---
_id: '9153'
abstract:
- lang: eng
text: Internal tide driven mixing plays a key role in sustaining the deep ocean
stratification and meridional overturning circulation. Internal tides can be generated
by topographic horizontal scales ranging from hundreds of meters to tens of kilometers.
State of the art topographic products barely resolve scales smaller than ∼10 km
in the deep ocean. On these scales abyssal hills dominate ocean floor roughness.
The impact of abyssal hill roughness on internal‐tide generation is evaluated
in this study. The conversion of M2 barotropic to baroclinic tidal energy is calculated
based on linear wave theory both in real and spectral space using the Shuttle
Radar Topography Mission SRTM30_PLUS bathymetric product at 1/120° resolution
with and without the addition of synthetic abyssal hill roughness. Internal tide
generation by abyssal hills integrates to 0.1 TW globally or 0.03 TW when the
energy flux is empirically corrected for supercritical slope (i.e., ∼10% of the
energy flux due to larger topographic scales resolved in standard products in
both cases). The abyssal hill driven energy conversion is dominated by mid‐ocean
ridges, where abyssal hill roughness is large. Focusing on two regions located
over the Mid‐Atlantic Ridge and the East Pacific Rise, it is shown that regionally
linear theory predicts an increase of the energy flux due to abyssal hills of
up to 100% or 60% when an empirical correction for supercritical slopes is attempted.
Therefore, abyssal hills, unresolved in state of the art topographic products,
can have a strong impact on internal tide generation, especially over mid‐ocean
ridges.
article_processing_charge: No
article_type: original
author:
- first_name: Angélique
full_name: Melet, Angélique
last_name: Melet
- first_name: Maxim
full_name: Nikurashin, Maxim
last_name: Nikurashin
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: S.
full_name: Falahat, S.
last_name: Falahat
- first_name: Jonas
full_name: Nycander, Jonas
last_name: Nycander
- first_name: Patrick G.
full_name: Timko, Patrick G.
last_name: Timko
- first_name: Brian K.
full_name: Arbic, Brian K.
last_name: Arbic
- first_name: John A.
full_name: Goff, John A.
last_name: Goff
citation:
ama: 'Melet A, Nikurashin M, Muller CJ, et al. Internal tide generation by abyssal
hills using analytical theory. Journal of Geophysical Research: Oceans.
2013;118(11):6303-6318. doi:10.1002/2013jc009212'
apa: 'Melet, A., Nikurashin, M., Muller, C. J., Falahat, S., Nycander, J., Timko,
P. G., … Goff, J. A. (2013). Internal tide generation by abyssal hills using analytical
theory. Journal of Geophysical Research: Oceans. American Geophysical Union.
https://doi.org/10.1002/2013jc009212'
chicago: 'Melet, Angélique, Maxim Nikurashin, Caroline J Muller, S. Falahat, Jonas
Nycander, Patrick G. Timko, Brian K. Arbic, and John A. Goff. “Internal Tide Generation
by Abyssal Hills Using Analytical Theory.” Journal of Geophysical Research:
Oceans. American Geophysical Union, 2013. https://doi.org/10.1002/2013jc009212.'
ieee: 'A. Melet et al., “Internal tide generation by abyssal hills using
analytical theory,” Journal of Geophysical Research: Oceans, vol. 118,
no. 11. American Geophysical Union, pp. 6303–6318, 2013.'
ista: 'Melet A, Nikurashin M, Muller CJ, Falahat S, Nycander J, Timko PG, Arbic
BK, Goff JA. 2013. Internal tide generation by abyssal hills using analytical
theory. Journal of Geophysical Research: Oceans. 118(11), 6303–6318.'
mla: 'Melet, Angélique, et al. “Internal Tide Generation by Abyssal Hills Using
Analytical Theory.” Journal of Geophysical Research: Oceans, vol. 118,
no. 11, American Geophysical Union, 2013, pp. 6303–18, doi:10.1002/2013jc009212.'
short: 'A. Melet, M. Nikurashin, C.J. Muller, S. Falahat, J. Nycander, P.G. Timko,
B.K. Arbic, J.A. Goff, Journal of Geophysical Research: Oceans 118 (2013) 6303–6318.'
date_created: 2021-02-15T15:11:39Z
date_published: 2013-11-07T00:00:00Z
date_updated: 2022-01-24T13:46:15Z
day: '07'
doi: 10.1002/2013jc009212
extern: '1'
intvolume: ' 118'
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/2013JC009212
month: '11'
oa: 1
oa_version: Published Version
page: 6303-6318
publication: 'Journal of Geophysical Research: Oceans'
publication_identifier:
issn:
- 2169-9275
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
status: public
title: Internal tide generation by abyssal hills using analytical theory
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 118
year: '2013'
...
---
_id: '9154'
abstract:
- lang: eng
text: "In this study the response of tropical precipitation extremes to warming
in organized convection is examined using a cloud-resolving model. Vertical shear
is imposed to organize the convection into squall lines. Earlier studies show
that in disorganized convection, the fractional increase of precipitation extremes
is similar to that of surface water vapor, which is substantially smaller than
the increase in column water vapor. It has been suggested that organized convection
could lead to stronger amplifications.\r\nRegardless of the strength of the shear,
amplifications of precipitation extremes in the cloud-resolving simulations are
comparable to those of surface water vapor and are substantially less than increases
in column water vapor. The results without shear and with critical shear, for
which the squall lines are perpendicular to the shear, are surprisingly similar
with a fractional rate of increase of precipitation extremes slightly smaller
than that of surface water vapor. Interestingly, the dependence on shear is nonmonotonic,
and stronger supercritical shear yields larger rates, close to or slightly larger
than surface humidity.\r\nA scaling is used to evaluate the thermodynamic and
dynamic contributions to precipitation extreme changes. To first order, they are
dominated by the thermodynamic component, which has the same magnitude for all
shears, close to the change in surface water vapor. The dynamic contribution plays
a secondary role and tends to weaken extremes without shear and with critical
shear, while it strengthens extremes with supercritical shear. These different
dynamic contributions for different shears are due to different responses of convective
mass fluxes in individual updrafts to warming."
article_processing_charge: No
article_type: original
author:
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
citation:
ama: Muller CJ. Impact of convective organization on the response of tropical precipitation
extremes to warming. Journal of Climate. 2013;26(14):5028-5043. doi:10.1175/jcli-d-12-00655.1
apa: Muller, C. J. (2013). Impact of convective organization on the response of
tropical precipitation extremes to warming. Journal of Climate. American
Meteorological Society. https://doi.org/10.1175/jcli-d-12-00655.1
chicago: Muller, Caroline J. “Impact of Convective Organization on the Response
of Tropical Precipitation Extremes to Warming.” Journal of Climate. American
Meteorological Society, 2013. https://doi.org/10.1175/jcli-d-12-00655.1.
ieee: C. J. Muller, “Impact of convective organization on the response of tropical
precipitation extremes to warming,” Journal of Climate, vol. 26, no. 14.
American Meteorological Society, pp. 5028–5043, 2013.
ista: Muller CJ. 2013. Impact of convective organization on the response of tropical
precipitation extremes to warming. Journal of Climate. 26(14), 5028–5043.
mla: Muller, Caroline J. “Impact of Convective Organization on the Response of Tropical
Precipitation Extremes to Warming.” Journal of Climate, vol. 26, no. 14,
American Meteorological Society, 2013, pp. 5028–43, doi:10.1175/jcli-d-12-00655.1.
short: C.J. Muller, Journal of Climate 26 (2013) 5028–5043.
date_created: 2021-02-15T15:26:39Z
date_published: 2013-07-15T00:00:00Z
date_updated: 2022-01-24T13:46:41Z
day: '15'
doi: 10.1175/jcli-d-12-00655.1
extern: '1'
intvolume: ' 26'
issue: '14'
keyword:
- Atmospheric Science
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1175/JCLI-D-12-00655.1
month: '07'
oa: 1
oa_version: Published Version
page: 5028-5043
publication: Journal of Climate
publication_identifier:
issn:
- 0894-8755
- 1520-0442
publication_status: published
publisher: American Meteorological Society
quality_controlled: '1'
status: public
title: Impact of convective organization on the response of tropical precipitation
extremes to warming
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 26
year: '2013'
...
---
_id: '9167'
abstract:
- lang: eng
text: We introduce a self-propelled colloidal hematite docker that can be steered
to a small particle cargo many times its size, dock, transport the cargo to a
remote location, and then release it. The self-propulsion and docking are reversible
and activated by visible light. The docker can be steered either by a weak uniform
magnetic field or by nanoscale tracks in a textured substrate. The light-activated
motion and docking originate from osmotic/phoretic particle transport in a concentration
gradient of fuel, hydrogen peroxide, induced by the photocatalytic activity of
the hematite. The docking mechanism is versatile and can be applied to various
materials and shapes. The hematite dockers are simple single-component particles
and are synthesized in bulk quantities. This system opens up new possibilities
for designing complex micrometer-size factories as well as new biomimetic systems.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: Stefano
full_name: Sacanna, Stefano
last_name: Sacanna
- first_name: Adrian
full_name: Vatchinsky, Adrian
last_name: Vatchinsky
- first_name: Paul M.
full_name: Chaikin, Paul M.
last_name: Chaikin
- first_name: David J.
full_name: Pine, David J.
last_name: Pine
citation:
ama: Palacci JA, Sacanna S, Vatchinsky A, Chaikin PM, Pine DJ. Photoactivated colloidal
dockers for cargo transportation. Journal of the American Chemical Society.
2013;135(43):15978-15981. doi:10.1021/ja406090s
apa: Palacci, J. A., Sacanna, S., Vatchinsky, A., Chaikin, P. M., & Pine, D.
J. (2013). Photoactivated colloidal dockers for cargo transportation. Journal
of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja406090s
chicago: Palacci, Jérémie A, Stefano Sacanna, Adrian Vatchinsky, Paul M. Chaikin,
and David J. Pine. “Photoactivated Colloidal Dockers for Cargo Transportation.”
Journal of the American Chemical Society. American Chemical Society, 2013.
https://doi.org/10.1021/ja406090s.
ieee: J. A. Palacci, S. Sacanna, A. Vatchinsky, P. M. Chaikin, and D. J. Pine, “Photoactivated
colloidal dockers for cargo transportation,” Journal of the American Chemical
Society, vol. 135, no. 43. American Chemical Society, pp. 15978–15981, 2013.
ista: Palacci JA, Sacanna S, Vatchinsky A, Chaikin PM, Pine DJ. 2013. Photoactivated
colloidal dockers for cargo transportation. Journal of the American Chemical Society.
135(43), 15978–15981.
mla: Palacci, Jérémie A., et al. “Photoactivated Colloidal Dockers for Cargo Transportation.”
Journal of the American Chemical Society, vol. 135, no. 43, American Chemical
Society, 2013, pp. 15978–81, doi:10.1021/ja406090s.
short: J.A. Palacci, S. Sacanna, A. Vatchinsky, P.M. Chaikin, D.J. Pine, Journal
of the American Chemical Society 135 (2013) 15978–15981.
date_created: 2021-02-18T14:31:26Z
date_published: 2013-10-30T00:00:00Z
date_updated: 2021-02-22T10:10:41Z
day: '30'
doi: 10.1021/ja406090s
extern: '1'
external_id:
arxiv:
- '1310.5724'
pmid:
- '24131488'
intvolume: ' 135'
issue: '43'
keyword:
- Colloid and Surface Chemistry
- Biochemistry
- General Chemistry
- Catalysis
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1310.5724
month: '10'
oa: 1
oa_version: Preprint
page: 15978-15981
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
eissn:
- '15205126'
issn:
- '00027863'
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Photoactivated colloidal dockers for cargo transportation
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 135
year: '2013'
...
---
_id: '921'
abstract:
- lang: eng
text: Recent experiments have shown that spreading epithelial sheets exhibit a long-range
coordination of motility forces that leads to a buildup of tension in the tissue,
which may enhance cell division and the speed of wound healing. Furthermore, the
edges of these epithelial sheets commonly show finger-like protrusions whereas
the bulk often displays spontaneous swirls of motile cells. To explain these experimental
observations, we propose a simple flocking-type mechanism, in which cells tend
to align their motility forceswith their velocity. Implementing this idea in amechanical
tissue simulation, the proposed model gives rise to efficient spreading and can
explain the experimentally observed long-range alignment of motility forces in
highly disordered patterns, as well as the buildup of tensile stress throughout
the tissue. Our model also qualitatively reproduces the dependence of swirl size
and swirl velocity on cell density reported in experiments and exhibits an undulation
instability at the edge of the spreading tissue commonly observed in vivo. Finally,
we study the dependence of colony spreading speed on important physical and biological
parameters and derive simple scaling relations that show that coordination of
motility forces leads to an improvement of the wound healing process for realistic
tissue parameters.
acknowledgement: "This work was supported by National Science Foundation (NSF) Grant
DMS-1068869 and by the NSF Center for Theoretical Biological Physics (Grant NSF
PHY-0822283).\r\nWe acknowledge useful discussions with Eshel Ben-Jacob and Assaf
Zaritsky. "
article_processing_charge: No
author:
- first_name: Markus
full_name: Basan, Markus
last_name: Basan
- first_name: Jens
full_name: Elgeti, Jens
last_name: Elgeti
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Wouter
full_name: Rappel, Wouter
last_name: Rappel
- first_name: Herbert
full_name: Levine, Herbert
last_name: Levine
citation:
ama: Basan M, Elgeti J, Hannezo EB, Rappel W, Levine H. Alignment of cellular motility
forces with tissue flow as a mechanism for efficient wound healing. PNAS.
2013;110(7):2452-2459. doi:10.1073/pnas.1219937110
apa: Basan, M., Elgeti, J., Hannezo, E. B., Rappel, W., & Levine, H. (2013).
Alignment of cellular motility forces with tissue flow as a mechanism for efficient
wound healing. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1219937110
chicago: Basan, Markus, Jens Elgeti, Edouard B Hannezo, Wouter Rappel, and Herbert
Levine. “Alignment of Cellular Motility Forces with Tissue Flow as a Mechanism
for Efficient Wound Healing.” PNAS. National Academy of Sciences, 2013.
https://doi.org/10.1073/pnas.1219937110.
ieee: M. Basan, J. Elgeti, E. B. Hannezo, W. Rappel, and H. Levine, “Alignment of
cellular motility forces with tissue flow as a mechanism for efficient wound healing,”
PNAS, vol. 110, no. 7. National Academy of Sciences, pp. 2452–2459, 2013.
ista: Basan M, Elgeti J, Hannezo EB, Rappel W, Levine H. 2013. Alignment of cellular
motility forces with tissue flow as a mechanism for efficient wound healing. PNAS.
110(7), 2452–2459.
mla: Basan, Markus, et al. “Alignment of Cellular Motility Forces with Tissue Flow
as a Mechanism for Efficient Wound Healing.” PNAS, vol. 110, no. 7, National
Academy of Sciences, 2013, pp. 2452–59, doi:10.1073/pnas.1219937110.
short: M. Basan, J. Elgeti, E.B. Hannezo, W. Rappel, H. Levine, PNAS 110 (2013)
2452–2459.
date_created: 2018-12-11T11:49:12Z
date_published: 2013-02-12T00:00:00Z
date_updated: 2021-01-12T08:21:55Z
day: '12'
doi: 10.1073/pnas.1219937110
extern: '1'
intvolume: ' 110'
issue: '7'
language:
- iso: eng
month: '02'
oa_version: None
page: 2452 - 2459
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6518'
status: public
title: Alignment of cellular motility forces with tissue flow as a mechanism for efficient
wound healing
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '7306'
abstract:
- lang: eng
text: Rechargeable lithium–air (O2) batteries are receiving intense interest because
their high theoretical specific energy exceeds that of lithium-ion batteries.
If the Li–O2 battery is ever to succeed, highly reversible formation/decomposition
of Li2O2 must take place at the cathode on cycling. However, carbon, used ubiquitously
as the basis of the cathode, decomposes during Li2O2 oxidation on charge and actively
promotes electrolyte decomposition on cycling. Replacing carbon with a nanoporous
gold cathode, when in contact with a dimethyl sulphoxide-based electrolyte, does
seem to demonstrate better stability. However, nanoporous gold is not a suitable
cathode; its high mass destroys the key advantage of Li–O2 over Li ion (specific
energy), it is too expensive and too difficult to fabricate. Identifying a suitable
cathode material for the Li–O2 cell is one of the greatest challenges at present.
Here we show that a TiC-based cathode reduces greatly side reactions (arising
from the electrolyte and electrode degradation) compared with carbon and exhibits
better reversible formation/decomposition of Li2O2 even than nanoporous gold (>98%
capacity retention after 100 cycles, compared with 95% for nanoporous gold); it
is also four times lighter, of lower cost and easier to fabricate. The stability
may originate from the presence of TiO2 (along with some TiOC) on the surface
of TiC. In contrast to carbon or nanoporous gold, TiC seems to represent a more
viable, stable, cathode for aprotic Li–O2 cells.
article_processing_charge: No
article_type: original
author:
- first_name: Muhammed M.
full_name: Ottakam Thotiyl, Muhammed M.
last_name: Ottakam Thotiyl
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Zhangquan
full_name: Peng, Zhangquan
last_name: Peng
- first_name: Yuhui
full_name: Chen, Yuhui
last_name: Chen
- first_name: Zheng
full_name: Liu, Zheng
last_name: Liu
- first_name: Peter G.
full_name: Bruce, Peter G.
last_name: Bruce
citation:
ama: Ottakam Thotiyl MM, Freunberger SA, Peng Z, Chen Y, Liu Z, Bruce PG. A stable
cathode for the aprotic Li–O2 battery. Nature Materials. 2013;12(11):1050-1056.
doi:10.1038/nmat3737
apa: Ottakam Thotiyl, M. M., Freunberger, S. A., Peng, Z., Chen, Y., Liu, Z., &
Bruce, P. G. (2013). A stable cathode for the aprotic Li–O2 battery. Nature
Materials. Springer Nature. https://doi.org/10.1038/nmat3737
chicago: Ottakam Thotiyl, Muhammed M., Stefan Alexander Freunberger, Zhangquan Peng,
Yuhui Chen, Zheng Liu, and Peter G. Bruce. “A Stable Cathode for the Aprotic Li–O2 Battery.”
Nature Materials. Springer Nature, 2013. https://doi.org/10.1038/nmat3737.
ieee: M. M. Ottakam Thotiyl, S. A. Freunberger, Z. Peng, Y. Chen, Z. Liu, and P.
G. Bruce, “A stable cathode for the aprotic Li–O2 battery,” Nature Materials,
vol. 12, no. 11. Springer Nature, pp. 1050–1056, 2013.
ista: Ottakam Thotiyl MM, Freunberger SA, Peng Z, Chen Y, Liu Z, Bruce PG. 2013.
A stable cathode for the aprotic Li–O2 battery. Nature Materials. 12(11), 1050–1056.
mla: Ottakam Thotiyl, Muhammed M., et al. “A Stable Cathode for the Aprotic Li–O2 Battery.”
Nature Materials, vol. 12, no. 11, Springer Nature, 2013, pp. 1050–56,
doi:10.1038/nmat3737.
short: M.M. Ottakam Thotiyl, S.A. Freunberger, Z. Peng, Y. Chen, Z. Liu, P.G. Bruce,
Nature Materials 12 (2013) 1050–1056.
date_created: 2020-01-15T12:18:29Z
date_published: 2013-09-01T00:00:00Z
date_updated: 2021-01-12T08:12:55Z
day: '01'
doi: 10.1038/nmat3737
extern: '1'
intvolume: ' 12'
issue: '11'
language:
- iso: eng
month: '09'
oa_version: None
page: 1050-1056
publication: Nature Materials
publication_identifier:
issn:
- 1476-1122
- 1476-4660
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: A stable cathode for the aprotic Li–O2 battery
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2013'
...
---
_id: '7307'
abstract:
- lang: eng
text: The non-aqueous Li–air (O2) battery is receiving intense interest because
its theoretical specific energy exceeds that of Li-ion batteries. Recharging the
Li–O2 battery depends on oxidizing solid lithium peroxide (Li2O2), which is formed
on discharge within the porous cathode. However, transporting charge between Li2O2
particles and the solid electrode surface is at best very difficult and leads
to voltage polarization on charging, even at modest rates. This is a significant
problem facing the non-aqueous Li–O2 battery. Here we show that incorporation
of a redox mediator, tetrathiafulvalene (TTF), enables recharging at rates that
are impossible for the cell in the absence of the mediator. On charging, TTF is
oxidized to TTF+ at the cathode surface; TTF+ in turn oxidizes the solid Li2O2,
which results in the regeneration of TTF. The mediator acts as an electron–hole
transfer agent that permits efficient oxidation of solid Li2O2. The cell with
the mediator demonstrated 100 charge/discharge cycles.
article_processing_charge: No
article_type: original
author:
- first_name: Yuhui
full_name: Chen, Yuhui
last_name: Chen
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Zhangquan
full_name: Peng, Zhangquan
last_name: Peng
- first_name: Olivier
full_name: Fontaine, Olivier
last_name: Fontaine
- first_name: Peter G.
full_name: Bruce, Peter G.
last_name: Bruce
citation:
ama: Chen Y, Freunberger SA, Peng Z, Fontaine O, Bruce PG. Charging a Li–O2 battery
using a redox mediator. Nature Chemistry. 2013;5(6):489-494. doi:10.1038/nchem.1646
apa: Chen, Y., Freunberger, S. A., Peng, Z., Fontaine, O., & Bruce, P. G. (2013).
Charging a Li–O2 battery using a redox mediator. Nature Chemistry. Springer
Nature. https://doi.org/10.1038/nchem.1646
chicago: Chen, Yuhui, Stefan Alexander Freunberger, Zhangquan Peng, Olivier Fontaine,
and Peter G. Bruce. “Charging a Li–O2 Battery Using a Redox Mediator.” Nature
Chemistry. Springer Nature, 2013. https://doi.org/10.1038/nchem.1646.
ieee: Y. Chen, S. A. Freunberger, Z. Peng, O. Fontaine, and P. G. Bruce, “Charging
a Li–O2 battery using a redox mediator,” Nature Chemistry, vol. 5, no.
6. Springer Nature, pp. 489–494, 2013.
ista: Chen Y, Freunberger SA, Peng Z, Fontaine O, Bruce PG. 2013. Charging a Li–O2
battery using a redox mediator. Nature Chemistry. 5(6), 489–494.
mla: Chen, Yuhui, et al. “Charging a Li–O2 Battery Using a Redox Mediator.” Nature
Chemistry, vol. 5, no. 6, Springer Nature, 2013, pp. 489–94, doi:10.1038/nchem.1646.
short: Y. Chen, S.A. Freunberger, Z. Peng, O. Fontaine, P.G. Bruce, Nature Chemistry
5 (2013) 489–494.
date_created: 2020-01-15T12:18:43Z
date_published: 2013-05-12T00:00:00Z
date_updated: 2021-01-12T08:12:56Z
day: '12'
doi: 10.1038/nchem.1646
extern: '1'
intvolume: ' 5'
issue: '6'
language:
- iso: eng
month: '05'
oa_version: None
page: 489-494
publication: Nature Chemistry
publication_identifier:
issn:
- 1755-4330
- 1755-4349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Charging a Li–O2 battery using a redox mediator
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2013'
...
---
_id: '7595'
abstract:
- lang: eng
text: Inositol 1,3,4-trisphosphate 5/6 kinase (ITPK) phosphorylates inositol 1,3,4-trisphosphate
to form inositol 1,3,4,5-tetrakisphosphate and inositol 1,3,4,6-tetrakisphosphate
which can be finally transferred to inositol hexaphosphate (IP6) and play important
roles during plant growth and development. There are 4 putative ITPK members in
Arabidopsis. Expression pattern analysis showed that ITPK2 is constitutively expressed
in various tissues. A T-DNA knockout mutant of ITPK2 was identified and scanning
electron microscopy (SEM) analysis showed that the epidermis structure of seed
coat was irregularly formed in seeds of itpk2-1 mutant, resulting in the increased
permeability of seed coat to tetrazolium salts. Further analysis by gas chromatography
coupled with mass spectrometry of lipid polyester monomers in cell wall confirmed
a dramatic decrease in composition of suberin and cutin, which relate to the permeability
of seed coat and the formation of which is accompanied with seed coat development.
These results indicate that ITPK2 plays an essential role in seed coat development
and lipid polyester barrier formation.
article_processing_charge: No
article_type: original
author:
- first_name: Yong
full_name: Tang, Yong
last_name: Tang
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Hongwei
full_name: Xue, Hongwei
last_name: Xue
citation:
ama: Tang Y, Tan S, Xue H. Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2
is required for seed coat development. Acta Biochimica et Biophysica Sinica.
2013;45(7):549-560. doi:10.1093/abbs/gmt039
apa: Tang, Y., Tan, S., & Xue, H. (2013). Arabidopsis inositol 1,3,4-trisphosphate
5/6 kinase 2 is required for seed coat development. Acta Biochimica et Biophysica
Sinica. Oxford University Press. https://doi.org/10.1093/abbs/gmt039
chicago: Tang, Yong, Shutang Tan, and Hongwei Xue. “Arabidopsis Inositol 1,3,4-Trisphosphate
5/6 Kinase 2 Is Required for Seed Coat Development.” Acta Biochimica et Biophysica
Sinica. Oxford University Press, 2013. https://doi.org/10.1093/abbs/gmt039.
ieee: Y. Tang, S. Tan, and H. Xue, “Arabidopsis inositol 1,3,4-trisphosphate 5/6
kinase 2 is required for seed coat development,” Acta Biochimica et Biophysica
Sinica, vol. 45, no. 7. Oxford University Press, pp. 549–560, 2013.
ista: Tang Y, Tan S, Xue H. 2013. Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase
2 is required for seed coat development. Acta Biochimica et Biophysica Sinica.
45(7), 549–560.
mla: Tang, Yong, et al. “Arabidopsis Inositol 1,3,4-Trisphosphate 5/6 Kinase 2 Is
Required for Seed Coat Development.” Acta Biochimica et Biophysica Sinica,
vol. 45, no. 7, Oxford University Press, 2013, pp. 549–60, doi:10.1093/abbs/gmt039.
short: Y. Tang, S. Tan, H. Xue, Acta Biochimica et Biophysica Sinica 45 (2013) 549–560.
date_created: 2020-03-21T16:06:36Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2021-01-12T08:14:23Z
day: '01'
doi: 10.1093/abbs/gmt039
extern: '1'
external_id:
pmid:
- '23595027'
intvolume: ' 45'
issue: '7'
language:
- iso: eng
month: '07'
oa_version: None
page: 549-560
pmid: 1
publication: Acta Biochimica et Biophysica Sinica
publication_identifier:
issn:
- 1745-7270
- 1672-9145
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed
coat development
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2013'
...
---
_id: '7596'
abstract:
- lang: eng
text: Casein kinase1 (CK1) plays crucial roles in regulating growth and development
via phosphorylating various substrates throughout the eukaryote kingdom. Blue
light is crucial for normal growth of both plants and animals, and blue light
receptor cryptochrome2 (CRY2) undergoes blue light–dependent phosphorylation and
degradation in planta. To study the function of plant CK1s, systematic genetic
analysis showed that deficiency of two paralogous Arabidopsis thaliana CK1s, CK1.3
and CK1.4, caused shortened hypocotyls, especially under blue light, while overexpression
of either CK1.3 or CK1.4 resulted in the insensitive response to blue light and
delayed flowering under long-day conditions. CK1.3 or CK1.4 act dependently on
CRY2, and overexpression of CK1.3 or CK1.4 significantly suppresses the hypersensitive
response to blue light by CRY2 overexpression. Biochemical studies showed that
CK1.3 and CK1.4 directly phosphorylate CRY2 at Ser-587 and Thr-603 in vitro and
negatively regulate CRY2 stability in planta, which are stimulated by blue light,
further confirming the crucial roles of CK1.3 and CK1.4 in blue light responses
through phosphorylating CRY2. Interestingly, expression of CK1.3 and CK1.4 is
stimulated by blue light and feedback regulated by CRY2-mediated signaling. These
results provide direct evidence for CRY2 phosphorylation and informative clues
on the mechanisms of CRY2-mediated light responses.
article_processing_charge: No
article_type: original
author:
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: C.
full_name: Dai, C.
last_name: Dai
- first_name: H.-T.
full_name: Liu, H.-T.
last_name: Liu
- first_name: H.-W.
full_name: Xue, H.-W.
last_name: Xue
citation:
ama: Tan S, Dai C, Liu H-T, Xue H-W. Arabidopsis casein kinase1 proteins CK1.3 and
CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling. The Plant
Cell. 2013;25(7):2618-2632. doi:10.1105/tpc.113.114322
apa: Tan, S., Dai, C., Liu, H.-T., & Xue, H.-W. (2013). Arabidopsis casein kinase1
proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling.
The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.113.114322
chicago: Tan, Shutang, C. Dai, H.-T. Liu, and H.-W. Xue. “Arabidopsis Casein Kinase1
Proteins CK1.3 and CK1.4 Phosphorylate Cryptochrome2 to Regulate Blue Light Signaling.”
The Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.114322.
ieee: S. Tan, C. Dai, H.-T. Liu, and H.-W. Xue, “Arabidopsis casein kinase1 proteins
CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling,”
The Plant Cell, vol. 25, no. 7. American Society of Plant Biologists, pp.
2618–2632, 2013.
ista: Tan S, Dai C, Liu H-T, Xue H-W. 2013. Arabidopsis casein kinase1 proteins
CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling.
The Plant Cell. 25(7), 2618–2632.
mla: Tan, Shutang, et al. “Arabidopsis Casein Kinase1 Proteins CK1.3 and CK1.4 Phosphorylate
Cryptochrome2 to Regulate Blue Light Signaling.” The Plant Cell, vol. 25,
no. 7, American Society of Plant Biologists, 2013, pp. 2618–32, doi:10.1105/tpc.113.114322.
short: S. Tan, C. Dai, H.-T. Liu, H.-W. Xue, The Plant Cell 25 (2013) 2618–2632.
date_created: 2020-03-21T16:06:55Z
date_published: 2013-08-26T00:00:00Z
date_updated: 2021-01-12T08:14:24Z
day: '26'
doi: 10.1105/tpc.113.114322
extern: '1'
external_id:
pmid:
- '23897926'
intvolume: ' 25'
issue: '7'
language:
- iso: eng
month: '08'
oa_version: None
page: 2618-2632
pmid: 1
publication: The Plant Cell
publication_identifier:
issn:
- 1040-4651
- 1532-298X
publication_status: published
publisher: American Society of Plant Biologists
quality_controlled: '1'
status: public
title: Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2
to regulate blue light signaling
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2013'
...
---
_id: '765'
abstract:
- lang: eng
text: Renaming is a classic distributed coordination task in which a set of processes
must pick distinct identifiers from a small namespace. In this paper, we consider
the time complexity of this problem when the namespace is linear in the number
of participants, a variant known as loose renaming. We give a non-adaptive algorithm
with O(log log n) (individual) step complexity, where n is a known upper bound
on contention, and an adaptive algorithm with step complexity O((log log k)2),
where k is the actual contention in the execution. We also present a variant of
the adaptive algorithm which requires O(k log log k) total process steps. All
upper bounds hold with high probability against a strong adaptive adversary. We
complement the algorithms with an ω(log log n) expected time lower bound on the
complexity of randomized renaming using test-and-set operations and linear space.
The result is based on a new coupling technique, and is the first to apply to
non-adaptive randomized renaming. Since our algorithms use O(n) test-and-set objects,
our results provide matching bounds on the cost of loose renaming in this setting.
acknowledgement: "Dan Alistarh - This author was supported by the SNF Postdoctoral
Fellows Program, NSF grant CCF-1217921, DoE ASCR grant\r\nER26116/DE-SC0008923,
\ and by grants from the Oracle\r\nand Intel corporations.\r\nJames Aspnes
- Supported in part by NSF grant CCF-0916389.\r\nGeorge Giakkoupis - This work was
funded in part by INRIA Associate Team\r\nRADCON, and ERC Starting Grant GOSSPLE
204742.\r\nPhilipp Woelfel - This research was undertaken, in part, thanks to funding\r\nfrom
the Canada Research Chairs program and the HP Labs\r\nInnovation Research Program."
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: James
full_name: Aspnes, James
last_name: Aspnes
- first_name: George
full_name: Giakkoupis, George
last_name: Giakkoupis
- first_name: Philipp
full_name: Woelfel, Philipp
last_name: Woelfel
citation:
ama: 'Alistarh D-A, Aspnes J, Giakkoupis G, Woelfel P. Randomized loose renaming
in O(loglogn) time. In: ACM; 2013:200-209. doi:10.1145/2484239.2484240'
apa: 'Alistarh, D.-A., Aspnes, J., Giakkoupis, G., & Woelfel, P. (2013). Randomized
loose renaming in O(loglogn) time (pp. 200–209). Presented at the PODC: Principles
of Distributed Computing, ACM. https://doi.org/10.1145/2484239.2484240'
chicago: Alistarh, Dan-Adrian, James Aspnes, George Giakkoupis, and Philipp Woelfel.
“Randomized Loose Renaming in O(Loglogn) Time,” 200–209. ACM, 2013. https://doi.org/10.1145/2484239.2484240.
ieee: 'D.-A. Alistarh, J. Aspnes, G. Giakkoupis, and P. Woelfel, “Randomized loose
renaming in O(loglogn) time,” presented at the PODC: Principles of Distributed
Computing, 2013, pp. 200–209.'
ista: 'Alistarh D-A, Aspnes J, Giakkoupis G, Woelfel P. 2013. Randomized loose renaming
in O(loglogn) time. PODC: Principles of Distributed Computing, 200–209.'
mla: Alistarh, Dan-Adrian, et al. Randomized Loose Renaming in O(Loglogn) Time.
ACM, 2013, pp. 200–09, doi:10.1145/2484239.2484240.
short: D.-A. Alistarh, J. Aspnes, G. Giakkoupis, P. Woelfel, in:, ACM, 2013, pp.
200–209.
conference:
name: 'PODC: Principles of Distributed Computing'
date_created: 2018-12-11T11:48:23Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2023-02-23T13:13:14Z
day: '01'
doi: 10.1145/2484239.2484240
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 200 - 209
publication_status: published
publisher: ACM
publist_id: '6889'
status: public
title: Randomized loose renaming in O(loglogn) time
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '7745'
abstract:
- lang: eng
text: The underlying basis of genetic variation in quantitative traits, in terms
of the number of causal variants and the size of their effects, is largely unknown
in natural populations. The expectation is that complex quantitative trait variation
is attributable to many, possibly interacting, causal variants, whose effects
may depend upon the sex, age and the environment in which they are expressed.
A recently developed methodology in animal breeding derives a value of relatedness
among individuals from high‐density genomic marker data, to estimate additive
genetic variance within livestock populations. Here, we adapt and test the effectiveness
of these methods to partition genetic variation for complex traits across genomic
regions within ecological study populations where individuals have varying degrees
of relatedness. We then apply this approach for the first time to a natural population
and demonstrate that genetic variation in wing length in the great tit (Parus
major) reflects contributions from multiple genomic regions. We show that a polygenic
additive mode of gene action best describes the patterns observed, and we find
no evidence of dosage compensation for the sex chromosome. Our results suggest
that most of the genomic regions that influence wing length have the same effects
in both sexes. We found a limited amount of genetic variance in males that is
attributed to regions that have no effects in females, which could facilitate
the sexual dimorphism observed for this trait. Although this exploratory work
focuses on one complex trait, the methodology is generally applicable to any trait
for any laboratory or wild population, paving the way for investigating sex‐,
age‐ and environment‐specific genetic effects and thus the underlying genetic
architecture of phenotype in biological study systems.
article_processing_charge: No
article_type: original
author:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Anna W.
full_name: Santure, Anna W.
last_name: Santure
- first_name: Isabelle
full_name: DeCauwer, Isabelle
last_name: DeCauwer
- first_name: Ben C.
full_name: Sheldon, Ben C.
last_name: Sheldon
- first_name: Jon
full_name: Slate, Jon
last_name: Slate
citation:
ama: Robinson MR, Santure AW, DeCauwer I, Sheldon BC, Slate J. Partitioning of genetic
variation across the genome using multimarker methods in a wild bird population.
Molecular Ecology. 2013;22(15):3963-3980. doi:10.1111/mec.12375
apa: Robinson, M. R., Santure, A. W., DeCauwer, I., Sheldon, B. C., & Slate,
J. (2013). Partitioning of genetic variation across the genome using multimarker
methods in a wild bird population. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.12375
chicago: Robinson, Matthew Richard, Anna W. Santure, Isabelle DeCauwer, Ben C. Sheldon,
and Jon Slate. “Partitioning of Genetic Variation across the Genome Using Multimarker
Methods in a Wild Bird Population.” Molecular Ecology. Wiley, 2013. https://doi.org/10.1111/mec.12375.
ieee: M. R. Robinson, A. W. Santure, I. DeCauwer, B. C. Sheldon, and J. Slate, “Partitioning
of genetic variation across the genome using multimarker methods in a wild bird
population,” Molecular Ecology, vol. 22, no. 15. Wiley, pp. 3963–3980,
2013.
ista: Robinson MR, Santure AW, DeCauwer I, Sheldon BC, Slate J. 2013. Partitioning
of genetic variation across the genome using multimarker methods in a wild bird
population. Molecular Ecology. 22(15), 3963–3980.
mla: Robinson, Matthew Richard, et al. “Partitioning of Genetic Variation across
the Genome Using Multimarker Methods in a Wild Bird Population.” Molecular
Ecology, vol. 22, no. 15, Wiley, 2013, pp. 3963–80, doi:10.1111/mec.12375.
short: M.R. Robinson, A.W. Santure, I. DeCauwer, B.C. Sheldon, J. Slate, Molecular
Ecology 22 (2013) 3963–3980.
date_created: 2020-04-30T11:00:15Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T08:15:14Z
day: '01'
doi: 10.1111/mec.12375
extern: '1'
intvolume: ' 22'
issue: '15'
language:
- iso: eng
month: '08'
oa_version: None
page: 3963-3980
publication: Molecular Ecology
publication_identifier:
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Partitioning of genetic variation across the genome using multimarker methods
in a wild bird population
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2013'
...
---
_id: '7746'
abstract:
- lang: eng
text: Clutch size and egg mass are life history traits that have been extensively
studied in wild bird populations, as life history theory predicts a negative trade‐off
between them, either at the phenotypic or at the genetic level. Here, we analyse
the genomic architecture of these heritable traits in a wild great tit (Parus
major) population, using three marker‐based approaches – chromosome partitioning,
quantitative trait locus (QTL) mapping and a genome‐wide association study (GWAS).
The variance explained by each great tit chromosome scales with predicted chromosome
size, no location in the genome contains genome‐wide significant QTL, and no individual
SNPs are associated with a large proportion of phenotypic variation, all of which
may suggest that variation in both traits is due to many loci of small effect,
located across the genome. There is no evidence that any regions of the genome
contribute significantly to both traits, which combined with a small, nonsignificant
negative genetic covariance between the traits, suggests the absence of genetic
constraints on the independent evolution of these traits. Our findings support
the hypothesis that variation in life history traits in natural populations is
likely to be determined by many loci of small effect spread throughout the genome,
which are subject to continued input of variation by mutation and migration, although
we cannot exclude the possibility of an additional input of major effect genes
influencing either trait.
article_processing_charge: No
article_type: original
author:
- first_name: Anna W.
full_name: Santure, Anna W.
last_name: Santure
- first_name: Isabelle
full_name: De Cauwer, Isabelle
last_name: De Cauwer
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Jocelyn
full_name: Poissant, Jocelyn
last_name: Poissant
- first_name: Ben C.
full_name: Sheldon, Ben C.
last_name: Sheldon
- first_name: Jon
full_name: Slate, Jon
last_name: Slate
citation:
ama: Santure AW, De Cauwer I, Robinson MR, Poissant J, Sheldon BC, Slate J. Genomic
dissection of variation in clutch size and egg mass in a wild great tit (Parus
major) population. Molecular Ecology. 2013;22(15):3949-3962. doi:10.1111/mec.12376
apa: Santure, A. W., De Cauwer, I., Robinson, M. R., Poissant, J., Sheldon, B. C.,
& Slate, J. (2013). Genomic dissection of variation in clutch size and egg
mass in a wild great tit (Parus major) population. Molecular Ecology. Wiley.
https://doi.org/10.1111/mec.12376
chicago: Santure, Anna W., Isabelle De Cauwer, Matthew Richard Robinson, Jocelyn
Poissant, Ben C. Sheldon, and Jon Slate. “Genomic Dissection of Variation in Clutch
Size and Egg Mass in a Wild Great Tit (Parus Major) Population.” Molecular
Ecology. Wiley, 2013. https://doi.org/10.1111/mec.12376.
ieee: A. W. Santure, I. De Cauwer, M. R. Robinson, J. Poissant, B. C. Sheldon, and
J. Slate, “Genomic dissection of variation in clutch size and egg mass in a wild
great tit (Parus major) population,” Molecular Ecology, vol. 22, no. 15.
Wiley, pp. 3949–3962, 2013.
ista: Santure AW, De Cauwer I, Robinson MR, Poissant J, Sheldon BC, Slate J. 2013.
Genomic dissection of variation in clutch size and egg mass in a wild great tit
(Parus major) population. Molecular Ecology. 22(15), 3949–3962.
mla: Santure, Anna W., et al. “Genomic Dissection of Variation in Clutch Size and
Egg Mass in a Wild Great Tit (Parus Major) Population.” Molecular Ecology,
vol. 22, no. 15, Wiley, 2013, pp. 3949–62, doi:10.1111/mec.12376.
short: A.W. Santure, I. De Cauwer, M.R. Robinson, J. Poissant, B.C. Sheldon, J.
Slate, Molecular Ecology 22 (2013) 3949–3962.
date_created: 2020-04-30T11:00:32Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T08:15:14Z
day: '01'
doi: 10.1111/mec.12376
extern: '1'
intvolume: ' 22'
issue: '15'
language:
- iso: eng
month: '08'
oa_version: None
page: 3949-3962
publication: Molecular Ecology
publication_identifier:
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Genomic dissection of variation in clutch size and egg mass in a wild great
tit (Parus major) population
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2013'
...
---
_id: '7747'
abstract:
- lang: eng
text: Acquisition and allocation of resources are central to life‐history theory.
However, empirical work typically focuses only on allocation despite the fact
that relationships between fitness components may be governed by differences in
the ability of individuals to acquire resources across environments. Here, we
outline a statistical framework to partition the genetic basis of multivariate
plasticity into independent axes of genetic variation, and quantify for the first
time, the extent to which specific traits drive multitrait genotype–environment
interactions. Our framework generalises to analyses of plasticity, growth and
ageing. We apply this approach to a unique, large‐scale, multivariate study of
acquisition, allocation and plasticity in the life history of the cricket, Gryllus
firmus. We demonstrate that resource acquisition and allocation are genetically
correlated, and that plasticity in trade‐offs between allocation to components
of fitness is 90% dependent on genetic variance for total resource acquisition.
These results suggest that genotype–environment effects for resource acquisition
can maintain variation in life‐history components that are typically observed
in the wild.
article_processing_charge: No
article_type: original
author:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Andrew P.
full_name: Beckerman, Andrew P.
last_name: Beckerman
citation:
ama: 'Robinson MR, Beckerman AP. Quantifying multivariate plasticity: Genetic variation
in resource acquisition drives plasticity in resource allocation to components
of life history. Ecology Letters. 2013;16(3):281-290. doi:10.1111/ele.12047'
apa: 'Robinson, M. R., & Beckerman, A. P. (2013). Quantifying multivariate plasticity:
Genetic variation in resource acquisition drives plasticity in resource allocation
to components of life history. Ecology Letters. Wiley. https://doi.org/10.1111/ele.12047'
chicago: 'Robinson, Matthew Richard, and Andrew P. Beckerman. “Quantifying Multivariate
Plasticity: Genetic Variation in Resource Acquisition Drives Plasticity in Resource
Allocation to Components of Life History.” Ecology Letters. Wiley, 2013.
https://doi.org/10.1111/ele.12047.'
ieee: 'M. R. Robinson and A. P. Beckerman, “Quantifying multivariate plasticity:
Genetic variation in resource acquisition drives plasticity in resource allocation
to components of life history,” Ecology Letters, vol. 16, no. 3. Wiley,
pp. 281–290, 2013.'
ista: 'Robinson MR, Beckerman AP. 2013. Quantifying multivariate plasticity: Genetic
variation in resource acquisition drives plasticity in resource allocation to
components of life history. Ecology Letters. 16(3), 281–290.'
mla: 'Robinson, Matthew Richard, and Andrew P. Beckerman. “Quantifying Multivariate
Plasticity: Genetic Variation in Resource Acquisition Drives Plasticity in Resource
Allocation to Components of Life History.” Ecology Letters, vol. 16, no.
3, Wiley, 2013, pp. 281–90, doi:10.1111/ele.12047.'
short: M.R. Robinson, A.P. Beckerman, Ecology Letters 16 (2013) 281–290.
date_created: 2020-04-30T11:00:49Z
date_published: 2013-03-01T00:00:00Z
date_updated: 2021-01-12T08:15:15Z
day: '01'
doi: 10.1111/ele.12047
extern: '1'
intvolume: ' 16'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 281-290
publication: Ecology Letters
publication_identifier:
issn:
- 1461-023X
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: 'Quantifying multivariate plasticity: Genetic variation in resource acquisition
drives plasticity in resource allocation to components of life history'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2013'
...
---
_id: '7774'
abstract:
- lang: eng
text: In 2005, Wyart et al. [Europhys. Lett., 2005, 72, 486] showed that the low
frequency vibrational properties of jammed amorphous sphere packings can be understood
in terms of a length scale, called l*, that diverges as the system becomes marginally
unstable. Despite the tremendous success of this theory, it has been difficult
to connect the counting argument that defines l* to other length scales that diverge
near the jamming transition. We present an alternate derivation of l* based on
the onset of rigidity. This phenomenological approach reveals the physical mechanism
underlying the length scale and is relevant to a range of systems for which the
original argument breaks down. It also allows us to present the first direct numerical
measurement of l*.
article_number: '10993'
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Wouter G.
full_name: Ellenbroek, Wouter G.
last_name: Ellenbroek
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
citation:
ama: 'Goodrich CP, Ellenbroek WG, Liu AJ. Stability of jammed packings I: The rigidity
length scale. Soft Matter. 2013;9(46). doi:10.1039/c3sm51095f'
apa: 'Goodrich, C. P., Ellenbroek, W. G., & Liu, A. J. (2013). Stability of
jammed packings I: The rigidity length scale. Soft Matter. Royal Society
of Chemistry. https://doi.org/10.1039/c3sm51095f'
chicago: 'Goodrich, Carl Peter, Wouter G. Ellenbroek, and Andrea J. Liu. “Stability
of Jammed Packings I: The Rigidity Length Scale.” Soft Matter. Royal Society
of Chemistry, 2013. https://doi.org/10.1039/c3sm51095f.'
ieee: 'C. P. Goodrich, W. G. Ellenbroek, and A. J. Liu, “Stability of jammed packings
I: The rigidity length scale,” Soft Matter, vol. 9, no. 46. Royal Society
of Chemistry, 2013.'
ista: 'Goodrich CP, Ellenbroek WG, Liu AJ. 2013. Stability of jammed packings I:
The rigidity length scale. Soft Matter. 9(46), 10993.'
mla: 'Goodrich, Carl Peter, et al. “Stability of Jammed Packings I: The Rigidity
Length Scale.” Soft Matter, vol. 9, no. 46, 10993, Royal Society of Chemistry,
2013, doi:10.1039/c3sm51095f.'
short: C.P. Goodrich, W.G. Ellenbroek, A.J. Liu, Soft Matter 9 (2013).
date_created: 2020-04-30T11:43:42Z
date_published: 2013-10-08T00:00:00Z
date_updated: 2021-01-12T08:15:27Z
day: '08'
doi: 10.1039/c3sm51095f
extern: '1'
intvolume: ' 9'
issue: '46'
language:
- iso: eng
month: '10'
oa_version: None
publication: Soft Matter
publication_identifier:
issn:
- 1744-683X
- 1744-6848
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
status: public
title: 'Stability of jammed packings I: The rigidity length scale'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2013'
...
---
_id: '7775'
abstract:
- lang: eng
text: As a function of packing fraction at zero temperature and applied stress,
an amorphous packing of spheres exhibits a jamming transition where the system
is sensitive to boundary conditions even in the thermodynamic limit. Upon further
compression, the system should become insensitive to boundary conditions provided
it is sufficiently large. Here we explore the linear response to a large class
of boundary perturbations in 2 and 3 dimensions. We consider each finite packing
with periodic-boundary conditions as the basis of an infinite square or cubic
lattice and study properties of vibrational modes at arbitrary wave vector. We
find that the stability of such modes can be understood in terms of a competition
between plane waves and the anomalous vibrational modes associated with the jamming
transition; infinitesimal boundary perturbations become irrelevant for systems
that are larger than a length scale that characterizes the transverse excitations.
This previously identified length diverges at the jamming transition.
article_number: '11000'
article_processing_charge: No
article_type: original
author:
- first_name: Samuel S.
full_name: Schoenholz, Samuel S.
last_name: Schoenholz
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Oleg
full_name: Kogan, Oleg
last_name: Kogan
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: 'Schoenholz SS, Goodrich CP, Kogan O, Liu AJ, Nagel SR. Stability of jammed
packings II: The transverse length scale. Soft Matter. 2013;9(46). doi:10.1039/c3sm51096d'
apa: 'Schoenholz, S. S., Goodrich, C. P., Kogan, O., Liu, A. J., & Nagel, S.
R. (2013). Stability of jammed packings II: The transverse length scale. Soft
Matter. Royal Society of Chemistry. https://doi.org/10.1039/c3sm51096d'
chicago: 'Schoenholz, Samuel S., Carl Peter Goodrich, Oleg Kogan, Andrea J. Liu,
and Sidney R. Nagel. “Stability of Jammed Packings II: The Transverse Length Scale.”
Soft Matter. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3sm51096d.'
ieee: 'S. S. Schoenholz, C. P. Goodrich, O. Kogan, A. J. Liu, and S. R. Nagel, “Stability
of jammed packings II: The transverse length scale,” Soft Matter, vol.
9, no. 46. Royal Society of Chemistry, 2013.'
ista: 'Schoenholz SS, Goodrich CP, Kogan O, Liu AJ, Nagel SR. 2013. Stability of
jammed packings II: The transverse length scale. Soft Matter. 9(46), 11000.'
mla: 'Schoenholz, Samuel S., et al. “Stability of Jammed Packings II: The Transverse
Length Scale.” Soft Matter, vol. 9, no. 46, 11000, Royal Society of Chemistry,
2013, doi:10.1039/c3sm51096d.'
short: S.S. Schoenholz, C.P. Goodrich, O. Kogan, A.J. Liu, S.R. Nagel, Soft Matter
9 (2013).
date_created: 2020-04-30T11:43:58Z
date_published: 2013-10-08T00:00:00Z
date_updated: 2021-01-12T08:15:27Z
day: '08'
doi: 10.1039/c3sm51096d
extern: '1'
intvolume: ' 9'
issue: '46'
language:
- iso: eng
month: '10'
oa_version: None
publication: Soft Matter
publication_identifier:
issn:
- 1744-683X
- 1744-6848
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
status: public
title: 'Stability of jammed packings II: The transverse length scale'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2013'
...
---
_id: '7785'
abstract:
- lang: eng
text: Neural circuit assembly requires selection of specific cell fates, axonal
trajectories, and synaptic targets. By analyzing the function of a secreted semaphorin,
Sema-2b, in Drosophila olfactory receptor neuron (ORN) development, we identified
multiple molecular and cellular mechanisms that link these events. Notch signaling
limits Sema-2b expression to ventromedial ORN classes, within which Sema-2b cell-autonomously
sensitizes ORN axons to external semaphorins. Central-brain-derived Sema-2a and
Sema-2b attract Sema-2b-expressing axons to the ventromedial trajectory. In addition,
Sema-2b/PlexB-mediated axon-axon interactions consolidate this trajectory choice
and promote ventromedial axon-bundle formation. Selecting the correct developmental
trajectory is ultimately essential for proper target choice. These findings demonstrate
that Sema-2b couples ORN axon guidance to postsynaptic target neuron dendrite
patterning well before the final target selection phase, and exemplify how a single
guidance molecule can drive consecutive stages of neural circuit assembly with
the help of sophisticated spatial and temporal regulation.
article_processing_charge: No
article_type: original
author:
- first_name: William J.
full_name: Joo, William J.
last_name: Joo
- first_name: Lora Beatrice Jaeger
full_name: Sweeney, Lora Beatrice Jaeger
id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
last_name: Sweeney
orcid: 0000-0001-9242-5601
- first_name: Liang
full_name: Liang, Liang
last_name: Liang
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
citation:
ama: 'Joo WJ, Sweeney LB, Liang L, Luo L. Linking cell fate, trajectory choice,
and target selection: Genetic analysis of sema-2b in olfactory axon targeting.
Neuron. 2013;78(4):673-686. doi:10.1016/j.neuron.2013.03.022'
apa: 'Joo, W. J., Sweeney, L. B., Liang, L., & Luo, L. (2013). Linking cell
fate, trajectory choice, and target selection: Genetic analysis of sema-2b in
olfactory axon targeting. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2013.03.022'
chicago: 'Joo, William J., Lora B. Sweeney, Liang Liang, and Liqun Luo. “Linking
Cell Fate, Trajectory Choice, and Target Selection: Genetic Analysis of Sema-2b
in Olfactory Axon Targeting.” Neuron. Elsevier, 2013. https://doi.org/10.1016/j.neuron.2013.03.022.'
ieee: 'W. J. Joo, L. B. Sweeney, L. Liang, and L. Luo, “Linking cell fate, trajectory
choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting,”
Neuron, vol. 78, no. 4. Elsevier, pp. 673–686, 2013.'
ista: 'Joo WJ, Sweeney LB, Liang L, Luo L. 2013. Linking cell fate, trajectory choice,
and target selection: Genetic analysis of sema-2b in olfactory axon targeting.
Neuron. 78(4), 673–686.'
mla: 'Joo, William J., et al. “Linking Cell Fate, Trajectory Choice, and Target
Selection: Genetic Analysis of Sema-2b in Olfactory Axon Targeting.” Neuron,
vol. 78, no. 4, Elsevier, 2013, pp. 673–86, doi:10.1016/j.neuron.2013.03.022.'
short: W.J. Joo, L.B. Sweeney, L. Liang, L. Luo, Neuron 78 (2013) 673–686.
date_created: 2020-04-30T13:19:59Z
date_published: 2013-05-22T00:00:00Z
date_updated: 2024-01-31T10:15:25Z
day: '22'
doi: 10.1016/j.neuron.2013.03.022
extern: '1'
intvolume: ' 78'
issue: '4'
language:
- iso: eng
month: '05'
oa_version: None
page: 673-686
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Linking cell fate, trajectory choice, and target selection: Genetic analysis
of sema-2b in olfactory axon targeting'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 78
year: '2013'
...
---
_id: '8030'
abstract:
- lang: eng
text: While the plasticity of excitatory synaptic connections in the brain has been
widely studied, the plasticity of inhibitory connections is much less understood.
Here, we present recent experimental and theoretical findings concerning the rules
of spike timing-dependent inhibitory plasticity and their putative network function.
This is a summary of a workshop at the COSYNE conference 2012.
article_number: '119'
article_processing_charge: No
article_type: original
author:
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: R. C.
full_name: Froemke, R. C.
last_name: Froemke
- first_name: N.
full_name: Doyon, N.
last_name: Doyon
- first_name: M.
full_name: Gilson, M.
last_name: Gilson
- first_name: J. S.
full_name: Haas, J. S.
last_name: Haas
- first_name: R.
full_name: Liu, R.
last_name: Liu
- first_name: A.
full_name: Maffei, A.
last_name: Maffei
- first_name: P.
full_name: Miller, P.
last_name: Miller
- first_name: C. J.
full_name: Wierenga, C. J.
last_name: Wierenga
- first_name: M. A.
full_name: Woodin, M. A.
last_name: Woodin
- first_name: F.
full_name: Zenke, F.
last_name: Zenke
- first_name: H.
full_name: Sprekeler, H.
last_name: Sprekeler
citation:
ama: 'Vogels TP, Froemke RC, Doyon N, et al. Inhibitory synaptic plasticity: Spike
timing-dependence and putative network function. Frontiers in Neural Circuits.
2013;7. doi:10.3389/fncir.2013.00119'
apa: 'Vogels, T. P., Froemke, R. C., Doyon, N., Gilson, M., Haas, J. S., Liu, R.,
… Sprekeler, H. (2013). Inhibitory synaptic plasticity: Spike timing-dependence
and putative network function. Frontiers in Neural Circuits. Frontiers
Media. https://doi.org/10.3389/fncir.2013.00119'
chicago: 'Vogels, Tim P, R. C. Froemke, N. Doyon, M. Gilson, J. S. Haas, R. Liu,
A. Maffei, et al. “Inhibitory Synaptic Plasticity: Spike Timing-Dependence and
Putative Network Function.” Frontiers in Neural Circuits. Frontiers Media,
2013. https://doi.org/10.3389/fncir.2013.00119.'
ieee: 'T. P. Vogels et al., “Inhibitory synaptic plasticity: Spike timing-dependence
and putative network function,” Frontiers in Neural Circuits, vol. 7. Frontiers
Media, 2013.'
ista: 'Vogels TP, Froemke RC, Doyon N, Gilson M, Haas JS, Liu R, Maffei A, Miller
P, Wierenga CJ, Woodin MA, Zenke F, Sprekeler H. 2013. Inhibitory synaptic plasticity:
Spike timing-dependence and putative network function. Frontiers in Neural Circuits.
7, 119.'
mla: 'Vogels, Tim P., et al. “Inhibitory Synaptic Plasticity: Spike Timing-Dependence
and Putative Network Function.” Frontiers in Neural Circuits, vol. 7, 119,
Frontiers Media, 2013, doi:10.3389/fncir.2013.00119.'
short: T.P. Vogels, R.C. Froemke, N. Doyon, M. Gilson, J.S. Haas, R. Liu, A. Maffei,
P. Miller, C.J. Wierenga, M.A. Woodin, F. Zenke, H. Sprekeler, Frontiers in Neural
Circuits 7 (2013).
date_created: 2020-06-25T13:23:50Z
date_published: 2013-07-18T00:00:00Z
date_updated: 2021-01-12T08:16:38Z
day: '18'
ddc:
- '570'
doi: 10.3389/fncir.2013.00119
extern: '1'
external_id:
pmid:
- '23882186'
file:
- access_level: open_access
checksum: 9c321cb12977d84048712eefa7f0c497
content_type: application/pdf
creator: cziletti
date_created: 2020-07-16T11:23:40Z
date_updated: 2020-07-16T11:23:40Z
file_id: '8123'
file_name: 2013_FrontNeurCirc_Vogels.pdf
file_size: 1530469
relation: main_file
success: 1
file_date_updated: 2020-07-16T11:23:40Z
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Neural Circuits
publication_identifier:
eissn:
- 1662-5110
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
status: public
title: 'Inhibitory synaptic plasticity: Spike timing-dependence and putative network
function'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2013'
...
---
_id: '810'
abstract:
- lang: eng
text: Cryo-electron tomography combined with image processing by sub-tomogram averaging
is unique in its power to resolve the structures of proteins and macromolecular
complexes in situ. Limitations of the method, including the low signal to noise
ratio within individual images from cryo-tomographic datasets and difficulties
in determining the defocus at which the data was collected, mean that to date
the very best structures obtained by sub-tomogram averaging are limited to a resolution
of approximately 15. Å. Here, by optimizing data collection and defocus determination
steps, we have determined the structure of assembled Mason-Pfizer monkey virus
Gag protein using sub-tomogram averaging to a resolution of 8.5. Å. At this resolution
alpha-helices can be directly and clearly visualized. These data demonstrate for
the first time that high-resolution structural information can be obtained from
cryo-electron tomograms using sub-tomogram averaging. Sub-tomogram averaging has
the potential to allow detailed studies of unsolved and biologically relevant
structures under biologically relevant conditions.
acknowledgement: The M-PMV ΔPro CANC tubes imaged in this study were a kind gift from
Pavel Ulbrich and Tomas Ruml, Institute of Chemical Technology, Prague. The cryo-EM
grids were prepared by Tanmay Bharat. This study was technically supported by EMBL’s
IT services unit and by Frank Thommen. We thank Martin Schorb and Svetlana Dodonova
for discussions and advice; Khanh Huy Bui for advice and scripts to streamline tomogram
reconstruction; and Giulia Zanetti, Tanmay Bharat, and Martin Beck for comments
on the manuscript. This study was supported by Deutsche Forschungsgemeinschaft grant
BR 3635/2-1 to JAGB.
author:
- first_name: Florian
full_name: Florian Schur
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Wim
full_name: Hagen, Wim J
last_name: Hagen
- first_name: Alex
full_name: De Marco, Alex
last_name: De Marco
- first_name: John
full_name: Briggs, John A
last_name: Briggs
citation:
ama: Schur FK, Hagen W, De Marco A, Briggs J. Determination of protein structure
at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging.
Journal of Structural Biology. 2013;184(3):394-400. doi:10.1016/j.jsb.2013.10.015
apa: Schur, F. K., Hagen, W., De Marco, A., & Briggs, J. (2013). Determination
of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram
averaging. Journal of Structural Biology. Academic Press. https://doi.org/10.1016/j.jsb.2013.10.015
chicago: Schur, Florian KM, Wim Hagen, Alex De Marco, and John Briggs. “Determination
of Protein Structure at 8.5Å Resolution Using Cryo-Electron Tomography and Sub-Tomogram
Averaging.” Journal of Structural Biology. Academic Press, 2013. https://doi.org/10.1016/j.jsb.2013.10.015.
ieee: F. K. Schur, W. Hagen, A. De Marco, and J. Briggs, “Determination of protein
structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging,”
Journal of Structural Biology, vol. 184, no. 3. Academic Press, pp. 394–400,
2013.
ista: Schur FK, Hagen W, De Marco A, Briggs J. 2013. Determination of protein structure
at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging.
Journal of Structural Biology. 184(3), 394–400.
mla: Schur, Florian KM, et al. “Determination of Protein Structure at 8.5Å Resolution
Using Cryo-Electron Tomography and Sub-Tomogram Averaging.” Journal of Structural
Biology, vol. 184, no. 3, Academic Press, 2013, pp. 394–400, doi:10.1016/j.jsb.2013.10.015.
short: F.K. Schur, W. Hagen, A. De Marco, J. Briggs, Journal of Structural Biology
184 (2013) 394–400.
date_created: 2018-12-11T11:48:37Z
date_published: 2013-12-01T00:00:00Z
date_updated: 2021-01-12T08:16:54Z
day: '01'
doi: 10.1016/j.jsb.2013.10.015
extern: 1
intvolume: ' 184'
issue: '3'
month: '12'
page: 394 - 400
publication: Journal of Structural Biology
publication_status: published
publisher: Academic Press
publist_id: '6839'
quality_controlled: 0
status: public
title: Determination of protein structure at 8.5Å resolution using cryo-electron tomography
and sub-tomogram averaging
type: journal_article
volume: 184
year: '2013'
...
---
_id: '811'
abstract:
- lang: eng
text: Cell migration is commonly accompanied by protrusion of membrane ruffles and
lamellipodia. In two-dimensional migration, protrusion of these thin sheets of
cytoplasm is considered relevant to both exploration of new space and initiation
of nascent adhesion to the substratum. Lamellipodium formation can be potently
stimulated by Rho GTPases of the Rac subfamily, but alsoby RhoG or Cdc42. Here
we describe viable fibroblast cell lines geneticallydeficient for Rac1 that lack
detectable levels of Rac2 and Rac3. Rac-deficient cells were devoid of apparent
lamellipodia, but these structures were restored by expression of either Rac subfamily
member, but not by Cdc42 or RhoG. Cells deficient in Rac showed strong reduction
in wound closure and random cell migration and a notable loss of sensitivity to
a chemotactic gradient. Despite these defects, Rac-deficient cells were able to
spread, formed filopodia and established focal adhesions. Spreading in these cells
was achieved by the extension of filopodia followed by the advancement of cytoplasmic
veils between them. The number and size of focal adhesions as well as their intensity
were largely unaffected by genetic removal of Rac1. However, Rac deficiency increased
the mobility of different components in focal adhesions, potentially explaining
how Rac - although not essential - can contribute to focal adhesion assembly.
Together, our data demonstrate that Rac signaling is essential for lamellipodium
protrusion and for efficient cell migration, but not for spreading or filopodium
formation. Our findings also suggest that Rac GTPases are crucial to the establishment
or maintenance of polarity in chemotactic migration.
acknowledgement: |-
This work was supported in part by the Deutsche Forschungsgemeinschaft [grants within programs SFB621 to K.R., and FOR629 and SFB629 to T.E.B.S.]. Deposited in PMC for immediate release.
We thank Brigitte Denker and Gerd Landsberg for excellent technical assistance. We are grateful to Robert Geffers (HZI Braunschweig, Germany) for microarray analyses and to Mirko Himmel (UKE Hamburg, Germany) for valuable advice on FRAP analysis.
author:
- first_name: Anika
full_name: Steffen, Anika
last_name: Steffen
- first_name: Markus
full_name: Ladwein, Markus
last_name: Ladwein
- first_name: Georgi A
full_name: Georgi Dimchev
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
- first_name: Anke
full_name: Hein, Anke
last_name: Hein
- first_name: Lisa
full_name: Schwenkmezger, Lisa
last_name: Schwenkmezger
- first_name: Stefan
full_name: Arens, Stefan
last_name: Arens
- first_name: Kathrin
full_name: Ladwein, Kathrin I
last_name: Ladwein
- first_name: J.
full_name: Holleboom, J. Margit
last_name: Holleboom
- first_name: Florian
full_name: Florian Schur
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: John
full_name: Small, John V
last_name: Small
- first_name: Janett
full_name: Schwarz, Janett
last_name: Schwarz
- first_name: Ralf
full_name: Gerhard, Ralf
last_name: Gerhard
- first_name: Jan
full_name: Faix, Jan
last_name: Faix
- first_name: Theresia
full_name: Stradal, Theresia E
last_name: Stradal
- first_name: Cord
full_name: Brakebusch, Cord H
last_name: Brakebusch
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
citation:
ama: Steffen A, Ladwein M, Dimchev GA, et al. Rac function is crucial for cell migration
but is not required for spreading and focal adhesion formation. Journal of
Cell Science. 2013;126(20):4572-4588. doi:10.1242/jcs.118232
apa: Steffen, A., Ladwein, M., Dimchev, G. A., Hein, A., Schwenkmezger, L., Arens,
S., … Rottner, K. (2013). Rac function is crucial for cell migration but is not
required for spreading and focal adhesion formation. Journal of Cell Science.
Company of Biologists. https://doi.org/10.1242/jcs.118232
chicago: Steffen, Anika, Markus Ladwein, Georgi A Dimchev, Anke Hein, Lisa Schwenkmezger,
Stefan Arens, Kathrin Ladwein, et al. “Rac Function Is Crucial for Cell Migration
but Is Not Required for Spreading and Focal Adhesion Formation.” Journal of
Cell Science. Company of Biologists, 2013. https://doi.org/10.1242/jcs.118232.
ieee: A. Steffen et al., “Rac function is crucial for cell migration but
is not required for spreading and focal adhesion formation,” Journal of Cell
Science, vol. 126, no. 20. Company of Biologists, pp. 4572–4588, 2013.
ista: Steffen A, Ladwein M, Dimchev GA, Hein A, Schwenkmezger L, Arens S, Ladwein
K, Holleboom J, Schur FK, Small J, Schwarz J, Gerhard R, Faix J, Stradal T, Brakebusch
C, Rottner K. 2013. Rac function is crucial for cell migration but is not required
for spreading and focal adhesion formation. Journal of Cell Science. 126(20),
4572–4588.
mla: Steffen, Anika, et al. “Rac Function Is Crucial for Cell Migration but Is Not
Required for Spreading and Focal Adhesion Formation.” Journal of Cell Science,
vol. 126, no. 20, Company of Biologists, 2013, pp. 4572–88, doi:10.1242/jcs.118232.
short: A. Steffen, M. Ladwein, G.A. Dimchev, A. Hein, L. Schwenkmezger, S. Arens,
K. Ladwein, J. Holleboom, F.K. Schur, J. Small, J. Schwarz, R. Gerhard, J. Faix,
T. Stradal, C. Brakebusch, K. Rottner, Journal of Cell Science 126 (2013) 4572–4588.
date_created: 2018-12-11T11:48:38Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T08:16:57Z
day: '01'
doi: 10.1242/jcs.118232
extern: 1
intvolume: ' 126'
issue: '20'
month: '01'
page: 4572 - 4588
publication: Journal of Cell Science
publication_status: published
publisher: Company of Biologists
publist_id: '6840'
quality_controlled: 0
status: public
title: Rac function is crucial for cell migration but is not required for spreading
and focal adhesion formation
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: 126
year: '2013'
...
---
_id: '812'
abstract:
- lang: eng
text: Lamellipodia are sheet-like protrusions formed during migration or phagocytosis
and comprise a network of actin filaments. Filament formation in this network
is initiated by nucleation/branching through the actin-related protein 2/3 (Arp2/3)
complex downstream of its activator, suppressor of cAMP receptor/WASP-family verprolin
homologous (Scar/WAVE), but the relative relevance of Arp2/3-mediated branching
versus actin filament elongation is unknown. Here we use instantaneous interference
with Arp2/3 complex function in live fibroblasts with established lamellipodia.
This allows direct examination of both the fate of elongating filaments upon instantaneous
suppression of Arp2/3 complex activity and the consequences of this treatment
on the dynamics of other lamellipodial regulators. We show that Arp2/3 complex
is an essential organizer of treadmilling actin filament arrays but has little
effect on the net rate of actin filament turnover at the cell periphery. In addition,
Arp2/3 complex serves as key upstream factor for the recruitment of modulators
of lamellipodia formation such as capping protein or cofilin. Arp2/3 complex is
thus decisive for filament organization and geometry within the network not only
by generating branches and novel filament ends, but also by directing capping
or severing activities to the lamellipodium. Arp2/3 complex is also crucial to
lamellipodia-based migration of keratocytes.
acknowledgement: "This work was supported in part by Deutsche Forschungsgemeinschaft
Grants RO2414/3-1 (to K.R.) and FA330/6-1 (to J.F.), Austrian \nScience Fund Projects
FWF 1516-B09 and FWF P21292-B09 (to J.V.S.), the Vienna Science and Technology
\ Fund (WWTF, to \nJ.V.S. and C.S.), and Australian National Health and
\ Medical \nResearch Council Grant APP1004175 (to P.W.G.). We thank J. Adams, \nR.
Chisholm, A. Hall, L. Machesky, H. G. Mannherz, D. Schafer, and \nR. Wedlich-Söldner
\ for expression constructs and B. Denker, \nP. Hagendorff, and G. Landsberg
for technical assistance."
author:
- first_name: Stefan
full_name: Koestler, Stefan A
last_name: Koestler
- first_name: Anika
full_name: Steffen, Anika
last_name: Steffen
- first_name: Maria
full_name: Maria Nemethova
id: 34E27F1C-F248-11E8-B48F-1D18A9856A87
last_name: Nemethova
- first_name: Moritz
full_name: Winterhoff, Moritz
last_name: Winterhoff
- first_name: Ningning
full_name: Luo, Ningning
last_name: Luo
- first_name: J.
full_name: Holleboom, J. Margit
last_name: Holleboom
- first_name: Jessica
full_name: Krupp, Jessica
last_name: Krupp
- first_name: Sonja
full_name: Jacob, Sonja
last_name: Jacob
- first_name: Marlene
full_name: Vinzenz, Marlene
last_name: Vinzenz
- first_name: Florian
full_name: Florian Schur
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Kai
full_name: Schlüter, Kai
last_name: Schlüter
- first_name: Peter
full_name: Gunning, Peter W
last_name: Gunning
- first_name: Christoph
full_name: Winkler, Christoph
last_name: Winkler
- first_name: Christian
full_name: Schmeiser, Christian
last_name: Schmeiser
- first_name: Jan
full_name: Faix, Jan
last_name: Faix
- first_name: Theresia
full_name: Stradal, Theresia E
last_name: Stradal
- first_name: John
full_name: Small, John V
last_name: Small
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
citation:
ama: Koestler S, Steffen A, Nemethova M, et al. Arp2/3 complex is essential for
actin network treadmilling as well as for targeting of capping protein and cofilin.
Molecular Biology of the Cell. 2013;24(18):2861-2875. doi:10.1091/mbc.E12-12-0857
apa: Koestler, S., Steffen, A., Nemethova, M., Winterhoff, M., Luo, N., Holleboom,
J., … Rottner, K. (2013). Arp2/3 complex is essential for actin network treadmilling
as well as for targeting of capping protein and cofilin. Molecular Biology
of the Cell. American Society for Biology. https://doi.org/10.1091/mbc.E12-12-0857
chicago: Koestler, Stefan, Anika Steffen, Maria Nemethova, Moritz Winterhoff, Ningning
Luo, J. Holleboom, Jessica Krupp, et al. “Arp2/3 Complex Is Essential for Actin
Network Treadmilling as Well as for Targeting of Capping Protein and Cofilin.”
Molecular Biology of the Cell. American Society for Biology, 2013. https://doi.org/10.1091/mbc.E12-12-0857.
ieee: S. Koestler et al., “Arp2/3 complex is essential for actin network
treadmilling as well as for targeting of capping protein and cofilin,” Molecular
Biology of the Cell, vol. 24, no. 18. American Society for Biology, pp. 2861–2875,
2013.
ista: Koestler S, Steffen A, Nemethova M, Winterhoff M, Luo N, Holleboom J, Krupp
J, Jacob S, Vinzenz M, Schur FK, Schlüter K, Gunning P, Winkler C, Schmeiser C,
Faix J, Stradal T, Small J, Rottner K. 2013. Arp2/3 complex is essential for actin
network treadmilling as well as for targeting of capping protein and cofilin.
Molecular Biology of the Cell. 24(18), 2861–2875.
mla: Koestler, Stefan, et al. “Arp2/3 Complex Is Essential for Actin Network Treadmilling
as Well as for Targeting of Capping Protein and Cofilin.” Molecular Biology
of the Cell, vol. 24, no. 18, American Society for Biology, 2013, pp. 2861–75,
doi:10.1091/mbc.E12-12-0857.
short: S. Koestler, A. Steffen, M. Nemethova, M. Winterhoff, N. Luo, J. Holleboom,
J. Krupp, S. Jacob, M. Vinzenz, F.K. Schur, K. Schlüter, P. Gunning, C. Winkler,
C. Schmeiser, J. Faix, T. Stradal, J. Small, K. Rottner, Molecular Biology of
the Cell 24 (2013) 2861–2875.
date_created: 2018-12-11T11:48:38Z
date_published: 2013-09-15T00:00:00Z
date_updated: 2021-01-12T08:17:00Z
day: '15'
doi: 10.1091/mbc.E12-12-0857
extern: 1
intvolume: ' 24'
issue: '18'
month: '09'
page: 2861 - 2875
publication: Molecular Biology of the Cell
publication_status: published
publisher: American Society for Biology
publist_id: '6841'
quality_controlled: 0
status: public
title: Arp2/3 complex is essential for actin network treadmilling as well as for targeting
of capping protein and cofilin
type: journal_article
volume: 24
year: '2013'
...
---
_id: '1726'
abstract:
- lang: eng
text: The development of a functional tissue requires coordination of the amplification
of progenitors and their differentiation into specific cell types. The molecular
basis for this coordination during myotome ontogeny is not well understood. Dermomytome
progenitors that colonize the myotome first acquire myocyte identity and subsequently
proliferate as Pax7-expressing progenitors before undergoing terminal differentiation.
We show that the dynamics of sonic hedgehog (Shh) signaling is crucial for this
transition in both avian and mouse embryos. Initially, Shh ligand emanating from
notochord/floor plate reaches the dermomyotome, where it both maintains the proliferation
of dermomyotome cells and promotes myogenic differentiation of progenitors that
colonized the myotome. Interfering with Shh signaling at this stage produces small
myotomes and accumulation of Pax7-expressing progenitors. An in vivo reporter
of Shh activity combined with mouse genetics revealed the existence of both activator
and repressor Shh activities operating on distinct subsets of cells during the
epaxial myotomal maturation. In contrast to observations in mice, in avians Shh
promotes the differentiation of both epaxial and hypaxial myotome domains. Subsequently,
myogenic progenitors become refractory to Shh; this is likely to occur at the
level of, or upstream of, smoothened signaling. The end of responsiveness to Shh
coincides with, and is thus likely to enable, the transition into the growth phase
of the myotome.
acknowledgement: This study was supported by grants from the Israel Science Foundation
(ISF) [11/09 to C.K.]; the Association Francaise contre les Myopathies (AFM) [15642
to C.K.]; the German Research Foundation (DFG) [UN 34/27-1 to C.K.]; the UK Medical
Research Council (MRC) [U117560541 to J.B. and A.K.]; Fondation Pour la Recherche
Médicale (FRM) (post-doctoral fellowship to V.R.). Deposited in PMC for release
after 6 months
author:
- first_name: Nitza
full_name: Kahane, Nitza
last_name: Kahane
- first_name: Vanessa
full_name: Ribes, Vanessa
last_name: Ribes
- first_name: Anna
full_name: Anna Kicheva
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: James
full_name: Briscoe, James
last_name: Briscoe
- first_name: Chaya
full_name: Kalcheim, Chaya
last_name: Kalcheim
citation:
ama: Kahane N, Ribes V, Kicheva A, Briscoe J, Kalcheim C. The transition from differentiation
to growth during dermomyotome-derived myogenesis depends on temporally restricted
hedgehog signaling. Development. 2013;140(8):1740-1750. doi:10.1242/dev.092726
apa: Kahane, N., Ribes, V., Kicheva, A., Briscoe, J., & Kalcheim, C. (2013).
The transition from differentiation to growth during dermomyotome-derived myogenesis
depends on temporally restricted hedgehog signaling. Development. Company
of Biologists. https://doi.org/10.1242/dev.092726
chicago: Kahane, Nitza, Vanessa Ribes, Anna Kicheva, James Briscoe, and Chaya Kalcheim.
“The Transition from Differentiation to Growth during Dermomyotome-Derived Myogenesis
Depends on Temporally Restricted Hedgehog Signaling.” Development. Company
of Biologists, 2013. https://doi.org/10.1242/dev.092726.
ieee: N. Kahane, V. Ribes, A. Kicheva, J. Briscoe, and C. Kalcheim, “The transition
from differentiation to growth during dermomyotome-derived myogenesis depends
on temporally restricted hedgehog signaling,” Development, vol. 140, no.
8. Company of Biologists, pp. 1740–1750, 2013.
ista: Kahane N, Ribes V, Kicheva A, Briscoe J, Kalcheim C. 2013. The transition
from differentiation to growth during dermomyotome-derived myogenesis depends
on temporally restricted hedgehog signaling. Development. 140(8), 1740–1750.
mla: Kahane, Nitza, et al. “The Transition from Differentiation to Growth during
Dermomyotome-Derived Myogenesis Depends on Temporally Restricted Hedgehog Signaling.”
Development, vol. 140, no. 8, Company of Biologists, 2013, pp. 1740–50,
doi:10.1242/dev.092726.
short: N. Kahane, V. Ribes, A. Kicheva, J. Briscoe, C. Kalcheim, Development 140
(2013) 1740–1750.
date_created: 2018-12-11T11:53:41Z
date_published: 2013-04-18T00:00:00Z
date_updated: 2021-01-12T06:52:47Z
day: '18'
doi: 10.1242/dev.092726
extern: 1
intvolume: ' 140'
issue: '8'
month: '04'
page: 1740 - 1750
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '5402'
quality_controlled: 0
status: public
title: The transition from differentiation to growth during dermomyotome-derived myogenesis
depends on temporally restricted hedgehog signaling
type: journal_article
volume: 140
year: '2013'
...