---
_id: '7768'
abstract:
- lang: eng
text: We investigate the vibrational modes of quasi-two-dimensional disordered colloidal
packings of hard colloidal spheres with short-range attractions as a function
of packing fraction. Certain properties of the vibrational density of states (vDOS)
are shown to correlate with the density and structure of the samples (i.e., in
sparsely versus densely packed samples). Specifically, a crossover from dense
glassy to sparse gel-like states is suggested by an excess of phonon modes at
low frequency and by a variation in the slope of the vDOS with frequency at low
frequency. This change in phonon mode distribution is demonstrated to arise largely
from localized vibrations that involve individual and/or small clusters of particles
with few local bonds. Conventional order parameters and void statistics did not
exhibit obvious gel-glass signatures as a function of volume fraction. These mode
behaviors and accompanying structural insights offer a potentially new set of
indicators for identification of glass-gel transitions and for assignment of gel-like
versus glass-like character to a disordered solid material.
article_number: '062305'
article_processing_charge: No
article_type: original
author:
- first_name: Matthew A.
full_name: Lohr, Matthew A.
last_name: Lohr
- first_name: Tim
full_name: Still, Tim
last_name: Still
- first_name: Raman
full_name: Ganti, Raman
last_name: Ganti
- first_name: Matthew D.
full_name: Gratale, Matthew D.
last_name: Gratale
- first_name: Zoey S.
full_name: Davidson, Zoey S.
last_name: Davidson
- first_name: Kevin B.
full_name: Aptowicz, Kevin B.
last_name: Aptowicz
- 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: Daniel M.
full_name: Sussman, Daniel M.
last_name: Sussman
- first_name: A. G.
full_name: Yodh, A. G.
last_name: Yodh
citation:
ama: Lohr MA, Still T, Ganti R, et al. Vibrational and structural signatures of
the crossover between dense glassy and sparse gel-like attractive colloidal packings.
Physical Review E. 2014;90(6). doi:10.1103/physreve.90.062305
apa: Lohr, M. A., Still, T., Ganti, R., Gratale, M. D., Davidson, Z. S., Aptowicz,
K. B., … Yodh, A. G. (2014). Vibrational and structural signatures of the crossover
between dense glassy and sparse gel-like attractive colloidal packings. Physical
Review E. American Physical Society. https://doi.org/10.1103/physreve.90.062305
chicago: Lohr, Matthew A., Tim Still, Raman Ganti, Matthew D. Gratale, Zoey S. Davidson,
Kevin B. Aptowicz, Carl Peter Goodrich, Daniel M. Sussman, and A. G. Yodh. “Vibrational
and Structural Signatures of the Crossover between Dense Glassy and Sparse Gel-like
Attractive Colloidal Packings.” Physical Review E. American Physical Society,
2014. https://doi.org/10.1103/physreve.90.062305.
ieee: M. A. Lohr et al., “Vibrational and structural signatures of the crossover
between dense glassy and sparse gel-like attractive colloidal packings,” Physical
Review E, vol. 90, no. 6. American Physical Society, 2014.
ista: Lohr MA, Still T, Ganti R, Gratale MD, Davidson ZS, Aptowicz KB, Goodrich
CP, Sussman DM, Yodh AG. 2014. Vibrational and structural signatures of the crossover
between dense glassy and sparse gel-like attractive colloidal packings. Physical
Review E. 90(6), 062305.
mla: Lohr, Matthew A., et al. “Vibrational and Structural Signatures of the Crossover
between Dense Glassy and Sparse Gel-like Attractive Colloidal Packings.” Physical
Review E, vol. 90, no. 6, 062305, American Physical Society, 2014, doi:10.1103/physreve.90.062305.
short: M.A. Lohr, T. Still, R. Ganti, M.D. Gratale, Z.S. Davidson, K.B. Aptowicz,
C.P. Goodrich, D.M. Sussman, A.G. Yodh, Physical Review E 90 (2014).
date_created: 2020-04-30T11:41:54Z
date_published: 2014-12-05T00:00:00Z
date_updated: 2021-01-12T08:15:24Z
day: '05'
doi: 10.1103/physreve.90.062305
extern: '1'
intvolume: ' 90'
issue: '6'
language:
- iso: eng
month: '12'
oa_version: None
publication: Physical Review E
publication_identifier:
issn:
- 1539-3755
- 1550-2376
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Vibrational and structural signatures of the crossover between dense glassy
and sparse gel-like attractive colloidal packings
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 90
year: '2014'
...
---
_id: '7769'
abstract:
- lang: eng
text: 'Athermal packings of soft repulsive spheres exhibit a sharp jamming transition
in the thermodynamic limit. Upon further compression, various structural and mechanical
properties display clean power-law behavior over many decades in pressure. As
with any phase transition, the rounding of such behavior in finite systems close
to the transition plays an important role in understanding the nature of the transition
itself. The situation for jamming is surprisingly rich: the assumption that jammed
packings are isotropic is only strictly true in the large-size limit, and finite-size
has a profound effect on the very meaning of jamming. Here, we provide a comprehensive
numerical study of finite-size effects in sphere packings above the jamming transition,
focusing on stability as well as the scaling of the contact number and the elastic
response.'
article_number: '022138'
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: Simon
full_name: Dagois-Bohy, Simon
last_name: Dagois-Bohy
- first_name: Brian P.
full_name: Tighe, Brian P.
last_name: Tighe
- first_name: Martin
full_name: van Hecke, Martin
last_name: van Hecke
- 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: 'Goodrich CP, Dagois-Bohy S, Tighe BP, van Hecke M, Liu AJ, Nagel SR. Jamming
in finite systems: Stability, anisotropy, fluctuations, and scaling. Physical
Review E. 2014;90(2). doi:10.1103/physreve.90.022138'
apa: 'Goodrich, C. P., Dagois-Bohy, S., Tighe, B. P., van Hecke, M., Liu, A. J.,
& Nagel, S. R. (2014). Jamming in finite systems: Stability, anisotropy, fluctuations,
and scaling. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.90.022138'
chicago: 'Goodrich, Carl Peter, Simon Dagois-Bohy, Brian P. Tighe, Martin van Hecke,
Andrea J. Liu, and Sidney R. Nagel. “Jamming in Finite Systems: Stability, Anisotropy,
Fluctuations, and Scaling.” Physical Review E. American Physical Society,
2014. https://doi.org/10.1103/physreve.90.022138.'
ieee: 'C. P. Goodrich, S. Dagois-Bohy, B. P. Tighe, M. van Hecke, A. J. Liu, and
S. R. Nagel, “Jamming in finite systems: Stability, anisotropy, fluctuations,
and scaling,” Physical Review E, vol. 90, no. 2. American Physical Society,
2014.'
ista: 'Goodrich CP, Dagois-Bohy S, Tighe BP, van Hecke M, Liu AJ, Nagel SR. 2014.
Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling. Physical
Review E. 90(2), 022138.'
mla: 'Goodrich, Carl Peter, et al. “Jamming in Finite Systems: Stability, Anisotropy,
Fluctuations, and Scaling.” Physical Review E, vol. 90, no. 2, 022138,
American Physical Society, 2014, doi:10.1103/physreve.90.022138.'
short: C.P. Goodrich, S. Dagois-Bohy, B.P. Tighe, M. van Hecke, A.J. Liu, S.R. Nagel,
Physical Review E 90 (2014).
date_created: 2020-04-30T11:42:09Z
date_published: 2014-08-27T00:00:00Z
date_updated: 2021-01-12T08:15:24Z
day: '27'
doi: 10.1103/physreve.90.022138
extern: '1'
intvolume: ' 90'
issue: '2'
language:
- iso: eng
month: '08'
oa_version: None
publication: Physical Review E
publication_identifier:
issn:
- 1539-3755
- 1550-2376
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: 'Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 90
year: '2014'
...
---
_id: '7770'
abstract:
- lang: eng
text: Packings of frictionless athermal particles that interact only when they overlap
experience a jamming transition as a function of packing density. Such packings
provide the foundation for the theory of jamming. This theory rests on the observation
that, despite the multitude of disordered configurations, the mechanical response
to linear order depends only on the distance to the transition. We investigate
the validity and utility of such measurements that invoke the harmonic approximation
and show that, despite particles coming in and out of contact, there is a well-defined
linear regime in the thermodynamic limit.
article_number: '022201'
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: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: Goodrich CP, Liu AJ, Nagel SR. Contact nonlinearities and linear response in
jammed particulate packings. Physical Review E. 2014;90(2). doi:10.1103/physreve.90.022201
apa: Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2014). Contact nonlinearities
and linear response in jammed particulate packings. Physical Review E.
American Physical Society. https://doi.org/10.1103/physreve.90.022201
chicago: Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Contact Nonlinearities
and Linear Response in Jammed Particulate Packings.” Physical Review E.
American Physical Society, 2014. https://doi.org/10.1103/physreve.90.022201.
ieee: C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Contact nonlinearities and linear
response in jammed particulate packings,” Physical Review E, vol. 90, no.
2. American Physical Society, 2014.
ista: Goodrich CP, Liu AJ, Nagel SR. 2014. Contact nonlinearities and linear response
in jammed particulate packings. Physical Review E. 90(2), 022201.
mla: Goodrich, Carl Peter, et al. “Contact Nonlinearities and Linear Response in
Jammed Particulate Packings.” Physical Review E, vol. 90, no. 2, 022201,
American Physical Society, 2014, doi:10.1103/physreve.90.022201.
short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review E 90 (2014).
date_created: 2020-04-30T11:42:24Z
date_published: 2014-08-04T00:00:00Z
date_updated: 2021-01-12T08:15:25Z
day: '04'
doi: 10.1103/physreve.90.022201
extern: '1'
intvolume: ' 90'
issue: '2'
language:
- iso: eng
month: '08'
oa_version: None
publication: Physical Review E
publication_identifier:
issn:
- 1539-3755
- 1550-2376
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Contact nonlinearities and linear response in jammed particulate packings
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 90
year: '2014'
...
---
_id: '7771'
abstract:
- lang: eng
text: 'In their Letter, Schreck, Bertrand, O''Hern and Shattuck [Phys. Rev. Lett.
107, 078301 (2011)] study nonlinearities in jammed particulate systems that arise
when contacts are altered. They conclude that there is "no harmonic regime in
the large system limit for all compressions" and "at jamming onset for any system
size." Their argument rests on the claim that for finite-range repulsive potentials,
of the form used in studies of jamming, the breaking or forming of a single contact
is sufficient to destroy the linear regime. We dispute these conclusions and argue
that linear response is both justified and essential for understanding the nature
of the jammed solid. '
article_number: '049801 '
article_processing_charge: No
article_type: letter_note
arxiv: 1
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: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: Goodrich CP, Liu AJ, Nagel SR. Comment on “Repulsive contact interactions make
jammed particulate systems inherently nonharmonic.” Physical Review Letters.
2014;112(4). doi:10.1103/physrevlett.112.049801
apa: Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2014). Comment on “Repulsive
contact interactions make jammed particulate systems inherently nonharmonic.”
Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.112.049801
chicago: Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Comment on ‘Repulsive
Contact Interactions Make Jammed Particulate Systems Inherently Nonharmonic.’”
Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/physrevlett.112.049801.
ieee: C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Comment on ‘Repulsive contact
interactions make jammed particulate systems inherently nonharmonic,’” Physical
Review Letters, vol. 112, no. 4. American Physical Society, 2014.
ista: Goodrich CP, Liu AJ, Nagel SR. 2014. Comment on “Repulsive contact interactions
make jammed particulate systems inherently nonharmonic”. Physical Review Letters.
112(4), 049801.
mla: Goodrich, Carl Peter, et al. “Comment on ‘Repulsive Contact Interactions Make
Jammed Particulate Systems Inherently Nonharmonic.’” Physical Review Letters,
vol. 112, no. 4, 049801, American Physical Society, 2014, doi:10.1103/physrevlett.112.049801.
short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 112 (2014).
date_created: 2020-04-30T11:42:39Z
date_published: 2014-04-20T00:00:00Z
date_updated: 2021-01-12T08:15:26Z
day: '20'
doi: 10.1103/physrevlett.112.049801
extern: '1'
external_id:
arxiv:
- '1306.1285'
intvolume: ' 112'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1306.1285
month: '04'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_identifier:
issn:
- 0031-9007
- 1079-7114
publication_status: published
publisher: American Physical Society
status: public
title: Comment on “Repulsive contact interactions make jammed particulate systems
inherently nonharmonic”
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2014'
...
---
_id: '7772'
abstract:
- lang: eng
text: Particle tracking and displacement covariance matrix techniques are employed
to investigate the phonon dispersion relations of two-dimensional colloidal glasses
composed of soft, thermoresponsive microgel particles whose temperature-sensitive
size permits in situ variation of particle packing fraction. Bulk, B, and shear,
G, moduli of the colloidal glasses are extracted from the dispersion relations
as a function of packing fraction, and variation of the ratio G/B with packing
fraction is found to agree quantitatively with predictions for jammed packings
of frictional soft particles. In addition, G and B individually agree with numerical
predictions for frictional particles. This remarkable level of agreement enabled
us to extract an energy scale for the interparticle interaction from the individual
elastic constants and to derive an approximate estimate for the interparticle
friction coefficient.
article_number: '012301'
article_processing_charge: No
article_type: original
author:
- first_name: Tim
full_name: Still, Tim
last_name: Still
- 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: Ke
full_name: Chen, Ke
last_name: Chen
- first_name: Peter J.
full_name: Yunker, Peter J.
last_name: Yunker
- first_name: Samuel
full_name: Schoenholz, Samuel
last_name: Schoenholz
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: A. G.
full_name: Yodh, A. G.
last_name: Yodh
citation:
ama: Still T, Goodrich CP, Chen K, et al. Phonon dispersion and elastic moduli of
two-dimensional disordered colloidal packings of soft particles with frictional
interactions. Physical Review E. 2014;89(1). doi:10.1103/physreve.89.012301
apa: Still, T., Goodrich, C. P., Chen, K., Yunker, P. J., Schoenholz, S., Liu, A.
J., & Yodh, A. G. (2014). Phonon dispersion and elastic moduli of two-dimensional
disordered colloidal packings of soft particles with frictional interactions.
Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.89.012301
chicago: Still, Tim, Carl Peter Goodrich, Ke Chen, Peter J. Yunker, Samuel Schoenholz,
Andrea J. Liu, and A. G. Yodh. “Phonon Dispersion and Elastic Moduli of Two-Dimensional
Disordered Colloidal Packings of Soft Particles with Frictional Interactions.”
Physical Review E. American Physical Society, 2014. https://doi.org/10.1103/physreve.89.012301.
ieee: T. Still et al., “Phonon dispersion and elastic moduli of two-dimensional
disordered colloidal packings of soft particles with frictional interactions,”
Physical Review E, vol. 89, no. 1. American Physical Society, 2014.
ista: Still T, Goodrich CP, Chen K, Yunker PJ, Schoenholz S, Liu AJ, Yodh AG. 2014.
Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings
of soft particles with frictional interactions. Physical Review E. 89(1), 012301.
mla: Still, Tim, et al. “Phonon Dispersion and Elastic Moduli of Two-Dimensional
Disordered Colloidal Packings of Soft Particles with Frictional Interactions.”
Physical Review E, vol. 89, no. 1, 012301, American Physical Society, 2014,
doi:10.1103/physreve.89.012301.
short: T. Still, C.P. Goodrich, K. Chen, P.J. Yunker, S. Schoenholz, A.J. Liu, A.G.
Yodh, Physical Review E 89 (2014).
date_created: 2020-04-30T11:43:02Z
date_published: 2014-01-03T00:00:00Z
date_updated: 2021-01-12T08:15:26Z
day: '03'
doi: 10.1103/physreve.89.012301
extern: '1'
intvolume: ' 89'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
publication: Physical Review E
publication_identifier:
issn:
- 1539-3755
- 1550-2376
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Phonon dispersion and elastic moduli of two-dimensional disordered colloidal
packings of soft particles with frictional interactions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2014'
...
---
_id: '7773'
abstract:
- lang: eng
text: 'For more than a century, physicists have described real solids in terms of
perturbations about perfect crystalline order1. Such an approach takes us only
so far: a glass, another ubiquitous form of rigid matter, cannot be described
in any meaningful sense as a defected crystal2. Is there an opposite extreme to
a crystal—a solid with complete disorder—that forms an alternative starting point
for understanding real materials? Here, we argue that the solid comprising particles
with finite-ranged interactions at the jamming transition3,4,5 constitutes such
a limit. It has been shown that the physics associated with this transition can
be extended to interactions that are long ranged6. We demonstrate that jamming
physics is not restricted to amorphous systems, but dominates the behaviour of
solids with surprisingly high order. Just as the free-electron and tight-binding
models represent two idealized cases from which to understand electronic structure1,
we identify two extreme limits of mechanical behaviour. Thus, the physics of jamming
can be set side by side with the physics of crystals to provide an organizing
structure for understanding the mechanical properties of solids over the entire
spectrum of disorder.'
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: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: Goodrich CP, Liu AJ, Nagel SR. Solids between the mechanical extremes of order
and disorder. Nature Physics. 2014;10(8):578-581. doi:10.1038/nphys3006
apa: Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2014). Solids between the
mechanical extremes of order and disorder. Nature Physics. Springer Nature.
https://doi.org/10.1038/nphys3006
chicago: Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Solids between
the Mechanical Extremes of Order and Disorder.” Nature Physics. Springer
Nature, 2014. https://doi.org/10.1038/nphys3006.
ieee: C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Solids between the mechanical
extremes of order and disorder,” Nature Physics, vol. 10, no. 8. Springer
Nature, pp. 578–581, 2014.
ista: Goodrich CP, Liu AJ, Nagel SR. 2014. Solids between the mechanical extremes
of order and disorder. Nature Physics. 10(8), 578–581.
mla: Goodrich, Carl Peter, et al. “Solids between the Mechanical Extremes of Order
and Disorder.” Nature Physics, vol. 10, no. 8, Springer Nature, 2014, pp.
578–81, doi:10.1038/nphys3006.
short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Nature Physics 10 (2014) 578–581.
date_created: 2020-04-30T11:43:29Z
date_published: 2014-07-06T00:00:00Z
date_updated: 2021-01-12T08:15:26Z
day: '06'
doi: 10.1038/nphys3006
extern: '1'
intvolume: ' 10'
issue: '8'
language:
- iso: eng
month: '07'
oa_version: None
page: 578-581
publication: Nature Physics
publication_identifier:
issn:
- 1745-2473
- 1745-2481
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Solids between the mechanical extremes of order and disorder
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2014'
...
---
_id: '8021'
abstract:
- lang: eng
text: 'Most excitatory inputs in the mammalian brain are made on dendritic spines,
rather than on dendritic shafts. Spines compartmentalize calcium, and this biochemical
isolation can underlie input-specific synaptic plasticity, providing a raison
d''etre for spines. However, recent results indicate that the spine can experience
a membrane potential different from that in the parent dendrite, as though the
spine neck electrically isolated the spine. Here we use two-photon calcium imaging
of mouse neocortical pyramidal neurons to analyze the correlation between the
morphologies of spines activated under minimal synaptic stimulation and the excitatory
postsynaptic potentials they generate. We find that excitatory postsynaptic potential
amplitudes are inversely correlated with spine neck lengths. Furthermore, a spike
timing-dependent plasticity protocol, in which two-photon glutamate uncaging over
a spine is paired with postsynaptic spikes, produces rapid shrinkage of the spine
neck and concomitant increases in the amplitude of the evoked spine potentials.
Using numerical simulations, we explore the parameter regimes for the spine neck
resistance and synaptic conductance changes necessary to explain our observations.
Our data, directly correlating synaptic and morphological plasticity, imply that
long-necked spines have small or negligible somatic voltage contributions, but
that, upon synaptic stimulation paired with postsynaptic activity, they can shorten
their necks and increase synaptic efficacy, thus changing the input/output gain
of pyramidal neurons. '
article_processing_charge: No
article_type: original
author:
- first_name: R.
full_name: Araya, R.
last_name: Araya
- 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.
full_name: Yuste, R.
last_name: Yuste
citation:
ama: Araya R, Vogels TP, Yuste R. Activity-dependent dendritic spine neck changes
are correlated with synaptic strength. Proceedings of the National Academy
of Sciences. 2014;111(28):E2895-E2904. doi:10.1073/pnas.1321869111
apa: Araya, R., Vogels, T. P., & Yuste, R. (2014). Activity-dependent dendritic
spine neck changes are correlated with synaptic strength. Proceedings of the
National Academy of Sciences. Proceedings of the National Academy of Sciences.
https://doi.org/10.1073/pnas.1321869111
chicago: Araya, R., Tim P Vogels, and R. Yuste. “Activity-Dependent Dendritic Spine
Neck Changes Are Correlated with Synaptic Strength.” Proceedings of the National
Academy of Sciences. Proceedings of the National Academy of Sciences, 2014.
https://doi.org/10.1073/pnas.1321869111.
ieee: R. Araya, T. P. Vogels, and R. Yuste, “Activity-dependent dendritic spine
neck changes are correlated with synaptic strength,” Proceedings of the National
Academy of Sciences, vol. 111, no. 28. Proceedings of the National Academy
of Sciences, pp. E2895–E2904, 2014.
ista: Araya R, Vogels TP, Yuste R. 2014. Activity-dependent dendritic spine neck
changes are correlated with synaptic strength. Proceedings of the National Academy
of Sciences. 111(28), E2895–E2904.
mla: Araya, R., et al. “Activity-Dependent Dendritic Spine Neck Changes Are Correlated
with Synaptic Strength.” Proceedings of the National Academy of Sciences,
vol. 111, no. 28, Proceedings of the National Academy of Sciences, 2014, pp. E2895–904,
doi:10.1073/pnas.1321869111.
short: R. Araya, T.P. Vogels, R. Yuste, Proceedings of the National Academy of Sciences
111 (2014) E2895–E2904.
date_created: 2020-06-25T13:06:24Z
date_published: 2014-07-15T00:00:00Z
date_updated: 2021-01-12T08:16:34Z
day: '15'
doi: 10.1073/pnas.1321869111
extern: '1'
external_id:
pmid:
- '24982196'
intvolume: ' 111'
issue: '28'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104910/
month: '07'
oa: 1
oa_version: Published Version
page: E2895-E2904
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: Activity-dependent dendritic spine neck changes are correlated with synaptic
strength
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 111
year: '2014'
...
---
_id: '8022'
abstract:
- lang: eng
text: Populations of neurons in motor cortex engage in complex transient dynamics
of large amplitude during the execution of limb movements. Traditional network
models with stochastically assigned synapses cannot reproduce this behavior. Here
we introduce a class of cortical architectures with strong and random excitatory
recurrence that is stabilized by intricate, fine-tuned inhibition, optimized from
a control theory perspective. Such networks transiently amplify specific activity
states and can be used to reliably execute multidimensional movement patterns.
Similar to the experimental observations, these transients must be preceded by
a steady-state initialization phase from which the network relaxes back into the
background state by way of complex internal dynamics. In our networks, excitation
and inhibition are as tightly balanced as recently reported in experiments across
several brain areas, suggesting inhibitory control of complex excitatory recurrence
as a generic organizational principle in cortex.
article_processing_charge: No
article_type: original
author:
- first_name: Guillaume
full_name: Hennequin, Guillaume
last_name: Hennequin
- 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: Wulfram
full_name: Gerstner, Wulfram
last_name: Gerstner
citation:
ama: Hennequin G, Vogels TP, Gerstner W. Optimal control of transient dynamics in
balanced networks supports generation of complex movements. Neuron. 2014;82(6):1394-1406.
doi:10.1016/j.neuron.2014.04.045
apa: Hennequin, G., Vogels, T. P., & Gerstner, W. (2014). Optimal control of
transient dynamics in balanced networks supports generation of complex movements.
Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.04.045
chicago: Hennequin, Guillaume, Tim P Vogels, and Wulfram Gerstner. “Optimal Control
of Transient Dynamics in Balanced Networks Supports Generation of Complex Movements.”
Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.04.045.
ieee: G. Hennequin, T. P. Vogels, and W. Gerstner, “Optimal control of transient
dynamics in balanced networks supports generation of complex movements,” Neuron,
vol. 82, no. 6. Elsevier, pp. 1394–1406, 2014.
ista: Hennequin G, Vogels TP, Gerstner W. 2014. Optimal control of transient dynamics
in balanced networks supports generation of complex movements. Neuron. 82(6),
1394–1406.
mla: Hennequin, Guillaume, et al. “Optimal Control of Transient Dynamics in Balanced
Networks Supports Generation of Complex Movements.” Neuron, vol. 82, no.
6, Elsevier, 2014, pp. 1394–406, doi:10.1016/j.neuron.2014.04.045.
short: G. Hennequin, T.P. Vogels, W. Gerstner, Neuron 82 (2014) 1394–1406.
date_created: 2020-06-25T13:07:37Z
date_published: 2014-06-18T00:00:00Z
date_updated: 2021-01-12T08:16:35Z
day: '18'
doi: 10.1016/j.neuron.2014.04.045
extern: '1'
external_id:
pmid:
- '24945778'
intvolume: ' 82'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364799/
month: '06'
oa: 1
oa_version: Submitted Version
page: 1394-1406
pmid: 1
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Optimal control of transient dynamics in balanced networks supports generation
of complex movements
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 82
year: '2014'
...
---
_id: '8023'
abstract:
- lang: eng
text: Uniform random sparse network architectures are ubiquitous in computational
neuroscience, but the implicit hypothesis that they are a good representation
of real neuronal networks has been met with skepticism. Here we used two experimental
data sets, a study of triplet connectivity statistics and a data set measuring
neuronal responses to channelrhodopsin stimuli, to evaluate the fidelity of thousands
of model networks. Network architectures comprised three neuron types (excitatory,
fast spiking, and nonfast spiking inhibitory) and were created from a set of rules
that govern the statistics of the resulting connection types. In a high-dimensional
parameter scan, we varied the degree distributions (i.e., how many cells each
neuron connects with) and the synaptic weight correlations of synapses from or
onto the same neuron. These variations converted initially uniform random and
homogeneously connected networks, in which every neuron sent and received equal
numbers of synapses with equal synaptic strength distributions, to highly heterogeneous
networks in which the number of synapses per neuron, as well as average synaptic
strength of synapses from or to a neuron were variable. By evaluating the impact
of each variable on the network structure and dynamics, and their similarity to
the experimental data, we could falsify the uniform random sparse connectivity
hypothesis for 7 of 36 connectivity parameters, but we also confirmed the hypothesis
in 8 cases. Twenty-one parameters had no substantial impact on the results of
the test protocols we used.
article_processing_charge: No
article_type: original
author:
- first_name: Christian
full_name: Tomm, Christian
last_name: Tomm
- first_name: Michael
full_name: Avermann, Michael
last_name: Avermann
- first_name: Carl
full_name: Petersen, Carl
last_name: Petersen
- first_name: Wulfram
full_name: Gerstner, Wulfram
last_name: Gerstner
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: Tomm C, Avermann M, Petersen C, Gerstner W, Vogels TP. Connection-type-specific
biases make uniform random network models consistent with cortical recordings.
Journal of Neurophysiology. 2014;112(8):1801-1814. doi:10.1152/jn.00629.2013
apa: Tomm, C., Avermann, M., Petersen, C., Gerstner, W., & Vogels, T. P. (2014).
Connection-type-specific biases make uniform random network models consistent
with cortical recordings. Journal of Neurophysiology. American Physiological
Society. https://doi.org/10.1152/jn.00629.2013
chicago: Tomm, Christian, Michael Avermann, Carl Petersen, Wulfram Gerstner, and
Tim P Vogels. “Connection-Type-Specific Biases Make Uniform Random Network Models
Consistent with Cortical Recordings.” Journal of Neurophysiology. American
Physiological Society, 2014. https://doi.org/10.1152/jn.00629.2013.
ieee: C. Tomm, M. Avermann, C. Petersen, W. Gerstner, and T. P. Vogels, “Connection-type-specific
biases make uniform random network models consistent with cortical recordings,”
Journal of Neurophysiology, vol. 112, no. 8. American Physiological Society,
pp. 1801–1814, 2014.
ista: Tomm C, Avermann M, Petersen C, Gerstner W, Vogels TP. 2014. Connection-type-specific
biases make uniform random network models consistent with cortical recordings.
Journal of Neurophysiology. 112(8), 1801–1814.
mla: Tomm, Christian, et al. “Connection-Type-Specific Biases Make Uniform Random
Network Models Consistent with Cortical Recordings.” Journal of Neurophysiology,
vol. 112, no. 8, American Physiological Society, 2014, pp. 1801–14, doi:10.1152/jn.00629.2013.
short: C. Tomm, M. Avermann, C. Petersen, W. Gerstner, T.P. Vogels, Journal of Neurophysiology
112 (2014) 1801–1814.
date_created: 2020-06-25T13:08:30Z
date_published: 2014-10-15T00:00:00Z
date_updated: 2021-01-12T08:16:35Z
day: '15'
ddc:
- '570'
doi: 10.1152/jn.00629.2013
extern: '1'
external_id:
pmid:
- '24944218'
file:
- access_level: open_access
checksum: 7c06a086da6f924342650de6dc555c3f
content_type: application/pdf
creator: cziletti
date_created: 2020-07-16T10:12:13Z
date_updated: 2020-07-16T10:12:13Z
file_id: '8122'
file_name: 2014_JNeurophysiol_Tomm.pdf
file_size: 1632295
relation: main_file
success: 1
file_date_updated: 2020-07-16T10:12:13Z
has_accepted_license: '1'
intvolume: ' 112'
issue: '8'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '10'
oa: 1
oa_version: Published Version
page: 1801-1814
pmid: 1
publication: Journal of Neurophysiology
publication_identifier:
eissn:
- 1522-1598
issn:
- 0022-3077
publication_status: published
publisher: American Physiological Society
quality_controlled: '1'
status: public
title: Connection-type-specific biases make uniform random network models consistent
with cortical recordings
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: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 112
year: '2014'
...
---
_id: '8044'
abstract:
- lang: eng
text: Many questions concerning models in quantum mechanics require a detailed analysis
of the spectrum of the corresponding Hamiltonian, a linear operator on a suitable
Hilbert space. Of particular relevance for an understanding of the low-temperature
properties of a system is the structure of the excitation spectrum, which is the
part of the spectrum close to the spectral bottom. We present recent progress
on this question for bosonic many-body quantum systems with weak two-body interactions.
Such system are currently of great interest, due to their experimental realization
in ultra-cold atomic gases. We investigate the accuracy of the Bogoliubov approximations,
which predicts that the low-energy spectrum is made up of sums of elementary excitations,
with linear dispersion law at low momentum. The latter property is crucial for
the superfluid behavior the system.
article_processing_charge: No
author:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Seiringer R. Structure of the excitation spectrum for many-body quantum systems.
In: Proceeding of the International Congress of Mathematicans. Vol 3. International
Congress of Mathematicians; 2014:1175-1194.'
apa: 'Seiringer, R. (2014). Structure of the excitation spectrum for many-body quantum
systems. In Proceeding of the International Congress of Mathematicans (Vol.
3, pp. 1175–1194). Seoul, South Korea: International Congress of Mathematicians.'
chicago: Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body
Quantum Systems.” In Proceeding of the International Congress of Mathematicans,
3:1175–94. International Congress of Mathematicians, 2014.
ieee: R. Seiringer, “Structure of the excitation spectrum for many-body quantum
systems,” in Proceeding of the International Congress of Mathematicans,
Seoul, South Korea, 2014, vol. 3, pp. 1175–1194.
ista: 'Seiringer R. 2014. Structure of the excitation spectrum for many-body quantum
systems. Proceeding of the International Congress of Mathematicans. ICM: International
Congress of Mathematicans vol. 3, 1175–1194.'
mla: Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body Quantum
Systems.” Proceeding of the International Congress of Mathematicans, vol.
3, International Congress of Mathematicians, 2014, pp. 1175–94.
short: R. Seiringer, in:, Proceeding of the International Congress of Mathematicans,
International Congress of Mathematicians, 2014, pp. 1175–1194.
conference:
end_date: 2014-08-21
location: Seoul, South Korea
name: 'ICM: International Congress of Mathematicans'
start_date: 2014-08-13
date_created: 2020-06-29T07:59:35Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2023-10-17T11:12:33Z
day: '01'
department:
- _id: RoSe
intvolume: ' 3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.icm2014.org/en/vod/proceedings.html
month: '08'
oa: 1
oa_version: Published Version
page: 1175-1194
publication: Proceeding of the International Congress of Mathematicans
publication_identifier:
isbn:
- '9788961058063'
publication_status: published
publisher: International Congress of Mathematicians
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure of the excitation spectrum for many-body quantum systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2014'
...
---
_id: '809'
abstract:
- lang: eng
text: The assembly of HIV-1 is mediated by oligomerization of the major structural
polyprotein, Gag, into a hexameric protein lattice at the plasma membrane of the
infected cell. This leads to budding and release of progeny immature virus particles.
Subsequent proteolytic cleavage of Gag triggers rearrangement of the particles
to form mature infectious virions. Obtaining a structural model of the assembled
lattice of Gag within immature virus particles is necessary to understand the
interactions that mediate assembly of HIV-1 particles in the infected cell, and
to describe the substrate that is subsequently cleaved by the viral protease.
An 8-Å resolution structure of an immature virus-like tubular array assembled
from a Gag-derived protein of the related retrovirus Mason-Pfizer monkey virus
(M-PMV) has previously been reported, and a model for the arrangement of the HIV-1
capsid (CA) domains has been generated based on homology to this structure. Here
we have assembled tubular arrays of a HIV-1 Gag-derived protein with an immature-like
arrangement of the C-terminal CA domains and have solved their structure by using
hybrid cryo-EM and tomography analysis. The structure reveals the arrangement
of the C-terminal domain of CA within an immature-like HIV-1 Gag lattice, and
provides, to our knowledge, the first high-resolution view of the region immediately
downstream of CA, which is essential for assembly, and is significantly different
from the respective region in M-PMV. Our results reveal a hollow column of density
for this region in HIV-1 that is compatible with the presence of a six-helix bundle
at this position.
acknowledgement: 'The authors thank Leonardo Trabuco for help with running MDFF, Maria
Anders for preparing amprenavir-inhibited virus, Marie-Christine Vaney for help
with X-ray data processing and structure refinement, Ahmed Haouz and Patrick Weber
(robotized crystallization facility Proteopole, Institut Pasteur) for help in crystal
screening, and the European Molecular Biology Laboratory (EMBL) Information Technology
Services Unit and Frank Thommen for technical support. This study was supported
by Deutsche Forschungsgemeinschaft Grants BR 3635/2-1 (to J.A.G.B.) and KR 906/7-1
(to H.-G.K.) and a Federation of European Biochemical Societies long-term fellowship
(to T.A.M.B.). The laboratory of J.A.G.B. acknowledges financial support from EMBL
and the Chica und Heinz Schaller Stiftung. '
author:
- first_name: Tanmay
full_name: Bharata, Tanmay A
last_name: Bharata
- first_name: Luis
full_name: Menendez, Luis R
last_name: Menendez
- first_name: Wim
full_name: Hagena, Wim J
last_name: Hagena
- first_name: Vanda
full_name: Luxd, Vanda
last_name: Luxd
- first_name: Sebastien
full_name: Igonete, Sebastien
last_name: Igonete
- first_name: Martin
full_name: Schorba, Martin
last_name: Schorba
- first_name: Florian
full_name: Florian Schur
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Hans
full_name: Kraüsslich, Hans Georg
last_name: Kraüsslich
- first_name: John
full_name: Briggsa, John A
last_name: Briggsa
citation:
ama: Bharata T, Menendez L, Hagena W, et al. Cryo electron microscopy of tubular
arrays of HIV-1 Gag resolves structures essential for immature virus assembly.
PNAS. 2014;111(22):8233-8238. doi:10.1073/pnas.1401455111
apa: Bharata, T., Menendez, L., Hagena, W., Luxd, V., Igonete, S., Schorba, M.,
… Briggsa, J. (2014). Cryo electron microscopy of tubular arrays of HIV-1 Gag
resolves structures essential for immature virus assembly. PNAS. National
Academy of Sciences. https://doi.org/10.1073/pnas.1401455111
chicago: Bharata, Tanmay, Luis Menendez, Wim Hagena, Vanda Luxd, Sebastien Igonete,
Martin Schorba, Florian KM Schur, Hans Kraüsslich, and John Briggsa. “Cryo Electron
Microscopy of Tubular Arrays of HIV-1 Gag Resolves Structures Essential for Immature
Virus Assembly.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1401455111.
ieee: T. Bharata et al., “Cryo electron microscopy of tubular arrays of HIV-1
Gag resolves structures essential for immature virus assembly,” PNAS, vol.
111, no. 22. National Academy of Sciences, pp. 8233–8238, 2014.
ista: Bharata T, Menendez L, Hagena W, Luxd V, Igonete S, Schorba M, Schur FK, Kraüsslich
H, Briggsa J. 2014. Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves
structures essential for immature virus assembly. PNAS. 111(22), 8233–8238.
mla: Bharata, Tanmay, et al. “Cryo Electron Microscopy of Tubular Arrays of HIV-1
Gag Resolves Structures Essential for Immature Virus Assembly.” PNAS, vol.
111, no. 22, National Academy of Sciences, 2014, pp. 8233–38, doi:10.1073/pnas.1401455111.
short: T. Bharata, L. Menendez, W. Hagena, V. Luxd, S. Igonete, M. Schorba, F.K.
Schur, H. Kraüsslich, J. Briggsa, PNAS 111 (2014) 8233–8238.
date_created: 2018-12-11T11:48:37Z
date_published: 2014-06-03T00:00:00Z
date_updated: 2021-01-12T08:16:50Z
day: '03'
doi: 10.1073/pnas.1401455111
extern: 1
intvolume: ' 111'
issue: '22'
month: '06'
page: 8233 - 8238
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6838'
quality_controlled: 0
status: public
title: Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures
essential for immature virus assembly
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
volume: 111
year: '2014'
...
---
_id: '8244'
abstract:
- lang: eng
text: Passive immunotherapy with monoclonal antibodies represents a cornerstone
of human anticancer therapies, but has not been established in veterinary medicine
yet. As the tumor-associated antigen EGFR (ErbB-1) is highly conserved between
humans and dogs, and considering the effectiveness of the anti-EGFR antibody cetuximab
in human clinical oncology, we present here a “caninized” version of this antibody,
can225IgG, for comparative oncology studies. Variable region genes of 225, the
murine precursor of cetuximab, were fused with canine constant heavy gamma and
kappa chain genes, respectively, and transfected into Chinese hamster ovary (CHO)
DUKX-B11 cells. Of note, 480 clones were screened and the best clones were selected
according to productivity and highest specificity in EGFR-coated ELISA. Upon purification
with Protein G, the recombinant cetuximab-like canine IgG was tested for integrity,
correct assembly, and functionality. Specific binding to the surface of EGFR-overexpressing
cells was assessed by flow cytometry and immunofluorescence; moreover, binding
to canine mammary tissue was demonstrated by immunohistochemistry. In cell viability
and proliferation assays, incubation with can225IgG led to significant tumor cell
growth inhibition. Moreover, this antibody mediated significant tumor cell killing
via phagocytosis in vitro. We thus present here, for the first time, the generation
of a canine IgG antibody and its hypothetical structure. On the basis of its cetuximab-like
binding site, on the one hand, and the expression of a 91% homologous EGFR molecule
in canine cancer, on the other hand, this antibody may be a promising research
compound to establish passive immunotherapy in dog patients with cancer.
article_processing_charge: No
article_type: original
author:
- first_name: J.
full_name: Singer, J.
last_name: Singer
- first_name: Judit
full_name: Fazekas, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas
orcid: 0000-0002-8777-3502
- first_name: W.
full_name: Wang, W.
last_name: Wang
- first_name: M.
full_name: Weichselbaumer, M.
last_name: Weichselbaumer
- first_name: M.
full_name: Matz, M.
last_name: Matz
- first_name: A.
full_name: Mader, A.
last_name: Mader
- first_name: W.
full_name: Steinfellner, W.
last_name: Steinfellner
- first_name: S.
full_name: Meitz, S.
last_name: Meitz
- first_name: D.
full_name: Mechtcheriakova, D.
last_name: Mechtcheriakova
- first_name: Y.
full_name: Sobanov, Y.
last_name: Sobanov
- first_name: M.
full_name: Willmann, M.
last_name: Willmann
- first_name: T.
full_name: Stockner, T.
last_name: Stockner
- first_name: E.
full_name: Spillner, E.
last_name: Spillner
- first_name: R.
full_name: Kunert, R.
last_name: Kunert
- first_name: E.
full_name: Jensen-Jarolim, E.
last_name: Jensen-Jarolim
citation:
ama: Singer J, Singer J, Wang W, et al. Generation of a canine anti-EGFR (ErbB-1)
antibody for passive immunotherapy in dog cancer patients. Molecular Cancer
Therapeutics. 2014;13(7):1777-1790. doi:10.1158/1535-7163.mct-13-0288
apa: Singer, J., Singer, J., Wang, W., Weichselbaumer, M., Matz, M., Mader, A.,
… Jensen-Jarolim, E. (2014). Generation of a canine anti-EGFR (ErbB-1) antibody
for passive immunotherapy in dog cancer patients. Molecular Cancer Therapeutics.
American Association for Cancer Research. https://doi.org/10.1158/1535-7163.mct-13-0288
chicago: Singer, J., Judit Singer, W. Wang, M. Weichselbaumer, M. Matz, A. Mader,
W. Steinfellner, et al. “Generation of a Canine Anti-EGFR (ErbB-1) Antibody for
Passive Immunotherapy in Dog Cancer Patients.” Molecular Cancer Therapeutics.
American Association for Cancer Research, 2014. https://doi.org/10.1158/1535-7163.mct-13-0288.
ieee: J. Singer et al., “Generation of a canine anti-EGFR (ErbB-1) antibody
for passive immunotherapy in dog cancer patients,” Molecular Cancer Therapeutics,
vol. 13, no. 7. American Association for Cancer Research, pp. 1777–1790, 2014.
ista: Singer J, Singer J, Wang W, Weichselbaumer M, Matz M, Mader A, Steinfellner
W, Meitz S, Mechtcheriakova D, Sobanov Y, Willmann M, Stockner T, Spillner E,
Kunert R, Jensen-Jarolim E. 2014. Generation of a canine anti-EGFR (ErbB-1) antibody
for passive immunotherapy in dog cancer patients. Molecular Cancer Therapeutics.
13(7), 1777–1790.
mla: Singer, J., et al. “Generation of a Canine Anti-EGFR (ErbB-1) Antibody for
Passive Immunotherapy in Dog Cancer Patients.” Molecular Cancer Therapeutics,
vol. 13, no. 7, American Association for Cancer Research, 2014, pp. 1777–90, doi:10.1158/1535-7163.mct-13-0288.
short: J. Singer, J. Singer, W. Wang, M. Weichselbaumer, M. Matz, A. Mader, W. Steinfellner,
S. Meitz, D. Mechtcheriakova, Y. Sobanov, M. Willmann, T. Stockner, E. Spillner,
R. Kunert, E. Jensen-Jarolim, Molecular Cancer Therapeutics 13 (2014) 1777–1790.
date_created: 2020-08-10T11:54:29Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2021-01-12T08:17:42Z
day: '01'
doi: 10.1158/1535-7163.mct-13-0288
extern: '1'
intvolume: ' 13'
issue: '7'
language:
- iso: eng
month: '07'
oa_version: None
page: 1777-1790
publication: Molecular Cancer Therapeutics
publication_identifier:
issn:
- 1535-7163
- 1538-8514
publication_status: published
publisher: American Association for Cancer Research
quality_controlled: '1'
status: public
title: Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy
in dog cancer patients
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2014'
...
---
_id: '845'
abstract:
- lang: eng
text: Recombination between double-stranded DNA molecules is a key genetic process
which occurs in a wide variety of organisms. Usually, crossing-over (CO) occurs
during meiosis between genotypes with 98.0-99.9% sequence identity, because within-population
nucleotide diversity only rarely exceeds 2%. However, some species are hypervariable
and it is unclear how CO can occur between genotypes with less than 90% sequence
identity. Here, we study CO in Schizophyllum commune, a hypervariable cosmopolitan
basidiomycete mushroom, a frequently encountered decayer of woody substrates.
We crossed two haploid individuals, from the United States and from Russia, and
obtained genome sequences for their 17 offspring. The average genetic distance
between the parents was 14%, making it possible to study CO at very high resolution.
We found reduced levels of linkage disequilibrium between loci flanking the CO
sites indicating that they are mostly confined to hotspots of recombination. Furthermore,
CO events preferentially occurred in regions under stronger negative selection,
in particular within exons that showed reduced levels of nucleotide diversity.
Apparently, in hypervariable species CO must avoid regions of higher divergence
between the recombining genomes due to limitations imposed by the mismatch repair
system, with regions under strong negative selection providing the opportunity
for recombination. These patterns are opposite to those observed in a number of
less variable species indicating that population genomics of hypervariable species
may reveal novel biological phenomena.
acknowledgement: The authors are grateful to Georgii Bazykin for valuable discussion
and to the DNA sequencing facility at Engelhardt Institute of Molecular Biology
for Sanger sequencing. This study was supported by the Russian government grant
No 11.G34.31.0008 and by Plan Nacional (BFU2012-31329), Howard Hughes Medical Institute
International Early Career Scientist Award and EMBO Young Investigator Program,
and core funds provided by the University of Michigan.
author:
- first_name: Vladimir
full_name: Seplyarskiy, Vladimir B
last_name: Seplyarskiy
- first_name: Maria
full_name: Logacheva, Maria D
last_name: Logacheva
- first_name: Aleksey
full_name: Penin, Aleksey A
last_name: Penin
- first_name: Maria
full_name: Baranová, Maria A
last_name: Baranová
- first_name: Evgeny
full_name: Leushkin, Evgeny V
last_name: Leushkin
- first_name: Natalia
full_name: Demidenko, Natalia V
last_name: Demidenko
- first_name: Anna
full_name: Klepikova, Anna V
last_name: Klepikova
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
- first_name: Timothy
full_name: James, Timothy Y
last_name: James
citation:
ama: Seplyarskiy V, Logacheva M, Penin A, et al. Crossing-over in a hypervariable
species preferentially occurs in regions of high local similarity. Molecular
Biology and Evolution. 2014;31(11):3016-3025. doi:10.1093/molbev/msu242
apa: Seplyarskiy, V., Logacheva, M., Penin, A., Baranová, M., Leushkin, E., Demidenko,
N., … James, T. (2014). Crossing-over in a hypervariable species preferentially
occurs in regions of high local similarity. Molecular Biology and Evolution.
Oxford University Press. https://doi.org/10.1093/molbev/msu242
chicago: Seplyarskiy, Vladimir, Maria Logacheva, Aleksey Penin, Maria Baranová,
Evgeny Leushkin, Natalia Demidenko, Anna Klepikova, Fyodor Kondrashov, Alexey
Kondrashov, and Timothy James. “Crossing-over in a Hypervariable Species Preferentially
Occurs in Regions of High Local Similarity.” Molecular Biology and Evolution.
Oxford University Press, 2014. https://doi.org/10.1093/molbev/msu242.
ieee: V. Seplyarskiy et al., “Crossing-over in a hypervariable species preferentially
occurs in regions of high local similarity,” Molecular Biology and Evolution,
vol. 31, no. 11. Oxford University Press, pp. 3016–3025, 2014.
ista: Seplyarskiy V, Logacheva M, Penin A, Baranová M, Leushkin E, Demidenko N,
Klepikova A, Kondrashov F, Kondrashov A, James T. 2014. Crossing-over in a hypervariable
species preferentially occurs in regions of high local similarity. Molecular Biology
and Evolution. 31(11), 3016–3025.
mla: Seplyarskiy, Vladimir, et al. “Crossing-over in a Hypervariable Species Preferentially
Occurs in Regions of High Local Similarity.” Molecular Biology and Evolution,
vol. 31, no. 11, Oxford University Press, 2014, pp. 3016–25, doi:10.1093/molbev/msu242.
short: V. Seplyarskiy, M. Logacheva, A. Penin, M. Baranová, E. Leushkin, N. Demidenko,
A. Klepikova, F. Kondrashov, A. Kondrashov, T. James, Molecular Biology and Evolution
31 (2014) 3016–3025.
date_created: 2018-12-11T11:48:48Z
date_published: 2014-11-01T00:00:00Z
date_updated: 2021-01-12T08:19:21Z
day: '01'
doi: 10.1093/molbev/msu242
extern: 1
intvolume: ' 31'
issue: '11'
month: '11'
page: 3016 - 3025
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6801'
quality_controlled: 0
status: public
title: Crossing-over in a hypervariable species preferentially occurs in regions of
high local similarity
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: 31
year: '2014'
...
---
_id: '8458'
abstract:
- lang: eng
text: The maintenance of bacterial cell shape and integrity is largely attributed
to peptidoglycan, a highly cross-linked biopolymer. The transpeptidases that perform
this cross-linking are important targets for antibiotics. Despite this biomedical
importance, to date no structure of a protein in complex with an intact bacterial
peptidoglycan has been resolved, primarily due to the large size and flexibility
of peptidoglycan sacculi. Here we use solid-state NMR spectroscopy to derive for
the first time an atomic model of an l,d-transpeptidase from Bacillus subtilis
bound to its natural substrate, the intact B. subtilis peptidoglycan. Importantly,
the model obtained from protein chemical shift perturbation data shows that both
domains—the catalytic domain as well as the proposed peptidoglycan recognition
domain—are important for the interaction and reveals a novel binding motif that
involves residues outside of the classical enzymatic pocket. Experiments on mutants
and truncated protein constructs independently confirm the binding site and the
implication of both domains. Through measurements of dipolar-coupling derived
order parameters of bond motion we show that protein binding reduces the flexibility
of peptidoglycan. This first report of an atomic model of a protein–peptidoglycan
complex paves the way for the design of new antibiotic drugs targeting l,d-transpeptidases.
The strategy developed here can be extended to the study of a large variety of
enzymes involved in peptidoglycan morphogenesis.
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Sébastien
full_name: Triboulet, Sébastien
last_name: Triboulet
- first_name: Cédric
full_name: Laguri, Cédric
last_name: Laguri
- first_name: Catherine M.
full_name: Bougault, Catherine M.
last_name: Bougault
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Morgane
full_name: Callon, Morgane
last_name: Callon
- first_name: Michel
full_name: Arthur, Michel
last_name: Arthur
- first_name: Jean-Pierre
full_name: Simorre, Jean-Pierre
last_name: Simorre
citation:
ama: Schanda P, Triboulet S, Laguri C, et al. Atomic model of a cell-wall cross-linking
enzyme in complex with an intact bacterial peptidoglycan. Journal of the American
Chemical Society. 2014;136(51):17852-17860. doi:10.1021/ja5105987
apa: Schanda, P., Triboulet, S., Laguri, C., Bougault, C. M., Ayala, I., Callon,
M., … Simorre, J.-P. (2014). Atomic model of a cell-wall cross-linking enzyme
in complex with an intact bacterial peptidoglycan. Journal of the American
Chemical Society. American Chemical Society. https://doi.org/10.1021/ja5105987
chicago: Schanda, Paul, Sébastien Triboulet, Cédric Laguri, Catherine M. Bougault,
Isabel Ayala, Morgane Callon, Michel Arthur, and Jean-Pierre Simorre. “Atomic
Model of a Cell-Wall Cross-Linking Enzyme in Complex with an Intact Bacterial
Peptidoglycan.” Journal of the American Chemical Society. American Chemical
Society, 2014. https://doi.org/10.1021/ja5105987.
ieee: P. Schanda et al., “Atomic model of a cell-wall cross-linking enzyme
in complex with an intact bacterial peptidoglycan,” Journal of the American
Chemical Society, vol. 136, no. 51. American Chemical Society, pp. 17852–17860,
2014.
ista: Schanda P, Triboulet S, Laguri C, Bougault CM, Ayala I, Callon M, Arthur M,
Simorre J-P. 2014. Atomic model of a cell-wall cross-linking enzyme in complex
with an intact bacterial peptidoglycan. Journal of the American Chemical Society.
136(51), 17852–17860.
mla: Schanda, Paul, et al. “Atomic Model of a Cell-Wall Cross-Linking Enzyme in
Complex with an Intact Bacterial Peptidoglycan.” Journal of the American Chemical
Society, vol. 136, no. 51, American Chemical Society, 2014, pp. 17852–60,
doi:10.1021/ja5105987.
short: P. Schanda, S. Triboulet, C. Laguri, C.M. Bougault, I. Ayala, M. Callon,
M. Arthur, J.-P. Simorre, Journal of the American Chemical Society 136 (2014)
17852–17860.
date_created: 2020-09-18T10:07:52Z
date_published: 2014-11-27T00:00:00Z
date_updated: 2021-01-12T08:19:24Z
day: '27'
doi: 10.1021/ja5105987
extern: '1'
intvolume: ' 136'
issue: '51'
language:
- iso: eng
month: '11'
oa_version: None
page: 17852-17860
publication: Journal of the American Chemical Society
publication_identifier:
issn:
- 0002-7863
- 1520-5126
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Atomic model of a cell-wall cross-linking enzyme in complex with an intact
bacterial peptidoglycan
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 136
year: '2014'
...
---
_id: '8459'
abstract:
- lang: eng
text: Nuclear magnetic resonance (NMR) is a powerful tool for observing the motion
of biomolecules at the atomic level. One technique, the analysis of relaxation
dispersion phenomenon, is highly suited for studying the kinetics and thermodynamics
of biological processes. Built on top of the relax computational environment for
NMR dynamics is a new dispersion analysis designed to be comprehensive, accurate
and easy-to-use. The software supports more models, both numeric and analytic,
than current solutions. An automated protocol, available for scripting and driving
the graphical user interface (GUI), is designed to simplify the analysis of dispersion
data for NMR spectroscopists. Decreases in optimization time are granted by parallelization
for running on computer clusters and by skipping an initial grid search by using
parameters from one solution as the starting point for another —using analytic
model results for the numeric models, taking advantage of model nesting, and using
averaged non-clustered results for the clustered analysis.
article_processing_charge: No
article_type: original
author:
- first_name: Sébastien
full_name: Morin, Sébastien
last_name: Morin
- first_name: Troels E
full_name: Linnet, Troels E
last_name: Linnet
- first_name: Mathilde
full_name: Lescanne, Mathilde
last_name: Lescanne
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Gary S
full_name: Thompson, Gary S
last_name: Thompson
- first_name: Martin
full_name: Tollinger, Martin
last_name: Tollinger
- first_name: Kaare
full_name: Teilum, Kaare
last_name: Teilum
- first_name: Stéphane
full_name: Gagné, Stéphane
last_name: Gagné
- first_name: Dominique
full_name: Marion, Dominique
last_name: Marion
- first_name: Christian
full_name: Griesinger, Christian
last_name: Griesinger
- first_name: Martin
full_name: Blackledge, Martin
last_name: Blackledge
- first_name: Edward J
full_name: d’Auvergne, Edward J
last_name: d’Auvergne
citation:
ama: 'Morin S, Linnet TE, Lescanne M, et al. Relax: The analysis of biomolecular
kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics.
2014;30(15):2219-2220. doi:10.1093/bioinformatics/btu166'
apa: 'Morin, S., Linnet, T. E., Lescanne, M., Schanda, P., Thompson, G. S., Tollinger,
M., … d’Auvergne, E. J. (2014). Relax: The analysis of biomolecular kinetics and
thermodynamics using NMR relaxation dispersion data. Bioinformatics. Oxford
University Press. https://doi.org/10.1093/bioinformatics/btu166'
chicago: 'Morin, Sébastien, Troels E Linnet, Mathilde Lescanne, Paul Schanda, Gary
S Thompson, Martin Tollinger, Kaare Teilum, et al. “Relax: The Analysis of Biomolecular
Kinetics and Thermodynamics Using NMR Relaxation Dispersion Data.” Bioinformatics.
Oxford University Press, 2014. https://doi.org/10.1093/bioinformatics/btu166.'
ieee: 'S. Morin et al., “Relax: The analysis of biomolecular kinetics and
thermodynamics using NMR relaxation dispersion data,” Bioinformatics, vol.
30, no. 15. Oxford University Press, pp. 2219–2220, 2014.'
ista: 'Morin S, Linnet TE, Lescanne M, Schanda P, Thompson GS, Tollinger M, Teilum
K, Gagné S, Marion D, Griesinger C, Blackledge M, d’Auvergne EJ. 2014. Relax:
The analysis of biomolecular kinetics and thermodynamics using NMR relaxation
dispersion data. Bioinformatics. 30(15), 2219–2220.'
mla: 'Morin, Sébastien, et al. “Relax: The Analysis of Biomolecular Kinetics and
Thermodynamics Using NMR Relaxation Dispersion Data.” Bioinformatics, vol.
30, no. 15, Oxford University Press, 2014, pp. 2219–20, doi:10.1093/bioinformatics/btu166.'
short: S. Morin, T.E. Linnet, M. Lescanne, P. Schanda, G.S. Thompson, M. Tollinger,
K. Teilum, S. Gagné, D. Marion, C. Griesinger, M. Blackledge, E.J. d’Auvergne,
Bioinformatics 30 (2014) 2219–2220.
date_created: 2020-09-18T10:08:07Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2021-01-12T08:19:25Z
day: '01'
doi: 10.1093/bioinformatics/btu166
extern: '1'
intvolume: ' 30'
issue: '15'
keyword:
- Statistics and Probability
- Computational Theory and Mathematics
- Biochemistry
- Molecular Biology
- Computational Mathematics
- Computer Science Applications
language:
- iso: eng
month: '08'
oa_version: None
page: 2219-2220
publication: Bioinformatics
publication_identifier:
issn:
- 1367-4803
- 1460-2059
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1093/bioinformatics/btz397
status: public
title: 'Relax: The analysis of biomolecular kinetics and thermodynamics using NMR
relaxation dispersion data'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2014'
...
---
_id: '8460'
abstract:
- lang: eng
text: The function of proteins depends on their ability to sample a variety of states
differing in structure and free energy. Deciphering how the various thermally
accessible conformations are connected, and understanding their structures and
relative energies is crucial in rationalizing protein function. Many biomolecular
reactions take place within microseconds to milliseconds, and this timescale is
therefore of central functional importance. Here we show that R1ρ relaxation dispersion
experiments in magic‐angle‐spinning solid‐state NMR spectroscopy make it possible
to investigate the thermodynamics and kinetics of such exchange process, and gain
insight into structural features of short‐lived states.
article_processing_charge: No
article_type: original
author:
- first_name: Peixiang
full_name: Ma, Peixiang
last_name: Ma
- first_name: Jens D.
full_name: Haller, Jens D.
last_name: Haller
- first_name: Jérémy
full_name: Zajakala, Jérémy
last_name: Zajakala
- first_name: Pavel
full_name: Macek, Pavel
last_name: Macek
- first_name: Astrid C.
full_name: Sivertsen, Astrid C.
last_name: Sivertsen
- first_name: Dieter
full_name: Willbold, Dieter
last_name: Willbold
- first_name: Jérôme
full_name: Boisbouvier, Jérôme
last_name: Boisbouvier
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Ma P, Haller JD, Zajakala J, et al. Probing transient conformational states
of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte
Chemie International Edition. 2014;53(17):4312-4317. doi:10.1002/anie.201311275
apa: Ma, P., Haller, J. D., Zajakala, J., Macek, P., Sivertsen, A. C., Willbold,
D., … Schanda, P. (2014). Probing transient conformational states of proteins
by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie
International Edition. Wiley. https://doi.org/10.1002/anie.201311275
chicago: Ma, Peixiang, Jens D. Haller, Jérémy Zajakala, Pavel Macek, Astrid C. Sivertsen,
Dieter Willbold, Jérôme Boisbouvier, and Paul Schanda. “Probing Transient Conformational
States of Proteins by Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.”
Angewandte Chemie International Edition. Wiley, 2014. https://doi.org/10.1002/anie.201311275.
ieee: P. Ma et al., “Probing transient conformational states of proteins
by solid-state R1ρ relaxation-dispersion NMR spectroscopy,” Angewandte Chemie
International Edition, vol. 53, no. 17. Wiley, pp. 4312–4317, 2014.
ista: Ma P, Haller JD, Zajakala J, Macek P, Sivertsen AC, Willbold D, Boisbouvier
J, Schanda P. 2014. Probing transient conformational states of proteins by solid-state
R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie International Edition.
53(17), 4312–4317.
mla: Ma, Peixiang, et al. “Probing Transient Conformational States of Proteins by
Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.” Angewandte Chemie
International Edition, vol. 53, no. 17, Wiley, 2014, pp. 4312–17, doi:10.1002/anie.201311275.
short: P. Ma, J.D. Haller, J. Zajakala, P. Macek, A.C. Sivertsen, D. Willbold, J.
Boisbouvier, P. Schanda, Angewandte Chemie International Edition 53 (2014) 4312–4317.
date_created: 2020-09-18T10:08:53Z
date_published: 2014-03-18T00:00:00Z
date_updated: 2021-01-12T08:19:25Z
day: '18'
doi: 10.1002/anie.201311275
extern: '1'
intvolume: ' 53'
issue: '17'
language:
- iso: eng
month: '03'
oa_version: None
page: 4312-4317
publication: Angewandte Chemie International Edition
publication_identifier:
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion
NMR spectroscopy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 53
year: '2014'
...
---
_id: '8500'
abstract:
- lang: eng
text: The main model studied in this paper is a lattice of pendula with a nearest‐neighbor
coupling. If the coupling is weak, then the system is near‐integrable and KAM
tori fill most of the phase space. For all KAM trajectories the energy of each
pendulum stays within a narrow band for all time. Still, we show that for an arbitrarily
weak coupling of a certain localized type, the neighboring pendula can exchange
energy. In fact, the energy can be transferred between the pendula in any prescribed
way.
article_processing_charge: No
article_type: original
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Mark
full_name: Levi, Mark
last_name: Levi
- first_name: Maria
full_name: Saprykina, Maria
last_name: Saprykina
citation:
ama: Kaloshin V, Levi M, Saprykina M. Arnol′d diffusion in a pendulum lattice. Communications
on Pure and Applied Mathematics. 2014;67(5):748-775. doi:10.1002/cpa.21509
apa: Kaloshin, V., Levi, M., & Saprykina, M. (2014). Arnol′d diffusion in a
pendulum lattice. Communications on Pure and Applied Mathematics. Wiley.
https://doi.org/10.1002/cpa.21509
chicago: Kaloshin, Vadim, Mark Levi, and Maria Saprykina. “Arnol′d Diffusion in
a Pendulum Lattice.” Communications on Pure and Applied Mathematics. Wiley,
2014. https://doi.org/10.1002/cpa.21509.
ieee: V. Kaloshin, M. Levi, and M. Saprykina, “Arnol′d diffusion in a pendulum lattice,”
Communications on Pure and Applied Mathematics, vol. 67, no. 5. Wiley,
pp. 748–775, 2014.
ista: Kaloshin V, Levi M, Saprykina M. 2014. Arnol′d diffusion in a pendulum lattice.
Communications on Pure and Applied Mathematics. 67(5), 748–775.
mla: Kaloshin, Vadim, et al. “Arnol′d Diffusion in a Pendulum Lattice.” Communications
on Pure and Applied Mathematics, vol. 67, no. 5, Wiley, 2014, pp. 748–75,
doi:10.1002/cpa.21509.
short: V. Kaloshin, M. Levi, M. Saprykina, Communications on Pure and Applied Mathematics
67 (2014) 748–775.
date_created: 2020-09-18T10:47:01Z
date_published: 2014-05-01T00:00:00Z
date_updated: 2022-08-25T13:58:13Z
day: '01'
doi: 10.1002/cpa.21509
extern: '1'
intvolume: ' 67'
issue: '5'
keyword:
- Applied Mathematics
- General Mathematics
language:
- iso: eng
month: '05'
oa_version: None
page: 748-775
publication: Communications on Pure and Applied Mathematics
publication_identifier:
issn:
- 0010-3640
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Arnol′d diffusion in a pendulum lattice
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 67
year: '2014'
...
---
_id: '8501'
abstract:
- lang: eng
text: In this paper, we study small perturbations of a class of non-convex integrable
Hamiltonians with two degrees of freedom, and we prove a result of diffusion for
an open and dense set of perturbations, with an optimal time of diffusion which
grows linearly with respect to the inverse of the size of the perturbation.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Abed
full_name: Bounemoura, Abed
last_name: Bounemoura
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: Bounemoura A, Kaloshin V. Generic fast diffusion for a class of non-convex
Hamiltonians with two degrees of freedom. Moscow Mathematical Journal.
2014;14(2):181-203. doi:10.17323/1609-4514-2014-14-2-181-203
apa: Bounemoura, A., & Kaloshin, V. (2014). Generic fast diffusion for a class
of non-convex Hamiltonians with two degrees of freedom. Moscow Mathematical
Journal. Independent University of Moscow. https://doi.org/10.17323/1609-4514-2014-14-2-181-203
chicago: Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class
of Non-Convex Hamiltonians with Two Degrees of Freedom.” Moscow Mathematical
Journal. Independent University of Moscow, 2014. https://doi.org/10.17323/1609-4514-2014-14-2-181-203.
ieee: A. Bounemoura and V. Kaloshin, “Generic fast diffusion for a class of non-convex
Hamiltonians with two degrees of freedom,” Moscow Mathematical Journal,
vol. 14, no. 2. Independent University of Moscow, pp. 181–203, 2014.
ista: Bounemoura A, Kaloshin V. 2014. Generic fast diffusion for a class of non-convex
Hamiltonians with two degrees of freedom. Moscow Mathematical Journal. 14(2),
181–203.
mla: Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class of
Non-Convex Hamiltonians with Two Degrees of Freedom.” Moscow Mathematical Journal,
vol. 14, no. 2, Independent University of Moscow, 2014, pp. 181–203, doi:10.17323/1609-4514-2014-14-2-181-203.
short: A. Bounemoura, V. Kaloshin, Moscow Mathematical Journal 14 (2014) 181–203.
date_created: 2020-09-18T10:47:09Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T08:19:43Z
day: '01'
doi: 10.17323/1609-4514-2014-14-2-181-203
extern: '1'
external_id:
arxiv:
- '1304.3050'
intvolume: ' 14'
issue: '2'
keyword:
- General Mathematics
language:
- iso: eng
month: '04'
oa_version: Preprint
page: 181-203
publication: Moscow Mathematical Journal
publication_identifier:
issn:
- 1609-3321
- 1609-4514
publication_status: published
publisher: Independent University of Moscow
quality_controlled: '1'
status: public
title: Generic fast diffusion for a class of non-convex Hamiltonians with two degrees
of freedom
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2014'
...
---
_id: '852'
abstract:
- lang: eng
text: 'Rapid divergence of gene copies after duplication is thought to determine
the fate of the copies and evolution of novel protein functions. However, data
on howlong the gene copies continue to experience an elevated rate of evolution
remain scarce. Standard theory of gene duplications based on some level of genetic
redundancy of gene copies predicts that the period of accelerated evolutionmust
end relatively quickly. Using a maximum-likelihood approach we estimate preduplication,
initial postduplication, and recent postduplication rates of evolution that occurred
in themammalian lineage.Wefind that both gene copies experience a similar in magnitude
acceleration in their rate of evolution. The copy located in the original genomic
position typically returns to the preduplication rates of evolution in a short
period of time. The burst of faster evolution of the copy that is located in a
new genomic position typically lasts longer. Furthermore, the fast-evolving copies
on average continue to evolve faster than the preduplication rates far longer
than predicted by standard theory of gene duplications.We hypothesize that the
prolonged elevated rates of evolution are determined by functional properties
that were acquired during, or soon after, the gene duplication event. '
author:
- first_name: Oriol
full_name: Rosello, Oriol P
last_name: Rosello
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Rosello O, Kondrashov F. Long-Term asymmetrical acceleration of protein evolution
after gene duplication. Genome Biology and Evolution. 2014;6(8):1949-1955.
doi:10.1093/gbe/evu159
apa: Rosello, O., & Kondrashov, F. (2014). Long-Term asymmetrical acceleration
of protein evolution after gene duplication. Genome Biology and Evolution.
Oxford University Press. https://doi.org/10.1093/gbe/evu159
chicago: Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration
of Protein Evolution after Gene Duplication.” Genome Biology and Evolution.
Oxford University Press, 2014. https://doi.org/10.1093/gbe/evu159.
ieee: O. Rosello and F. Kondrashov, “Long-Term asymmetrical acceleration of protein
evolution after gene duplication,” Genome Biology and Evolution, vol. 6,
no. 8. Oxford University Press, pp. 1949–1955, 2014.
ista: Rosello O, Kondrashov F. 2014. Long-Term asymmetrical acceleration of protein
evolution after gene duplication. Genome Biology and Evolution. 6(8), 1949–1955.
mla: Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration
of Protein Evolution after Gene Duplication.” Genome Biology and Evolution,
vol. 6, no. 8, Oxford University Press, 2014, pp. 1949–55, doi:10.1093/gbe/evu159.
short: O. Rosello, F. Kondrashov, Genome Biology and Evolution 6 (2014) 1949–1955.
date_created: 2018-12-11T11:48:51Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2021-01-12T08:19:51Z
day: '01'
doi: 10.1093/gbe/evu159
extern: 1
intvolume: ' 6'
issue: '8'
month: '08'
page: 1949 - 1955
publication: Genome Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6797'
quality_controlled: 0
status: public
title: Long-Term asymmetrical acceleration of protein evolution after gene duplication
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: 6
year: '2014'
...
---
_id: '856'
abstract:
- lang: eng
text: The emergence of new genes throughout evolution requires rewiring and extension
of regulatory networks. However, the molecular details of how the transcriptional
regulation of new gene copies evolves remain largely unexplored. Here we show
how duplication of a transcription factor gene allowed the emergence of two independent
regulatory circuits. Interestingly, the ancestral transcription factor was promiscuous
and could bind different motifs in its target promoters. After duplication, one
paralogue evolved increased binding specificity so that it only binds one type
of motif, whereas the other copy evolved a decreased activity so that it only
activates promoters that contain multiple binding sites. Interestingly, only a
few mutations in both the DNA-binding domains and in the promoter binding sites
were required to gradually disentangle the two networks. These results reveal
how duplication of a promiscuous transcription factor followed by concerted cis
and trans mutations allows expansion of a regulatory network.
acknowledgement: 'K.P. acknowledges financial support from TRIPLE I and a Belspo mobility
grant from the Belgian Federal Science Policy Office co-funded by the Marie Curie
Actions from the European Commission. Research in the lab of K.J.V. is supported
by ERC Starting Grant 241426, HFSP programme grant RGP0050/2013, VIB, EMBO YIP programme,
KU Leuven Programme Financing, FWO, and IWT. A.V. acknowledges RIKEN for the FPR
grant. The work of F.A.K. was supported by a grant of the HHMI International Early
Career Scientist Programme (grant #55007424), the Spanish Ministry of Economy and
Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP programme, two grants
from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia
Severo Ochoa 2013–2017 (grant #Sev-2012-0208)’ and (grant #BES-2013-064004) funded
by the European Regional Development Fund (ERDF), the European Union and the European
Research Council (grant #335980_EinME). K.V. is supported by an FWO postdoctoral
fellowship. Funders had no role in study design, data collection and analysis, decision
to publish or preparation of the manuscript.'
author:
- first_name: Ksenia
full_name: Pougach, Ksenia S
last_name: Pougach
- first_name: Arnout
full_name: Voet, Arnout R
last_name: Voet
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Karin
full_name: Voordeckers, Karin
last_name: Voordeckers
- first_name: Joaquin
full_name: Christiaens, Joaquin F
last_name: Christiaens
- first_name: Bianka
full_name: Baying, Bianka
last_name: Baying
- first_name: Vladimı́R
full_name: Bénès, Vladimı́r
last_name: Bénès
- first_name: Ryo
full_name: Sakai, Ryo
last_name: Sakai
- first_name: Jan
full_name: Aerts, Jan A
last_name: Aerts
- first_name: Bo
full_name: Zhu, Bo
last_name: Zhu
- first_name: Patrick
full_name: Van Dijck, Patrick
last_name: Van Dijck
- first_name: Kevin
full_name: Verstrepen, Kevin J
last_name: Verstrepen
citation:
ama: Pougach K, Voet A, Kondrashov F, et al. Duplication of a promiscuous transcription
factor drives the emergence of a new regulatory network. Nature Communications.
2014;5. doi:10.1038/ncomms5868
apa: Pougach, K., Voet, A., Kondrashov, F., Voordeckers, K., Christiaens, J., Baying,
B., … Verstrepen, K. (2014). Duplication of a promiscuous transcription factor
drives the emergence of a new regulatory network. Nature Communications.
Nature Publishing Group. https://doi.org/10.1038/ncomms5868
chicago: Pougach, Ksenia, Arnout Voet, Fyodor Kondrashov, Karin Voordeckers, Joaquin
Christiaens, Bianka Baying, Vladimı́R Bénès, et al. “Duplication of a Promiscuous
Transcription Factor Drives the Emergence of a New Regulatory Network.” Nature
Communications. Nature Publishing Group, 2014. https://doi.org/10.1038/ncomms5868.
ieee: K. Pougach et al., “Duplication of a promiscuous transcription factor
drives the emergence of a new regulatory network,” Nature Communications,
vol. 5. Nature Publishing Group, 2014.
ista: Pougach K, Voet A, Kondrashov F, Voordeckers K, Christiaens J, Baying B, Bénès
V, Sakai R, Aerts J, Zhu B, Van Dijck P, Verstrepen K. 2014. Duplication of a
promiscuous transcription factor drives the emergence of a new regulatory network.
Nature Communications. 5.
mla: Pougach, Ksenia, et al. “Duplication of a Promiscuous Transcription Factor
Drives the Emergence of a New Regulatory Network.” Nature Communications,
vol. 5, Nature Publishing Group, 2014, doi:10.1038/ncomms5868.
short: K. Pougach, A. Voet, F. Kondrashov, K. Voordeckers, J. Christiaens, B. Baying,
V. Bénès, R. Sakai, J. Aerts, B. Zhu, P. Van Dijck, K. Verstrepen, Nature Communications
5 (2014).
date_created: 2018-12-11T11:48:52Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T08:20:01Z
day: '01'
doi: 10.1038/ncomms5868
extern: 1
intvolume: ' 5'
month: '01'
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '6790'
quality_controlled: 0
status: public
title: Duplication of a promiscuous transcription factor drives the emergence of a
new regulatory network
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: 5
year: '2014'
...