---
_id: '811'
abstract:
- lang: eng
text: Cell migration is commonly accompanied by protrusion of membrane ruffles and
lamellipodia. In two-dimensional migration, protrusion of these thin sheets of
cytoplasm is considered relevant to both exploration of new space and initiation
of nascent adhesion to the substratum. Lamellipodium formation can be potently
stimulated by Rho GTPases of the Rac subfamily, but alsoby RhoG or Cdc42. Here
we describe viable fibroblast cell lines geneticallydeficient for Rac1 that lack
detectable levels of Rac2 and Rac3. Rac-deficient cells were devoid of apparent
lamellipodia, but these structures were restored by expression of either Rac subfamily
member, but not by Cdc42 or RhoG. Cells deficient in Rac showed strong reduction
in wound closure and random cell migration and a notable loss of sensitivity to
a chemotactic gradient. Despite these defects, Rac-deficient cells were able to
spread, formed filopodia and established focal adhesions. Spreading in these cells
was achieved by the extension of filopodia followed by the advancement of cytoplasmic
veils between them. The number and size of focal adhesions as well as their intensity
were largely unaffected by genetic removal of Rac1. However, Rac deficiency increased
the mobility of different components in focal adhesions, potentially explaining
how Rac - although not essential - can contribute to focal adhesion assembly.
Together, our data demonstrate that Rac signaling is essential for lamellipodium
protrusion and for efficient cell migration, but not for spreading or filopodium
formation. Our findings also suggest that Rac GTPases are crucial to the establishment
or maintenance of polarity in chemotactic migration.
acknowledgement: |-
This work was supported in part by the Deutsche Forschungsgemeinschaft [grants within programs SFB621 to K.R., and FOR629 and SFB629 to T.E.B.S.]. Deposited in PMC for immediate release.
We thank Brigitte Denker and Gerd Landsberg for excellent technical assistance. We are grateful to Robert Geffers (HZI Braunschweig, Germany) for microarray analyses and to Mirko Himmel (UKE Hamburg, Germany) for valuable advice on FRAP analysis.
author:
- first_name: Anika
full_name: Steffen, Anika
last_name: Steffen
- first_name: Markus
full_name: Ladwein, Markus
last_name: Ladwein
- first_name: Georgi A
full_name: Georgi Dimchev
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
- first_name: Anke
full_name: Hein, Anke
last_name: Hein
- first_name: Lisa
full_name: Schwenkmezger, Lisa
last_name: Schwenkmezger
- first_name: Stefan
full_name: Arens, Stefan
last_name: Arens
- first_name: Kathrin
full_name: Ladwein, Kathrin I
last_name: Ladwein
- first_name: J.
full_name: Holleboom, J. Margit
last_name: Holleboom
- first_name: Florian
full_name: Florian Schur
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: John
full_name: Small, John V
last_name: Small
- first_name: Janett
full_name: Schwarz, Janett
last_name: Schwarz
- first_name: Ralf
full_name: Gerhard, Ralf
last_name: Gerhard
- first_name: Jan
full_name: Faix, Jan
last_name: Faix
- first_name: Theresia
full_name: Stradal, Theresia E
last_name: Stradal
- first_name: Cord
full_name: Brakebusch, Cord H
last_name: Brakebusch
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
citation:
ama: Steffen A, Ladwein M, Dimchev GA, et al. Rac function is crucial for cell migration
but is not required for spreading and focal adhesion formation. Journal of
Cell Science. 2013;126(20):4572-4588. doi:10.1242/jcs.118232
apa: Steffen, A., Ladwein, M., Dimchev, G. A., Hein, A., Schwenkmezger, L., Arens,
S., … Rottner, K. (2013). Rac function is crucial for cell migration but is not
required for spreading and focal adhesion formation. Journal of Cell Science.
Company of Biologists. https://doi.org/10.1242/jcs.118232
chicago: Steffen, Anika, Markus Ladwein, Georgi A Dimchev, Anke Hein, Lisa Schwenkmezger,
Stefan Arens, Kathrin Ladwein, et al. “Rac Function Is Crucial for Cell Migration
but Is Not Required for Spreading and Focal Adhesion Formation.” Journal of
Cell Science. Company of Biologists, 2013. https://doi.org/10.1242/jcs.118232.
ieee: A. Steffen et al., “Rac function is crucial for cell migration but
is not required for spreading and focal adhesion formation,” Journal of Cell
Science, vol. 126, no. 20. Company of Biologists, pp. 4572–4588, 2013.
ista: Steffen A, Ladwein M, Dimchev GA, Hein A, Schwenkmezger L, Arens S, Ladwein
K, Holleboom J, Schur FK, Small J, Schwarz J, Gerhard R, Faix J, Stradal T, Brakebusch
C, Rottner K. 2013. Rac function is crucial for cell migration but is not required
for spreading and focal adhesion formation. Journal of Cell Science. 126(20),
4572–4588.
mla: Steffen, Anika, et al. “Rac Function Is Crucial for Cell Migration but Is Not
Required for Spreading and Focal Adhesion Formation.” Journal of Cell Science,
vol. 126, no. 20, Company of Biologists, 2013, pp. 4572–88, doi:10.1242/jcs.118232.
short: A. Steffen, M. Ladwein, G.A. Dimchev, A. Hein, L. Schwenkmezger, S. Arens,
K. Ladwein, J. Holleboom, F.K. Schur, J. Small, J. Schwarz, R. Gerhard, J. Faix,
T. Stradal, C. Brakebusch, K. Rottner, Journal of Cell Science 126 (2013) 4572–4588.
date_created: 2018-12-11T11:48:38Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T08:16:57Z
day: '01'
doi: 10.1242/jcs.118232
extern: 1
intvolume: ' 126'
issue: '20'
month: '01'
page: 4572 - 4588
publication: Journal of Cell Science
publication_status: published
publisher: Company of Biologists
publist_id: '6840'
quality_controlled: 0
status: public
title: Rac function is crucial for cell migration but is not required for spreading
and focal adhesion formation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 126
year: '2013'
...
---
_id: '812'
abstract:
- lang: eng
text: Lamellipodia are sheet-like protrusions formed during migration or phagocytosis
and comprise a network of actin filaments. Filament formation in this network
is initiated by nucleation/branching through the actin-related protein 2/3 (Arp2/3)
complex downstream of its activator, suppressor of cAMP receptor/WASP-family verprolin
homologous (Scar/WAVE), but the relative relevance of Arp2/3-mediated branching
versus actin filament elongation is unknown. Here we use instantaneous interference
with Arp2/3 complex function in live fibroblasts with established lamellipodia.
This allows direct examination of both the fate of elongating filaments upon instantaneous
suppression of Arp2/3 complex activity and the consequences of this treatment
on the dynamics of other lamellipodial regulators. We show that Arp2/3 complex
is an essential organizer of treadmilling actin filament arrays but has little
effect on the net rate of actin filament turnover at the cell periphery. In addition,
Arp2/3 complex serves as key upstream factor for the recruitment of modulators
of lamellipodia formation such as capping protein or cofilin. Arp2/3 complex is
thus decisive for filament organization and geometry within the network not only
by generating branches and novel filament ends, but also by directing capping
or severing activities to the lamellipodium. Arp2/3 complex is also crucial to
lamellipodia-based migration of keratocytes.
acknowledgement: "This work was supported in part by Deutsche Forschungsgemeinschaft
Grants RO2414/3-1 (to K.R.) and FA330/6-1 (to J.F.), Austrian \nScience Fund Projects
FWF 1516-B09 and FWF P21292-B09 (to J.V.S.), the Vienna Science and Technology
\ Fund (WWTF, to \nJ.V.S. and C.S.), and Australian National Health and
\ Medical \nResearch Council Grant APP1004175 (to P.W.G.). We thank J. Adams, \nR.
Chisholm, A. Hall, L. Machesky, H. G. Mannherz, D. Schafer, and \nR. Wedlich-Söldner
\ for expression constructs and B. Denker, \nP. Hagendorff, and G. Landsberg
for technical assistance."
author:
- first_name: Stefan
full_name: Koestler, Stefan A
last_name: Koestler
- first_name: Anika
full_name: Steffen, Anika
last_name: Steffen
- first_name: Maria
full_name: Maria Nemethova
id: 34E27F1C-F248-11E8-B48F-1D18A9856A87
last_name: Nemethova
- first_name: Moritz
full_name: Winterhoff, Moritz
last_name: Winterhoff
- first_name: Ningning
full_name: Luo, Ningning
last_name: Luo
- first_name: J.
full_name: Holleboom, J. Margit
last_name: Holleboom
- first_name: Jessica
full_name: Krupp, Jessica
last_name: Krupp
- first_name: Sonja
full_name: Jacob, Sonja
last_name: Jacob
- first_name: Marlene
full_name: Vinzenz, Marlene
last_name: Vinzenz
- first_name: Florian
full_name: Florian Schur
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Kai
full_name: Schlüter, Kai
last_name: Schlüter
- first_name: Peter
full_name: Gunning, Peter W
last_name: Gunning
- first_name: Christoph
full_name: Winkler, Christoph
last_name: Winkler
- first_name: Christian
full_name: Schmeiser, Christian
last_name: Schmeiser
- first_name: Jan
full_name: Faix, Jan
last_name: Faix
- first_name: Theresia
full_name: Stradal, Theresia E
last_name: Stradal
- first_name: John
full_name: Small, John V
last_name: Small
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
citation:
ama: Koestler S, Steffen A, Nemethova M, et al. Arp2/3 complex is essential for
actin network treadmilling as well as for targeting of capping protein and cofilin.
Molecular Biology of the Cell. 2013;24(18):2861-2875. doi:10.1091/mbc.E12-12-0857
apa: Koestler, S., Steffen, A., Nemethova, M., Winterhoff, M., Luo, N., Holleboom,
J., … Rottner, K. (2013). Arp2/3 complex is essential for actin network treadmilling
as well as for targeting of capping protein and cofilin. Molecular Biology
of the Cell. American Society for Biology. https://doi.org/10.1091/mbc.E12-12-0857
chicago: Koestler, Stefan, Anika Steffen, Maria Nemethova, Moritz Winterhoff, Ningning
Luo, J. Holleboom, Jessica Krupp, et al. “Arp2/3 Complex Is Essential for Actin
Network Treadmilling as Well as for Targeting of Capping Protein and Cofilin.”
Molecular Biology of the Cell. American Society for Biology, 2013. https://doi.org/10.1091/mbc.E12-12-0857.
ieee: S. Koestler et al., “Arp2/3 complex is essential for actin network
treadmilling as well as for targeting of capping protein and cofilin,” Molecular
Biology of the Cell, vol. 24, no. 18. American Society for Biology, pp. 2861–2875,
2013.
ista: Koestler S, Steffen A, Nemethova M, Winterhoff M, Luo N, Holleboom J, Krupp
J, Jacob S, Vinzenz M, Schur FK, Schlüter K, Gunning P, Winkler C, Schmeiser C,
Faix J, Stradal T, Small J, Rottner K. 2013. Arp2/3 complex is essential for actin
network treadmilling as well as for targeting of capping protein and cofilin.
Molecular Biology of the Cell. 24(18), 2861–2875.
mla: Koestler, Stefan, et al. “Arp2/3 Complex Is Essential for Actin Network Treadmilling
as Well as for Targeting of Capping Protein and Cofilin.” Molecular Biology
of the Cell, vol. 24, no. 18, American Society for Biology, 2013, pp. 2861–75,
doi:10.1091/mbc.E12-12-0857.
short: S. Koestler, A. Steffen, M. Nemethova, M. Winterhoff, N. Luo, J. Holleboom,
J. Krupp, S. Jacob, M. Vinzenz, F.K. Schur, K. Schlüter, P. Gunning, C. Winkler,
C. Schmeiser, J. Faix, T. Stradal, J. Small, K. Rottner, Molecular Biology of
the Cell 24 (2013) 2861–2875.
date_created: 2018-12-11T11:48:38Z
date_published: 2013-09-15T00:00:00Z
date_updated: 2021-01-12T08:17:00Z
day: '15'
doi: 10.1091/mbc.E12-12-0857
extern: 1
intvolume: ' 24'
issue: '18'
month: '09'
page: 2861 - 2875
publication: Molecular Biology of the Cell
publication_status: published
publisher: American Society for Biology
publist_id: '6841'
quality_controlled: 0
status: public
title: Arp2/3 complex is essential for actin network treadmilling as well as for targeting
of capping protein and cofilin
type: journal_article
volume: 24
year: '2013'
...
---
_id: '8245'
abstract:
- lang: eng
text: "Background: Monoclonal antibodies (mAb), such as trastuzumab are a valuable
addition to breast cancer therapy.\r\nData obtained from neoadjuvant settings
revealed that antibody-dependent cell-mediated cytotoxicity (ADCC) is a\r\nmajor
mechanism of action for the mAb trastuzumab. Conflicting results still call into
question whether disease\r\nprogression, prolonged treatment or concomitant chemotherapy
influences ADCC and related immunological\r\nphenomena.\r\nMethods: We analyzed
the activity of ADCC and antibody-dependent cell-mediated phagocytosis (ADCP)
of\r\nperipheral blood mononuclear cells (PBMCs) from human epidermal growth factor
receptor 2 (HER2/neu) positive\r\nbreast cancer patients receiving trastuzumab
therapy either in an adjuvant (n = 13) or metastatic (n = 15) setting as\r\nwell
as from trastuzumab treatment-naive (t-naive) HER2/neu negative patients (n =
15). PBMCs from healthy volunteers\r\n(n = 24) were used as controls. ADCC and
ADCP activity was correlated with the expression of antibody binding\r\nFc-gamma
receptor (FcγR)I (CD64), FcγRII (CD32) and FcγRIII (CD16) on CD14+ (monocytes)
and CD56+ (NK) cells, as well as the expression of CD107a+ (LAMP-1) on CD56+ cells
and the total amount of CD4+CD25+FOXP3+ (Treg) cells. In metastatic patients,
markers were correlated with progression-free survival (PFS).\r\nResults: ADCC
activity was significantly down regulated in metastatic, adjuvant and t-naive
patient cohorts as compared to healthy controls. Reduced ADCC activity was inversely
correlated with the expression of CD107a on CD56+\r\ncells in adjuvant patients.
ADCC and ADCP activity of the patient cohorts were similar, regardless of treatment
duration\r\nor additional chemotherapy. PFS in metastatic patients inversely correlated
with the number of peripheral Treg cells.\r\nConclusion: The reduction of ADCC
in patients as compared to healthy controls calls for adjuvant strategies, such
as\r\nimmune-enhancing agents, to improve the activity of trastuzumab. However,
efficacy of trastuzumab-specific ADCC\r\nand ADCP appears not to be affected by
treatment duration, disease progression or concomitant chemotherapy. This\r\nfinding
supports the application of trastuzumab at any stage of the disease."
article_number: '307'
article_processing_charge: No
author:
- first_name: Branka
full_name: Petricevic, Branka
last_name: Petricevic
- first_name: Johannes
full_name: Laengle, Johannes
last_name: Laengle
- first_name: Josef
full_name: Singer, Josef
last_name: Singer
- first_name: Monika
full_name: Sachet, Monika
last_name: Sachet
- first_name: Judit
full_name: Fazekas, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas
orcid: 0000-0002-8777-3502
- first_name: Guenther
full_name: Steger, Guenther
last_name: Steger
- first_name: Rupert
full_name: Bartsch, Rupert
last_name: Bartsch
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
- first_name: Michael
full_name: Bergmann, Michael
last_name: Bergmann
citation:
ama: Petricevic B, Laengle J, Singer J, et al. Trastuzumab mediates antibody-dependent
cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant
and metastatic HER2/neu breast cancer patients. Journal of Translational Medicine.
2013;11. doi:10.1186/1479-5876-11-307
apa: Petricevic, B., Laengle, J., Singer, J., Sachet, M., Singer, J., Steger, G.,
… Bergmann, M. (2013). Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity
and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast
cancer patients. Journal of Translational Medicine. Springer Nature. https://doi.org/10.1186/1479-5876-11-307
chicago: Petricevic, Branka, Johannes Laengle, Josef Singer, Monika Sachet, Judit
Singer, Guenther Steger, Rupert Bartsch, Erika Jensen-Jarolim, and Michael Bergmann.
“Trastuzumab Mediates Antibody-Dependent Cell-Mediated Cytotoxicity and Phagocytosis
to the Same Extent in Both Adjuvant and Metastatic HER2/Neu Breast Cancer Patients.”
Journal of Translational Medicine. Springer Nature, 2013. https://doi.org/10.1186/1479-5876-11-307.
ieee: B. Petricevic et al., “Trastuzumab mediates antibody-dependent cell-mediated
cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic
HER2/neu breast cancer patients,” Journal of Translational Medicine, vol.
11. Springer Nature, 2013.
ista: Petricevic B, Laengle J, Singer J, Sachet M, Singer J, Steger G, Bartsch R,
Jensen-Jarolim E, Bergmann M. 2013. Trastuzumab mediates antibody-dependent cell-mediated
cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic
HER2/neu breast cancer patients. Journal of Translational Medicine. 11, 307.
mla: Petricevic, Branka, et al. “Trastuzumab Mediates Antibody-Dependent Cell-Mediated
Cytotoxicity and Phagocytosis to the Same Extent in Both Adjuvant and Metastatic
HER2/Neu Breast Cancer Patients.” Journal of Translational Medicine, vol.
11, 307, Springer Nature, 2013, doi:10.1186/1479-5876-11-307.
short: B. Petricevic, J. Laengle, J. Singer, M. Sachet, J. Singer, G. Steger, R.
Bartsch, E. Jensen-Jarolim, M. Bergmann, Journal of Translational Medicine 11
(2013).
date_created: 2020-08-10T11:54:34Z
date_published: 2013-12-12T00:00:00Z
date_updated: 2022-08-25T14:52:39Z
day: '12'
ddc:
- '570'
doi: 10.1186/1479-5876-11-307
extern: '1'
external_id:
pmid:
- '24330813'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-08-10T13:45:19Z
date_updated: 2020-08-10T13:45:19Z
file_id: '8247'
file_name: 2013_JoTM_Petricevic.pdf
file_size: 777311
relation: main_file
success: 1
file_date_updated: 2020-08-10T13:45:19Z
has_accepted_license: '1'
intvolume: ' 11'
language:
- iso: eng
month: '12'
oa: 1
oa_version: None
pmid: 1
publication: Journal of Translational Medicine
publication_identifier:
issn:
- 1479-5876
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis
to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2013'
...
---
_id: '827'
abstract:
- lang: eng
text: As sessile organisms, plants have to be able to adapt to a continuously changing
environment. Plants that perceive some of these changes as stress signals activate
signaling pathways to modulate their development and to enable them to survive.
The complex responses to environmental cues are to a large extent mediated by
plant hormones that together orchestrate the final plant response. The phytohormone
cytokinin is involved in many plant developmental processes. Recently, it has
been established that cytokinin plays an important role in stress responses, but
does not act alone. Indeed, the hormonal control of plant development and stress
adaptation is the outcome of a complex network of multiple synergistic and antagonistic
interactions between various hormones. Here, we review the recent findings on
the cytokinin function as part of this hormonal network. We focus on the importance
of the crosstalk between cytokinin and other hormones, such as abscisic acid,
jasmonate, salicylic acid, ethylene, and auxin in the modulation of plant development
and stress adaptation. Finally, the impact of the current research in the biotechnological
industry will be discussed.
article_number: '451'
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).
date_created: 2018-12-11T11:48:43Z
date_published: 2013-11-19T00:00:00Z
date_updated: 2021-01-12T08:17:50Z
day: '19'
ddc:
- '580'
department:
- _id: EvBe
doi: 10.3389/fpls.2013.00451
ec_funded: 1
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'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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'
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).
date_created: 2018-12-11T11:48:43Z
date_published: 2013-12-26T00:00:00Z
date_updated: 2021-01-12T08:17:52Z
day: '26'
ddc:
- '580'
department:
- _id: EvBe
doi: 10.3389/fpls.2013.00537
ec_funded: 1
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'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2013'
...
---
_id: '830'
abstract:
- lang: eng
text: Upon hormonal signaling, ovules develop as lateral organs from the placenta.
Ovule numbers ultimately determine the number of seeds that develop, and thereby
contribute to the final seed yield in crop plants. We demonstrate here that CUP-SHAPED
COTYLEDON 1 (CUC1), CUC2 and AINTEGUMENTA (ANT) have additive effects on ovule
primordia formation. We show that expression of the CUC1 and CUC2 genes is required
to redundantly regulate expression of PINFORMED1 (PIN1), which in turn is required
for ovule primordia formation. Furthermore, our results suggest that the auxin
response factor MONOPTEROS (MP/ARF5) may directly bind ANT, CUC1 and CUC2 and
promote their transcription. Based on our findings, we propose an integrative
model to describe the molecular mechanisms of the early stages of ovule development.
acknowledgement: The project and F.G. were supported by the CARIPLO Foundation (project
2009-2990) and COST (European Cooperation in Science and Technology) action HAPRECI
(Harnessing Plant Reproduction for Crop Improvement). E.B. and C.C. were supported
by the European Research Council through a ‘Starting Independent Research’ grant
(ERC-2007-Stg-207362-HCPO). We thank A.P. MacCabe (Consejo Superior de Investigaciones
Científicas, Valencia, Spain) for critical reading of the manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Francesca
full_name: Galbiati, Francesca
last_name: Galbiati
- first_name: Dola
full_name: Sinha Roy, Dola
last_name: Sinha Roy
- first_name: Sara
full_name: Simonini, Sara
last_name: Simonini
- first_name: Mara
full_name: Cucinotta, Mara
last_name: Cucinotta
- first_name: Luca
full_name: Ceccato, Luca
last_name: Ceccato
- first_name: Candela
full_name: Cuesta, Candela
id: 33A3C818-F248-11E8-B48F-1D18A9856A87
last_name: Cuesta
orcid: 0000-0003-1923-2410
- first_name: Mária
full_name: Šimášková, Mária
last_name: Šimášková
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Yuri
full_name: Kamiuchi, Yuri
last_name: Kamiuchi
- first_name: Mitsuhiro
full_name: Aida, Mitsuhiro
last_name: Aida
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Rüdiger
full_name: Simon, Rüdiger
last_name: Simon
- first_name: Simona
full_name: Masiero, Simona
last_name: Masiero
- first_name: Lucia
full_name: Colombo, Lucia
last_name: Colombo
citation:
ama: Galbiati F, Sinha Roy D, Simonini S, et al. An integrative model of the control
of ovule primordia formation. The Plant journal for cell and molecular biology.
2013;76(3):446-455. doi:10.1111/tpj.12309
apa: Galbiati, F., Sinha Roy, D., Simonini, S., Cucinotta, M., Ceccato, L., Cuesta,
C., … Colombo, L. (2013). An integrative model of the control of ovule primordia
formation. The Plant Journal for Cell and Molecular Biology. Wiley-Blackwell.
https://doi.org/10.1111/tpj.12309
chicago: Galbiati, Francesca, Dola Sinha Roy, Sara Simonini, Mara Cucinotta, Luca
Ceccato, Candela Cuesta, Mária Šimášková, et al. “An Integrative Model of the
Control of Ovule Primordia Formation.” The Plant Journal for Cell and Molecular
Biology. Wiley-Blackwell, 2013. https://doi.org/10.1111/tpj.12309.
ieee: F. Galbiati et al., “An integrative model of the control of ovule primordia
formation,” The Plant journal for cell and molecular biology, vol. 76,
no. 3. Wiley-Blackwell, pp. 446–455, 2013.
ista: Galbiati F, Sinha Roy D, Simonini S, Cucinotta M, Ceccato L, Cuesta C, Šimášková
M, Benková E, Kamiuchi Y, Aida M, Weijers D, Simon R, Masiero S, Colombo L. 2013.
An integrative model of the control of ovule primordia formation. The Plant journal
for cell and molecular biology. 76(3), 446–455.
mla: Galbiati, Francesca, et al. “An Integrative Model of the Control of Ovule Primordia
Formation.” The Plant Journal for Cell and Molecular Biology, vol. 76,
no. 3, Wiley-Blackwell, 2013, pp. 446–55, doi:10.1111/tpj.12309.
short: F. Galbiati, D. Sinha Roy, S. Simonini, M. Cucinotta, L. Ceccato, C. Cuesta,
M. Šimášková, E. Benková, Y. Kamiuchi, M. Aida, D. Weijers, R. Simon, S. Masiero,
L. Colombo, The Plant Journal for Cell and Molecular Biology 76 (2013) 446–455.
date_created: 2018-12-11T11:48:44Z
date_published: 2013-09-19T00:00:00Z
date_updated: 2022-03-21T07:17:26Z
day: '19'
doi: 10.1111/tpj.12309
extern: '1'
external_id:
pmid:
- '23941199'
intvolume: ' 76'
issue: '3'
language:
- iso: eng
month: '09'
oa_version: None
page: 446 - 455
pmid: 1
publication: The Plant journal for cell and molecular biology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6818'
quality_controlled: '1'
scopus_import: '1'
status: public
title: An integrative model of the control of ovule primordia formation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 76
year: '2013'
...
---
_id: '831'
abstract:
- lang: eng
text: In Arabidopsis, lateral roots originate from pericycle cells deep within the
primary root. New lateral root primordia (LRP) have to emerge through several
overlaying tissues. Here, we report that auxin produced in new LRP is transported
towards the outer tissues where it triggers cell separation by inducing both the
auxin influx carrier LAX3 and cell-wall enzymes. LAX3 is expressed in just two
cell files overlaying new LRP. To understand how this striking pattern of LAX3
expression is regulated, we developed a mathematical model that captures the network
regulating its expression and auxin transport within realistic three-dimensional
cell and tissue geometries. Our model revealed that, for the LAX3 spatial expression
to be robust to natural variations in root tissue geometry, an efflux carrier
is required--later identified to be PIN3. To prevent LAX3 from being transiently
expressed in multiple cell files, PIN3 and LAX3 must be induced consecutively,
which we later demonstrated to be the case. Our study exemplifies how mathematical
models can be used to direct experiments to elucidate complex developmental processes.
acknowledgement: This work was supported by an FEBS Long‐Term Fellowship (BP), an
Intra‐European Fellowship for Career Development under the 7th framework of the
European Commission (IEF‐2008‐220506 to BP), an EMBO Long‐Term Fellowship (BP),
an European Reintegration Grant under the 7th framework of the European Commission
(ERG‐2010‐276662 to BP) and the Swedish Research Council (VR 621‐2010‐5720 to IS,
GS and KL). AMM, APF, AL, LRB, SP, NM, DMW, MO, JRK and MJB acknowledge the support
of the Biotechnology and Biological Sciences Research Council (BBSRC) and Engineering
and Physical Sciences Research Council (EPSRC) funding to the Centre for Plant Integrative
Biology (CPIB); BBSRC Professorial Research Fellowship funding to DMW and MJB; Belgian
Scientific policy (BELSPO contract MARS) to TB and MJB. We thank Bert de Rybel for
his help in Multisite Gateway cloning.
author:
- first_name: Benjamin
full_name: Péret, Benjamin
last_name: Péret
- first_name: Alistair
full_name: Middleton, Alistair M
last_name: Middleton
- first_name: Andrew
full_name: French, Andrew P
last_name: French
- first_name: Antoine
full_name: Larrieu, Antoine
last_name: Larrieu
- first_name: Anthony
full_name: Bishopp, Anthony
last_name: Bishopp
- first_name: Maria
full_name: Njo, Maria
last_name: Njo
- first_name: Darren
full_name: Wells, Darren M
last_name: Wells
- first_name: Silvana
full_name: Porco, Silvana
last_name: Porco
- first_name: Nathan
full_name: Mellor, Nathan
last_name: Mellor
- first_name: Leah
full_name: Band, Leah R
last_name: Band
- first_name: Ilda
full_name: Casimiro, Ilda
last_name: Casimiro
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Ilkka
full_name: Sairanen, Ilkka
last_name: Sairanen
- first_name: Romain
full_name: Mallet, Romain
last_name: Mallet
- first_name: Göran
full_name: Sandberg, Göran
last_name: Sandberg
- first_name: Karin
full_name: Ljung, Karin
last_name: Ljung
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Eric
full_name: Kramer, Eric
last_name: Kramer
- first_name: John
full_name: King, John R
last_name: King
- first_name: Ive
full_name: De Smet, Ive
last_name: De Smet
- first_name: Tony
full_name: Pridmore, Tony
last_name: Pridmore
- first_name: Markus
full_name: Owen, Markus
last_name: Owen
- first_name: Malcolm
full_name: Bennett, Malcolm J
last_name: Bennett
citation:
ama: Péret B, Middleton A, French A, et al. Sequential induction of auxin efflux
and influx carriers regulates lateral root emergence. Molecular Systems Biology.
2013;9. doi:10.1038/msb.2013.43
apa: Péret, B., Middleton, A., French, A., Larrieu, A., Bishopp, A., Njo, M., …
Bennett, M. (2013). Sequential induction of auxin efflux and influx carriers regulates
lateral root emergence. Molecular Systems Biology. Nature Publishing Group.
https://doi.org/10.1038/msb.2013.43
chicago: Péret, Benjamin, Alistair Middleton, Andrew French, Antoine Larrieu, Anthony
Bishopp, Maria Njo, Darren Wells, et al. “Sequential Induction of Auxin Efflux
and Influx Carriers Regulates Lateral Root Emergence.” Molecular Systems Biology.
Nature Publishing Group, 2013. https://doi.org/10.1038/msb.2013.43.
ieee: B. Péret et al., “Sequential induction of auxin efflux and influx carriers
regulates lateral root emergence,” Molecular Systems Biology, vol. 9. Nature
Publishing Group, 2013.
ista: Péret B, Middleton A, French A, Larrieu A, Bishopp A, Njo M, Wells D, Porco
S, Mellor N, Band L, Casimiro I, Kleine Vehn J, Vanneste S, Sairanen I, Mallet
R, Sandberg G, Ljung K, Beeckman T, Benková E, Friml J, Kramer E, King J, De Smet
I, Pridmore T, Owen M, Bennett M. 2013. Sequential induction of auxin efflux and
influx carriers regulates lateral root emergence. Molecular Systems Biology. 9.
mla: Péret, Benjamin, et al. “Sequential Induction of Auxin Efflux and Influx Carriers
Regulates Lateral Root Emergence.” Molecular Systems Biology, vol. 9, Nature
Publishing Group, 2013, doi:10.1038/msb.2013.43.
short: B. Péret, A. Middleton, A. French, A. Larrieu, A. Bishopp, M. Njo, D. Wells,
S. Porco, N. Mellor, L. Band, I. Casimiro, J. Kleine Vehn, S. Vanneste, I. Sairanen,
R. Mallet, G. Sandberg, K. Ljung, T. Beeckman, E. Benková, J. Friml, E. Kramer,
J. King, I. De Smet, T. Pridmore, M. Owen, M. Bennett, Molecular Systems Biology
9 (2013).
date_created: 2018-12-11T11:48:44Z
date_published: 2013-10-22T00:00:00Z
date_updated: 2021-01-12T08:18:03Z
day: '22'
doi: 10.1038/msb.2013.43
extern: 1
intvolume: ' 9'
month: '10'
publication: Molecular Systems Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '6817'
quality_controlled: 0
status: public
title: Sequential induction of auxin efflux and influx carriers regulates lateral
root emergence
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
volume: 9
year: '2013'
...
---
_id: '8461'
abstract:
- lang: eng
text: Solid-state NMR provides insight into protein motion over time scales ranging
from picoseconds to seconds. While in solution state the methodology to measure
protein dynamics is well established, there is currently no such consensus protocol
for measuring dynamics in solids. In this article, we perform a detailed investigation
of measurement protocols for fast motions, i.e. motions ranging from picoseconds
to a few microseconds, which is the range covered by dipolar coupling and relaxation
experiments. We perform a detailed theoretical investigation how dipolar couplings
and relaxation data can provide information about amplitudes and time scales of
local motion. We show that the measurement of dipolar couplings is crucial for
obtaining accurate motional parameters, while systematic errors are found when
only relaxation data are used. Based on this realization, we investigate how the
REDOR experiment can provide such data in a very accurate manner. We identify
that with accurate rf calibration, and explicit consideration of rf field inhomogeneities,
one can obtain highly accurate absolute order parameters. We then perform joint
model-free analyses of 6 relaxation data sets and dipolar couplings, based on
previously existing, as well as new data sets on microcrystalline ubiquitin. We
show that nanosecond motion can be detected primarily in loop regions, and compare
solid-state data to solution-state relaxation and RDC analyses. The protocols
investigated here will serve as a useful basis towards the establishment of a
routine protocol for the characterization of ps–μs motions in proteins by solid-state
NMR.
article_processing_charge: No
article_type: original
author:
- first_name: Jens D.
full_name: Haller, Jens D.
last_name: Haller
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Haller JD, Schanda P. Amplitudes and time scales of picosecond-to-microsecond
motion in proteins studied by solid-state NMR: a critical evaluation of experimental
approaches and application to crystalline ubiquitin. Journal of Biomolecular
NMR. 2013;57(3):263-280. doi:10.1007/s10858-013-9787-x'
apa: 'Haller, J. D., & Schanda, P. (2013). Amplitudes and time scales of picosecond-to-microsecond
motion in proteins studied by solid-state NMR: a critical evaluation of experimental
approaches and application to crystalline ubiquitin. Journal of Biomolecular
NMR. Springer Nature. https://doi.org/10.1007/s10858-013-9787-x'
chicago: 'Haller, Jens D., and Paul Schanda. “Amplitudes and Time Scales of Picosecond-to-Microsecond
Motion in Proteins Studied by Solid-State NMR: A Critical Evaluation of Experimental
Approaches and Application to Crystalline Ubiquitin.” Journal of Biomolecular
NMR. Springer Nature, 2013. https://doi.org/10.1007/s10858-013-9787-x.'
ieee: 'J. D. Haller and P. Schanda, “Amplitudes and time scales of picosecond-to-microsecond
motion in proteins studied by solid-state NMR: a critical evaluation of experimental
approaches and application to crystalline ubiquitin,” Journal of Biomolecular
NMR, vol. 57, no. 3. Springer Nature, pp. 263–280, 2013.'
ista: 'Haller JD, Schanda P. 2013. Amplitudes and time scales of picosecond-to-microsecond
motion in proteins studied by solid-state NMR: a critical evaluation of experimental
approaches and application to crystalline ubiquitin. Journal of Biomolecular NMR.
57(3), 263–280.'
mla: 'Haller, Jens D., and Paul Schanda. “Amplitudes and Time Scales of Picosecond-to-Microsecond
Motion in Proteins Studied by Solid-State NMR: A Critical Evaluation of Experimental
Approaches and Application to Crystalline Ubiquitin.” Journal of Biomolecular
NMR, vol. 57, no. 3, Springer Nature, 2013, pp. 263–80, doi:10.1007/s10858-013-9787-x.'
short: J.D. Haller, P. Schanda, Journal of Biomolecular NMR 57 (2013) 263–280.
date_created: 2020-09-18T10:09:05Z
date_published: 2013-10-09T00:00:00Z
date_updated: 2021-01-12T08:19:26Z
day: '09'
doi: 10.1007/s10858-013-9787-x
extern: '1'
intvolume: ' 57'
issue: '3'
keyword:
- Spectroscopy
- Biochemistry
language:
- iso: eng
month: '10'
oa_version: None
page: 263-280
publication: Journal of Biomolecular NMR
publication_identifier:
issn:
- 0925-2738
- 1573-5001
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: 'Amplitudes and time scales of picosecond-to-microsecond motion in proteins
studied by solid-state NMR: a critical evaluation of experimental approaches and
application to crystalline ubiquitin'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2013'
...
---
_id: '8462'
abstract:
- lang: eng
text: The transition of proteins from their soluble functional state to amyloid
fibrils and aggregates is associated with the onset of several human diseases.
Protein aggregation often requires some structural reshaping and the subsequent
formation of intermolecular contacts. Therefore, the study of the conformation
of excited protein states and their ability to form oligomers is of primary importance
for understanding the molecular basis of amyloid fibril formation. Here, we investigated
the oligomerization processes that occur along the folding of the amyloidogenic
human protein β2-microglobulin. The combination of real-time two-dimensional NMR
data with real-time small-angle X-ray scattering measurements allowed us to derive
thermodynamic and kinetic information on protein oligomerization of different
conformational states populated along the folding pathways. In particular, we
could demonstrate that a long-lived folding intermediate (I-state) has a higher
propensity to oligomerize compared to the native state. Our data agree well with
a simple five-state kinetic model that involves only monomeric and dimeric species.
The dimers have an elongated shape with the dimerization interface located at
the apical side of β2-microglobulin close to Pro32, the residue that has a trans
conformation in the I-state and a cis conformation in the native (N) state. Our
experimental data suggest that partial unfolding in the apical half of the protein
close to Pro32 leads to an excited state conformation with enhanced propensity
for oligomerization. This excited state becomes more populated in the transient
I-state due to the destabilization of the native conformation by the trans-Pro32
configuration.
article_processing_charge: No
article_type: original
author:
- first_name: E.
full_name: Rennella, E.
last_name: Rennella
- first_name: T.
full_name: Cutuil, T.
last_name: Cutuil
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: I.
full_name: Ayala, I.
last_name: Ayala
- first_name: F.
full_name: Gabel, F.
last_name: Gabel
- first_name: V.
full_name: Forge, V.
last_name: Forge
- first_name: A.
full_name: Corazza, A.
last_name: Corazza
- first_name: G.
full_name: Esposito, G.
last_name: Esposito
- first_name: B.
full_name: Brutscher, B.
last_name: Brutscher
citation:
ama: 'Rennella E, Cutuil T, Schanda P, et al. Oligomeric states along the folding
pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. Journal
of Molecular Biology. 2013;425(15):2722-2736. doi:10.1016/j.jmb.2013.04.028'
apa: 'Rennella, E., Cutuil, T., Schanda, P., Ayala, I., Gabel, F., Forge, V., …
Brutscher, B. (2013). Oligomeric states along the folding pathways of β2-microglobulin:
Kinetics, thermodynamics, and structure. Journal of Molecular Biology.
Elsevier. https://doi.org/10.1016/j.jmb.2013.04.028'
chicago: 'Rennella, E., T. Cutuil, Paul Schanda, I. Ayala, F. Gabel, V. Forge, A.
Corazza, G. Esposito, and B. Brutscher. “Oligomeric States along the Folding Pathways
of Β2-Microglobulin: Kinetics, Thermodynamics, and Structure.” Journal of Molecular
Biology. Elsevier, 2013. https://doi.org/10.1016/j.jmb.2013.04.028.'
ieee: 'E. Rennella et al., “Oligomeric states along the folding pathways
of β2-microglobulin: Kinetics, thermodynamics, and structure,” Journal of Molecular
Biology, vol. 425, no. 15. Elsevier, pp. 2722–2736, 2013.'
ista: 'Rennella E, Cutuil T, Schanda P, Ayala I, Gabel F, Forge V, Corazza A, Esposito
G, Brutscher B. 2013. Oligomeric states along the folding pathways of β2-microglobulin:
Kinetics, thermodynamics, and structure. Journal of Molecular Biology. 425(15),
2722–2736.'
mla: 'Rennella, E., et al. “Oligomeric States along the Folding Pathways of Β2-Microglobulin:
Kinetics, Thermodynamics, and Structure.” Journal of Molecular Biology,
vol. 425, no. 15, Elsevier, 2013, pp. 2722–36, doi:10.1016/j.jmb.2013.04.028.'
short: E. Rennella, T. Cutuil, P. Schanda, I. Ayala, F. Gabel, V. Forge, A. Corazza,
G. Esposito, B. Brutscher, Journal of Molecular Biology 425 (2013) 2722–2736.
date_created: 2020-09-18T10:09:12Z
date_published: 2013-08-09T00:00:00Z
date_updated: 2022-08-25T14:56:24Z
day: '09'
doi: 10.1016/j.jmb.2013.04.028
extern: '1'
intvolume: ' 425'
issue: '15'
keyword:
- Molecular Biology
language:
- iso: eng
month: '08'
oa_version: None
page: 2722-2736
publication: Journal of Molecular Biology
publication_identifier:
issn:
- 0022-2836
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Oligomeric states along the folding pathways of β2-microglobulin: Kinetics,
thermodynamics, and structure'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 425
year: '2013'
...
---
_id: '894'
abstract:
- lang: eng
text: 'Background: Genetic variation at the melanocortin-1 receptor (MC1R) gene
is correlated with melanin color variation in many birds. Feral pigeons (Columba
livia) show two major melanin-based colorations: a red coloration due to pheomelanic
pigment and a black coloration due to eumelanic pigment. Furthermore, within each
color type, feral pigeons display continuous variation in the amount of melanin
pigment present in the feathers, with individuals varying from pure white to a
full dark melanic color. Coloration is highly heritable and it has been suggested
that it is under natural or sexual selection, or both. Our objective was to investigate
whether MC1R allelic variants are associated with plumage color in feral pigeons.
Findings. We sequenced 888 bp of the coding sequence of MC1R among pigeons varying
both in the type, eumelanin or pheomelanin, and the amount of melanin in their
feathers. We detected 10 non-synonymous substitutions and 2 synonymous substitution
but none of them were associated with a plumage type. It remains possible that
non-synonymous substitutions that influence coloration are present in the short
MC1R fragment that we did not sequence but this seems unlikely because we analyzed
the entire functionally important region of the gene. Conclusions: Our results
show that color differences among feral pigeons are probably not attributable
to amino acid variation at the MC1R locus. Therefore, variation in regulatory
regions of MC1R or variation in other genes may be responsible for the color polymorphism
of feral pigeons.'
acknowledgement: Romain Derelle was supported by grant from Plan Nacional 004302 BFU2012-31329.
Fyodor A Kondrashov was supported by grants HHMI (Howard Hughes Medical Institute)
003803 and EMBO 003691 EUI-EURYIP-2011-4320.
author:
- first_name: Romain
full_name: Derelle, Romain
last_name: Derelle
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Vladimir
full_name: Arkhipov, Vladimir
last_name: Arkhipov
- first_name: Hélène
full_name: Corbel, Hélène
last_name: Corbel
- first_name: Adrien
full_name: Frantz, Adrien
last_name: Frantz
- first_name: Julien
full_name: Gasparini, Julien
last_name: Gasparini
- first_name: Lisa
full_name: Jacquin, Lisa
last_name: Jacquin
- first_name: Gwenaël
full_name: Jacob, Gwenaël
last_name: Jacob
- first_name: Sophie
full_name: Thibault, Sophie
last_name: Thibault
- first_name: Emmanuelle
full_name: Baudry, Emmanuelle
last_name: Baudry
citation:
ama: Derelle R, Kondrashov F, Arkhipov V, et al. Color differences among feral pigeons
(Columba livia) are not attributable to sequence variation in the coding region
of the melanocortin-1 receptor gene MC1R. BMC Research Notes. 2013;6(1).
doi:10.1186/1756-0500-6-310
apa: Derelle, R., Kondrashov, F., Arkhipov, V., Corbel, H., Frantz, A., Gasparini,
J., … Baudry, E. (2013). Color differences among feral pigeons (Columba livia)
are not attributable to sequence variation in the coding region of the melanocortin-1
receptor gene MC1R. BMC Research Notes. BioMed Central. https://doi.org/10.1186/1756-0500-6-310
chicago: Derelle, Romain, Fyodor Kondrashov, Vladimir Arkhipov, Hélène Corbel, Adrien
Frantz, Julien Gasparini, Lisa Jacquin, Gwenaël Jacob, Sophie Thibault, and Emmanuelle
Baudry. “Color Differences among Feral Pigeons (Columba Livia) Are Not Attributable
to Sequence Variation in the Coding Region of the Melanocortin-1 Receptor Gene
MC1R.” BMC Research Notes. BioMed Central, 2013. https://doi.org/10.1186/1756-0500-6-310.
ieee: R. Derelle et al., “Color differences among feral pigeons (Columba
livia) are not attributable to sequence variation in the coding region of the
melanocortin-1 receptor gene MC1R,” BMC Research Notes, vol. 6, no. 1.
BioMed Central, 2013.
ista: Derelle R, Kondrashov F, Arkhipov V, Corbel H, Frantz A, Gasparini J, Jacquin
L, Jacob G, Thibault S, Baudry E. 2013. Color differences among feral pigeons
(Columba livia) are not attributable to sequence variation in the coding region
of the melanocortin-1 receptor gene MC1R. BMC Research Notes. 6(1).
mla: Derelle, Romain, et al. “Color Differences among Feral Pigeons (Columba Livia)
Are Not Attributable to Sequence Variation in the Coding Region of the Melanocortin-1
Receptor Gene MC1R.” BMC Research Notes, vol. 6, no. 1, BioMed Central,
2013, doi:10.1186/1756-0500-6-310.
short: R. Derelle, F. Kondrashov, V. Arkhipov, H. Corbel, A. Frantz, J. Gasparini,
L. Jacquin, G. Jacob, S. Thibault, E. Baudry, BMC Research Notes 6 (2013).
date_created: 2018-12-11T11:49:04Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T08:21:25Z
day: '01'
doi: 10.1186/1756-0500-6-310
extern: '1'
intvolume: ' 6'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
publication: BMC Research Notes
publication_status: published
publisher: BioMed Central
publist_id: '6752'
status: public
title: Color differences among feral pigeons (Columba livia) are not attributable
to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2013'
...
---
_id: '899'
abstract:
- lang: eng
text: Understanding fitness landscapes, a conceptual depiction of the genotype-to-phenotype
relationship, is crucial to many areas of biology. Two aspects of fitness landscapes
are the focus of contemporary studies of molecular evolution. First, the local
shape of the fitness landscape defined by the contribution of individual alleles
to fitness that is independent of all genetic interactions. Second, the global,
multidimensional fitness landscape shape determined by how interactions between
alleles at different loci change each other’s fitness impact, or epistasis. In
explaining the high amino-acid usage (u), we focused on the global shape of the
fitness landscape, ignoring the perturbations at individual sites.
author:
- first_name: Michael
full_name: Breen, Michael S
last_name: Breen
- first_name: Carsten
full_name: Kemena, Carsten
last_name: Kemena
- first_name: Peter
full_name: Vlasov, Peter K
last_name: Vlasov
- first_name: Cédric
full_name: Notredame, Cédric
last_name: Notredame
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. Breen et al. reply.
Nature. 2013;497(7451):E2-E3. doi:10.1038/nature12220
apa: Breen, M., Kemena, C., Vlasov, P., Notredame, C., & Kondrashov, F. (2013).
Breen et al. reply. Nature. Nature Publishing Group. https://doi.org/10.1038/nature12220
chicago: Breen, Michael, Carsten Kemena, Peter Vlasov, Cédric Notredame, and Fyodor
Kondrashov. “Breen et Al. Reply.” Nature. Nature Publishing Group, 2013.
https://doi.org/10.1038/nature12220.
ieee: M. Breen, C. Kemena, P. Vlasov, C. Notredame, and F. Kondrashov, “Breen et
al. reply,” Nature, vol. 497, no. 7451. Nature Publishing Group, pp. E2–E3,
2013.
ista: Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. 2013. Breen et al.
reply. Nature. 497(7451), E2–E3.
mla: Breen, Michael, et al. “Breen et Al. Reply.” Nature, vol. 497, no. 7451,
Nature Publishing Group, 2013, pp. E2–3, doi:10.1038/nature12220.
short: M. Breen, C. Kemena, P. Vlasov, C. Notredame, F. Kondrashov, Nature 497 (2013)
E2–E3.
date_created: 2018-12-11T11:49:05Z
date_published: 2013-05-30T00:00:00Z
date_updated: 2021-01-12T08:21:40Z
day: '30'
doi: 10.1038/nature12220
extern: 1
intvolume: ' 497'
issue: '7451'
month: '05'
page: E2 - E3
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6747'
quality_controlled: 0
status: public
title: Breen et al. reply
type: journal_article
volume: 497
year: '2013'
...
---
_id: '1726'
abstract:
- lang: eng
text: The development of a functional tissue requires coordination of the amplification
of progenitors and their differentiation into specific cell types. The molecular
basis for this coordination during myotome ontogeny is not well understood. Dermomytome
progenitors that colonize the myotome first acquire myocyte identity and subsequently
proliferate as Pax7-expressing progenitors before undergoing terminal differentiation.
We show that the dynamics of sonic hedgehog (Shh) signaling is crucial for this
transition in both avian and mouse embryos. Initially, Shh ligand emanating from
notochord/floor plate reaches the dermomyotome, where it both maintains the proliferation
of dermomyotome cells and promotes myogenic differentiation of progenitors that
colonized the myotome. Interfering with Shh signaling at this stage produces small
myotomes and accumulation of Pax7-expressing progenitors. An in vivo reporter
of Shh activity combined with mouse genetics revealed the existence of both activator
and repressor Shh activities operating on distinct subsets of cells during the
epaxial myotomal maturation. In contrast to observations in mice, in avians Shh
promotes the differentiation of both epaxial and hypaxial myotome domains. Subsequently,
myogenic progenitors become refractory to Shh; this is likely to occur at the
level of, or upstream of, smoothened signaling. The end of responsiveness to Shh
coincides with, and is thus likely to enable, the transition into the growth phase
of the myotome.
acknowledgement: This study was supported by grants from the Israel Science Foundation
(ISF) [11/09 to C.K.]; the Association Francaise contre les Myopathies (AFM) [15642
to C.K.]; the German Research Foundation (DFG) [UN 34/27-1 to C.K.]; the UK Medical
Research Council (MRC) [U117560541 to J.B. and A.K.]; Fondation Pour la Recherche
Médicale (FRM) (post-doctoral fellowship to V.R.). Deposited in PMC for release
after 6 months
author:
- first_name: Nitza
full_name: Kahane, Nitza
last_name: Kahane
- first_name: Vanessa
full_name: Ribes, Vanessa
last_name: Ribes
- first_name: Anna
full_name: Anna Kicheva
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: James
full_name: Briscoe, James
last_name: Briscoe
- first_name: Chaya
full_name: Kalcheim, Chaya
last_name: Kalcheim
citation:
ama: Kahane N, Ribes V, Kicheva A, Briscoe J, Kalcheim C. The transition from differentiation
to growth during dermomyotome-derived myogenesis depends on temporally restricted
hedgehog signaling. Development. 2013;140(8):1740-1750. doi:10.1242/dev.092726
apa: Kahane, N., Ribes, V., Kicheva, A., Briscoe, J., & Kalcheim, C. (2013).
The transition from differentiation to growth during dermomyotome-derived myogenesis
depends on temporally restricted hedgehog signaling. Development. Company
of Biologists. https://doi.org/10.1242/dev.092726
chicago: Kahane, Nitza, Vanessa Ribes, Anna Kicheva, James Briscoe, and Chaya Kalcheim.
“The Transition from Differentiation to Growth during Dermomyotome-Derived Myogenesis
Depends on Temporally Restricted Hedgehog Signaling.” Development. Company
of Biologists, 2013. https://doi.org/10.1242/dev.092726.
ieee: N. Kahane, V. Ribes, A. Kicheva, J. Briscoe, and C. Kalcheim, “The transition
from differentiation to growth during dermomyotome-derived myogenesis depends
on temporally restricted hedgehog signaling,” Development, vol. 140, no.
8. Company of Biologists, pp. 1740–1750, 2013.
ista: Kahane N, Ribes V, Kicheva A, Briscoe J, Kalcheim C. 2013. The transition
from differentiation to growth during dermomyotome-derived myogenesis depends
on temporally restricted hedgehog signaling. Development. 140(8), 1740–1750.
mla: Kahane, Nitza, et al. “The Transition from Differentiation to Growth during
Dermomyotome-Derived Myogenesis Depends on Temporally Restricted Hedgehog Signaling.”
Development, vol. 140, no. 8, Company of Biologists, 2013, pp. 1740–50,
doi:10.1242/dev.092726.
short: N. Kahane, V. Ribes, A. Kicheva, J. Briscoe, C. Kalcheim, Development 140
(2013) 1740–1750.
date_created: 2018-12-11T11:53:41Z
date_published: 2013-04-18T00:00:00Z
date_updated: 2021-01-12T06:52:47Z
day: '18'
doi: 10.1242/dev.092726
extern: 1
intvolume: ' 140'
issue: '8'
month: '04'
page: 1740 - 1750
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '5402'
quality_controlled: 0
status: public
title: The transition from differentiation to growth during dermomyotome-derived myogenesis
depends on temporally restricted hedgehog signaling
type: journal_article
volume: 140
year: '2013'
...
---
_id: '1727'
abstract:
- lang: eng
text: 'Cells at different positions in a developing tissue receive different concentrations
of signaling molecules, called morphogens, and this influences their cell fate.
Morphogen concentration gradients have been proposed to control patterning as
well as growth in many developing tissues. Some outstanding questions about tissue
patterning by morphogen gradients are the following: What are the mechanisms that
regulate gradient formation and shape? Is the positional information encoded in
the gradient sufficiently precise to determine the positions of target gene domain
boundaries? What are the temporal dynamics of gradients and how do they relate
to patterning and growth? These questions are inherently quantitative in nature
and addressing them requires measuring morphogen concentrations in cells, levels
of downstream signaling activity, and kinetics of morphogen transport. Here we
first present methods for quantifying morphogen gradient shape in which the measurements
can be calibrated to reflect actual morphogen concentrations. We then discuss
using fluorescence recovery after photobleaching to study the kinetics of morphogen
transport at the tissue level. Finally, we present particle tracking as a method
to study morphogen intracellular trafficking.'
author:
- first_name: Anna
full_name: Anna Kicheva
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Laurent
full_name: Holtzer, Laurent
last_name: Holtzer
- first_name: Ortrud
full_name: Wartlick, Ortrud
last_name: Wartlick
- first_name: Thomas
full_name: Schmidt, Thomas S
last_name: Schmidt
- first_name: Marcos
full_name: González-Gaitán, Marcos A
last_name: González Gaitán
citation:
ama: Kicheva A, Holtzer L, Wartlick O, Schmidt T, González Gaitán M. Quantitative
imaging of morphogen gradients in drosophila imaginal discs. Cold Spring Harbor
Protocols. 2013;8(5):387-403. doi:10.1101/pdb.top074237
apa: Kicheva, A., Holtzer, L., Wartlick, O., Schmidt, T., & González Gaitán,
M. (2013). Quantitative imaging of morphogen gradients in drosophila imaginal
discs. Cold Spring Harbor Protocols. Cold Spring Harbor Laboratory Press.
https://doi.org/10.1101/pdb.top074237
chicago: Kicheva, Anna, Laurent Holtzer, Ortrud Wartlick, Thomas Schmidt, and Marcos
González Gaitán. “Quantitative Imaging of Morphogen Gradients in Drosophila Imaginal
Discs.” Cold Spring Harbor Protocols. Cold Spring Harbor Laboratory Press,
2013. https://doi.org/10.1101/pdb.top074237.
ieee: A. Kicheva, L. Holtzer, O. Wartlick, T. Schmidt, and M. González Gaitán, “Quantitative
imaging of morphogen gradients in drosophila imaginal discs,” Cold Spring Harbor
Protocols, vol. 8, no. 5. Cold Spring Harbor Laboratory Press, pp. 387–403,
2013.
ista: Kicheva A, Holtzer L, Wartlick O, Schmidt T, González Gaitán M. 2013. Quantitative
imaging of morphogen gradients in drosophila imaginal discs. Cold Spring Harbor
Protocols. 8(5), 387–403.
mla: Kicheva, Anna, et al. “Quantitative Imaging of Morphogen Gradients in Drosophila
Imaginal Discs.” Cold Spring Harbor Protocols, vol. 8, no. 5, Cold Spring
Harbor Laboratory Press, 2013, pp. 387–403, doi:10.1101/pdb.top074237.
short: A. Kicheva, L. Holtzer, O. Wartlick, T. Schmidt, M. González Gaitán, Cold
Spring Harbor Protocols 8 (2013) 387–403.
date_created: 2018-12-11T11:53:41Z
date_published: 2013-05-01T00:00:00Z
date_updated: 2021-01-12T06:52:47Z
day: '01'
doi: 10.1101/pdb.top074237
extern: 1
intvolume: ' 8'
issue: '5'
month: '05'
page: 387 - 403
publication: Cold Spring Harbor Protocols
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '5401'
quality_controlled: 0
status: public
title: Quantitative imaging of morphogen gradients in drosophila imaginal discs
type: journal_article
volume: 8
year: '2013'
...
---
_id: '1759'
abstract:
- lang: eng
text: We report an electric-field-induced giant modulation of the hole g factor
in SiGe nanocrystals. The observed effect is ascribed to a so-far overlooked contribution
to the g factor that stems from the mixing between heavy- and light-hole wave
functions. We show that the relative displacement between the confined heavy-
and light-hole states, occurring upon application of the electric field, alters
their mixing strength leading to a strong nonmonotonic modulation of the g factor.
acknowledgement: We acknowledge financial support from the Nanosciences Foundation
(Grenoble, France), DOE under Contract No. DEFG02-08ER46482 (Yale), the Agence Nationale
de la Recherche, and the European Starting Grant. G. K. acknowledges support from
the European Commission via a Marie Curie Carrer Integration Grant and the FWF for
a Lise-Meitner Fellowship
author:
- first_name: Natalia
full_name: Ares, Natalia
last_name: Ares
- first_name: Vitaly
full_name: Golovach, Vitaly N
last_name: Golovach
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Mathieu
full_name: Stoffel, Mathieu
last_name: Stoffel
- first_name: Frank
full_name: Fournel, Frank
last_name: Fournel
- first_name: Leonid
full_name: Glazman, Leonid I
last_name: Glazman
- first_name: Oliver
full_name: Schmidt, Oliver G
last_name: Schmidt
- first_name: Silvano
full_name: De Franceschi, Silvano
last_name: De Franceschi
citation:
ama: Ares N, Golovach V, Katsaros G, et al. Nature of tunable hole g factors in
quantum dots. Physical Review Letters. 2013;110(4). doi:10.1103/PhysRevLett.110.046602
apa: Ares, N., Golovach, V., Katsaros, G., Stoffel, M., Fournel, F., Glazman, L.,
… De Franceschi, S. (2013). Nature of tunable hole g factors in quantum dots.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.110.046602
chicago: Ares, Natalia, Vitaly Golovach, Georgios Katsaros, Mathieu Stoffel, Frank
Fournel, Leonid Glazman, Oliver Schmidt, and Silvano De Franceschi. “Nature of
Tunable Hole g Factors in Quantum Dots.” Physical Review Letters. American
Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.046602.
ieee: N. Ares et al., “Nature of tunable hole g factors in quantum dots,”
Physical Review Letters, vol. 110, no. 4. American Physical Society, 2013.
ista: Ares N, Golovach V, Katsaros G, Stoffel M, Fournel F, Glazman L, Schmidt O,
De Franceschi S. 2013. Nature of tunable hole g factors in quantum dots. Physical
Review Letters. 110(4).
mla: Ares, Natalia, et al. “Nature of Tunable Hole g Factors in Quantum Dots.” Physical
Review Letters, vol. 110, no. 4, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.046602.
short: N. Ares, V. Golovach, G. Katsaros, M. Stoffel, F. Fournel, L. Glazman, O.
Schmidt, S. De Franceschi, Physical Review Letters 110 (2013).
date_created: 2018-12-11T11:53:51Z
date_published: 2013-01-23T00:00:00Z
date_updated: 2021-01-12T06:53:01Z
day: '23'
doi: 10.1103/PhysRevLett.110.046602
extern: 1
intvolume: ' 110'
issue: '4'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1208.0476
month: '01'
oa: 1
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5365'
quality_controlled: 0
status: public
title: Nature of tunable hole g factors in quantum dots
type: journal_article
volume: 110
year: '2013'
...
---
_id: '1760'
abstract:
- lang: eng
text: We report on hole g-factor measurements in three terminal SiGe self-assembled
quantum dot devices with a top gate electrode positioned very close to the nanostructure.
Measurements of both the perpendicular as well as the parallel g-factor reveal
significant changes for a small modulation of the top gate voltage. From the observed
modulations, we estimate that, for realistic experimental conditions, hole spins
can be electrically manipulated with Rabi frequencies in the order of 100 MHz.
This work emphasises the potential of hole-based nano-devices for efficient spin
manipulation by means of the g-tensor modulation technique.
acknowledgement: We acknowledge the financial support from the Nanosciences Foundation
(Grenoble, France), the Commission for a Marie Curie Carrer Integration Grant, the
Austrian Science Fund (FWF) for a Lise-Meitner Fellowship (M1435-N30), the DOE under
Contract No. DE-FG02-08ER46482 (Yale), the European Starting Grant program, and
the Agence Nationale de la Recherche
author:
- first_name: Natalia
full_name: Ares, Natalia
last_name: Ares
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Vitaly
full_name: Golovach, Vitaly N
last_name: Golovach
- first_name: Jianjun
full_name: Zhang, Jianjun
last_name: Zhang
- first_name: Aaron
full_name: Prager, Aaron A
last_name: Prager
- first_name: Leonid
full_name: Glazman, Leonid I
last_name: Glazman
- first_name: Oliver
full_name: Schmidt, Oliver G
last_name: Schmidt
- first_name: Silvano
full_name: De Franceschi, Silvano
last_name: De Franceschi
citation:
ama: Ares N, Katsaros G, Golovach V, et al. SiGe quantum dots for fast hole spin
Rabi oscillations. Applied Physics Letters. 2013;103(26). doi:10.1063/1.4858959
apa: Ares, N., Katsaros, G., Golovach, V., Zhang, J., Prager, A., Glazman, L., …
De Franceschi, S. (2013). SiGe quantum dots for fast hole spin Rabi oscillations.
Applied Physics Letters. American Institute of Physics. https://doi.org/10.1063/1.4858959
chicago: Ares, Natalia, Georgios Katsaros, Vitaly Golovach, Jianjun Zhang, Aaron
Prager, Leonid Glazman, Oliver Schmidt, and Silvano De Franceschi. “SiGe Quantum
Dots for Fast Hole Spin Rabi Oscillations.” Applied Physics Letters. American
Institute of Physics, 2013. https://doi.org/10.1063/1.4858959.
ieee: N. Ares et al., “SiGe quantum dots for fast hole spin Rabi oscillations,”
Applied Physics Letters, vol. 103, no. 26. American Institute of Physics,
2013.
ista: Ares N, Katsaros G, Golovach V, Zhang J, Prager A, Glazman L, Schmidt O, De
Franceschi S. 2013. SiGe quantum dots for fast hole spin Rabi oscillations. Applied
Physics Letters. 103(26).
mla: Ares, Natalia, et al. “SiGe Quantum Dots for Fast Hole Spin Rabi Oscillations.”
Applied Physics Letters, vol. 103, no. 26, American Institute of Physics,
2013, doi:10.1063/1.4858959.
short: N. Ares, G. Katsaros, V. Golovach, J. Zhang, A. Prager, L. Glazman, O. Schmidt,
S. De Franceschi, Applied Physics Letters 103 (2013).
date_created: 2018-12-11T11:53:52Z
date_published: 2013-01-23T00:00:00Z
date_updated: 2021-01-12T06:53:02Z
day: '23'
doi: 10.1063/1.4858959
extern: 1
intvolume: ' 103'
issue: '26'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1307.7196
month: '01'
oa: 1
publication: Applied Physics Letters
publication_status: published
publisher: American Institute of Physics
publist_id: '5364'
quality_controlled: 0
status: public
title: SiGe quantum dots for fast hole spin Rabi oscillations
type: journal_article
volume: 103
year: '2013'
...
---
_id: '1785'
abstract:
- lang: eng
text: The geometric aspects of quantum mechanics are emphasized most prominently
by the concept of geometric phases, which are acquired whenever a quantum system
evolves along a path in Hilbert space, that is, the space of quantum states of
the system. The geometric phase is determined only by the shape of this path and
is, in its simplest form, a real number. However, if the system has degenerate
energy levels, then matrix-valued geometric state transformations, known as non-Abelian
holonomies-the effect of which depends on the order of two consecutive paths-can
be obtained. They are important, for example, for the creation of synthetic gauge
fields in cold atomic gases or the description of non-Abelian anyon statistics.
Moreover, there are proposals to exploit non-Abelian holonomic gates for the purposes
of noise-resilient quantum computation. In contrast to Abelian geometric operations,
non-Abelian ones have been observed only in nuclear quadrupole resonance experiments
with a large number of spins, and without full characterization of the geometric
process and its non-commutative nature. Here we realize non-Abelian non-adiabatic
holonomic quantum operations on a single, superconducting, artificial three-level
atom by applying a well-controlled, two-tone microwave drive. Using quantum process
tomography, we determine fidelities of the resulting non-commuting gates that
exceed 95 per cent. We show that two different quantum gates, originating from
two distinct paths in Hilbert space, yield non-equivalent transformations when
applied in different orders. This provides evidence for the non-Abelian character
of the implemented holonomic quantum operations. In combination with a non-trivial
two-quantum-bit gate, our method suggests a way to universal holonomic quantum
computing.
acknowledgement: This work is supported financially by GEOMDISS, the Swiss National
Science Foundation and ETH Zurich
author:
- first_name: Abdufarrukh
full_name: Abdumalikov, Abdufarrukh A
last_name: Abdumalikov
- first_name: Johannes M
full_name: Johannes Fink
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: K
full_name: Juliusson, K
last_name: Juliusson
- first_name: M
full_name: Pechal, M
last_name: Pechal
- first_name: Stefan
full_name: Berger, Stefan T
last_name: Berger
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
- first_name: Stefan
full_name: Filipp, Stefan
last_name: Filipp
citation:
ama: Abdumalikov A, Fink JM, Juliusson K, et al. Experimental realization of non-Abelian
non-adiabatic geometric gates. Nature. 2013;496(7446):482-485. doi:10.1038/nature12010
apa: Abdumalikov, A., Fink, J. M., Juliusson, K., Pechal, M., Berger, S., Wallraff,
A., & Filipp, S. (2013). Experimental realization of non-Abelian non-adiabatic
geometric gates. Nature. Nature Publishing Group. https://doi.org/10.1038/nature12010
chicago: Abdumalikov, Abdufarrukh, Johannes M Fink, K Juliusson, M Pechal, Stefan
Berger, Andreas Wallraff, and Stefan Filipp. “Experimental Realization of Non-Abelian
Non-Adiabatic Geometric Gates.” Nature. Nature Publishing Group, 2013.
https://doi.org/10.1038/nature12010.
ieee: A. Abdumalikov et al., “Experimental realization of non-Abelian non-adiabatic
geometric gates,” Nature, vol. 496, no. 7446. Nature Publishing Group,
pp. 482–485, 2013.
ista: Abdumalikov A, Fink JM, Juliusson K, Pechal M, Berger S, Wallraff A, Filipp
S. 2013. Experimental realization of non-Abelian non-adiabatic geometric gates.
Nature. 496(7446), 482–485.
mla: Abdumalikov, Abdufarrukh, et al. “Experimental Realization of Non-Abelian Non-Adiabatic
Geometric Gates.” Nature, vol. 496, no. 7446, Nature Publishing Group,
2013, pp. 482–85, doi:10.1038/nature12010.
short: A. Abdumalikov, J.M. Fink, K. Juliusson, M. Pechal, S. Berger, A. Wallraff,
S. Filipp, Nature 496 (2013) 482–485.
date_created: 2018-12-11T11:54:00Z
date_published: 2013-04-25T00:00:00Z
date_updated: 2021-01-12T06:53:11Z
day: '25'
doi: 10.1038/nature12010
extern: 1
intvolume: ' 496'
issue: '7446'
month: '04'
page: 482 - 485
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '5329'
quality_controlled: 0
status: public
title: Experimental realization of non-Abelian non-adiabatic geometric gates
type: journal_article
volume: 496
year: '2013'
...
---
_id: '1786'
abstract:
- lang: eng
text: We report the experimental observation and a theoretical explanation of collective
suppression of linewidths for multiple superconducting qubits coupled to a good
cavity. This demonstrates how strong qubit-cavity coupling can significantly modify
the dephasing and dissipation processes that might be expected for individual
qubits, and can potentially improve coherence times in many-body circuit QED.
acknowledgement: J. K. acknowledges financial support from EPSRC program “TOPNES”
(EP/I031014/1) and EPSRC (EP/G004714/2)
author:
- first_name: Felix
full_name: Nissen, Felix
last_name: Nissen
- first_name: Johannes M
full_name: Johannes Fink
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Jonas
full_name: Mlynek, Jonas A
last_name: Mlynek
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
- first_name: Jonathan
full_name: Keeling, Jonathan M
last_name: Keeling
citation:
ama: Nissen F, Fink JM, Mlynek J, Wallraff A, Keeling J. Collective suppression
of linewidths in circuit QED. Physical Review Letters. 2013;110(20). doi:10.1103/PhysRevLett.110.203602
apa: Nissen, F., Fink, J. M., Mlynek, J., Wallraff, A., & Keeling, J. (2013).
Collective suppression of linewidths in circuit QED. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.110.203602
chicago: Nissen, Felix, Johannes M Fink, Jonas Mlynek, Andreas Wallraff, and Jonathan
Keeling. “Collective Suppression of Linewidths in Circuit QED.” Physical Review
Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.203602.
ieee: F. Nissen, J. M. Fink, J. Mlynek, A. Wallraff, and J. Keeling, “Collective
suppression of linewidths in circuit QED,” Physical Review Letters, vol.
110, no. 20. American Physical Society, 2013.
ista: Nissen F, Fink JM, Mlynek J, Wallraff A, Keeling J. 2013. Collective suppression
of linewidths in circuit QED. Physical Review Letters. 110(20).
mla: Nissen, Felix, et al. “Collective Suppression of Linewidths in Circuit QED.”
Physical Review Letters, vol. 110, no. 20, American Physical Society, 2013,
doi:10.1103/PhysRevLett.110.203602.
short: F. Nissen, J.M. Fink, J. Mlynek, A. Wallraff, J. Keeling, Physical Review
Letters 110 (2013).
date_created: 2018-12-11T11:54:00Z
date_published: 2013-05-15T00:00:00Z
date_updated: 2021-01-12T06:53:11Z
day: '15'
doi: 10.1103/PhysRevLett.110.203602
extern: 1
intvolume: ' 110'
issue: '20'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1302.0665
month: '05'
oa: 1
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5328'
quality_controlled: 0
status: public
title: Collective suppression of linewidths in circuit QED
type: journal_article
volume: 110
year: '2013'
...
---
_id: '1787'
abstract:
- lang: eng
text: When two indistinguishable single photons impinge at the two inputs of a beam
splitter they coalesce into a pair of photons appearing in either one of its two
outputs. This effect is due to the bosonic nature of photons and was first experimentally
observed by Hong, Ou and Mandel. Here, we present the observation of the Hong-Ou-Mandel
effect with two independent single-photon sources in the microwave frequency domain.
We probe the indistinguishability of single photons, created with a controllable
delay, in time-resolved second-order cross- and auto-correlation function measurements.
Using quadrature amplitude detection we are able to resolve different photon numbers
and detect coherence in and between the output arms. This scheme allows us to
fully characterize the two-mode entanglement of the spatially separated beam-splitter
output modes. Our experiments constitute a first step towards using two-photon
interference at microwave frequencies for quantum communication and information
processing.
acknowledgement: This work was supported by the European Research Council (ERC) through
a Starting Grant and by ETHZ. L.S. was supported by EU IP SOLID. A.B. and M.J.W.
were supported by NSERC, CIFAR and the Alfred P. Sloan Foundation
author:
- first_name: C
full_name: Lang, C
last_name: Lang
- first_name: Christopher
full_name: Eichler, Christopher
last_name: Eichler
- first_name: L.
full_name: Steffen, L. Kraig
last_name: Steffen
- first_name: Johannes M
full_name: Johannes Fink
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Matthew
full_name: Woolley, Matthew J
last_name: Woolley
- first_name: Alexandre
full_name: Blais, Alexandre
last_name: Blais
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
citation:
ama: Lang C, Eichler C, Steffen L, et al. Correlations, indistinguishability and
entanglement in Hong-Ou-Mandel experiments at microwave frequencies. Nature
Physics. 2013;9(6):345-348. doi:10.1038/nphys2612
apa: Lang, C., Eichler, C., Steffen, L., Fink, J. M., Woolley, M., Blais, A., &
Wallraff, A. (2013). Correlations, indistinguishability and entanglement in Hong-Ou-Mandel
experiments at microwave frequencies. Nature Physics. Nature Publishing
Group. https://doi.org/10.1038/nphys2612
chicago: Lang, C, Christopher Eichler, L. Steffen, Johannes M Fink, Matthew Woolley,
Alexandre Blais, and Andreas Wallraff. “Correlations, Indistinguishability and
Entanglement in Hong-Ou-Mandel Experiments at Microwave Frequencies.” Nature
Physics. Nature Publishing Group, 2013. https://doi.org/10.1038/nphys2612.
ieee: C. Lang et al., “Correlations, indistinguishability and entanglement
in Hong-Ou-Mandel experiments at microwave frequencies,” Nature Physics,
vol. 9, no. 6. Nature Publishing Group, pp. 345–348, 2013.
ista: Lang C, Eichler C, Steffen L, Fink JM, Woolley M, Blais A, Wallraff A. 2013.
Correlations, indistinguishability and entanglement in Hong-Ou-Mandel experiments
at microwave frequencies. Nature Physics. 9(6), 345–348.
mla: Lang, C., et al. “Correlations, Indistinguishability and Entanglement in Hong-Ou-Mandel
Experiments at Microwave Frequencies.” Nature Physics, vol. 9, no. 6, Nature
Publishing Group, 2013, pp. 345–48, doi:10.1038/nphys2612.
short: C. Lang, C. Eichler, L. Steffen, J.M. Fink, M. Woolley, A. Blais, A. Wallraff,
Nature Physics 9 (2013) 345–348.
date_created: 2018-12-11T11:54:00Z
date_published: 2013-06-01T00:00:00Z
date_updated: 2021-01-12T06:53:11Z
day: '01'
doi: 10.1038/nphys2612
extern: 1
intvolume: ' 9'
issue: '6'
month: '06'
page: 345 - 348
publication: Nature Physics
publication_status: published
publisher: Nature Publishing Group
publist_id: '5327'
quality_controlled: 0
status: public
title: Correlations, indistinguishability and entanglement in Hong-Ou-Mandel experiments
at microwave frequencies
type: journal_article
volume: 9
year: '2013'
...
---
_id: '1790'
abstract:
- lang: eng
text: In the September 12, 2013 issue of Nature, the Epi4K Consortium (. Allen etal.,
2013) reported sequencing 264patient trios with epileptic encephalopathies. The
Consortium focused on genes exceptionally intolerant to sequence variations and
found substantial interconnections with autism and intellectual disability gene
networks.
author:
- first_name: Gaia
full_name: Gaia Novarino
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Seungtae
full_name: Baek, SeungTae
last_name: Baek
- first_name: Joseph
full_name: Gleeson, Joseph G
last_name: Gleeson
citation:
ama: 'Novarino G, Baek S, Gleeson J. The sacred disease: The puzzling genetics of
epileptic disorders. Neuron. 2013;80(1):9-11. doi:10.1016/j.neuron.2013.09.019'
apa: 'Novarino, G., Baek, S., & Gleeson, J. (2013). The sacred disease: The
puzzling genetics of epileptic disorders. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2013.09.019'
chicago: 'Novarino, Gaia, Seungtae Baek, and Joseph Gleeson. “The Sacred Disease:
The Puzzling Genetics of Epileptic Disorders.” Neuron. Elsevier, 2013.
https://doi.org/10.1016/j.neuron.2013.09.019.'
ieee: 'G. Novarino, S. Baek, and J. Gleeson, “The sacred disease: The puzzling genetics
of epileptic disorders,” Neuron, vol. 80, no. 1. Elsevier, pp. 9–11, 2013.'
ista: 'Novarino G, Baek S, Gleeson J. 2013. The sacred disease: The puzzling genetics
of epileptic disorders. Neuron. 80(1), 9–11.'
mla: 'Novarino, Gaia, et al. “The Sacred Disease: The Puzzling Genetics of Epileptic
Disorders.” Neuron, vol. 80, no. 1, Elsevier, 2013, pp. 9–11, doi:10.1016/j.neuron.2013.09.019.'
short: G. Novarino, S. Baek, J. Gleeson, Neuron 80 (2013) 9–11.
date_created: 2018-12-11T11:54:01Z
date_published: 2013-10-02T00:00:00Z
date_updated: 2021-01-12T06:53:13Z
day: '02'
doi: 10.1016/j.neuron.2013.09.019
extern: 1
intvolume: ' 80'
issue: '1'
month: '10'
page: 9 - 11
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '5323'
quality_controlled: 0
status: public
title: 'The sacred disease: The puzzling genetics of epileptic disorders'
type: journal_article
volume: 80
year: '2013'
...
---
_id: '1977'
abstract:
- lang: eng
text: Complex I (NADH:ubiquinone oxidoreductase) is central to cellular energy production,
being the first and largest enzyme of the respiratory chain in mitochondria. It
couples electron transfer from NADH to ubiquinone with proton translocation across
the inner mitochondrial membrane and is involved in a wide range of human neurodegenerative
disorders. Mammalian complex I is composed of 44 different subunits, whereas the
'minimal' bacterial version contains 14 highly conserved 'core' subunits. The
L-shaped assembly consists of hydrophilic and membrane domains. We have determined
all known atomic structures of complex I, starting from the hydrophilic domain
of Thermus thermophilus enzyme (eight subunits, nine Fe-S clusters), followed
by the membrane domains of the Escherichia coli (six subunits, 55 transmembrane
helices) and T. thermophilus (seven subunits, 64 transmembrane helices) enzymes,
and finally culminating in a recent crystal structure of the entire intact complex
I from T. thermophilus (536 kDa, 16 subunits, nine Fe-S clusters, 64 transmembrane
helices). The structure suggests an unusual and unique coupling mechanism via
longrange conformational changes. Determination of the structure of the entire
complex was possible only through this step-by-step approach, building on from
smaller subcomplexes towards the entire assembly. Large membrane proteins are
notoriously difficult to crystallize, and so various non-standard and sometimes
counterintuitive approaches were employed in order to achieve crystal diffraction
to high resolution and solve the structures. These steps, as well as the implications
from the final structure, are discussed in the present review.
acknowledgement: This work was funded by the Medical Research Council.
author:
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
- first_name: Rozbeh
full_name: 'Baradaran, Rozbeh '
last_name: Baradaran
- first_name: Rouslan
full_name: Efremov, Rouslan G
last_name: Efremov
- first_name: John
full_name: Berrisford, John M
last_name: Berrisford
- first_name: Gurdeep
full_name: Minhas, Gurdeep S
last_name: Minhas
citation:
ama: Sazanov LA, Baradaran R, Efremov R, Berrisford J, Minhas G. A long road towards
the structure of respiratory complex I, a giant molecular proton pump. Biochemical
Society Transactions. 2013;41(5):1265-1271. doi:10.1042/BST20130193
apa: Sazanov, L. A., Baradaran, R., Efremov, R., Berrisford, J., & Minhas, G.
(2013). A long road towards the structure of respiratory complex I, a giant molecular
proton pump. Biochemical Society Transactions. Portland Press. https://doi.org/10.1042/BST20130193
chicago: Sazanov, Leonid A, Rozbeh Baradaran, Rouslan Efremov, John Berrisford,
and Gurdeep Minhas. “A Long Road towards the Structure of Respiratory Complex
I, a Giant Molecular Proton Pump.” Biochemical Society Transactions. Portland
Press, 2013. https://doi.org/10.1042/BST20130193.
ieee: L. A. Sazanov, R. Baradaran, R. Efremov, J. Berrisford, and G. Minhas, “A
long road towards the structure of respiratory complex I, a giant molecular proton
pump,” Biochemical Society Transactions, vol. 41, no. 5. Portland Press,
pp. 1265–1271, 2013.
ista: Sazanov LA, Baradaran R, Efremov R, Berrisford J, Minhas G. 2013. A long road
towards the structure of respiratory complex I, a giant molecular proton pump.
Biochemical Society Transactions. 41(5), 1265–1271.
mla: Sazanov, Leonid A., et al. “A Long Road towards the Structure of Respiratory
Complex I, a Giant Molecular Proton Pump.” Biochemical Society Transactions,
vol. 41, no. 5, Portland Press, 2013, pp. 1265–71, doi:10.1042/BST20130193.
short: L.A. Sazanov, R. Baradaran, R. Efremov, J. Berrisford, G. Minhas, Biochemical
Society Transactions 41 (2013) 1265–1271.
date_created: 2018-12-11T11:55:00Z
date_published: 2013-10-01T00:00:00Z
date_updated: 2021-01-12T06:54:28Z
day: '01'
doi: 10.1042/BST20130193
extern: 1
intvolume: ' 41'
issue: '5'
month: '10'
page: 1265 - 1271
publication: Biochemical Society Transactions
publication_status: published
publisher: Portland Press
publist_id: '5106'
quality_controlled: 0
status: public
title: A long road towards the structure of respiratory complex I, a giant molecular
proton pump
type: journal_article
volume: 41
year: '2013'
...