl, Y. Haxhimusa, A. Ion, in:, Springer, 2012, pp. 11–20.
conference:
end_date: 2012-08-31
location: Graz, Austria
name: Pattern Recognition
start_date: 2012-08-28
date_created: 2018-12-11T12:00:37Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2021-01-12T07:40:10Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/978-3-642-32717-9_2
intvolume: ' 7476'
language:
- iso: eng
month: '01'
oa_version: None
page: 11 - 20
publication_status: published
publisher: Springer
publist_id: '3737'
quality_controlled: '1'
scopus_import: 1
status: public
title: Interactive labeling of image segmentation hierarchies
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7476
year: '2012'
...
---
_id: '2972'
abstract:
- lang: eng
text: 'Energy parity games are infinite two-player turn-based games played on weighted
graphs. The objective of the game combines a (qualitative) parity condition with
the (quantitative) requirement that the sum of the weights (i.e., the level of
energy in the game) must remain positive. Beside their own interest in the design
and synthesis of resource-constrained omega-regular specifications, energy parity
games provide one of the simplest model of games with combined qualitative and
quantitative objectives. Our main results are as follows: (a) exponential memory
is sufficient and may be necessary for winning strategies in energy parity games;
(b) the problem of deciding the winner in energy parity games can be solved in
NP ∩ coNP; and (c) we give an algorithm to solve energy parity by reduction to
energy games. We also show that the problem of deciding the winner in energy parity
games is logspace-equivalent to the problem of deciding the winner in mean-payoff
parity games, which can thus be solved in NP ∩ coNP. As a consequence we also
obtain a conceptually simple algorithm to solve mean-payoff parity games.'
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
citation:
ama: Chatterjee K, Doyen L. Energy parity games. Theoretical Computer Science.
2012;458:49-60. doi:10.1016/j.tcs.2012.07.038
apa: Chatterjee, K., & Doyen, L. (2012). Energy parity games. Theoretical
Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2012.07.038
chicago: Chatterjee, Krishnendu, and Laurent Doyen. “Energy Parity Games.” Theoretical
Computer Science. Elsevier, 2012. https://doi.org/10.1016/j.tcs.2012.07.038.
ieee: K. Chatterjee and L. Doyen, “Energy parity games,” Theoretical Computer
Science, vol. 458. Elsevier, pp. 49–60, 2012.
ista: Chatterjee K, Doyen L. 2012. Energy parity games. Theoretical Computer Science.
458, 49–60.
mla: Chatterjee, Krishnendu, and Laurent Doyen. “Energy Parity Games.” Theoretical
Computer Science, vol. 458, Elsevier, 2012, pp. 49–60, doi:10.1016/j.tcs.2012.07.038.
short: K. Chatterjee, L. Doyen, Theoretical Computer Science 458 (2012) 49–60.
date_created: 2018-12-11T12:00:37Z
date_published: 2012-11-02T00:00:00Z
date_updated: 2023-02-23T11:45:29Z
day: '02'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.1016/j.tcs.2012.07.038
ec_funded: 1
external_id:
arxiv:
- '1001.5183'
file:
- access_level: open_access
checksum: 719e4a5af5a01ad3f2f7f7f05b3c2b09
content_type: application/pdf
creator: kschuh
date_created: 2019-02-06T11:56:22Z
date_updated: 2020-07-14T12:45:57Z
file_id: '5935'
file_name: 2012_Elsevier_Chatterjee.pdf
file_size: 351271
relation: main_file
file_date_updated: 2020-07-14T12:45:57Z
has_accepted_license: '1'
intvolume: ' 458'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '11'
oa: 1
oa_version: Published Version
page: 49 - 60
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Theoretical Computer Science
publication_status: published
publisher: Elsevier
publist_id: '3736'
pubrep_id: '935'
quality_controlled: '1'
related_material:
record:
- id: '3851'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Energy parity games
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 458
year: '2012'
...
---
_id: '2974'
abstract:
- lang: eng
text: "We construct a perfectly binding string commitment scheme whose security
is based on the learning parity with noise (LPN) assumption, or equivalently,
the hardness of decoding random linear codes. Our scheme not only allows for a
simple and efficient zero-knowledge proof of knowledge for committed values (essentially
a Σ-protocol), but also for such proofs showing any kind of relation amongst committed
values, i.e. proving that messages m_0,...,m_u, are such that m_0=C(m_1,...,m_u)
for any circuit C.\r\n\r\nTo get soundness which is exponentially small in a security
parameter t, and when the zero-knowledge property relies on the LPN problem with
secrets of length l, our 3 round protocol has communication complexity O(t|C|l
log(l)) and computational complexity of O(t|C|l) bit operations. The hidden constants
are small, and the computation consists mostly of computing inner products of
bit-vectors."
acknowledgement: "We are grateful to Petros Mol for helpful discussions on the reduction
for the hardness of the xLPN problem.\r\n"
alternative_title:
- LNCS
author:
- first_name: Abhishek
full_name: Jain, Abhishek
last_name: Jain
- first_name: Stephan
full_name: Krenn, Stephan
id: 329FCCF0-F248-11E8-B48F-1D18A9856A87
last_name: Krenn
orcid: 0000-0003-2835-9093
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Aris
full_name: Tentes, Aris
last_name: Tentes
citation:
ama: 'Jain A, Krenn S, Pietrzak KZ, Tentes A. Commitments and efficient zero knowledge
proofs from learning parity with noise. In: Wang X, Sako K, eds. Vol 7658. Springer;
2012:663-680. doi:10.1007/978-3-642-34961-4_40'
apa: 'Jain, A., Krenn, S., Pietrzak, K. Z., & Tentes, A. (2012). Commitments
and efficient zero knowledge proofs from learning parity with noise. In X. Wang
& K. Sako (Eds.) (Vol. 7658, pp. 663–680). Presented at the ASIACRYPT: Theory
and Application of Cryptology and Information Security, Beijing, China: Springer.
https://doi.org/10.1007/978-3-642-34961-4_40'
chicago: Jain, Abhishek, Stephan Krenn, Krzysztof Z Pietrzak, and Aris Tentes. “Commitments
and Efficient Zero Knowledge Proofs from Learning Parity with Noise.” edited by
Xiaoyun Wang and Kazue Sako, 7658:663–80. Springer, 2012. https://doi.org/10.1007/978-3-642-34961-4_40.
ieee: 'A. Jain, S. Krenn, K. Z. Pietrzak, and A. Tentes, “Commitments and efficient
zero knowledge proofs from learning parity with noise,” presented at the ASIACRYPT:
Theory and Application of Cryptology and Information Security, Beijing, China,
2012, vol. 7658, pp. 663–680.'
ista: 'Jain A, Krenn S, Pietrzak KZ, Tentes A. 2012. Commitments and efficient zero
knowledge proofs from learning parity with noise. ASIACRYPT: Theory and Application
of Cryptology and Information Security, LNCS, vol. 7658, 663–680.'
mla: Jain, Abhishek, et al. Commitments and Efficient Zero Knowledge Proofs from
Learning Parity with Noise. Edited by Xiaoyun Wang and Kazue Sako, vol. 7658,
Springer, 2012, pp. 663–80, doi:10.1007/978-3-642-34961-4_40.
short: A. Jain, S. Krenn, K.Z. Pietrzak, A. Tentes, in:, X. Wang, K. Sako (Eds.),
Springer, 2012, pp. 663–680.
conference:
end_date: 2012-12-06
location: Beijing, China
name: 'ASIACRYPT: Theory and Application of Cryptology and Information Security'
start_date: 2012-12-02
date_created: 2018-12-11T12:00:38Z
date_published: 2012-12-01T00:00:00Z
date_updated: 2021-01-12T07:40:11Z
day: '01'
ddc:
- '004'
- '005'
department:
- _id: KrPi
doi: 10.1007/978-3-642-34961-4_40
ec_funded: 1
editor:
- first_name: Xiaoyun
full_name: Wang, Xiaoyun
last_name: Wang
- first_name: Kazue
full_name: Sako, Kazue
last_name: Sako
file:
- access_level: open_access
checksum: ab879537385efc4cb4203e7ef0fea17b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:00Z
date_updated: 2020-07-14T12:45:58Z
file_id: '5048'
file_name: IST-2016-721-v1+1_513.pdf
file_size: 482570
relation: main_file
file_date_updated: 2020-07-14T12:45:58Z
has_accepted_license: '1'
intvolume: ' 7658'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Submitted Version
page: 663 - 680
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '3730'
pubrep_id: '721'
scopus_import: 1
status: public
title: Commitments and efficient zero knowledge proofs from learning parity with noise
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: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7658
year: '2012'
...
---
_id: '3104'
abstract:
- lang: eng
text: |2-
Gradients of the plant hormone auxin, which depend on its active intercellular transport, are crucial for the maintenance of root meristematic activity. This directional transport is largely orchestrated by a complex interaction of specific influx and efflux carriers that mediate the auxin flow into and out of cells, respectively. Besides these transport proteins, plant-specific polyphenolic compounds knownasflavonols have beenshownto act as endogenous regulators of auxin transport. However, only limited information is available on how flavonol synthesis is developmentally regulated. Using reduction-of-function and overexpression approaches in parallel, we demonstrate that the WRKY23 transcription factor is needed for proper root growth and development by stimulating the local biosynthesis of flavonols. The expression of WRKY23 itself is controlled by auxin through the AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 transcriptional response pathway. Our results suggest a model in which WRKY23 is part of a transcriptional feedback loop of auxin on its own transport through local regulation of flavonol biosynthesis.
author:
- first_name: Wim
full_name: Grunewald, Wim
last_name: Grunewald
- first_name: Ive
full_name: De Smet, Ive
last_name: De Smet
- first_name: Daniel
full_name: Lewis, Daniel R
last_name: Lewis
- first_name: Christian
full_name: Löfke, Christian
last_name: Löfke
- first_name: Leentje
full_name: Jansen, Leentje
last_name: Jansen
- first_name: Geert
full_name: Goeminne, Geert
last_name: Goeminne
- first_name: Robin
full_name: Vanden Bossche, Robin
last_name: Vanden Bossche
- first_name: Mansour
full_name: Karimi, Mansour
last_name: Karimi
- first_name: Bert
full_name: De Rybel, Bert
last_name: De Rybel
- first_name: Bartel
full_name: Vanholme, Bartel
last_name: Vanholme
- first_name: Thomas
full_name: Teichmann, Thomas
last_name: Teichmann
- first_name: Wout
full_name: Boerjan, Wout
last_name: Boerjan
- first_name: Marc
full_name: Van Montagu, Marc C
last_name: Van Montagu
- first_name: Godelieve
full_name: Gheysen, Godelieve
last_name: Gheysen
- first_name: Gloria
full_name: Muday, Gloria K
last_name: Muday
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
citation:
ama: Grunewald W, De Smet I, Lewis D, et al. Transcription factor WRKY23 assists
auxin distribution patterns during Arabidopsis root development through local
control on flavonol biosynthesis. PNAS. 2012;109(5):1554-1559. doi:10.1073/pnas.1121134109
apa: Grunewald, W., De Smet, I., Lewis, D., Löfke, C., Jansen, L., Goeminne, G.,
… Beeckman, T. (2012). Transcription factor WRKY23 assists auxin distribution
patterns during Arabidopsis root development through local control on flavonol
biosynthesis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1121134109
chicago: Grunewald, Wim, Ive De Smet, Daniel Lewis, Christian Löfke, Leentje Jansen,
Geert Goeminne, Robin Vanden Bossche, et al. “Transcription Factor WRKY23 Assists
Auxin Distribution Patterns during Arabidopsis Root Development through Local
Control on Flavonol Biosynthesis.” PNAS. National Academy of Sciences,
2012. https://doi.org/10.1073/pnas.1121134109.
ieee: W. Grunewald et al., “Transcription factor WRKY23 assists auxin distribution
patterns during Arabidopsis root development through local control on flavonol
biosynthesis,” PNAS, vol. 109, no. 5. National Academy of Sciences, pp.
1554–1559, 2012.
ista: Grunewald W, De Smet I, Lewis D, Löfke C, Jansen L, Goeminne G, Vanden Bossche
R, Karimi M, De Rybel B, Vanholme B, Teichmann T, Boerjan W, Van Montagu M, Gheysen
G, Muday G, Friml J, Beeckman T. 2012. Transcription factor WRKY23 assists auxin
distribution patterns during Arabidopsis root development through local control
on flavonol biosynthesis. PNAS. 109(5), 1554–1559.
mla: Grunewald, Wim, et al. “Transcription Factor WRKY23 Assists Auxin Distribution
Patterns during Arabidopsis Root Development through Local Control on Flavonol
Biosynthesis.” PNAS, vol. 109, no. 5, National Academy of Sciences, 2012,
pp. 1554–59, doi:10.1073/pnas.1121134109.
short: W. Grunewald, I. De Smet, D. Lewis, C. Löfke, L. Jansen, G. Goeminne, R.
Vanden Bossche, M. Karimi, B. De Rybel, B. Vanholme, T. Teichmann, W. Boerjan,
M. Van Montagu, G. Gheysen, G. Muday, J. Friml, T. Beeckman, PNAS 109 (2012) 1554–1559.
date_created: 2018-12-11T12:01:24Z
date_published: 2012-01-31T00:00:00Z
date_updated: 2021-01-12T07:41:05Z
day: '31'
doi: 10.1073/pnas.1121134109
extern: 1
intvolume: ' 109'
issue: '5'
month: '01'
page: 1554 - 1559
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3595'
quality_controlled: 0
status: public
title: Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis
root development through local control on flavonol biosynthesis
type: journal_article
volume: 109
year: '2012'
...
---
_id: '3105'
abstract:
- lang: eng
text: Growth and development are coordinated by an array of intercellular communications.
Known plant signaling molecules include phytohormones and hormone peptides. Although
both classes can be implicated in the same developmental processes, little is
known about the interplay between phytohormone action and peptide signaling within
the cellular microenvironment. We show that genes coding for small secretory peptides,
designated GOLVEN (GLV), modulate the distribution of the phytohormone auxin.
The deregulation of the GLV function impairs the formation of auxin gradients
and alters the reorientation of shoots and roots after a gravity stimulus. Specifically,
the GLV signal modulates the trafficking dynamics of the auxin efflux carrier
PIN-FORMED2 involved in root tropic responses and meristem organization. Our work
links the local action of secretory peptides with phytohormone transport. Root
growth factor (RGF) or GOLVEN (GLV) secreted peptides have previously been implicated
in meristem regulation. Whitford et al. now show that RGF/GLV peptides induce
rapid relocalization of the auxin efflux regulator PIN2, regulate auxin gradients,
and modulate auxin-dependent root responses to specific stimuli.
author:
- first_name: Ryan
full_name: Whitford, Ryan
last_name: Whitford
- first_name: Ana
full_name: Fernandez, Ana
last_name: Fernandez
- first_name: Ricardo
full_name: Tejos, Ricardo
last_name: Tejos
- first_name: Amparo
full_name: Pérez, Amparo Cuéllar
last_name: Pérez
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Andrzej
full_name: Drozdzecki, Andrzej
last_name: Drozdzecki
- first_name: Johannes
full_name: Leitner, Johannes
last_name: Leitner
- first_name: Lindy
full_name: Abas, Lindy
last_name: Abas
- first_name: Maarten
full_name: Aerts, Maarten
last_name: Aerts
- first_name: Kurt
full_name: Hoogewijs, Kurt
last_name: Hoogewijs
- first_name: Pawel
full_name: Pawel Baster
id: 3028BD74-F248-11E8-B48F-1D18A9856A87
last_name: Baster
- first_name: Ruth
full_name: De Groodt, Ruth
last_name: De Groodt
- first_name: Yao
full_name: Lin, Yao-Cheng
last_name: Lin
- first_name: Véronique
full_name: Storme, Véronique
last_name: Storme
- first_name: Yves
full_name: Van de Peer, Yves
last_name: Van De Peer
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Annemieke
full_name: Madder, Annemieke
last_name: Madder
- first_name: Bart
full_name: Devreese, Bart
last_name: Devreese
- first_name: Christian
full_name: Luschnig, Christian
last_name: Luschnig
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Pierre
full_name: Hilson, Pierre
last_name: Hilson
citation:
ama: Whitford R, Fernandez A, Tejos R, et al. GOLVEN secretory peptides regulate
auxin carrier turnover during plant gravitropic responses. Developmental Cell.
2012;22(3):678-685. doi:10.1016/j.devcel.2012.02.002
apa: Whitford, R., Fernandez, A., Tejos, R., Pérez, A., Kleine Vehn, J., Vanneste,
S., … Hilson, P. (2012). GOLVEN secretory peptides regulate auxin carrier turnover
during plant gravitropic responses. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2012.02.002
chicago: Whitford, Ryan, Ana Fernandez, Ricardo Tejos, Amparo Pérez, Jürgen Kleine
Vehn, Steffen Vanneste, Andrzej Drozdzecki, et al. “GOLVEN Secretory Peptides
Regulate Auxin Carrier Turnover during Plant Gravitropic Responses.” Developmental
Cell. Cell Press, 2012. https://doi.org/10.1016/j.devcel.2012.02.002.
ieee: R. Whitford et al., “GOLVEN secretory peptides regulate auxin carrier
turnover during plant gravitropic responses,” Developmental Cell, vol.
22, no. 3. Cell Press, pp. 678–685, 2012.
ista: Whitford R, Fernandez A, Tejos R, Pérez A, Kleine Vehn J, Vanneste S, Drozdzecki
A, Leitner J, Abas L, Aerts M, Hoogewijs K, Baster P, De Groodt R, Lin Y, Storme
V, Van De Peer Y, Beeckman T, Madder A, Devreese B, Luschnig C, Friml J, Hilson
P. 2012. GOLVEN secretory peptides regulate auxin carrier turnover during plant
gravitropic responses. Developmental Cell. 22(3), 678–685.
mla: Whitford, Ryan, et al. “GOLVEN Secretory Peptides Regulate Auxin Carrier Turnover
during Plant Gravitropic Responses.” Developmental Cell, vol. 22, no. 3,
Cell Press, 2012, pp. 678–85, doi:10.1016/j.devcel.2012.02.002.
short: R. Whitford, A. Fernandez, R. Tejos, A. Pérez, J. Kleine Vehn, S. Vanneste,
A. Drozdzecki, J. Leitner, L. Abas, M. Aerts, K. Hoogewijs, P. Baster, R. De Groodt,
Y. Lin, V. Storme, Y. Van De Peer, T. Beeckman, A. Madder, B. Devreese, C. Luschnig,
J. Friml, P. Hilson, Developmental Cell 22 (2012) 678–685.
date_created: 2018-12-11T12:01:25Z
date_published: 2012-03-13T00:00:00Z
date_updated: 2021-01-12T07:41:06Z
day: '13'
doi: 10.1016/j.devcel.2012.02.002
extern: 1
intvolume: ' 22'
issue: '3'
month: '03'
page: 678 - 685
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '3594'
quality_controlled: 0
status: public
title: GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic
responses
type: journal_article
volume: 22
year: '2012'
...
---
_id: '3106'
abstract:
- lang: eng
text: Cell polarization via asymmetrical distribution of structures or molecules
is essential for diverse cellular functions and development of organisms, but
how polarity is developmentally controlled has been poorly understood. In plants,
the asymmetrical distribution of the PIN-FORMED (PIN) proteins involved in the
cellular efflux of the quintessential phytohormone auxin plays a central role
in developmental patterning, morphogenesis, and differential growth. Recently
we showed that auxin promotes cell interdigitation by activating the Rho family
ROP GTPases in leaf epidermal pavement cells. Here we found that auxin activation
of the ROP2 signaling pathway regulates the asymmetric distribution of PIN1 by
inhibiting its endocytosis. ROP2 inhibits PIN1 endocytosis via the accumulation
of cortical actin microfilaments induced by the ROP2 effector protein RIC4. Our
findings suggest a link between the developmental auxin signal and polar PIN1
distribution via Rho-dependent cytoskeletal reorganization and reveal the conservation
of a design principle for cell polarization that is based on Rho GTPase-mediated
inhibition of endocytosis.
author:
- first_name: Shingo
full_name: Nagawa, Shingo
last_name: Nagawa
- first_name: Tongda
full_name: Xu, Tongda
last_name: Xu
- first_name: Deshu
full_name: Lin, Deshu
last_name: Lin
- first_name: Pankaj
full_name: Dhonukshe, Pankaj
last_name: Dhonukshe
- first_name: Xingxing
full_name: Zhang, Xingxing
last_name: Zhang
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Ben
full_name: Scheres, Ben
last_name: Scheres
- first_name: Ying
full_name: Fu, Ying
last_name: Fu
- first_name: Zhenbiao
full_name: Yang, Zhenbiao
last_name: Yang
citation:
ama: Nagawa S, Xu T, Lin D, et al. ROP GTPase-dependent actin microfilaments promote
PIN1 polarization by localized inhibition of clathrin-dependent endocytosis. PLoS
Biology. 2012;10(4). doi:10.1371/journal.pbio.1001299
apa: Nagawa, S., Xu, T., Lin, D., Dhonukshe, P., Zhang, X., Friml, J., … Yang, Z.
(2012). ROP GTPase-dependent actin microfilaments promote PIN1 polarization by
localized inhibition of clathrin-dependent endocytosis. PLoS Biology. Public
Library of Science. https://doi.org/10.1371/journal.pbio.1001299
chicago: Nagawa, Shingo, Tongda Xu, Deshu Lin, Pankaj Dhonukshe, Xingxing Zhang,
Jiří Friml, Ben Scheres, Ying Fu, and Zhenbiao Yang. “ROP GTPase-Dependent Actin
Microfilaments Promote PIN1 Polarization by Localized Inhibition of Clathrin-Dependent
Endocytosis.” PLoS Biology. Public Library of Science, 2012. https://doi.org/10.1371/journal.pbio.1001299.
ieee: S. Nagawa et al., “ROP GTPase-dependent actin microfilaments promote
PIN1 polarization by localized inhibition of clathrin-dependent endocytosis,”
PLoS Biology, vol. 10, no. 4. Public Library of Science, 2012.
ista: Nagawa S, Xu T, Lin D, Dhonukshe P, Zhang X, Friml J, Scheres B, Fu Y, Yang
Z. 2012. ROP GTPase-dependent actin microfilaments promote PIN1 polarization by
localized inhibition of clathrin-dependent endocytosis. PLoS Biology. 10(4).
mla: Nagawa, Shingo, et al. “ROP GTPase-Dependent Actin Microfilaments Promote PIN1
Polarization by Localized Inhibition of Clathrin-Dependent Endocytosis.” PLoS
Biology, vol. 10, no. 4, Public Library of Science, 2012, doi:10.1371/journal.pbio.1001299.
short: S. Nagawa, T. Xu, D. Lin, P. Dhonukshe, X. Zhang, J. Friml, B. Scheres, Y.
Fu, Z. Yang, PLoS Biology 10 (2012).
date_created: 2018-12-11T12:01:25Z
date_published: 2012-04-01T00:00:00Z
date_updated: 2021-01-12T07:41:06Z
day: '01'
doi: 10.1371/journal.pbio.1001299
extern: 1
intvolume: ' 10'
issue: '4'
month: '04'
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '3593'
quality_controlled: 0
status: public
title: ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized
inhibition of clathrin-dependent endocytosis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 10
year: '2012'
...
---
_id: '3107'
author:
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Vanneste S, Friml J. Plant Signaling: Deconstructing Auxin Sensing.
Vol 8. Nature Publishing Group; 2012:415-416. doi:10.1038/nchembio.943'
apa: 'Vanneste, S., & Friml, J. (2012). Plant signaling: Deconstructing auxin
sensing. Nature Chemical Biology (Vol. 8, pp. 415–416). Nature Publishing
Group. https://doi.org/10.1038/nchembio.943'
chicago: 'Vanneste, Steffen, and Jiří Friml. Plant Signaling: Deconstructing
Auxin Sensing. Nature Chemical Biology. Vol. 8. Nature Publishing Group,
2012. https://doi.org/10.1038/nchembio.943.'
ieee: 'S. Vanneste and J. Friml, Plant signaling: Deconstructing auxin sensing,
vol. 8, no. 5. Nature Publishing Group, 2012, pp. 415–416.'
ista: 'Vanneste S, Friml J. 2012. Plant signaling: Deconstructing auxin sensing,
Nature Publishing Group,p.'
mla: 'Vanneste, Steffen, and Jiří Friml. “Plant Signaling: Deconstructing Auxin
Sensing.” Nature Chemical Biology, vol. 8, no. 5, Nature Publishing Group,
2012, pp. 415–16, doi:10.1038/nchembio.943.'
short: 'S. Vanneste, J. Friml, Plant Signaling: Deconstructing Auxin Sensing, Nature
Publishing Group, 2012.'
date_created: 2018-12-11T12:01:26Z
date_published: 2012-05-01T00:00:00Z
date_updated: 2021-01-12T07:41:06Z
day: '01'
doi: 10.1038/nchembio.943
extern: '1'
intvolume: ' 8'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 415 - 416
publication: Nature Chemical Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '3592'
quality_controlled: '1'
status: public
title: 'Plant signaling: Deconstructing auxin sensing'
type: other_academic_publication
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2012'
...
---
_id: '3108'
abstract:
- lang: eng
text: The phytohormone auxin acts as a prominent signal, providing, by its local
accumulation or depletion in selected cells, a spatial and temporal reference
for changes in the developmental program. The distribution of auxin depends on
both auxin metabolism (biosynthesis, conjugation and degradation) and cellular
auxin transport. We identified in silico a novel putative auxin transport facilitator
family, called PIN-LIKES (PILS). Here we illustrate that PILS proteins are required
for auxin-dependent regulation of plant growth by determining the cellular sensitivity
to auxin. PILS proteins regulate intracellular auxin accumulation at the endoplasmic
reticulum and thus auxin availability for nuclear auxin signalling. PILS activity
affects the level of endogenous auxin indole-3-acetic acid (IAA), presumably via
intracellular accumulation and metabolism. Our findings reveal that the transport
machinery to compartmentalize auxin within the cell is of an unexpected molecular
complexity and demonstrate this compartmentalization to be functionally important
for a number of developmental processes.
author:
- first_name: Elke
full_name: Barbez, Elke
last_name: Barbez
- first_name: Martin
full_name: Kubeš, Martin
last_name: Kubeš
- first_name: Jakub
full_name: Rolčík, Jakub
last_name: Rolčík
- first_name: Chloe
full_name: Béziat, Chloe
last_name: Béziat
- first_name: Aleš
full_name: Pěnčík, Aleš
last_name: Pěnčík
- first_name: Bangjun
full_name: Wang, Bangjun
last_name: Wang
- first_name: Michel
full_name: Rosquete, Michel Ruiz
last_name: Rosquete
- first_name: Jinsheng
full_name: Zhu, Jinsheng
last_name: Zhu
- first_name: Petre
full_name: Dobrev, Petre I
last_name: Dobrev
- first_name: Yuree
full_name: Lee, Yuree
last_name: Lee
- first_name: Eva
full_name: Zašímalová, Eva
last_name: Zašímalová
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Markus
full_name: Geisler, Markus
last_name: Geisler
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
citation:
ama: Barbez E, Kubeš M, Rolčík J, et al. A novel putative auxin carrier family regulates
intracellular auxin homeostasis in plants. Nature. 2012;485(7396):119-122.
doi:10.1038/nature11001
apa: Barbez, E., Kubeš, M., Rolčík, J., Béziat, C., Pěnčík, A., Wang, B., … Kleine
Vehn, J. (2012). A novel putative auxin carrier family regulates intracellular
auxin homeostasis in plants. Nature. Nature Publishing Group. https://doi.org/10.1038/nature11001
chicago: Barbez, Elke, Martin Kubeš, Jakub Rolčík, Chloe Béziat, Aleš Pěnčík, Bangjun
Wang, Michel Rosquete, et al. “A Novel Putative Auxin Carrier Family Regulates
Intracellular Auxin Homeostasis in Plants.” Nature. Nature Publishing Group,
2012. https://doi.org/10.1038/nature11001.
ieee: E. Barbez et al., “A novel putative auxin carrier family regulates
intracellular auxin homeostasis in plants,” Nature, vol. 485, no. 7396.
Nature Publishing Group, pp. 119–122, 2012.
ista: Barbez E, Kubeš M, Rolčík J, Béziat C, Pěnčík A, Wang B, Rosquete M, Zhu J,
Dobrev P, Lee Y, Zašímalová E, Petrášek J, Geisler M, Friml J, Kleine Vehn J.
2012. A novel putative auxin carrier family regulates intracellular auxin homeostasis
in plants. Nature. 485(7396), 119–122.
mla: Barbez, Elke, et al. “A Novel Putative Auxin Carrier Family Regulates Intracellular
Auxin Homeostasis in Plants.” Nature, vol. 485, no. 7396, Nature Publishing
Group, 2012, pp. 119–22, doi:10.1038/nature11001.
short: E. Barbez, M. Kubeš, J. Rolčík, C. Béziat, A. Pěnčík, B. Wang, M. Rosquete,
J. Zhu, P. Dobrev, Y. Lee, E. Zašímalová, J. Petrášek, M. Geisler, J. Friml, J.
Kleine Vehn, Nature 485 (2012) 119–122.
date_created: 2018-12-11T12:01:26Z
date_published: 2012-05-03T00:00:00Z
date_updated: 2021-01-12T07:41:07Z
day: '03'
doi: 10.1038/nature11001
extern: 1
intvolume: ' 485'
issue: '7396'
month: '05'
page: 119 - 122
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '3591'
quality_controlled: 0
status: public
title: A novel putative auxin carrier family regulates intracellular auxin homeostasis
in plants
type: journal_article
volume: 485
year: '2012'
...
---
_id: '3109'
abstract:
- lang: eng
text: Receptor-mediated endocytosis is an integral part of signal transduction as
it mediates signal attenuation and provides spatial and temporal dimensions to
signaling events. One of the best-studied leucine-rich repeat receptor-like kinases
in plants, BRASSINOSTEROID INSENSITIVE 1 (BRI1), perceives its ligand, the brassinosteroid
(BR) hormone, at the cell surface and is constitutively endocytosed. However,
the importance of endocytosis for BR signaling remains unclear. Here we developed
a bioactive, fluorescent BR analog, Alexa Fluor 647-castasterone (AFCS), and visualized
the endocytosis of BRI1-AFCS complexes in living Arabidopsis thaliana cells. Impairment
of endocytosis dependent on clathrin and the guanine nucleotide exchange factor
for ARF GTPases (ARF-GEF) GNOM enhanced BR signaling by retaining active BRI1-ligand
complexes at the plasma membrane. Increasing the trans-Golgi network/early endosome
pool of BRI1-BR complexes did not affect BR signaling. Our findings provide what
is to our knowledge the first visualization of receptor-ligand complexes in plants
and reveal clathrin-and ARF-GEF-dependent endocytic regulation of BR signaling
from the plasma membrane.
author:
- first_name: Niloufer
full_name: Irani, Niloufer G
last_name: Irani
- first_name: Simone
full_name: Di Rubbo, Simone
last_name: Di Rubbo
- first_name: Evelien
full_name: Mylle, Evelien
last_name: Mylle
- first_name: Jos
full_name: Van Den Begin, Jos
last_name: Van Den Begin
- first_name: Joanna
full_name: Schneider-Pizoń, Joanna
last_name: Schneider Pizoń
- first_name: Jaroslava
full_name: Hniliková, Jaroslava
last_name: Hniliková
- first_name: Miroslav
full_name: Šíša, Miroslav
last_name: Šíša
- first_name: Dieter
full_name: Buyst, Dieter
last_name: Buyst
- first_name: Josep
full_name: Vilarrasa-Blasi, Josep
last_name: Vilarrasa Blasi
- first_name: Anna
full_name: Szatmári, Anna-Maria
last_name: Szatmári
- first_name: Daniël
full_name: Van Damme, Daniël
last_name: Van Damme
- first_name: Kiril
full_name: Mishev, Kiril
last_name: Mishev
- first_name: Mirela
full_name: Codreanu, Mirela-Corina
last_name: Codreanu
- first_name: Ladislav
full_name: Kohout, Ladislav
last_name: Kohout
- first_name: Miroslav
full_name: Strnad, Miroslav
last_name: Strnad
- first_name: Ana
full_name: Caño-Delgado, Ana I
last_name: Caño Delgado
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Annemieke
full_name: Madder, Annemieke
last_name: Madder
- first_name: Eugenia
full_name: Russinova, Eugenia
last_name: Russinova
citation:
ama: Irani N, Di Rubbo S, Mylle E, et al. Fluorescent castasterone reveals BRI1
signaling from the plasma membrane. Nature Chemical Biology. 2012;8(6):583-589.
doi:10.1038/nchembio.958
apa: Irani, N., Di Rubbo, S., Mylle, E., Van Den Begin, J., Schneider Pizoń, J.,
Hniliková, J., … Russinova, E. (2012). Fluorescent castasterone reveals BRI1 signaling
from the plasma membrane. Nature Chemical Biology. Nature Publishing Group.
https://doi.org/10.1038/nchembio.958
chicago: Irani, Niloufer, Simone Di Rubbo, Evelien Mylle, Jos Van Den Begin, Joanna
Schneider Pizoń, Jaroslava Hniliková, Miroslav Šíša, et al. “Fluorescent Castasterone
Reveals BRI1 Signaling from the Plasma Membrane.” Nature Chemical Biology.
Nature Publishing Group, 2012. https://doi.org/10.1038/nchembio.958.
ieee: N. Irani et al., “Fluorescent castasterone reveals BRI1 signaling from
the plasma membrane,” Nature Chemical Biology, vol. 8, no. 6. Nature Publishing
Group, pp. 583–589, 2012.
ista: Irani N, Di Rubbo S, Mylle E, Van Den Begin J, Schneider Pizoń J, Hniliková
J, Šíša M, Buyst D, Vilarrasa Blasi J, Szatmári A, Van Damme D, Mishev K, Codreanu
M, Kohout L, Strnad M, Caño Delgado A, Friml J, Madder A, Russinova E. 2012. Fluorescent
castasterone reveals BRI1 signaling from the plasma membrane. Nature Chemical
Biology. 8(6), 583–589.
mla: Irani, Niloufer, et al. “Fluorescent Castasterone Reveals BRI1 Signaling from
the Plasma Membrane.” Nature Chemical Biology, vol. 8, no. 6, Nature Publishing
Group, 2012, pp. 583–89, doi:10.1038/nchembio.958.
short: N. Irani, S. Di Rubbo, E. Mylle, J. Van Den Begin, J. Schneider Pizoń, J.
Hniliková, M. Šíša, D. Buyst, J. Vilarrasa Blasi, A. Szatmári, D. Van Damme, K.
Mishev, M. Codreanu, L. Kohout, M. Strnad, A. Caño Delgado, J. Friml, A. Madder,
E. Russinova, Nature Chemical Biology 8 (2012) 583–589.
date_created: 2018-12-11T12:01:26Z
date_published: 2012-06-01T00:00:00Z
date_updated: 2021-01-12T07:41:07Z
day: '01'
doi: 10.1038/nchembio.958
extern: 1
intvolume: ' 8'
issue: '6'
month: '06'
page: 583 - 589
publication: Nature Chemical Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '3590'
quality_controlled: 0
status: public
title: Fluorescent castasterone reveals BRI1 signaling from the plasma membrane
type: journal_article
volume: 8
year: '2012'
...
---
_id: '3110'
abstract:
- lang: eng
text: 'The directional transport of the phytohormone auxin depends on the phosphorylation
status and polar localization of PIN-FORMED (PIN) auxin efflux proteins. While
PINIOD (PID) kinase is directly involved in the phosphorylation of PIN proteins,
the phosphatase holoenzyme complexes that dephosphorylate PIN proteins remain
elusive. Here, we demonstrate that mutations simultaneously disrupting the function
of Arabidopsis thaliana FyPP1 (for Phytochrome-associated serine/threonine protein
phosphatase1) and FyPP3, two homologous genes encoding the catalytic subunits
of protein phosphatase6 (PP6), cause elevated accumulation of phosphorylated PIN
proteins, correlating with a basal-to-apical shift in subcellular PIN localization.
The changes in PIN polarity result in increased root basipetal auxin transport
and severe defects, including shorter roots, fewer lateral roots, defective columella
cells, root meristem collapse, abnormal cotyledons (small, cup-shaped, or fused
cotyledons), and altered leaf venation. Our molecular, biochemical, and genetic
data support the notion that FyPP1/3, SAL (for SAPS DOMAIN-LIKE), and PP2AA proteins
(RCN1 [for ROOTS CURL IN NAPHTHYLPHTHALAMIC ACID1] or PP2AA1, PP2AA2, and PP2AA3)
physically interact to form a novel PP6-type heterotrimeric holoenzyme complex.
We also show that FyPP1/3, SAL, and PP2AA interact with a subset of PIN proteins
and that for SAL the strength of the interaction depends on the PIN phosphorylation
status. Thus, an Arabidopsis PP6-type phosphatase holoenzyme acts antagonistically
with PID to direct auxin transport polarity and plant development by directly
regulating PIN phosphorylation. '
author:
- first_name: Mingqiu
full_name: Dai, Mingqiu
last_name: Dai
- first_name: Chen
full_name: Zhang, Chen
last_name: Zhang
- first_name: Urszula
full_name: Urszula Kania
id: 4AE5C486-F248-11E8-B48F-1D18A9856A87
last_name: Kania
- first_name: Fang
full_name: Chen, Fang
last_name: Chen
- first_name: Qin
full_name: Xue, Qin
last_name: Xue
- first_name: Tyra
full_name: McCray, Tyra
last_name: Mccray
- first_name: Gang
full_name: Li, Gang
last_name: Li
- first_name: Genji
full_name: Qin, Genji
last_name: Qin
- first_name: Michelle
full_name: Wakeley, Michelle
last_name: Wakeley
- first_name: William
full_name: Terzaghi, William
last_name: Terzaghi
- first_name: Jianmin
full_name: Wan, Jianmin
last_name: Wan
- first_name: Yunde
full_name: Zhao, Yunde
last_name: Zhao
- first_name: Jian
full_name: Xu, Jian
last_name: Xu
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Xing
full_name: Deng, Xing W
last_name: Deng
- first_name: Haiyang
full_name: Wang, Haiyang
last_name: Wang
citation:
ama: Dai M, Zhang C, Kania U, et al. A PP6 type phosphatase holoenzyme directly
regulates PIN phosphorylation and auxin efflux in Arabidopsis. Plant Cell.
2012;24(6):2497-2514. doi:10.1105/tpc.112.098905
apa: Dai, M., Zhang, C., Kania, U., Chen, F., Xue, Q., Mccray, T., … Wang, H. (2012).
A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin
efflux in Arabidopsis. Plant Cell. American Society of Plant Biologists.
https://doi.org/10.1105/tpc.112.098905
chicago: Dai, Mingqiu, Chen Zhang, Urszula Kania, Fang Chen, Qin Xue, Tyra Mccray,
Gang Li, et al. “A PP6 Type Phosphatase Holoenzyme Directly Regulates PIN Phosphorylation
and Auxin Efflux in Arabidopsis.” Plant Cell. American Society of Plant
Biologists, 2012. https://doi.org/10.1105/tpc.112.098905.
ieee: M. Dai et al., “A PP6 type phosphatase holoenzyme directly regulates
PIN phosphorylation and auxin efflux in Arabidopsis,” Plant Cell, vol.
24, no. 6. American Society of Plant Biologists, pp. 2497–2514, 2012.
ista: Dai M, Zhang C, Kania U, Chen F, Xue Q, Mccray T, Li G, Qin G, Wakeley M,
Terzaghi W, Wan J, Zhao Y, Xu J, Friml J, Deng X, Wang H. 2012. A PP6 type phosphatase
holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis.
Plant Cell. 24(6), 2497–2514.
mla: Dai, Mingqiu, et al. “A PP6 Type Phosphatase Holoenzyme Directly Regulates
PIN Phosphorylation and Auxin Efflux in Arabidopsis.” Plant Cell, vol.
24, no. 6, American Society of Plant Biologists, 2012, pp. 2497–514, doi:10.1105/tpc.112.098905.
short: M. Dai, C. Zhang, U. Kania, F. Chen, Q. Xue, T. Mccray, G. Li, G. Qin, M.
Wakeley, W. Terzaghi, J. Wan, Y. Zhao, J. Xu, J. Friml, X. Deng, H. Wang, Plant
Cell 24 (2012) 2497–2514.
date_created: 2018-12-11T12:01:27Z
date_published: 2012-06-01T00:00:00Z
date_updated: 2021-01-12T07:41:08Z
day: '01'
doi: 10.1105/tpc.112.098905
extern: 1
intvolume: ' 24'
issue: '6'
month: '06'
page: 2497 - 2514
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3589'
quality_controlled: 0
status: public
title: A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and
auxin efflux in Arabidopsis
type: journal_article
volume: 24
year: '2012'
...
---
_id: '3111'
abstract:
- lang: eng
text: PIN-FORMED (PIN) protein-mediated auxin polar transport is critically important
for development, pattern formation, and morphogenesis in plants. Auxin has been
implicated in the regulation of polar auxin transport by inhibiting PIN endocytosis
[1, 2], but how auxin regulates this process is poorly understood. Our genetic
screen identified the Arabidopsis SPIKE1 (SPK1) gene whose loss-of-function mutations
increased lateral root density and retarded gravitropic responses, as do pin2
knockout mutations [3]. SPK1 belongs to the conserved DHR2-Dock family of Rho
guanine nucleotide exchange factors [4-6]. The spk1 mutations induced PIN2 internalization
that was not suppressed by auxin, as did the loss-of-function mutations for Rho-like
GTPase from Plants 6 (ROP6)-GTPase or its effector RIC1. Furthermore, SPK1 was
required for auxin induction of ROP6 activation. Our results have established
a Rho GTPase-based auxin signaling pathway that maintains PIN2 polar distribution
to the plasma membrane via inhibition of its internalization in Arabidopsis roots.
Our findings provide new insights into signaling mechanisms that underlie the
regulation of the dynamic trafficking of PINs required for long-distance auxin
transport and that link auxin signaling to PIN-mediated pattern formation and
morphogenesis.
author:
- first_name: Deshu
full_name: Lin, Deshu
last_name: Lin
- first_name: Shingo
full_name: Nagawa, Shingo
last_name: Nagawa
- first_name: Jisheng
full_name: Chen, Jisheng
last_name: Chen
- first_name: Lingyan
full_name: Cao, Lingyan
last_name: Cao
- first_name: Xu
full_name: Xu Chen
id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Tongda
full_name: Xu, Tongda
last_name: Xu
- first_name: Hongjiang
full_name: Hongjiang Li
id: 33CA54A6-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0001-5039-9660
- first_name: Pankaj
full_name: Dhonukshe, Pankaj
last_name: Dhonukshe
- first_name: Chizuko
full_name: Yamamuro, Chizuko
last_name: Yamamuro
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Ben
full_name: Scheres, Ben
last_name: Scheres
- first_name: Ying
full_name: Fu, Ying
last_name: Fu
- first_name: Zhenbiao
full_name: Yang, Zhenbiao
last_name: Yang
citation:
ama: Lin D, Nagawa S, Chen J, et al. A ROP GTPase dependent auxin signaling pathway
regulates the subcellular distribution of PIN2 in Arabidopsis roots. Current
Biology. 2012;22(14):1319-1325. doi:10.1016/j.cub.2012.05.019
apa: Lin, D., Nagawa, S., Chen, J., Cao, L., Chen, X., Xu, T., … Yang, Z. (2012).
A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution
of PIN2 in Arabidopsis roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2012.05.019
chicago: Lin, Deshu, Shingo Nagawa, Jisheng Chen, Lingyan Cao, Xu Chen, Tongda Xu,
Hongjiang Li, et al. “A ROP GTPase Dependent Auxin Signaling Pathway Regulates
the Subcellular Distribution of PIN2 in Arabidopsis Roots.” Current Biology.
Cell Press, 2012. https://doi.org/10.1016/j.cub.2012.05.019.
ieee: D. Lin et al., “A ROP GTPase dependent auxin signaling pathway regulates
the subcellular distribution of PIN2 in Arabidopsis roots,” Current Biology,
vol. 22, no. 14. Cell Press, pp. 1319–1325, 2012.
ista: Lin D, Nagawa S, Chen J, Cao L, Chen X, Xu T, Li H, Dhonukshe P, Yamamuro
C, Friml J, Scheres B, Fu Y, Yang Z. 2012. A ROP GTPase dependent auxin signaling
pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots. Current
Biology. 22(14), 1319–1325.
mla: Lin, Deshu, et al. “A ROP GTPase Dependent Auxin Signaling Pathway Regulates
the Subcellular Distribution of PIN2 in Arabidopsis Roots.” Current Biology,
vol. 22, no. 14, Cell Press, 2012, pp. 1319–25, doi:10.1016/j.cub.2012.05.019.
short: D. Lin, S. Nagawa, J. Chen, L. Cao, X. Chen, T. Xu, H. Li, P. Dhonukshe,
C. Yamamuro, J. Friml, B. Scheres, Y. Fu, Z. Yang, Current Biology 22 (2012) 1319–1325.
date_created: 2018-12-11T12:01:27Z
date_published: 2012-07-24T00:00:00Z
date_updated: 2021-01-12T07:41:08Z
day: '24'
doi: 10.1016/j.cub.2012.05.019
extern: 1
intvolume: ' 22'
issue: '14'
month: '07'
page: 1319 - 1325
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '3588'
quality_controlled: 0
status: public
title: A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution
of PIN2 in Arabidopsis roots
type: journal_article
volume: 22
year: '2012'
...
---
_id: '3112'
abstract:
- lang: eng
text: The dynamic spatial and temporal distribution of the crucial plant signaling
molecule auxin is achieved by feedback coordination of auxin signaling and intercellular
auxin transport pathways [1, 2]. Developmental roles of auxin have been attributed
predominantly to its effect on transcription; however, an alternative pathway
involving AUXIN BINDING PROTEIN1 (ABP1) has been proposed to regulate clathrin-mediated
endocytosis in roots and Rho-like GTPase (ROP)-dependent pavement cell interdigitation
in leaves [3, 4]. In this study, we show that ROP6 and its downstream effector
RIC1 regulate clathrin association with the plasma membrane for clathrin-mediated
endocytosis, as well as for its feedback regulation by auxin. Genetic analysis
revealed that ROP6/RIC1 acts downstream of ABP1 to regulate endocytosis. This
signaling circuit is also involved in the feedback regulation of PIN-FORMED 1
(PIN1) and PIN2 auxin transporters activity (via its constitutive endocytosis)
and corresponding auxin transport-mediated processes, including root gravitropism
and leave vascular tissue patterning. Our findings suggest that the signaling
module auxin-ABP1-ROP6/RIC1-clathrin-PIN1/PIN2 is a shared component of the feedback
regulation of auxin transport during both root and aerial development.
author:
- first_name: Xu
full_name: Xu Chen
id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Ricardo
full_name: Tejos, Ricardo
last_name: Tejos
- first_name: Christian
full_name: Löfke, Christian
last_name: Löfke
- first_name: Deshu
full_name: Lin, Deshu
last_name: Lin
- first_name: Zhenbiao
full_name: Yang, Zhenbiao
last_name: Yang
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Chen X, Naramoto S, Robert S, et al. ABP1 and ROP6 GTPase signaling regulate
clathrin mediated endocytosis in Arabidopsis roots. Current Biology. 2012;22(14):1326-1332.
doi:10.1016/j.cub.2012.05.020
apa: Chen, X., Naramoto, S., Robert, S., Tejos, R., Löfke, C., Lin, D., … Friml,
J. (2012). ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis
in Arabidopsis roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2012.05.020
chicago: Chen, Xu, Satoshi Naramoto, Stéphanie Robert, Ricardo Tejos, Christian
Löfke, Deshu Lin, Zhenbiao Yang, and Jiří Friml. “ABP1 and ROP6 GTPase Signaling
Regulate Clathrin Mediated Endocytosis in Arabidopsis Roots.” Current Biology.
Cell Press, 2012. https://doi.org/10.1016/j.cub.2012.05.020.
ieee: X. Chen et al., “ABP1 and ROP6 GTPase signaling regulate clathrin mediated
endocytosis in Arabidopsis roots,” Current Biology, vol. 22, no. 14. Cell
Press, pp. 1326–1332, 2012.
ista: Chen X, Naramoto S, Robert S, Tejos R, Löfke C, Lin D, Yang Z, Friml J. 2012.
ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis
roots. Current Biology. 22(14), 1326–1332.
mla: Chen, Xu, et al. “ABP1 and ROP6 GTPase Signaling Regulate Clathrin Mediated
Endocytosis in Arabidopsis Roots.” Current Biology, vol. 22, no. 14, Cell
Press, 2012, pp. 1326–32, doi:10.1016/j.cub.2012.05.020.
short: X. Chen, S. Naramoto, S. Robert, R. Tejos, C. Löfke, D. Lin, Z. Yang, J.
Friml, Current Biology 22 (2012) 1326–1332.
date_created: 2018-12-11T12:01:27Z
date_published: 2012-07-24T00:00:00Z
date_updated: 2021-01-12T07:41:08Z
day: '24'
doi: 10.1016/j.cub.2012.05.020
extern: 1
intvolume: ' 22'
issue: '14'
month: '07'
page: 1326 - 1332
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '3587'
quality_controlled: 0
status: public
title: ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis
roots
type: journal_article
volume: 22
year: '2012'
...
---
_id: '3113'
abstract:
- lang: eng
text: A cell membrane can be considered a liquid-phase plane in which lipids and
proteins theoretically are free to diffuse. Numerous reports,however, describe
retarded diffusion ofmembrane proteins in animal cells. This anomalous diffusion
results from a combination of structuring factors including protein-protein interactions,
cytoskeleton corralling, and lipid organization into microdomains. In plant cells,
plasma-membrane (PM) proteins have been described as relatively immobile, but
the control mechanisms that structure the PM have not been studied. Here, we use
fluorescence recovery after photobleaching to estimate mobility of a set of minimal
PM proteins. These proteins consist only of a PM-anchoring domain fused to a fluorescent
protein, but their mobilities remained limited, as is the case for many full-length
proteins. Neither the cytoskeleton nor membrane microdomain structure was involved
in constraining the diffusion of these proteins. The cell wall, however, was shown
to have a crucial role in immobilizing PM proteins. In addition, by single-molecule
fluorescence imaging we confirmed that the pattern of cellulose deposition in
the cell wall affects the trajectory and speed ofPMprotein diffusion. Regulation
ofPMprotein dynamics by the plant cell wall can be interpreted as a mechanism
for regulating protein interactions in processes such as trafficking and signal
transduction.
author:
- first_name: Alexandre
full_name: Martinière, Alexandre
last_name: Martinière
- first_name: Irene
full_name: Lavagi, Irene
last_name: Lavagi
- first_name: Gayathri
full_name: Nageswaran, Gayathri
last_name: Nageswaran
- first_name: Daniel
full_name: Rolfe, Daniel J
last_name: Rolfe
- first_name: Lilly
full_name: Maneta-Peyret, Lilly
last_name: Maneta Peyret
- first_name: Doan
full_name: Luu, Doan-Trung
last_name: Luu
- first_name: Stanley
full_name: Botchway, Stanley W
last_name: Botchway
- first_name: Stephen
full_name: Webb, Stephen E
last_name: Webb
- first_name: Sebastien
full_name: Mongrand, Sebastien
last_name: Mongrand
- first_name: Christophe
full_name: Maurel, Christophe
last_name: Maurel
- first_name: Marisa
full_name: Martin-Fernandez, Marisa L
last_name: Martin Fernandez
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Patrick
full_name: Moreau, Patrick
last_name: Moreau
- first_name: John
full_name: Runions, John
last_name: Runions
citation:
ama: Martinière A, Lavagi I, Nageswaran G, et al. Cell wall constrains lateral diffusion
of plant plasma membrane proteins. PNAS. 2012;109(31):12805-12810. doi:10.1073/pnas.1202040109
apa: Martinière, A., Lavagi, I., Nageswaran, G., Rolfe, D., Maneta Peyret, L., Luu,
D., … Runions, J. (2012). Cell wall constrains lateral diffusion of plant plasma
membrane proteins. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1202040109
chicago: Martinière, Alexandre, Irene Lavagi, Gayathri Nageswaran, Daniel Rolfe,
Lilly Maneta Peyret, Doan Luu, Stanley Botchway, et al. “Cell Wall Constrains
Lateral Diffusion of Plant Plasma Membrane Proteins.” PNAS. National Academy
of Sciences, 2012. https://doi.org/10.1073/pnas.1202040109.
ieee: A. Martinière et al., “Cell wall constrains lateral diffusion of plant
plasma membrane proteins,” PNAS, vol. 109, no. 31. National Academy of
Sciences, pp. 12805–12810, 2012.
ista: Martinière A, Lavagi I, Nageswaran G, Rolfe D, Maneta Peyret L, Luu D, Botchway
S, Webb S, Mongrand S, Maurel C, Martin Fernandez M, Kleine Vehn J, Friml J, Moreau
P, Runions J. 2012. Cell wall constrains lateral diffusion of plant plasma membrane
proteins. PNAS. 109(31), 12805–12810.
mla: Martinière, Alexandre, et al. “Cell Wall Constrains Lateral Diffusion of Plant
Plasma Membrane Proteins.” PNAS, vol. 109, no. 31, National Academy of
Sciences, 2012, pp. 12805–10, doi:10.1073/pnas.1202040109.
short: A. Martinière, I. Lavagi, G. Nageswaran, D. Rolfe, L. Maneta Peyret, D. Luu,
S. Botchway, S. Webb, S. Mongrand, C. Maurel, M. Martin Fernandez, J. Kleine Vehn,
J. Friml, P. Moreau, J. Runions, PNAS 109 (2012) 12805–12810.
date_created: 2018-12-11T12:01:28Z
date_published: 2012-07-31T00:00:00Z
date_updated: 2021-01-12T07:41:09Z
day: '31'
doi: 10.1073/pnas.1202040109
extern: 1
intvolume: ' 109'
issue: '31'
month: '07'
page: 12805 - 12810
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3586'
quality_controlled: 0
status: public
title: Cell wall constrains lateral diffusion of plant plasma membrane proteins
type: journal_article
volume: 109
year: '2012'
...
---
_id: '3114'
abstract:
- lang: eng
text: Auxin is a key coordinative signal required for many aspects of plant development
and its levels are controlled by auxin metabolism and intercellular auxin transport.
Here we find that a member of PIN auxin transporter family, PIN8 is expressed
in male gametophyte of Arabidopsis thaliana and has a crucial role in pollen development
and functionality. Ectopic expression in sporophytic tissues establishes a role
of PIN8 in regulating auxin homoeostasis and metabolism. PIN8 co-localizes with
PIN5 to the endoplasmic reticulum (ER) where it acts as an auxin transporter.
Genetic analyses reveal an antagonistic action of PIN5 and PIN8 in the regulation
of intracellular auxin homoeostasis and gametophyte as well as sporophyte development.
Our results reveal a role of the auxin transport in male gametophyte development
in which the distinct actions of ER-localized PIN transporters regulate cellular
auxin homoeostasis and maintain the auxin levels optimal for pollen development
and pollen tube growth.
author:
- first_name: Zhaojun
full_name: Ding, Zhaojun
last_name: Ding
- first_name: Bangjun
full_name: Wang, Bangjun
last_name: Wang
- first_name: Ignacio
full_name: Moreno, Ignacio
last_name: Moreno
- first_name: Nikoleta
full_name: Dupláková, Nikoleta
last_name: Dupláková
- first_name: Sibu
full_name: Sibu Simon
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Nicola
full_name: Carraro, Nicola
last_name: Carraro
- first_name: Jesica
full_name: Reemmer, Jesica
last_name: Reemmer
- first_name: Aleš
full_name: Pěnčík, Aleš
last_name: Pěnčík
- first_name: Xu
full_name: Xu Chen
id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Ricardo
full_name: Tejos, Ricardo I
last_name: Tejos
- first_name: Petr
full_name: Skůpa, Petr
last_name: Skůpa
- first_name: Stephan
full_name: Pollmann, Stephan
last_name: Pollmann
- first_name: Jozef
full_name: Mravec, Jozef
last_name: Mravec
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: David
full_name: Honys, David
last_name: Honys
- first_name: Jakub
full_name: Rolčík, Jakub
last_name: Rolčík
- first_name: Angus
full_name: Murphy, Angus S
last_name: Murphy
- first_name: Ariel
full_name: Orellana, Ariel
last_name: Orellana
- first_name: Markus
full_name: Geisler, Markus
last_name: Geisler
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Ding Z, Wang B, Moreno I, et al. ER-localized auxin transporter PIN8 regulates
auxin homeostasis and male gametophyte development in Arabidopsis. Nature Communications.
2012;3(AN 941). doi:10.1038/ncomms1941
apa: Ding, Z., Wang, B., Moreno, I., Dupláková, N., Simon, S., Carraro, N., … Friml,
J. (2012). ER-localized auxin transporter PIN8 regulates auxin homeostasis and
male gametophyte development in Arabidopsis. Nature Communications. Nature
Publishing Group. https://doi.org/10.1038/ncomms1941
chicago: Ding, Zhaojun, Bangjun Wang, Ignacio Moreno, Nikoleta Dupláková, Sibu Simon,
Nicola Carraro, Jesica Reemmer, et al. “ER-Localized Auxin Transporter PIN8 Regulates
Auxin Homeostasis and Male Gametophyte Development in Arabidopsis.” Nature
Communications. Nature Publishing Group, 2012. https://doi.org/10.1038/ncomms1941.
ieee: Z. Ding et al., “ER-localized auxin transporter PIN8 regulates auxin
homeostasis and male gametophyte development in Arabidopsis,” Nature Communications,
vol. 3, no. AN 941. Nature Publishing Group, 2012.
ista: Ding Z, Wang B, Moreno I, Dupláková N, Simon S, Carraro N, Reemmer J, Pěnčík
A, Chen X, Tejos R, Skůpa P, Pollmann S, Mravec J, Petrášek J, Zažímalová E, Honys
D, Rolčík J, Murphy A, Orellana A, Geisler M, Friml J. 2012. ER-localized auxin
transporter PIN8 regulates auxin homeostasis and male gametophyte development
in Arabidopsis. Nature Communications. 3(AN 941).
mla: Ding, Zhaojun, et al. “ER-Localized Auxin Transporter PIN8 Regulates Auxin
Homeostasis and Male Gametophyte Development in Arabidopsis.” Nature Communications,
vol. 3, no. AN 941, Nature Publishing Group, 2012, doi:10.1038/ncomms1941.
short: Z. Ding, B. Wang, I. Moreno, N. Dupláková, S. Simon, N. Carraro, J. Reemmer,
A. Pěnčík, X. Chen, R. Tejos, P. Skůpa, S. Pollmann, J. Mravec, J. Petrášek, E.
Zažímalová, D. Honys, J. Rolčík, A. Murphy, A. Orellana, M. Geisler, J. Friml,
Nature Communications 3 (2012).
date_created: 2018-12-11T12:01:28Z
date_published: 2012-07-03T00:00:00Z
date_updated: 2021-01-12T07:41:09Z
day: '03'
doi: 10.1038/ncomms1941
extern: 1
intvolume: ' 3'
issue: AN 941
month: '07'
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '3585'
quality_controlled: 0
status: public
title: ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte
development in Arabidopsis
type: journal_article
volume: 3
year: '2012'
...
---
_id: '3115'
abstract:
- lang: eng
text: 'We consider the offset-deconstruction problem: Given a polygonal shape Q
with n vertices, can it be expressed, up to a tolerance ε in Hausdorff distance,
as the Minkowski sum of another polygonal shape P with a disk of fixed radius?
If it does, we also seek a preferably simple-looking solution P; then, P''s offset
constitutes an accurate, vertex-reduced, and smoothened approximation of Q. We
give an O(nlogn)-time exact decision algorithm that handles any polygonal shape,
assuming the real-RAM model of computation. A variant of the algorithm, which
we have implemented using the cgal library, is based on rational arithmetic and
answers the same deconstruction problem up to an uncertainty parameter δ its running
time additionally depends on δ. If the input shape is found to be approximable,
this algorithm also computes an approximate solution for the problem. It also
allows us to solve parameter-optimization problems induced by the offset-deconstruction
problem. For convex shapes, the complexity of the exact decision algorithm drops
to O(n), which is also the time required to compute a solution P with at most
one more vertex than a vertex-minimal one.'
acknowledgement: "We thank Eyal Flato (Plataine Ltd.) for raising the offset-deconstruction
problem in connection with wood cutting. We also thank Tim Bretl (UIUC) for suggesting
the digital-pen offset-deconstruction problem. This work has been supported in part
by the Israel Science Foundation (grant no. 1102/11), by the German–Israeli Foundation
(grant no. 969/07), by the Hermann Minkowski–Minerva Center for Geometry at Tel
Aviv University, and by the EU Project under Contract No. 255827 (CGL—Computational
Geometry Learning).\r\n"
arxiv: 1
author:
- first_name: Eric
full_name: Berberich, Eric
last_name: Berberich
- first_name: Dan
full_name: Halperin, Dan
last_name: Halperin
- first_name: Michael
full_name: Kerber, Michael
id: 36E4574A-F248-11E8-B48F-1D18A9856A87
last_name: Kerber
orcid: 0000-0002-8030-9299
- first_name: Roza
full_name: Pogalnikova, Roza
last_name: Pogalnikova
citation:
ama: Berberich E, Halperin D, Kerber M, Pogalnikova R. Deconstructing approximate
offsets. Discrete & Computational Geometry. 2012;48(4):964-989. doi:10.1007/s00454-012-9441-5
apa: Berberich, E., Halperin, D., Kerber, M., & Pogalnikova, R. (2012). Deconstructing
approximate offsets. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-012-9441-5
chicago: Berberich, Eric, Dan Halperin, Michael Kerber, and Roza Pogalnikova. “Deconstructing
Approximate Offsets.” Discrete & Computational Geometry. Springer,
2012. https://doi.org/10.1007/s00454-012-9441-5.
ieee: E. Berberich, D. Halperin, M. Kerber, and R. Pogalnikova, “Deconstructing
approximate offsets,” Discrete & Computational Geometry, vol. 48, no.
4. Springer, pp. 964–989, 2012.
ista: Berberich E, Halperin D, Kerber M, Pogalnikova R. 2012. Deconstructing approximate
offsets. Discrete & Computational Geometry. 48(4), 964–989.
mla: Berberich, Eric, et al. “Deconstructing Approximate Offsets.” Discrete &
Computational Geometry, vol. 48, no. 4, Springer, 2012, pp. 964–89, doi:10.1007/s00454-012-9441-5.
short: E. Berberich, D. Halperin, M. Kerber, R. Pogalnikova, Discrete & Computational
Geometry 48 (2012) 964–989.
date_created: 2018-12-11T12:01:28Z
date_published: 2012-12-01T00:00:00Z
date_updated: 2023-02-23T11:22:30Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/s00454-012-9441-5
external_id:
arxiv:
- '1109.2158'
intvolume: ' 48'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1109.2158
month: '12'
oa: 1
oa_version: Preprint
page: 964 - 989
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '3584'
quality_controlled: '1'
related_material:
record:
- id: '3329'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Deconstructing approximate offsets
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 48
year: '2012'
...
---
_id: '3117'
abstract:
- lang: eng
text: We consider the problem of minimizing a function represented as a sum of submodular
terms. We assume each term allows an efficient computation of exchange capacities.
This holds, for example, for terms depending on a small number of variables, or
for certain cardinality-dependent terms. A naive application of submodular minimization
algorithms would not exploit the existence of specialized exchange capacity subroutines
for individual terms. To overcome this, we cast the problem as a submodular flow
(SF) problem in an auxiliary graph in such a way that applying most existing SF
algorithms would rely only on these subroutines. We then explore in more detail
Iwata's capacity scaling approach for submodular flows (Iwata 1997 [19]). In particular,
we show how to improve its complexity in the case when the function contains cardinality-dependent
terms.
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: Kolmogorov V. Minimizing a sum of submodular functions. Discrete Applied
Mathematics. 2012;160(15):2246-2258. doi:10.1016/j.dam.2012.05.025
apa: Kolmogorov, V. (2012). Minimizing a sum of submodular functions. Discrete
Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2012.05.025
chicago: Kolmogorov, Vladimir. “Minimizing a Sum of Submodular Functions.” Discrete
Applied Mathematics. Elsevier, 2012. https://doi.org/10.1016/j.dam.2012.05.025.
ieee: V. Kolmogorov, “Minimizing a sum of submodular functions,” Discrete Applied
Mathematics, vol. 160, no. 15. Elsevier, pp. 2246–2258, 2012.
ista: Kolmogorov V. 2012. Minimizing a sum of submodular functions. Discrete Applied
Mathematics. 160(15), 2246–2258.
mla: Kolmogorov, Vladimir. “Minimizing a Sum of Submodular Functions.” Discrete
Applied Mathematics, vol. 160, no. 15, Elsevier, 2012, pp. 2246–58, doi:10.1016/j.dam.2012.05.025.
short: V. Kolmogorov, Discrete Applied Mathematics 160 (2012) 2246–2258.
date_created: 2018-12-11T12:01:29Z
date_published: 2012-10-01T00:00:00Z
date_updated: 2021-01-12T07:41:11Z
day: '01'
department:
- _id: VlKo
doi: 10.1016/j.dam.2012.05.025
intvolume: ' 160'
issue: '15'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1006.1990
month: '10'
oa: 1
oa_version: Preprint
page: 2246 - 2258
publication: Discrete Applied Mathematics
publication_status: published
publisher: Elsevier
publist_id: '3582'
quality_controlled: '1'
scopus_import: 1
status: public
title: Minimizing a sum of submodular functions
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 160
year: '2012'
...
---
_id: '3118'
abstract:
- lang: eng
text: We present a method for recovering a temporally coherent, deforming triangle
mesh with arbitrarily changing topology from an incoherent sequence of static
closed surfaces. We solve this problem using the surface geometry alone, without
any prior information like surface templates or velocity fields. Our system combines
a proven strategy for triangle mesh improvement, a robust multi-resolution non-rigid
registration routine, and a reliable technique for changing surface mesh topology.
We also introduce a novel topological constraint enforcement algorithm to ensure
that the output and input always have similar topology. We apply our technique
to a series of diverse input data from video reconstructions, physics simulations,
and artistic morphs. The structured output of our algorithm allows us to efficiently
track information like colors and displacement maps, recover velocity information,
and solve PDEs on the mesh as a post process.
acknowledgement: "This work is supported by the SNF fellowship PBEZP2-134464.\r\nWe
would like to thank Xiaochen Hu for implementing mesh con- version tools, Duygu
Ceylan for helping with the rendering, and Art Tevs for the human performance data
comparison. We also thank Nils Thuerey and Christopher Batty for helpful discussions. "
alternative_title:
- SIGGRAPH
article_number: '53'
article_processing_charge: No
article_type: original
author:
- first_name: Morten
full_name: Bojsen-Hansen, Morten
id: 439F0C8C-F248-11E8-B48F-1D18A9856A87
last_name: Bojsen-Hansen
orcid: 0000-0002-4417-3224
- first_name: Hao
full_name: Li, Hao
last_name: Li
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Bojsen-Hansen M, Li H, Wojtan C. Tracking surfaces with evolving topology.
ACM Transactions on Graphics. 2012;31(4). doi:10.1145/2185520.2185549
apa: Bojsen-Hansen, M., Li, H., & Wojtan, C. (2012). Tracking surfaces with
evolving topology. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2185520.2185549
chicago: Bojsen-Hansen, Morten, Hao Li, and Chris Wojtan. “Tracking Surfaces with
Evolving Topology.” ACM Transactions on Graphics. ACM, 2012. https://doi.org/10.1145/2185520.2185549.
ieee: M. Bojsen-Hansen, H. Li, and C. Wojtan, “Tracking surfaces with evolving topology,”
ACM Transactions on Graphics, vol. 31, no. 4. ACM, 2012.
ista: Bojsen-Hansen M, Li H, Wojtan C. 2012. Tracking surfaces with evolving topology.
ACM Transactions on Graphics. 31(4), 53.
mla: Bojsen-Hansen, Morten, et al. “Tracking Surfaces with Evolving Topology.” ACM
Transactions on Graphics, vol. 31, no. 4, 53, ACM, 2012, doi:10.1145/2185520.2185549.
short: M. Bojsen-Hansen, H. Li, C. Wojtan, ACM Transactions on Graphics 31 (2012).
date_created: 2018-12-11T12:01:29Z
date_published: 2012-07-01T00:00:00Z
date_updated: 2022-05-24T08:21:11Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2185520.2185549
file:
- access_level: open_access
checksum: 1e219c5bf4e5552c1290c62eefa5cd60
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:37Z
date_updated: 2020-07-14T12:46:00Z
file_id: '5359'
file_name: IST-2016-602-v1+1_topoReg.pdf
file_size: 44538518
relation: main_file
file_date_updated: 2020-07-14T12:46:00Z
has_accepted_license: '1'
intvolume: ' 31'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '3581'
pubrep_id: '602'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tracking surfaces with evolving topology
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2012'
...