---
_id: '7746'
abstract:
- lang: eng
text: Clutch size and egg mass are life history traits that have been extensively
studied in wild bird populations, as life history theory predicts a negative trade‐off
between them, either at the phenotypic or at the genetic level. Here, we analyse
the genomic architecture of these heritable traits in a wild great tit (Parus
major) population, using three marker‐based approaches – chromosome partitioning,
quantitative trait locus (QTL) mapping and a genome‐wide association study (GWAS).
The variance explained by each great tit chromosome scales with predicted chromosome
size, no location in the genome contains genome‐wide significant QTL, and no individual
SNPs are associated with a large proportion of phenotypic variation, all of which
may suggest that variation in both traits is due to many loci of small effect,
located across the genome. There is no evidence that any regions of the genome
contribute significantly to both traits, which combined with a small, nonsignificant
negative genetic covariance between the traits, suggests the absence of genetic
constraints on the independent evolution of these traits. Our findings support
the hypothesis that variation in life history traits in natural populations is
likely to be determined by many loci of small effect spread throughout the genome,
which are subject to continued input of variation by mutation and migration, although
we cannot exclude the possibility of an additional input of major effect genes
influencing either trait.
article_processing_charge: No
article_type: original
author:
- first_name: Anna W.
full_name: Santure, Anna W.
last_name: Santure
- first_name: Isabelle
full_name: De Cauwer, Isabelle
last_name: De Cauwer
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Jocelyn
full_name: Poissant, Jocelyn
last_name: Poissant
- first_name: Ben C.
full_name: Sheldon, Ben C.
last_name: Sheldon
- first_name: Jon
full_name: Slate, Jon
last_name: Slate
citation:
ama: Santure AW, De Cauwer I, Robinson MR, Poissant J, Sheldon BC, Slate J. Genomic
dissection of variation in clutch size and egg mass in a wild great tit (Parus
major) population. Molecular Ecology. 2013;22(15):3949-3962. doi:10.1111/mec.12376
apa: Santure, A. W., De Cauwer, I., Robinson, M. R., Poissant, J., Sheldon, B. C.,
& Slate, J. (2013). Genomic dissection of variation in clutch size and egg
mass in a wild great tit (Parus major) population. Molecular Ecology. Wiley.
https://doi.org/10.1111/mec.12376
chicago: Santure, Anna W., Isabelle De Cauwer, Matthew Richard Robinson, Jocelyn
Poissant, Ben C. Sheldon, and Jon Slate. “Genomic Dissection of Variation in Clutch
Size and Egg Mass in a Wild Great Tit (Parus Major) Population.” Molecular
Ecology. Wiley, 2013. https://doi.org/10.1111/mec.12376.
ieee: A. W. Santure, I. De Cauwer, M. R. Robinson, J. Poissant, B. C. Sheldon, and
J. Slate, “Genomic dissection of variation in clutch size and egg mass in a wild
great tit (Parus major) population,” Molecular Ecology, vol. 22, no. 15.
Wiley, pp. 3949–3962, 2013.
ista: Santure AW, De Cauwer I, Robinson MR, Poissant J, Sheldon BC, Slate J. 2013.
Genomic dissection of variation in clutch size and egg mass in a wild great tit
(Parus major) population. Molecular Ecology. 22(15), 3949–3962.
mla: Santure, Anna W., et al. “Genomic Dissection of Variation in Clutch Size and
Egg Mass in a Wild Great Tit (Parus Major) Population.” Molecular Ecology,
vol. 22, no. 15, Wiley, 2013, pp. 3949–62, doi:10.1111/mec.12376.
short: A.W. Santure, I. De Cauwer, M.R. Robinson, J. Poissant, B.C. Sheldon, J.
Slate, Molecular Ecology 22 (2013) 3949–3962.
date_created: 2020-04-30T11:00:32Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T08:15:14Z
day: '01'
doi: 10.1111/mec.12376
extern: '1'
intvolume: ' 22'
issue: '15'
language:
- iso: eng
month: '08'
oa_version: None
page: 3949-3962
publication: Molecular Ecology
publication_identifier:
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Genomic dissection of variation in clutch size and egg mass in a wild great
tit (Parus major) population
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2013'
...
---
_id: '7747'
abstract:
- lang: eng
text: Acquisition and allocation of resources are central to life‐history theory.
However, empirical work typically focuses only on allocation despite the fact
that relationships between fitness components may be governed by differences in
the ability of individuals to acquire resources across environments. Here, we
outline a statistical framework to partition the genetic basis of multivariate
plasticity into independent axes of genetic variation, and quantify for the first
time, the extent to which specific traits drive multitrait genotype–environment
interactions. Our framework generalises to analyses of plasticity, growth and
ageing. We apply this approach to a unique, large‐scale, multivariate study of
acquisition, allocation and plasticity in the life history of the cricket, Gryllus
firmus. We demonstrate that resource acquisition and allocation are genetically
correlated, and that plasticity in trade‐offs between allocation to components
of fitness is 90% dependent on genetic variance for total resource acquisition.
These results suggest that genotype–environment effects for resource acquisition
can maintain variation in life‐history components that are typically observed
in the wild.
article_processing_charge: No
article_type: original
author:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Andrew P.
full_name: Beckerman, Andrew P.
last_name: Beckerman
citation:
ama: 'Robinson MR, Beckerman AP. Quantifying multivariate plasticity: Genetic variation
in resource acquisition drives plasticity in resource allocation to components
of life history. Ecology Letters. 2013;16(3):281-290. doi:10.1111/ele.12047'
apa: 'Robinson, M. R., & Beckerman, A. P. (2013). Quantifying multivariate plasticity:
Genetic variation in resource acquisition drives plasticity in resource allocation
to components of life history. Ecology Letters. Wiley. https://doi.org/10.1111/ele.12047'
chicago: 'Robinson, Matthew Richard, and Andrew P. Beckerman. “Quantifying Multivariate
Plasticity: Genetic Variation in Resource Acquisition Drives Plasticity in Resource
Allocation to Components of Life History.” Ecology Letters. Wiley, 2013.
https://doi.org/10.1111/ele.12047.'
ieee: 'M. R. Robinson and A. P. Beckerman, “Quantifying multivariate plasticity:
Genetic variation in resource acquisition drives plasticity in resource allocation
to components of life history,” Ecology Letters, vol. 16, no. 3. Wiley,
pp. 281–290, 2013.'
ista: 'Robinson MR, Beckerman AP. 2013. Quantifying multivariate plasticity: Genetic
variation in resource acquisition drives plasticity in resource allocation to
components of life history. Ecology Letters. 16(3), 281–290.'
mla: 'Robinson, Matthew Richard, and Andrew P. Beckerman. “Quantifying Multivariate
Plasticity: Genetic Variation in Resource Acquisition Drives Plasticity in Resource
Allocation to Components of Life History.” Ecology Letters, vol. 16, no.
3, Wiley, 2013, pp. 281–90, doi:10.1111/ele.12047.'
short: M.R. Robinson, A.P. Beckerman, Ecology Letters 16 (2013) 281–290.
date_created: 2020-04-30T11:00:49Z
date_published: 2013-03-01T00:00:00Z
date_updated: 2021-01-12T08:15:15Z
day: '01'
doi: 10.1111/ele.12047
extern: '1'
intvolume: ' 16'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 281-290
publication: Ecology Letters
publication_identifier:
issn:
- 1461-023X
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: 'Quantifying multivariate plasticity: Genetic variation in resource acquisition
drives plasticity in resource allocation to components of life history'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2013'
...
---
_id: '7774'
abstract:
- lang: eng
text: In 2005, Wyart et al. [Europhys. Lett., 2005, 72, 486] showed that the low
frequency vibrational properties of jammed amorphous sphere packings can be understood
in terms of a length scale, called l*, that diverges as the system becomes marginally
unstable. Despite the tremendous success of this theory, it has been difficult
to connect the counting argument that defines l* to other length scales that diverge
near the jamming transition. We present an alternate derivation of l* based on
the onset of rigidity. This phenomenological approach reveals the physical mechanism
underlying the length scale and is relevant to a range of systems for which the
original argument breaks down. It also allows us to present the first direct numerical
measurement of l*.
article_number: '10993'
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Wouter G.
full_name: Ellenbroek, Wouter G.
last_name: Ellenbroek
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
citation:
ama: 'Goodrich CP, Ellenbroek WG, Liu AJ. Stability of jammed packings I: The rigidity
length scale. Soft Matter. 2013;9(46). doi:10.1039/c3sm51095f'
apa: 'Goodrich, C. P., Ellenbroek, W. G., & Liu, A. J. (2013). Stability of
jammed packings I: The rigidity length scale. Soft Matter. Royal Society
of Chemistry. https://doi.org/10.1039/c3sm51095f'
chicago: 'Goodrich, Carl Peter, Wouter G. Ellenbroek, and Andrea J. Liu. “Stability
of Jammed Packings I: The Rigidity Length Scale.” Soft Matter. Royal Society
of Chemistry, 2013. https://doi.org/10.1039/c3sm51095f.'
ieee: 'C. P. Goodrich, W. G. Ellenbroek, and A. J. Liu, “Stability of jammed packings
I: The rigidity length scale,” Soft Matter, vol. 9, no. 46. Royal Society
of Chemistry, 2013.'
ista: 'Goodrich CP, Ellenbroek WG, Liu AJ. 2013. Stability of jammed packings I:
The rigidity length scale. Soft Matter. 9(46), 10993.'
mla: 'Goodrich, Carl Peter, et al. “Stability of Jammed Packings I: The Rigidity
Length Scale.” Soft Matter, vol. 9, no. 46, 10993, Royal Society of Chemistry,
2013, doi:10.1039/c3sm51095f.'
short: C.P. Goodrich, W.G. Ellenbroek, A.J. Liu, Soft Matter 9 (2013).
date_created: 2020-04-30T11:43:42Z
date_published: 2013-10-08T00:00:00Z
date_updated: 2021-01-12T08:15:27Z
day: '08'
doi: 10.1039/c3sm51095f
extern: '1'
intvolume: ' 9'
issue: '46'
language:
- iso: eng
month: '10'
oa_version: None
publication: Soft Matter
publication_identifier:
issn:
- 1744-683X
- 1744-6848
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
status: public
title: 'Stability of jammed packings I: The rigidity length scale'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2013'
...
---
_id: '7775'
abstract:
- lang: eng
text: As a function of packing fraction at zero temperature and applied stress,
an amorphous packing of spheres exhibits a jamming transition where the system
is sensitive to boundary conditions even in the thermodynamic limit. Upon further
compression, the system should become insensitive to boundary conditions provided
it is sufficiently large. Here we explore the linear response to a large class
of boundary perturbations in 2 and 3 dimensions. We consider each finite packing
with periodic-boundary conditions as the basis of an infinite square or cubic
lattice and study properties of vibrational modes at arbitrary wave vector. We
find that the stability of such modes can be understood in terms of a competition
between plane waves and the anomalous vibrational modes associated with the jamming
transition; infinitesimal boundary perturbations become irrelevant for systems
that are larger than a length scale that characterizes the transverse excitations.
This previously identified length diverges at the jamming transition.
article_number: '11000'
article_processing_charge: No
article_type: original
author:
- first_name: Samuel S.
full_name: Schoenholz, Samuel S.
last_name: Schoenholz
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Oleg
full_name: Kogan, Oleg
last_name: Kogan
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: 'Schoenholz SS, Goodrich CP, Kogan O, Liu AJ, Nagel SR. Stability of jammed
packings II: The transverse length scale. Soft Matter. 2013;9(46). doi:10.1039/c3sm51096d'
apa: 'Schoenholz, S. S., Goodrich, C. P., Kogan, O., Liu, A. J., & Nagel, S.
R. (2013). Stability of jammed packings II: The transverse length scale. Soft
Matter. Royal Society of Chemistry. https://doi.org/10.1039/c3sm51096d'
chicago: 'Schoenholz, Samuel S., Carl Peter Goodrich, Oleg Kogan, Andrea J. Liu,
and Sidney R. Nagel. “Stability of Jammed Packings II: The Transverse Length Scale.”
Soft Matter. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3sm51096d.'
ieee: 'S. S. Schoenholz, C. P. Goodrich, O. Kogan, A. J. Liu, and S. R. Nagel, “Stability
of jammed packings II: The transverse length scale,” Soft Matter, vol.
9, no. 46. Royal Society of Chemistry, 2013.'
ista: 'Schoenholz SS, Goodrich CP, Kogan O, Liu AJ, Nagel SR. 2013. Stability of
jammed packings II: The transverse length scale. Soft Matter. 9(46), 11000.'
mla: 'Schoenholz, Samuel S., et al. “Stability of Jammed Packings II: The Transverse
Length Scale.” Soft Matter, vol. 9, no. 46, 11000, Royal Society of Chemistry,
2013, doi:10.1039/c3sm51096d.'
short: S.S. Schoenholz, C.P. Goodrich, O. Kogan, A.J. Liu, S.R. Nagel, Soft Matter
9 (2013).
date_created: 2020-04-30T11:43:58Z
date_published: 2013-10-08T00:00:00Z
date_updated: 2021-01-12T08:15:27Z
day: '08'
doi: 10.1039/c3sm51096d
extern: '1'
intvolume: ' 9'
issue: '46'
language:
- iso: eng
month: '10'
oa_version: None
publication: Soft Matter
publication_identifier:
issn:
- 1744-683X
- 1744-6848
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
status: public
title: 'Stability of jammed packings II: The transverse length scale'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2013'
...
---
_id: '7785'
abstract:
- lang: eng
text: Neural circuit assembly requires selection of specific cell fates, axonal
trajectories, and synaptic targets. By analyzing the function of a secreted semaphorin,
Sema-2b, in Drosophila olfactory receptor neuron (ORN) development, we identified
multiple molecular and cellular mechanisms that link these events. Notch signaling
limits Sema-2b expression to ventromedial ORN classes, within which Sema-2b cell-autonomously
sensitizes ORN axons to external semaphorins. Central-brain-derived Sema-2a and
Sema-2b attract Sema-2b-expressing axons to the ventromedial trajectory. In addition,
Sema-2b/PlexB-mediated axon-axon interactions consolidate this trajectory choice
and promote ventromedial axon-bundle formation. Selecting the correct developmental
trajectory is ultimately essential for proper target choice. These findings demonstrate
that Sema-2b couples ORN axon guidance to postsynaptic target neuron dendrite
patterning well before the final target selection phase, and exemplify how a single
guidance molecule can drive consecutive stages of neural circuit assembly with
the help of sophisticated spatial and temporal regulation.
article_processing_charge: No
article_type: original
author:
- first_name: William J.
full_name: Joo, William J.
last_name: Joo
- first_name: Lora Beatrice Jaeger
full_name: Sweeney, Lora Beatrice Jaeger
id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
last_name: Sweeney
orcid: 0000-0001-9242-5601
- first_name: Liang
full_name: Liang, Liang
last_name: Liang
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
citation:
ama: 'Joo WJ, Sweeney LB, Liang L, Luo L. Linking cell fate, trajectory choice,
and target selection: Genetic analysis of sema-2b in olfactory axon targeting.
Neuron. 2013;78(4):673-686. doi:10.1016/j.neuron.2013.03.022'
apa: 'Joo, W. J., Sweeney, L. B., Liang, L., & Luo, L. (2013). Linking cell
fate, trajectory choice, and target selection: Genetic analysis of sema-2b in
olfactory axon targeting. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2013.03.022'
chicago: 'Joo, William J., Lora B. Sweeney, Liang Liang, and Liqun Luo. “Linking
Cell Fate, Trajectory Choice, and Target Selection: Genetic Analysis of Sema-2b
in Olfactory Axon Targeting.” Neuron. Elsevier, 2013. https://doi.org/10.1016/j.neuron.2013.03.022.'
ieee: 'W. J. Joo, L. B. Sweeney, L. Liang, and L. Luo, “Linking cell fate, trajectory
choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting,”
Neuron, vol. 78, no. 4. Elsevier, pp. 673–686, 2013.'
ista: 'Joo WJ, Sweeney LB, Liang L, Luo L. 2013. Linking cell fate, trajectory choice,
and target selection: Genetic analysis of sema-2b in olfactory axon targeting.
Neuron. 78(4), 673–686.'
mla: 'Joo, William J., et al. “Linking Cell Fate, Trajectory Choice, and Target
Selection: Genetic Analysis of Sema-2b in Olfactory Axon Targeting.” Neuron,
vol. 78, no. 4, Elsevier, 2013, pp. 673–86, doi:10.1016/j.neuron.2013.03.022.'
short: W.J. Joo, L.B. Sweeney, L. Liang, L. Luo, Neuron 78 (2013) 673–686.
date_created: 2020-04-30T13:19:59Z
date_published: 2013-05-22T00:00:00Z
date_updated: 2024-01-31T10:15:25Z
day: '22'
doi: 10.1016/j.neuron.2013.03.022
extern: '1'
intvolume: ' 78'
issue: '4'
language:
- iso: eng
month: '05'
oa_version: None
page: 673-686
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Linking cell fate, trajectory choice, and target selection: Genetic analysis
of sema-2b in olfactory axon targeting'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 78
year: '2013'
...
---
_id: '8030'
abstract:
- lang: eng
text: While the plasticity of excitatory synaptic connections in the brain has been
widely studied, the plasticity of inhibitory connections is much less understood.
Here, we present recent experimental and theoretical findings concerning the rules
of spike timing-dependent inhibitory plasticity and their putative network function.
This is a summary of a workshop at the COSYNE conference 2012.
article_number: '119'
article_processing_charge: No
article_type: original
author:
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: R. C.
full_name: Froemke, R. C.
last_name: Froemke
- first_name: N.
full_name: Doyon, N.
last_name: Doyon
- first_name: M.
full_name: Gilson, M.
last_name: Gilson
- first_name: J. S.
full_name: Haas, J. S.
last_name: Haas
- first_name: R.
full_name: Liu, R.
last_name: Liu
- first_name: A.
full_name: Maffei, A.
last_name: Maffei
- first_name: P.
full_name: Miller, P.
last_name: Miller
- first_name: C. J.
full_name: Wierenga, C. J.
last_name: Wierenga
- first_name: M. A.
full_name: Woodin, M. A.
last_name: Woodin
- first_name: F.
full_name: Zenke, F.
last_name: Zenke
- first_name: H.
full_name: Sprekeler, H.
last_name: Sprekeler
citation:
ama: 'Vogels TP, Froemke RC, Doyon N, et al. Inhibitory synaptic plasticity: Spike
timing-dependence and putative network function. Frontiers in Neural Circuits.
2013;7. doi:10.3389/fncir.2013.00119'
apa: 'Vogels, T. P., Froemke, R. C., Doyon, N., Gilson, M., Haas, J. S., Liu, R.,
… Sprekeler, H. (2013). Inhibitory synaptic plasticity: Spike timing-dependence
and putative network function. Frontiers in Neural Circuits. Frontiers
Media. https://doi.org/10.3389/fncir.2013.00119'
chicago: 'Vogels, Tim P, R. C. Froemke, N. Doyon, M. Gilson, J. S. Haas, R. Liu,
A. Maffei, et al. “Inhibitory Synaptic Plasticity: Spike Timing-Dependence and
Putative Network Function.” Frontiers in Neural Circuits. Frontiers Media,
2013. https://doi.org/10.3389/fncir.2013.00119.'
ieee: 'T. P. Vogels et al., “Inhibitory synaptic plasticity: Spike timing-dependence
and putative network function,” Frontiers in Neural Circuits, vol. 7. Frontiers
Media, 2013.'
ista: 'Vogels TP, Froemke RC, Doyon N, Gilson M, Haas JS, Liu R, Maffei A, Miller
P, Wierenga CJ, Woodin MA, Zenke F, Sprekeler H. 2013. Inhibitory synaptic plasticity:
Spike timing-dependence and putative network function. Frontiers in Neural Circuits.
7, 119.'
mla: 'Vogels, Tim P., et al. “Inhibitory Synaptic Plasticity: Spike Timing-Dependence
and Putative Network Function.” Frontiers in Neural Circuits, vol. 7, 119,
Frontiers Media, 2013, doi:10.3389/fncir.2013.00119.'
short: T.P. Vogels, R.C. Froemke, N. Doyon, M. Gilson, J.S. Haas, R. Liu, A. Maffei,
P. Miller, C.J. Wierenga, M.A. Woodin, F. Zenke, H. Sprekeler, Frontiers in Neural
Circuits 7 (2013).
date_created: 2020-06-25T13:23:50Z
date_published: 2013-07-18T00:00:00Z
date_updated: 2021-01-12T08:16:38Z
day: '18'
ddc:
- '570'
doi: 10.3389/fncir.2013.00119
extern: '1'
external_id:
pmid:
- '23882186'
file:
- access_level: open_access
checksum: 9c321cb12977d84048712eefa7f0c497
content_type: application/pdf
creator: cziletti
date_created: 2020-07-16T11:23:40Z
date_updated: 2020-07-16T11:23:40Z
file_id: '8123'
file_name: 2013_FrontNeurCirc_Vogels.pdf
file_size: 1530469
relation: main_file
success: 1
file_date_updated: 2020-07-16T11:23:40Z
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Neural Circuits
publication_identifier:
eissn:
- 1662-5110
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
status: public
title: 'Inhibitory synaptic plasticity: Spike timing-dependence and putative network
function'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2013'
...
---
_id: '810'
abstract:
- lang: eng
text: Cryo-electron tomography combined with image processing by sub-tomogram averaging
is unique in its power to resolve the structures of proteins and macromolecular
complexes in situ. Limitations of the method, including the low signal to noise
ratio within individual images from cryo-tomographic datasets and difficulties
in determining the defocus at which the data was collected, mean that to date
the very best structures obtained by sub-tomogram averaging are limited to a resolution
of approximately 15. Å. Here, by optimizing data collection and defocus determination
steps, we have determined the structure of assembled Mason-Pfizer monkey virus
Gag protein using sub-tomogram averaging to a resolution of 8.5. Å. At this resolution
alpha-helices can be directly and clearly visualized. These data demonstrate for
the first time that high-resolution structural information can be obtained from
cryo-electron tomograms using sub-tomogram averaging. Sub-tomogram averaging has
the potential to allow detailed studies of unsolved and biologically relevant
structures under biologically relevant conditions.
acknowledgement: The M-PMV ΔPro CANC tubes imaged in this study were a kind gift from
Pavel Ulbrich and Tomas Ruml, Institute of Chemical Technology, Prague. The cryo-EM
grids were prepared by Tanmay Bharat. This study was technically supported by EMBL’s
IT services unit and by Frank Thommen. We thank Martin Schorb and Svetlana Dodonova
for discussions and advice; Khanh Huy Bui for advice and scripts to streamline tomogram
reconstruction; and Giulia Zanetti, Tanmay Bharat, and Martin Beck for comments
on the manuscript. This study was supported by Deutsche Forschungsgemeinschaft grant
BR 3635/2-1 to JAGB.
author:
- first_name: Florian
full_name: Florian Schur
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Wim
full_name: Hagen, Wim J
last_name: Hagen
- first_name: Alex
full_name: De Marco, Alex
last_name: De Marco
- first_name: John
full_name: Briggs, John A
last_name: Briggs
citation:
ama: Schur FK, Hagen W, De Marco A, Briggs J. Determination of protein structure
at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging.
Journal of Structural Biology. 2013;184(3):394-400. doi:10.1016/j.jsb.2013.10.015
apa: Schur, F. K., Hagen, W., De Marco, A., & Briggs, J. (2013). Determination
of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram
averaging. Journal of Structural Biology. Academic Press. https://doi.org/10.1016/j.jsb.2013.10.015
chicago: Schur, Florian KM, Wim Hagen, Alex De Marco, and John Briggs. “Determination
of Protein Structure at 8.5Å Resolution Using Cryo-Electron Tomography and Sub-Tomogram
Averaging.” Journal of Structural Biology. Academic Press, 2013. https://doi.org/10.1016/j.jsb.2013.10.015.
ieee: F. K. Schur, W. Hagen, A. De Marco, and J. Briggs, “Determination of protein
structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging,”
Journal of Structural Biology, vol. 184, no. 3. Academic Press, pp. 394–400,
2013.
ista: Schur FK, Hagen W, De Marco A, Briggs J. 2013. Determination of protein structure
at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging.
Journal of Structural Biology. 184(3), 394–400.
mla: Schur, Florian KM, et al. “Determination of Protein Structure at 8.5Å Resolution
Using Cryo-Electron Tomography and Sub-Tomogram Averaging.” Journal of Structural
Biology, vol. 184, no. 3, Academic Press, 2013, pp. 394–400, doi:10.1016/j.jsb.2013.10.015.
short: F.K. Schur, W. Hagen, A. De Marco, J. Briggs, Journal of Structural Biology
184 (2013) 394–400.
date_created: 2018-12-11T11:48:37Z
date_published: 2013-12-01T00:00:00Z
date_updated: 2021-01-12T08:16:54Z
day: '01'
doi: 10.1016/j.jsb.2013.10.015
extern: 1
intvolume: ' 184'
issue: '3'
month: '12'
page: 394 - 400
publication: Journal of Structural Biology
publication_status: published
publisher: Academic Press
publist_id: '6839'
quality_controlled: 0
status: public
title: Determination of protein structure at 8.5Å resolution using cryo-electron tomography
and sub-tomogram averaging
type: journal_article
volume: 184
year: '2013'
...
---
_id: '811'
abstract:
- lang: eng
text: Cell migration is commonly accompanied by protrusion of membrane ruffles and
lamellipodia. In two-dimensional migration, protrusion of these thin sheets of
cytoplasm is considered relevant to both exploration of new space and initiation
of nascent adhesion to the substratum. Lamellipodium formation can be potently
stimulated by Rho GTPases of the Rac subfamily, but alsoby RhoG or Cdc42. Here
we describe viable fibroblast cell lines geneticallydeficient for Rac1 that lack
detectable levels of Rac2 and Rac3. Rac-deficient cells were devoid of apparent
lamellipodia, but these structures were restored by expression of either Rac subfamily
member, but not by Cdc42 or RhoG. Cells deficient in Rac showed strong reduction
in wound closure and random cell migration and a notable loss of sensitivity to
a chemotactic gradient. Despite these defects, Rac-deficient cells were able to
spread, formed filopodia and established focal adhesions. Spreading in these cells
was achieved by the extension of filopodia followed by the advancement of cytoplasmic
veils between them. The number and size of focal adhesions as well as their intensity
were largely unaffected by genetic removal of Rac1. However, Rac deficiency increased
the mobility of different components in focal adhesions, potentially explaining
how Rac - although not essential - can contribute to focal adhesion assembly.
Together, our data demonstrate that Rac signaling is essential for lamellipodium
protrusion and for efficient cell migration, but not for spreading or filopodium
formation. Our findings also suggest that Rac GTPases are crucial to the establishment
or maintenance of polarity in chemotactic migration.
acknowledgement: |-
This work was supported in part by the Deutsche Forschungsgemeinschaft [grants within programs SFB621 to K.R., and FOR629 and SFB629 to T.E.B.S.]. Deposited in PMC for immediate release.
We thank Brigitte Denker and Gerd Landsberg for excellent technical assistance. We are grateful to Robert Geffers (HZI Braunschweig, Germany) for microarray analyses and to Mirko Himmel (UKE Hamburg, Germany) for valuable advice on FRAP analysis.
author:
- first_name: Anika
full_name: Steffen, Anika
last_name: Steffen
- first_name: Markus
full_name: Ladwein, Markus
last_name: Ladwein
- first_name: Georgi A
full_name: Georgi Dimchev
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
- first_name: Anke
full_name: Hein, Anke
last_name: Hein
- first_name: Lisa
full_name: Schwenkmezger, Lisa
last_name: Schwenkmezger
- first_name: Stefan
full_name: Arens, Stefan
last_name: Arens
- first_name: Kathrin
full_name: Ladwein, Kathrin I
last_name: Ladwein
- first_name: J.
full_name: Holleboom, J. Margit
last_name: Holleboom
- first_name: Florian
full_name: Florian Schur
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: John
full_name: Small, John V
last_name: Small
- first_name: Janett
full_name: Schwarz, Janett
last_name: Schwarz
- first_name: Ralf
full_name: Gerhard, Ralf
last_name: Gerhard
- first_name: Jan
full_name: Faix, Jan
last_name: Faix
- first_name: Theresia
full_name: Stradal, Theresia E
last_name: Stradal
- first_name: Cord
full_name: Brakebusch, Cord H
last_name: Brakebusch
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
citation:
ama: Steffen A, Ladwein M, Dimchev GA, et al. Rac function is crucial for cell migration
but is not required for spreading and focal adhesion formation. Journal of
Cell Science. 2013;126(20):4572-4588. doi:10.1242/jcs.118232
apa: Steffen, A., Ladwein, M., Dimchev, G. A., Hein, A., Schwenkmezger, L., Arens,
S., … Rottner, K. (2013). Rac function is crucial for cell migration but is not
required for spreading and focal adhesion formation. Journal of Cell Science.
Company of Biologists. https://doi.org/10.1242/jcs.118232
chicago: Steffen, Anika, Markus Ladwein, Georgi A Dimchev, Anke Hein, Lisa Schwenkmezger,
Stefan Arens, Kathrin Ladwein, et al. “Rac Function Is Crucial for Cell Migration
but Is Not Required for Spreading and Focal Adhesion Formation.” Journal of
Cell Science. Company of Biologists, 2013. https://doi.org/10.1242/jcs.118232.
ieee: A. Steffen et al., “Rac function is crucial for cell migration but
is not required for spreading and focal adhesion formation,” Journal of Cell
Science, vol. 126, no. 20. Company of Biologists, pp. 4572–4588, 2013.
ista: Steffen A, Ladwein M, Dimchev GA, Hein A, Schwenkmezger L, Arens S, Ladwein
K, Holleboom J, Schur FK, Small J, Schwarz J, Gerhard R, Faix J, Stradal T, Brakebusch
C, Rottner K. 2013. Rac function is crucial for cell migration but is not required
for spreading and focal adhesion formation. Journal of Cell Science. 126(20),
4572–4588.
mla: Steffen, Anika, et al. “Rac Function Is Crucial for Cell Migration but Is Not
Required for Spreading and Focal Adhesion Formation.” Journal of Cell Science,
vol. 126, no. 20, Company of Biologists, 2013, pp. 4572–88, doi:10.1242/jcs.118232.
short: A. Steffen, M. Ladwein, G.A. Dimchev, A. Hein, L. Schwenkmezger, S. Arens,
K. Ladwein, J. Holleboom, F.K. Schur, J. Small, J. Schwarz, R. Gerhard, J. Faix,
T. Stradal, C. Brakebusch, K. Rottner, Journal of Cell Science 126 (2013) 4572–4588.
date_created: 2018-12-11T11:48:38Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T08:16:57Z
day: '01'
doi: 10.1242/jcs.118232
extern: 1
intvolume: ' 126'
issue: '20'
month: '01'
page: 4572 - 4588
publication: Journal of Cell Science
publication_status: published
publisher: Company of Biologists
publist_id: '6840'
quality_controlled: 0
status: public
title: Rac function is crucial for cell migration but is not required for spreading
and focal adhesion formation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 126
year: '2013'
...
---
_id: '812'
abstract:
- lang: eng
text: Lamellipodia are sheet-like protrusions formed during migration or phagocytosis
and comprise a network of actin filaments. Filament formation in this network
is initiated by nucleation/branching through the actin-related protein 2/3 (Arp2/3)
complex downstream of its activator, suppressor of cAMP receptor/WASP-family verprolin
homologous (Scar/WAVE), but the relative relevance of Arp2/3-mediated branching
versus actin filament elongation is unknown. Here we use instantaneous interference
with Arp2/3 complex function in live fibroblasts with established lamellipodia.
This allows direct examination of both the fate of elongating filaments upon instantaneous
suppression of Arp2/3 complex activity and the consequences of this treatment
on the dynamics of other lamellipodial regulators. We show that Arp2/3 complex
is an essential organizer of treadmilling actin filament arrays but has little
effect on the net rate of actin filament turnover at the cell periphery. In addition,
Arp2/3 complex serves as key upstream factor for the recruitment of modulators
of lamellipodia formation such as capping protein or cofilin. Arp2/3 complex is
thus decisive for filament organization and geometry within the network not only
by generating branches and novel filament ends, but also by directing capping
or severing activities to the lamellipodium. Arp2/3 complex is also crucial to
lamellipodia-based migration of keratocytes.
acknowledgement: "This work was supported in part by Deutsche Forschungsgemeinschaft
Grants RO2414/3-1 (to K.R.) and FA330/6-1 (to J.F.), Austrian \nScience Fund Projects
FWF 1516-B09 and FWF P21292-B09 (to J.V.S.), the Vienna Science and Technology
\ Fund (WWTF, to \nJ.V.S. and C.S.), and Australian National Health and
\ Medical \nResearch Council Grant APP1004175 (to P.W.G.). We thank J. Adams, \nR.
Chisholm, A. Hall, L. Machesky, H. G. Mannherz, D. Schafer, and \nR. Wedlich-Söldner
\ for expression constructs and B. Denker, \nP. Hagendorff, and G. Landsberg
for technical assistance."
author:
- first_name: Stefan
full_name: Koestler, Stefan A
last_name: Koestler
- first_name: Anika
full_name: Steffen, Anika
last_name: Steffen
- first_name: Maria
full_name: Maria Nemethova
id: 34E27F1C-F248-11E8-B48F-1D18A9856A87
last_name: Nemethova
- first_name: Moritz
full_name: Winterhoff, Moritz
last_name: Winterhoff
- first_name: Ningning
full_name: Luo, Ningning
last_name: Luo
- first_name: J.
full_name: Holleboom, J. Margit
last_name: Holleboom
- first_name: Jessica
full_name: Krupp, Jessica
last_name: Krupp
- first_name: Sonja
full_name: Jacob, Sonja
last_name: Jacob
- first_name: Marlene
full_name: Vinzenz, Marlene
last_name: Vinzenz
- first_name: Florian
full_name: Florian Schur
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Kai
full_name: Schlüter, Kai
last_name: Schlüter
- first_name: Peter
full_name: Gunning, Peter W
last_name: Gunning
- first_name: Christoph
full_name: Winkler, Christoph
last_name: Winkler
- first_name: Christian
full_name: Schmeiser, Christian
last_name: Schmeiser
- first_name: Jan
full_name: Faix, Jan
last_name: Faix
- first_name: Theresia
full_name: Stradal, Theresia E
last_name: Stradal
- first_name: John
full_name: Small, John V
last_name: Small
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
citation:
ama: Koestler S, Steffen A, Nemethova M, et al. Arp2/3 complex is essential for
actin network treadmilling as well as for targeting of capping protein and cofilin.
Molecular Biology of the Cell. 2013;24(18):2861-2875. doi:10.1091/mbc.E12-12-0857
apa: Koestler, S., Steffen, A., Nemethova, M., Winterhoff, M., Luo, N., Holleboom,
J., … Rottner, K. (2013). Arp2/3 complex is essential for actin network treadmilling
as well as for targeting of capping protein and cofilin. Molecular Biology
of the Cell. American Society for Biology. https://doi.org/10.1091/mbc.E12-12-0857
chicago: Koestler, Stefan, Anika Steffen, Maria Nemethova, Moritz Winterhoff, Ningning
Luo, J. Holleboom, Jessica Krupp, et al. “Arp2/3 Complex Is Essential for Actin
Network Treadmilling as Well as for Targeting of Capping Protein and Cofilin.”
Molecular Biology of the Cell. American Society for Biology, 2013. https://doi.org/10.1091/mbc.E12-12-0857.
ieee: S. Koestler et al., “Arp2/3 complex is essential for actin network
treadmilling as well as for targeting of capping protein and cofilin,” Molecular
Biology of the Cell, vol. 24, no. 18. American Society for Biology, pp. 2861–2875,
2013.
ista: Koestler S, Steffen A, Nemethova M, Winterhoff M, Luo N, Holleboom J, Krupp
J, Jacob S, Vinzenz M, Schur FK, Schlüter K, Gunning P, Winkler C, Schmeiser C,
Faix J, Stradal T, Small J, Rottner K. 2013. Arp2/3 complex is essential for actin
network treadmilling as well as for targeting of capping protein and cofilin.
Molecular Biology of the Cell. 24(18), 2861–2875.
mla: Koestler, Stefan, et al. “Arp2/3 Complex Is Essential for Actin Network Treadmilling
as Well as for Targeting of Capping Protein and Cofilin.” Molecular Biology
of the Cell, vol. 24, no. 18, American Society for Biology, 2013, pp. 2861–75,
doi:10.1091/mbc.E12-12-0857.
short: S. Koestler, A. Steffen, M. Nemethova, M. Winterhoff, N. Luo, J. Holleboom,
J. Krupp, S. Jacob, M. Vinzenz, F.K. Schur, K. Schlüter, P. Gunning, C. Winkler,
C. Schmeiser, J. Faix, T. Stradal, J. Small, K. Rottner, Molecular Biology of
the Cell 24 (2013) 2861–2875.
date_created: 2018-12-11T11:48:38Z
date_published: 2013-09-15T00:00:00Z
date_updated: 2021-01-12T08:17:00Z
day: '15'
doi: 10.1091/mbc.E12-12-0857
extern: 1
intvolume: ' 24'
issue: '18'
month: '09'
page: 2861 - 2875
publication: Molecular Biology of the Cell
publication_status: published
publisher: American Society for Biology
publist_id: '6841'
quality_controlled: 0
status: public
title: Arp2/3 complex is essential for actin network treadmilling as well as for targeting
of capping protein and cofilin
type: journal_article
volume: 24
year: '2013'
...
---
_id: '1726'
abstract:
- lang: eng
text: The development of a functional tissue requires coordination of the amplification
of progenitors and their differentiation into specific cell types. The molecular
basis for this coordination during myotome ontogeny is not well understood. Dermomytome
progenitors that colonize the myotome first acquire myocyte identity and subsequently
proliferate as Pax7-expressing progenitors before undergoing terminal differentiation.
We show that the dynamics of sonic hedgehog (Shh) signaling is crucial for this
transition in both avian and mouse embryos. Initially, Shh ligand emanating from
notochord/floor plate reaches the dermomyotome, where it both maintains the proliferation
of dermomyotome cells and promotes myogenic differentiation of progenitors that
colonized the myotome. Interfering with Shh signaling at this stage produces small
myotomes and accumulation of Pax7-expressing progenitors. An in vivo reporter
of Shh activity combined with mouse genetics revealed the existence of both activator
and repressor Shh activities operating on distinct subsets of cells during the
epaxial myotomal maturation. In contrast to observations in mice, in avians Shh
promotes the differentiation of both epaxial and hypaxial myotome domains. Subsequently,
myogenic progenitors become refractory to Shh; this is likely to occur at the
level of, or upstream of, smoothened signaling. The end of responsiveness to Shh
coincides with, and is thus likely to enable, the transition into the growth phase
of the myotome.
acknowledgement: This study was supported by grants from the Israel Science Foundation
(ISF) [11/09 to C.K.]; the Association Francaise contre les Myopathies (AFM) [15642
to C.K.]; the German Research Foundation (DFG) [UN 34/27-1 to C.K.]; the UK Medical
Research Council (MRC) [U117560541 to J.B. and A.K.]; Fondation Pour la Recherche
Médicale (FRM) (post-doctoral fellowship to V.R.). Deposited in PMC for release
after 6 months
author:
- first_name: Nitza
full_name: Kahane, Nitza
last_name: Kahane
- first_name: Vanessa
full_name: Ribes, Vanessa
last_name: Ribes
- first_name: Anna
full_name: Anna Kicheva
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: James
full_name: Briscoe, James
last_name: Briscoe
- first_name: Chaya
full_name: Kalcheim, Chaya
last_name: Kalcheim
citation:
ama: Kahane N, Ribes V, Kicheva A, Briscoe J, Kalcheim C. The transition from differentiation
to growth during dermomyotome-derived myogenesis depends on temporally restricted
hedgehog signaling. Development. 2013;140(8):1740-1750. doi:10.1242/dev.092726
apa: Kahane, N., Ribes, V., Kicheva, A., Briscoe, J., & Kalcheim, C. (2013).
The transition from differentiation to growth during dermomyotome-derived myogenesis
depends on temporally restricted hedgehog signaling. Development. Company
of Biologists. https://doi.org/10.1242/dev.092726
chicago: Kahane, Nitza, Vanessa Ribes, Anna Kicheva, James Briscoe, and Chaya Kalcheim.
“The Transition from Differentiation to Growth during Dermomyotome-Derived Myogenesis
Depends on Temporally Restricted Hedgehog Signaling.” Development. Company
of Biologists, 2013. https://doi.org/10.1242/dev.092726.
ieee: N. Kahane, V. Ribes, A. Kicheva, J. Briscoe, and C. Kalcheim, “The transition
from differentiation to growth during dermomyotome-derived myogenesis depends
on temporally restricted hedgehog signaling,” Development, vol. 140, no.
8. Company of Biologists, pp. 1740–1750, 2013.
ista: Kahane N, Ribes V, Kicheva A, Briscoe J, Kalcheim C. 2013. The transition
from differentiation to growth during dermomyotome-derived myogenesis depends
on temporally restricted hedgehog signaling. Development. 140(8), 1740–1750.
mla: Kahane, Nitza, et al. “The Transition from Differentiation to Growth during
Dermomyotome-Derived Myogenesis Depends on Temporally Restricted Hedgehog Signaling.”
Development, vol. 140, no. 8, Company of Biologists, 2013, pp. 1740–50,
doi:10.1242/dev.092726.
short: N. Kahane, V. Ribes, A. Kicheva, J. Briscoe, C. Kalcheim, Development 140
(2013) 1740–1750.
date_created: 2018-12-11T11:53:41Z
date_published: 2013-04-18T00:00:00Z
date_updated: 2021-01-12T06:52:47Z
day: '18'
doi: 10.1242/dev.092726
extern: 1
intvolume: ' 140'
issue: '8'
month: '04'
page: 1740 - 1750
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '5402'
quality_controlled: 0
status: public
title: The transition from differentiation to growth during dermomyotome-derived myogenesis
depends on temporally restricted hedgehog signaling
type: journal_article
volume: 140
year: '2013'
...
---
_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'
...
---
_id: '1978'
abstract:
- lang: eng
text: Complex I is the first and largest enzyme of the respiratory chain and has
a central role in cellular energy production through the coupling of NADH:ubiquinone
electron transfer to proton translocation. It is also implicated in many common
human neurodegenerative diseases. Here, we report the first crystal structure
of the entire, intact complex I (from Thermus thermophilus) at 3.3 Å resolution.
The structure of the 536-kDa complex comprises 16 different subunits, with a total
of 64 transmembrane helices and 9 iron-sulphur clusters. The core fold of subunit
Nqo8 (ND1 in humans) is, unexpectedly, similar to a half-channel of the antiporter-like
subunits. Small subunits nearby form a linked second half-channel, which completes
the fourth proton-translocation pathway (present in addition to the channels in
three antiporter-like subunits). The quinone-binding site is unusually long, narrow
and enclosed. The quinone headgroup binds at the deep end of this chamber, near
iron-sulphur cluster N2. Notably, the chamber is linked to the fourth channel
by a 'funnel' of charged residues. The link continues over the entire membrane
domain as a flexible central axis of charged and polar residues, and probably
has a leading role in the propagation of conformational changes, aided by coupling
elements. The structure suggests that a unique, out-of-the-membrane quinone-reaction
chamber enables the redox energy to drive concerted long-range conformational
changes in the four antiporter-like domains, resulting in translocation of four
protons per cycle.
acknowledgement: This work was funded by the Medical Research Council.
author:
- first_name: Rozbeh
full_name: 'Baradaran, Rozbeh '
last_name: Baradaran
- first_name: John
full_name: Berrisford, John M
last_name: Berrisford
- first_name: Gurdeep
full_name: Minhas, Gurdeep S
last_name: Minhas
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Baradaran R, Berrisford J, Minhas G, Sazanov LA. Crystal structure of the entire
respiratory complex i. Nature. 2013;494(7438):443-448. doi:10.1038/nature11871
apa: Baradaran, R., Berrisford, J., Minhas, G., & Sazanov, L. A. (2013). Crystal
structure of the entire respiratory complex i. Nature. Nature Publishing
Group. https://doi.org/10.1038/nature11871
chicago: Baradaran, Rozbeh, John Berrisford, Gurdeep Minhas, and Leonid A Sazanov.
“Crystal Structure of the Entire Respiratory Complex I.” Nature. Nature
Publishing Group, 2013. https://doi.org/10.1038/nature11871.
ieee: R. Baradaran, J. Berrisford, G. Minhas, and L. A. Sazanov, “Crystal structure
of the entire respiratory complex i,” Nature, vol. 494, no. 7438. Nature
Publishing Group, pp. 443–448, 2013.
ista: Baradaran R, Berrisford J, Minhas G, Sazanov LA. 2013. Crystal structure of
the entire respiratory complex i. Nature. 494(7438), 443–448.
mla: Baradaran, Rozbeh, et al. “Crystal Structure of the Entire Respiratory Complex
I.” Nature, vol. 494, no. 7438, Nature Publishing Group, 2013, pp. 443–48,
doi:10.1038/nature11871.
short: R. Baradaran, J. Berrisford, G. Minhas, L.A. Sazanov, Nature 494 (2013) 443–448.
date_created: 2018-12-11T11:55:01Z
date_published: 2013-02-28T00:00:00Z
date_updated: 2021-01-12T06:54:28Z
day: '28'
doi: 10.1038/nature11871
extern: 1
intvolume: ' 494'
issue: '7438'
month: '02'
page: 443 - 448
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '5107'
quality_controlled: 0
status: public
title: Crystal structure of the entire respiratory complex i
type: journal_article
volume: 494
year: '2013'
...
---
_id: '1988'
abstract:
- lang: eng
text: The rod-shaped bacterium Escherichia coli selects the cell center as site
of division with the help of the proteins MinC, MinD, and MinE. This protein system
collectively oscillates between the two cell poles by alternately binding to the
membrane in one of the two cell halves. This dynamic behavior, which emerges from
the interaction of the ATPase MinD and its activator MinE on the cell membrane,
has become a paradigm for protein self-organization. Recently, it has been found
that not only the binding of MinD to the membrane, but also interactions of MinE
with the membrane contribute to Min-protein self-organization. Here, we show that
by accounting for this finding in a computational model, we can comprehensively
describe all observed Min-protein patterns in vivo and in vitro. Furthermore,
by varying the system's geometry, our computations predict patterns that have
not yet been reported. We confirm these predictions experimentally.
author:
- first_name: Mike
full_name: 'Bonny, Mike '
last_name: Bonny
- first_name: Elisabeth
full_name: Fischer-Friedrich, Elisabeth
last_name: Fischer Friedrich
- first_name: Martin
full_name: Martin Loose
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Petra
full_name: 'Schwille, Petra '
last_name: Schwille
- first_name: Karsten
full_name: Kruse, Karsten
last_name: Kruse
citation:
ama: Bonny M, Fischer Friedrich E, Loose M, Schwille P, Kruse K. Membrane binding
of MinE allows for a comprehensive description of Min-protein pattern formation.
PLoS Computational Biology. 2013;9(12). doi:10.1371/journal.pcbi.1003347
apa: Bonny, M., Fischer Friedrich, E., Loose, M., Schwille, P., & Kruse, K.
(2013). Membrane binding of MinE allows for a comprehensive description of Min-protein
pattern formation. PLoS Computational Biology. Public Library of Science.
https://doi.org/10.1371/journal.pcbi.1003347
chicago: Bonny, Mike, Elisabeth Fischer Friedrich, Martin Loose, Petra Schwille,
and Karsten Kruse. “Membrane Binding of MinE Allows for a Comprehensive Description
of Min-Protein Pattern Formation.” PLoS Computational Biology. Public Library
of Science, 2013. https://doi.org/10.1371/journal.pcbi.1003347.
ieee: M. Bonny, E. Fischer Friedrich, M. Loose, P. Schwille, and K. Kruse, “Membrane
binding of MinE allows for a comprehensive description of Min-protein pattern
formation,” PLoS Computational Biology, vol. 9, no. 12. Public Library
of Science, 2013.
ista: Bonny M, Fischer Friedrich E, Loose M, Schwille P, Kruse K. 2013. Membrane
binding of MinE allows for a comprehensive description of Min-protein pattern
formation. PLoS Computational Biology. 9(12).
mla: Bonny, Mike, et al. “Membrane Binding of MinE Allows for a Comprehensive Description
of Min-Protein Pattern Formation.” PLoS Computational Biology, vol. 9,
no. 12, Public Library of Science, 2013, doi:10.1371/journal.pcbi.1003347.
short: M. Bonny, E. Fischer Friedrich, M. Loose, P. Schwille, K. Kruse, PLoS Computational
Biology 9 (2013).
date_created: 2018-12-11T11:55:04Z
date_published: 2013-12-01T00:00:00Z
date_updated: 2021-01-12T06:54:32Z
day: '01'
doi: 10.1371/journal.pcbi.1003347
extern: 1
intvolume: ' 9'
issue: '12'
month: '12'
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5095'
quality_controlled: 0
status: public
title: Membrane binding of MinE allows for a comprehensive description of Min-protein
pattern formation
type: journal_article
volume: 9
year: '2013'
...