---
_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: '8245'
abstract:
- lang: eng
text: "Background: Monoclonal antibodies (mAb), such as trastuzumab are a valuable
addition to breast cancer therapy.\r\nData obtained from neoadjuvant settings
revealed that antibody-dependent cell-mediated cytotoxicity (ADCC) is a\r\nmajor
mechanism of action for the mAb trastuzumab. Conflicting results still call into
question whether disease\r\nprogression, prolonged treatment or concomitant chemotherapy
influences ADCC and related immunological\r\nphenomena.\r\nMethods: We analyzed
the activity of ADCC and antibody-dependent cell-mediated phagocytosis (ADCP)
of\r\nperipheral blood mononuclear cells (PBMCs) from human epidermal growth factor
receptor 2 (HER2/neu) positive\r\nbreast cancer patients receiving trastuzumab
therapy either in an adjuvant (n = 13) or metastatic (n = 15) setting as\r\nwell
as from trastuzumab treatment-naive (t-naive) HER2/neu negative patients (n =
15). PBMCs from healthy volunteers\r\n(n = 24) were used as controls. ADCC and
ADCP activity was correlated with the expression of antibody binding\r\nFc-gamma
receptor (FcγR)I (CD64), FcγRII (CD32) and FcγRIII (CD16) on CD14+ (monocytes)
and CD56+ (NK) cells, as well as the expression of CD107a+ (LAMP-1) on CD56+ cells
and the total amount of CD4+CD25+FOXP3+ (Treg) cells. In metastatic patients,
markers were correlated with progression-free survival (PFS).\r\nResults: ADCC
activity was significantly down regulated in metastatic, adjuvant and t-naive
patient cohorts as compared to healthy controls. Reduced ADCC activity was inversely
correlated with the expression of CD107a on CD56+\r\ncells in adjuvant patients.
ADCC and ADCP activity of the patient cohorts were similar, regardless of treatment
duration\r\nor additional chemotherapy. PFS in metastatic patients inversely correlated
with the number of peripheral Treg cells.\r\nConclusion: The reduction of ADCC
in patients as compared to healthy controls calls for adjuvant strategies, such
as\r\nimmune-enhancing agents, to improve the activity of trastuzumab. However,
efficacy of trastuzumab-specific ADCC\r\nand ADCP appears not to be affected by
treatment duration, disease progression or concomitant chemotherapy. This\r\nfinding
supports the application of trastuzumab at any stage of the disease."
article_number: '307'
article_processing_charge: No
author:
- first_name: Branka
full_name: Petricevic, Branka
last_name: Petricevic
- first_name: Johannes
full_name: Laengle, Johannes
last_name: Laengle
- first_name: Josef
full_name: Singer, Josef
last_name: Singer
- first_name: Monika
full_name: Sachet, Monika
last_name: Sachet
- first_name: Judit
full_name: Fazekas, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas
orcid: 0000-0002-8777-3502
- first_name: Guenther
full_name: Steger, Guenther
last_name: Steger
- first_name: Rupert
full_name: Bartsch, Rupert
last_name: Bartsch
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
- first_name: Michael
full_name: Bergmann, Michael
last_name: Bergmann
citation:
ama: Petricevic B, Laengle J, Singer J, et al. Trastuzumab mediates antibody-dependent
cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant
and metastatic HER2/neu breast cancer patients. Journal of Translational Medicine.
2013;11. doi:10.1186/1479-5876-11-307
apa: Petricevic, B., Laengle, J., Singer, J., Sachet, M., Singer, J., Steger, G.,
… Bergmann, M. (2013). Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity
and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast
cancer patients. Journal of Translational Medicine. Springer Nature. https://doi.org/10.1186/1479-5876-11-307
chicago: Petricevic, Branka, Johannes Laengle, Josef Singer, Monika Sachet, Judit
Singer, Guenther Steger, Rupert Bartsch, Erika Jensen-Jarolim, and Michael Bergmann.
“Trastuzumab Mediates Antibody-Dependent Cell-Mediated Cytotoxicity and Phagocytosis
to the Same Extent in Both Adjuvant and Metastatic HER2/Neu Breast Cancer Patients.”
Journal of Translational Medicine. Springer Nature, 2013. https://doi.org/10.1186/1479-5876-11-307.
ieee: B. Petricevic et al., “Trastuzumab mediates antibody-dependent cell-mediated
cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic
HER2/neu breast cancer patients,” Journal of Translational Medicine, vol.
11. Springer Nature, 2013.
ista: Petricevic B, Laengle J, Singer J, Sachet M, Singer J, Steger G, Bartsch R,
Jensen-Jarolim E, Bergmann M. 2013. Trastuzumab mediates antibody-dependent cell-mediated
cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic
HER2/neu breast cancer patients. Journal of Translational Medicine. 11, 307.
mla: Petricevic, Branka, et al. “Trastuzumab Mediates Antibody-Dependent Cell-Mediated
Cytotoxicity and Phagocytosis to the Same Extent in Both Adjuvant and Metastatic
HER2/Neu Breast Cancer Patients.” Journal of Translational Medicine, vol.
11, 307, Springer Nature, 2013, doi:10.1186/1479-5876-11-307.
short: B. Petricevic, J. Laengle, J. Singer, M. Sachet, J. Singer, G. Steger, R.
Bartsch, E. Jensen-Jarolim, M. Bergmann, Journal of Translational Medicine 11
(2013).
date_created: 2020-08-10T11:54:34Z
date_published: 2013-12-12T00:00:00Z
date_updated: 2022-08-25T14:52:39Z
day: '12'
ddc:
- '570'
doi: 10.1186/1479-5876-11-307
extern: '1'
external_id:
pmid:
- '24330813'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-08-10T13:45:19Z
date_updated: 2020-08-10T13:45:19Z
file_id: '8247'
file_name: 2013_JoTM_Petricevic.pdf
file_size: 777311
relation: main_file
success: 1
file_date_updated: 2020-08-10T13:45:19Z
has_accepted_license: '1'
intvolume: ' 11'
language:
- iso: eng
month: '12'
oa: 1
oa_version: None
pmid: 1
publication: Journal of Translational Medicine
publication_identifier:
issn:
- 1479-5876
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis
to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2013'
...
---
_id: '827'
abstract:
- lang: eng
text: As sessile organisms, plants have to be able to adapt to a continuously changing
environment. Plants that perceive some of these changes as stress signals activate
signaling pathways to modulate their development and to enable them to survive.
The complex responses to environmental cues are to a large extent mediated by
plant hormones that together orchestrate the final plant response. The phytohormone
cytokinin is involved in many plant developmental processes. Recently, it has
been established that cytokinin plays an important role in stress responses, but
does not act alone. Indeed, the hormonal control of plant development and stress
adaptation is the outcome of a complex network of multiple synergistic and antagonistic
interactions between various hormones. Here, we review the recent findings on
the cytokinin function as part of this hormonal network. We focus on the importance
of the crosstalk between cytokinin and other hormones, such as abscisic acid,
jasmonate, salicylic acid, ethylene, and auxin in the modulation of plant development
and stress adaptation. Finally, the impact of the current research in the biotechnological
industry will be discussed.
article_number: '451'
article_processing_charge: No
author:
- first_name: José
full_name: O'Brien, José
last_name: O'Brien
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: O’Brien J, Benková E. Cytokinin cross talking during biotic and abiotic stress
responses. Frontiers in Plant Science. 2013;4. doi:10.3389/fpls.2013.00451
apa: O’Brien, J., & Benková, E. (2013). Cytokinin cross talking during biotic
and abiotic stress responses. Frontiers in Plant Science. Frontiers Research
Foundation. https://doi.org/10.3389/fpls.2013.00451
chicago: O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic
and Abiotic Stress Responses.” Frontiers in Plant Science. Frontiers Research
Foundation, 2013. https://doi.org/10.3389/fpls.2013.00451.
ieee: J. O’Brien and E. Benková, “Cytokinin cross talking during biotic and abiotic
stress responses,” Frontiers in Plant Science, vol. 4. Frontiers Research
Foundation, 2013.
ista: O’Brien J, Benková E. 2013. Cytokinin cross talking during biotic and abiotic
stress responses. Frontiers in Plant Science. 4, 451.
mla: O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and
Abiotic Stress Responses.” Frontiers in Plant Science, vol. 4, 451, Frontiers
Research Foundation, 2013, doi:10.3389/fpls.2013.00451.
short: J. O’Brien, E. Benková, Frontiers in Plant Science 4 (2013).
corr_author: '1'
date_created: 2018-12-11T11:48:43Z
date_published: 2013-11-19T00:00:00Z
date_updated: 2025-09-29T14:33:09Z
day: '19'
ddc:
- '580'
department:
- _id: EvBe
doi: 10.3389/fpls.2013.00451
ec_funded: 1
external_id:
isi:
- '000331445200001'
file:
- access_level: open_access
checksum: fdc25ddd1bf9a99b99f662cdbafeddd4
content_type: application/pdf
creator: dernst
date_created: 2019-01-31T10:40:38Z
date_updated: 2020-07-14T12:48:11Z
file_id: '5903'
file_name: 2013_FrontiersPlant_OBrien.pdf
file_size: 953299
relation: main_file
file_date_updated: 2020-07-14T12:48:11Z
has_accepted_license: '1'
intvolume: ' 4'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
publication: Frontiers in Plant Science
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '6821'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cytokinin cross talking during biotic and abiotic stress responses
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 4
year: '2013'
...
---
_id: '828'
abstract:
- lang: eng
text: The plant root system is essential for providing anchorage to the soil, supplying
minerals and water, and synthesizing metabolites. It is a dynamic organ modulated
by external cues such as environmental signals, water and nutrients availability,
salinity and others. Lateral roots (LRs) are initiated from the primary root post-embryonically,
after which they progress through discrete developmental stages which can be independently
controlled, providing a high level of plasticity during root system formation.
Within this review, main contributions are presented, from the classical forward
genetic screens to the more recent high-throughput approaches, combined with computer
model predictions, dissecting how LRs and thereby root system architecture is
established and developed.
article_number: '537'
article_processing_charge: No
author:
- first_name: Candela
full_name: Cuesta, Candela
id: 33A3C818-F248-11E8-B48F-1D18A9856A87
last_name: Cuesta
orcid: 0000-0003-1923-2410
- 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: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Cuesta C, Wabnik KT, Benková E. Systems approaches to study root architecture
dynamics. Frontiers in Plant Science. 2013;4. doi:10.3389/fpls.2013.00537
apa: Cuesta, C., Wabnik, K. T., & Benková, E. (2013). Systems approaches to
study root architecture dynamics. Frontiers in Plant Science. Frontiers
Research Foundation. https://doi.org/10.3389/fpls.2013.00537
chicago: Cuesta, Candela, Krzysztof T Wabnik, and Eva Benková. “Systems Approaches
to Study Root Architecture Dynamics.” Frontiers in Plant Science. Frontiers
Research Foundation, 2013. https://doi.org/10.3389/fpls.2013.00537.
ieee: C. Cuesta, K. T. Wabnik, and E. Benková, “Systems approaches to study root
architecture dynamics,” Frontiers in Plant Science, vol. 4. Frontiers Research
Foundation, 2013.
ista: Cuesta C, Wabnik KT, Benková E. 2013. Systems approaches to study root architecture
dynamics. Frontiers in Plant Science. 4, 537.
mla: Cuesta, Candela, et al. “Systems Approaches to Study Root Architecture Dynamics.”
Frontiers in Plant Science, vol. 4, 537, Frontiers Research Foundation,
2013, doi:10.3389/fpls.2013.00537.
short: C. Cuesta, K.T. Wabnik, E. Benková, Frontiers in Plant Science 4 (2013).
corr_author: '1'
date_created: 2018-12-11T11:48:43Z
date_published: 2013-12-26T00:00:00Z
date_updated: 2025-09-29T14:32:42Z
day: '26'
ddc:
- '580'
department:
- _id: EvBe
doi: 10.3389/fpls.2013.00537
ec_funded: 1
external_id:
isi:
- '000331533500002'
file:
- access_level: open_access
checksum: 0185b3c4d7df9a94bd3ce5a66d213506
content_type: application/pdf
creator: dernst
date_created: 2019-01-31T10:36:43Z
date_updated: 2020-07-14T12:48:11Z
file_id: '5902'
file_name: 2013_FrontiersPlant_Cuesta.pdf
file_size: 710835
relation: main_file
file_date_updated: 2020-07-14T12:48:11Z
has_accepted_license: '1'
intvolume: ' 4'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
publication: Frontiers in Plant Science
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '6820'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Systems approaches to study root architecture dynamics
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 4
year: '2013'
...
---
_id: '830'
abstract:
- lang: eng
text: Upon hormonal signaling, ovules develop as lateral organs from the placenta.
Ovule numbers ultimately determine the number of seeds that develop, and thereby
contribute to the final seed yield in crop plants. We demonstrate here that CUP-SHAPED
COTYLEDON 1 (CUC1), CUC2 and AINTEGUMENTA (ANT) have additive effects on ovule
primordia formation. We show that expression of the CUC1 and CUC2 genes is required
to redundantly regulate expression of PINFORMED1 (PIN1), which in turn is required
for ovule primordia formation. Furthermore, our results suggest that the auxin
response factor MONOPTEROS (MP/ARF5) may directly bind ANT, CUC1 and CUC2 and
promote their transcription. Based on our findings, we propose an integrative
model to describe the molecular mechanisms of the early stages of ovule development.
acknowledgement: The project and F.G. were supported by the CARIPLO Foundation (project
2009-2990) and COST (European Cooperation in Science and Technology) action HAPRECI
(Harnessing Plant Reproduction for Crop Improvement). E.B. and C.C. were supported
by the European Research Council through a ‘Starting Independent Research’ grant
(ERC-2007-Stg-207362-HCPO). We thank A.P. MacCabe (Consejo Superior de Investigaciones
Científicas, Valencia, Spain) for critical reading of the manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Francesca
full_name: Galbiati, Francesca
last_name: Galbiati
- first_name: Dola
full_name: Sinha Roy, Dola
last_name: Sinha Roy
- first_name: Sara
full_name: Simonini, Sara
last_name: Simonini
- first_name: Mara
full_name: Cucinotta, Mara
last_name: Cucinotta
- first_name: Luca
full_name: Ceccato, Luca
last_name: Ceccato
- first_name: Candela
full_name: Cuesta, Candela
id: 33A3C818-F248-11E8-B48F-1D18A9856A87
last_name: Cuesta
orcid: 0000-0003-1923-2410
- first_name: Mária
full_name: Šimášková, Mária
last_name: Šimášková
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Yuri
full_name: Kamiuchi, Yuri
last_name: Kamiuchi
- first_name: Mitsuhiro
full_name: Aida, Mitsuhiro
last_name: Aida
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Rüdiger
full_name: Simon, Rüdiger
last_name: Simon
- first_name: Simona
full_name: Masiero, Simona
last_name: Masiero
- first_name: Lucia
full_name: Colombo, Lucia
last_name: Colombo
citation:
ama: Galbiati F, Sinha Roy D, Simonini S, et al. An integrative model of the control
of ovule primordia formation. The Plant journal for cell and molecular biology.
2013;76(3):446-455. doi:10.1111/tpj.12309
apa: Galbiati, F., Sinha Roy, D., Simonini, S., Cucinotta, M., Ceccato, L., Cuesta,
C., … Colombo, L. (2013). An integrative model of the control of ovule primordia
formation. The Plant Journal for Cell and Molecular Biology. Wiley-Blackwell.
https://doi.org/10.1111/tpj.12309
chicago: Galbiati, Francesca, Dola Sinha Roy, Sara Simonini, Mara Cucinotta, Luca
Ceccato, Candela Cuesta, Mária Šimášková, et al. “An Integrative Model of the
Control of Ovule Primordia Formation.” The Plant Journal for Cell and Molecular
Biology. Wiley-Blackwell, 2013. https://doi.org/10.1111/tpj.12309.
ieee: F. Galbiati et al., “An integrative model of the control of ovule primordia
formation,” The Plant journal for cell and molecular biology, vol. 76,
no. 3. Wiley-Blackwell, pp. 446–455, 2013.
ista: Galbiati F, Sinha Roy D, Simonini S, Cucinotta M, Ceccato L, Cuesta C, Šimášková
M, Benková E, Kamiuchi Y, Aida M, Weijers D, Simon R, Masiero S, Colombo L. 2013.
An integrative model of the control of ovule primordia formation. The Plant journal
for cell and molecular biology. 76(3), 446–455.
mla: Galbiati, Francesca, et al. “An Integrative Model of the Control of Ovule Primordia
Formation.” The Plant Journal for Cell and Molecular Biology, vol. 76,
no. 3, Wiley-Blackwell, 2013, pp. 446–55, doi:10.1111/tpj.12309.
short: F. Galbiati, D. Sinha Roy, S. Simonini, M. Cucinotta, L. Ceccato, C. Cuesta,
M. Šimášková, E. Benková, Y. Kamiuchi, M. Aida, D. Weijers, R. Simon, S. Masiero,
L. Colombo, The Plant Journal for Cell and Molecular Biology 76 (2013) 446–455.
date_created: 2018-12-11T11:48:44Z
date_published: 2013-09-19T00:00:00Z
date_updated: 2022-03-21T07:17:26Z
day: '19'
doi: 10.1111/tpj.12309
extern: '1'
external_id:
pmid:
- '23941199'
intvolume: ' 76'
issue: '3'
language:
- iso: eng
month: '09'
oa_version: None
page: 446 - 455
pmid: 1
publication: The Plant journal for cell and molecular biology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6818'
quality_controlled: '1'
scopus_import: '1'
status: public
title: An integrative model of the control of ovule primordia formation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 76
year: '2013'
...
---
_id: '831'
abstract:
- lang: eng
text: In Arabidopsis, lateral roots originate from pericycle cells deep within the
primary root. New lateral root primordia (LRP) have to emerge through several
overlaying tissues. Here, we report that auxin produced in new LRP is transported
towards the outer tissues where it triggers cell separation by inducing both the
auxin influx carrier LAX3 and cell-wall enzymes. LAX3 is expressed in just two
cell files overlaying new LRP. To understand how this striking pattern of LAX3
expression is regulated, we developed a mathematical model that captures the network
regulating its expression and auxin transport within realistic three-dimensional
cell and tissue geometries. Our model revealed that, for the LAX3 spatial expression
to be robust to natural variations in root tissue geometry, an efflux carrier
is required--later identified to be PIN3. To prevent LAX3 from being transiently
expressed in multiple cell files, PIN3 and LAX3 must be induced consecutively,
which we later demonstrated to be the case. Our study exemplifies how mathematical
models can be used to direct experiments to elucidate complex developmental processes.
acknowledgement: This work was supported by an FEBS Long‐Term Fellowship (BP), an
Intra‐European Fellowship for Career Development under the 7th framework of the
European Commission (IEF‐2008‐220506 to BP), an EMBO Long‐Term Fellowship (BP),
an European Reintegration Grant under the 7th framework of the European Commission
(ERG‐2010‐276662 to BP) and the Swedish Research Council (VR 621‐2010‐5720 to IS,
GS and KL). AMM, APF, AL, LRB, SP, NM, DMW, MO, JRK and MJB acknowledge the support
of the Biotechnology and Biological Sciences Research Council (BBSRC) and Engineering
and Physical Sciences Research Council (EPSRC) funding to the Centre for Plant Integrative
Biology (CPIB); BBSRC Professorial Research Fellowship funding to DMW and MJB; Belgian
Scientific policy (BELSPO contract MARS) to TB and MJB. We thank Bert de Rybel for
his help in Multisite Gateway cloning.
author:
- first_name: Benjamin
full_name: Péret, Benjamin
last_name: Péret
- first_name: Alistair
full_name: Middleton, Alistair M
last_name: Middleton
- first_name: Andrew
full_name: French, Andrew P
last_name: French
- first_name: Antoine
full_name: Larrieu, Antoine
last_name: Larrieu
- first_name: Anthony
full_name: Bishopp, Anthony
last_name: Bishopp
- first_name: Maria
full_name: Njo, Maria
last_name: Njo
- first_name: Darren
full_name: Wells, Darren M
last_name: Wells
- first_name: Silvana
full_name: Porco, Silvana
last_name: Porco
- first_name: Nathan
full_name: Mellor, Nathan
last_name: Mellor
- first_name: Leah
full_name: Band, Leah R
last_name: Band
- first_name: Ilda
full_name: Casimiro, Ilda
last_name: Casimiro
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Ilkka
full_name: Sairanen, Ilkka
last_name: Sairanen
- first_name: Romain
full_name: Mallet, Romain
last_name: Mallet
- first_name: Göran
full_name: Sandberg, Göran
last_name: Sandberg
- first_name: Karin
full_name: Ljung, Karin
last_name: Ljung
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- 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
- first_name: Eric
full_name: Kramer, Eric
last_name: Kramer
- first_name: John
full_name: King, John R
last_name: King
- first_name: Ive
full_name: De Smet, Ive
last_name: De Smet
- first_name: Tony
full_name: Pridmore, Tony
last_name: Pridmore
- first_name: Markus
full_name: Owen, Markus
last_name: Owen
- first_name: Malcolm
full_name: Bennett, Malcolm J
last_name: Bennett
citation:
ama: Péret B, Middleton A, French A, et al. Sequential induction of auxin efflux
and influx carriers regulates lateral root emergence. Molecular Systems Biology.
2013;9. doi:10.1038/msb.2013.43
apa: Péret, B., Middleton, A., French, A., Larrieu, A., Bishopp, A., Njo, M., …
Bennett, M. (2013). Sequential induction of auxin efflux and influx carriers regulates
lateral root emergence. Molecular Systems Biology. Nature Publishing Group.
https://doi.org/10.1038/msb.2013.43
chicago: Péret, Benjamin, Alistair Middleton, Andrew French, Antoine Larrieu, Anthony
Bishopp, Maria Njo, Darren Wells, et al. “Sequential Induction of Auxin Efflux
and Influx Carriers Regulates Lateral Root Emergence.” Molecular Systems Biology.
Nature Publishing Group, 2013. https://doi.org/10.1038/msb.2013.43.
ieee: B. Péret et al., “Sequential induction of auxin efflux and influx carriers
regulates lateral root emergence,” Molecular Systems Biology, vol. 9. Nature
Publishing Group, 2013.
ista: Péret B, Middleton A, French A, Larrieu A, Bishopp A, Njo M, Wells D, Porco
S, Mellor N, Band L, Casimiro I, Kleine Vehn J, Vanneste S, Sairanen I, Mallet
R, Sandberg G, Ljung K, Beeckman T, Benková E, Friml J, Kramer E, King J, De Smet
I, Pridmore T, Owen M, Bennett M. 2013. Sequential induction of auxin efflux and
influx carriers regulates lateral root emergence. Molecular Systems Biology. 9.
mla: Péret, Benjamin, et al. “Sequential Induction of Auxin Efflux and Influx Carriers
Regulates Lateral Root Emergence.” Molecular Systems Biology, vol. 9, Nature
Publishing Group, 2013, doi:10.1038/msb.2013.43.
short: B. Péret, A. Middleton, A. French, A. Larrieu, A. Bishopp, M. Njo, D. Wells,
S. Porco, N. Mellor, L. Band, I. Casimiro, J. Kleine Vehn, S. Vanneste, I. Sairanen,
R. Mallet, G. Sandberg, K. Ljung, T. Beeckman, E. Benková, J. Friml, E. Kramer,
J. King, I. De Smet, T. Pridmore, M. Owen, M. Bennett, Molecular Systems Biology
9 (2013).
date_created: 2018-12-11T11:48:44Z
date_published: 2013-10-22T00:00:00Z
date_updated: 2021-01-12T08:18:03Z
day: '22'
doi: 10.1038/msb.2013.43
extern: 1
intvolume: ' 9'
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '10'
publication: Molecular Systems Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '6817'
quality_controlled: 0
status: public
title: Sequential induction of auxin efflux and influx carriers regulates lateral
root emergence
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
volume: 9
year: '2013'
...
---
_id: '8461'
abstract:
- lang: eng
text: Solid-state NMR provides insight into protein motion over time scales ranging
from picoseconds to seconds. While in solution state the methodology to measure
protein dynamics is well established, there is currently no such consensus protocol
for measuring dynamics in solids. In this article, we perform a detailed investigation
of measurement protocols for fast motions, i.e. motions ranging from picoseconds
to a few microseconds, which is the range covered by dipolar coupling and relaxation
experiments. We perform a detailed theoretical investigation how dipolar couplings
and relaxation data can provide information about amplitudes and time scales of
local motion. We show that the measurement of dipolar couplings is crucial for
obtaining accurate motional parameters, while systematic errors are found when
only relaxation data are used. Based on this realization, we investigate how the
REDOR experiment can provide such data in a very accurate manner. We identify
that with accurate rf calibration, and explicit consideration of rf field inhomogeneities,
one can obtain highly accurate absolute order parameters. We then perform joint
model-free analyses of 6 relaxation data sets and dipolar couplings, based on
previously existing, as well as new data sets on microcrystalline ubiquitin. We
show that nanosecond motion can be detected primarily in loop regions, and compare
solid-state data to solution-state relaxation and RDC analyses. The protocols
investigated here will serve as a useful basis towards the establishment of a
routine protocol for the characterization of ps–μs motions in proteins by solid-state
NMR.
article_processing_charge: No
article_type: original
author:
- first_name: Jens D.
full_name: Haller, Jens D.
last_name: Haller
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Haller JD, Schanda P. Amplitudes and time scales of picosecond-to-microsecond
motion in proteins studied by solid-state NMR: a critical evaluation of experimental
approaches and application to crystalline ubiquitin. Journal of Biomolecular
NMR. 2013;57(3):263-280. doi:10.1007/s10858-013-9787-x'
apa: 'Haller, J. D., & Schanda, P. (2013). Amplitudes and time scales of picosecond-to-microsecond
motion in proteins studied by solid-state NMR: a critical evaluation of experimental
approaches and application to crystalline ubiquitin. Journal of Biomolecular
NMR. Springer Nature. https://doi.org/10.1007/s10858-013-9787-x'
chicago: 'Haller, Jens D., and Paul Schanda. “Amplitudes and Time Scales of Picosecond-to-Microsecond
Motion in Proteins Studied by Solid-State NMR: A Critical Evaluation of Experimental
Approaches and Application to Crystalline Ubiquitin.” Journal of Biomolecular
NMR. Springer Nature, 2013. https://doi.org/10.1007/s10858-013-9787-x.'
ieee: 'J. D. Haller and P. Schanda, “Amplitudes and time scales of picosecond-to-microsecond
motion in proteins studied by solid-state NMR: a critical evaluation of experimental
approaches and application to crystalline ubiquitin,” Journal of Biomolecular
NMR, vol. 57, no. 3. Springer Nature, pp. 263–280, 2013.'
ista: 'Haller JD, Schanda P. 2013. Amplitudes and time scales of picosecond-to-microsecond
motion in proteins studied by solid-state NMR: a critical evaluation of experimental
approaches and application to crystalline ubiquitin. Journal of Biomolecular NMR.
57(3), 263–280.'
mla: 'Haller, Jens D., and Paul Schanda. “Amplitudes and Time Scales of Picosecond-to-Microsecond
Motion in Proteins Studied by Solid-State NMR: A Critical Evaluation of Experimental
Approaches and Application to Crystalline Ubiquitin.” Journal of Biomolecular
NMR, vol. 57, no. 3, Springer Nature, 2013, pp. 263–80, doi:10.1007/s10858-013-9787-x.'
short: J.D. Haller, P. Schanda, Journal of Biomolecular NMR 57 (2013) 263–280.
date_created: 2020-09-18T10:09:05Z
date_published: 2013-10-09T00:00:00Z
date_updated: 2021-01-12T08:19:26Z
day: '09'
doi: 10.1007/s10858-013-9787-x
extern: '1'
intvolume: ' 57'
issue: '3'
keyword:
- Spectroscopy
- Biochemistry
language:
- iso: eng
month: '10'
oa_version: None
page: 263-280
publication: Journal of Biomolecular NMR
publication_identifier:
issn:
- 0925-2738
- 1573-5001
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: 'Amplitudes and time scales of picosecond-to-microsecond motion in proteins
studied by solid-state NMR: a critical evaluation of experimental approaches and
application to crystalline ubiquitin'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2013'
...
---
_id: '8462'
abstract:
- lang: eng
text: The transition of proteins from their soluble functional state to amyloid
fibrils and aggregates is associated with the onset of several human diseases.
Protein aggregation often requires some structural reshaping and the subsequent
formation of intermolecular contacts. Therefore, the study of the conformation
of excited protein states and their ability to form oligomers is of primary importance
for understanding the molecular basis of amyloid fibril formation. Here, we investigated
the oligomerization processes that occur along the folding of the amyloidogenic
human protein β2-microglobulin. The combination of real-time two-dimensional NMR
data with real-time small-angle X-ray scattering measurements allowed us to derive
thermodynamic and kinetic information on protein oligomerization of different
conformational states populated along the folding pathways. In particular, we
could demonstrate that a long-lived folding intermediate (I-state) has a higher
propensity to oligomerize compared to the native state. Our data agree well with
a simple five-state kinetic model that involves only monomeric and dimeric species.
The dimers have an elongated shape with the dimerization interface located at
the apical side of β2-microglobulin close to Pro32, the residue that has a trans
conformation in the I-state and a cis conformation in the native (N) state. Our
experimental data suggest that partial unfolding in the apical half of the protein
close to Pro32 leads to an excited state conformation with enhanced propensity
for oligomerization. This excited state becomes more populated in the transient
I-state due to the destabilization of the native conformation by the trans-Pro32
configuration.
article_processing_charge: No
article_type: original
author:
- first_name: E.
full_name: Rennella, E.
last_name: Rennella
- first_name: T.
full_name: Cutuil, T.
last_name: Cutuil
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: I.
full_name: Ayala, I.
last_name: Ayala
- first_name: F.
full_name: Gabel, F.
last_name: Gabel
- first_name: V.
full_name: Forge, V.
last_name: Forge
- first_name: A.
full_name: Corazza, A.
last_name: Corazza
- first_name: G.
full_name: Esposito, G.
last_name: Esposito
- first_name: B.
full_name: Brutscher, B.
last_name: Brutscher
citation:
ama: 'Rennella E, Cutuil T, Schanda P, et al. Oligomeric states along the folding
pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. Journal
of Molecular Biology. 2013;425(15):2722-2736. doi:10.1016/j.jmb.2013.04.028'
apa: 'Rennella, E., Cutuil, T., Schanda, P., Ayala, I., Gabel, F., Forge, V., …
Brutscher, B. (2013). Oligomeric states along the folding pathways of β2-microglobulin:
Kinetics, thermodynamics, and structure. Journal of Molecular Biology.
Elsevier. https://doi.org/10.1016/j.jmb.2013.04.028'
chicago: 'Rennella, E., T. Cutuil, Paul Schanda, I. Ayala, F. Gabel, V. Forge, A.
Corazza, G. Esposito, and B. Brutscher. “Oligomeric States along the Folding Pathways
of Β2-Microglobulin: Kinetics, Thermodynamics, and Structure.” Journal of Molecular
Biology. Elsevier, 2013. https://doi.org/10.1016/j.jmb.2013.04.028.'
ieee: 'E. Rennella et al., “Oligomeric states along the folding pathways
of β2-microglobulin: Kinetics, thermodynamics, and structure,” Journal of Molecular
Biology, vol. 425, no. 15. Elsevier, pp. 2722–2736, 2013.'
ista: 'Rennella E, Cutuil T, Schanda P, Ayala I, Gabel F, Forge V, Corazza A, Esposito
G, Brutscher B. 2013. Oligomeric states along the folding pathways of β2-microglobulin:
Kinetics, thermodynamics, and structure. Journal of Molecular Biology. 425(15),
2722–2736.'
mla: 'Rennella, E., et al. “Oligomeric States along the Folding Pathways of Β2-Microglobulin:
Kinetics, Thermodynamics, and Structure.” Journal of Molecular Biology,
vol. 425, no. 15, Elsevier, 2013, pp. 2722–36, doi:10.1016/j.jmb.2013.04.028.'
short: E. Rennella, T. Cutuil, P. Schanda, I. Ayala, F. Gabel, V. Forge, A. Corazza,
G. Esposito, B. Brutscher, Journal of Molecular Biology 425 (2013) 2722–2736.
date_created: 2020-09-18T10:09:12Z
date_published: 2013-08-09T00:00:00Z
date_updated: 2022-08-25T14:56:24Z
day: '09'
doi: 10.1016/j.jmb.2013.04.028
extern: '1'
intvolume: ' 425'
issue: '15'
keyword:
- Molecular Biology
language:
- iso: eng
month: '08'
oa_version: None
page: 2722-2736
publication: Journal of Molecular Biology
publication_identifier:
issn:
- 0022-2836
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Oligomeric states along the folding pathways of β2-microglobulin: Kinetics,
thermodynamics, and structure'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 425
year: '2013'
...
---
_id: '894'
abstract:
- lang: eng
text: 'Background: Genetic variation at the melanocortin-1 receptor (MC1R) gene
is correlated with melanin color variation in many birds. Feral pigeons (Columba
livia) show two major melanin-based colorations: a red coloration due to pheomelanic
pigment and a black coloration due to eumelanic pigment. Furthermore, within each
color type, feral pigeons display continuous variation in the amount of melanin
pigment present in the feathers, with individuals varying from pure white to a
full dark melanic color. Coloration is highly heritable and it has been suggested
that it is under natural or sexual selection, or both. Our objective was to investigate
whether MC1R allelic variants are associated with plumage color in feral pigeons.
Findings. We sequenced 888 bp of the coding sequence of MC1R among pigeons varying
both in the type, eumelanin or pheomelanin, and the amount of melanin in their
feathers. We detected 10 non-synonymous substitutions and 2 synonymous substitution
but none of them were associated with a plumage type. It remains possible that
non-synonymous substitutions that influence coloration are present in the short
MC1R fragment that we did not sequence but this seems unlikely because we analyzed
the entire functionally important region of the gene. Conclusions: Our results
show that color differences among feral pigeons are probably not attributable
to amino acid variation at the MC1R locus. Therefore, variation in regulatory
regions of MC1R or variation in other genes may be responsible for the color polymorphism
of feral pigeons.'
acknowledgement: Romain Derelle was supported by grant from Plan Nacional 004302 BFU2012-31329.
Fyodor A Kondrashov was supported by grants HHMI (Howard Hughes Medical Institute)
003803 and EMBO 003691 EUI-EURYIP-2011-4320.
author:
- first_name: Romain
full_name: Derelle, Romain
last_name: Derelle
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Vladimir
full_name: Arkhipov, Vladimir
last_name: Arkhipov
- first_name: Hélène
full_name: Corbel, Hélène
last_name: Corbel
- first_name: Adrien
full_name: Frantz, Adrien
last_name: Frantz
- first_name: Julien
full_name: Gasparini, Julien
last_name: Gasparini
- first_name: Lisa
full_name: Jacquin, Lisa
last_name: Jacquin
- first_name: Gwenaël
full_name: Jacob, Gwenaël
last_name: Jacob
- first_name: Sophie
full_name: Thibault, Sophie
last_name: Thibault
- first_name: Emmanuelle
full_name: Baudry, Emmanuelle
last_name: Baudry
citation:
ama: Derelle R, Kondrashov F, Arkhipov V, et al. Color differences among feral pigeons
(Columba livia) are not attributable to sequence variation in the coding region
of the melanocortin-1 receptor gene MC1R. BMC Research Notes. 2013;6(1).
doi:10.1186/1756-0500-6-310
apa: Derelle, R., Kondrashov, F., Arkhipov, V., Corbel, H., Frantz, A., Gasparini,
J., … Baudry, E. (2013). Color differences among feral pigeons (Columba livia)
are not attributable to sequence variation in the coding region of the melanocortin-1
receptor gene MC1R. BMC Research Notes. BioMed Central. https://doi.org/10.1186/1756-0500-6-310
chicago: Derelle, Romain, Fyodor Kondrashov, Vladimir Arkhipov, Hélène Corbel, Adrien
Frantz, Julien Gasparini, Lisa Jacquin, Gwenaël Jacob, Sophie Thibault, and Emmanuelle
Baudry. “Color Differences among Feral Pigeons (Columba Livia) Are Not Attributable
to Sequence Variation in the Coding Region of the Melanocortin-1 Receptor Gene
MC1R.” BMC Research Notes. BioMed Central, 2013. https://doi.org/10.1186/1756-0500-6-310.
ieee: R. Derelle et al., “Color differences among feral pigeons (Columba
livia) are not attributable to sequence variation in the coding region of the
melanocortin-1 receptor gene MC1R,” BMC Research Notes, vol. 6, no. 1.
BioMed Central, 2013.
ista: Derelle R, Kondrashov F, Arkhipov V, Corbel H, Frantz A, Gasparini J, Jacquin
L, Jacob G, Thibault S, Baudry E. 2013. Color differences among feral pigeons
(Columba livia) are not attributable to sequence variation in the coding region
of the melanocortin-1 receptor gene MC1R. BMC Research Notes. 6(1).
mla: Derelle, Romain, et al. “Color Differences among Feral Pigeons (Columba Livia)
Are Not Attributable to Sequence Variation in the Coding Region of the Melanocortin-1
Receptor Gene MC1R.” BMC Research Notes, vol. 6, no. 1, BioMed Central,
2013, doi:10.1186/1756-0500-6-310.
short: R. Derelle, F. Kondrashov, V. Arkhipov, H. Corbel, A. Frantz, J. Gasparini,
L. Jacquin, G. Jacob, S. Thibault, E. Baudry, BMC Research Notes 6 (2013).
date_created: 2018-12-11T11:49:04Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T08:21:25Z
day: '01'
doi: 10.1186/1756-0500-6-310
extern: '1'
intvolume: ' 6'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
publication: BMC Research Notes
publication_status: published
publisher: BioMed Central
publist_id: '6752'
status: public
title: Color differences among feral pigeons (Columba livia) are not attributable
to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2013'
...
---
_id: '899'
abstract:
- lang: eng
text: Understanding fitness landscapes, a conceptual depiction of the genotype-to-phenotype
relationship, is crucial to many areas of biology. Two aspects of fitness landscapes
are the focus of contemporary studies of molecular evolution. First, the local
shape of the fitness landscape defined by the contribution of individual alleles
to fitness that is independent of all genetic interactions. Second, the global,
multidimensional fitness landscape shape determined by how interactions between
alleles at different loci change each other’s fitness impact, or epistasis. In
explaining the high amino-acid usage (u), we focused on the global shape of the
fitness landscape, ignoring the perturbations at individual sites.
author:
- first_name: Michael
full_name: Breen, Michael S
last_name: Breen
- first_name: Carsten
full_name: Kemena, Carsten
last_name: Kemena
- first_name: Peter
full_name: Vlasov, Peter K
last_name: Vlasov
- first_name: Cédric
full_name: Notredame, Cédric
last_name: Notredame
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. Breen et al. reply.
Nature. 2013;497(7451):E2-E3. doi:10.1038/nature12220
apa: Breen, M., Kemena, C., Vlasov, P., Notredame, C., & Kondrashov, F. (2013).
Breen et al. reply. Nature. Nature Publishing Group. https://doi.org/10.1038/nature12220
chicago: Breen, Michael, Carsten Kemena, Peter Vlasov, Cédric Notredame, and Fyodor
Kondrashov. “Breen et Al. Reply.” Nature. Nature Publishing Group, 2013.
https://doi.org/10.1038/nature12220.
ieee: M. Breen, C. Kemena, P. Vlasov, C. Notredame, and F. Kondrashov, “Breen et
al. reply,” Nature, vol. 497, no. 7451. Nature Publishing Group, pp. E2–E3,
2013.
ista: Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. 2013. Breen et al.
reply. Nature. 497(7451), E2–E3.
mla: Breen, Michael, et al. “Breen et Al. Reply.” Nature, vol. 497, no. 7451,
Nature Publishing Group, 2013, pp. E2–3, doi:10.1038/nature12220.
short: M. Breen, C. Kemena, P. Vlasov, C. Notredame, F. Kondrashov, Nature 497 (2013)
E2–E3.
date_created: 2018-12-11T11:49:05Z
date_published: 2013-05-30T00:00:00Z
date_updated: 2021-01-12T08:21:40Z
day: '30'
doi: 10.1038/nature12220
extern: 1
intvolume: ' 497'
issue: '7451'
month: '05'
page: E2 - E3
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6747'
quality_controlled: 0
status: public
title: Breen et al. reply
type: journal_article
volume: 497
year: '2013'
...
---
_id: '905'
abstract:
- lang: eng
text: A survey of avifauna was carried out in the Mys Shmidta area, north Chukotka,
Russia from 8 June to 12 July 2011. A total of 90 species was recorded in the
area, which together with literature data made a final list of 104 species. For
several species this area is beyond the northern, north-eastern or north-western
limits of their known distribution. We collected new data for 19 globally or locally
threatened species. Tundra Swan Cygnus columbianus, Emperor Goose Anser canagica,
American Golden Plover Pluvialis dominica, Western Sandpiper Calidris mauri, Semipalmated
Sandpiper C. pusilla, Northern House Martin Delichon urbica and Barn Swallow Hirundo
rustica were all confirmed to be breeding. Breeding of Brent Goose Branta bernicla
nigricans, Spectacled Eider Somateria fischeri and Steller's Eider Polysticta
stelleri was judged to be 'very likely'. There was no evidence for breeding of
Ross's Gull Rhodostethia rosea despite several records. Two Eurasian Dotterels
Eudromias morinellus were recorded displaying for the first time in the area,
but the status of the species is unclear. The area is important for Snowy Owl
Nyctea scandiaca, and as moulting grounds for Emperor Goose. Canada Goose Branta
canadensis, Baikal Teal Anas formosa, Bar-tailed Godwit Limosa lapponica, Slaty-backed
Gull Larus schistisagus, Thayer's Gull L. thayeri, Black-headed Gull L. ridibundus,
White-tailed Eagle Haliaeetus albicilla, Steller's Sea Eagle H. pelagicus, Osprey
Pandion haliaetus, Arctic Warbler Phylloscopus borealis and House Sparrow Passer
domesticus are more likely to be rare vagrants or migrants. An observation of
a Pine Siskin Carduelis pinus is the first record for Eurasia.
acknowledgement: We thank Natalya Kveten and Oksana Makarova, heads of administrations
of Mys Shmidta and Ryrkaypiy for hospitality and for help with organising our excursions.
Warm thanks too to Pavel Tomkovich for useful comments on local birds and ornithological
literature. We are very grateful to The David and Lucile Packard Foundation for
the support to Birds Russia’s Spoon-billed Sandpiper conservation programme in 2011
and to Evgeny Syroechkovsky Jr, the leader of the Spoon-billed Sandpiper conservation
team in Russia.
author:
- first_name: Vladimir
full_name: Arkhipov, Vladimir Y
last_name: Arkhipov
- first_name: T
full_name: Noah T
last_name: Noah
- first_name: Steffen
full_name: Koschkar, Steffen
last_name: Koschkar
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Arkhipov V, Noah T, Koschkar S, Kondrashov F. Birds of Mys Shmidta, north Chukotka,
Russia. Forktail. 2013;(29):25-30.
apa: Arkhipov, V., Noah, T., Koschkar, S., & Kondrashov, F. (2013). Birds of
Mys Shmidta, north Chukotka, Russia. Forktail. Oriental Bird Club.
chicago: Arkhipov, Vladimir, T Noah, Steffen Koschkar, and Fyodor Kondrashov. “Birds
of Mys Shmidta, North Chukotka, Russia.” Forktail. Oriental Bird Club,
2013.
ieee: V. Arkhipov, T. Noah, S. Koschkar, and F. Kondrashov, “Birds of Mys Shmidta,
north Chukotka, Russia,” Forktail, no. 29. Oriental Bird Club, pp. 25–30,
2013.
ista: Arkhipov V, Noah T, Koschkar S, Kondrashov F. 2013. Birds of Mys Shmidta,
north Chukotka, Russia. Forktail. (29), 25–30.
mla: Arkhipov, Vladimir, et al. “Birds of Mys Shmidta, North Chukotka, Russia.”
Forktail, no. 29, Oriental Bird Club, 2013, pp. 25–30.
short: V. Arkhipov, T. Noah, S. Koschkar, F. Kondrashov, Forktail (2013) 25–30.
date_created: 2018-12-11T11:49:07Z
date_published: 2013-09-01T00:00:00Z
date_updated: 2021-01-12T08:21:48Z
day: '01'
extern: 1
issue: '29'
main_file_link:
- open_access: '1'
url: http://orientalbirdclub.org/forktail29/
month: '09'
oa: 1
page: 25 - 30
publication: Forktail
publication_status: published
publisher: Oriental Bird Club
publist_id: '6741'
quality_controlled: 0
status: public
title: Birds of Mys Shmidta, north Chukotka, Russia
type: journal_article
year: '2013'
...
---
_id: '9055'
abstract:
- lang: eng
text: Spontaneous formation of colonies of bacteria or flocks of birds are examples
of self-organization in active living matter. Here, we demonstrate a form of self-organization
from nonequilibrium driving forces in a suspension of synthetic photoactivated
colloidal particles. They lead to two-dimensional "living crystals," which form,
break, explode, and re-form elsewhere. The dynamic assembly results from a competition
between self-propulsion of particles and an attractive interaction induced respectively
by osmotic and phoretic effects and activated by light. We measured a transition
from normal to giant-number fluctuations. Our experiments are quantitatively described
by simple numerical simulations. We show that the existence of the living crystals
is intrinsically related to the out-of-equilibrium collisions of the self-propelled
particles.
article_processing_charge: No
article_type: original
author:
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: S.
full_name: Sacanna, S.
last_name: Sacanna
- first_name: A. P.
full_name: Steinberg, A. P.
last_name: Steinberg
- first_name: D. J.
full_name: Pine, D. J.
last_name: Pine
- first_name: P. M.
full_name: Chaikin, P. M.
last_name: Chaikin
citation:
ama: Palacci JA, Sacanna S, Steinberg AP, Pine DJ, Chaikin PM. Living crystals of
light-activated colloidal surfers. Science. 2013;339(6122):936-940. doi:10.1126/science.1230020
apa: Palacci, J. A., Sacanna, S., Steinberg, A. P., Pine, D. J., & Chaikin,
P. M. (2013). Living crystals of light-activated colloidal surfers. Science.
American Association for the Advancement of Science . https://doi.org/10.1126/science.1230020
chicago: Palacci, Jérémie A, S. Sacanna, A. P. Steinberg, D. J. Pine, and P. M.
Chaikin. “Living Crystals of Light-Activated Colloidal Surfers.” Science.
American Association for the Advancement of Science , 2013. https://doi.org/10.1126/science.1230020.
ieee: J. A. Palacci, S. Sacanna, A. P. Steinberg, D. J. Pine, and P. M. Chaikin,
“Living crystals of light-activated colloidal surfers,” Science, vol. 339,
no. 6122. American Association for the Advancement of Science , pp. 936–940, 2013.
ista: Palacci JA, Sacanna S, Steinberg AP, Pine DJ, Chaikin PM. 2013. Living crystals
of light-activated colloidal surfers. Science. 339(6122), 936–940.
mla: Palacci, Jérémie A., et al. “Living Crystals of Light-Activated Colloidal Surfers.”
Science, vol. 339, no. 6122, American Association for the Advancement of
Science , 2013, pp. 936–40, doi:10.1126/science.1230020.
short: J.A. Palacci, S. Sacanna, A.P. Steinberg, D.J. Pine, P.M. Chaikin, Science
339 (2013) 936–940.
date_created: 2021-02-01T14:37:29Z
date_published: 2013-02-22T00:00:00Z
date_updated: 2022-08-25T14:57:43Z
day: '22'
doi: 10.1126/science.1230020
extern: '1'
external_id:
pmid:
- '23371555'
intvolume: ' 339'
issue: '6122'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '02'
oa_version: None
page: 936-940
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: 'American Association for the Advancement of Science '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Living crystals of light-activated colloidal surfers
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 339
year: '2013'
...
---
_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'
...