---
_id: '1809'
abstract:
- lang: eng
text: 'Background: Indirect genetic effects (IGEs) occur when genes expressed in
one individual alter the expression of traits in social partners. Previous studies
focused on the evolutionary consequences and evolutionary dynamics of IGEs, using
equilibrium solutions to predict phenotypes in subsequent generations. However,
whether or not such steady states may be reached may depend on the dynamics of
interactions themselves. Results: In our study, we focus on the dynamics of social
interactions and indirect genetic effects and investigate how they modify phenotypes
over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics;
rather we consider within-individual phenotypic changes, also referred to as phenotypic
plasticity. We analyse iterative interactions, when individuals interact in a
series of discontinuous events, and investigate the stability of steady state
solutions and the dependence on model parameters, such as population size, strength,
and the nature of interactions. We show that for interactions where a feedback
loop occurs, the possible parameter space of interaction strength is fairly limited,
affecting the evolutionary consequences of IGEs. We discuss the implications of
our results for current IGE model predictions and their limitations.'
author:
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Reinmar
full_name: Hager, Reinmar
last_name: Hager
citation:
ama: Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of
social interactions. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0126907
apa: Trubenova, B., Novak, S., & Hager, R. (2015). Indirect genetic effects
and the dynamics of social interactions. PLoS One. Public Library of Science.
https://doi.org/10.1371/journal.pone.0126907
chicago: Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic
Effects and the Dynamics of Social Interactions.” PLoS One. Public Library
of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.
ieee: B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics
of social interactions,” PLoS One, vol. 10, no. 5. Public Library of Science,
2015.
ista: Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics
of social interactions. PLoS One. 10(5).
mla: Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social
Interactions.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015,
doi:10.1371/journal.pone.0126907.
short: B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015).
date_created: 2018-12-11T11:54:07Z
date_published: 2015-05-18T00:00:00Z
date_updated: 2023-02-23T14:07:48Z
day: '18'
ddc:
- '570'
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pone.0126907
file:
- access_level: open_access
checksum: d3a4a58ef4bd3b3e2f32b7fd7af4a743
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:07Z
date_updated: 2020-07-14T12:45:17Z
file_id: '4730'
file_name: IST-2016-453-v1+1_journal.pone.0126907.pdf
file_size: 2748982
relation: main_file
file_date_updated: 2020-07-14T12:45:17Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '5299'
pubrep_id: '453'
quality_controlled: '1'
related_material:
record:
- id: '9715'
relation: research_data
status: public
- id: '9772'
relation: research_data
status: public
scopus_import: 1
status: public
title: Indirect genetic effects and the dynamics of social interactions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2015'
...
---
_id: '9772'
article_processing_charge: No
author:
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Reinmar
full_name: Hager, Reinmar
last_name: Hager
citation:
ama: Trubenova B, Novak S, Hager R. Description of the agent based simulations.
2015. doi:10.1371/journal.pone.0126907.s003
apa: Trubenova, B., Novak, S., & Hager, R. (2015). Description of the agent
based simulations. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s003
chicago: Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Description of
the Agent Based Simulations.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s003.
ieee: B. Trubenova, S. Novak, and R. Hager, “Description of the agent based simulations.”
Public Library of Science, 2015.
ista: Trubenova B, Novak S, Hager R. 2015. Description of the agent based simulations,
Public Library of Science, 10.1371/journal.pone.0126907.s003.
mla: Trubenova, Barbora, et al. Description of the Agent Based Simulations.
Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.s003.
short: B. Trubenova, S. Novak, R. Hager, (2015).
date_created: 2021-08-05T12:55:20Z
date_published: 2015-05-18T00:00:00Z
date_updated: 2023-02-23T10:15:25Z
day: '18'
department:
- _id: NiBa
doi: 10.1371/journal.pone.0126907.s003
month: '05'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1809'
relation: used_in_publication
status: public
status: public
title: Description of the agent based simulations
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '9773'
article_processing_charge: No
author:
- first_name: Tamar
full_name: Friedlander, Tamar
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Avraham E.
full_name: Mayo, Avraham E.
last_name: Mayo
- first_name: Tsvi
full_name: Tlusty, Tsvi
last_name: Tlusty
- first_name: Uri
full_name: Alon, Uri
last_name: Alon
citation:
ama: Friedlander T, Mayo AE, Tlusty T, Alon U. Evolutionary simulation code. 2015.
doi:10.1371/journal.pcbi.1004055.s002
apa: Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Evolutionary
simulation code. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s002
chicago: Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Evolutionary
Simulation Code.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.s002.
ieee: T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Evolutionary simulation
code.” Public Library of Science, 2015.
ista: Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Evolutionary simulation code,
Public Library of Science, 10.1371/journal.pcbi.1004055.s002.
mla: Friedlander, Tamar, et al. Evolutionary Simulation Code. Public Library
of Science, 2015, doi:10.1371/journal.pcbi.1004055.s002.
short: T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).
date_created: 2021-08-05T12:58:07Z
date_published: 2015-03-23T00:00:00Z
date_updated: 2023-02-23T10:16:13Z
day: '23'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1004055.s002
month: '03'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1827'
relation: used_in_publication
status: public
status: public
title: Evolutionary simulation code
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '981'
abstract:
- lang: eng
text: The tunability of topological surface states and controllable opening of the
Dirac gap are of fundamental and practical interest in the field of topological
materials. In the newly discovered topological crystalline insulators (TCIs),
theory predicts that the Dirac node is protected by a crystalline symmetry and
that the surface state electrons can acquire a mass if this symmetry is broken.
Recent studies have detected signatures of a spontaneously generated Dirac gap
in TCIs; however, the mechanism of mass formation remains elusive. In this work,
we present scanning tunnelling microscopy (STM) measurements of the TCI Pb 1â'x
Sn x Se for a wide range of alloy compositions spanning the topological and non-topological
regimes. The STM topographies reveal a symmetry-breaking distortion on the surface,
which imparts mass to the otherwise massless Dirac electrons-a mechanism analogous
to the long sought-after Higgs mechanism in particle physics. Interestingly, the
measured Dirac gap decreases on approaching the trivial phase, whereas the magnitude
of the distortion remains nearly constant. Our data and calculations reveal that
the penetration depth of Dirac surface states controls the magnitude of the Dirac
mass. At the limit of the critical composition, the penetration depth is predicted
to go to infinity, resulting in zero mass, consistent with our measurements. Finally,
we discover the existence of surface states in the non-topological regime, which
have the characteristics of gapped, double-branched Dirac fermions and could be
exploited in realizing superconductivity in these materials.
acknowledgement: We thank R. Buczko, C. Chamon, J. C. Seamus Davis, M. El-Batanouny,
A. Mesaros, Y. Ran and A. Soumyanarayanan for useful conversations and G. McMahon
for help with EDS measurements. V.M. gratefully acknowledges funding from the US
Department of Energy, Scanned Probe Division under Award Number DE-FG02-12ER46880
for the support of I.Z., Y.O., W.Z. and D.W. for this project. Work at Massachusetts
Institute of Technology is supported by US Department of Energy, Office of Basic
Energy Sciences, Division of Materials Sciences and Engineering under Award DE-SC0010526
(L.F.), and NSF-DMR-1104498 (M.S.). H.L. acknowledges the Singapore National Research
Foundation for support under NRF Award No. NRF-NRFF2013-03. Y.O. was partly supported
by JSPS KAKENHI Grant Numbers 26707016 and 00707656. The work at Northeastern University
is supported by the US Department of Energy grant number DE-FG02-07ER46352, and
benefited from Northeastern University’s Advanced Scientific Computation Center
(ASCC), theory support at the Advanced Light Source, Berkeley and the allocation
of supercomputer time at the NERSC through DOE grant number DE-AC02-05CH11231. Work
at Princeton University is supported by the US National Science Foundation Grant,
NSF-DMR-1006492. F.C. acknowledges the support provided by MOST-Taiwan under project
number NSC-102-2119-M-002-004.
author:
- first_name: Ilija
full_name: Zeljkovic, Ilija
last_name: Zeljkovic
- first_name: Yoshinori
full_name: Okada, Yoshinori
last_name: Okada
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Raman
full_name: Sankar, Raman
last_name: Sankar
- first_name: Daniel
full_name: Walkup, Daniel
last_name: Walkup
- first_name: Wenwen
full_name: Zhou, Wenwen
last_name: Zhou
- first_name: Junwei
full_name: Liu, Junwei
last_name: Liu
- first_name: Guoqing
full_name: Chang, Guoqing
last_name: Chang
- first_name: Yungjui
full_name: Wang, Yungjui
last_name: Wang
- first_name: Md
full_name: Hasan, Md Z
last_name: Hasan
- first_name: Fangcheng
full_name: Chou, Fangcheng
last_name: Chou
- first_name: Hsin
full_name: Lin, Hsin
last_name: Lin
- first_name: Arun
full_name: Bansil, Arun
last_name: Bansil
- first_name: Liang
full_name: Fu, Liang
last_name: Fu
- first_name: Vidya
full_name: Madhavan, Vidya
last_name: Madhavan
citation:
ama: Zeljkovic I, Okada Y, Serbyn M, et al. Dirac mass generation from crystal symmetry
breaking on the surfaces of topological crystalline insulators. Nature Materials.
2015;14(3):318-324. doi:10.1038/nmat4215
apa: Zeljkovic, I., Okada, Y., Serbyn, M., Sankar, R., Walkup, D., Zhou, W., … Madhavan,
V. (2015). Dirac mass generation from crystal symmetry breaking on the surfaces
of topological crystalline insulators. Nature Materials. Nature Publishing
Group. https://doi.org/10.1038/nmat4215
chicago: Zeljkovic, Ilija, Yoshinori Okada, Maksym Serbyn, Raman Sankar, Daniel
Walkup, Wenwen Zhou, Junwei Liu, et al. “Dirac Mass Generation from Crystal Symmetry
Breaking on the Surfaces of Topological Crystalline Insulators.” Nature Materials.
Nature Publishing Group, 2015. https://doi.org/10.1038/nmat4215.
ieee: I. Zeljkovic et al., “Dirac mass generation from crystal symmetry breaking
on the surfaces of topological crystalline insulators,” Nature Materials,
vol. 14, no. 3. Nature Publishing Group, pp. 318–324, 2015.
ista: Zeljkovic I, Okada Y, Serbyn M, Sankar R, Walkup D, Zhou W, Liu J, Chang G,
Wang Y, Hasan M, Chou F, Lin H, Bansil A, Fu L, Madhavan V. 2015. Dirac mass generation
from crystal symmetry breaking on the surfaces of topological crystalline insulators.
Nature Materials. 14(3), 318–324.
mla: Zeljkovic, Ilija, et al. “Dirac Mass Generation from Crystal Symmetry Breaking
on the Surfaces of Topological Crystalline Insulators.” Nature Materials,
vol. 14, no. 3, Nature Publishing Group, 2015, pp. 318–24, doi:10.1038/nmat4215.
short: I. Zeljkovic, Y. Okada, M. Serbyn, R. Sankar, D. Walkup, W. Zhou, J. Liu,
G. Chang, Y. Wang, M. Hasan, F. Chou, H. Lin, A. Bansil, L. Fu, V. Madhavan, Nature
Materials 14 (2015) 318–324.
date_created: 2018-12-11T11:49:31Z
date_published: 2015-03-01T00:00:00Z
date_updated: 2021-01-12T08:22:24Z
day: '01'
doi: 10.1038/nmat4215
extern: 1
intvolume: ' 14'
issue: '3'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1403.4906
month: '03'
oa: 1
page: 318 - 324
publication: Nature Materials
publication_status: published
publisher: Nature Publishing Group
publist_id: '6419'
quality_controlled: 0
status: public
title: Dirac mass generation from crystal symmetry breaking on the surfaces of topological
crystalline insulators
type: journal_article
volume: 14
year: '2015'
...
---
_id: '982'
abstract:
- lang: eng
text: We propose a new approach to probing ergodicity and its breakdown in one-dimensional
quantum manybody systems based on their response to a local perturbation. We study
the distribution of matrix elements of a local operator between the system's eigenstates,
finding a qualitatively different behavior in the manybody localized (MBL) and
ergodic phases. To characterize how strongly a local perturbation modifies the
eigenstates, we introduce the parameter g(L) = (In (Vnm/δ)) which represents the
disorder-averaged ratio of a typical matrix element of a local operator V to energy
level spacing δ this parameter is reminiscent of the Thouless conductance in the
single-particle localization. We show that the parameter g(L) decreases with system
size L in the MBL phase and grows in the ergodic phase. We surmise that the delocalization
transition occurs when g(L) is independent of system size, g(L)=gc ~ 1. We illustrate
our approach by studying the many-body localization transition and resolving the
many-body mobility edge in a disordered one-dimensional XXZ spin-1=2 chain using
exact diagonalization and time-evolving block-decimation methods. Our criterion
for the MBL transition gives insights into microscopic details of transition.
Its direct physical consequences, in particular, logarithmically slow transport
at the transition and extensive entanglement entropy of the eigenstates, are consistent
with recent renormalization-group predictions.
acknowledgement: We acknowledge helpful discussions with Sid Parameswaran, Andrew
Potter, Antonello Scardicchio, Romain Vasseur, and especially with Ehud Altman and
David Huse. We would like to thank Miles Stoudenmire for the assistance with ITensor
library. Research at Perimeter Institute is supported by the Government of Canada
through Industry Canada and by the Province of Ontario through the Ministry of Economic
Development & Innovation. This research was supported by Gordon and Betty Moore
Foundation EPiQS Initiative through Grant No. GBMF4307 (M. S.), Sloan Foundation,
NSERC, and Early Researcher Award of Ontario (D. A.). This work made use of the
facilities of N8 HPC Centre of Excellence, provided and funded by the N8 consortium
and EPSRC (Grant No. EP/K000225/1). The Centre is coordinated by the Universities
of Leeds and Manchester.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
- first_name: Dmitry
full_name: Abanin, Dmitry A
last_name: Abanin
citation:
ama: Serbyn M, Papić Z, Abanin D. Criterion for many-body localization-delocalization
phase transition. Physical Review X. 2015;5(4). doi:10.1103/PhysRevX.5.041047
apa: Serbyn, M., Papić, Z., & Abanin, D. (2015). Criterion for many-body localization-delocalization
phase transition. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.5.041047
chicago: Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Criterion for Many-Body
Localization-Delocalization Phase Transition.” Physical Review X. American
Physical Society, 2015. https://doi.org/10.1103/PhysRevX.5.041047.
ieee: M. Serbyn, Z. Papić, and D. Abanin, “Criterion for many-body localization-delocalization
phase transition,” Physical Review X, vol. 5, no. 4. American Physical
Society, 2015.
ista: Serbyn M, Papić Z, Abanin D. 2015. Criterion for many-body localization-delocalization
phase transition. Physical Review X. 5(4).
mla: Serbyn, Maksym, et al. “Criterion for Many-Body Localization-Delocalization
Phase Transition.” Physical Review X, vol. 5, no. 4, American Physical
Society, 2015, doi:10.1103/PhysRevX.5.041047.
short: M. Serbyn, Z. Papić, D. Abanin, Physical Review X 5 (2015).
date_created: 2018-12-11T11:49:32Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T08:22:25Z
day: '01'
doi: 10.1103/PhysRevX.5.041047
extern: 1
intvolume: ' 5'
issue: '4'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1507.01635
month: '01'
oa: 1
publication: Physical Review X
publication_status: published
publisher: American Physical Society
publist_id: '6418'
quality_controlled: 0
status: public
title: Criterion for many-body localization-delocalization phase transition
type: journal_article
volume: 5
year: '2015'
...
---
_id: '99'
abstract:
- lang: eng
text: Quasiparticle excitations can compromise the performance of superconducting
devices, causing high-frequency dissipation, decoherence in Josephson qubits,
and braiding errors in proposed Majorana-based topological quantum computers.
Quasiparticle dynamics have been studied in detail in metallic superconductors
but remain relatively unexplored in semiconductor-superconductor structures, which
are now being intensely pursued in the context of topological superconductivity.
To this end, we use a system comprising a gate-confined semiconductor nanowire
with an epitaxially grown superconductor layer, yielding an isolated, proximitized
nanowire segment. We identify bound states in the semiconductor by means of bias
spectroscopy, determine the characteristic temperatures and magnetic fields for
quasiparticle excitations, and extract a parity lifetime (poisoning time) of the
bound state in the semiconductor exceeding 10 ms.
acknowledgement: Research support by Microsoft Project Q, the Danish National Research
Foundation, the Lundbeck Foundation, the Carlsberg Foundation, and the European
Commission. A.P.H. acknowledges support from the US Department of Energy, C.M.M.
acknowledges support from the Villum Foundation.
author:
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: S M
full_name: Albrecht, S M
last_name: Albrecht
- first_name: Gediminas
full_name: Kiršanskas, Gediminas
last_name: Kiršanskas
- first_name: W
full_name: Chang, W
last_name: Chang
- first_name: Ferdinand
full_name: Kuemmeth, Ferdinand
last_name: Kuemmeth
- first_name: Peter
full_name: Krogstrup, Peter
last_name: Krogstrup
- first_name: Thomas
full_name: Jespersen, Thomas
last_name: Jespersen
- first_name: Jesper
full_name: Nygård, Jesper
last_name: Nygård
- first_name: Karsten
full_name: Flensberg, Karsten
last_name: Flensberg
- first_name: Charles
full_name: Marcus, Charles
last_name: Marcus
citation:
ama: Higginbotham AP, Albrecht SM, Kiršanskas G, et al. Parity lifetime of bound
states in a proximitized semiconductor nanowire. Nature Physics. 2015;11(12):1017-1021.
doi:10.1038/nphys3461
apa: Higginbotham, A. P., Albrecht, S. M., Kiršanskas, G., Chang, W., Kuemmeth,
F., Krogstrup, P., … Marcus, C. (2015). Parity lifetime of bound states in a proximitized
semiconductor nanowire. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys3461
chicago: Higginbotham, Andrew P, S M Albrecht, Gediminas Kiršanskas, W Chang, Ferdinand
Kuemmeth, Peter Krogstrup, Thomas Jespersen, Jesper Nygård, Karsten Flensberg,
and Charles Marcus. “Parity Lifetime of Bound States in a Proximitized Semiconductor
Nanowire.” Nature Physics. Nature Publishing Group, 2015. https://doi.org/10.1038/nphys3461.
ieee: A. P. Higginbotham et al., “Parity lifetime of bound states in a proximitized
semiconductor nanowire,” Nature Physics, vol. 11, no. 12. Nature Publishing
Group, pp. 1017–1021, 2015.
ista: Higginbotham AP, Albrecht SM, Kiršanskas G, Chang W, Kuemmeth F, Krogstrup
P, Jespersen T, Nygård J, Flensberg K, Marcus C. 2015. Parity lifetime of bound
states in a proximitized semiconductor nanowire. Nature Physics. 11(12), 1017–1021.
mla: Higginbotham, Andrew P., et al. “Parity Lifetime of Bound States in a Proximitized
Semiconductor Nanowire.” Nature Physics, vol. 11, no. 12, Nature Publishing
Group, 2015, pp. 1017–21, doi:10.1038/nphys3461.
short: A.P. Higginbotham, S.M. Albrecht, G. Kiršanskas, W. Chang, F. Kuemmeth, P.
Krogstrup, T. Jespersen, J. Nygård, K. Flensberg, C. Marcus, Nature Physics 11
(2015) 1017–1021.
date_created: 2018-12-11T11:44:37Z
date_published: 2015-09-14T00:00:00Z
date_updated: 2021-01-12T08:22:28Z
day: '14'
doi: 10.1038/nphys3461
extern: '1'
external_id:
arxiv:
- '1501.05155'
intvolume: ' 11'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1501.05155
month: '09'
oa: 1
oa_version: Preprint
page: 1017 - 1021
publication: Nature Physics
publication_status: published
publisher: Nature Publishing Group
publist_id: '7955'
quality_controlled: '1'
status: public
title: Parity lifetime of bound states in a proximitized semiconductor nanowire
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2015'
...
---
_id: '8495'
abstract:
- lang: eng
text: 'In this note, we consider the dynamics associated to a perturbation of an
integrable Hamiltonian system in action-angle coordinates in any number of degrees
of freedom and we prove the following result of ``micro-diffusion'''': under generic
assumptions on $ h$ and $ f$, there exists an orbit of the system for which the
drift of its action variables is at least of order $ \sqrt {\varepsilon }$, after
a time of order $ \sqrt {\varepsilon }^{-1}$. The assumptions, which are essentially
minimal, are that there exists a resonant point for $ h$ and that the corresponding
averaged perturbation is non-constant. The conclusions, although very weak when
compared to usual instability phenomena, are also essentially optimal within this
setting.'
article_processing_charge: No
article_type: letter_note
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. A note on micro-instability for Hamiltonian systems
close to integrable. Proceedings of the American Mathematical Society.
2015;144(4):1553-1560. doi:10.1090/proc/12796
apa: Bounemoura, A., & Kaloshin, V. (2015). A note on micro-instability for
Hamiltonian systems close to integrable. Proceedings of the American Mathematical
Society. American Mathematical Society. https://doi.org/10.1090/proc/12796
chicago: Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for
Hamiltonian Systems Close to Integrable.” Proceedings of the American Mathematical
Society. American Mathematical Society, 2015. https://doi.org/10.1090/proc/12796.
ieee: A. Bounemoura and V. Kaloshin, “A note on micro-instability for Hamiltonian
systems close to integrable,” Proceedings of the American Mathematical Society,
vol. 144, no. 4. American Mathematical Society, pp. 1553–1560, 2015.
ista: Bounemoura A, Kaloshin V. 2015. A note on micro-instability for Hamiltonian
systems close to integrable. Proceedings of the American Mathematical Society.
144(4), 1553–1560.
mla: Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for Hamiltonian
Systems Close to Integrable.” Proceedings of the American Mathematical Society,
vol. 144, no. 4, American Mathematical Society, 2015, pp. 1553–60, doi:10.1090/proc/12796.
short: A. Bounemoura, V. Kaloshin, Proceedings of the American Mathematical Society
144 (2015) 1553–1560.
date_created: 2020-09-18T10:46:14Z
date_published: 2015-12-21T00:00:00Z
date_updated: 2021-01-12T08:19:40Z
day: '21'
doi: 10.1090/proc/12796
extern: '1'
intvolume: ' 144'
issue: '4'
language:
- iso: eng
month: '12'
oa_version: None
page: 1553-1560
publication: Proceedings of the American Mathematical Society
publication_identifier:
issn:
- 0002-9939
- 1088-6826
publication_status: published
publisher: American Mathematical Society
quality_controlled: '1'
status: public
title: A note on micro-instability for Hamiltonian systems close to integrable
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 144
year: '2015'
...
---
_id: '866'
abstract:
- lang: eng
text: Proteases play important roles in many biologic processes and are key mediators
of cancer, inflammation, and thrombosis. However, comprehensive and quantitative
techniques to define the substrate specificity profile of proteases are lacking.
The metalloprotease ADAMTS13 regulates blood coagulation by cleaving von Willebrand
factor (VWF), reducing its procoagulant activity. A mutagenized substrate phage
display library based on a 73-amino acid fragment of VWF was constructed, and
the ADAMTS13-dependent change in library complexity was evaluated over reaction
time points, using high-throughput sequencing. Reaction rate constants (kcat/KM)
were calculated for nearly every possible single amino acid substitution within
this fragment. This massively parallel enzyme kinetics analysis detailed the specificity
of ADAMTS13 and demonstrated the critical importance of the P1-P1' substrate residues
while defining exosite binding domains. These data provided empirical evidence
for the propensity for epistasis within VWF and showed strong correlation to conservation
across orthologs, highlighting evolutionary selective pressures for VWF.
acknowledgement: |
We thank Isabel Wang and Vivian Cheung from the Life Sciences Institute, University of Michigan, for assistance with high- throughput sequencing experiments and valuable discussions. We also thank J. Evan Sadler (Washington University) and Sriram Krishnaswamy (Children’s Hospital of Philadelphia) for helpful discussions. We thank Jeff Weitz (McMaster University), Jim Fredenburgh (McMaster University), and Steve Weiss (University of Michigan) for critical review of the manuscript. C.A.K. was awarded the Judith Graham Pool Fellowship from National Hemophilia Foundation. This work was supported by the National Institutes of Health (R01 HL039693), the National Heart, Lung, and Blood Institute (P01- HL057346), Ministerio de Economía y Competitividad Grants BFU2012- 31329 and Sev-2012-0208, and European Research Council Starting Grant 335980_EinME. D.G. is an investigator of the Howard Hughes Medical In- stitute, and F.A.K. is a Howard Hughes Medical Institute International Early Career Scientist.
author:
- first_name: Colin
full_name: Kretz, Colin A
last_name: Kretz
- first_name: Manhong
full_name: Dai, Manhong
last_name: Dai
- first_name: Onuralp
full_name: Soylemez, Onuralp
last_name: Soylemez
- first_name: Andrew
full_name: Yee, Andrew
last_name: Yee
- first_name: Karl
full_name: Desch, Karl C
last_name: Desch
- first_name: David
full_name: Siemieniak, David R
last_name: Siemieniak
- first_name: Kärt
full_name: Tomberg, Kärt
last_name: Tomberg
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Fan
full_name: Meng, Fan
last_name: Meng
- first_name: David
full_name: Ginsburg, David B
last_name: Ginsburg
citation:
ama: Kretz C, Dai M, Soylemez O, et al. Massively parallel enzyme kinetics reveals
the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS.
2015;112(30):9328-9333. doi:10.1073/pnas.1511328112
apa: Kretz, C., Dai, M., Soylemez, O., Yee, A., Desch, K., Siemieniak, D., … Ginsburg,
D. (2015). Massively parallel enzyme kinetics reveals the substrate recognition
landscape of the metalloprotease ADAMTS13. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.1511328112
chicago: Kretz, Colin, Manhong Dai, Onuralp Soylemez, Andrew Yee, Karl Desch, David
Siemieniak, Kärt Tomberg, Fyodor Kondrashov, Fan Meng, and David Ginsburg. “Massively
Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease
ADAMTS13.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1511328112.
ieee: C. Kretz et al., “Massively parallel enzyme kinetics reveals the substrate
recognition landscape of the metalloprotease ADAMTS13,” PNAS, vol. 112,
no. 30. National Academy of Sciences, pp. 9328–9333, 2015.
ista: Kretz C, Dai M, Soylemez O, Yee A, Desch K, Siemieniak D, Tomberg K, Kondrashov
F, Meng F, Ginsburg D. 2015. Massively parallel enzyme kinetics reveals the substrate
recognition landscape of the metalloprotease ADAMTS13. PNAS. 112(30), 9328–9333.
mla: Kretz, Colin, et al. “Massively Parallel Enzyme Kinetics Reveals the Substrate
Recognition Landscape of the Metalloprotease ADAMTS13.” PNAS, vol. 112,
no. 30, National Academy of Sciences, 2015, pp. 9328–33, doi:10.1073/pnas.1511328112.
short: C. Kretz, M. Dai, O. Soylemez, A. Yee, K. Desch, D. Siemieniak, K. Tomberg,
F. Kondrashov, F. Meng, D. Ginsburg, PNAS 112 (2015) 9328–9333.
date_created: 2018-12-11T11:48:55Z
date_published: 2015-07-28T00:00:00Z
date_updated: 2021-01-12T08:20:26Z
day: '28'
doi: 10.1073/pnas.1511328112
extern: 1
intvolume: ' 112'
issue: '30'
month: '07'
page: 9328 - 9333
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6783'
quality_controlled: 0
status: public
title: Massively parallel enzyme kinetics reveals the substrate recognition landscape
of the metalloprotease ADAMTS13
type: journal_article
volume: 112
year: '2015'
...
---
_id: '886'
abstract:
- lang: eng
text: The factors that determine the tempo and mode of protein evolution continue
to be a central question in molecular evolution. Traditionally, studies of protein
evolution focused on the rates of amino acid substitutions. More recently, with
the availability of sequence data and advanced experimental techniques, the focus
of attention has shifted toward the study of evolutionary trajectories and the
overall layout of protein fitness landscapes. In this review we describe the effect
of epistasis on the topology of evolutionary pathways that are likely to be found
in fitness landscapes and develop a simple theory to connect the number of maladapted
genotypes to the topology of fitness landscapes with epistatic interactions. Finally,
we review recent studies that have probed the extent of epistatic interactions
and have begun to chart the fitness landscapes in protein sequence space.
acknowledgement: 'This work has been supported by a grant from the HHMI International
Early Career Scientist Program (#55007424), the Spanish Ministry of Economy and
Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP program, two grants
from the Spanish Ministry of Economy and Competitiveness, Centro de Excelencia Severo
Ochoa 2013–2017 (#Sev-2012-0208) and BES-2013-064004 funded by the European Regional
Development Fund (ERDF), the European Union, and the European Research Council under
grant agreement no 335980_EinME.'
author:
- first_name: Dmitry
full_name: Kondrashov, Dmitry A
last_name: Kondrashov
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kondrashov D, Kondrashov F. Topological features of rugged fitness landscapes
in sequence space. Trends in Genetics. 2015;31(1):24-33. doi:10.1016/j.tig.2014.09.009
apa: Kondrashov, D., & Kondrashov, F. (2015). Topological features of rugged
fitness landscapes in sequence space. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2014.09.009
chicago: Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged
Fitness Landscapes in Sequence Space.” Trends in Genetics. Elsevier, 2015.
https://doi.org/10.1016/j.tig.2014.09.009.
ieee: D. Kondrashov and F. Kondrashov, “Topological features of rugged fitness landscapes
in sequence space,” Trends in Genetics, vol. 31, no. 1. Elsevier, pp. 24–33,
2015.
ista: Kondrashov D, Kondrashov F. 2015. Topological features of rugged fitness landscapes
in sequence space. Trends in Genetics. 31(1), 24–33.
mla: Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged
Fitness Landscapes in Sequence Space.” Trends in Genetics, vol. 31, no.
1, Elsevier, 2015, pp. 24–33, doi:10.1016/j.tig.2014.09.009.
short: D. Kondrashov, F. Kondrashov, Trends in Genetics 31 (2015) 24–33.
date_created: 2018-12-11T11:49:01Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T08:21:16Z
day: '01'
doi: 10.1016/j.tig.2014.09.009
extern: 1
intvolume: ' 31'
issue: '1'
month: '01'
page: 24 - 33
publication: Trends in Genetics
publication_status: published
publisher: Elsevier
publist_id: '6764'
quality_controlled: 0
status: public
title: Topological features of rugged fitness landscapes in sequence space
type: journal_article
volume: 31
year: '2015'
...
---
_id: '9017'
abstract:
- lang: eng
text: MCM2 is a subunit of the replicative helicase machinery shown to interact
with histones H3 and H4 during the replication process through its N-terminal
domain. During replication, this interaction has been proposed to assist disassembly
and assembly of nucleosomes on DNA. However, how this interaction participates
in crosstalk with histone chaperones at the replication fork remains to be elucidated.
Here, we solved the crystal structure of the ternary complex between the histone-binding
domain of Mcm2 and the histones H3-H4 at 2.9 Å resolution. Histones H3 and H4
assemble as a tetramer in the crystal structure, but MCM2 interacts only with
a single molecule of H3-H4. The latter interaction exploits binding surfaces that
contact either DNA or H2B when H3-H4 dimers are incorporated in the nucleosome
core particle. Upon binding of the ternary complex with the histone chaperone
ASF1, the histone tetramer dissociates and both MCM2 and ASF1 interact simultaneously
with the histones forming a 1:1:1:1 heteromeric complex. Thermodynamic analysis
of the quaternary complex together with structural modeling support that ASF1
and MCM2 could form a chaperoning module for histones H3 and H4 protecting them
from promiscuous interactions. This suggests an additional function for MCM2 outside
its helicase function as a proper histone chaperone connected to the replication
pathway.
article_processing_charge: No
article_type: original
author:
- first_name: Nicolas
full_name: Richet, Nicolas
last_name: Richet
- first_name: Danni
full_name: Liu, Danni
last_name: Liu
- first_name: Pierre
full_name: Legrand, Pierre
last_name: Legrand
- first_name: Christophe
full_name: Velours, Christophe
last_name: Velours
- first_name: Armelle
full_name: Corpet, Armelle
last_name: Corpet
- first_name: Albane
full_name: Gaubert, Albane
last_name: Gaubert
- first_name: May M
full_name: Bakail, May M
id: FB3C3F8E-522F-11EA-B186-22963DDC885E
last_name: Bakail
orcid: 0000-0002-9592-1587
- first_name: Gwenaelle
full_name: Moal-Raisin, Gwenaelle
last_name: Moal-Raisin
- first_name: Raphael
full_name: Guerois, Raphael
last_name: Guerois
- first_name: Christel
full_name: Compper, Christel
last_name: Compper
- first_name: Arthur
full_name: Besle, Arthur
last_name: Besle
- first_name: Berengère
full_name: Guichard, Berengère
last_name: Guichard
- first_name: Genevieve
full_name: Almouzni, Genevieve
last_name: Almouzni
- first_name: Françoise
full_name: Ochsenbein, Françoise
last_name: Ochsenbein
citation:
ama: Richet N, Liu D, Legrand P, et al. Structural insight into how the human helicase
subunit MCM2 may act as a histone chaperone together with ASF1 at the replication
fork. Nucleic Acids Research. 2015;43(3):1905-1917. doi:10.1093/nar/gkv021
apa: Richet, N., Liu, D., Legrand, P., Velours, C., Corpet, A., Gaubert, A., … Ochsenbein,
F. (2015). Structural insight into how the human helicase subunit MCM2 may act
as a histone chaperone together with ASF1 at the replication fork. Nucleic
Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkv021
chicago: Richet, Nicolas, Danni Liu, Pierre Legrand, Christophe Velours, Armelle
Corpet, Albane Gaubert, May M Bakail, et al. “Structural Insight into How the
Human Helicase Subunit MCM2 May Act as a Histone Chaperone Together with ASF1
at the Replication Fork.” Nucleic Acids Research. Oxford University Press,
2015. https://doi.org/10.1093/nar/gkv021.
ieee: N. Richet et al., “Structural insight into how the human helicase subunit
MCM2 may act as a histone chaperone together with ASF1 at the replication fork,”
Nucleic Acids Research, vol. 43, no. 3. Oxford University Press, pp. 1905–1917,
2015.
ista: Richet N, Liu D, Legrand P, Velours C, Corpet A, Gaubert A, Bakail MM, Moal-Raisin
G, Guerois R, Compper C, Besle A, Guichard B, Almouzni G, Ochsenbein F. 2015.
Structural insight into how the human helicase subunit MCM2 may act as a histone
chaperone together with ASF1 at the replication fork. Nucleic Acids Research.
43(3), 1905–1917.
mla: Richet, Nicolas, et al. “Structural Insight into How the Human Helicase Subunit
MCM2 May Act as a Histone Chaperone Together with ASF1 at the Replication Fork.”
Nucleic Acids Research, vol. 43, no. 3, Oxford University Press, 2015,
pp. 1905–17, doi:10.1093/nar/gkv021.
short: N. Richet, D. Liu, P. Legrand, C. Velours, A. Corpet, A. Gaubert, M.M. Bakail,
G. Moal-Raisin, R. Guerois, C. Compper, A. Besle, B. Guichard, G. Almouzni, F.
Ochsenbein, Nucleic Acids Research 43 (2015) 1905–1917.
date_created: 2021-01-19T11:01:01Z
date_published: 2015-02-18T00:00:00Z
date_updated: 2023-02-23T13:46:50Z
day: '18'
doi: 10.1093/nar/gkv021
extern: '1'
external_id:
pmid:
- '25618846'
intvolume: ' 43'
issue: '3'
language:
- iso: eng
month: '02'
oa_version: Published Version
page: 1905-1917
pmid: 1
publication: Nucleic Acids Research
publication_identifier:
issn:
- 1362-4962
- 0305-1048
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: Structural insight into how the human helicase subunit MCM2 may act as a histone
chaperone together with ASF1 at the replication fork
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2015'
...
---
_id: '924'
abstract:
- lang: eng
text: This paper presents a numerical study of a Capillary Pumped Loop evaporator.
A two-dimensional unsteady mathematical model of a flat evaporator is developed
to simulate heat and mass transfer in unsaturated porous wick with phase change.
The liquid-vapor phase change inside the porous wick is described by Langmuir's
law. The governing equations are solved by the Finite Element Method. The results
are presented then for a sintered nickel wick and methanol as a working fluid.
The heat flux required to the transition from the all-liquid wick to the vapor-liquid
wick is calculated. The dynamic and thermodynamic behavior of the working fluid
in the capillary structure are discussed in this paper.
acknowledgement: The work presented in this paper is supported by Alstom Transport,
site de Tarbes (Contract number is 11099).
article_processing_charge: No
author:
- first_name: Riadh
full_name: Boubaker, Riadh
last_name: Boubaker
- first_name: Vincent
full_name: Platel, Vincent
last_name: Platel
- first_name: Alexis
full_name: Bergès, Alexis
last_name: Bergès
- first_name: Mathieu
full_name: Bancelin, Mathieu
last_name: Bancelin
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
citation:
ama: Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. Dynamic model of heat
and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied
Thermal Engineering. 2015;76:1-8. doi:10.1016/j.applthermaleng.2014.10.009
apa: Boubaker, R., Platel, V., Bergès, A., Bancelin, M., & Hannezo, E. B. (2015).
Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary
pumped loop. Applied Thermal Engineering. Elsevier. https://doi.org/10.1016/j.applthermaleng.2014.10.009
chicago: Boubaker, Riadh, Vincent Platel, Alexis Bergès, Mathieu Bancelin, and Edouard
B Hannezo. “Dynamic Model of Heat and Mass Transfer in an Unsaturated Porous Wick
of Capillary Pumped Loop.” Applied Thermal Engineering. Elsevier, 2015.
https://doi.org/10.1016/j.applthermaleng.2014.10.009.
ieee: R. Boubaker, V. Platel, A. Bergès, M. Bancelin, and E. B. Hannezo, “Dynamic
model of heat and mass transfer in an unsaturated porous wick of capillary pumped
loop,” Applied Thermal Engineering, vol. 76. Elsevier, pp. 1–8, 2015.
ista: Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. 2015. Dynamic model
of heat and mass transfer in an unsaturated porous wick of capillary pumped loop.
Applied Thermal Engineering. 76, 1–8.
mla: Boubaker, Riadh, et al. “Dynamic Model of Heat and Mass Transfer in an Unsaturated
Porous Wick of Capillary Pumped Loop.” Applied Thermal Engineering, vol.
76, Elsevier, 2015, pp. 1–8, doi:10.1016/j.applthermaleng.2014.10.009.
short: R. Boubaker, V. Platel, A. Bergès, M. Bancelin, E.B. Hannezo, Applied Thermal
Engineering 76 (2015) 1–8.
date_created: 2018-12-11T11:49:13Z
date_published: 2015-02-05T00:00:00Z
date_updated: 2021-01-12T08:21:56Z
day: '05'
doi: 10.1016/j.applthermaleng.2014.10.009
extern: '1'
intvolume: ' 76'
language:
- iso: eng
month: '02'
oa_version: None
page: 1 - 8
publication: Applied Thermal Engineering
publication_status: published
publisher: Elsevier
publist_id: '6514'
status: public
title: Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary
pumped loop
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 76
year: '2015'
...
---
_id: '929'
abstract:
- lang: eng
text: 'An essential question of morphogenesis is how patterns arise without preexisting
positional information, as inspired by Turing. In the past few years, cytoskeletal
flows in the cell cortex have been identified as a key mechanism of molecular
patterning at the subcellular level. Theoretical and in vitro studies have suggested
that biological polymers such as actomyosin gels have the property to self-organize,
but the applicability of this concept in an in vivo setting remains unclear. Here,
we report that the regular spacing pattern of supracellular actin rings in the
Drosophila tracheal tubule is governed by a self-organizing principle. We propose
a simple biophysical model where pattern formation arises from the interplay of
myosin contractility and actin turnover. We validate the hypotheses of the model
using photobleaching experiments and report that the formation of actin rings
is contractility dependent. Moreover, genetic and pharmacological perturbations
of the physical properties of the actomyosin gel modify the spacing of the pattern,
as the model predicted. In addition, our model posited a role of cortical friction
in stabilizing the spacing pattern of actin rings. Consistently, genetic depletion
of apical extracellular matrix caused strikingly dynamic movements of actin rings,
mirroring our model prediction of a transition from steady to chaotic actin patterns
at low cortical friction. Our results therefore demonstrate quantitatively that
a hydrodynamical instability of the actin cortex can trigger regular pattern formation
and drive morphogenesis in an in vivo setting. '
acknowledgement: We thank H. Oda, R. E. Ward, K. Saigo, T. Nishimura, D. Pinheiro,
Y. Bellaiche, the Bloomington Stock Center, Drosophila Genetic Resource Center (Kyoto),
and the Developmental Studies Hybridoma Bank for generously providing antibodies
and fly stocks; A. Hayashi for sharing phalloidin staining samples; Y. H. Zhang
for plasmid and protocol for CBP preparation; and T. Kondo and J. Prost for suggestions
and discussion. This work was supported by the Taishan Scholar Program of Shandong
and the Fundamental Research Funds for the Central Universities in China (3005000-841412019)
(to B.D.) and a Grant-in-Aid for Scientific Research on Innovative Areas from Ministry
of Education, Culture, Sports, Science and Technology of Japan (to S.H.). E.H. acknowledges
support from the Young Researcher Prize of the Bettencourt-Schueller Foundation.
article_processing_charge: No
author:
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Bo
full_name: Dong, Bo
last_name: Dong
- first_name: Pierre
full_name: Recho, Pierre
last_name: Recho
- first_name: Jean
full_name: Joanny, Jean
last_name: Joanny
- first_name: Shigeo
full_name: Hayashi, Shigeo
last_name: Hayashi
citation:
ama: Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. Cortical instability drives
periodic supracellular actin pattern formation in epithelial tubes. PNAS.
2015;112(28):8620-8625. doi:10.1073/pnas.1504762112
apa: Hannezo, E. B., Dong, B., Recho, P., Joanny, J., & Hayashi, S. (2015).
Cortical instability drives periodic supracellular actin pattern formation in
epithelial tubes. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1504762112
chicago: Hannezo, Edouard B, Bo Dong, Pierre Recho, Jean Joanny, and Shigeo Hayashi.
“Cortical Instability Drives Periodic Supracellular Actin Pattern Formation in
Epithelial Tubes.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1504762112.
ieee: E. B. Hannezo, B. Dong, P. Recho, J. Joanny, and S. Hayashi, “Cortical instability
drives periodic supracellular actin pattern formation in epithelial tubes,” PNAS,
vol. 112, no. 28. National Academy of Sciences, pp. 8620–8625, 2015.
ista: Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. 2015. Cortical instability
drives periodic supracellular actin pattern formation in epithelial tubes. PNAS.
112(28), 8620–8625.
mla: Hannezo, Edouard B., et al. “Cortical Instability Drives Periodic Supracellular
Actin Pattern Formation in Epithelial Tubes.” PNAS, vol. 112, no. 28, National
Academy of Sciences, 2015, pp. 8620–25, doi:10.1073/pnas.1504762112.
short: E.B. Hannezo, B. Dong, P. Recho, J. Joanny, S. Hayashi, PNAS 112 (2015) 8620–8625.
date_created: 2018-12-11T11:49:15Z
date_published: 2015-07-14T00:00:00Z
date_updated: 2021-01-12T08:21:59Z
day: '14'
doi: 10.1073/pnas.1504762112
extern: '1'
intvolume: ' 112'
issue: '28'
language:
- iso: eng
month: '07'
oa_version: None
page: 8620 - 8625
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6513'
status: public
title: Cortical instability drives periodic supracellular actin pattern formation
in epithelial tubes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '933'
abstract:
- lang: eng
text: Although collective cell motion plays an important role, for example during
wound healing, embryogenesis, or cancer progression, the fundamental rules governing
this motion are still not well understood, in particular at high cell density.
We study here the motion of human bronchial epithelial cells within a monolayer,
over long times. We observe that, as the monolayer ages, the cells slow down monotonously,
while the velocity correlation length first increases as the cells slow down but
eventually decreases at the slowest motions. By comparing experiments, analytic
model, and detailed particle-based simulations, we shed light on this biological
amorphous solidification process, demonstrating that the observed dynamics can
be explained as a consequence of the combined maturation and strengthening of
cell-cell and cell-substrate adhesions. Surprisingly, the increase of cell surface
density due to proliferation is only secondary in this process. This analysis
is confirmed with two other cell types. The very general relations between the
mean cell velocity and velocity correlation lengths, which apply for aggregates
of self-propelled particles, as well as motile cells, can possibly be used to
discriminate between various parameter changes in vivo, from noninvasive microscopy
data.
author:
- first_name: Simón
full_name: García, Simón
last_name: García
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Jens
full_name: Elgeti, Jens
last_name: Elgeti
- first_name: Jean
full_name: Joanny, Jean
last_name: Joanny
- first_name: Pascal
full_name: Silberzan, Pascal
last_name: Silberzan
- first_name: Nir
full_name: Gov, Nir
last_name: Gov
citation:
ama: García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. Physics of active
jamming during collective cellular motion in a monolayer. PNAS. 2015;112(50):15314-15319.
doi:10.1073/pnas.1510973112
apa: García, S., Hannezo, E. B., Elgeti, J., Joanny, J., Silberzan, P., & Gov,
N. (2015). Physics of active jamming during collective cellular motion in a monolayer.
PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1510973112
chicago: García, Simón, Edouard B Hannezo, Jens Elgeti, Jean Joanny, Pascal Silberzan,
and Nir Gov. “Physics of Active Jamming during Collective Cellular Motion in a
Monolayer.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1510973112.
ieee: S. García, E. B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, and N. Gov,
“Physics of active jamming during collective cellular motion in a monolayer,”
PNAS, vol. 112, no. 50. National Academy of Sciences, pp. 15314–15319,
2015.
ista: García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. 2015. Physics
of active jamming during collective cellular motion in a monolayer. PNAS. 112(50),
15314–15319.
mla: García, Simón, et al. “Physics of Active Jamming during Collective Cellular
Motion in a Monolayer.” PNAS, vol. 112, no. 50, National Academy of Sciences,
2015, pp. 15314–19, doi:10.1073/pnas.1510973112.
short: S. García, E.B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, N. Gov, PNAS
112 (2015) 15314–15319.
date_created: 2018-12-11T11:49:16Z
date_published: 2015-12-15T00:00:00Z
date_updated: 2021-01-12T08:22:01Z
day: '15'
doi: 10.1073/pnas.1510973112
extern: '1'
external_id:
pmid:
- '26627719'
intvolume: ' 112'
issue: '50'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.pnas.org/content/pnas/112/50/15314.full.pdf
month: '12'
oa: 1
oa_version: None
page: 15314 - 15319
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6511'
quality_controlled: '1'
status: public
title: Physics of active jamming during collective cellular motion in a monolayer
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '9532'
abstract:
- lang: eng
text: Genomic imprinting, an inherently epigenetic phenomenon defined by parent
of origin-dependent gene expression, is observed in mammals and flowering plants.
Genome-scale surveys of imprinted expression and the underlying differential epigenetic
marks have led to the discovery of hundreds of imprinted plant genes and confirmed
DNA and histone methylation as key regulators of plant imprinting. However, the
biological roles of the vast majority of imprinted plant genes are unknown, and
the evolutionary forces shaping plant imprinting remain rather opaque. Here, we
review the mechanisms of plant genomic imprinting and discuss theories of imprinting
evolution and biological significance in light of recent findings.
article_processing_charge: No
article_type: review
author:
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in
plants. Genes and Development. 2015;29(24):2517–2531. doi:10.1101/gad.269902.115
apa: Rodrigues, J. A., & Zilberman, D. (2015). Evolution and function of genomic
imprinting in plants. Genes and Development. Cold Spring Harbor Laboratory
Press. https://doi.org/10.1101/gad.269902.115
chicago: Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of
Genomic Imprinting in Plants.” Genes and Development. Cold Spring Harbor
Laboratory Press, 2015. https://doi.org/10.1101/gad.269902.115.
ieee: J. A. Rodrigues and D. Zilberman, “Evolution and function of genomic imprinting
in plants,” Genes and Development, vol. 29, no. 24. Cold Spring Harbor
Laboratory Press, pp. 2517–2531, 2015.
ista: Rodrigues JA, Zilberman D. 2015. Evolution and function of genomic imprinting
in plants. Genes and Development. 29(24), 2517–2531.
mla: Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic
Imprinting in Plants.” Genes and Development, vol. 29, no. 24, Cold Spring
Harbor Laboratory Press, 2015, pp. 2517–2531, doi:10.1101/gad.269902.115.
short: J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531.
date_created: 2021-06-08T09:56:24Z
date_published: 2015-12-15T00:00:00Z
date_updated: 2021-12-14T07:58:15Z
day: '15'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.1101/gad.269902.115
extern: '1'
external_id:
pmid:
- '26680300'
file:
- access_level: open_access
checksum: 086a88cfca4677646da26ed960cb02e9
content_type: application/pdf
creator: asandaue
date_created: 2021-06-08T09:55:10Z
date_updated: 2021-06-08T09:55:10Z
file_id: '9533'
file_name: 2015_GenesAndDevelopment_Rodrigues.pdf
file_size: 1116846
relation: main_file
success: 1
file_date_updated: 2021-06-08T09:55:10Z
has_accepted_license: '1'
intvolume: ' 29'
issue: '24'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 2517–2531
pmid: 1
publication: Genes and Development
publication_identifier:
eissn:
- 1549-5477
issn:
- 0890-9369
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolution and function of genomic imprinting in plants
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 29
year: '2015'
...
---
_id: '9684'
abstract:
- lang: eng
text: The size dependence of the strength of nano- and micron-sized crystals is
studied using a new simulation approach in which the dynamics of the density functions
of dislocations are modeled. Since any quantity of dislocations can be represented
by a density, this approach can handle large systems containing large quantities
of dislocations, which may handicap discrete dislocation dynamics schemes due
to the excessive computation time involved. For this reason, pillar sizes spanning
a large range, from the sub-micron to micron regimes, can be simulated. The simulation
results reveal the power-law relationship between strength and specimen size up
to a certain size, beyond which the strength varies much more slowly with size.
For specimens smaller than ~4000b, their strength is found to be controlled by
the dislocation depletion condition, in which the total dislocation density remains
almost constant throughout the loading process. In specimens larger than ~4000b,
the initial dislocation distribution is of critical importance since the presence
of dislocation entanglements is found to obstruct deformation in the neighboring
regions within a distance of ~2000b. This length scale suggests that the effects
of dense dislocation clusters are greater in intermediate-sized specimens (e.g.
4000b and 8000b) than in larger specimens (e.g. 16 000b), according to the weakest-link
concept.
article_number: '035001'
article_processing_charge: No
article_type: original
author:
- first_name: P S S
full_name: Leung, P S S
last_name: Leung
- first_name: H S
full_name: Leung, H S
last_name: Leung
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: A H W
full_name: Ngan, A H W
last_name: Ngan
citation:
ama: Leung PSS, Leung HS, Cheng B, Ngan AHW. Size dependence of yield strength simulated
by a dislocation-density function dynamics approach. Modelling and Simulation
in Materials Science and Engineering. 2015;23(3). doi:10.1088/0965-0393/23/3/035001
apa: Leung, P. S. S., Leung, H. S., Cheng, B., & Ngan, A. H. W. (2015). Size
dependence of yield strength simulated by a dislocation-density function dynamics
approach. Modelling and Simulation in Materials Science and Engineering.
IOP Publishing. https://doi.org/10.1088/0965-0393/23/3/035001
chicago: Leung, P S S, H S Leung, Bingqing Cheng, and A H W Ngan. “Size Dependence
of Yield Strength Simulated by a Dislocation-Density Function Dynamics Approach.”
Modelling and Simulation in Materials Science and Engineering. IOP Publishing,
2015. https://doi.org/10.1088/0965-0393/23/3/035001.
ieee: P. S. S. Leung, H. S. Leung, B. Cheng, and A. H. W. Ngan, “Size dependence
of yield strength simulated by a dislocation-density function dynamics approach,”
Modelling and Simulation in Materials Science and Engineering, vol. 23,
no. 3. IOP Publishing, 2015.
ista: Leung PSS, Leung HS, Cheng B, Ngan AHW. 2015. Size dependence of yield strength
simulated by a dislocation-density function dynamics approach. Modelling and Simulation
in Materials Science and Engineering. 23(3), 035001.
mla: Leung, P. S. S., et al. “Size Dependence of Yield Strength Simulated by a Dislocation-Density
Function Dynamics Approach.” Modelling and Simulation in Materials Science
and Engineering, vol. 23, no. 3, 035001, IOP Publishing, 2015, doi:10.1088/0965-0393/23/3/035001.
short: P.S.S. Leung, H.S. Leung, B. Cheng, A.H.W. Ngan, Modelling and Simulation
in Materials Science and Engineering 23 (2015).
date_created: 2021-07-19T09:11:12Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2023-02-23T14:04:54Z
day: '01'
doi: 10.1088/0965-0393/23/3/035001
extern: '1'
intvolume: ' 23'
issue: '3'
language:
- iso: eng
month: '04'
oa_version: None
publication: Modelling and Simulation in Materials Science and Engineering
publication_identifier:
eissn:
- 1361-651X
issn:
- 0965-0393
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Size dependence of yield strength simulated by a dislocation-density function
dynamics approach
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 23
year: '2015'
...
---
_id: '1566'
abstract:
- lang: eng
text: Deposits of misfolded proteins in the human brain are associated with the
development of many neurodegenerative diseases. Recent studies show that these
proteins have common traits even at the monomer level. Among them, a polyglutamine
region that is present in huntingtin is known to exhibit a correlation between
the length of the chain and the severity as well as the earliness of the onset
of Huntington disease. Here, we apply bias exchange molecular dynamics to generate
structures of polyglutamine expansions of several lengths and characterize the
resulting independent conformations. We compare the properties of these conformations
to those of the standard proteins, as well as to other homopolymeric tracts. We
find that, similar to the previously studied polyvaline chains, the set of possible
transient folds is much broader than the set of known-to-date folds, although
the conformations have different structures. We show that the mechanical stability
is not related to any simple geometrical characteristics of the structures. We
demonstrate that long polyglutamine expansions result in higher mechanical stability
than the shorter ones. They also have a longer life span and are substantially
more prone to form knotted structures. The knotted region has an average length
of 35 residues, similar to the typical threshold for most polyglutamine-related
diseases. Similarly, changes in shape and mechanical stability appear once the
total length of the peptide exceeds this threshold of 35 glutamine residues. We
suggest that knotted conformers may also harm the cellular machinery and thus
lead to disease.
acknowledgement: 'We acknowledge the support by the EU Joint Programme in Neurodegenerative
Diseases (JPND AC14/00037) project. The project is supported through the following
funding organisations under the aegis of JPND—www.jpnd.eu: Ireland, HRB; Poland,
National Science Centre; and Spain, ISCIII. '
article_number: e1004541
author:
- first_name: Àngel
full_name: Gómez Sicilia, Àngel
last_name: Gómez Sicilia
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Marek
full_name: Cieplak, Marek
last_name: Cieplak
- first_name: Mariano
full_name: Carrión Vázquez, Mariano
last_name: Carrión Vázquez
citation:
ama: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of
the universe of polyglutamine structures. PLoS Computational Biology. 2015;11(10).
doi:10.1371/journal.pcbi.1004541
apa: Gómez Sicilia, À., Sikora, M. K., Cieplak, M., & Carrión Vázquez, M. (2015).
An exploration of the universe of polyglutamine structures. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004541
chicago: Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión
Vázquez. “An Exploration of the Universe of Polyglutamine Structures.” PLoS
Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004541.
ieee: À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration
of the universe of polyglutamine structures,” PLoS Computational Biology,
vol. 11, no. 10. Public Library of Science, 2015.
ista: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration
of the universe of polyglutamine structures. PLoS Computational Biology. 11(10),
e1004541.
mla: Gómez Sicilia, Àngel, et al. “An Exploration of the Universe of Polyglutamine
Structures.” PLoS Computational Biology, vol. 11, no. 10, e1004541, Public
Library of Science, 2015, doi:10.1371/journal.pcbi.1004541.
short: À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, PLoS Computational
Biology 11 (2015).
date_created: 2018-12-11T11:52:45Z
date_published: 2015-10-23T00:00:00Z
date_updated: 2023-02-23T14:05:55Z
day: '23'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1371/journal.pcbi.1004541
file:
- access_level: open_access
checksum: 8b67d729be663bfc9af04bfd94459655
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:21Z
date_updated: 2020-07-14T12:45:02Z
file_id: '5207'
file_name: IST-2016-478-v1+1_journal.pcbi.1004541.pdf
file_size: 1412511
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5605'
pubrep_id: '478'
quality_controlled: '1'
related_material:
record:
- id: '9714'
relation: research_data
status: public
scopus_import: 1
status: public
title: An exploration of the universe of polyglutamine structures
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2015'
...
---
_id: '9712'
article_processing_charge: No
author:
- first_name: Murat
full_name: Tugrul, Murat
id: 37C323C6-F248-11E8-B48F-1D18A9856A87
last_name: Tugrul
orcid: 0000-0002-8523-0758
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Tugrul M, Paixao T, Barton NH, Tkačik G. Other fitness models for comparison
& for interacting TFBSs. 2015. doi:10.1371/journal.pgen.1005639.s001
apa: Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Other fitness
models for comparison & for interacting TFBSs. Public Library of Science.
https://doi.org/10.1371/journal.pgen.1005639.s001
chicago: Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Other
Fitness Models for Comparison & for Interacting TFBSs.” Public Library of
Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.s001.
ieee: M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for
comparison & for interacting TFBSs.” Public Library of Science, 2015.
ista: Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Other fitness models for comparison
& for interacting TFBSs, Public Library of Science, 10.1371/journal.pgen.1005639.s001.
mla: Tugrul, Murat, et al. Other Fitness Models for Comparison & for Interacting
TFBSs. Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.s001.
short: M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015).
date_created: 2021-07-23T12:00:37Z
date_published: 2015-11-06T00:00:00Z
date_updated: 2023-02-23T10:09:08Z
day: '06'
department:
- _id: NiBa
- _id: CaGu
- _id: GaTk
doi: 10.1371/journal.pgen.1005639.s001
month: '11'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1666'
relation: used_in_publication
status: public
status: public
title: Other fitness models for comparison & for interacting TFBSs
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '9714'
article_processing_charge: No
author:
- first_name: Àngel
full_name: Gómez Sicilia, Àngel
last_name: Gómez Sicilia
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Marek
full_name: Cieplak, Marek
last_name: Cieplak
- first_name: Mariano
full_name: Carrión Vázquez, Mariano
last_name: Carrión Vázquez
citation:
ama: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of
the universe of polyglutamine structures - submission to PLOS journals. 2015.
doi:10.1371/journal.pcbi.1004541.s001
apa: Gómez Sicilia, À., Sikora, M. K., Cieplak, M., & Carrión Vázquez, M. (2015).
An exploration of the universe of polyglutamine structures - submission to PLOS
journals. Public Library of Science . https://doi.org/10.1371/journal.pcbi.1004541.s001
chicago: Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión
Vázquez. “An Exploration of the Universe of Polyglutamine Structures - Submission
to PLOS Journals.” Public Library of Science , 2015. https://doi.org/10.1371/journal.pcbi.1004541.s001.
ieee: À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration
of the universe of polyglutamine structures - submission to PLOS journals.” Public
Library of Science , 2015.
ista: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration
of the universe of polyglutamine structures - submission to PLOS journals, Public
Library of Science , 10.1371/journal.pcbi.1004541.s001.
mla: Gómez Sicilia, Àngel, et al. An Exploration of the Universe of Polyglutamine
Structures - Submission to PLOS Journals. Public Library of Science , 2015,
doi:10.1371/journal.pcbi.1004541.s001.
short: À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, (2015).
date_created: 2021-07-23T12:05:28Z
date_published: 2015-10-23T00:00:00Z
date_updated: 2023-02-23T10:04:35Z
day: '23'
department:
- _id: CaHe
doi: 10.1371/journal.pcbi.1004541.s001
month: '10'
oa_version: Published Version
publisher: 'Public Library of Science '
related_material:
record:
- id: '1566'
relation: used_in_publication
status: public
status: public
title: An exploration of the universe of polyglutamine structures - submission to
PLOS journals
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '9715'
article_processing_charge: No
author:
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Reinmar
full_name: Hager, Reinmar
last_name: Hager
citation:
ama: Trubenova B, Novak S, Hager R. Mathematical inference of the results. 2015.
doi:10.1371/journal.pone.0126907.s001
apa: Trubenova, B., Novak, S., & Hager, R. (2015). Mathematical inference of
the results. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s001
chicago: Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Mathematical Inference
of the Results.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s001.
ieee: B. Trubenova, S. Novak, and R. Hager, “Mathematical inference of the results.”
Public Library of Science, 2015.
ista: Trubenova B, Novak S, Hager R. 2015. Mathematical inference of the results,
Public Library of Science, 10.1371/journal.pone.0126907.s001.
mla: Trubenova, Barbora, et al. Mathematical Inference of the Results. Public
Library of Science, 2015, doi:10.1371/journal.pone.0126907.s001.
short: B. Trubenova, S. Novak, R. Hager, (2015).
date_created: 2021-07-23T12:11:30Z
date_published: 2015-05-18T00:00:00Z
date_updated: 2023-02-23T10:15:25Z
day: '18'
department:
- _id: NiBa
doi: 10.1371/journal.pone.0126907.s001
month: '05'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1809'
relation: used_in_publication
status: public
status: public
title: Mathematical inference of the results
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '1993'
abstract:
- lang: eng
text: 'The fitness effects of symbionts on their hosts can be context-dependent,
with usually benign symbionts causing detrimental effects when their hosts are
stressed, or typically parasitic symbionts providing protection towards their
hosts (e.g. against pathogen infection). Here, we studied the novel association
between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia
formicarum for potential costs and benefits. We tested ants with different Laboulbenia
levels for their survival and immunity under resource limitation and exposure
to the obligate killing entomopathogen Metarhizium brunneum. While survival of
L. neglectus workers under starvation was significantly decreased with increasing
Laboulbenia levels, host survival under Metarhizium exposure increased with higher
levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection,
which seems to be driven mechanistically by both improved sanitary behaviours
and an upregulated immune system. Ants with high Laboulbenia levels showed significantly
longer self-grooming and elevated expression of immune genes relevant for wound
repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase),
compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont
Laboulbenia formicarum weakens its ant host by either direct resource exploitation
or the costs of an upregulated behavioural and immunological response, which,
however, provides a prophylactic protection upon later exposure to pathogens. '
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: "Funding was obtained by the German Research Foundation (CR 118–2)
and an ERC StG (243071) by the European Research Council (both to S.C.).\r\nWe thank
Line V. Ugelvig for help with ant collection and statistical discussion, Xavier
Espadaler for detailed information on the ant collection site, Birgit Lautenschläger
for the electron microscopy images and Eva Sixt for ant drawings. We further thank
Jørgen Eilenberg for the fungal strain, Meghan L. Vyleta for genetic strain characterization
and immune gene primer development, Paul Schmid-Hempel for discussion, and Line
V. Ugelvig, Xavier Espadaler and Christopher D. Pull for comments on the manuscript.
S.C., M.K. and S.T. conceived the study; M.K. and A.V.G. performed the experiments;
M.K. performed the statistical analysis; S.C. and M.K. wrote the manuscript with
intense contributions of A.V.G. and S.T.; all authors approved the manuscript."
article_number: '20141976'
article_processing_charge: No
article_type: original
author:
- first_name: Matthias
full_name: Konrad, Matthias
id: 46528076-F248-11E8-B48F-1D18A9856A87
last_name: Konrad
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Simon
full_name: Tragust, Simon
id: 35A7A418-F248-11E8-B48F-1D18A9856A87
last_name: Tragust
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Konrad M, Grasse AV, Tragust S, Cremer S. Anti-pathogen protection versus survival
costs mediated by an ectosymbiont in an ant host. Proceedings of the Royal
Society of London Series B Biological Sciences. 2015;282(1799). doi:10.1098/rspb.2014.1976
apa: Konrad, M., Grasse, A. V., Tragust, S., & Cremer, S. (2015). Anti-pathogen
protection versus survival costs mediated by an ectosymbiont in an ant host. Proceedings
of the Royal Society of London Series B Biological Sciences. The Royal Society.
https://doi.org/10.1098/rspb.2014.1976
chicago: Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Anti-Pathogen
Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.”
Proceedings of the Royal Society of London Series B Biological Sciences.
The Royal Society, 2015. https://doi.org/10.1098/rspb.2014.1976.
ieee: M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Anti-pathogen protection
versus survival costs mediated by an ectosymbiont in an ant host,” Proceedings
of the Royal Society of London Series B Biological Sciences, vol. 282, no.
1799. The Royal Society, 2015.
ista: Konrad M, Grasse AV, Tragust S, Cremer S. 2015. Anti-pathogen protection versus
survival costs mediated by an ectosymbiont in an ant host. Proceedings of the
Royal Society of London Series B Biological Sciences. 282(1799), 20141976.
mla: Konrad, Matthias, et al. “Anti-Pathogen Protection versus Survival Costs Mediated
by an Ectosymbiont in an Ant Host.” Proceedings of the Royal Society of London
Series B Biological Sciences, vol. 282, no. 1799, 20141976, The Royal Society,
2015, doi:10.1098/rspb.2014.1976.
short: M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, Proceedings of the Royal Society
of London Series B Biological Sciences 282 (2015).
date_created: 2018-12-11T11:55:06Z
date_published: 2015-01-22T00:00:00Z
date_updated: 2023-02-23T14:06:41Z
day: '22'
department:
- _id: SyCr
doi: 10.1098/rspb.2014.1976
ec_funded: 1
external_id:
pmid:
- '25473011'
intvolume: ' 282'
issue: '1799'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286035/
month: '01'
oa: 1
oa_version: Submitted Version
pmid: 1
project:
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '243071'
name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
Effects'
- _id: 25DAF0B2-B435-11E9-9278-68D0E5697425
grant_number: CR-118/3-1
name: Host-Parasite Coevolution
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_identifier:
eissn:
- 1471-2954
issn:
- 0962-8452
publication_status: published
publisher: The Royal Society
publist_id: '5090'
quality_controlled: '1'
related_material:
record:
- id: '9740'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Anti-pathogen protection versus survival costs mediated by an ectosymbiont
in an ant host
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 282
year: '2015'
...