---
_id: '10385'
abstract:
- lang: eng
text: We show how self-assembly of sticky nanoparticles can drive radial collapse
of thin-walled nanotubes. Using numerical simulations, we study the transition
as a function of the geometric and elastic parameters of the nanotube and the
binding strength of the nanoparticles. We find that it is possible to derive a
simple scaling law relating all these parameters, and estimate bounds for the
onset conditions leading to the collapse of the nanotube. We also study the reverse
process – the nanoparticle release from the folded state – and find that the stability
of the collapsed state can be greatly improved by increasing the bending rigidity
of the nanotubes. Our results suggest ways to strengthen the mechanical properties
of nanotubes, but also indicate that the control of nanoparticle self-assembly
on these nanotubes can lead to nanoparticle-laden responsive materials.
acknowledgement: This work was supported by the National Science Foundation under
Career Grant no. DMR-0846426.
article_processing_charge: No
article_type: original
author:
- first_name: Joseph A.
full_name: Napoli, Joseph A.
last_name: Napoli
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Angelo
full_name: Cacciuto, Angelo
last_name: Cacciuto
citation:
ama: Napoli JA, Šarić A, Cacciuto A. Collapsing nanoparticle-laden nanotubes. Soft
Matter. 2013;9(37):8881-8886. doi:10.1039/c3sm51495a
apa: Napoli, J. A., Šarić, A., & Cacciuto, A. (2013). Collapsing nanoparticle-laden
nanotubes. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c3sm51495a
chicago: Napoli, Joseph A., Anđela Šarić, and Angelo Cacciuto. “Collapsing Nanoparticle-Laden
Nanotubes.” Soft Matter. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3sm51495a.
ieee: J. A. Napoli, A. Šarić, and A. Cacciuto, “Collapsing nanoparticle-laden nanotubes,”
Soft Matter, vol. 9, no. 37. Royal Society of Chemistry, pp. 8881–8886,
2013.
ista: Napoli JA, Šarić A, Cacciuto A. 2013. Collapsing nanoparticle-laden nanotubes.
Soft Matter. 9(37), 8881–8886.
mla: Napoli, Joseph A., et al. “Collapsing Nanoparticle-Laden Nanotubes.” Soft
Matter, vol. 9, no. 37, Royal Society of Chemistry, 2013, pp. 8881–86, doi:10.1039/c3sm51495a.
short: J.A. Napoli, A. Šarić, A. Cacciuto, Soft Matter 9 (2013) 8881–8886.
date_created: 2021-11-29T13:31:24Z
date_published: 2013-08-08T00:00:00Z
date_updated: 2021-11-29T14:05:23Z
day: '08'
doi: 10.1039/c3sm51495a
extern: '1'
intvolume: ' 9'
issue: '37'
keyword:
- condensed matter physics
- general chemistry
language:
- iso: eng
month: '08'
oa_version: None
page: 8881-8886
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Collapsing nanoparticle-laden nanotubes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9
year: '2013'
...
---
_id: '10386'
abstract:
- lang: eng
text: In this paper we review recent numerical and theoretical developments of particle
self-assembly on fluid and elastic membranes and compare them to available experimental
realizations. We discuss the problem and its applications in biology and materials
science, and give an overview of numerical models and strategies to study these
systems across all length-scales. As this is a very broad field, this review focuses
exclusively on surface-driven aggregation of nanoparticles that are at least one
order of magnitude larger than the surface thickness and are adsorbed onto it.
In this regime, all chemical details of the surface can be ignored in favor of
a coarse-grained representation, and the collective behavior of many particles
can be monitored and analyzed. We review the existing literature on how the mechanical
properties and the geometry of the surface affect the structure of the particle
aggregates and how these can drive shape deformation on the surface.
acknowledgement: This work was supported by the National Science Foundation under
Career Grant No. DMR 0846426. The authors thank J. C. Pàmies for many fruitful discussions
on the subject.
article_number: '6677'
article_processing_charge: No
article_type: original
author:
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Angelo
full_name: Cacciuto, Angelo
last_name: Cacciuto
citation:
ama: Šarić A, Cacciuto A. Self-assembly of nanoparticles adsorbed on fluid and elastic
membranes. Soft Matter. 2013;9(29). doi:10.1039/c3sm50188d
apa: Šarić, A., & Cacciuto, A. (2013). Self-assembly of nanoparticles adsorbed
on fluid and elastic membranes. Soft Matter. Royal Society of Chemistry.
https://doi.org/10.1039/c3sm50188d
chicago: Šarić, Anđela, and Angelo Cacciuto. “Self-Assembly of Nanoparticles Adsorbed
on Fluid and Elastic Membranes.” Soft Matter. Royal Society of Chemistry,
2013. https://doi.org/10.1039/c3sm50188d.
ieee: A. Šarić and A. Cacciuto, “Self-assembly of nanoparticles adsorbed on fluid
and elastic membranes,” Soft Matter, vol. 9, no. 29. Royal Society of Chemistry,
2013.
ista: Šarić A, Cacciuto A. 2013. Self-assembly of nanoparticles adsorbed on fluid
and elastic membranes. Soft Matter. 9(29), 6677.
mla: Šarić, Anđela, and Angelo Cacciuto. “Self-Assembly of Nanoparticles Adsorbed
on Fluid and Elastic Membranes.” Soft Matter, vol. 9, no. 29, 6677, Royal
Society of Chemistry, 2013, doi:10.1039/c3sm50188d.
short: A. Šarić, A. Cacciuto, Soft Matter 9 (2013).
date_created: 2021-11-29T14:06:32Z
date_published: 2013-05-03T00:00:00Z
date_updated: 2021-11-29T14:29:31Z
day: '03'
doi: 10.1039/c3sm50188d
extern: '1'
intvolume: ' 9'
issue: '29'
keyword:
- condensed matter physics
- general chemistry
language:
- iso: eng
main_file_link:
- url: https://pubs.rsc.org/en/content/articlehtml/2013/sm/c3sm50188d
month: '05'
oa_version: None
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Self-assembly of nanoparticles adsorbed on fluid and elastic membranes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9
year: '2013'
...
---
_id: '10396'
abstract:
- lang: eng
text: Stimfit is a free cross-platform software package for viewing and analyzing
electrophysiological data. It supports most standard file types for cellular neurophysiology
and other biomedical formats. Its analysis algorithms have been used and validated
in several experimental laboratories. Its embedded Python scripting interface
makes Stimfit highly extensible and customizable.
article_number: '000010151520134181'
article_processing_charge: No
article_type: original
author:
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: C.
full_name: Schmidt-Hieber, C.
last_name: Schmidt-Hieber
- first_name: S. J.
full_name: Guzman, S. J.
last_name: Guzman
citation:
ama: 'Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. Stimfit: A fast visualization
and analysis environment for cellular neurophysiology. Biomedical Engineering
/ Biomedizinische Technik. 2013;58(SI-1-Track-G). doi:10.1515/bmt-2013-4181'
apa: 'Schlögl, A., Jonas, P. M., Schmidt-Hieber, C., & Guzman, S. J. (2013).
Stimfit: A fast visualization and analysis environment for cellular neurophysiology.
Biomedical Engineering / Biomedizinische Technik. Graz, Austria: De Gruyter.
https://doi.org/10.1515/bmt-2013-4181'
chicago: 'Schlögl, Alois, Peter M Jonas, C. Schmidt-Hieber, and S. J. Guzman. “Stimfit:
A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” Biomedical
Engineering / Biomedizinische Technik. De Gruyter, 2013. https://doi.org/10.1515/bmt-2013-4181.'
ieee: 'A. Schlögl, P. M. Jonas, C. Schmidt-Hieber, and S. J. Guzman, “Stimfit: A
fast visualization and analysis environment for cellular neurophysiology,” Biomedical
Engineering / Biomedizinische Technik, vol. 58, no. SI-1-Track-G. De Gruyter,
2013.'
ista: 'Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. 2013. Stimfit: A fast visualization
and analysis environment for cellular neurophysiology. Biomedical Engineering
/ Biomedizinische Technik. 58(SI-1-Track-G), 000010151520134181.'
mla: 'Schlögl, Alois, et al. “Stimfit: A Fast Visualization and Analysis Environment
for Cellular Neurophysiology.” Biomedical Engineering / Biomedizinische Technik,
vol. 58, no. SI-1-Track-G, 000010151520134181, De Gruyter, 2013, doi:10.1515/bmt-2013-4181.'
short: A. Schlögl, P.M. Jonas, C. Schmidt-Hieber, S.J. Guzman, Biomedical Engineering
/ Biomedizinische Technik 58 (2013).
conference:
end_date: 2013-09-21
location: Graz, Austria
name: 'BMT: Biomedizinische Technik '
start_date: 2013-09-19
corr_author: '1'
date_created: 2021-12-01T14:35:35Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2025-09-30T07:31:23Z
day: '01'
ddc:
- '005'
- '610'
department:
- _id: PeJo
doi: 10.1515/bmt-2013-4181
external_id:
isi:
- '000497714000034'
pmid:
- '24042795'
file:
- access_level: open_access
checksum: cdfc5339b530a25d6079f7223f0b1f16
content_type: application/pdf
creator: schloegl
date_created: 2021-12-01T14:38:08Z
date_updated: 2021-12-01T14:38:08Z
file_id: '10397'
file_name: Schloegl_Abstract-BMT2013.pdf
file_size: 149825
relation: main_file
success: 1
file_date_updated: 2021-12-01T14:38:08Z
has_accepted_license: '1'
intvolume: ' 58'
isi: 1
issue: SI-1-Track-G
keyword:
- biomedical engineering
- data analysis
- free software
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Biomedical Engineering / Biomedizinische Technik
publication_identifier:
eissn:
- 1862-278X
issn:
- 0013-5585
publication_status: published
publisher: De Gruyter
quality_controlled: '1'
status: public
title: 'Stimfit: A fast visualization and analysis environment for cellular neurophysiology'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 58
year: '2013'
...
---
_id: '10749'
abstract:
- lang: eng
text: Fluxoid quantization provides a direct means to study phase coherence. In
cuprate superconductors, there have been observations which suggest that phase
coherent superconducting fluctuations may persist at temperatures significantly
above Tc. The focus of this work is to study the vortex states in mesoscopic cuprate
superconducting samples to directly probe phase coherence over a wide range of
temperatures. We present cantilever torque susceptometry measurements of micron
and sub-micron size Bi2212 rings and disks. The high sensitivity of this technique
allowed observation of transitions between different fluxoid states of a single
ring, and the discrete vortex states of micron size disks. The dependence of magnetic
susceptibility on diameter and wall thickness of the ring was investigated. Measurements
were made at different values of the in-plane magnetic field, and over a wide
range of temperatures.
acknowledgement: This work was supported by the Center for Emergent Superconductivity,
an Energy Frontier Research Center funded by the US DOE, Office of Science.
alternative_title:
- Bulletin of the American Physical Society
article_number: N36.00001
article_processing_charge: No
author:
- first_name: Hryhoriy
full_name: Polshyn, Hryhoriy
id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
last_name: Polshyn
orcid: 0000-0001-8223-8896
- first_name: Raffi
full_name: Budakian, Raffi
last_name: Budakian
- first_name: Genda
full_name: Gu, Genda
last_name: Gu
citation:
ama: 'Polshyn H, Budakian R, Gu G. Cantilever micro-susceptometry of mesoscopic
Bi2212 samples. In: APS March Meeting 2013. Vol 58. American Physical Society;
2013.'
apa: 'Polshyn, H., Budakian, R., & Gu, G. (2013). Cantilever micro-susceptometry
of mesoscopic Bi2212 samples. In APS March Meeting 2013 (Vol. 58). Baltimore,
MD, United States: American Physical Society.'
chicago: Polshyn, Hryhoriy, Raffi Budakian, and Genda Gu. “Cantilever Micro-Susceptometry
of Mesoscopic Bi2212 Samples.” In APS March Meeting 2013, Vol. 58. American
Physical Society, 2013.
ieee: H. Polshyn, R. Budakian, and G. Gu, “Cantilever micro-susceptometry of mesoscopic
Bi2212 samples,” in APS March Meeting 2013, Baltimore, MD, United States,
2013, vol. 58, no. 1.
ista: 'Polshyn H, Budakian R, Gu G. 2013. Cantilever micro-susceptometry of mesoscopic
Bi2212 samples. APS March Meeting 2013. APS: American Physical Society, Bulletin
of the American Physical Society, vol. 58, N36.00001.'
mla: Polshyn, Hryhoriy, et al. “Cantilever Micro-Susceptometry of Mesoscopic Bi2212
Samples.” APS March Meeting 2013, vol. 58, no. 1, N36.00001, American Physical
Society, 2013.
short: H. Polshyn, R. Budakian, G. Gu, in:, APS March Meeting 2013, American Physical
Society, 2013.
conference:
end_date: 2013-03-22
location: Baltimore, MD, United States
name: 'APS: American Physical Society'
start_date: 2013-03-18
date_created: 2022-02-08T10:34:29Z
date_published: 2013-03-01T00:00:00Z
date_updated: 2022-02-08T10:48:06Z
day: '01'
extern: '1'
intvolume: ' 58'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://meetings.aps.org/Meeting/MAR13/Event/186873
month: '03'
oa: 1
oa_version: Published Version
publication: APS March Meeting 2013
publication_identifier:
issn:
- 0003-0503
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Cantilever micro-susceptometry of mesoscopic Bi2212 samples
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 58
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'
license: https://creativecommons.org/licenses/by/4.0/
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'
...