---
_id: '2413'
abstract:
- lang: eng
text: 'Progress in understanding the global brain dynamics has remained slow to
date in large part because of the highly multiscale nature of brain activity.
Indeed, normal brain dynamics is characterized by complex interactions between
multiple levels: from the microscopic scale of single neurons to the mesoscopic
level of local groups of neurons, and finally to the macroscopic level of the
whole brain. Among the most difficult tasks are those of identifying which scales
are significant for a given particular function and describing how the scales
affect each other. It is important to realize that the scales of time and space
are linked together, or even intertwined, and that causal inference is far more
ambiguous between than within levels. We approach this problem from the perspective
of our recent work on simultaneous recording from micro- and macroelectrodes in
the human brain. We propose a physiological description of these multilevel interactions,
based on phase–amplitude coupling of neuronal oscillations that operate at multiple
frequencies and on different spatial scales. Specifically, the amplitude of the
oscillations on a particular spatial scale is modulated by phasic variations in
neuronal excitability induced by lower frequency oscillations that emerge on a
larger spatial scale. Following this general principle, it is possible to scale
up or scale down the multiscale brain dynamics. It is expected that large-scale
network oscillations in the low-frequency range, mediating downward effects, may
play an important role in attention and consciousness.'
alternative_title:
- Reviews of Nonlinear Dynamics and Complexity
author:
- first_name: Mario
full_name: Valderrama, Mario
last_name: Valderrama
- first_name: Vicente
full_name: Botella Soler, Vicente
id: 421234E8-F248-11E8-B48F-1D18A9856A87
last_name: Botella Soler
orcid: 0000-0002-8790-1914
- first_name: Michel
full_name: Le Van Quyen, Michel
last_name: Le Van Quyen
citation:
ama: 'Valderrama M, Botella Soler V, Le Van Quyen M. Neuronal oscillations scale
up and scale down the brain dynamics . In: Meyer M, Pesenson Z, eds. Multiscale
Analysis and Nonlinear Dynamics: From Genes to the Brain. Wiley-VCH; 2013.
doi:10.1002/9783527671632.ch08'
apa: 'Valderrama, M., Botella Soler, V., & Le Van Quyen, M. (2013). Neuronal
oscillations scale up and scale down the brain dynamics . In M. Meyer & Z.
Pesenson (Eds.), Multiscale Analysis and Nonlinear Dynamics: From Genes to
the Brain. Wiley-VCH. https://doi.org/10.1002/9783527671632.ch08'
chicago: 'Valderrama, Mario, Vicente Botella Soler, and Michel Le Van Quyen. “Neuronal
Oscillations Scale up and Scale down the Brain Dynamics .” In Multiscale Analysis
and Nonlinear Dynamics: From Genes to the Brain, edited by Misha Meyer and
Z. Pesenson. Wiley-VCH, 2013. https://doi.org/10.1002/9783527671632.ch08.'
ieee: 'M. Valderrama, V. Botella Soler, and M. Le Van Quyen, “Neuronal oscillations
scale up and scale down the brain dynamics ,” in Multiscale Analysis and Nonlinear
Dynamics: From Genes to the Brain, M. Meyer and Z. Pesenson, Eds. Wiley-VCH,
2013.'
ista: 'Valderrama M, Botella Soler V, Le Van Quyen M. 2013.Neuronal oscillations
scale up and scale down the brain dynamics . In: Multiscale Analysis and Nonlinear
Dynamics: From Genes to the Brain. Reviews of Nonlinear Dynamics and Complexity,
.'
mla: 'Valderrama, Mario, et al. “Neuronal Oscillations Scale up and Scale down the
Brain Dynamics .” Multiscale Analysis and Nonlinear Dynamics: From Genes to
the Brain, edited by Misha Meyer and Z. Pesenson, Wiley-VCH, 2013, doi:10.1002/9783527671632.ch08.'
short: 'M. Valderrama, V. Botella Soler, M. Le Van Quyen, in:, M. Meyer, Z. Pesenson
(Eds.), Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, Wiley-VCH,
2013.'
date_created: 2018-12-11T11:57:31Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T06:57:20Z
day: '01'
department:
- _id: GaTk
doi: 10.1002/9783527671632.ch08
editor:
- first_name: Misha
full_name: Meyer, Misha
last_name: Meyer
- first_name: Z.
full_name: Pesenson, Z.
last_name: Pesenson
language:
- iso: eng
month: '08'
oa_version: None
publication: 'Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain'
publication_identifier:
eisbn:
- '9783527671632'
isbn:
- '9783527411986 '
publication_status: published
publisher: Wiley-VCH
publist_id: '4513'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Neuronal oscillations scale up and scale down the brain dynamics '
type: book_chapter
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '6768'
abstract:
- lang: eng
text: The paper presents an algorithm that applies a stack filter simulating the
Mean Curvature Motion equation via a finite difference scheme.
article_type: original
author:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: Mondelli M. A finite difference scheme for the stack filter simulating the
MCM. Image Processing On Line. 2013;3:68-111. doi:10.5201/ipol.2013.53
apa: Mondelli, M. (2013). A finite difference scheme for the stack filter simulating
the MCM. Image Processing On Line. Image Processing On Line. https://doi.org/10.5201/ipol.2013.53
chicago: Mondelli, Marco. “A Finite Difference Scheme for the Stack Filter Simulating
the MCM.” Image Processing On Line. Image Processing On Line, 2013. https://doi.org/10.5201/ipol.2013.53.
ieee: M. Mondelli, “A finite difference scheme for the stack filter simulating the
MCM,” Image Processing On Line, vol. 3. Image Processing On Line, pp. 68–111,
2013.
ista: Mondelli M. 2013. A finite difference scheme for the stack filter simulating
the MCM. Image Processing On Line. 3, 68–111.
mla: Mondelli, Marco. “A Finite Difference Scheme for the Stack Filter Simulating
the MCM.” Image Processing On Line, vol. 3, Image Processing On Line, 2013,
pp. 68–111, doi:10.5201/ipol.2013.53.
short: M. Mondelli, Image Processing On Line 3 (2013) 68–111.
date_created: 2019-08-05T12:30:38Z
date_published: 2013-07-11T00:00:00Z
date_updated: 2021-01-12T08:08:56Z
day: '11'
ddc:
- '510'
doi: 10.5201/ipol.2013.53
extern: '1'
file:
- access_level: open_access
checksum: 83b7d429bc248c6c461229d3504fb139
content_type: application/pdf
creator: dernst
date_created: 2019-08-05T12:33:40Z
date_updated: 2020-07-14T12:47:40Z
file_id: '6769'
file_name: 2013_IPOL_Mondelli.pdf
file_size: 4306158
relation: main_file
file_date_updated: 2020-07-14T12:47:40Z
has_accepted_license: '1'
intvolume: ' 3'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 68-111
publication: Image Processing On Line
publication_identifier:
issn:
- 2105-1232
publication_status: published
publisher: Image Processing On Line
quality_controlled: '1'
status: public
title: A finite difference scheme for the stack filter simulating the MCM
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
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2013'
...
---
_id: '7306'
abstract:
- lang: eng
text: Rechargeable lithium–air (O2) batteries are receiving intense interest because
their high theoretical specific energy exceeds that of lithium-ion batteries.
If the Li–O2 battery is ever to succeed, highly reversible formation/decomposition
of Li2O2 must take place at the cathode on cycling. However, carbon, used ubiquitously
as the basis of the cathode, decomposes during Li2O2 oxidation on charge and actively
promotes electrolyte decomposition on cycling. Replacing carbon with a nanoporous
gold cathode, when in contact with a dimethyl sulphoxide-based electrolyte, does
seem to demonstrate better stability. However, nanoporous gold is not a suitable
cathode; its high mass destroys the key advantage of Li–O2 over Li ion (specific
energy), it is too expensive and too difficult to fabricate. Identifying a suitable
cathode material for the Li–O2 cell is one of the greatest challenges at present.
Here we show that a TiC-based cathode reduces greatly side reactions (arising
from the electrolyte and electrode degradation) compared with carbon and exhibits
better reversible formation/decomposition of Li2O2 even than nanoporous gold (>98%
capacity retention after 100 cycles, compared with 95% for nanoporous gold); it
is also four times lighter, of lower cost and easier to fabricate. The stability
may originate from the presence of TiO2 (along with some TiOC) on the surface
of TiC. In contrast to carbon or nanoporous gold, TiC seems to represent a more
viable, stable, cathode for aprotic Li–O2 cells.
article_processing_charge: No
article_type: original
author:
- first_name: Muhammed M.
full_name: Ottakam Thotiyl, Muhammed M.
last_name: Ottakam Thotiyl
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Zhangquan
full_name: Peng, Zhangquan
last_name: Peng
- first_name: Yuhui
full_name: Chen, Yuhui
last_name: Chen
- first_name: Zheng
full_name: Liu, Zheng
last_name: Liu
- first_name: Peter G.
full_name: Bruce, Peter G.
last_name: Bruce
citation:
ama: Ottakam Thotiyl MM, Freunberger SA, Peng Z, Chen Y, Liu Z, Bruce PG. A stable
cathode for the aprotic Li–O2 battery. Nature Materials. 2013;12(11):1050-1056.
doi:10.1038/nmat3737
apa: Ottakam Thotiyl, M. M., Freunberger, S. A., Peng, Z., Chen, Y., Liu, Z., &
Bruce, P. G. (2013). A stable cathode for the aprotic Li–O2 battery. Nature
Materials. Springer Nature. https://doi.org/10.1038/nmat3737
chicago: Ottakam Thotiyl, Muhammed M., Stefan Alexander Freunberger, Zhangquan Peng,
Yuhui Chen, Zheng Liu, and Peter G. Bruce. “A Stable Cathode for the Aprotic Li–O2 Battery.”
Nature Materials. Springer Nature, 2013. https://doi.org/10.1038/nmat3737.
ieee: M. M. Ottakam Thotiyl, S. A. Freunberger, Z. Peng, Y. Chen, Z. Liu, and P.
G. Bruce, “A stable cathode for the aprotic Li–O2 battery,” Nature Materials,
vol. 12, no. 11. Springer Nature, pp. 1050–1056, 2013.
ista: Ottakam Thotiyl MM, Freunberger SA, Peng Z, Chen Y, Liu Z, Bruce PG. 2013.
A stable cathode for the aprotic Li–O2 battery. Nature Materials. 12(11), 1050–1056.
mla: Ottakam Thotiyl, Muhammed M., et al. “A Stable Cathode for the Aprotic Li–O2 Battery.”
Nature Materials, vol. 12, no. 11, Springer Nature, 2013, pp. 1050–56,
doi:10.1038/nmat3737.
short: M.M. Ottakam Thotiyl, S.A. Freunberger, Z. Peng, Y. Chen, Z. Liu, P.G. Bruce,
Nature Materials 12 (2013) 1050–1056.
date_created: 2020-01-15T12:18:29Z
date_published: 2013-09-01T00:00:00Z
date_updated: 2021-01-12T08:12:55Z
day: '01'
doi: 10.1038/nmat3737
extern: '1'
intvolume: ' 12'
issue: '11'
language:
- iso: eng
month: '09'
oa_version: None
page: 1050-1056
publication: Nature Materials
publication_identifier:
issn:
- 1476-1122
- 1476-4660
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: A stable cathode for the aprotic Li–O2 battery
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2013'
...
---
_id: '7307'
abstract:
- lang: eng
text: The non-aqueous Li–air (O2) battery is receiving intense interest because
its theoretical specific energy exceeds that of Li-ion batteries. Recharging the
Li–O2 battery depends on oxidizing solid lithium peroxide (Li2O2), which is formed
on discharge within the porous cathode. However, transporting charge between Li2O2
particles and the solid electrode surface is at best very difficult and leads
to voltage polarization on charging, even at modest rates. This is a significant
problem facing the non-aqueous Li–O2 battery. Here we show that incorporation
of a redox mediator, tetrathiafulvalene (TTF), enables recharging at rates that
are impossible for the cell in the absence of the mediator. On charging, TTF is
oxidized to TTF+ at the cathode surface; TTF+ in turn oxidizes the solid Li2O2,
which results in the regeneration of TTF. The mediator acts as an electron–hole
transfer agent that permits efficient oxidation of solid Li2O2. The cell with
the mediator demonstrated 100 charge/discharge cycles.
article_processing_charge: No
article_type: original
author:
- first_name: Yuhui
full_name: Chen, Yuhui
last_name: Chen
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Zhangquan
full_name: Peng, Zhangquan
last_name: Peng
- first_name: Olivier
full_name: Fontaine, Olivier
last_name: Fontaine
- first_name: Peter G.
full_name: Bruce, Peter G.
last_name: Bruce
citation:
ama: Chen Y, Freunberger SA, Peng Z, Fontaine O, Bruce PG. Charging a Li–O2 battery
using a redox mediator. Nature Chemistry. 2013;5(6):489-494. doi:10.1038/nchem.1646
apa: Chen, Y., Freunberger, S. A., Peng, Z., Fontaine, O., & Bruce, P. G. (2013).
Charging a Li–O2 battery using a redox mediator. Nature Chemistry. Springer
Nature. https://doi.org/10.1038/nchem.1646
chicago: Chen, Yuhui, Stefan Alexander Freunberger, Zhangquan Peng, Olivier Fontaine,
and Peter G. Bruce. “Charging a Li–O2 Battery Using a Redox Mediator.” Nature
Chemistry. Springer Nature, 2013. https://doi.org/10.1038/nchem.1646.
ieee: Y. Chen, S. A. Freunberger, Z. Peng, O. Fontaine, and P. G. Bruce, “Charging
a Li–O2 battery using a redox mediator,” Nature Chemistry, vol. 5, no.
6. Springer Nature, pp. 489–494, 2013.
ista: Chen Y, Freunberger SA, Peng Z, Fontaine O, Bruce PG. 2013. Charging a Li–O2
battery using a redox mediator. Nature Chemistry. 5(6), 489–494.
mla: Chen, Yuhui, et al. “Charging a Li–O2 Battery Using a Redox Mediator.” Nature
Chemistry, vol. 5, no. 6, Springer Nature, 2013, pp. 489–94, doi:10.1038/nchem.1646.
short: Y. Chen, S.A. Freunberger, Z. Peng, O. Fontaine, P.G. Bruce, Nature Chemistry
5 (2013) 489–494.
date_created: 2020-01-15T12:18:43Z
date_published: 2013-05-12T00:00:00Z
date_updated: 2021-01-12T08:12:56Z
day: '12'
doi: 10.1038/nchem.1646
extern: '1'
intvolume: ' 5'
issue: '6'
language:
- iso: eng
month: '05'
oa_version: None
page: 489-494
publication: Nature Chemistry
publication_identifier:
issn:
- 1755-4330
- 1755-4349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Charging a Li–O2 battery using a redox mediator
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2013'
...
---
_id: '7595'
abstract:
- lang: eng
text: Inositol 1,3,4-trisphosphate 5/6 kinase (ITPK) phosphorylates inositol 1,3,4-trisphosphate
to form inositol 1,3,4,5-tetrakisphosphate and inositol 1,3,4,6-tetrakisphosphate
which can be finally transferred to inositol hexaphosphate (IP6) and play important
roles during plant growth and development. There are 4 putative ITPK members in
Arabidopsis. Expression pattern analysis showed that ITPK2 is constitutively expressed
in various tissues. A T-DNA knockout mutant of ITPK2 was identified and scanning
electron microscopy (SEM) analysis showed that the epidermis structure of seed
coat was irregularly formed in seeds of itpk2-1 mutant, resulting in the increased
permeability of seed coat to tetrazolium salts. Further analysis by gas chromatography
coupled with mass spectrometry of lipid polyester monomers in cell wall confirmed
a dramatic decrease in composition of suberin and cutin, which relate to the permeability
of seed coat and the formation of which is accompanied with seed coat development.
These results indicate that ITPK2 plays an essential role in seed coat development
and lipid polyester barrier formation.
article_processing_charge: No
article_type: original
author:
- first_name: Yong
full_name: Tang, Yong
last_name: Tang
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Hongwei
full_name: Xue, Hongwei
last_name: Xue
citation:
ama: Tang Y, Tan S, Xue H. Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2
is required for seed coat development. Acta Biochimica et Biophysica Sinica.
2013;45(7):549-560. doi:10.1093/abbs/gmt039
apa: Tang, Y., Tan, S., & Xue, H. (2013). Arabidopsis inositol 1,3,4-trisphosphate
5/6 kinase 2 is required for seed coat development. Acta Biochimica et Biophysica
Sinica. Oxford University Press. https://doi.org/10.1093/abbs/gmt039
chicago: Tang, Yong, Shutang Tan, and Hongwei Xue. “Arabidopsis Inositol 1,3,4-Trisphosphate
5/6 Kinase 2 Is Required for Seed Coat Development.” Acta Biochimica et Biophysica
Sinica. Oxford University Press, 2013. https://doi.org/10.1093/abbs/gmt039.
ieee: Y. Tang, S. Tan, and H. Xue, “Arabidopsis inositol 1,3,4-trisphosphate 5/6
kinase 2 is required for seed coat development,” Acta Biochimica et Biophysica
Sinica, vol. 45, no. 7. Oxford University Press, pp. 549–560, 2013.
ista: Tang Y, Tan S, Xue H. 2013. Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase
2 is required for seed coat development. Acta Biochimica et Biophysica Sinica.
45(7), 549–560.
mla: Tang, Yong, et al. “Arabidopsis Inositol 1,3,4-Trisphosphate 5/6 Kinase 2 Is
Required for Seed Coat Development.” Acta Biochimica et Biophysica Sinica,
vol. 45, no. 7, Oxford University Press, 2013, pp. 549–60, doi:10.1093/abbs/gmt039.
short: Y. Tang, S. Tan, H. Xue, Acta Biochimica et Biophysica Sinica 45 (2013) 549–560.
date_created: 2020-03-21T16:06:36Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2021-01-12T08:14:23Z
day: '01'
doi: 10.1093/abbs/gmt039
extern: '1'
external_id:
pmid:
- '23595027'
intvolume: ' 45'
issue: '7'
language:
- iso: eng
month: '07'
oa_version: None
page: 549-560
pmid: 1
publication: Acta Biochimica et Biophysica Sinica
publication_identifier:
issn:
- 1745-7270
- 1672-9145
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed
coat development
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2013'
...
---
_id: '7596'
abstract:
- lang: eng
text: Casein kinase1 (CK1) plays crucial roles in regulating growth and development
via phosphorylating various substrates throughout the eukaryote kingdom. Blue
light is crucial for normal growth of both plants and animals, and blue light
receptor cryptochrome2 (CRY2) undergoes blue light–dependent phosphorylation and
degradation in planta. To study the function of plant CK1s, systematic genetic
analysis showed that deficiency of two paralogous Arabidopsis thaliana CK1s, CK1.3
and CK1.4, caused shortened hypocotyls, especially under blue light, while overexpression
of either CK1.3 or CK1.4 resulted in the insensitive response to blue light and
delayed flowering under long-day conditions. CK1.3 or CK1.4 act dependently on
CRY2, and overexpression of CK1.3 or CK1.4 significantly suppresses the hypersensitive
response to blue light by CRY2 overexpression. Biochemical studies showed that
CK1.3 and CK1.4 directly phosphorylate CRY2 at Ser-587 and Thr-603 in vitro and
negatively regulate CRY2 stability in planta, which are stimulated by blue light,
further confirming the crucial roles of CK1.3 and CK1.4 in blue light responses
through phosphorylating CRY2. Interestingly, expression of CK1.3 and CK1.4 is
stimulated by blue light and feedback regulated by CRY2-mediated signaling. These
results provide direct evidence for CRY2 phosphorylation and informative clues
on the mechanisms of CRY2-mediated light responses.
article_processing_charge: No
article_type: original
author:
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: C.
full_name: Dai, C.
last_name: Dai
- first_name: H.-T.
full_name: Liu, H.-T.
last_name: Liu
- first_name: H.-W.
full_name: Xue, H.-W.
last_name: Xue
citation:
ama: Tan S, Dai C, Liu H-T, Xue H-W. Arabidopsis casein kinase1 proteins CK1.3 and
CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling. The Plant
Cell. 2013;25(7):2618-2632. doi:10.1105/tpc.113.114322
apa: Tan, S., Dai, C., Liu, H.-T., & Xue, H.-W. (2013). Arabidopsis casein kinase1
proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling.
The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.113.114322
chicago: Tan, Shutang, C. Dai, H.-T. Liu, and H.-W. Xue. “Arabidopsis Casein Kinase1
Proteins CK1.3 and CK1.4 Phosphorylate Cryptochrome2 to Regulate Blue Light Signaling.”
The Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.114322.
ieee: S. Tan, C. Dai, H.-T. Liu, and H.-W. Xue, “Arabidopsis casein kinase1 proteins
CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling,”
The Plant Cell, vol. 25, no. 7. American Society of Plant Biologists, pp.
2618–2632, 2013.
ista: Tan S, Dai C, Liu H-T, Xue H-W. 2013. Arabidopsis casein kinase1 proteins
CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling.
The Plant Cell. 25(7), 2618–2632.
mla: Tan, Shutang, et al. “Arabidopsis Casein Kinase1 Proteins CK1.3 and CK1.4 Phosphorylate
Cryptochrome2 to Regulate Blue Light Signaling.” The Plant Cell, vol. 25,
no. 7, American Society of Plant Biologists, 2013, pp. 2618–32, doi:10.1105/tpc.113.114322.
short: S. Tan, C. Dai, H.-T. Liu, H.-W. Xue, The Plant Cell 25 (2013) 2618–2632.
date_created: 2020-03-21T16:06:55Z
date_published: 2013-08-26T00:00:00Z
date_updated: 2021-01-12T08:14:24Z
day: '26'
doi: 10.1105/tpc.113.114322
extern: '1'
external_id:
pmid:
- '23897926'
intvolume: ' 25'
issue: '7'
language:
- iso: eng
month: '08'
oa_version: None
page: 2618-2632
pmid: 1
publication: The Plant Cell
publication_identifier:
issn:
- 1040-4651
- 1532-298X
publication_status: published
publisher: American Society of Plant Biologists
quality_controlled: '1'
status: public
title: Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2
to regulate blue light signaling
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2013'
...
---
_id: '765'
abstract:
- lang: eng
text: Renaming is a classic distributed coordination task in which a set of processes
must pick distinct identifiers from a small namespace. In this paper, we consider
the time complexity of this problem when the namespace is linear in the number
of participants, a variant known as loose renaming. We give a non-adaptive algorithm
with O(log log n) (individual) step complexity, where n is a known upper bound
on contention, and an adaptive algorithm with step complexity O((log log k)2),
where k is the actual contention in the execution. We also present a variant of
the adaptive algorithm which requires O(k log log k) total process steps. All
upper bounds hold with high probability against a strong adaptive adversary. We
complement the algorithms with an ω(log log n) expected time lower bound on the
complexity of randomized renaming using test-and-set operations and linear space.
The result is based on a new coupling technique, and is the first to apply to
non-adaptive randomized renaming. Since our algorithms use O(n) test-and-set objects,
our results provide matching bounds on the cost of loose renaming in this setting.
acknowledgement: "Dan Alistarh - This author was supported by the SNF Postdoctoral
Fellows Program, NSF grant CCF-1217921, DoE ASCR grant\r\nER26116/DE-SC0008923,
\ and by grants from the Oracle\r\nand Intel corporations.\r\nJames Aspnes
- Supported in part by NSF grant CCF-0916389.\r\nGeorge Giakkoupis - This work was
funded in part by INRIA Associate Team\r\nRADCON, and ERC Starting Grant GOSSPLE
204742.\r\nPhilipp Woelfel - This research was undertaken, in part, thanks to funding\r\nfrom
the Canada Research Chairs program and the HP Labs\r\nInnovation Research Program."
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: James
full_name: Aspnes, James
last_name: Aspnes
- first_name: George
full_name: Giakkoupis, George
last_name: Giakkoupis
- first_name: Philipp
full_name: Woelfel, Philipp
last_name: Woelfel
citation:
ama: 'Alistarh D-A, Aspnes J, Giakkoupis G, Woelfel P. Randomized loose renaming
in O(loglogn) time. In: ACM; 2013:200-209. doi:10.1145/2484239.2484240'
apa: 'Alistarh, D.-A., Aspnes, J., Giakkoupis, G., & Woelfel, P. (2013). Randomized
loose renaming in O(loglogn) time (pp. 200–209). Presented at the PODC: Principles
of Distributed Computing, ACM. https://doi.org/10.1145/2484239.2484240'
chicago: Alistarh, Dan-Adrian, James Aspnes, George Giakkoupis, and Philipp Woelfel.
“Randomized Loose Renaming in O(Loglogn) Time,” 200–209. ACM, 2013. https://doi.org/10.1145/2484239.2484240.
ieee: 'D.-A. Alistarh, J. Aspnes, G. Giakkoupis, and P. Woelfel, “Randomized loose
renaming in O(loglogn) time,” presented at the PODC: Principles of Distributed
Computing, 2013, pp. 200–209.'
ista: 'Alistarh D-A, Aspnes J, Giakkoupis G, Woelfel P. 2013. Randomized loose renaming
in O(loglogn) time. PODC: Principles of Distributed Computing, 200–209.'
mla: Alistarh, Dan-Adrian, et al. Randomized Loose Renaming in O(Loglogn) Time.
ACM, 2013, pp. 200–09, doi:10.1145/2484239.2484240.
short: D.-A. Alistarh, J. Aspnes, G. Giakkoupis, P. Woelfel, in:, ACM, 2013, pp.
200–209.
conference:
name: 'PODC: Principles of Distributed Computing'
date_created: 2018-12-11T11:48:23Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2023-02-23T13:13:14Z
day: '01'
doi: 10.1145/2484239.2484240
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 200 - 209
publication_status: published
publisher: ACM
publist_id: '6889'
status: public
title: Randomized loose renaming in O(loglogn) time
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '7745'
abstract:
- lang: eng
text: The underlying basis of genetic variation in quantitative traits, in terms
of the number of causal variants and the size of their effects, is largely unknown
in natural populations. The expectation is that complex quantitative trait variation
is attributable to many, possibly interacting, causal variants, whose effects
may depend upon the sex, age and the environment in which they are expressed.
A recently developed methodology in animal breeding derives a value of relatedness
among individuals from high‐density genomic marker data, to estimate additive
genetic variance within livestock populations. Here, we adapt and test the effectiveness
of these methods to partition genetic variation for complex traits across genomic
regions within ecological study populations where individuals have varying degrees
of relatedness. We then apply this approach for the first time to a natural population
and demonstrate that genetic variation in wing length in the great tit (Parus
major) reflects contributions from multiple genomic regions. We show that a polygenic
additive mode of gene action best describes the patterns observed, and we find
no evidence of dosage compensation for the sex chromosome. Our results suggest
that most of the genomic regions that influence wing length have the same effects
in both sexes. We found a limited amount of genetic variance in males that is
attributed to regions that have no effects in females, which could facilitate
the sexual dimorphism observed for this trait. Although this exploratory work
focuses on one complex trait, the methodology is generally applicable to any trait
for any laboratory or wild population, paving the way for investigating sex‐,
age‐ and environment‐specific genetic effects and thus the underlying genetic
architecture of phenotype in biological study systems.
article_processing_charge: No
article_type: original
author:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Anna W.
full_name: Santure, Anna W.
last_name: Santure
- first_name: Isabelle
full_name: DeCauwer, Isabelle
last_name: DeCauwer
- first_name: Ben C.
full_name: Sheldon, Ben C.
last_name: Sheldon
- first_name: Jon
full_name: Slate, Jon
last_name: Slate
citation:
ama: Robinson MR, Santure AW, DeCauwer I, Sheldon BC, Slate J. Partitioning of genetic
variation across the genome using multimarker methods in a wild bird population.
Molecular Ecology. 2013;22(15):3963-3980. doi:10.1111/mec.12375
apa: Robinson, M. R., Santure, A. W., DeCauwer, I., Sheldon, B. C., & Slate,
J. (2013). Partitioning of genetic variation across the genome using multimarker
methods in a wild bird population. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.12375
chicago: Robinson, Matthew Richard, Anna W. Santure, Isabelle DeCauwer, Ben C. Sheldon,
and Jon Slate. “Partitioning of Genetic Variation across the Genome Using Multimarker
Methods in a Wild Bird Population.” Molecular Ecology. Wiley, 2013. https://doi.org/10.1111/mec.12375.
ieee: M. R. Robinson, A. W. Santure, I. DeCauwer, B. C. Sheldon, and J. Slate, “Partitioning
of genetic variation across the genome using multimarker methods in a wild bird
population,” Molecular Ecology, vol. 22, no. 15. Wiley, pp. 3963–3980,
2013.
ista: Robinson MR, Santure AW, DeCauwer I, Sheldon BC, Slate J. 2013. Partitioning
of genetic variation across the genome using multimarker methods in a wild bird
population. Molecular Ecology. 22(15), 3963–3980.
mla: Robinson, Matthew Richard, et al. “Partitioning of Genetic Variation across
the Genome Using Multimarker Methods in a Wild Bird Population.” Molecular
Ecology, vol. 22, no. 15, Wiley, 2013, pp. 3963–80, doi:10.1111/mec.12375.
short: M.R. Robinson, A.W. Santure, I. DeCauwer, B.C. Sheldon, J. Slate, Molecular
Ecology 22 (2013) 3963–3980.
date_created: 2020-04-30T11:00:15Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T08:15:14Z
day: '01'
doi: 10.1111/mec.12375
extern: '1'
intvolume: ' 22'
issue: '15'
language:
- iso: eng
month: '08'
oa_version: None
page: 3963-3980
publication: Molecular Ecology
publication_identifier:
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Partitioning of genetic variation across the genome using multimarker methods
in a wild bird population
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2013'
...
---
_id: '7746'
abstract:
- lang: eng
text: Clutch size and egg mass are life history traits that have been extensively
studied in wild bird populations, as life history theory predicts a negative trade‐off
between them, either at the phenotypic or at the genetic level. Here, we analyse
the genomic architecture of these heritable traits in a wild great tit (Parus
major) population, using three marker‐based approaches – chromosome partitioning,
quantitative trait locus (QTL) mapping and a genome‐wide association study (GWAS).
The variance explained by each great tit chromosome scales with predicted chromosome
size, no location in the genome contains genome‐wide significant QTL, and no individual
SNPs are associated with a large proportion of phenotypic variation, all of which
may suggest that variation in both traits is due to many loci of small effect,
located across the genome. There is no evidence that any regions of the genome
contribute significantly to both traits, which combined with a small, nonsignificant
negative genetic covariance between the traits, suggests the absence of genetic
constraints on the independent evolution of these traits. Our findings support
the hypothesis that variation in life history traits in natural populations is
likely to be determined by many loci of small effect spread throughout the genome,
which are subject to continued input of variation by mutation and migration, although
we cannot exclude the possibility of an additional input of major effect genes
influencing either trait.
article_processing_charge: No
article_type: original
author:
- first_name: Anna W.
full_name: Santure, Anna W.
last_name: Santure
- first_name: Isabelle
full_name: De Cauwer, Isabelle
last_name: De Cauwer
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Jocelyn
full_name: Poissant, Jocelyn
last_name: Poissant
- first_name: Ben C.
full_name: Sheldon, Ben C.
last_name: Sheldon
- first_name: Jon
full_name: Slate, Jon
last_name: Slate
citation:
ama: Santure AW, De Cauwer I, Robinson MR, Poissant J, Sheldon BC, Slate J. Genomic
dissection of variation in clutch size and egg mass in a wild great tit (Parus
major) population. Molecular Ecology. 2013;22(15):3949-3962. doi:10.1111/mec.12376
apa: Santure, A. W., De Cauwer, I., Robinson, M. R., Poissant, J., Sheldon, B. C.,
& Slate, J. (2013). Genomic dissection of variation in clutch size and egg
mass in a wild great tit (Parus major) population. Molecular Ecology. Wiley.
https://doi.org/10.1111/mec.12376
chicago: Santure, Anna W., Isabelle De Cauwer, Matthew Richard Robinson, Jocelyn
Poissant, Ben C. Sheldon, and Jon Slate. “Genomic Dissection of Variation in Clutch
Size and Egg Mass in a Wild Great Tit (Parus Major) Population.” Molecular
Ecology. Wiley, 2013. https://doi.org/10.1111/mec.12376.
ieee: A. W. Santure, I. De Cauwer, M. R. Robinson, J. Poissant, B. C. Sheldon, and
J. Slate, “Genomic dissection of variation in clutch size and egg mass in a wild
great tit (Parus major) population,” Molecular Ecology, vol. 22, no. 15.
Wiley, pp. 3949–3962, 2013.
ista: Santure AW, De Cauwer I, Robinson MR, Poissant J, Sheldon BC, Slate J. 2013.
Genomic dissection of variation in clutch size and egg mass in a wild great tit
(Parus major) population. Molecular Ecology. 22(15), 3949–3962.
mla: Santure, Anna W., et al. “Genomic Dissection of Variation in Clutch Size and
Egg Mass in a Wild Great Tit (Parus Major) Population.” Molecular Ecology,
vol. 22, no. 15, Wiley, 2013, pp. 3949–62, doi:10.1111/mec.12376.
short: A.W. Santure, I. De Cauwer, M.R. Robinson, J. Poissant, B.C. Sheldon, J.
Slate, Molecular Ecology 22 (2013) 3949–3962.
date_created: 2020-04-30T11:00:32Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T08:15:14Z
day: '01'
doi: 10.1111/mec.12376
extern: '1'
intvolume: ' 22'
issue: '15'
language:
- iso: eng
month: '08'
oa_version: None
page: 3949-3962
publication: Molecular Ecology
publication_identifier:
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Genomic dissection of variation in clutch size and egg mass in a wild great
tit (Parus major) population
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2013'
...
---
_id: '7747'
abstract:
- lang: eng
text: Acquisition and allocation of resources are central to life‐history theory.
However, empirical work typically focuses only on allocation despite the fact
that relationships between fitness components may be governed by differences in
the ability of individuals to acquire resources across environments. Here, we
outline a statistical framework to partition the genetic basis of multivariate
plasticity into independent axes of genetic variation, and quantify for the first
time, the extent to which specific traits drive multitrait genotype–environment
interactions. Our framework generalises to analyses of plasticity, growth and
ageing. We apply this approach to a unique, large‐scale, multivariate study of
acquisition, allocation and plasticity in the life history of the cricket, Gryllus
firmus. We demonstrate that resource acquisition and allocation are genetically
correlated, and that plasticity in trade‐offs between allocation to components
of fitness is 90% dependent on genetic variance for total resource acquisition.
These results suggest that genotype–environment effects for resource acquisition
can maintain variation in life‐history components that are typically observed
in the wild.
article_processing_charge: No
article_type: original
author:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Andrew P.
full_name: Beckerman, Andrew P.
last_name: Beckerman
citation:
ama: 'Robinson MR, Beckerman AP. Quantifying multivariate plasticity: Genetic variation
in resource acquisition drives plasticity in resource allocation to components
of life history. Ecology Letters. 2013;16(3):281-290. doi:10.1111/ele.12047'
apa: 'Robinson, M. R., & Beckerman, A. P. (2013). Quantifying multivariate plasticity:
Genetic variation in resource acquisition drives plasticity in resource allocation
to components of life history. Ecology Letters. Wiley. https://doi.org/10.1111/ele.12047'
chicago: 'Robinson, Matthew Richard, and Andrew P. Beckerman. “Quantifying Multivariate
Plasticity: Genetic Variation in Resource Acquisition Drives Plasticity in Resource
Allocation to Components of Life History.” Ecology Letters. Wiley, 2013.
https://doi.org/10.1111/ele.12047.'
ieee: 'M. R. Robinson and A. P. Beckerman, “Quantifying multivariate plasticity:
Genetic variation in resource acquisition drives plasticity in resource allocation
to components of life history,” Ecology Letters, vol. 16, no. 3. Wiley,
pp. 281–290, 2013.'
ista: 'Robinson MR, Beckerman AP. 2013. Quantifying multivariate plasticity: Genetic
variation in resource acquisition drives plasticity in resource allocation to
components of life history. Ecology Letters. 16(3), 281–290.'
mla: 'Robinson, Matthew Richard, and Andrew P. Beckerman. “Quantifying Multivariate
Plasticity: Genetic Variation in Resource Acquisition Drives Plasticity in Resource
Allocation to Components of Life History.” Ecology Letters, vol. 16, no.
3, Wiley, 2013, pp. 281–90, doi:10.1111/ele.12047.'
short: M.R. Robinson, A.P. Beckerman, Ecology Letters 16 (2013) 281–290.
date_created: 2020-04-30T11:00:49Z
date_published: 2013-03-01T00:00:00Z
date_updated: 2021-01-12T08:15:15Z
day: '01'
doi: 10.1111/ele.12047
extern: '1'
intvolume: ' 16'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 281-290
publication: Ecology Letters
publication_identifier:
issn:
- 1461-023X
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: 'Quantifying multivariate plasticity: Genetic variation in resource acquisition
drives plasticity in resource allocation to components of life history'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2013'
...
---
_id: '476'
abstract:
- lang: eng
text: 'Maternal exposure to infection occurring mid-gestation produces a three-fold
increase in the risk of schizophrenia in the offspring. The critical initiating
factor appears to be the maternal immune activation (MIA) that follows infection.
This process can be induced in rodents by exposure of pregnant dams to the viral
mimic Poly I:C, which triggers an immune response that results in structural,
functional, behavioral, and electrophysiological phenotypes in the adult offspring
that model those seen in schizophrenia. We used this model to explore the role
of synchronization in brain neural networks, a process thought to be dysfunctional
in schizophrenia and previously associated with positive, negative, and cognitive
symptoms of schizophrenia. Exposure of pregnant dams to Poly I:C on GD15 produced
an impairment in long-range neural synchrony in adult offspring between two regions
implicated in schizophrenia pathology; the hippocampus and the medial prefrontal
cortex (mPFC). This reduction in synchrony was ameliorated by acute doses of the
antipsychotic clozapine. MIA animals have previously been shown to have impaired
pre-pulse inhibition (PPI), a gold-standard measure of schizophrenia-like deficits
in animal models. Our data showed that deficits in synchrony were positively correlated
with the impairments in PPI. Subsequent analysis of LFP activity during the PPI
response also showed that reduced coupling between the mPFC and the hippocampus
following processing of the pre-pulse was associated with reduced PPI. The ability
of the MIA intervention to model neurodevelopmental aspects of schizophrenia pathology
provides a useful platform from which to investigate the ontogeny of aberrant
synchronous processes. Further, the way in which the model expresses translatable
deficits such as aberrant synchrony and reduced PPI will allow researchers to
explore novel intervention strategies targeted to these changes. '
author:
- first_name: Desiree
full_name: Dickerson, Desiree
id: 444EB89E-F248-11E8-B48F-1D18A9856A87
last_name: Dickerson
- first_name: David
full_name: Bilkey, David
last_name: Bilkey
citation:
ama: 'Dickerson D, Bilkey D. Aberrant neural synchrony in the maternal immune activation
model: Using translatable measures to explore targeted interventions. Frontiers
in Behavioral Neuroscience. 2013;7(DEC). doi:10.3389/fnbeh.2013.00217'
apa: 'Dickerson, D., & Bilkey, D. (2013). Aberrant neural synchrony in the maternal
immune activation model: Using translatable measures to explore targeted interventions.
Frontiers in Behavioral Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fnbeh.2013.00217'
chicago: 'Dickerson, Desiree, and David Bilkey. “Aberrant Neural Synchrony in the
Maternal Immune Activation Model: Using Translatable Measures to Explore Targeted
Interventions.” Frontiers in Behavioral Neuroscience. Frontiers Research
Foundation, 2013. https://doi.org/10.3389/fnbeh.2013.00217.'
ieee: 'D. Dickerson and D. Bilkey, “Aberrant neural synchrony in the maternal immune
activation model: Using translatable measures to explore targeted interventions,”
Frontiers in Behavioral Neuroscience, vol. 7, no. DEC. Frontiers Research
Foundation, 2013.'
ista: 'Dickerson D, Bilkey D. 2013. Aberrant neural synchrony in the maternal immune
activation model: Using translatable measures to explore targeted interventions.
Frontiers in Behavioral Neuroscience. 7(DEC).'
mla: 'Dickerson, Desiree, and David Bilkey. “Aberrant Neural Synchrony in the Maternal
Immune Activation Model: Using Translatable Measures to Explore Targeted Interventions.”
Frontiers in Behavioral Neuroscience, vol. 7, no. DEC, Frontiers Research
Foundation, 2013, doi:10.3389/fnbeh.2013.00217.'
short: D. Dickerson, D. Bilkey, Frontiers in Behavioral Neuroscience 7 (2013).
date_created: 2018-12-11T11:46:41Z
date_published: 2013-12-27T00:00:00Z
date_updated: 2021-01-12T08:00:53Z
day: '27'
ddc:
- '571'
department:
- _id: JoCs
doi: 10.3389/fnbeh.2013.00217
file:
- access_level: open_access
checksum: cd7183121e56251176100ccac165c95c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:10Z
date_updated: 2020-07-14T12:46:35Z
file_id: '5128'
file_name: IST-2018-953-v1+1_2013_Dickerson_Aberrant_neural.pdf
file_size: 530134
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 7'
issue: DEC
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Frontiers in Behavioral Neuroscience
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '7346'
pubrep_id: '953'
quality_controlled: '1'
status: public
title: 'Aberrant neural synchrony in the maternal immune activation model: Using translatable
measures to explore targeted interventions'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2013'
...
---
_id: '499'
abstract:
- lang: eng
text: Exposure of an isogenic bacterial population to a cidal antibiotic typically
fails to eliminate a small fraction of refractory cells. Historically, fractional
killing has been attributed to infrequently dividing or nondividing "persisters."
Using microfluidic cultures and time-lapse microscopy, we found that Mycobacterium
smegmatis persists by dividing in the presence of the drug isoniazid (INH). Although
persistence in these studies was characterized by stable numbers of cells, this
apparent stability was actually a dynamic state of balanced division and death.
Single cells expressed catalase-peroxidase (KatG), which activates INH, in stochastic
pulses that were negatively correlated with cell survival. These behaviors may
reflect epigenetic effects, because KatG pulsing and death were correlated between
sibling cells. Selection of lineages characterized by infrequent KatG pulsing
could allow nonresponsive adaptation during prolonged drug exposure.
author:
- first_name: Yurichi
full_name: Wakamoto, Yurichi
last_name: Wakamoto
- first_name: Neraaj
full_name: Dhar, Neraaj
last_name: Dhar
- first_name: Remy P
full_name: Chait, Remy P
id: 3464AE84-F248-11E8-B48F-1D18A9856A87
last_name: Chait
orcid: 0000-0003-0876-3187
- first_name: Katrin
full_name: Schneider, Katrin
last_name: Schneider
- first_name: François
full_name: Signorino Gelo, François
last_name: Signorino Gelo
- first_name: Stanislas
full_name: Leibler, Stanislas
last_name: Leibler
- first_name: John
full_name: Mckinney, John
last_name: Mckinney
citation:
ama: Wakamoto Y, Dhar N, Chait RP, et al. Dynamic persistence of antibiotic-stressed
mycobacteria. Science. 2013;339(6115):91-95. doi:10.1126/science.1229858
apa: Wakamoto, Y., Dhar, N., Chait, R. P., Schneider, K., Signorino Gelo, F., Leibler,
S., & Mckinney, J. (2013). Dynamic persistence of antibiotic-stressed mycobacteria.
Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1229858
chicago: Wakamoto, Yurichi, Neraaj Dhar, Remy P Chait, Katrin Schneider, François
Signorino Gelo, Stanislas Leibler, and John Mckinney. “Dynamic Persistence of
Antibiotic-Stressed Mycobacteria.” Science. American Association for the
Advancement of Science, 2013. https://doi.org/10.1126/science.1229858.
ieee: Y. Wakamoto et al., “Dynamic persistence of antibiotic-stressed mycobacteria,”
Science, vol. 339, no. 6115. American Association for the Advancement of
Science, pp. 91–95, 2013.
ista: Wakamoto Y, Dhar N, Chait RP, Schneider K, Signorino Gelo F, Leibler S, Mckinney
J. 2013. Dynamic persistence of antibiotic-stressed mycobacteria. Science. 339(6115),
91–95.
mla: Wakamoto, Yurichi, et al. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.”
Science, vol. 339, no. 6115, American Association for the Advancement of
Science, 2013, pp. 91–95, doi:10.1126/science.1229858.
short: Y. Wakamoto, N. Dhar, R.P. Chait, K. Schneider, F. Signorino Gelo, S. Leibler,
J. Mckinney, Science 339 (2013) 91–95.
date_created: 2018-12-11T11:46:48Z
date_published: 2013-01-04T00:00:00Z
date_updated: 2021-01-12T08:01:06Z
day: '04'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1126/science.1229858
intvolume: ' 339'
issue: '6115'
language:
- iso: eng
month: '01'
oa_version: None
page: 91 - 95
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '7321'
quality_controlled: '1'
scopus_import: 1
status: public
title: Dynamic persistence of antibiotic-stressed mycobacteria
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 339
year: '2013'
...
---
_id: '500'
abstract:
- lang: eng
text: 'Background: Reassortment between the RNA segments encoding haemagglutinin
(HA) and neuraminidase (NA), the major antigenic influenza proteins, produces
viruses with novel HA and NA subtype combinations and has preceded the emergence
of pandemic strains. It has been suggested that productive viral infection requires
a balance in the level of functional activity of HA and NA, arising from their
closely interacting roles in the viral life cycle, and that this functional balance
could be mediated by genetic changes in the HA and NA. Here, we investigate how
the selective pressure varies for H7 avian influenza HA on different NA subtype
backgrounds. Results: By extending Bayesian stochastic mutational mapping methods
to calculate the ratio of the rate of non-synonymous change to the rate of synonymous
change (d N/d S), we found the average d N/d S across the avian influenza H7 HA1
region to be significantly greater on an N2 NA subtype background than on an N1,
N3 or N7 background. Observed differences in evolutionary rates of H7 HA on different
NA subtype backgrounds could not be attributed to underlying differences between
avian host species or virus pathogenicity. Examination of d N/d S values for each
subtype on a site-by-site basis indicated that the elevated d N/d S on the N2
NA background was a result of increased selection, rather than a relaxation of
selective constraint. Conclusions: Our results are consistent with the hypothesis
that reassortment exposes influenza HA to significant changes in selective pressure
through genetic interactions with NA. Such epistatic effects might be explicitly
accounted for in future models of influenza evolution.'
acknowledgement: "This work was supported by the Biotechnology and Biological Sciences
Research Council, the Government of the Republic of Panama, the Interdisciplinary
Centre for Human and Avian Influenza Research (www.ichair-flu.org) funded by the
Scottish Funding Council, and the Institute for Science and Technology Austria.\r\nCC
BY 2.0\r\n"
article_number: '222'
author:
- first_name: Melissa
full_name: Ward, Melissa
last_name: Ward
- first_name: Samantha
full_name: Lycett, Samantha
last_name: Lycett
- first_name: Dorita
full_name: Avila, Dorita
last_name: Avila
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Andrew
full_name: Leigh Brown, Andrew
last_name: Leigh Brown
citation:
ama: Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. Evolutionary interactions
between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary
Biology. 2013;13(1). doi:10.1186/1471-2148-13-222
apa: Ward, M., Lycett, S., Avila, D., Bollback, J. P., & Leigh Brown, A. (2013).
Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza.
BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-13-222
chicago: Ward, Melissa, Samantha Lycett, Dorita Avila, Jonathan P Bollback, and
Andrew Leigh Brown. “Evolutionary Interactions between Haemagglutinin and Neuraminidase
in Avian Influenza.” BMC Evolutionary Biology. BioMed Central, 2013. https://doi.org/10.1186/1471-2148-13-222.
ieee: M. Ward, S. Lycett, D. Avila, J. P. Bollback, and A. Leigh Brown, “Evolutionary
interactions between haemagglutinin and neuraminidase in avian influenza,” BMC
Evolutionary Biology, vol. 13, no. 1. BioMed Central, 2013.
ista: Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. 2013. Evolutionary
interactions between haemagglutinin and neuraminidase in avian influenza. BMC
Evolutionary Biology. 13(1), 222.
mla: Ward, Melissa, et al. “Evolutionary Interactions between Haemagglutinin and
Neuraminidase in Avian Influenza.” BMC Evolutionary Biology, vol. 13, no.
1, 222, BioMed Central, 2013, doi:10.1186/1471-2148-13-222.
short: M. Ward, S. Lycett, D. Avila, J.P. Bollback, A. Leigh Brown, BMC Evolutionary
Biology 13 (2013).
date_created: 2018-12-11T11:46:49Z
date_published: 2013-10-09T00:00:00Z
date_updated: 2021-01-12T08:01:08Z
day: '09'
ddc:
- '576'
department:
- _id: JoBo
doi: 10.1186/1471-2148-13-222
file:
- access_level: open_access
checksum: 52cf48a7c1794676ae8b0029573a84a9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:59Z
date_updated: 2020-07-14T12:46:36Z
file_id: '4722'
file_name: IST-2018-941-v1+1_2013_Bollback_Evolutionary_interactionspdf.pdf
file_size: 1150052
relation: main_file
file_date_updated: 2020-07-14T12:46:36Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: BMC Evolutionary Biology
publication_status: published
publisher: BioMed Central
publist_id: '7320'
pubrep_id: '941'
quality_controlled: '1'
scopus_import: 1
status: public
title: Evolutionary interactions between haemagglutinin and neuraminidase in avian
influenza
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2013'
...
---
_id: '501'
abstract:
- lang: eng
text: 'All known species of extant tapirs are allopatric: 1 in southeastern Asia
and 3 in Central and South America. The fossil record for tapirs, however, is
much wider in geographical range, including Europe, Asia, and North and South
America, going back to the late Oligocene, making the present distribution a relict
of the original one. We here describe a new species of living Tapirus from the
Amazon rain forest, the 1st since T. bairdii Gill, 1865, and the 1st new Perissodactyla
in more than 100 years, from both morphological and molecular characters. It is
shorter in stature than T. terrestris (Linnaeus, 1758) and has distinctive skull
morphology, and it is basal to the clade formed by T. terrestris and T. pinchaque
(Roulin, 1829). This highlights the unrecognized biodiversity in western Amazonia,
where the biota faces increasing threats. Local peoples have long recognized our
new species, suggesting a key role for traditional knowledge in understanding
the biodiversity of the region.'
author:
- first_name: Mario
full_name: Cozzuol, Mario
last_name: Cozzuol
- first_name: Camila
full_name: Clozato, Camila
last_name: Clozato
- first_name: Elizete
full_name: Holanda, Elizete
last_name: Holanda
- first_name: Flávio
full_name: Rodrigues, Flávio
last_name: Rodrigues
- first_name: Samuel
full_name: Nienow, Samuel
last_name: Nienow
- first_name: Benoit
full_name: De Thoisy, Benoit
last_name: De Thoisy
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Fabrício
full_name: Santos, Fabrício
last_name: Santos
citation:
ama: Cozzuol M, Clozato C, Holanda E, et al. A new species of tapir from the Amazon.
Journal of Mammalogy. 2013;94(6):1331-1345. doi:10.1644/12-MAMM-A-169.1
apa: Cozzuol, M., Clozato, C., Holanda, E., Rodrigues, F., Nienow, S., De Thoisy,
B., … Santos, F. (2013). A new species of tapir from the Amazon. Journal of
Mammalogy. Oxford University Press. https://doi.org/10.1644/12-MAMM-A-169.1
chicago: Cozzuol, Mario, Camila Clozato, Elizete Holanda, Flávio Rodrigues, Samuel
Nienow, Benoit De Thoisy, Rodrigo A Fernandes Redondo, and Fabrício Santos. “A
New Species of Tapir from the Amazon.” Journal of Mammalogy. Oxford University
Press, 2013. https://doi.org/10.1644/12-MAMM-A-169.1.
ieee: M. Cozzuol et al., “A new species of tapir from the Amazon,” Journal
of Mammalogy, vol. 94, no. 6. Oxford University Press, pp. 1331–1345, 2013.
ista: Cozzuol M, Clozato C, Holanda E, Rodrigues F, Nienow S, De Thoisy B, Fernandes
Redondo RA, Santos F. 2013. A new species of tapir from the Amazon. Journal of
Mammalogy. 94(6), 1331–1345.
mla: Cozzuol, Mario, et al. “A New Species of Tapir from the Amazon.” Journal
of Mammalogy, vol. 94, no. 6, Oxford University Press, 2013, pp. 1331–45,
doi:10.1644/12-MAMM-A-169.1.
short: M. Cozzuol, C. Clozato, E. Holanda, F. Rodrigues, S. Nienow, B. De Thoisy,
R.A. Fernandes Redondo, F. Santos, Journal of Mammalogy 94 (2013) 1331–1345.
date_created: 2018-12-11T11:46:49Z
date_published: 2013-12-01T00:00:00Z
date_updated: 2021-01-12T08:01:09Z
day: '01'
ddc:
- '570'
department:
- _id: JoBo
doi: 10.1644/12-MAMM-A-169.1
file:
- access_level: open_access
checksum: 8007815078dccac21ecd1cf73a269dc6
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:59Z
date_updated: 2020-07-14T12:46:36Z
file_id: '4980'
file_name: IST-2018-940-v1+1_2013_Redondo_A_new.pdf
file_size: 1040765
relation: main_file
file_date_updated: 2020-07-14T12:46:36Z
has_accepted_license: '1'
intvolume: ' 94'
issue: '6'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '12'
oa: 1
oa_version: Published Version
page: 1331 - 1345
publication: Journal of Mammalogy
publication_status: published
publisher: Oxford University Press
publist_id: '7319'
pubrep_id: '940'
quality_controlled: '1'
scopus_import: 1
status: public
title: A new species of tapir from the Amazon
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 94
year: '2013'
...
---
_id: '502'
abstract:
- lang: eng
text: 'Blind signatures allow users to obtain signatures on messages hidden from
the signer; moreover, the signer cannot link the resulting message/signature pair
to the signing session. This paper presents blind signature schemes, in which
the number of interactions between the user and the signer is minimal and whose
blind signatures are short. Our schemes are defined over bilinear groups and are
proved secure in the common-reference-string model without random oracles and
under standard assumptions: CDH and the decision-linear assumption. (We also give
variants over asymmetric groups based on similar assumptions.) The blind signatures
are Waters signatures, which consist of 2 group elements. Moreover, we instantiate
partially blind signatures, where the message consists of a part hidden from the
signer and a commonly known public part, and schemes achieving perfect blindness.
We propose new variants of blind signatures, such as signer-friendly partially
blind signatures, where the public part can be chosen by the signer without prior
agreement, 3-party blind signatures, as well as blind signatures on multiple aggregated
messages provided by independent sources. We also extend Waters signatures to
non-binary alphabets by proving a new result on the underlying hash function. '
author:
- first_name: Olivier
full_name: Blazy, Olivier
last_name: Blazy
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: David
full_name: Pointcheval, David
last_name: Pointcheval
- first_name: Damien
full_name: Vergnaud, Damien
last_name: Vergnaud
citation:
ama: Blazy O, Fuchsbauer G, Pointcheval D, Vergnaud D. Short blind signatures. Journal
of Computer Security. 2013;21(5):627-661. doi:10.3233/JCS-130477
apa: Blazy, O., Fuchsbauer, G., Pointcheval, D., & Vergnaud, D. (2013). Short
blind signatures. Journal of Computer Security. IOS Press. https://doi.org/10.3233/JCS-130477
chicago: Blazy, Olivier, Georg Fuchsbauer, David Pointcheval, and Damien Vergnaud.
“Short Blind Signatures.” Journal of Computer Security. IOS Press, 2013.
https://doi.org/10.3233/JCS-130477.
ieee: O. Blazy, G. Fuchsbauer, D. Pointcheval, and D. Vergnaud, “Short blind signatures,”
Journal of Computer Security, vol. 21, no. 5. IOS Press, pp. 627–661, 2013.
ista: Blazy O, Fuchsbauer G, Pointcheval D, Vergnaud D. 2013. Short blind signatures.
Journal of Computer Security. 21(5), 627–661.
mla: Blazy, Olivier, et al. “Short Blind Signatures.” Journal of Computer Security,
vol. 21, no. 5, IOS Press, 2013, pp. 627–61, doi:10.3233/JCS-130477.
short: O. Blazy, G. Fuchsbauer, D. Pointcheval, D. Vergnaud, Journal of Computer
Security 21 (2013) 627–661.
date_created: 2018-12-11T11:46:50Z
date_published: 2013-11-22T00:00:00Z
date_updated: 2021-01-12T08:01:09Z
day: '22'
department:
- _id: KrPi
doi: 10.3233/JCS-130477
intvolume: ' 21'
issue: '5'
language:
- iso: eng
month: '11'
oa_version: None
page: 627 - 661
publication: Journal of Computer Security
publication_status: published
publisher: IOS Press
publist_id: '7318'
quality_controlled: '1'
scopus_import: 1
status: public
title: Short blind signatures
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2013'
...
---
_id: '505'
abstract:
- lang: eng
text: Alkyd resins are polyesters containing unsaturated fatty acids that are used
as binding agents in paints and coatings. Chemical drying of these polyesters
is based on heavy metal catalyzed cross-linking of the unsaturated fatty acid
moieties. Among the heavy-metal catalysts, cobalt complexes are the most effective,
yet they have been proven to be carcinogenic. Therefore, strategies to replace
the cobalt-based catalyst by environmentally friendlier and less toxic alternatives
are under development. Here, we demonstrate for the first time that a laccase-mediator
system can effectively replace the heavy-metal catalyst and cross-link alkyd resins.
Interestingly, the biocatalytic reaction does not only work in aqueous media,
but also in a solid film, where enzyme diffusion is limited. Within the catalytic
cycle, the mediator oxidizes the alkyd resin and is regenerated by the laccase,
which is uniformly distributed within the drying film as evidenced by confocal
laser scanning microscopy. During gradual build-up of molecular weight, there
is a concomitant decrease of the oxygen content in the film. A new optical sensor
to follow oxygen consumption during the cross-linking reaction was developed and
validated with state of the art techniques. A remarkable feature is the low sample
amount required, which allows faster screening of new catalysts.
acknowledgement: "This study was performed within the Austrian Centre of Indus-\r\ntrial
Biotechnology ACIB and the COST Action 868. This work\r\nhas been supported by the
Federal Ministry of Economy,\r\nFamily and Youth (BMWFJ), the Federal Ministry of
Tra\r\nffi\r\nc,\r\nInnovation and Technology (bmvit), the Styrian Business\r\nPromotion
Agency SFG, the Standortagentur Tirol and ZIT\r\n–\r\nTechnology Agency of the
\ City of Vienna through the\r\nCOMET-Funding Program managed by the Austrian
Research\r\nPromotion Agency FFG. Dr Massimiliano Cardinale (Institute of\r\nEnvironmental
Biotechnology, TU Graz) is gratefully acknowl-\r\nedged for technical support with
the CLSM measurements."
author:
- first_name: Katrin
full_name: Greimel, Katrin
last_name: Greimel
- first_name: Veronika
full_name: Perz, Veronika
last_name: Perz
- first_name: Klaus
full_name: Koren, Klaus
id: 382FBD6A-F248-11E8-B48F-1D18A9856A87
last_name: Koren
- first_name: Roland
full_name: Feola, Roland
last_name: Feola
- first_name: Armin
full_name: Temel, Armin
last_name: Temel
- first_name: Christian
full_name: Sohar, Christian
last_name: Sohar
- first_name: Enrique
full_name: Herrero Acero, Enrique
last_name: Herrero Acero
- first_name: Ingo
full_name: Klimant, Ingo
last_name: Klimant
- first_name: Georg
full_name: Guebitz, Georg
last_name: Guebitz
citation:
ama: 'Greimel K, Perz V, Koren K, et al. Banning toxic heavy-metal catalysts from
paints: Enzymatic cross-linking of alkyd resins. Green Chemistry. 2013;15(2):381-388.
doi:10.1039/c2gc36666e'
apa: 'Greimel, K., Perz, V., Koren, K., Feola, R., Temel, A., Sohar, C., … Guebitz,
G. (2013). Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking
of alkyd resins. Green Chemistry. Royal Society of Chemistry. https://doi.org/10.1039/c2gc36666e'
chicago: 'Greimel, Katrin, Veronika Perz, Klaus Koren, Roland Feola, Armin Temel,
Christian Sohar, Enrique Herrero Acero, Ingo Klimant, and Georg Guebitz. “Banning
Toxic Heavy-Metal Catalysts from Paints: Enzymatic Cross-Linking of Alkyd Resins.”
Green Chemistry. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c2gc36666e.'
ieee: 'K. Greimel et al., “Banning toxic heavy-metal catalysts from paints:
Enzymatic cross-linking of alkyd resins,” Green Chemistry, vol. 15, no.
2. Royal Society of Chemistry, pp. 381–388, 2013.'
ista: 'Greimel K, Perz V, Koren K, Feola R, Temel A, Sohar C, Herrero Acero E, Klimant
I, Guebitz G. 2013. Banning toxic heavy-metal catalysts from paints: Enzymatic
cross-linking of alkyd resins. Green Chemistry. 15(2), 381–388.'
mla: 'Greimel, Katrin, et al. “Banning Toxic Heavy-Metal Catalysts from Paints:
Enzymatic Cross-Linking of Alkyd Resins.” Green Chemistry, vol. 15, no.
2, Royal Society of Chemistry, 2013, pp. 381–88, doi:10.1039/c2gc36666e.'
short: K. Greimel, V. Perz, K. Koren, R. Feola, A. Temel, C. Sohar, E. Herrero Acero,
I. Klimant, G. Guebitz, Green Chemistry 15 (2013) 381–388.
date_created: 2018-12-11T11:46:51Z
date_published: 2013-02-01T00:00:00Z
date_updated: 2021-01-12T08:01:11Z
day: '01'
department:
- _id: HaJa
doi: 10.1039/c2gc36666e
intvolume: ' 15'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 381 - 388
publication: Green Chemistry
publication_status: published
publisher: Royal Society of Chemistry
publist_id: '7313'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of
alkyd resins'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2013'
...
---
_id: '507'
abstract:
- lang: eng
text: Fertilization in flowering plants requires the temporal and spatial coordination
of many developmental processes, including pollen production, anther dehiscence,
ovule production, and pollen tube elongation. However, it remains elusive as to
how this coordination occurs during reproduction. Here, we present evidence that
endocytosis, involving heterotetrameric adaptor protein complex 2 (AP-2), plays
a crucial role in fertilization. An Arabidopsis thaliana mutant ap2m displays
multiple defects in pollen production and viability, as well as elongation of
staminal filaments and pollen tubes, all of which are pivotal processes needed
for fertilization. Of these abnormalities, the defects in elongation of staminal
filaments and pollen tubes were partially rescued by exogenous auxin. Moreover,
DR5rev:GFP (for green fluorescent protein) expression was greatly reduced in filaments
and anthers in ap2m mutant plants. At the cellular level, ap2m mutants displayed
defects in both endocytosis of N-(3-triethylammonium-propyl)-4- (4-diethylaminophenylhexatrienyl)
pyridinium dibromide, a lypophilic dye used as an endocytosis marker, and polar
localization of auxin-efflux carrier PIN FORMED2 (PIN2) in the stamen filaments.
Moreover, these defects were phenocopied by treatment with Tyrphostin A23, an
inhibitor of endocytosis. Based on these results, we propose that AP-2-dependent
endocytosis plays a crucial role in coordinating the multiple developmental aspects
of male reproductive organs by modulating cellular auxin level through the regulation
of the amount and polarity of PINs.
author:
- first_name: Soo
full_name: Kim, Soo
last_name: Kim
- first_name: Zheng
full_name: Xu, Zheng
last_name: Xu
- first_name: Kyungyoung
full_name: Song, Kyungyoung
last_name: Song
- first_name: Dae
full_name: Kim, Dae
last_name: Kim
- first_name: Hyangju
full_name: Kang, Hyangju
last_name: Kang
- first_name: Ilka
full_name: Reichardt, Ilka
last_name: Reichardt
- first_name: Eun
full_name: Sohn, Eun
last_name: Sohn
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Gerd
full_name: Juergens, Gerd
last_name: Juergens
- first_name: Inhwan
full_name: Hwang, Inhwan
last_name: Hwang
citation:
ama: Kim S, Xu Z, Song K, et al. Adaptor protein complex 2-mediated endocytosis
is crucial for male reproductive organ development in arabidopsis. Plant Cell.
2013;25(8):2970-2985. doi:10.1105/tpc.113.114264
apa: Kim, S., Xu, Z., Song, K., Kim, D., Kang, H., Reichardt, I., … Hwang, I. (2013).
Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive
organ development in arabidopsis. Plant Cell. American Society of Plant
Biologists. https://doi.org/10.1105/tpc.113.114264
chicago: Kim, Soo, Zheng Xu, Kyungyoung Song, Dae Kim, Hyangju Kang, Ilka Reichardt,
Eun Sohn, Jiří Friml, Gerd Juergens, and Inhwan Hwang. “Adaptor Protein Complex
2-Mediated Endocytosis Is Crucial for Male Reproductive Organ Development in Arabidopsis.”
Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.114264.
ieee: S. Kim et al., “Adaptor protein complex 2-mediated endocytosis is crucial
for male reproductive organ development in arabidopsis,” Plant Cell, vol.
25, no. 8. American Society of Plant Biologists, pp. 2970–2985, 2013.
ista: Kim S, Xu Z, Song K, Kim D, Kang H, Reichardt I, Sohn E, Friml J, Juergens
G, Hwang I. 2013. Adaptor protein complex 2-mediated endocytosis is crucial for
male reproductive organ development in arabidopsis. Plant Cell. 25(8), 2970–2985.
mla: Kim, Soo, et al. “Adaptor Protein Complex 2-Mediated Endocytosis Is Crucial
for Male Reproductive Organ Development in Arabidopsis.” Plant Cell, vol.
25, no. 8, American Society of Plant Biologists, 2013, pp. 2970–85, doi:10.1105/tpc.113.114264.
short: S. Kim, Z. Xu, K. Song, D. Kim, H. Kang, I. Reichardt, E. Sohn, J. Friml,
G. Juergens, I. Hwang, Plant Cell 25 (2013) 2970–2985.
date_created: 2018-12-11T11:46:52Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T08:01:12Z
day: '01'
department:
- _id: JiFr
doi: 10.1105/tpc.113.114264
external_id:
pmid:
- '23975898'
intvolume: ' 25'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784592/
month: '08'
oa: 1
oa_version: Submitted Version
page: 2970 - 2985
pmid: 1
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '7312'
quality_controlled: '1'
scopus_import: 1
status: public
title: Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive
organ development in arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2013'
...
---
_id: '508'
abstract:
- lang: eng
text: The phagocyte NADPH oxidase catalyzes the reduction of O2 to reactive oxygen
species with microbicidal activity. It is composed of two membrane-spanning subunits,
gp91-phox and p22-phox (encoded by CYBB and CYBA, respectively), and three cytoplasmic
subunits, p40-phox, p47-phox, and p67-phox (encoded by NCF4, NCF1, and NCF2, respectively).
Mutations in any of these genes can result in chronic granulomatous disease, a
primary immunodeficiency characterized by recurrent infections. Using evolutionary
mapping, we determined that episodes of adaptive natural selection have shaped
the extracellular portion of gp91-phox during the evolution of mammals, which
suggests that this region may have a function in host-pathogen interactions. On
the basis of a resequencing analysis of approximately 35 kb of CYBB, CYBA, NCF2,
and NCF4 in 102 ethnically diverse individuals (24 of African ancestry, 31 of
European ancestry, 24 of Asian/Oceanians, and 23 US Hispanics), we show that the
pattern of CYBA diversity is compatible with balancing natural selection, perhaps
mediated by catalase-positive pathogens. NCF2 in Asian populations shows a pattern
of diversity characterized by a differentiated haplotype structure. Our study
provides insight into the role of pathogen-driven natural selection in an innate
immune pathway and sheds light on the role of CYBA in endothelial, nonphagocytic
NADPH oxidases, which are relevant in the pathogenesis of cardiovascular and other
complex diseases.
author:
- first_name: Eduardo
full_name: Tarazona Santos, Eduardo
last_name: Tarazona Santos
- first_name: Moara
full_name: Machado, Moara
last_name: Machado
- first_name: Wagner
full_name: Magalhães, Wagner
last_name: Magalhães
- first_name: Renee
full_name: Chen, Renee
last_name: Chen
- first_name: Fernanda
full_name: Lyon, Fernanda
last_name: Lyon
- first_name: Laurie
full_name: Burdett, Laurie
last_name: Burdett
- first_name: Andrew
full_name: Crenshaw, Andrew
last_name: Crenshaw
- first_name: Cristina
full_name: Fabbri, Cristina
last_name: Fabbri
- first_name: Latife
full_name: Pereira, Latife
last_name: Pereira
- first_name: Laelia
full_name: Pinto, Laelia
last_name: Pinto
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Ben
full_name: Sestanovich, Ben
last_name: Sestanovich
- first_name: Meredith
full_name: Yeager, Meredith
last_name: Yeager
- first_name: Stephen
full_name: Chanock, Stephen
last_name: Chanock
citation:
ama: 'Tarazona Santos E, Machado M, Magalhães W, et al. Evolutionary dynamics of
the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications.
Molecular Biology and Evolution. 2013;30(9):2157-2167. doi:10.1093/molbev/mst119'
apa: 'Tarazona Santos, E., Machado, M., Magalhães, W., Chen, R., Lyon, F., Burdett,
L., … Chanock, S. (2013). Evolutionary dynamics of the human NADPH oxidase genes
CYBB, CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and
Evolution. Oxford University Press. https://doi.org/10.1093/molbev/mst119'
chicago: 'Tarazona Santos, Eduardo, Moara Machado, Wagner Magalhães, Renee Chen,
Fernanda Lyon, Laurie Burdett, Andrew Crenshaw, et al. “Evolutionary Dynamics
of the Human NADPH Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.”
Molecular Biology and Evolution. Oxford University Press, 2013. https://doi.org/10.1093/molbev/mst119.'
ieee: 'E. Tarazona Santos et al., “Evolutionary dynamics of the human NADPH
oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications,” Molecular
Biology and Evolution, vol. 30, no. 9. Oxford University Press, pp. 2157–2167,
2013.'
ista: 'Tarazona Santos E, Machado M, Magalhães W, Chen R, Lyon F, Burdett L, Crenshaw
A, Fabbri C, Pereira L, Pinto L, Fernandes Redondo RA, Sestanovich B, Yeager M,
Chanock S. 2013. Evolutionary dynamics of the human NADPH oxidase genes CYBB,
CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and Evolution.
30(9), 2157–2167.'
mla: 'Tarazona Santos, Eduardo, et al. “Evolutionary Dynamics of the Human NADPH
Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.” Molecular
Biology and Evolution, vol. 30, no. 9, Oxford University Press, 2013, pp.
2157–67, doi:10.1093/molbev/mst119.'
short: E. Tarazona Santos, M. Machado, W. Magalhães, R. Chen, F. Lyon, L. Burdett,
A. Crenshaw, C. Fabbri, L. Pereira, L. Pinto, R.A. Fernandes Redondo, B. Sestanovich,
M. Yeager, S. Chanock, Molecular Biology and Evolution 30 (2013) 2157–2167.
date_created: 2018-12-11T11:46:52Z
date_published: 2013-09-01T00:00:00Z
date_updated: 2021-01-12T08:01:12Z
day: '01'
department:
- _id: JoBo
doi: 10.1093/molbev/mst119
external_id:
pmid:
- '23821607'
intvolume: ' 30'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3748357/
month: '09'
oa: 1
oa_version: Submitted Version
page: 2157 - 2167
pmid: 1
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '7310'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and
NCF4: Functional implications'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2013'
...
---
_id: '509'
abstract:
- lang: eng
text: 'Clathrin-mediated endocytosis (CME) regulates many aspects of plant development,
including hormone signaling and responses to environmental stresses. Despite the
importance of this process, the machinery that regulates CME in plants is largely
unknown. In mammals, the heterotetrameric ADAPTOR PROTEIN COMPLEX-2 (AP-2) is
required for the formation of clathrin-coated vesicles at the plasma membrane
(PM). Although the existence of AP-2 has been predicted in Arabidopsis thaliana,
the biochemistry and functionality of the complex is still uncharacterized. Here,
we identified all the subunits of the Arabidopsis AP-2 by tandem affinity purification
and found that one of the large AP-2 subunits, AP2A1, localized at the PM and
interacted with clathrin. Furthermore, endocytosis of the leucine-rich repeat
receptor kinase, BRASSINOSTEROID INSENSITIVE1 (BRI1), was shown to depend on AP-2.
Knockdown of the two Arabidopsis AP2A genes or overexpression of a dominant-negative
version of the medium AP-2 subunit, AP2M, impaired BRI1 endocytosis and enhanced
the brassinosteroid signaling. Our data reveal that the CME machinery in Arabidopsis
is evolutionarily conserved and that AP-2 functions in receptormediated endocytosis. '
author:
- first_name: Simone
full_name: Di Rubbo, Simone
last_name: Di Rubbo
- first_name: Niloufer
full_name: Irani, Niloufer
last_name: Irani
- first_name: Soo
full_name: Kim, Soo
last_name: Kim
- first_name: Zheng
full_name: Xu, Zheng
last_name: Xu
- first_name: Astrid
full_name: Gadeyne, Astrid
last_name: Gadeyne
- first_name: Wim
full_name: Dejonghe, Wim
last_name: Dejonghe
- first_name: Isabelle
full_name: Vanhoutte, Isabelle
last_name: Vanhoutte
- first_name: Geert
full_name: Persiau, Geert
last_name: Persiau
- first_name: Dominique
full_name: Eeckhout, Dominique
last_name: Eeckhout
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Kyungyoung
full_name: Song, Kyungyoung
last_name: Song
- first_name: Jürgen
full_name: Kleine Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Geert
full_name: De Jaeger, Geert
last_name: De Jaeger
- first_name: Daniël
full_name: Van Damme, Daniël
last_name: Van Damme
- first_name: Inhwan
full_name: Hwang, Inhwan
last_name: Hwang
- first_name: Eugenia
full_name: Russinova, Eugenia
last_name: Russinova
citation:
ama: Di Rubbo S, Irani N, Kim S, et al. The clathrin adaptor complex AP-2 mediates
endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis. Plant Cell.
2013;25(8):2986-2997. doi:10.1105/tpc.113.114058
apa: Di Rubbo, S., Irani, N., Kim, S., Xu, Z., Gadeyne, A., Dejonghe, W., … Russinova,
E. (2013). The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid
INSENSITIVE1 in arabidopsis. Plant Cell. American Society of Plant Biologists.
https://doi.org/10.1105/tpc.113.114058
chicago: Di Rubbo, Simone, Niloufer Irani, Soo Kim, Zheng Xu, Astrid Gadeyne, Wim
Dejonghe, Isabelle Vanhoutte, et al. “The Clathrin Adaptor Complex AP-2 Mediates
Endocytosis of Brassinosteroid INSENSITIVE1 in Arabidopsis.” Plant Cell.
American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.114058.
ieee: S. Di Rubbo et al., “The clathrin adaptor complex AP-2 mediates endocytosis
of brassinosteroid INSENSITIVE1 in arabidopsis,” Plant Cell, vol. 25, no.
8. American Society of Plant Biologists, pp. 2986–2997, 2013.
ista: Di Rubbo S, Irani N, Kim S, Xu Z, Gadeyne A, Dejonghe W, Vanhoutte I, Persiau
G, Eeckhout D, Simon S, Song K, Kleine Vehn J, Friml J, De Jaeger G, Van Damme
D, Hwang I, Russinova E. 2013. The clathrin adaptor complex AP-2 mediates endocytosis
of brassinosteroid INSENSITIVE1 in arabidopsis. Plant Cell. 25(8), 2986–2997.
mla: Di Rubbo, Simone, et al. “The Clathrin Adaptor Complex AP-2 Mediates Endocytosis
of Brassinosteroid INSENSITIVE1 in Arabidopsis.” Plant Cell, vol. 25, no.
8, American Society of Plant Biologists, 2013, pp. 2986–97, doi:10.1105/tpc.113.114058.
short: S. Di Rubbo, N. Irani, S. Kim, Z. Xu, A. Gadeyne, W. Dejonghe, I. Vanhoutte,
G. Persiau, D. Eeckhout, S. Simon, K. Song, J. Kleine Vehn, J. Friml, G. De Jaeger,
D. Van Damme, I. Hwang, E. Russinova, Plant Cell 25 (2013) 2986–2997.
date_created: 2018-12-11T11:46:52Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T08:01:13Z
day: '01'
department:
- _id: JiFr
doi: 10.1105/tpc.113.114058
external_id:
pmid:
- '23975899'
intvolume: ' 25'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784593/
month: '08'
oa: 1
oa_version: Submitted Version
page: 2986 - 2997
pmid: 1
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '7311'
quality_controlled: '1'
scopus_import: 1
status: public
title: The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1
in arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2013'
...
---
_id: '511'
abstract:
- lang: eng
text: The native auxin, indole-3-acetic acid (IAA), is a major regulator of plant
growth and development. Its nonuniform distribution between cells and tissues
underlies the spatiotemporal coordination of many developmental events and responses
to environmental stimuli. The regulation of auxin gradients and the formation
of auxin maxima/minima most likely involve the regulation of both metabolic and
transport processes. In this article, we have demonstrated that 2-oxindole-3-acetic
acid (oxIAA) is a major primary IAA catabolite formed in Arabidopsis thaliana
root tissues. OxIAA had little biological activity and was formed rapidly and
irreversibly in response to increases in auxin levels. We further showed that
there is cell type-specific regulation of oxIAA levels in the Arabidopsis root
apex. We propose that oxIAA is an important element in the regulation of output
from auxin gradients and, therefore, in the regulation of auxin homeostasis and
response mechanisms.
author:
- first_name: Aleš
full_name: Pěnčík, Aleš
last_name: Pěnčík
- first_name: Biljana
full_name: Simonovik, Biljana
last_name: Simonovik
- first_name: Sara
full_name: Petersson, Sara
last_name: Petersson
- first_name: Eva
full_name: Henyková, Eva
last_name: Henyková
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Kathleen
full_name: Greenham, Kathleen
last_name: Greenham
- first_name: Yi
full_name: Zhang, Yi
last_name: Zhang
- first_name: Mariusz
full_name: Kowalczyk, Mariusz
last_name: Kowalczyk
- first_name: Mark
full_name: Estelle, Mark
last_name: Estelle
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Ondřej
full_name: Novák, Ondřej
last_name: Novák
- first_name: Göran
full_name: Sandberg, Göran
last_name: Sandberg
- first_name: Karin
full_name: Ljung, Karin
last_name: Ljung
citation:
ama: Pěnčík A, Simonovik B, Petersson S, et al. Regulation of auxin homeostasis
and gradients in Arabidopsis roots through the formation of the indole-3-acetic
acid catabolite 2-oxindole-3-acetic acid. Plant Cell. 2013;25(10):3858-3870.
doi:10.1105/tpc.113.114421
apa: Pěnčík, A., Simonovik, B., Petersson, S., Henyková, E., Simon, S., Greenham,
K., … Ljung, K. (2013). Regulation of auxin homeostasis and gradients in Arabidopsis
roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic
acid. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.113.114421
chicago: Pěnčík, Aleš, Biljana Simonovik, Sara Petersson, Eva Henyková, Sibu Simon,
Kathleen Greenham, Yi Zhang, et al. “Regulation of Auxin Homeostasis and Gradients
in Arabidopsis Roots through the Formation of the Indole-3-Acetic Acid Catabolite
2-Oxindole-3-Acetic Acid.” Plant Cell. American Society of Plant Biologists,
2013. https://doi.org/10.1105/tpc.113.114421.
ieee: A. Pěnčík et al., “Regulation of auxin homeostasis and gradients in
Arabidopsis roots through the formation of the indole-3-acetic acid catabolite
2-oxindole-3-acetic acid,” Plant Cell, vol. 25, no. 10. American Society
of Plant Biologists, pp. 3858–3870, 2013.
ista: Pěnčík A, Simonovik B, Petersson S, Henyková E, Simon S, Greenham K, Zhang
Y, Kowalczyk M, Estelle M, Zažímalová E, Novák O, Sandberg G, Ljung K. 2013. Regulation
of auxin homeostasis and gradients in Arabidopsis roots through the formation
of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid. Plant Cell. 25(10),
3858–3870.
mla: Pěnčík, Aleš, et al. “Regulation of Auxin Homeostasis and Gradients in Arabidopsis
Roots through the Formation of the Indole-3-Acetic Acid Catabolite 2-Oxindole-3-Acetic
Acid.” Plant Cell, vol. 25, no. 10, American Society of Plant Biologists,
2013, pp. 3858–70, doi:10.1105/tpc.113.114421.
short: A. Pěnčík, B. Simonovik, S. Petersson, E. Henyková, S. Simon, K. Greenham,
Y. Zhang, M. Kowalczyk, M. Estelle, E. Zažímalová, O. Novák, G. Sandberg, K. Ljung,
Plant Cell 25 (2013) 3858–3870.
date_created: 2018-12-11T11:46:53Z
date_published: 2013-10-01T00:00:00Z
date_updated: 2021-01-12T08:01:15Z
day: '01'
department:
- _id: JiFr
doi: 10.1105/tpc.113.114421
external_id:
pmid:
- '24163311'
intvolume: ' 25'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: www.doi.org/10.1105/tpc.113.114421
month: '10'
oa: 1
oa_version: Published Version
page: 3858 - 3870
pmid: 1
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '7309'
quality_controlled: '1'
scopus_import: 1
status: public
title: Regulation of auxin homeostasis and gradients in Arabidopsis roots through
the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2013'
...