---
_id: '3094'
abstract:
- lang: eng
text: Summary Gravitropism aligns plant growth with gravity. It involves gravity
perception and the asymmetric distribution of the phytohormone auxin. Here we
provide insights into the mechanism for hypocotyl gravitropic growth. We show
that the Arabidopsis thaliana PIN3 auxin transporter is required for the asymmetric
auxin distribution for the gravitropic response. Gravistimulation polarizes PIN3
to the bottom side of hypocotyl endodermal cells, which correlates with an increased
auxin response at the lower hypocotyl side. Both PIN3 polarization and hypocotyl
bending require the activity of the trafficking regulator GNOM and the protein
kinase PINOID. Our data suggest that gravity-induced PIN3 polarization diverts
the auxin flow to mediate the asymmetric distribution of auxin for gravitropic
shoot bending.
author:
- first_name: Hana
full_name: Rakusová, Hana
last_name: Rakusová
- first_name: Javier
full_name: Gallego-Bartolomé, Javier
last_name: Gallego Bartolomé
- first_name: Marleen
full_name: Vanstraelen, Marleen
last_name: Vanstraelen
- first_name: Hélène
full_name: Robert, Hélène S
last_name: Robert
- first_name: David
full_name: Alabadí, David
last_name: Alabadí
- first_name: Miguel
full_name: Blázquez, Miguel A
last_name: Blázquez
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Rakusová H, Gallego Bartolomé J, Vanstraelen M, et al. Polarization of PIN3
dependent auxin transport for hypocotyl gravitropic response in Arabidopsis thaliana.
Plant Journal. 2011;67(5):817-826. doi:10.1111/j.1365-313X.2011.04636.x
apa: Rakusová, H., Gallego Bartolomé, J., Vanstraelen, M., Robert, H., Alabadí,
D., Blázquez, M., … Friml, J. (2011). Polarization of PIN3 dependent auxin transport
for hypocotyl gravitropic response in Arabidopsis thaliana. Plant Journal.
Wiley-Blackwell. https://doi.org/10.1111/j.1365-313X.2011.04636.x
chicago: Rakusová, Hana, Javier Gallego Bartolomé, Marleen Vanstraelen, Hélène Robert,
David Alabadí, Miguel Blázquez, Eva Benková, and Jiří Friml. “Polarization of
PIN3 Dependent Auxin Transport for Hypocotyl Gravitropic Response in Arabidopsis
Thaliana.” Plant Journal. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1365-313X.2011.04636.x.
ieee: H. Rakusová et al., “Polarization of PIN3 dependent auxin transport
for hypocotyl gravitropic response in Arabidopsis thaliana,” Plant Journal,
vol. 67, no. 5. Wiley-Blackwell, pp. 817–826, 2011.
ista: Rakusová H, Gallego Bartolomé J, Vanstraelen M, Robert H, Alabadí D, Blázquez
M, Benková E, Friml J. 2011. Polarization of PIN3 dependent auxin transport for
hypocotyl gravitropic response in Arabidopsis thaliana. Plant Journal. 67(5),
817–826.
mla: Rakusová, Hana, et al. “Polarization of PIN3 Dependent Auxin Transport for
Hypocotyl Gravitropic Response in Arabidopsis Thaliana.” Plant Journal,
vol. 67, no. 5, Wiley-Blackwell, 2011, pp. 817–26, doi:10.1111/j.1365-313X.2011.04636.x.
short: H. Rakusová, J. Gallego Bartolomé, M. Vanstraelen, H. Robert, D. Alabadí,
M. Blázquez, E. Benková, J. Friml, Plant Journal 67 (2011) 817–826.
date_created: 2018-12-11T12:01:21Z
date_published: 2011-09-01T00:00:00Z
date_updated: 2021-01-12T07:41:01Z
day: '01'
doi: 10.1111/j.1365-313X.2011.04636.x
extern: 1
intvolume: ' 67'
issue: '5'
month: '09'
page: 817 - 826
publication: Plant Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3606'
quality_controlled: 0
status: public
title: Polarization of PIN3 dependent auxin transport for hypocotyl gravitropic response
in Arabidopsis thaliana
type: journal_article
volume: 67
year: '2011'
...
---
_id: '3095'
abstract:
- lang: eng
text: Root system architecture depends on lateral root (LR) initiation that takes
place in a relatively narrow developmental window (DW). Here, we analyzed the
role of auxin gradients established along the parent root in defining this DW
for LR initiation. Correlations between auxin distribution and response, and spatiotemporal
control of LR initiation were analyzed in Arabidopsis thaliana and tomato (Solanum
lycopersicum). In both Arabidopsis and tomato roots, a well defined zone, where
auxin content and response are minimal, demarcates the position of a DW for founder
cell specification and LR initiation. We show that in the zone of auxin minimum
pericycle cells have highest probability to become founder cells and that auxin
perception via the TIR1/AFB pathway, and polar auxin transport, are essential
for the establishment of this zone. Altogether, this study reveals that the same
morphogen-like molecule, auxin, can act simultaneously as a morphogenetic trigger
of LR founder cell identity and as a gradient-dependent signal defining positioning
of the founder cell specification. This auxin minimum zone might represent an
important control mechanism ensuring the LR initiation steadiness and the acropetal
LR initiation pattern. © 2011 The Authors. New Phytologist © 2011 New Phytologist
Trust.
author:
- first_name: Joseph
full_name: Dubrovsky, Joseph G
last_name: Dubrovsky
- first_name: Selene
full_name: Napsucialy-Mendivil, Selene
last_name: Napsucialy Mendivil
- first_name: Jérôme
full_name: Duclercq, Jérôme
last_name: Duclercq
- first_name: Yan
full_name: Cheng, Yan
last_name: Cheng
- first_name: Svetlana
full_name: Shishkova, Svetlana O
last_name: Shishkova
- first_name: Maria
full_name: Ivanchenko, Maria G
last_name: Ivanchenko
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Angus
full_name: Murphy, Angus S
last_name: Murphy
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Dubrovsky J, Napsucialy Mendivil S, Duclercq J, et al. Auxin minimum defines
a developmental window for lateral root initiation. New Phytologist. 2011;191(4):970-983.
doi: 10.1111/j.1469-8137.2011.03757.x
apa: Dubrovsky, J., Napsucialy Mendivil, S., Duclercq, J., Cheng, Y., Shishkova,
S., Ivanchenko, M., … Benková, E. (2011). Auxin minimum defines a developmental
window for lateral root initiation. New Phytologist. Wiley-Blackwell. https://doi.org/ 10.1111/j.1469-8137.2011.03757.x
chicago: Dubrovsky, Joseph, Selene Napsucialy Mendivil, Jérôme Duclercq, Yan Cheng,
Svetlana Shishkova, Maria Ivanchenko, Jiří Friml, Angus Murphy, and Eva Benková.
“Auxin Minimum Defines a Developmental Window for Lateral Root Initiation.” New
Phytologist. Wiley-Blackwell, 2011. https://doi.org/
10.1111/j.1469-8137.2011.03757.x.
ieee: J. Dubrovsky et al., “Auxin minimum defines a developmental window
for lateral root initiation,” New Phytologist, vol. 191, no. 4. Wiley-Blackwell,
pp. 970–983, 2011.
ista: Dubrovsky J, Napsucialy Mendivil S, Duclercq J, Cheng Y, Shishkova S, Ivanchenko
M, Friml J, Murphy A, Benková E. 2011. Auxin minimum defines a developmental window
for lateral root initiation. New Phytologist. 191(4), 970–983.
mla: Dubrovsky, Joseph, et al. “Auxin Minimum Defines a Developmental Window for
Lateral Root Initiation.” New Phytologist, vol. 191, no. 4, Wiley-Blackwell,
2011, pp. 970–83, doi:
10.1111/j.1469-8137.2011.03757.x.
short: J. Dubrovsky, S. Napsucialy Mendivil, J. Duclercq, Y. Cheng, S. Shishkova,
M. Ivanchenko, J. Friml, A. Murphy, E. Benková, New Phytologist 191 (2011) 970–983.
date_created: 2018-12-11T12:01:21Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:41:01Z
day: '01'
doi: ' 10.1111/j.1469-8137.2011.03757.x'
extern: 1
intvolume: ' 191'
issue: '4'
month: '01'
page: 970 - 983
publication: New Phytologist
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3605'
quality_controlled: 0
status: public
title: Auxin minimum defines a developmental window for lateral root initiation
type: journal_article
volume: 191
year: '2011'
...
---
_id: '3096'
abstract:
- lang: eng
text: Carrier-dependent, intercellular auxin transport is central to the developmental
patterning of higher plants (tracheophytes). The evolution of this polar auxin
transport might be linked to the translocation of some PIN auxin efflux carriers
from their presumably ancestral localization at the endoplasmic reticulum (ER)
to the polar domains at the plasma membrane. Here we propose an eventually ancient
mechanism of intercellular auxin distribution by ER-localized auxin transporters
involving intracellular auxin retention and switch-like release from the ER. The
proposed model integrates feedback circuits utilizing the conserved nuclear auxin
signaling for the regulation of PIN transcription and a hypothetical ER-based
signaling for the regulation of PIN-dependent transport activity at the ER. Computer
simulations of the model revealed its plausibility for generating auxin channels
and localized auxin maxima highlighting the possibility of this alternative mechanism
for polar auxin transport.
author:
- first_name: Krzysztof T
full_name: Wabnik, Krzysztof T
id: 4DE369A4-F248-11E8-B48F-1D18A9856A87
last_name: Wabnik
orcid: 0000-0001-7263-0560
- first_name: Jürgen
full_name: Kleine Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Willy
full_name: Govaerts, Willy
last_name: Govaerts
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Wabnik KT, Kleine Vehn J, Govaerts W, Friml J. Prototype cell-to-cell auxin
transport mechanism by intracellular auxin compartmentalization. Trends in
Plant Science. 2011;16(9):468-475. doi:10.1016/j.tplants.2011.05.002
apa: Wabnik, K. T., Kleine Vehn, J., Govaerts, W., & Friml, J. (2011). Prototype
cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization.
Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2011.05.002
chicago: Wabnik, Krzysztof T, Jürgen Kleine Vehn, Willy Govaerts, and Jiří Friml.
“Prototype Cell-to-Cell Auxin Transport Mechanism by Intracellular Auxin Compartmentalization.”
Trends in Plant Science. Cell Press, 2011. https://doi.org/10.1016/j.tplants.2011.05.002.
ieee: K. T. Wabnik, J. Kleine Vehn, W. Govaerts, and J. Friml, “Prototype cell-to-cell
auxin transport mechanism by intracellular auxin compartmentalization,” Trends
in Plant Science, vol. 16, no. 9. Cell Press, pp. 468–475, 2011.
ista: Wabnik KT, Kleine Vehn J, Govaerts W, Friml J. 2011. Prototype cell-to-cell
auxin transport mechanism by intracellular auxin compartmentalization. Trends
in Plant Science. 16(9), 468–475.
mla: Wabnik, Krzysztof T., et al. “Prototype Cell-to-Cell Auxin Transport Mechanism
by Intracellular Auxin Compartmentalization.” Trends in Plant Science,
vol. 16, no. 9, Cell Press, 2011, pp. 468–75, doi:10.1016/j.tplants.2011.05.002.
short: K.T. Wabnik, J. Kleine Vehn, W. Govaerts, J. Friml, Trends in Plant Science
16 (2011) 468–475.
date_created: 2018-12-11T12:01:21Z
date_published: 2011-09-01T00:00:00Z
date_updated: 2021-01-12T07:41:01Z
day: '01'
doi: 10.1016/j.tplants.2011.05.002
extern: '1'
intvolume: ' 16'
issue: '9'
language:
- iso: eng
month: '09'
oa_version: None
page: 468 - 475
publication: Trends in Plant Science
publication_status: published
publisher: Cell Press
publist_id: '3604'
quality_controlled: '1'
status: public
title: Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2011'
...
---
_id: '3097'
abstract:
- lang: eng
text: Cytokinin is an important regulator of plant growth and development. In Arabidopsis
thaliana, the two-component phosphorelay mediated through a family of histidine
kinases and response regulators is recognized as the principal cytokinin signal
transduction mechanism activating the complex transcriptional response to control
various developmental processes. Here, we identified an alternative mode of cytokinin
action that uses endocytic trafficking as a means to direct plant organogenesis.
This activity occurs downstream of known cytokinin receptors but through a branch
of the cytokinin signaling pathway that does not involve transcriptional regulation.
We show that cytokinin regulates endocytic recycling of the auxin efflux carrier
PINFORMED1 (PIN1) by redirecting it for lytic degradation in vacuoles. Stimulation
of the lytic PIN1 degradation is not a default effect for general downregulation
of proteins from plasma membranes, but a specific mechanism to rapidly modulate
the auxin distribution in cytokinin-mediated developmental processes.
author:
- first_name: Peter
full_name: Peter Marhavy
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Agnieszka
full_name: Bielach, Agnieszka
last_name: Bielach
- first_name: Lindy
full_name: Abas, Lindy
last_name: Abas
- first_name: Anas
full_name: Abuzeineh, Anas
last_name: Abuzeineh
- first_name: Jérôme
full_name: Duclercq, Jérôme
last_name: Duclercq
- first_name: Hirokazu
full_name: Tanaka, Hirokazu
last_name: Tanaka
- first_name: Markéta
full_name: Pařezová, Markéta
last_name: Pařezová
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- 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
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Marhavý P, Bielach A, Abas L, et al. Cytokinin modulates endocytic trafficking
of PIN1 auxin efflux carrier to control plant organogenesis. Developmental
Cell. 2011;21(4):796-804. doi:10.1016/j.devcel.2011.08.014
apa: Marhavý, P., Bielach, A., Abas, L., Abuzeineh, A., Duclercq, J., Tanaka, H.,
… Benková, E. (2011). Cytokinin modulates endocytic trafficking of PIN1 auxin
efflux carrier to control plant organogenesis. Developmental Cell. Cell
Press. https://doi.org/10.1016/j.devcel.2011.08.014
chicago: Marhavý, Peter, Agnieszka Bielach, Lindy Abas, Anas Abuzeineh, Jérôme Duclercq,
Hirokazu Tanaka, Markéta Pařezová, et al. “Cytokinin Modulates Endocytic Trafficking
of PIN1 Auxin Efflux Carrier to Control Plant Organogenesis.” Developmental
Cell. Cell Press, 2011. https://doi.org/10.1016/j.devcel.2011.08.014.
ieee: P. Marhavý et al., “Cytokinin modulates endocytic trafficking of PIN1
auxin efflux carrier to control plant organogenesis,” Developmental Cell,
vol. 21, no. 4. Cell Press, pp. 796–804, 2011.
ista: Marhavý P, Bielach A, Abas L, Abuzeineh A, Duclercq J, Tanaka H, Pařezová
M, Petrášek J, Friml J, Kleine Vehn J, Benková E. 2011. Cytokinin modulates endocytic
trafficking of PIN1 auxin efflux carrier to control plant organogenesis. Developmental
Cell. 21(4), 796–804.
mla: Marhavý, Peter, et al. “Cytokinin Modulates Endocytic Trafficking of PIN1 Auxin
Efflux Carrier to Control Plant Organogenesis.” Developmental Cell, vol.
21, no. 4, Cell Press, 2011, pp. 796–804, doi:10.1016/j.devcel.2011.08.014.
short: P. Marhavý, A. Bielach, L. Abas, A. Abuzeineh, J. Duclercq, H. Tanaka, M.
Pařezová, J. Petrášek, J. Friml, J. Kleine Vehn, E. Benková, Developmental Cell
21 (2011) 796–804.
date_created: 2018-12-11T12:01:22Z
date_published: 2011-10-18T00:00:00Z
date_updated: 2021-01-12T07:41:02Z
day: '18'
doi: 10.1016/j.devcel.2011.08.014
extern: 1
intvolume: ' 21'
issue: '4'
month: '10'
page: 796 - 804
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '3603'
quality_controlled: 0
status: public
title: Cytokinin modulates endocytic trafficking of PIN1 auxin efflux carrier to control
plant organogenesis
type: journal_article
volume: 21
year: '2011'
...
---
_id: '3098'
abstract:
- lang: eng
text: Cell polarity reflected by asymmetric distribution of proteins at the plasma
membrane is a fundamental feature of unicellular and multicellular organisms.
It remains conceptually unclear how cell polarity is kept in cell wall-encapsulated
plant cells. We have used super-resolution and semi-quantitative live-cell imaging
in combination with pharmacological, genetic, and computational approaches to
reveal insights into the mechanism of cell polarity maintenance in Arabidopsis
thaliana. We show that polar-competent PIN transporters for the phytohormone auxin
are delivered to the center of polar domains by super-polar recycling. Within
the plasma membrane, PINs are recruited into non-mobile membrane clusters and
their lateral diffusion is dramatically reduced, which ensures longer polar retention.
At the circumventing edges of the polar domain, spatially defined internalization
of escaped cargos occurs by clathrin-dependent endocytosis. Computer simulations
confirm that the combination of these processes provides a robust mechanism for
polarity maintenance in plant cells. Moreover, our study suggests that the regulation
of lateral diffusion and spatially defined endocytosis, but not super-polar exocytosis
have primary importance for PIN polarity maintenance.
author:
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Krzysztof T
full_name: Krzysztof Wabnik
id: 4DE369A4-F248-11E8-B48F-1D18A9856A87
last_name: Wabnik
orcid: 0000-0001-7263-0560
- first_name: Alexandre
full_name: Martinière, Alexandre
last_name: Martinière
- first_name: Łukasz
full_name: Łangowski, Łukasz
last_name: Łangowski
- first_name: Katrin
full_name: Willig, Katrin
last_name: Willig
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Johannes
full_name: Leitner, Johannes
last_name: Leitner
- first_name: Hirokazu
full_name: Tanaka, Hirokazu
last_name: Tanaka
- first_name: Stefan
full_name: Jakobs, Stefan
last_name: Jakobs
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Christian
full_name: Luschnig, Christian
last_name: Luschnig
- first_name: Willy
full_name: Govaerts, Willy J
last_name: Govaerts
- first_name: Stefan
full_name: Hell, Stefan W
last_name: Hell
- first_name: John
full_name: Runions, John
last_name: Runions
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Kleine Vehn J, Wabnik KT, Martinière A, et al. Recycling, clustering and endocytosis
jointly maintain PIN auxin carrier polarity at the plasma membrane. Molecular
Systems Biology. 2011;7. doi:10.1038/msb.2011.72
apa: Kleine Vehn, J., Wabnik, K. T., Martinière, A., Łangowski, Ł., Willig, K.,
Naramoto, S., … Friml, J. (2011). Recycling, clustering and endocytosis jointly
maintain PIN auxin carrier polarity at the plasma membrane. Molecular Systems
Biology. Nature Publishing Group. https://doi.org/10.1038/msb.2011.72
chicago: Kleine Vehn, Jürgen, Krzysztof T Wabnik, Alexandre Martinière, Łukasz Łangowski,
Katrin Willig, Satoshi Naramoto, Johannes Leitner, et al. “Recycling, Clustering
and Endocytosis Jointly Maintain PIN Auxin Carrier Polarity at the Plasma Membrane.”
Molecular Systems Biology. Nature Publishing Group, 2011. https://doi.org/10.1038/msb.2011.72.
ieee: J. Kleine Vehn et al., “Recycling, clustering and endocytosis jointly
maintain PIN auxin carrier polarity at the plasma membrane,” Molecular Systems
Biology, vol. 7. Nature Publishing Group, 2011.
ista: Kleine Vehn J, Wabnik KT, Martinière A, Łangowski Ł, Willig K, Naramoto S,
Leitner J, Tanaka H, Jakobs S, Robert S, Luschnig C, Govaerts W, Hell S, Runions
J, Friml J. 2011. Recycling, clustering and endocytosis jointly maintain PIN auxin
carrier polarity at the plasma membrane. Molecular Systems Biology. 7.
mla: Kleine Vehn, Jürgen, et al. “Recycling, Clustering and Endocytosis Jointly
Maintain PIN Auxin Carrier Polarity at the Plasma Membrane.” Molecular Systems
Biology, vol. 7, Nature Publishing Group, 2011, doi:10.1038/msb.2011.72.
short: J. Kleine Vehn, K.T. Wabnik, A. Martinière, Ł. Łangowski, K. Willig, S. Naramoto,
J. Leitner, H. Tanaka, S. Jakobs, S. Robert, C. Luschnig, W. Govaerts, S. Hell,
J. Runions, J. Friml, Molecular Systems Biology 7 (2011).
date_created: 2018-12-11T12:01:22Z
date_published: 2011-10-25T00:00:00Z
date_updated: 2021-01-12T07:41:02Z
day: '25'
doi: 10.1038/msb.2011.72
extern: 1
intvolume: ' 7'
month: '10'
publication: Molecular Systems Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '3601'
quality_controlled: 0
status: public
title: Recycling, clustering and endocytosis jointly maintain PIN auxin carrier polarity
at the plasma membrane
type: journal_article
volume: 7
year: '2011'
...
---
_id: '3099'
abstract:
- lang: eng
text: Endomembrane trafficking relies on the coordination of a highly complex, dynamic
network of intracellular vesicles. Understanding the network will require a dissection
of cargo and vesicle dynamics at the cellular level in vivo. This is also a key
to establishing a link between vesicular networks and their functional roles in
development. We used a high-content intracellular screen to discover small molecules
targeting endomembrane trafficking in vivo in a complex eukaryote, Arabidopsis
thaliana. Tens of thousands of molecules were prescreened and a selected subset
was interrogated against a panel of plasma membrane (PM) and other endomembrane
compartment markers to identify molecules that altered vesicle trafficking. The
extensive image dataset was transformed by a flexible algorithm into a marker-by-phenotype-by-treatment
time matrix and revealed groups of molecules that induced similar subcellular
fingerprints (clusters). This matrix provides a platform for a systems view of
trafficking. Molecules from distinct clusters presented avenues and enabled an
entry point to dissect recycling at the PM, vacuolar sorting, and cell-plate maturation.
Bioactivity in human cells indicated the value of the approach to identifying
small molecules that are active in diverse organisms for biology and drug discovery.
author:
- first_name: Georgia
full_name: Drakakaki, Georgia
last_name: Drakakaki
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Anna
full_name: Szatmári, Anna-Maria
last_name: Szatmári
- first_name: Michelle
full_name: Brown, Michelle Q
last_name: Brown
- first_name: Shingo
full_name: Nagawa, Shingo
last_name: Nagawa
- first_name: Daniël
full_name: Van Damme, Daniël
last_name: Van Damme
- first_name: Marylin
full_name: Leonard, Marylin
last_name: Leonard
- first_name: Zhenbiao
full_name: Yang, Zhenbiao
last_name: Yang
- first_name: Thomas
full_name: Girke, Thomas
last_name: Girke
- first_name: Sandra
full_name: Schmid, Sandra L
last_name: Schmid
- first_name: Eugenia
full_name: Russinova, Eugenia
last_name: Russinova
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Natasha
full_name: Raikhel, Natasha V
last_name: Raikhel
- first_name: Glen
full_name: Hicks, Glen R
last_name: Hicks
citation:
ama: Drakakaki G, Robert S, Szatmári A, et al. Clusters of bioactive compounds target
dynamic endomembrane networks in vivo. PNAS. 2011;108(43):17850-17855.
doi:10.1073/pnas.1108581108
apa: Drakakaki, G., Robert, S., Szatmári, A., Brown, M., Nagawa, S., Van Damme,
D., … Hicks, G. (2011). Clusters of bioactive compounds target dynamic endomembrane
networks in vivo. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1108581108
chicago: Drakakaki, Georgia, Stéphanie Robert, Anna Szatmári, Michelle Brown, Shingo
Nagawa, Daniël Van Damme, Marylin Leonard, et al. “Clusters of Bioactive Compounds
Target Dynamic Endomembrane Networks in Vivo.” PNAS. National Academy of
Sciences, 2011. https://doi.org/10.1073/pnas.1108581108.
ieee: G. Drakakaki et al., “Clusters of bioactive compounds target dynamic
endomembrane networks in vivo,” PNAS, vol. 108, no. 43. National Academy
of Sciences, pp. 17850–17855, 2011.
ista: Drakakaki G, Robert S, Szatmári A, Brown M, Nagawa S, Van Damme D, Leonard
M, Yang Z, Girke T, Schmid S, Russinova E, Friml J, Raikhel N, Hicks G. 2011.
Clusters of bioactive compounds target dynamic endomembrane networks in vivo.
PNAS. 108(43), 17850–17855.
mla: Drakakaki, Georgia, et al. “Clusters of Bioactive Compounds Target Dynamic
Endomembrane Networks in Vivo.” PNAS, vol. 108, no. 43, National Academy
of Sciences, 2011, pp. 17850–55, doi:10.1073/pnas.1108581108.
short: G. Drakakaki, S. Robert, A. Szatmári, M. Brown, S. Nagawa, D. Van Damme,
M. Leonard, Z. Yang, T. Girke, S. Schmid, E. Russinova, J. Friml, N. Raikhel,
G. Hicks, PNAS 108 (2011) 17850–17855.
date_created: 2018-12-11T12:01:23Z
date_published: 2011-10-25T00:00:00Z
date_updated: 2021-01-12T07:41:02Z
day: '25'
doi: 10.1073/pnas.1108581108
extern: 1
intvolume: ' 108'
issue: '43'
month: '10'
page: 17850 - 17855
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3602'
quality_controlled: 0
status: public
title: Clusters of bioactive compounds target dynamic endomembrane networks in vivo
type: journal_article
volume: 108
year: '2011'
...
---
_id: '3100'
abstract:
- lang: eng
text: In multicellular organisms, morphogenesis relies on a strict coordination
in time and space of cell proliferation and differentiation. In contrast to animals,
plant development displays continuous organ formation and adaptive growth responses
during their lifespan relying on a tight coordination of cell proliferation. How
developmental signals interact with the plant cell-cycle machinery is largely
unknown. Here, we characterize plant A2-type cyclins, a small gene family of mitotic
cyclins, and show how they contribute to the fine-tuning of local proliferation
during plant development. Moreover, the timely repression of CYCA2;3 expression
in newly formed guard cells is shown to require the stomatal transcription factors
FOUR LIPS/MYB124 and MYB88, providing a direct link between developmental programming
and cell-cycle exit in plants. Thus, transcriptional downregulation of CYCA2s
represents a critical mechanism to coordinate proliferation during plant development.
author:
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Frederik
full_name: Coppens, Frederik
last_name: Coppens
- first_name: Eunkyoung
full_name: Lee, EunKyoung
last_name: Lee
- first_name: Tyler
full_name: Donner, Tyler J
last_name: Donner
- first_name: Zidian
full_name: Xie, Zidian
last_name: Xie
- first_name: Gert
full_name: Van Isterdael, Gert
last_name: Van Isterdael
- first_name: Stijn
full_name: Dhondt, Stijn
last_name: Dhondt
- first_name: Freya
full_name: De Winter, Freya
last_name: De Winter
- first_name: Bert
full_name: De Rybel, Bert
last_name: De Rybel
- first_name: Marnik
full_name: Vuylsteke, Marnik
last_name: Vuylsteke
- first_name: Lieven
full_name: De Veylder, Lieven
last_name: De Veylder
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Dirk
full_name: Inzé, Dirk
last_name: Inzé
- first_name: Erich
full_name: Grotewold, Erich
last_name: Grotewold
- first_name: Enrico
full_name: Scarpella, Enrico
last_name: Scarpella
- first_name: Fred
full_name: Sack, Fred
last_name: Sack
- first_name: Gerrit
full_name: Beemster, Gerrit T
last_name: Beemster
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
citation:
ama: Vanneste S, Coppens F, Lee E, et al. Developmental regulation of CYCA2s contributes
to tissue-specific proliferation in Arabidopsis . EMBO Journal. 2011;30(16):3430-3441.
doi:10.1038/emboj.2011.240
apa: Vanneste, S., Coppens, F., Lee, E., Donner, T., Xie, Z., Van Isterdael, G.,
… Beeckman, T. (2011). Developmental regulation of CYCA2s contributes to tissue-specific
proliferation in Arabidopsis . EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2011.240
chicago: Vanneste, Steffen, Frederik Coppens, Eunkyoung Lee, Tyler Donner, Zidian
Xie, Gert Van Isterdael, Stijn Dhondt, et al. “Developmental Regulation of CYCA2s
Contributes to Tissue-Specific Proliferation in Arabidopsis .” EMBO Journal.
Wiley-Blackwell, 2011. https://doi.org/10.1038/emboj.2011.240.
ieee: S. Vanneste et al., “Developmental regulation of CYCA2s contributes
to tissue-specific proliferation in Arabidopsis ,” EMBO Journal, vol. 30,
no. 16. Wiley-Blackwell, pp. 3430–3441, 2011.
ista: Vanneste S, Coppens F, Lee E, Donner T, Xie Z, Van Isterdael G, Dhondt S,
De Winter F, De Rybel B, Vuylsteke M, De Veylder L, Friml J, Inzé D, Grotewold
E, Scarpella E, Sack F, Beemster G, Beeckman T. 2011. Developmental regulation
of CYCA2s contributes to tissue-specific proliferation in Arabidopsis . EMBO Journal.
30(16), 3430–3441.
mla: Vanneste, Steffen, et al. “Developmental Regulation of CYCA2s Contributes to
Tissue-Specific Proliferation in Arabidopsis .” EMBO Journal, vol. 30,
no. 16, Wiley-Blackwell, 2011, pp. 3430–41, doi:10.1038/emboj.2011.240.
short: S. Vanneste, F. Coppens, E. Lee, T. Donner, Z. Xie, G. Van Isterdael, S.
Dhondt, F. De Winter, B. De Rybel, M. Vuylsteke, L. De Veylder, J. Friml, D. Inzé,
E. Grotewold, E. Scarpella, F. Sack, G. Beemster, T. Beeckman, EMBO Journal 30
(2011) 3430–3441.
date_created: 2018-12-11T12:01:23Z
date_published: 2011-08-17T00:00:00Z
date_updated: 2021-01-12T07:41:04Z
day: '17'
doi: 10.1038/emboj.2011.240
extern: 1
intvolume: ' 30'
issue: '16'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3160660/
month: '08'
oa: 1
page: 3430 - 3441
publication: EMBO Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3600'
quality_controlled: 0
status: public
title: 'Developmental regulation of CYCA2s contributes to tissue-specific proliferation
in Arabidopsis '
type: journal_article
volume: 30
year: '2011'
...
---
_id: '3101'
abstract:
- lang: eng
text: Subcellular trafficking is required for a multitude of functions in eukaryotic
cells. It involves regulation of cargo sorting, vesicle formation, trafficking
and fusion processes at multiple levels. Adaptor protein (AP) complexes are key
regulators of cargo sorting into vesicles in yeast and mammals but their existence
and function in plants have not been demonstrated. Here we report the identification
of the protein-affected trafficking 4 (pat4) mutant defective in the putative
δ subunit of the AP-3 complex. pat4 and pat2, a mutant isolated from the same
GFP imaging-based forward genetic screen that lacks a functional putative AP-3
β, as well as dominant negative AP-3 μ transgenic lines display undistinguishable
phenotypes characterized by largely normal morphology and development, but strong
intracellular accumulation of membrane proteins in aberrant vacuolar structures.
All mutants are defective in morphology and function of lytic and protein storage
vacuoles (PSVs) but show normal sorting of reserve proteins to PSVs. Immunoprecipitation
experiments and genetic studies revealed tight functional and physical associations
of putative AP-3 β and AP-3 δ subunits. Furthermore, both proteins are closely
linked with putative AP-3 μ and σ subunits and several components of the clathrin
and dynamin machineries. Taken together, these results demonstrate that AP complexes,
similar to those in other eukaryotes, exist in plants, and that AP-3 plays a specific
role in the regulation of biogenesis and function of vacuoles in plant cells.
© 2011 IBCB, SIBS, CAS All rights reserved
author:
- first_name: Marta
full_name: Zwiewka, Marta
last_name: Zwiewka
- first_name: Elena
full_name: Feraru, Elena
last_name: Feraru
- first_name: Barbara
full_name: Möller, Barbara
last_name: Möller
- first_name: Inhwan
full_name: Hwang, Inhwan
last_name: Hwang
- first_name: Mugurel
full_name: Feraru, Mugurel I
last_name: Feraru
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Zwiewka M, Feraru E, Möller B, et al. The AP 3 adaptor complex is required
for vacuolar function in Arabidopsis. Cell Research. 2011;21(12):1711-1722.
doi:10.1038/cr.2011.99
apa: Zwiewka, M., Feraru, E., Möller, B., Hwang, I., Feraru, M., Kleine Vehn, J.,
… Friml, J. (2011). The AP 3 adaptor complex is required for vacuolar function
in Arabidopsis. Cell Research. Nature Publishing Group. https://doi.org/10.1038/cr.2011.99
chicago: Zwiewka, Marta, Elena Feraru, Barbara Möller, Inhwan Hwang, Mugurel Feraru,
Jürgen Kleine Vehn, Dolf Weijers, and Jiří Friml. “The AP 3 Adaptor Complex Is
Required for Vacuolar Function in Arabidopsis.” Cell Research. Nature Publishing
Group, 2011. https://doi.org/10.1038/cr.2011.99.
ieee: M. Zwiewka et al., “The AP 3 adaptor complex is required for vacuolar
function in Arabidopsis,” Cell Research, vol. 21, no. 12. Nature Publishing
Group, pp. 1711–1722, 2011.
ista: Zwiewka M, Feraru E, Möller B, Hwang I, Feraru M, Kleine Vehn J, Weijers D,
Friml J. 2011. The AP 3 adaptor complex is required for vacuolar function in Arabidopsis.
Cell Research. 21(12), 1711–1722.
mla: Zwiewka, Marta, et al. “The AP 3 Adaptor Complex Is Required for Vacuolar Function
in Arabidopsis.” Cell Research, vol. 21, no. 12, Nature Publishing Group,
2011, pp. 1711–22, doi:10.1038/cr.2011.99.
short: M. Zwiewka, E. Feraru, B. Möller, I. Hwang, M. Feraru, J. Kleine Vehn, D.
Weijers, J. Friml, Cell Research 21 (2011) 1711–1722.
date_created: 2018-12-11T12:01:23Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:41:04Z
day: '01'
doi: 10.1038/cr.2011.99
extern: 1
intvolume: ' 21'
issue: '12'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3357998/
month: '01'
oa: 1
page: 1711 - 1722
publication: Cell Research
publication_status: published
publisher: Nature Publishing Group
publist_id: '3597'
quality_controlled: 0
status: public
title: The AP 3 adaptor complex is required for vacuolar function in Arabidopsis
type: journal_article
volume: 21
year: '2011'
...
---
_id: '3102'
abstract:
- lang: eng
text: 'Multicellular organisms depend on cell production, cell fate specification,
and correct patterning to shape their adult body. In plants, auxin plays a prominent
role in the timely coordination of these different cellular processes. A well-studied
example is lateral root initiation, in which auxin triggers founder cell specification
and cell cycle activation of xylem pole–positioned pericycle cells. Here, we report
that the E2Fa transcription factor of Arabidopsis thaliana is an essential component
that regulates the asymmetric cell division marking lateral root initiation. Moreover,
we demonstrate that E2Fa expression is regulated by the LATERAL ORGAN BOUNDARY
DOMAIN18/LATERAL ORGAN BOUNDARY DOMAIN33 (LBD18/LBD33) dimer that is, in turn,
regulated by the auxin signaling pathway. LBD18/LBD33 mediates lateral root organogenesis
through E2Fa transcriptional activation, whereas E2Fa expression under control
of the LBD18 promoter eliminates the need for LBD18. Besides lateral root initiation,
vascular patterning is disrupted in E2Fa knockout plants, similarly as it is affected
in auxin signaling and lbd mutants, indicating that the transcriptional induction
of E2Fa through LBDs represents a general mechanism for auxin-dependent cell cycle
activation. Our data illustrate how a conserved mechanism driving cell cycle entry
has been adapted evolutionarily to connect auxin signaling with control of processes
determining plant architecture. '
author:
- first_name: Barbara
full_name: Berckmans, Barbara
last_name: Berckmans
- first_name: Valya
full_name: Vassileva, Valya
last_name: Vassileva
- first_name: Stephan
full_name: Schmid, Stephan P
last_name: Schmid
- first_name: Sara
full_name: Maes, Sara
last_name: Maes
- first_name: Boris
full_name: Parizot, Boris
last_name: Parizot
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Zoltan
full_name: Magyar, Zoltan
last_name: Magyar
- first_name: Claire
full_name: Lessa Alvim Kamei, Claire
last_name: Lessa Alvim Kamei
- first_name: Csaba
full_name: Koncz, Csaba
last_name: Koncz
- first_name: Laszlo
full_name: Bögre, Laszlo
last_name: Bögre
- first_name: Geert
full_name: Persiau, Geert
last_name: Persiau
- first_name: Geert
full_name: De Jaeger, Geert
last_name: De Jaeger
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Rüdiger
full_name: Simon, Rüdiger
last_name: Simon
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Lieven
full_name: de Veyldera, Lieven
last_name: De Veyldera
citation:
ama: Berckmans B, Vassileva V, Schmid S, et al. Auxin Dependent cell cycle reactivation
through transcriptional regulation of arabidopsis E2Fa by lateral organ boundary
proteins. Plant Cell. 2011;23(10):3671-3683. doi:10.1105/tpc.111.088377
apa: Berckmans, B., Vassileva, V., Schmid, S., Maes, S., Parizot, B., Naramoto,
S., … De Veyldera, L. (2011). Auxin Dependent cell cycle reactivation through
transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins.
Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.111.088377
chicago: Berckmans, Barbara, Valya Vassileva, Stephan Schmid, Sara Maes, Boris Parizot,
Satoshi Naramoto, Zoltan Magyar, et al. “Auxin Dependent Cell Cycle Reactivation
through Transcriptional Regulation of Arabidopsis E2Fa by Lateral Organ Boundary
Proteins.” Plant Cell. American Society of Plant Biologists, 2011. https://doi.org/10.1105/tpc.111.088377.
ieee: B. Berckmans et al., “Auxin Dependent cell cycle reactivation through
transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins,”
Plant Cell, vol. 23, no. 10. American Society of Plant Biologists, pp.
3671–3683, 2011.
ista: Berckmans B, Vassileva V, Schmid S, Maes S, Parizot B, Naramoto S, Magyar
Z, Lessa Alvim Kamei C, Koncz C, Bögre L, Persiau G, De Jaeger G, Friml J, Simon
R, Beeckman T, De Veyldera L. 2011. Auxin Dependent cell cycle reactivation through
transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins.
Plant Cell. 23(10), 3671–3683.
mla: Berckmans, Barbara, et al. “Auxin Dependent Cell Cycle Reactivation through
Transcriptional Regulation of Arabidopsis E2Fa by Lateral Organ Boundary Proteins.”
Plant Cell, vol. 23, no. 10, American Society of Plant Biologists, 2011,
pp. 3671–83, doi:10.1105/tpc.111.088377.
short: B. Berckmans, V. Vassileva, S. Schmid, S. Maes, B. Parizot, S. Naramoto,
Z. Magyar, C. Lessa Alvim Kamei, C. Koncz, L. Bögre, G. Persiau, G. De Jaeger,
J. Friml, R. Simon, T. Beeckman, L. De Veyldera, Plant Cell 23 (2011) 3671–3683.
date_created: 2018-12-11T12:01:24Z
date_published: 2011-10-14T00:00:00Z
date_updated: 2021-01-12T07:41:04Z
day: '14'
doi: 10.1105/tpc.111.088377
extern: 1
intvolume: ' 23'
issue: '10'
month: '10'
page: 3671 - 3683
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3598'
quality_controlled: 0
status: public
title: Auxin Dependent cell cycle reactivation through transcriptional regulation
of arabidopsis E2Fa by lateral organ boundary proteins
type: journal_article
volume: 23
year: '2011'
...
---
_id: '3103'
abstract:
- lang: eng
text: Endocytosis in plants has an essential role not only for basic cellular functions
but also for growth and development, hormonal signaling and communication with
the environment including nutrient delivery, toxin avoidance, and pathogen defense.
The major endocytic mechanism in plants depends on the coat protein clathrin.
It starts by clathrin-coated vesicle formation at the plasma membrane, where specific
cargoes are recognized and packaged for internalization. Recently, genetic, biochemical
and advanced microscopy studies provided initial insights into mechanisms and
roles of clathrin-mediated endocytosis in plants. Here we summarize the present
state of knowledge and compare mechanisms of clathrin-mediated endocytosis in
plants with animal and yeast paradigms as well as review plant-specific regulations
and roles of this process.
author:
- first_name: Xu
full_name: Chen, Xu
id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Niloufer
full_name: Irani, Niloufer
last_name: Irani
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Chen X, Irani N, Friml J. Clathrin-mediated endocytosis: The gateway into
plant cells. Current Opinion in Plant Biology. 2011;14(6):674-682. doi:10.1016/j.pbi.2011.08.006'
apa: 'Chen, X., Irani, N., & Friml, J. (2011). Clathrin-mediated endocytosis:
The gateway into plant cells. Current Opinion in Plant Biology. Elsevier.
https://doi.org/10.1016/j.pbi.2011.08.006'
chicago: 'Chen, Xu, Niloufer Irani, and Jiří Friml. “Clathrin-Mediated Endocytosis:
The Gateway into Plant Cells.” Current Opinion in Plant Biology. Elsevier,
2011. https://doi.org/10.1016/j.pbi.2011.08.006.'
ieee: 'X. Chen, N. Irani, and J. Friml, “Clathrin-mediated endocytosis: The gateway
into plant cells,” Current Opinion in Plant Biology, vol. 14, no. 6. Elsevier,
pp. 674–682, 2011.'
ista: 'Chen X, Irani N, Friml J. 2011. Clathrin-mediated endocytosis: The gateway
into plant cells. Current Opinion in Plant Biology. 14(6), 674–682.'
mla: 'Chen, Xu, et al. “Clathrin-Mediated Endocytosis: The Gateway into Plant Cells.”
Current Opinion in Plant Biology, vol. 14, no. 6, Elsevier, 2011, pp. 674–82,
doi:10.1016/j.pbi.2011.08.006.'
short: X. Chen, N. Irani, J. Friml, Current Opinion in Plant Biology 14 (2011) 674–682.
date_created: 2018-12-11T12:01:24Z
date_published: 2011-12-01T00:00:00Z
date_updated: 2021-01-12T07:41:05Z
day: '01'
doi: 10.1016/j.pbi.2011.08.006
extern: '1'
intvolume: ' 14'
issue: '6'
language:
- iso: eng
month: '12'
oa_version: None
page: 674 - 682
publication: Current Opinion in Plant Biology
publication_status: published
publisher: Elsevier
publist_id: '3596'
quality_controlled: '1'
status: public
title: 'Clathrin-mediated endocytosis: The gateway into plant cells'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2011'
...
---
_id: '3138'
abstract:
- lang: eng
text: Hippocampal sharp waves (SPWs) and associated fast ("ripple") oscillations
(SPW-Rs) in the CA1 region are among the most synchronous physiological patterns
in the mammalian brain. Using two-dimensional arrays of electrodes for recording
local field potentials and unit discharges in freely moving rats, we studied the
emergence of ripple oscillations (140-220 Hz) and compared their origin and cellular-synaptic
mechanisms with fast gamma oscillations (90-140 Hz). We show that (1) hippocampal
SPW-Rs and fast gamma oscillations are quantitatively distinct patterns but involve
the same networks and share similar mechanisms; (2) both the frequency and magnitude
of fast oscillations are positively correlated with the magnitude of SPWs; (3)
during both ripples and fast gamma oscillations the frequency of network oscillation
is higher in CA1 than in CA3; and (4) the emergence of CA3 population bursts,
a prerequisite for SPW-Rs, is biased by activity patterns in the dentate gyrus
and entorhinal cortex, with the highest probability of ripples associated with
an "optimum" level of dentate gamma power. We hypothesize that each
hippocampal subnetwork possesses distinct resonant properties, tuned by the magnitude
of the excitatory drive.
author:
- first_name: David
full_name: Sullivan, David W
last_name: Sullivan
- first_name: Jozsef L
full_name: Jozsef Csicsvari
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Kenji
full_name: Mizuseki, Kenji
last_name: Mizuseki
- first_name: Sean
full_name: Montgomery, Sean M
last_name: Montgomery
- first_name: Kamran
full_name: Diba, Kamran
last_name: Diba
- first_name: György
full_name: Buzsáki, György
last_name: Buzsáki
citation:
ama: Sullivan D, Csicsvari JL, Mizuseki K, Montgomery S, Diba K, Buzsáki G. Relationships
between hippocampal sharp waves ripples and fast gamma oscillation Influence of
dentate and entorhinal cortical activity. Journal of Neuroscience. 2011;31(23):8605-8616.
doi:10.1523/JNEUROSCI.0294-11.2011
apa: Sullivan, D., Csicsvari, J. L., Mizuseki, K., Montgomery, S., Diba, K., &
Buzsáki, G. (2011). Relationships between hippocampal sharp waves ripples and
fast gamma oscillation Influence of dentate and entorhinal cortical activity.
Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0294-11.2011
chicago: Sullivan, David, Jozsef L Csicsvari, Kenji Mizuseki, Sean Montgomery, Kamran
Diba, and György Buzsáki. “Relationships between Hippocampal Sharp Waves Ripples
and Fast Gamma Oscillation Influence of Dentate and Entorhinal Cortical Activity.”
Journal of Neuroscience. Society for Neuroscience, 2011. https://doi.org/10.1523/JNEUROSCI.0294-11.2011.
ieee: D. Sullivan, J. L. Csicsvari, K. Mizuseki, S. Montgomery, K. Diba, and G.
Buzsáki, “Relationships between hippocampal sharp waves ripples and fast gamma
oscillation Influence of dentate and entorhinal cortical activity,” Journal
of Neuroscience, vol. 31, no. 23. Society for Neuroscience, pp. 8605–8616,
2011.
ista: Sullivan D, Csicsvari JL, Mizuseki K, Montgomery S, Diba K, Buzsáki G. 2011.
Relationships between hippocampal sharp waves ripples and fast gamma oscillation
Influence of dentate and entorhinal cortical activity. Journal of Neuroscience.
31(23), 8605–8616.
mla: Sullivan, David, et al. “Relationships between Hippocampal Sharp Waves Ripples
and Fast Gamma Oscillation Influence of Dentate and Entorhinal Cortical Activity.”
Journal of Neuroscience, vol. 31, no. 23, Society for Neuroscience, 2011,
pp. 8605–16, doi:10.1523/JNEUROSCI.0294-11.2011.
short: D. Sullivan, J.L. Csicsvari, K. Mizuseki, S. Montgomery, K. Diba, G. Buzsáki,
Journal of Neuroscience 31 (2011) 8605–8616.
date_created: 2018-12-11T12:01:36Z
date_published: 2011-06-08T00:00:00Z
date_updated: 2021-01-12T07:41:19Z
day: '08'
doi: 10.1523/JNEUROSCI.0294-11.2011
extern: 1
intvolume: ' 31'
issue: '23'
month: '06'
page: 8605 - 8616
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '3559'
quality_controlled: 0
status: public
title: Relationships between hippocampal sharp waves ripples and fast gamma oscillation
Influence of dentate and entorhinal cortical activity
type: journal_article
volume: 31
year: '2011'
...
---
_id: '3145'
abstract:
- lang: eng
text: Microinjection of recombinant DNA into zygotic pronuclei has been widely used
for producing transgenic mice. However, with this method, the insertion site,
integrity, and copy number of the transgene cannot be controlled. Here, we present
an integrase-based approach to produce transgenic mice via pronuclear injection,
whereby an intact single-copy transgene can be inserted into predetermined chromosomal
loci with high efficiency (up to 40%), and faithfully transmitted through generations.
We show that neighboring transgenic elements and bacterial DNA within the transgene
cause profound silencing and expression variability of the transgenic marker.
Removal of these undesirable elements leads to global high-level marker expression
from transgenes driven by a ubiquitous promoter. We also obtained faithful marker
expression from a tissue-specific promoter. The technique presented here will
greatly facilitate murine transgenesis and precise structure/function dissection
of mammalian gene function and regulation in vivo.
author:
- first_name: Bosiljka
full_name: Tasic, Bosiljka
last_name: Tasic
- first_name: Simon
full_name: Simon Hippenmeyer
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Charlene
full_name: Wang, Charlene
last_name: Wang
- first_name: Matthew
full_name: Gamboa, Matthew
last_name: Gamboa
- first_name: Hui
full_name: Zong, Hui
last_name: Zong
- first_name: Yanru
full_name: Chen-Tsai, Yanru
last_name: Chen Tsai
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
citation:
ama: Tasic B, Hippenmeyer S, Wang C, et al. Site specific integrase mediated transgenesis
in mice via pronuclear injection. PNAS. 2011;108(19):7902-7907. doi:10.1073/pnas.1019507108
apa: Tasic, B., Hippenmeyer, S., Wang, C., Gamboa, M., Zong, H., Chen Tsai, Y.,
& Luo, L. (2011). Site specific integrase mediated transgenesis in mice via
pronuclear injection. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1019507108
chicago: Tasic, Bosiljka, Simon Hippenmeyer, Charlene Wang, Matthew Gamboa, Hui
Zong, Yanru Chen Tsai, and Liqun Luo. “Site Specific Integrase Mediated Transgenesis
in Mice via Pronuclear Injection.” PNAS. National Academy of Sciences,
2011. https://doi.org/10.1073/pnas.1019507108.
ieee: B. Tasic et al., “Site specific integrase mediated transgenesis in
mice via pronuclear injection,” PNAS, vol. 108, no. 19. National Academy
of Sciences, pp. 7902–7907, 2011.
ista: Tasic B, Hippenmeyer S, Wang C, Gamboa M, Zong H, Chen Tsai Y, Luo L. 2011.
Site specific integrase mediated transgenesis in mice via pronuclear injection.
PNAS. 108(19), 7902–7907.
mla: Tasic, Bosiljka, et al. “Site Specific Integrase Mediated Transgenesis in Mice
via Pronuclear Injection.” PNAS, vol. 108, no. 19, National Academy of
Sciences, 2011, pp. 7902–07, doi:10.1073/pnas.1019507108.
short: B. Tasic, S. Hippenmeyer, C. Wang, M. Gamboa, H. Zong, Y. Chen Tsai, L. Luo,
PNAS 108 (2011) 7902–7907.
date_created: 2018-12-11T12:01:39Z
date_published: 2011-05-10T00:00:00Z
date_updated: 2021-01-12T07:41:22Z
day: '10'
doi: 10.1073/pnas.1019507108
extern: 1
intvolume: ' 108'
issue: '19'
month: '05'
page: 7902 - 7907
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3549'
quality_controlled: 0
status: public
title: Site specific integrase mediated transgenesis in mice via pronuclear injection
type: journal_article
volume: 108
year: '2011'
...
---
_id: '3147'
abstract:
- lang: eng
text: Cancer cell of origin is difficult to identify by analyzing cells within terminal
stage tumors, whose identity could be concealed by the acquired plasticity. Thus,
an ideal approach to identify the cell of origin is to analyze proliferative abnormalities
in distinct lineages prior to malignancy. Here, we use mosaic analysis with double
markers (MADM) in mice to model gliomagenesis by initiating concurrent p53/Nf1
mutations sporadically in neural stem cells (NSCs). Surprisingly, MADM-based lineage
tracing revealed significant aberrant growth prior to malignancy only in oligodendrocyte
precursor cells (OPCs), but not in any other NSC-derived lineages or NSCs themselves.
Upon tumor formation, phenotypic and transcriptome analyses of tumor cells revealed
salient OPC features. Finally, introducing the same p53/Nf1 mutations directly
into OPCs consistently led to gliomagenesis. Our findings suggest OPCs as the
cell of origin in this model, even when initial mutations occur in NSCs, and highlight
the importance of analyzing premalignant stages to identify the cancer cell of
origin.
author:
- first_name: Chong
full_name: Liu, Chong
last_name: Liu
- first_name: Jonathan
full_name: Sage, Jonathan C
last_name: Sage
- first_name: Michael
full_name: Miller, Michael R
last_name: Miller
- first_name: Roel
full_name: Verhaak, Roel G
last_name: Verhaak
- first_name: Simon
full_name: Simon Hippenmeyer
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Hannes
full_name: Vogel, Hannes
last_name: Vogel
- first_name: Oded
full_name: Foreman, Oded
last_name: Foreman
- first_name: Roderick
full_name: Bronson, Roderick T
last_name: Bronson
- first_name: Akiko
full_name: Nishiyama, Akiko
last_name: Nishiyama
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
- first_name: Hui
full_name: Zong, Hui
last_name: Zong
citation:
ama: Liu C, Sage J, Miller M, et al. Mosaic analysis with double markers reveals
tumor cell of origin in glioma. Cell. 2011;146(2):209-221. doi:10.1016/j.cell.2011.06.014
apa: Liu, C., Sage, J., Miller, M., Verhaak, R., Hippenmeyer, S., Vogel, H., … Zong,
H. (2011). Mosaic analysis with double markers reveals tumor cell of origin in
glioma. Cell. Cell Press. https://doi.org/10.1016/j.cell.2011.06.014
chicago: Liu, Chong, Jonathan Sage, Michael Miller, Roel Verhaak, Simon Hippenmeyer,
Hannes Vogel, Oded Foreman, et al. “Mosaic Analysis with Double Markers Reveals
Tumor Cell of Origin in Glioma.” Cell. Cell Press, 2011. https://doi.org/10.1016/j.cell.2011.06.014.
ieee: C. Liu et al., “Mosaic analysis with double markers reveals tumor cell
of origin in glioma,” Cell, vol. 146, no. 2. Cell Press, pp. 209–221, 2011.
ista: Liu C, Sage J, Miller M, Verhaak R, Hippenmeyer S, Vogel H, Foreman O, Bronson
R, Nishiyama A, Luo L, Zong H. 2011. Mosaic analysis with double markers reveals
tumor cell of origin in glioma. Cell. 146(2), 209–221.
mla: Liu, Chong, et al. “Mosaic Analysis with Double Markers Reveals Tumor Cell
of Origin in Glioma.” Cell, vol. 146, no. 2, Cell Press, 2011, pp. 209–21,
doi:10.1016/j.cell.2011.06.014.
short: C. Liu, J. Sage, M. Miller, R. Verhaak, S. Hippenmeyer, H. Vogel, O. Foreman,
R. Bronson, A. Nishiyama, L. Luo, H. Zong, Cell 146 (2011) 209–221.
date_created: 2018-12-11T12:01:40Z
date_published: 2011-07-22T00:00:00Z
date_updated: 2021-01-12T07:41:23Z
day: '22'
doi: 10.1016/j.cell.2011.06.014
extern: 1
intvolume: ' 146'
issue: '2'
month: '07'
page: 209 - 221
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '3548'
quality_controlled: 0
status: public
title: Mosaic analysis with double markers reveals tumor cell of origin in glioma
type: journal_article
volume: 146
year: '2011'
...
---
_id: '3154'
abstract:
- lang: eng
text: Regulated adhesion between cells and their environment is critical for normal
cell migration. We have identified mutations in a gene encoding the Drosophila
hydrogen peroxide (H2O2)-degrading enzyme Jafrac1, which lead to germ cell adhesion
defects. During gastrulation, primordial germ cells (PGCs) associate tightly with
the invaginating midgut primordium as it enters the embryo; however, in embryos
from jafrac1 mutant mothers this association is disrupted, leaving some PGCs trailing
on the outside of the embryo. We observed similar phenotypes in embryos from DE-cadherin/shotgun
(shg) mutant mothers and were able to rescue the jafrac1 phenotype by increasing
DE-cadherin levels. This and our biochemical evidence strongly suggest that Jafrac1-mediated
reduction of H2O2 is required to maintain DE-cadherin protein levels in the early
embryo. Our results present in vivo evidence of a peroxiredoxin regulating DE-cadherin-mediated
adhesion.
author:
- first_name: Matthew
full_name: DeGennaro, Matthew
last_name: Degennaro
- first_name: Thomas
full_name: Hurd, Thomas R
last_name: Hurd
- first_name: Daria E
full_name: Daria Siekhaus
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Benoit
full_name: Biteau, Benoit
last_name: Biteau
- first_name: Heinrich
full_name: Jasper, Heinrich
last_name: Jasper
- first_name: Ruth
full_name: Lehmann, Ruth
last_name: Lehmann
citation:
ama: Degennaro M, Hurd T, Siekhaus DE, Biteau B, Jasper H, Lehmann R. Peroxiredoxin
stabilization of DE-cadherin promotes primordial germ cell adhesion. Developmental
Cell. 2011;20(2):233-243. doi:10.1016/j.devcel.2010.12.007
apa: Degennaro, M., Hurd, T., Siekhaus, D. E., Biteau, B., Jasper, H., & Lehmann,
R. (2011). Peroxiredoxin stabilization of DE-cadherin promotes primordial germ
cell adhesion. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2010.12.007
chicago: Degennaro, Matthew, Thomas Hurd, Daria E Siekhaus, Benoit Biteau, Heinrich
Jasper, and Ruth Lehmann. “Peroxiredoxin Stabilization of DE-Cadherin Promotes
Primordial Germ Cell Adhesion.” Developmental Cell. Cell Press, 2011. https://doi.org/10.1016/j.devcel.2010.12.007.
ieee: M. Degennaro, T. Hurd, D. E. Siekhaus, B. Biteau, H. Jasper, and R. Lehmann,
“Peroxiredoxin stabilization of DE-cadherin promotes primordial germ cell adhesion,”
Developmental Cell, vol. 20, no. 2. Cell Press, pp. 233–243, 2011.
ista: Degennaro M, Hurd T, Siekhaus DE, Biteau B, Jasper H, Lehmann R. 2011. Peroxiredoxin
stabilization of DE-cadherin promotes primordial germ cell adhesion. Developmental
Cell. 20(2), 233–243.
mla: Degennaro, Matthew, et al. “Peroxiredoxin Stabilization of DE-Cadherin Promotes
Primordial Germ Cell Adhesion.” Developmental Cell, vol. 20, no. 2, Cell
Press, 2011, pp. 233–43, doi:10.1016/j.devcel.2010.12.007.
short: M. Degennaro, T. Hurd, D.E. Siekhaus, B. Biteau, H. Jasper, R. Lehmann, Developmental
Cell 20 (2011) 233–243.
date_created: 2018-12-11T12:01:42Z
date_published: 2011-02-15T00:00:00Z
date_updated: 2021-01-12T07:41:26Z
day: '15'
doi: 10.1016/j.devcel.2010.12.007
extern: 1
intvolume: ' 20'
issue: '2'
month: '02'
page: 233 - 243
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '3541'
quality_controlled: 0
status: public
title: Peroxiredoxin stabilization of DE-cadherin promotes primordial germ cell adhesion
type: journal_article
volume: 20
year: '2011'
...
---
_id: '3163'
abstract:
- lang: eng
text: We study multi-label prediction for structured output sets, a problem that
occurs, for example, in object detection in images, secondary structure prediction
in computational biology, and graph matching with symmetries. Conventional multilabel
classification techniques are typically not applicable in this situation, because
they require explicit enumeration of the label set, which is infeasible in case
of structured outputs. Relying on techniques originally designed for single-label
structured prediction, in particular structured support vector machines, results
in reduced prediction accuracy, or leads to infeasible optimization problems.
In this work we derive a maximum-margin training formulation for multi-label structured
prediction that remains computationally tractable while achieving high prediction
accuracy. It also shares most beneficial properties with single-label maximum-margin
approaches, in particular formulation as a convex optimization problem, efficient
working set training, and PAC-Bayesian generalization bounds.
author:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Lampert C. Maximum margin multi-label structured prediction. In: Neural Information
Processing Systems; 2011.'
apa: 'Lampert, C. (2011). Maximum margin multi-label structured prediction. Presented
at the NIPS: Neural Information Processing Systems, Granada, Spain: Neural Information
Processing Systems.'
chicago: Lampert, Christoph. “Maximum Margin Multi-Label Structured Prediction.”
Neural Information Processing Systems, 2011.
ieee: 'C. Lampert, “Maximum margin multi-label structured prediction,” presented
at the NIPS: Neural Information Processing Systems, Granada, Spain, 2011.'
ista: 'Lampert C. 2011. Maximum margin multi-label structured prediction. NIPS:
Neural Information Processing Systems.'
mla: Lampert, Christoph. Maximum Margin Multi-Label Structured Prediction.
Neural Information Processing Systems, 2011.
short: C. Lampert, in:, Neural Information Processing Systems, 2011.
conference:
end_date: 2011-12-14
location: Granada, Spain
name: 'NIPS: Neural Information Processing Systems'
start_date: 2011-12-12
date_created: 2018-12-11T12:01:45Z
date_published: 2011-12-01T00:00:00Z
date_updated: 2023-10-17T11:47:35Z
day: '01'
department:
- _id: ChLa
language:
- iso: eng
month: '12'
oa_version: None
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '3522'
quality_controlled: '1'
related_material:
record:
- id: '3322'
relation: later_version
status: public
scopus_import: 1
status: public
title: Maximum margin multi-label structured prediction
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3204'
abstract:
- lang: eng
text: 'We introduce a new class of functions that can be minimized in polynomial
time in the value oracle model. These are functions f satisfying f(x) + f(y) ≥
f(x ∏ y) + f(x ∐ y) where the domain of each variable x i corresponds to nodes
of a rooted binary tree, and operations ∏,∐ are defined with respect to this tree.
Special cases include previously studied L-convex and bisubmodular functions,
which can be obtained with particular choices of trees. We present a polynomial-time
algorithm for minimizing functions in the new class. It combines Murota''s steepest
descent algorithm for L-convex functions with bisubmodular minimization algorithms. '
alternative_title:
- LNCS
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Kolmogorov V. Submodularity on a tree: Unifying Submodularity on a tree: Unifying
L-convex and bisubmodular functions convex and bisubmodular functions. In: Vol
6907. Springer; 2011:400-411. doi:10.1007/978-3-642-22993-0_37'
apa: 'Kolmogorov, V. (2011). Submodularity on a tree: Unifying Submodularity on
a tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions
(Vol. 6907, pp. 400–411). Presented at the MFCS: Mathematical Foundations of Computer
Science, Springer. https://doi.org/10.1007/978-3-642-22993-0_37'
chicago: 'Kolmogorov, Vladimir. “Submodularity on a Tree: Unifying Submodularity
on a Tree: Unifying L-Convex and Bisubmodular Functions Convex and Bisubmodular
Functions,” 6907:400–411. Springer, 2011. https://doi.org/10.1007/978-3-642-22993-0_37.'
ieee: 'V. Kolmogorov, “Submodularity on a tree: Unifying Submodularity on a tree:
Unifying L-convex and bisubmodular functions convex and bisubmodular functions,”
presented at the MFCS: Mathematical Foundations of Computer Science, 2011, vol.
6907, pp. 400–411.'
ista: 'Kolmogorov V. 2011. Submodularity on a tree: Unifying Submodularity on a
tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions.
MFCS: Mathematical Foundations of Computer Science, LNCS, vol. 6907, 400–411.'
mla: 'Kolmogorov, Vladimir. Submodularity on a Tree: Unifying Submodularity on
a Tree: Unifying L-Convex and Bisubmodular Functions Convex and Bisubmodular Functions.
Vol. 6907, Springer, 2011, pp. 400–11, doi:10.1007/978-3-642-22993-0_37.'
short: V. Kolmogorov, in:, Springer, 2011, pp. 400–411.
conference:
name: 'MFCS: Mathematical Foundations of Computer Science'
date_created: 2018-12-11T12:02:00Z
date_published: 2011-08-09T00:00:00Z
date_updated: 2021-01-12T07:41:47Z
day: '09'
doi: 10.1007/978-3-642-22993-0_37
extern: 1
intvolume: ' 6907'
main_file_link:
- open_access: '0'
url: http://arxiv.org/pdf/1007.1229v3
month: '08'
page: 400 - 411
publication_status: published
publisher: Springer
publist_id: '3478'
quality_controlled: 0
status: public
title: 'Submodularity on a tree: Unifying Submodularity on a tree: Unifying L-convex
and bisubmodular functions convex and bisubmodular functions'
type: conference
volume: 6907
year: '2011'
...
---
_id: '3205'
abstract:
- lang: eng
text: This paper proposes a novel Linear Programming (LP) based algorithm, called
Dynamic Tree-Block Coordinate Ascent (DT-BCA), for performing maximum a posteriori
(MAP) inference in probabilistic graphical models. Unlike traditional message
passing algorithms, which operate uniformly on the whole factor graph, our method
dynamically chooses regions of the factor graph on which to focus message-passing
efforts. We propose two criteria for selecting regions, including an efficiently
computable upper-bound on the increase in the objective possible by passing messages
in any particular region. This bound is derived from the theory of primal-dual
methods from combinatorial optimization, and the forest that maximizes the bounds
can be chosen efficiently using a maximum-spanning-tree-like algorithm. Experimental
results show that our dynamic schedules significantly speed up state-of-the-art
LP-based message-passing algorithms on a wide variety of real-world problems.
author:
- first_name: Daniel
full_name: Tarlow, Daniel
last_name: Tarlow
- first_name: Druv
full_name: Batra, Druv
last_name: Batra
- first_name: Pushmeet
full_name: Kohli, Pushmeet
last_name: Kohli
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Tarlow D, Batra D, Kohli P, Kolmogorov V. Dynamic tree block coordinate ascent.
In: Omnipress; 2011:113-120.'
apa: 'Tarlow, D., Batra, D., Kohli, P., & Kolmogorov, V. (2011). Dynamic tree
block coordinate ascent (pp. 113–120). Presented at the ICML: International Conference
on Machine Learning, Omnipress.'
chicago: Tarlow, Daniel, Druv Batra, Pushmeet Kohli, and Vladimir Kolmogorov. “Dynamic
Tree Block Coordinate Ascent,” 113–20. Omnipress, 2011.
ieee: 'D. Tarlow, D. Batra, P. Kohli, and V. Kolmogorov, “Dynamic tree block coordinate
ascent,” presented at the ICML: International Conference on Machine Learning,
2011, pp. 113–120.'
ista: 'Tarlow D, Batra D, Kohli P, Kolmogorov V. 2011. Dynamic tree block coordinate
ascent. ICML: International Conference on Machine Learning, 113–120.'
mla: Tarlow, Daniel, et al. Dynamic Tree Block Coordinate Ascent. Omnipress,
2011, pp. 113–20.
short: D. Tarlow, D. Batra, P. Kohli, V. Kolmogorov, in:, Omnipress, 2011, pp. 113–120.
conference:
name: 'ICML: International Conference on Machine Learning'
date_created: 2018-12-11T12:02:00Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:41:47Z
day: '01'
extern: 1
main_file_link:
- open_access: '0'
url: http://ttic.uchicago.edu/~dbatra/publications/assets/tbkk_icml11.pdf
month: '01'
page: 113 - 120
publication_status: published
publisher: Omnipress
publist_id: '3475'
quality_controlled: 0
status: public
title: Dynamic tree block coordinate ascent
type: conference
year: '2011'
...
---
_id: '3206'
abstract:
- lang: eng
text: In this paper we address the problem of finding the most probable state of
discrete Markov random field (MRF) with associative pairwise terms. Although of
practical importance, this problem is known to be NP-hard in general. We propose
a new type of MRF decomposition, submod-ular decomposition (SMD). Unlike existing
decomposition approaches SMD decomposes the initial problem into sub-problems
corresponding to a specific class label while preserving the graph structure of
each subproblem. Such decomposition enables us to take into account several types
of global constraints in an efficient manner. We study theoretical properties
of the proposed approach and demonstrate its applicability on a number of problems.
author:
- first_name: Anton
full_name: Osokin, Anton
last_name: Osokin
- first_name: Dmitry
full_name: Vetrov, Dmitry
last_name: Vetrov
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Osokin A, Vetrov D, Kolmogorov V. Submodular decomposition framework for inference
in associative Markov networks with global constraints. In: IEEE; 2011:1889-1896.
doi:10.1109/CVPR.2011.5995361'
apa: 'Osokin, A., Vetrov, D., & Kolmogorov, V. (2011). Submodular decomposition
framework for inference in associative Markov networks with global constraints
(pp. 1889–1896). Presented at the CVPR: Computer Vision and Pattern Recognition,
IEEE. https://doi.org/10.1109/CVPR.2011.5995361'
chicago: Osokin, Anton, Dmitry Vetrov, and Vladimir Kolmogorov. “Submodular Decomposition
Framework for Inference in Associative Markov Networks with Global Constraints,”
1889–96. IEEE, 2011. https://doi.org/10.1109/CVPR.2011.5995361.
ieee: 'A. Osokin, D. Vetrov, and V. Kolmogorov, “Submodular decomposition framework
for inference in associative Markov networks with global constraints,” presented
at the CVPR: Computer Vision and Pattern Recognition, 2011, pp. 1889–1896.'
ista: 'Osokin A, Vetrov D, Kolmogorov V. 2011. Submodular decomposition framework
for inference in associative Markov networks with global constraints. CVPR: Computer
Vision and Pattern Recognition, 1889–1896.'
mla: Osokin, Anton, et al. Submodular Decomposition Framework for Inference in
Associative Markov Networks with Global Constraints. IEEE, 2011, pp. 1889–96,
doi:10.1109/CVPR.2011.5995361.
short: A. Osokin, D. Vetrov, V. Kolmogorov, in:, IEEE, 2011, pp. 1889–1896.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:02:00Z
date_published: 2011-08-22T00:00:00Z
date_updated: 2021-01-12T07:41:47Z
day: '22'
doi: 10.1109/CVPR.2011.5995361
extern: 1
main_file_link:
- open_access: '0'
url: http://arxiv.org/pdf/1103.1077v1
month: '08'
page: 1889 - 1896
publication_status: published
publisher: IEEE
publist_id: '3476'
quality_controlled: 0
status: public
title: Submodular decomposition framework for inference in associative Markov networks
with global constraints
type: conference
year: '2011'
...
---
_id: '3207'
abstract:
- lang: eng
text: 'Cosegmentation is typically defined as the task of jointly segmenting something
similar in a given set of images. Existing methods are too generic and so far
have not demonstrated competitive results for any specific task. In this paper
we overcome this limitation by adding two new aspects to cosegmentation: (1) the
"something" has to be an object, and (2) the "similarity"
measure is learned. In this way, we are able to achieve excellent results on the
recently introduced iCoseg dataset, which contains small sets of images of either
the same object instance or similar objects of the same class. The challenge of
this dataset lies in the extreme changes in viewpoint, lighting, and object deformations
within each set. We are able to considerably outperform several competitors. To
achieve this performance, we borrow recent ideas from object recognition: the
use of powerful features extracted from a pool of candidate object-like segmentations.
We believe that our work will be beneficial to several application areas, such
as image retrieval.'
author:
- first_name: Sara
full_name: Vicente, Sara
last_name: Vicente
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Vicente S, Rother C, Kolmogorov V. Object cosegmentation. In: IEEE; 2011:2217-2224.
doi:10.1109/CVPR.2011.5995530'
apa: 'Vicente, S., Rother, C., & Kolmogorov, V. (2011). Object cosegmentation
(pp. 2217–2224). Presented at the CVPR: Computer Vision and Pattern Recognition,
IEEE. https://doi.org/10.1109/CVPR.2011.5995530'
chicago: Vicente, Sara, Carsten Rother, and Vladimir Kolmogorov. “Object Cosegmentation,”
2217–24. IEEE, 2011. https://doi.org/10.1109/CVPR.2011.5995530.
ieee: 'S. Vicente, C. Rother, and V. Kolmogorov, “Object cosegmentation,” presented
at the CVPR: Computer Vision and Pattern Recognition, 2011, pp. 2217–2224.'
ista: 'Vicente S, Rother C, Kolmogorov V. 2011. Object cosegmentation. CVPR: Computer
Vision and Pattern Recognition, 2217–2224.'
mla: Vicente, Sara, et al. Object Cosegmentation. IEEE, 2011, pp. 2217–24,
doi:10.1109/CVPR.2011.5995530.
short: S. Vicente, C. Rother, V. Kolmogorov, in:, IEEE, 2011, pp. 2217–2224.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:02:01Z
date_published: 2011-08-22T00:00:00Z
date_updated: 2021-01-12T07:41:48Z
day: '22'
doi: 10.1109/CVPR.2011.5995530
extern: 1
month: '08'
page: 2217 - 2224
publication_status: published
publisher: IEEE
publist_id: '3477'
quality_controlled: 0
status: public
title: Object cosegmentation
type: conference
year: '2011'
...
---
_id: '3236'
abstract:
- lang: eng
text: 'If a cryptographic primitive remains secure even if ℓ bits about the secret
key are leaked to the adversary, one would expect that at least one of n independent
instantiations of the scheme remains secure given n·ℓ bits of leakage. This intuition
has been proven true for schemes satisfying some special information-theoretic
properties by Alwen et al. [Eurocrypt''10]. On the negative side, Lewko and Waters
[FOCS''10] construct a CPA secure public-key encryption scheme for which this
intuition fails. The counterexample of Lewko and Waters leaves open the interesting
possibility that for any scheme there exists a constant c>0, such that n fold
repetition remains secure against c·n·ℓ bits of leakage. Furthermore, their counterexample
requires the n copies of the encryption scheme to share a common reference parameter,
leaving open the possibility that the intuition is true for all schemes without
common setup. In this work we give a stronger counterexample ruling out these
possibilities. We construct a signature scheme such that: 1. a single instantiation
remains secure given ℓ = log(k) bits of leakage where k is a security parameter.
2. any polynomial number of independent instantiations can be broken (in the strongest
sense of key-recovery) given ℓ′ = poly(k) bits of leakage. Note that ℓ does not
depend on the number of instances. The computational assumption underlying our
counterexample is that non-interactive computationally sound proofs exist. Moreover,
under a stronger (non-standard) assumption about such proofs, our counterexample
does not require a common reference parameter. The underlying idea of our counterexample
is rather generic and can be applied to other primitives like encryption schemes.
© 2011 International Association for Cryptologic Research.'
alternative_title:
- LNCS
author:
- first_name: Abhishek
full_name: Jain, Abhishek
last_name: Jain
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Jain A, Pietrzak KZ. Parallel repetition for leakage resilience amplification
revisited. In: Vol 6597. Springer; 2011:58-69. doi:10.1007/978-3-642-19571-6_5'
apa: 'Jain, A., & Pietrzak, K. Z. (2011). Parallel repetition for leakage resilience
amplification revisited (Vol. 6597, pp. 58–69). Presented at the TCC: Theory of
Cryptography Conference, Springer. https://doi.org/10.1007/978-3-642-19571-6_5'
chicago: Jain, Abhishek, and Krzysztof Z Pietrzak. “Parallel Repetition for Leakage
Resilience Amplification Revisited,” 6597:58–69. Springer, 2011. https://doi.org/10.1007/978-3-642-19571-6_5.
ieee: 'A. Jain and K. Z. Pietrzak, “Parallel repetition for leakage resilience amplification
revisited,” presented at the TCC: Theory of Cryptography Conference, 2011, vol.
6597, pp. 58–69.'
ista: 'Jain A, Pietrzak KZ. 2011. Parallel repetition for leakage resilience amplification
revisited. TCC: Theory of Cryptography Conference, LNCS, vol. 6597, 58–69.'
mla: Jain, Abhishek, and Krzysztof Z. Pietrzak. Parallel Repetition for Leakage
Resilience Amplification Revisited. Vol. 6597, Springer, 2011, pp. 58–69,
doi:10.1007/978-3-642-19571-6_5.
short: A. Jain, K.Z. Pietrzak, in:, Springer, 2011, pp. 58–69.
conference:
name: 'TCC: Theory of Cryptography Conference'
date_created: 2018-12-11T12:02:11Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:00Z
day: '01'
doi: 10.1007/978-3-642-19571-6_5
extern: 1
month: '01'
page: 58 - 69
publication_status: published
publisher: Springer
publist_id: '3443'
quality_controlled: 0
status: public
title: Parallel repetition for leakage resilience amplification revisited
type: conference
volume: '6597 '
year: '2011'
...