---
_id: '8453'
abstract:
- lang: eng
text: Transverse relaxation rate measurements in magic-angle spinning solid-state
nuclear magnetic resonance provide information about molecular motions occurring
on nanosecond-to-millisecond (ns–ms) time scales. The measurement of heteronuclear
(13C, 15N) relaxation rate constants in the presence of a spin-lock radiofrequency
field (R1ρ relaxation) provides access to such motions, and an increasing number
of studies involving R1ρ relaxation in proteins have been reported. However, two
factors that influence the observed relaxation rate constants have so far been
neglected, namely, (1) the role of CSA/dipolar cross-correlated relaxation (CCR)
and (2) the impact of fast proton spin flips (i.e., proton spin diffusion and
relaxation). We show that CSA/D CCR in R1ρ experiments is measurable and that
the CCR rate constant depends on ns–ms motions; it can thus provide insight into
dynamics. We find that proton spin diffusion attenuates this CCR due to its decoupling
effect on the doublet components. For measurements of dynamics, the use of R1ρ
rate constants has practical advantages over the use of CCR rates, and this article
reveals factors that have so far been disregarded and which are important for
accurate measurements and interpretation.
article_processing_charge: No
article_type: original
author:
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Emmanuelle
full_name: Weber, Emmanuelle
last_name: Weber
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Dominique
full_name: Marion, Dominique
last_name: Marion
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Kurauskas V, Weber E, Hessel A, Ayala I, Marion D, Schanda P. Cross-correlated
relaxation of dipolar coupling and chemical-shift anisotropy in magic-angle spinning
R1ρ NMR measurements: Application to protein backbone dynamics measurements. The
Journal of Physical Chemistry B. 2016;120(34):8905-8913. doi:10.1021/acs.jpcb.6b06129'
apa: 'Kurauskas, V., Weber, E., Hessel, A., Ayala, I., Marion, D., & Schanda,
P. (2016). Cross-correlated relaxation of dipolar coupling and chemical-shift
anisotropy in magic-angle spinning R1ρ NMR measurements: Application to protein
backbone dynamics measurements. The Journal of Physical Chemistry B. American
Chemical Society. https://doi.org/10.1021/acs.jpcb.6b06129'
chicago: 'Kurauskas, Vilius, Emmanuelle Weber, Audrey Hessel, Isabel Ayala, Dominique
Marion, and Paul Schanda. “Cross-Correlated Relaxation of Dipolar Coupling and
Chemical-Shift Anisotropy in Magic-Angle Spinning R1ρ NMR Measurements: Application
to Protein Backbone Dynamics Measurements.” The Journal of Physical Chemistry
B. American Chemical Society, 2016. https://doi.org/10.1021/acs.jpcb.6b06129.'
ieee: 'V. Kurauskas, E. Weber, A. Hessel, I. Ayala, D. Marion, and P. Schanda, “Cross-correlated
relaxation of dipolar coupling and chemical-shift anisotropy in magic-angle spinning
R1ρ NMR measurements: Application to protein backbone dynamics measurements,”
The Journal of Physical Chemistry B, vol. 120, no. 34. American Chemical
Society, pp. 8905–8913, 2016.'
ista: 'Kurauskas V, Weber E, Hessel A, Ayala I, Marion D, Schanda P. 2016. Cross-correlated
relaxation of dipolar coupling and chemical-shift anisotropy in magic-angle spinning
R1ρ NMR measurements: Application to protein backbone dynamics measurements. The
Journal of Physical Chemistry B. 120(34), 8905–8913.'
mla: 'Kurauskas, Vilius, et al. “Cross-Correlated Relaxation of Dipolar Coupling
and Chemical-Shift Anisotropy in Magic-Angle Spinning R1ρ NMR Measurements: Application
to Protein Backbone Dynamics Measurements.” The Journal of Physical Chemistry
B, vol. 120, no. 34, American Chemical Society, 2016, pp. 8905–13, doi:10.1021/acs.jpcb.6b06129.'
short: V. Kurauskas, E. Weber, A. Hessel, I. Ayala, D. Marion, P. Schanda, The Journal
of Physical Chemistry B 120 (2016) 8905–8913.
date_created: 2020-09-18T10:07:07Z
date_published: 2016-08-08T00:00:00Z
date_updated: 2021-01-12T08:19:22Z
day: '08'
doi: 10.1021/acs.jpcb.6b06129
extern: '1'
intvolume: ' 120'
issue: '34'
keyword:
- Physical and Theoretical Chemistry
- Materials Chemistry
- Surfaces
- Coatings and Films
language:
- iso: eng
month: '08'
oa_version: None
page: 8905-8913
publication: The Journal of Physical Chemistry B
publication_identifier:
issn:
- 1520-6106
- 1520-5207
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: 'Cross-correlated relaxation of dipolar coupling and chemical-shift anisotropy
in magic-angle spinning R1ρ NMR measurements: Application to protein backbone dynamics
measurements'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 120
year: '2016'
...
---
_id: '8454'
abstract:
- lang: eng
text: Magic-angle spinning solid-state NMR spectroscopy is an important technique
to study molecular structure, dynamics and interactions, and is rapidly gaining
importance in biomolecular sciences. Here we provide an overview of experimental
approaches to study molecular dynamics by MAS solid-state NMR, with an emphasis
on the underlying theoretical concepts and differences of MAS solid-state NMR
compared to solution-state NMR. The theoretical foundations of nuclear spin relaxation
are revisited, focusing on the particularities of spin relaxation in solid samples
under magic-angle spinning. We discuss the range of validity of Redfield theory,
as well as the inherent multi-exponential behavior of relaxation in solids. Experimental
challenges for measuring relaxation parameters in MAS solid-state NMR and a few
recently proposed relaxation approaches are discussed, which provide information
about time scales and amplitudes of motions ranging from picoseconds to milliseconds.
We also discuss the theoretical basis and experimental measurements of anisotropic
interactions (chemical-shift anisotropies, dipolar and quadrupolar couplings),
which give direct information about the amplitude of motions. The potential of
combining relaxation data with such measurements of dynamically-averaged anisotropic
interactions is discussed. Although the focus of this review is on the theoretical
foundations of dynamics studies rather than their application, we close by discussing
a small number of recent dynamics studies, where the dynamic properties of proteins
in crystals are compared to those in solution.
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: Matthias
full_name: Ernst, Matthias
last_name: Ernst
citation:
ama: 'Schanda P, Ernst M. Studying dynamics by magic-angle spinning solid-state
NMR spectroscopy: Principles and applications to biomolecules. Progress in
Nuclear Magnetic Resonance Spectroscopy. 2016;96(8):1-46. doi:10.1016/j.pnmrs.2016.02.001'
apa: 'Schanda, P., & Ernst, M. (2016). Studying dynamics by magic-angle spinning
solid-state NMR spectroscopy: Principles and applications to biomolecules. Progress
in Nuclear Magnetic Resonance Spectroscopy. Elsevier. https://doi.org/10.1016/j.pnmrs.2016.02.001'
chicago: 'Schanda, Paul, and Matthias Ernst. “Studying Dynamics by Magic-Angle Spinning
Solid-State NMR Spectroscopy: Principles and Applications to Biomolecules.” Progress
in Nuclear Magnetic Resonance Spectroscopy. Elsevier, 2016. https://doi.org/10.1016/j.pnmrs.2016.02.001.'
ieee: 'P. Schanda and M. Ernst, “Studying dynamics by magic-angle spinning solid-state
NMR spectroscopy: Principles and applications to biomolecules,” Progress in
Nuclear Magnetic Resonance Spectroscopy, vol. 96, no. 8. Elsevier, pp. 1–46,
2016.'
ista: 'Schanda P, Ernst M. 2016. Studying dynamics by magic-angle spinning solid-state
NMR spectroscopy: Principles and applications to biomolecules. Progress in Nuclear
Magnetic Resonance Spectroscopy. 96(8), 1–46.'
mla: 'Schanda, Paul, and Matthias Ernst. “Studying Dynamics by Magic-Angle Spinning
Solid-State NMR Spectroscopy: Principles and Applications to Biomolecules.” Progress
in Nuclear Magnetic Resonance Spectroscopy, vol. 96, no. 8, Elsevier, 2016,
pp. 1–46, doi:10.1016/j.pnmrs.2016.02.001.'
short: P. Schanda, M. Ernst, Progress in Nuclear Magnetic Resonance Spectroscopy
96 (2016) 1–46.
date_created: 2020-09-18T10:07:17Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2021-01-12T08:19:23Z
day: '01'
doi: 10.1016/j.pnmrs.2016.02.001
extern: '1'
intvolume: ' 96'
issue: '8'
language:
- iso: eng
month: '08'
oa_version: None
page: 1-46
publication: Progress in Nuclear Magnetic Resonance Spectroscopy
publication_identifier:
issn:
- 0079-6565
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Studying dynamics by magic-angle spinning solid-state NMR spectroscopy: Principles
and applications to biomolecules'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 96
year: '2016'
...
---
_id: '8455'
abstract:
- lang: eng
text: Solid-state NMR spectroscopy allows the characterization of the structure,
interactions and dynamics of insoluble and/or very large proteins. Sensitivity
and resolution are often major challenges for obtaining atomic-resolution information,
in particular for very large protein complexes. Here we show that the use of deuterated,
specifically CH3-labelled proteins result in significant sensitivity gains compared
to previously employed CHD2 labelling, while line widths increase only marginally.
We apply this labelling strategy to a 468 kDa-large dodecameric aminopeptidase,
TET2, and the 1.6 MDa-large 50S ribosome subunit of Thermus thermophilus.
article_processing_charge: No
article_type: original
author:
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Elodie
full_name: Crublet, Elodie
last_name: Crublet
- first_name: Pavel
full_name: Macek, Pavel
last_name: Macek
- first_name: Rime
full_name: Kerfah, Rime
last_name: Kerfah
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- 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: 'Kurauskas V, Crublet E, Macek P, et al. Sensitive proton-detected solid-state
NMR spectroscopy of large proteins with selective CH3labelling: Application to
the 50S ribosome subunit. Chemical Communications. 2016;52(61):9558-9561.
doi:10.1039/c6cc04484k'
apa: 'Kurauskas, V., Crublet, E., Macek, P., Kerfah, R., Gauto, D. F., Boisbouvier,
J., & Schanda, P. (2016). Sensitive proton-detected solid-state NMR spectroscopy
of large proteins with selective CH3labelling: Application to the 50S ribosome
subunit. Chemical Communications. Royal Society of Chemistry. https://doi.org/10.1039/c6cc04484k'
chicago: 'Kurauskas, Vilius, Elodie Crublet, Pavel Macek, Rime Kerfah, Diego F.
Gauto, Jérôme Boisbouvier, and Paul Schanda. “Sensitive Proton-Detected Solid-State
NMR Spectroscopy of Large Proteins with Selective CH3labelling: Application to
the 50S Ribosome Subunit.” Chemical Communications. Royal Society of Chemistry,
2016. https://doi.org/10.1039/c6cc04484k.'
ieee: 'V. Kurauskas et al., “Sensitive proton-detected solid-state NMR spectroscopy
of large proteins with selective CH3labelling: Application to the 50S ribosome
subunit,” Chemical Communications, vol. 52, no. 61. Royal Society of Chemistry,
pp. 9558–9561, 2016.'
ista: 'Kurauskas V, Crublet E, Macek P, Kerfah R, Gauto DF, Boisbouvier J, Schanda
P. 2016. Sensitive proton-detected solid-state NMR spectroscopy of large proteins
with selective CH3labelling: Application to the 50S ribosome subunit. Chemical
Communications. 52(61), 9558–9561.'
mla: 'Kurauskas, Vilius, et al. “Sensitive Proton-Detected Solid-State NMR Spectroscopy
of Large Proteins with Selective CH3labelling: Application to the 50S Ribosome
Subunit.” Chemical Communications, vol. 52, no. 61, Royal Society of Chemistry,
2016, pp. 9558–61, doi:10.1039/c6cc04484k.'
short: V. Kurauskas, E. Crublet, P. Macek, R. Kerfah, D.F. Gauto, J. Boisbouvier,
P. Schanda, Chemical Communications 52 (2016) 9558–9561.
date_created: 2020-09-18T10:07:29Z
date_published: 2016-07-04T00:00:00Z
date_updated: 2021-01-12T08:19:23Z
day: '04'
doi: 10.1039/c6cc04484k
extern: '1'
intvolume: ' 52'
issue: '61'
keyword:
- Materials Chemistry
- Electronic
- Optical and Magnetic Materials
- General Chemistry
- Surfaces
- Coatings and Films
- Metals and Alloys
- Ceramics and Composites
- Catalysis
language:
- iso: eng
month: '07'
oa_version: None
page: 9558-9561
publication: Chemical Communications
publication_identifier:
issn:
- 1359-7345
- 1364-548X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
status: public
title: 'Sensitive proton-detected solid-state NMR spectroscopy of large proteins with
selective CH3labelling: Application to the 50S ribosome subunit'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 52
year: '2016'
...
---
_id: '849'
abstract:
- lang: eng
text: Understanding the principles that led to the current complexity of the genetic
code is a central question in evolution. Expansion of the genetic code required
the selection of new transfer RNAs (tRNAs) with specific recognition signals that
allowed them to be matured, modified, aminoacylated, and processed by the ribosome
without compromising the fidelity or efficiency of protein synthesis. We show
that saturation of recognition signals blocks the emergence of new tRNA identities
and that the rate of nucleotide substitutions in tRNAs is higher in species with
fewer tRNA genes. We propose that the growth of the genetic code stalled because
a limit was reached in the number of identity elements that can be effectively
used in the tRNA structure.
acknowledgement: |-
We thank D. Söll, H. Grosjean, and L. Filonava for comments and suggestions.
M.O. and P.D.D. thank the Barcelona Supercomputing Center for CPU/GPU time on MareNostrum/
MinoTauro. P.D.D. is a PEDECIBA (Programa de Desarrollo de las Ciencias Básicas) and an SNI
(Sistema Nacional de Investigadores) (ANII, Uruguay) researcher. Funding: This work was
supported in part by the Spanish Ministry of Economy and Competitiveness (grants
BIO2012-32200, Sev-2012-0208, and BIO2012-32868 to L.R.d.P., F.A.K., and M.O., respectively)
and by the Catalan Government (grants 2014-SGR-0771, 2014-SGR-0974, and 2014-SGR-0134 to
L.R.d.P., F.A.K., and M.O., respectively). This work was also supported by the Howard Hughes
Medical Institute International Early Career Scientist Program (55007424), by a European Research
Council (ERC) Starting Grant (335980_EinME to F.K.), and by a grant from the ERC (ERC_SimDNA to
M.O). A.G.T. and C.B. are funded by the Spanish Ministry of Economy and Competitiveness
(FPDI-2013-17742 and BES-2013-064004, respectively).
author:
- first_name: Adélaïde
full_name: Saint-Léger, Adélaïde
last_name: Saint Léger
- first_name: Carla
full_name: Bello, Carla
last_name: Bello
- first_name: Pablo
full_name: Dans, Pablo D
last_name: Dans
- first_name: Adrian
full_name: Torres, Adrian G
last_name: Torres
- first_name: Eva
full_name: Novoa, Eva M
last_name: Novoa
- first_name: Noelia
full_name: Camacho, Noelia
last_name: Camacho
- first_name: Modesto
full_name: Orozco, Modesto
last_name: Orozco
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Lluís
full_name: Ribas De Pouplana, Lluís
last_name: Ribas De Pouplana
citation:
ama: Saint Léger A, Bello C, Dans P, et al. Saturation of recognition elements blocks
evolution of new tRNA identities. Science advances. 2016;2(4):e1501860-e1501860.
doi:10.1126/sciadv.1501860
apa: Saint Léger, A., Bello, C., Dans, P., Torres, A., Novoa, E., Camacho, N., …
Ribas De Pouplana, L. (2016). Saturation of recognition elements blocks evolution
of new tRNA identities. Science Advances. American Association for the
Advancement of Science. https://doi.org/10.1126/sciadv.1501860
chicago: Saint Léger, Adélaïde, Carla Bello, Pablo Dans, Adrian Torres, Eva Novoa,
Noelia Camacho, Modesto Orozco, Fyodor Kondrashov, and Lluís Ribas De Pouplana.
“Saturation of Recognition Elements Blocks Evolution of New TRNA Identities.”
Science Advances. American Association for the Advancement of Science,
2016. https://doi.org/10.1126/sciadv.1501860.
ieee: A. Saint Léger et al., “Saturation of recognition elements blocks evolution
of new tRNA identities,” Science advances, vol. 2, no. 4. American Association
for the Advancement of Science, pp. e1501860–e1501860, 2016.
ista: Saint Léger A, Bello C, Dans P, Torres A, Novoa E, Camacho N, Orozco M, Kondrashov
F, Ribas De Pouplana L. 2016. Saturation of recognition elements blocks evolution
of new tRNA identities. Science advances. 2(4), e1501860–e1501860.
mla: Saint Léger, Adélaïde, et al. “Saturation of Recognition Elements Blocks Evolution
of New TRNA Identities.” Science Advances, vol. 2, no. 4, American Association
for the Advancement of Science, 2016, pp. e1501860–e1501860, doi:10.1126/sciadv.1501860.
short: A. Saint Léger, C. Bello, P. Dans, A. Torres, E. Novoa, N. Camacho, M. Orozco,
F. Kondrashov, L. Ribas De Pouplana, Science Advances 2 (2016) e1501860–e1501860.
date_created: 2018-12-11T11:48:50Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-01-12T08:19:38Z
day: '01'
doi: 10.1126/sciadv.1501860
extern: 1
intvolume: ' 2'
issue: '4'
month: '04'
page: e1501860 - e1501860
publication: Science advances
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '6798'
quality_controlled: 0
status: public
title: Saturation of recognition elements blocks evolution of new tRNA identities
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
volume: 2
year: '2016'
...
---
_id: '8493'
abstract:
- lang: eng
text: In this paper we study a so-called separatrix map introduced by Zaslavskii–Filonenko
(Sov Phys JETP 27:851–857, 1968) and studied by Treschev (Physica D 116(1–2):21–43,
1998; J Nonlinear Sci 12(1):27–58, 2002), Piftankin (Nonlinearity (19):2617–2644,
2006) Piftankin and Treshchëv (Uspekhi Mat Nauk 62(2(374)):3–108, 2007). We derive
a second order expansion of this map for trigonometric perturbations. In Castejon
et al. (Random iteration of maps of a cylinder and diffusive behavior. Preprint
available at arXiv:1501.03319, 2015), Guardia and Kaloshin (Stochastic diffusive
behavior through big gaps in a priori unstable systems (in preparation), 2015),
and Kaloshin et al. (Normally Hyperbolic Invariant Laminations and diffusive behavior
for the generalized Arnold example away from resonances. Preprint available at
http://www.terpconnect.umd.edu/vkaloshi/, 2015), applying the results of the present
paper, we describe a class of nearly integrable deterministic systems with stochastic
diffusive behavior.
article_processing_charge: No
article_type: original
author:
- first_name: M.
full_name: Guardia, M.
last_name: Guardia
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: J.
full_name: Zhang, J.
last_name: Zhang
citation:
ama: Guardia M, Kaloshin V, Zhang J. A second order expansion of the separatrix
map for trigonometric perturbations of a priori unstable systems. Communications
in Mathematical Physics. 2016;348:321-361. doi:10.1007/s00220-016-2705-9
apa: Guardia, M., Kaloshin, V., & Zhang, J. (2016). A second order expansion
of the separatrix map for trigonometric perturbations of a priori unstable systems.
Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-016-2705-9
chicago: Guardia, M., Vadim Kaloshin, and J. Zhang. “A Second Order Expansion of
the Separatrix Map for Trigonometric Perturbations of a Priori Unstable Systems.”
Communications in Mathematical Physics. Springer Nature, 2016. https://doi.org/10.1007/s00220-016-2705-9.
ieee: M. Guardia, V. Kaloshin, and J. Zhang, “A second order expansion of the separatrix
map for trigonometric perturbations of a priori unstable systems,” Communications
in Mathematical Physics, vol. 348. Springer Nature, pp. 321–361, 2016.
ista: Guardia M, Kaloshin V, Zhang J. 2016. A second order expansion of the separatrix
map for trigonometric perturbations of a priori unstable systems. Communications
in Mathematical Physics. 348, 321–361.
mla: Guardia, M., et al. “A Second Order Expansion of the Separatrix Map for Trigonometric
Perturbations of a Priori Unstable Systems.” Communications in Mathematical
Physics, vol. 348, Springer Nature, 2016, pp. 321–61, doi:10.1007/s00220-016-2705-9.
short: M. Guardia, V. Kaloshin, J. Zhang, Communications in Mathematical Physics
348 (2016) 321–361.
date_created: 2020-09-18T10:45:50Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2021-01-12T08:19:39Z
day: '01'
doi: 10.1007/s00220-016-2705-9
extern: '1'
intvolume: ' 348'
language:
- iso: eng
month: '11'
oa_version: None
page: 321-361
publication: Communications in Mathematical Physics
publication_identifier:
issn:
- 0010-3616
- 1432-0916
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: A second order expansion of the separatrix map for trigonometric perturbations
of a priori unstable systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 348
year: '2016'
...
---
_id: '8494'
abstract:
- lang: eng
text: "We prove a form of Arnold diffusion in the a-priori stable case. Let\r\nH0(p)+ϵH1(θ,p,t),θ∈Tn,p∈Bn,t∈T=R/T,\r\nbe
a nearly integrable system of arbitrary degrees of freedom n⩾2 with a strictly
convex H0. We show that for a “generic” ϵH1, there exists an orbit (θ,p) satisfying\r\n∥p(t)−p(0)∥>l(H1)>0,\r\nwhere
l(H1) is independent of ϵ. The diffusion orbit travels along a codimension-1 resonance,
and the only obstruction to our construction is a finite set of additional resonances.\r\n\r\nFor
the proof we use a combination of geometric and variational methods, and manage
to adapt tools which have recently been developed in the a-priori unstable case."
article_processing_charge: No
article_type: original
author:
- first_name: Patrick
full_name: Bernard, Patrick
last_name: Bernard
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Ke
full_name: Zhang, Ke
last_name: Zhang
citation:
ama: Bernard P, Kaloshin V, Zhang K. Arnold diffusion in arbitrary degrees of freedom
and normally hyperbolic invariant cylinders. Acta Mathematica. 2016;217(1):1-79.
doi:10.1007/s11511-016-0141-5
apa: Bernard, P., Kaloshin, V., & Zhang, K. (2016). Arnold diffusion in arbitrary
degrees of freedom and normally hyperbolic invariant cylinders. Acta Mathematica.
Institut Mittag-Leffler. https://doi.org/10.1007/s11511-016-0141-5
chicago: Bernard, Patrick, Vadim Kaloshin, and Ke Zhang. “Arnold Diffusion in Arbitrary
Degrees of Freedom and Normally Hyperbolic Invariant Cylinders.” Acta Mathematica.
Institut Mittag-Leffler, 2016. https://doi.org/10.1007/s11511-016-0141-5.
ieee: P. Bernard, V. Kaloshin, and K. Zhang, “Arnold diffusion in arbitrary degrees
of freedom and normally hyperbolic invariant cylinders,” Acta Mathematica,
vol. 217, no. 1. Institut Mittag-Leffler, pp. 1–79, 2016.
ista: Bernard P, Kaloshin V, Zhang K. 2016. Arnold diffusion in arbitrary degrees
of freedom and normally hyperbolic invariant cylinders. Acta Mathematica. 217(1),
1–79.
mla: Bernard, Patrick, et al. “Arnold Diffusion in Arbitrary Degrees of Freedom
and Normally Hyperbolic Invariant Cylinders.” Acta Mathematica, vol. 217,
no. 1, Institut Mittag-Leffler, 2016, pp. 1–79, doi:10.1007/s11511-016-0141-5.
short: P. Bernard, V. Kaloshin, K. Zhang, Acta Mathematica 217 (2016) 1–79.
date_created: 2020-09-18T10:46:07Z
date_published: 2016-09-28T00:00:00Z
date_updated: 2021-01-12T08:19:39Z
day: '28'
doi: 10.1007/s11511-016-0141-5
extern: '1'
intvolume: ' 217'
issue: '1'
language:
- iso: eng
month: '09'
oa_version: None
page: 1-79
publication: Acta Mathematica
publication_identifier:
issn:
- 0001-5962
publication_status: published
publisher: Institut Mittag-Leffler
quality_controlled: '1'
status: public
title: Arnold diffusion in arbitrary degrees of freedom and normally hyperbolic invariant
cylinders
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 217
year: '2016'
...
---
_id: '8496'
article_processing_charge: No
article_type: original
author:
- first_name: Artur
full_name: Avila, Artur
last_name: Avila
- first_name: Jacopo
full_name: De Simoi, Jacopo
last_name: De Simoi
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: Avila A, De Simoi J, Kaloshin V. An integrable deformation of an ellipse of
small eccentricity is an ellipse. Annals of Mathematics. 2016;184(2):527-558.
doi:10.4007/annals.2016.184.2.5
apa: Avila, A., De Simoi, J., & Kaloshin, V. (2016). An integrable deformation
of an ellipse of small eccentricity is an ellipse. Annals of Mathematics.
Princeton University Press. https://doi.org/10.4007/annals.2016.184.2.5
chicago: Avila, Artur, Jacopo De Simoi, and Vadim Kaloshin. “An Integrable Deformation
of an Ellipse of Small Eccentricity Is an Ellipse.” Annals of Mathematics.
Princeton University Press, 2016. https://doi.org/10.4007/annals.2016.184.2.5.
ieee: A. Avila, J. De Simoi, and V. Kaloshin, “An integrable deformation of an ellipse
of small eccentricity is an ellipse,” Annals of Mathematics, vol. 184,
no. 2. Princeton University Press, pp. 527–558, 2016.
ista: Avila A, De Simoi J, Kaloshin V. 2016. An integrable deformation of an ellipse
of small eccentricity is an ellipse. Annals of Mathematics. 184(2), 527–558.
mla: Avila, Artur, et al. “An Integrable Deformation of an Ellipse of Small Eccentricity
Is an Ellipse.” Annals of Mathematics, vol. 184, no. 2, Princeton University
Press, 2016, pp. 527–58, doi:10.4007/annals.2016.184.2.5.
short: A. Avila, J. De Simoi, V. Kaloshin, Annals of Mathematics 184 (2016) 527–558.
date_created: 2020-09-18T10:46:22Z
date_published: 2016-09-01T00:00:00Z
date_updated: 2021-01-12T08:19:40Z
day: '01'
doi: 10.4007/annals.2016.184.2.5
extern: '1'
intvolume: ' 184'
issue: '2'
language:
- iso: eng
month: '09'
oa_version: None
page: 527-558
publication: Annals of Mathematics
publication_identifier:
issn:
- 0003-486X
publication_status: published
publisher: Princeton University Press
quality_controlled: '1'
status: public
title: An integrable deformation of an ellipse of small eccentricity is an ellipse
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 184
year: '2016'
...
---
_id: '8497'
abstract:
- lang: eng
text: "We study the dynamics of the restricted planar three-body problem near mean
motion resonances, i.e. a resonance involving the Keplerian periods of the two
lighter bodies revolving around the most massive one. This problem is often used
to model Sun–Jupiter–asteroid systems. For the primaries (Sun and Jupiter), we
pick a realistic mass ratio μ=10−3 and a small eccentricity e0>0. The main result
is a construction of a variety of non local diffusing orbits which show a drastic
change of the osculating (instant) eccentricity of the asteroid, while the osculating
semi major axis is kept almost constant. The proof relies on the careful analysis
of the circular problem, which has a hyperbolic structure, but for which diffusion
is prevented by KAM tori. In the proof we verify certain non-degeneracy conditions
numerically.\r\n\r\nBased on the work of Treschev, it is natural to conjecture
that the time of diffusion for this problem is ∼−ln(μe0)μ3/2e0. We expect our
instability mechanism to apply to realistic values of e0 and we give heuristic
arguments in its favor. If so, the applicability of Nekhoroshev theory to the
three-body problem as well as the long time stability become questionable.\r\n\r\nIt
is well known that, in the Asteroid Belt, located between the orbits of Mars and
Jupiter, the distribution of asteroids has the so-called Kirkwood gaps exactly
at mean motion resonances of low order. Our mechanism gives a possible explanation
of their existence. To relate the existence of Kirkwood gaps with Arnol'd diffusion,
we also state a conjecture on its existence for a typical ϵ-perturbation of the
product of the pendulum and the rotator. Namely, we predict that a positive conditional
measure of initial conditions concentrated in the main resonance exhibits Arnol’d
diffusion on time scales −lnϵϵ2."
article_processing_charge: No
article_type: original
author:
- first_name: Jacques
full_name: Féjoz, Jacques
last_name: Féjoz
- first_name: Marcel
full_name: Guàrdia, Marcel
last_name: Guàrdia
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Pablo
full_name: Roldán, Pablo
last_name: Roldán
citation:
ama: Féjoz J, Guàrdia M, Kaloshin V, Roldán P. Kirkwood gaps and diffusion along
mean motion resonances in the restricted planar three-body problem. Journal
of the European Mathematical Society. 2016;18(10):2315-2403. doi:10.4171/jems/642
apa: Féjoz, J., Guàrdia, M., Kaloshin, V., & Roldán, P. (2016). Kirkwood gaps
and diffusion along mean motion resonances in the restricted planar three-body
problem. Journal of the European Mathematical Society. European Mathematical
Society Publishing House. https://doi.org/10.4171/jems/642
chicago: Féjoz, Jacques, Marcel Guàrdia, Vadim Kaloshin, and Pablo Roldán. “Kirkwood
Gaps and Diffusion along Mean Motion Resonances in the Restricted Planar Three-Body
Problem.” Journal of the European Mathematical Society. European Mathematical
Society Publishing House, 2016. https://doi.org/10.4171/jems/642.
ieee: J. Féjoz, M. Guàrdia, V. Kaloshin, and P. Roldán, “Kirkwood gaps and diffusion
along mean motion resonances in the restricted planar three-body problem,” Journal
of the European Mathematical Society, vol. 18, no. 10. European Mathematical
Society Publishing House, pp. 2315–2403, 2016.
ista: Féjoz J, Guàrdia M, Kaloshin V, Roldán P. 2016. Kirkwood gaps and diffusion
along mean motion resonances in the restricted planar three-body problem. Journal
of the European Mathematical Society. 18(10), 2315–2403.
mla: Féjoz, Jacques, et al. “Kirkwood Gaps and Diffusion along Mean Motion Resonances
in the Restricted Planar Three-Body Problem.” Journal of the European Mathematical
Society, vol. 18, no. 10, European Mathematical Society Publishing House,
2016, pp. 2315–403, doi:10.4171/jems/642.
short: J. Féjoz, M. Guàrdia, V. Kaloshin, P. Roldán, Journal of the European Mathematical
Society 18 (2016) 2315–2403.
date_created: 2020-09-18T10:46:31Z
date_published: 2016-09-19T00:00:00Z
date_updated: 2021-01-12T08:19:41Z
day: '19'
doi: 10.4171/jems/642
extern: '1'
intvolume: ' 18'
issue: '10'
language:
- iso: eng
month: '09'
oa_version: None
page: 2315-2403
publication: Journal of the European Mathematical Society
publication_identifier:
issn:
- 1435-9855
publication_status: published
publisher: European Mathematical Society Publishing House
quality_controlled: '1'
status: public
title: Kirkwood gaps and diffusion along mean motion resonances in the restricted
planar three-body problem
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2016'
...
---
_id: '850'
abstract:
- lang: eng
text: Fitness landscapes depict how genotypes manifest at the phenotypic level and
form the basis of our understanding of many areas of biology, yet their properties
remain elusive. Previous studies have analysed specific genes, often using their
function as a proxy for fitness, experimentally assessing the effect on function
of single mutations and their combinations in a specific sequence or in different
sequences. However, systematic high-throughput studies of the local fitness landscape
of an entire protein have not yet been reported. Here we visualize an extensive
region of the local fitness landscape of the green fluorescent protein from Aequorea
Victoria (avGFP) by measuring the native function (fluorescence) of tens of thousands
of derivative genotypes of avGFP. We show that the fitness landscape of avGFP
is narrow, with 3/4 of the derivatives with a single mutation showing reduced
fluorescence and half of the derivatives with four mutations being completely
non-fluorescent. The narrowness is enhanced by epistasis, which was detected in
up to 30% of genotypes with multiple mutations and mostly occurred through the
cumulative effect of slightly deleterious mutations causing a threshold-like decrease
in protein stability and a concomitant loss of fluorescence. A model of orthologous
sequence divergence spanning hundreds of millions of years predicted the extent
of epistasis in our data, indicating congruence between the fitness landscape
properties at the local and global scales. The characterization of the local fitness
landscape of avGFP has important implications for several fields including molecular
evolution, population genetics and protein design.
acknowledgement: We thank Y. Kulikova and G. Filion for discussion on statistical
analysis and I. Osterman, R. Moretti and J. Meiler for technical assistance and
M. Friesen for a critical reading of the manuscript. We thank H. Himmelbauer, CRG
Genomic Unit and the Russian Science Foundation project (14-50-00150) for sequencing.
Experiments were partially carried out using the equipment provided by the IBCH
core facility (CKP IBCH). The work was supported by HHMI International Early Career
Scientist Program (55007424), the EMBO Young Investigator Programme, MINECO (BFU2012-31329),
Spanish Ministry of Economy and Competitiveness Centro de Excelencia Severo Ochoa
2013-2017 grant (SEV-2012-0208), Secretaria d'Universitats i Recerca del Departament
d'Economia i Coneixement de la Generalitat's AGAUR program (2014 SGR 0974), Russian
Science Foundation (14-25-00129) and the European Research Council under the European
Union's Seventh Framework Programme (FP7/2007-2013, ERC grant agreement, 335980-EinME).
author:
- first_name: Karen
full_name: Karen Sarkisyan
id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
last_name: Sarkisyan
orcid: 0000-0002-5375-6341
- first_name: Dmitry
full_name: Bolotin, Dmitry A
last_name: Bolotin
- first_name: Margarita
full_name: Meer, Margarita V
last_name: Meer
- first_name: Dinara
full_name: Usmanova, Dinara R
last_name: Usmanova
- first_name: Alexander
full_name: Mishin, Alexander S
last_name: Mishin
- first_name: George
full_name: Sharonov, George V
last_name: Sharonov
- first_name: Dmitry
full_name: Ivankov, Dmitry N
last_name: Ivankov
- first_name: Nina
full_name: Bozhanova, Nina G
last_name: Bozhanova
- first_name: Mikhail
full_name: Baranov, Mikhail S
last_name: Baranov
- first_name: Onuralp
full_name: Soylemez, Onuralp
last_name: Soylemez
- first_name: Natalya
full_name: Bogatyreva, Natalya S
last_name: Bogatyreva
- first_name: Peter
full_name: Vlasov, Peter K
last_name: Vlasov
- first_name: Evgeny
full_name: Egorov, Evgeny S
last_name: Egorov
- first_name: Maria
full_name: Logacheva, Maria D
last_name: Logacheva
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
- first_name: Dmitriy
full_name: Chudakov, Dmitriy M
last_name: Chudakov
- first_name: Ekaterina
full_name: Putintseva, Ekaterina V
last_name: Putintseva
- first_name: Ilgar
full_name: Mamedov, Ilgar Z
last_name: Mamedov
- first_name: Dan
full_name: Tawfik, Dan S
last_name: Tawfik
- first_name: Konstantin
full_name: Lukyanov, Konstantin A
last_name: Lukyanov
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Sarkisyan K, Bolotin D, Meer M, et al. Local fitness landscape of the green
fluorescent protein. Nature. 2016;533:397-401. doi:10.1038/nature17995
apa: Sarkisyan, K., Bolotin, D., Meer, M., Usmanova, D., Mishin, A., Sharonov, G.,
… Kondrashov, F. (2016). Local fitness landscape of the green fluorescent protein.
Nature. Nature Publishing Group. https://doi.org/10.1038/nature17995
chicago: Sarkisyan, Karen, Dmitry Bolotin, Margarita Meer, Dinara Usmanova, Alexander
Mishin, George Sharonov, Dmitry Ivankov, et al. “Local Fitness Landscape of the
Green Fluorescent Protein.” Nature. Nature Publishing Group, 2016. https://doi.org/10.1038/nature17995.
ieee: K. Sarkisyan et al., “Local fitness landscape of the green fluorescent
protein,” Nature, vol. 533. Nature Publishing Group, pp. 397–401, 2016.
ista: Sarkisyan K, Bolotin D, Meer M, Usmanova D, Mishin A, Sharonov G, Ivankov
D, Bozhanova N, Baranov M, Soylemez O, Bogatyreva N, Vlasov P, Egorov E, Logacheva
M, Kondrashov A, Chudakov D, Putintseva E, Mamedov I, Tawfik D, Lukyanov K, Kondrashov
F. 2016. Local fitness landscape of the green fluorescent protein. Nature. 533,
397–401.
mla: Sarkisyan, Karen, et al. “Local Fitness Landscape of the Green Fluorescent
Protein.” Nature, vol. 533, Nature Publishing Group, 2016, pp. 397–401,
doi:10.1038/nature17995.
short: K. Sarkisyan, D. Bolotin, M. Meer, D. Usmanova, A. Mishin, G. Sharonov, D.
Ivankov, N. Bozhanova, M. Baranov, O. Soylemez, N. Bogatyreva, P. Vlasov, E. Egorov,
M. Logacheva, A. Kondrashov, D. Chudakov, E. Putintseva, I. Mamedov, D. Tawfik,
K. Lukyanov, F. Kondrashov, Nature 533 (2016) 397–401.
date_created: 2018-12-11T11:48:50Z
date_published: 2016-05-11T00:00:00Z
date_updated: 2021-01-12T08:19:42Z
day: '11'
doi: 10.1038/nature17995
extern: 1
intvolume: ' 533'
month: '05'
page: 397 - 401
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6799'
quality_controlled: 0
status: public
title: Local fitness landscape of the green fluorescent protein
type: journal_article
volume: 533
year: '2016'
...
---
_id: '853'
abstract:
- lang: eng
text: A comparative analysis of the metagenomes from two 30 000-year-old permafrost
samples, one of lake-alluvial origin and the other from late Pleistocene Ice Complex
sediments, revealed significant differences within microbial communities. The
late Pleistocene Ice Complex sediments (which have been characterized by the absence
of methane with lower values of redox potential and Fe2+ content) showed a low
abundance of methanogenic archaea and enzymes from both the carbon and nitrogen
cycles, but a higher abundance of enzymes associated with the sulfur cycle. The
metagenomic and geochemical analyses described in the paper provide evidence that
the formation of the sampled late Pleistocene Ice Complex sediments likely took
place under much more aerobic conditions than lake-alluvial sediments.
acknowledgement: This work was supported by grants from the Russian Scientific Fund
(14-14-01115) to Elizaveta Rivkina; from the National Science Foundation (DEB-1442262)
to Tatiana Vish- nivetskaya; and from the HHMI International Early Career Scientist
Program (55007424), the EMBO Young Investigator Programme, MINECO (BFU2012-31329
and Sev-2012-0208), and the AGAUR program (2014 SGR 0974) to Fyodor Kondrashov.
Support from the Russian Scientific Fund (14-14-01115) was allocated for sample
collection, gDNA isolation, and analysis of metagenomic data.
author:
- first_name: Elizaveta
full_name: Rivkina, Elizaveta
last_name: Rivkina
- first_name: Lada
full_name: Petrovskaya, Lada E
last_name: Petrovskaya
- first_name: Tatiana
full_name: Vishnivetskaya, Tatiana A
last_name: Vishnivetskaya
- first_name: Kirill
full_name: Krivushin, Kirill V
last_name: Krivushin
- first_name: Lyubov
full_name: Shmakova, Lyubov A
last_name: Shmakova
- first_name: Maria
full_name: Tutukina, Maria
last_name: Tutukina
- first_name: Arthur
full_name: Meyers, Arthur J
last_name: Meyers
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Rivkina E, Petrovskaya L, Vishnivetskaya T, et al. Metagenomic analyses of
the late Pleistocene permafrost - Additional tools for reconstruction of environmental
conditions. Biogeosciences. 2016;13(7):2207-2219. doi:10.5194/bg-13-2207-2016
apa: Rivkina, E., Petrovskaya, L., Vishnivetskaya, T., Krivushin, K., Shmakova,
L., Tutukina, M., … Kondrashov, F. (2016). Metagenomic analyses of the late Pleistocene
permafrost - Additional tools for reconstruction of environmental conditions.
Biogeosciences. European Geosciences Union. https://doi.org/10.5194/bg-13-2207-2016
chicago: Rivkina, Elizaveta, Lada Petrovskaya, Tatiana Vishnivetskaya, Kirill Krivushin,
Lyubov Shmakova, Maria Tutukina, Arthur Meyers, and Fyodor Kondrashov. “Metagenomic
Analyses of the Late Pleistocene Permafrost - Additional Tools for Reconstruction
of Environmental Conditions.” Biogeosciences. European Geosciences Union,
2016. https://doi.org/10.5194/bg-13-2207-2016.
ieee: E. Rivkina et al., “Metagenomic analyses of the late Pleistocene permafrost
- Additional tools for reconstruction of environmental conditions,” Biogeosciences,
vol. 13, no. 7. European Geosciences Union, pp. 2207–2219, 2016.
ista: Rivkina E, Petrovskaya L, Vishnivetskaya T, Krivushin K, Shmakova L, Tutukina
M, Meyers A, Kondrashov F. 2016. Metagenomic analyses of the late Pleistocene
permafrost - Additional tools for reconstruction of environmental conditions.
Biogeosciences. 13(7), 2207–2219.
mla: Rivkina, Elizaveta, et al. “Metagenomic Analyses of the Late Pleistocene Permafrost
- Additional Tools for Reconstruction of Environmental Conditions.” Biogeosciences,
vol. 13, no. 7, European Geosciences Union, 2016, pp. 2207–19, doi:10.5194/bg-13-2207-2016.
short: E. Rivkina, L. Petrovskaya, T. Vishnivetskaya, K. Krivushin, L. Shmakova,
M. Tutukina, A. Meyers, F. Kondrashov, Biogeosciences 13 (2016) 2207–2219.
date_created: 2018-12-11T11:48:51Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-01-12T08:19:54Z
day: '01'
doi: 10.5194/bg-13-2207-2016
extern: 1
intvolume: ' 13'
issue: '7'
month: '04'
page: 2207 - 2219
publication: Biogeosciences
publication_status: published
publisher: European Geosciences Union
publist_id: '6793'
quality_controlled: 0
status: public
title: Metagenomic analyses of the late Pleistocene permafrost - Additional tools
for reconstruction of environmental conditions
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: 13
year: '2016'
...
---
_id: '896'
abstract:
- lang: eng
text: Multicellular eukaryotes have evolved a range of mechanisms for immune recognition.
A widespread family involved in innate immunity are the NACHT-domain and leucine-rich-repeat-containing
(NLR) proteins.Mammals have small numbers of NLR proteins, whereas in some species,
mostly those without adaptive immune systems, NLRs have expanded into very large
families.We describe a family of nearly 400NLR proteins encoded in the zebrafish
genome. The proteins share a defining overall structure, which arose in fishes
after a fusion of the core NLR domains with a B30.2 domain, but can be subdivided
into four groups based on their NACHT domains. Gene conversion acting differentially
on the NACHT and B30.2 domains has shaped the family and created the groups. Evidence
of positive selection in the B30.2 domain indicates that this domain rather than
the leucine-rich repeats acts as the pathogen recognition module. In an unusual
chromosomal organization, the majority of the genes are located on one chromosome
arm, interspersed with other large multigene families, including a new family
encoding zinc-finger proteins. The NLR-B30.2 proteins represent a new family with
diversity in the specific recognition module that is present in fishes in spite
of the parallel existence of an adaptive immune system.
acknowledgement: Financial support was provided by EMBO and the DFG SFB 670 'Zellautonome
Immunität' to M.L., DFG SFB 680 'Molecular basis of evolutionary innovation' to
T.W., DFG SPP1819 to M.L. and T.W., the HHMI International Early Career Scientist
Programme (55007424), MINECO (Sev-2012-0208), AGAUR programme (2014 SGR 0974), and
an ERC Starting Grant (335980-EinME) to F.K., the European Molecular Biology Laboratory
to J.M., the Wellcome Trust to K.H. (zebrafish genome sequencing project) and the
National Human Genome Research Institute (NHGRI) grant HG002659 to G.K.L. (gene
annotation), and a grant from the Volkswagen Foundation to P.H.S. We thank the CHEOPS
support team and the Bundesland Nordrhein Westfalen for making HPC applications
freely available at the University of Cologne.
author:
- first_name: Kerstin
full_name: Howe, Kerstin L
last_name: Howe
- first_name: Philipp
full_name: Schiffer, Philipp H
last_name: Schiffer
- first_name: Julia
full_name: Zielinski, Julia G
last_name: Zielinski
- first_name: Thomas
full_name: Wiehe, Thomas H
last_name: Wiehe
- first_name: Gavin
full_name: Laird, Gavin K
last_name: Laird
- first_name: John
full_name: Marioni, John C
last_name: Marioni
- first_name: Onuralp
full_name: Soylemez, Onuralp
last_name: Soylemez
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Maria
full_name: Leptin, Maria
last_name: Leptin
citation:
ama: Howe K, Schiffer P, Zielinski J, et al. Structure and evolutionary history
of a large family of NLR proteins in the zebrafish. Open Biology. 2016;6(4).
doi:10.1098/rsob.160009
apa: Howe, K., Schiffer, P., Zielinski, J., Wiehe, T., Laird, G., Marioni, J., …
Leptin, M. (2016). Structure and evolutionary history of a large family of NLR
proteins in the zebrafish. Open Biology. Royal Society, The. https://doi.org/10.1098/rsob.160009
chicago: Howe, Kerstin, Philipp Schiffer, Julia Zielinski, Thomas Wiehe, Gavin Laird,
John Marioni, Onuralp Soylemez, Fyodor Kondrashov, and Maria Leptin. “Structure
and Evolutionary History of a Large Family of NLR Proteins in the Zebrafish.”
Open Biology. Royal Society, The, 2016. https://doi.org/10.1098/rsob.160009.
ieee: K. Howe et al., “Structure and evolutionary history of a large family
of NLR proteins in the zebrafish,” Open Biology, vol. 6, no. 4. Royal Society,
The, 2016.
ista: Howe K, Schiffer P, Zielinski J, Wiehe T, Laird G, Marioni J, Soylemez O,
Kondrashov F, Leptin M. 2016. Structure and evolutionary history of a large family
of NLR proteins in the zebrafish. Open Biology. 6(4).
mla: Howe, Kerstin, et al. “Structure and Evolutionary History of a Large Family
of NLR Proteins in the Zebrafish.” Open Biology, vol. 6, no. 4, Royal Society,
The, 2016, doi:10.1098/rsob.160009.
short: K. Howe, P. Schiffer, J. Zielinski, T. Wiehe, G. Laird, J. Marioni, O. Soylemez,
F. Kondrashov, M. Leptin, Open Biology 6 (2016).
date_created: 2018-12-11T11:49:04Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T08:21:32Z
day: '01'
doi: 10.1098/rsob.160009
extern: 1
intvolume: ' 6'
issue: '4'
month: '01'
publication: Open Biology
publication_status: published
publisher: Royal Society, The
publist_id: '6754'
quality_controlled: 0
status: public
title: Structure and evolutionary history of a large family of NLR proteins in the
zebrafish
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: '2016'
...
---
_id: '9019'
abstract:
- lang: eng
text: Targeting protein–protein interactions has long been considered as a very
difficult if impossible task, but over the past decade, front lines have moved.
The number of successful examples is exponentially growing. This review presents
a rapid overview of recent advances in this field considering the strengths and
weaknesses of the small molecule approaches and alternative strategies such as
the selection or design of artificial antibodies, peptides or peptidomimetics.
- lang: fre
text: Cibler les interactions protéine–protéine a longtemps été considéré comme
une tâche très difficile, voire impossible, mais, depuis les dix dernières années,
les lignes ont bougé. Le nombre d’exemples de réussites s’accroît exponentiellement.
Cette revue présente un rapide panorama des avancées récentes dans ce domaine,
considérant les forces et les faiblesses de l’approche « petite molécule » ainsi
que des stratégies alternatives comme la sélection ou le design d’anticorps artificiels,
de peptides ou de peptidomimétiques.
article_processing_charge: No
article_type: original
author:
- 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: Francoise
full_name: Ochsenbein, Francoise
last_name: Ochsenbein
citation:
ama: Bakail MM, Ochsenbein F. Targeting protein–protein interactions, a wide open
field for drug design. Comptes Rendus Chimie. 2016;19(1-2):19-27. doi:10.1016/j.crci.2015.12.004
apa: Bakail, M. M., & Ochsenbein, F. (2016). Targeting protein–protein interactions,
a wide open field for drug design. Comptes Rendus Chimie. Elsevier. https://doi.org/10.1016/j.crci.2015.12.004
chicago: Bakail, May M, and Francoise Ochsenbein. “Targeting Protein–Protein Interactions,
a Wide Open Field for Drug Design.” Comptes Rendus Chimie. Elsevier, 2016.
https://doi.org/10.1016/j.crci.2015.12.004.
ieee: M. M. Bakail and F. Ochsenbein, “Targeting protein–protein interactions, a
wide open field for drug design,” Comptes Rendus Chimie, vol. 19, no. 1–2.
Elsevier, pp. 19–27, 2016.
ista: Bakail MM, Ochsenbein F. 2016. Targeting protein–protein interactions, a wide
open field for drug design. Comptes Rendus Chimie. 19(1–2), 19–27.
mla: Bakail, May M., and Francoise Ochsenbein. “Targeting Protein–Protein Interactions,
a Wide Open Field for Drug Design.” Comptes Rendus Chimie, vol. 19, no.
1–2, Elsevier, 2016, pp. 19–27, doi:10.1016/j.crci.2015.12.004.
short: M.M. Bakail, F. Ochsenbein, Comptes Rendus Chimie 19 (2016) 19–27.
date_created: 2021-01-19T11:11:54Z
date_published: 2016-02-06T00:00:00Z
date_updated: 2023-02-23T13:46:55Z
day: '06'
ddc:
- '570'
doi: 10.1016/j.crci.2015.12.004
extern: '1'
file:
- access_level: open_access
checksum: c262814ffdbfe95900256ab9ff42cdf5
content_type: application/pdf
creator: dernst
date_created: 2021-01-22T12:36:52Z
date_updated: 2021-01-22T12:36:52Z
file_id: '9035'
file_name: 2016_ComptesRendueChimie_Bakail.pdf
file_size: 2045260
relation: main_file
success: 1
file_date_updated: 2021-01-22T12:36:52Z
has_accepted_license: '1'
intvolume: ' 19'
issue: 1-2
keyword:
- General Chemistry
- General Chemical Engineering
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 19-27
publication: Comptes Rendus Chimie
publication_identifier:
issn:
- 1631-0748
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Targeting protein–protein interactions, a wide open field for drug design
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2016'
...
---
_id: '9051'
abstract:
- lang: eng
text: 'Biological systems often involve the self-assembly of basic components into
complex and functioning structures. Artificial systems that mimic such processes
can provide a well-controlled setting to explore the principles involved and also
synthesize useful micromachines. Our experiments show that immotile, but active,
components self-assemble into two types of structure that exhibit the fundamental
forms of motility: translation and rotation. Specifically, micron-scale metallic
rods are designed to induce extensile surface flows in the presence of a chemical
fuel; these rods interact with each other and pair up to form either a swimmer
or a rotor. Such pairs can transition reversibly between these two configurations,
leading to kinetics reminiscent of bacterial run-and-tumble motion.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Megan S.
full_name: Davies Wykes, Megan S.
last_name: Davies Wykes
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: Takuji
full_name: Adachi, Takuji
last_name: Adachi
- first_name: Leif
full_name: Ristroph, Leif
last_name: Ristroph
- first_name: Xiao
full_name: Zhong, Xiao
last_name: Zhong
- first_name: Michael D.
full_name: Ward, Michael D.
last_name: Ward
- first_name: Jun
full_name: Zhang, Jun
last_name: Zhang
- first_name: Michael J.
full_name: Shelley, Michael J.
last_name: Shelley
citation:
ama: Davies Wykes MS, Palacci JA, Adachi T, et al. Dynamic self-assembly of microscale
rotors and swimmers. Soft Matter. 2016;12(20):4584-4589. doi:10.1039/c5sm03127c
apa: Davies Wykes, M. S., Palacci, J. A., Adachi, T., Ristroph, L., Zhong, X., Ward,
M. D., … Shelley, M. J. (2016). Dynamic self-assembly of microscale rotors and
swimmers. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c5sm03127c
chicago: Davies Wykes, Megan S., Jérémie A Palacci, Takuji Adachi, Leif Ristroph,
Xiao Zhong, Michael D. Ward, Jun Zhang, and Michael J. Shelley. “Dynamic Self-Assembly
of Microscale Rotors and Swimmers.” Soft Matter. Royal Society of Chemistry,
2016. https://doi.org/10.1039/c5sm03127c.
ieee: M. S. Davies Wykes et al., “Dynamic self-assembly of microscale rotors
and swimmers,” Soft Matter, vol. 12, no. 20. Royal Society of Chemistry,
pp. 4584–4589, 2016.
ista: Davies Wykes MS, Palacci JA, Adachi T, Ristroph L, Zhong X, Ward MD, Zhang
J, Shelley MJ. 2016. Dynamic self-assembly of microscale rotors and swimmers.
Soft Matter. 12(20), 4584–4589.
mla: Davies Wykes, Megan S., et al. “Dynamic Self-Assembly of Microscale Rotors
and Swimmers.” Soft Matter, vol. 12, no. 20, Royal Society of Chemistry,
2016, pp. 4584–89, doi:10.1039/c5sm03127c.
short: M.S. Davies Wykes, J.A. Palacci, T. Adachi, L. Ristroph, X. Zhong, M.D. Ward,
J. Zhang, M.J. Shelley, Soft Matter 12 (2016) 4584–4589.
date_created: 2021-02-01T13:44:00Z
date_published: 2016-05-28T00:00:00Z
date_updated: 2023-02-23T13:47:38Z
day: '28'
doi: 10.1039/c5sm03127c
extern: '1'
external_id:
arxiv:
- '1509.06330'
pmid:
- '27121100'
intvolume: ' 12'
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1509.06330
month: '05'
oa: 1
oa_version: Preprint
page: 4584-4589
pmid: 1
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic self-assembly of microscale rotors and swimmers
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 12
year: '2016'
...
---
_id: '9052'
abstract:
- lang: eng
text: We describe colloidal Janus particles with metallic and dielectric faces that
swim vigorously when illuminated by defocused optical tweezers without consuming
any chemical fuel. Rather than wandering randomly, these optically-activated colloidal
swimmers circulate back and forth through the beam of light, tracing out sinuous
rosette patterns. We propose a model for this mode of light-activated transport
that accounts for the observed behavior through a combination of self-thermophoresis
and optically-induced torque. In the deterministic limit, this model yields trajectories
that resemble rosette curves known as hypotrochoids.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Henrique
full_name: Moyses, Henrique
last_name: Moyses
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: Stefano
full_name: Sacanna, Stefano
last_name: Sacanna
- first_name: David G.
full_name: Grier, David G.
last_name: Grier
citation:
ama: Moyses H, Palacci JA, Sacanna S, Grier DG. Trochoidal trajectories of self-propelled
Janus particles in a diverging laser beam. Soft Matter. 2016;12(30):6357-6364.
doi:10.1039/c6sm01163b
apa: Moyses, H., Palacci, J. A., Sacanna, S., & Grier, D. G. (2016). Trochoidal
trajectories of self-propelled Janus particles in a diverging laser beam. Soft
Matter. Royal Society of Chemistry . https://doi.org/10.1039/c6sm01163b
chicago: Moyses, Henrique, Jérémie A Palacci, Stefano Sacanna, and David G. Grier.
“Trochoidal Trajectories of Self-Propelled Janus Particles in a Diverging Laser
Beam.” Soft Matter. Royal Society of Chemistry , 2016. https://doi.org/10.1039/c6sm01163b.
ieee: H. Moyses, J. A. Palacci, S. Sacanna, and D. G. Grier, “Trochoidal trajectories
of self-propelled Janus particles in a diverging laser beam,” Soft Matter,
vol. 12, no. 30. Royal Society of Chemistry , pp. 6357–6364, 2016.
ista: Moyses H, Palacci JA, Sacanna S, Grier DG. 2016. Trochoidal trajectories of
self-propelled Janus particles in a diverging laser beam. Soft Matter. 12(30),
6357–6364.
mla: Moyses, Henrique, et al. “Trochoidal Trajectories of Self-Propelled Janus Particles
in a Diverging Laser Beam.” Soft Matter, vol. 12, no. 30, Royal Society
of Chemistry , 2016, pp. 6357–64, doi:10.1039/c6sm01163b.
short: H. Moyses, J.A. Palacci, S. Sacanna, D.G. Grier, Soft Matter 12 (2016) 6357–6364.
date_created: 2021-02-01T13:44:15Z
date_published: 2016-08-14T00:00:00Z
date_updated: 2023-02-23T13:47:40Z
day: '14'
doi: 10.1039/c6sm01163b
extern: '1'
external_id:
arxiv:
- '1609.01497'
pmid:
- '27338294'
intvolume: ' 12'
issue: '30'
keyword:
- General Chemistry
- Condensed Matter Physics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1609.01497
month: '08'
oa: 1
oa_version: Preprint
page: 6357-6364
pmid: 1
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: 'Royal Society of Chemistry '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Trochoidal trajectories of self-propelled Janus particles in a diverging laser
beam
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 12
year: '2016'
...
---
_id: '9140'
abstract:
- lang: eng
text: 'Expected changes to future extreme precipitation remain a key uncertainty
associated with anthropogenic climate change. Extreme precipitation has been proposed
to scale with the precipitable water content in the atmosphere. Assuming constant
relative humidity, this implies an increase of precipitation extremes at a rate
of about 7% °C−1 globally as indicated by the Clausius‐Clapeyron relationship.
Increases faster and slower than Clausius‐Clapeyron have also been reported. In
this work, we examine the scaling between precipitation extremes and temperature
in the present climate using simulations and measurements from surface weather
stations collected in the frame of the HyMeX and MED‐CORDEX programs in Southern
France. Of particular interest are departures from the Clausius‐Clapeyron thermodynamic
expectation, their spatial and temporal distribution, and their origin. Looking
at the scaling of precipitation extreme with temperature, two regimes emerge which
form a hook shape: one at low temperatures (cooler than around 15°C) with rates
of increase close to the Clausius‐Clapeyron rate and one at high temperatures
(warmer than about 15°C) with sub‐Clausius‐Clapeyron rates and most often negative
rates. On average, the region of focus does not seem to exhibit super Clausius‐Clapeyron
behavior except at some stations, in contrast to earlier studies. Many factors
can contribute to departure from Clausius‐Clapeyron scaling: time and spatial
averaging, choice of scaling temperature (surface versus condensation level),
and precipitation efficiency and vertical velocity in updrafts that are not necessarily
constant with temperature. But most importantly, the dynamical contribution of
orography to precipitation in the fall over this area during the so‐called “Cevenoles”
events, explains the hook shape of the scaling of precipitation extremes.'
article_processing_charge: No
article_type: original
author:
- first_name: P.
full_name: Drobinski, P.
last_name: Drobinski
- first_name: B.
full_name: Alonzo, B.
last_name: Alonzo
- first_name: S.
full_name: Bastin, S.
last_name: Bastin
- first_name: N. Da
full_name: Silva, N. Da
last_name: Silva
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
citation:
ama: 'Drobinski P, Alonzo B, Bastin S, Silva ND, Muller CJ. Scaling of precipitation
extremes with temperature in the French Mediterranean region: What explains the
hook shape? Journal of Geophysical Research: Atmospheres. 2016;121(7):3100-3119.
doi:10.1002/2015jd023497'
apa: 'Drobinski, P., Alonzo, B., Bastin, S., Silva, N. D., & Muller, C. J. (2016).
Scaling of precipitation extremes with temperature in the French Mediterranean
region: What explains the hook shape? Journal of Geophysical Research: Atmospheres.
American Geophysical Union. https://doi.org/10.1002/2015jd023497'
chicago: 'Drobinski, P., B. Alonzo, S. Bastin, N. Da Silva, and Caroline J Muller.
“Scaling of Precipitation Extremes with Temperature in the French Mediterranean
Region: What Explains the Hook Shape?” Journal of Geophysical Research: Atmospheres.
American Geophysical Union, 2016. https://doi.org/10.1002/2015jd023497.'
ieee: 'P. Drobinski, B. Alonzo, S. Bastin, N. D. Silva, and C. J. Muller, “Scaling
of precipitation extremes with temperature in the French Mediterranean region:
What explains the hook shape?,” Journal of Geophysical Research: Atmospheres,
vol. 121, no. 7. American Geophysical Union, pp. 3100–3119, 2016.'
ista: 'Drobinski P, Alonzo B, Bastin S, Silva ND, Muller CJ. 2016. Scaling of precipitation
extremes with temperature in the French Mediterranean region: What explains the
hook shape? Journal of Geophysical Research: Atmospheres. 121(7), 3100–3119.'
mla: 'Drobinski, P., et al. “Scaling of Precipitation Extremes with Temperature
in the French Mediterranean Region: What Explains the Hook Shape?” Journal
of Geophysical Research: Atmospheres, vol. 121, no. 7, American Geophysical
Union, 2016, pp. 3100–19, doi:10.1002/2015jd023497.'
short: 'P. Drobinski, B. Alonzo, S. Bastin, N.D. Silva, C.J. Muller, Journal of
Geophysical Research: Atmospheres 121 (2016) 3100–3119.'
date_created: 2021-02-15T14:21:16Z
date_published: 2016-03-16T00:00:00Z
date_updated: 2022-01-24T13:41:02Z
day: '16'
doi: 10.1002/2015jd023497
extern: '1'
intvolume: ' 121'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/2015JD023497
month: '03'
oa: 1
oa_version: Published Version
page: 3100-3119
publication: 'Journal of Geophysical Research: Atmospheres'
publication_identifier:
issn:
- 2169-897X
- 2169-8996
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
status: public
title: 'Scaling of precipitation extremes with temperature in the French Mediterranean
region: What explains the hook shape?'
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 121
year: '2016'
...
---
_id: '92'
abstract:
- lang: eng
text: 'Advanced organic nonlinear optical (NLO) materials have attracted increasing
attention due to their multitude of applications in modern telecommunication devices.
Arguably the most important advantage of organic NLO materials, relative to traditionally
used inorganic NLO materials, is their short optical response time. Geminal amido
esters with their donor-π-acceptor (D-π-A) architecture exhibit high levels of
electron delocalization and substantial intramolecular charge transfer, which
should endow these materials with short optical response times and large molecular
(hyper)polarizabilities. In order to test this hypothesis, the linear and second-order
nonlinear optical properties of five geminal amido esters, (E)-ethyl 3-(X-phenylamino)-2-(Y-phenylcarbamoyl)acrylate
(1, X = 4-H, Y = 4-H; 2, X = 4-CH3, Y = 4-CH3; 3, X = 4-NO2, Y = 2,5-OCH3; 4,
X = 2-Cl, Y = 2-Cl; 5, X = 4-Cl, Y = 4-Cl) were synthesized and characterized,
whereby NLO structure-function relationships were established including intramolecular
charge transfer characteristics, crystal field effects, and molecular first hyperpolarizabilities
(β). Given the typically large errors (10-30%) associated with the determination
of β coefficients, three independent methods were used: (i) density functional
theory, (ii) hyper-Rayleigh scattering, and (iii) high-resolution X-ray diffraction
data analysis based on multipolar modeling of electron densities at each atom.
These three methods delivered consistent values of β, and based on these results,
3 should hold the most promise for NLO applications. The correlation between the
molecular structure of these geminal amido esters and their linear and nonlinear
optical properties thus provide molecular design guidelines for organic NLO materials;
this leads to the ultimate goal of generating bespoke organic molecules to suit
a given NLO device application.'
acknowledgement: J.M.C. thanks the 1851 Royal Commission of the Great Exhibition for
a Design Fellowship, hosted by Argonne National Laboratory where work done was supported
by the DOE Office of Science, Office of Basic Energy Sciences, under Contract No.
DE-AC02-06CH11357. T.-C.L acknowledges the Taiwanese Government for a Studying Abroad
Scholarship. C.M.A is indebted to the EPSRC UK for a DTA Ph.D. studentship (Grants
EP/J500380/1 and EP/L504920/1). Y.T. is grateful for a Cavendish-NUDT Scholarship.
The Swiss-Norwegian Collaborative Research Group at the ESRF, Grenoble, France,
is thanked for access to synchrotron facilities. The OPAL reactor, ANSTO, Australia,
is acknowledged for access to neutron scattering facilities via a program proposal,
ID 1236. J.P-M. is grateful to Skidmore College for supporting this work via a full-year
sabbatical with enhancement. All authors thank the EPSRC UK National Service for
Computational Chemistry Software (NSCCS) and acknowledge contributions from its
staff in supporting this work.
author:
- first_name: Jaqueline
full_name: Cole, Jaqueline
last_name: Cole
- first_name: Tzechia
full_name: Lin, Tzechia
last_name: Lin
- first_name: Christopher
full_name: Ashcroft, Christopher
last_name: Ashcroft
- first_name: Javier
full_name: Pérez Moreno, Javier
last_name: Pérez Moreno
- first_name: Yizhou
full_name: Tan, Yizhou
last_name: Tan
- first_name: Perumal
full_name: Venkatesan, Perumal
last_name: Venkatesan
- 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: Philip
full_name: Pattison, Philip
last_name: Pattison
- first_name: Alison
full_name: Edwards, Alison
last_name: Edwards
- first_name: Ross
full_name: Piltz, Ross
last_name: Piltz
- first_name: Koen
full_name: Clays, Koen
last_name: Clays
- first_name: Andivelu
full_name: Ilangovan, Andivelu
last_name: Ilangovan
citation:
ama: Cole J, Lin T, Ashcroft C, et al. Relating the structure of geminal Amido Esters
to their molecular hyperpolarizability. Journal of Physical Chemistry C.
2016;120(51):29439-29448. doi:10.1021/acs.jpcc.6b10724
apa: Cole, J., Lin, T., Ashcroft, C., Pérez Moreno, J., Tan, Y., Venkatesan, P.,
… Ilangovan, A. (2016). Relating the structure of geminal Amido Esters to their
molecular hyperpolarizability. Journal of Physical Chemistry C. American
Chemical Society. https://doi.org/10.1021/acs.jpcc.6b10724
chicago: Cole, Jaqueline, Tzechia Lin, Christopher Ashcroft, Javier Pérez Moreno,
Yizhou Tan, Perumal Venkatesan, Andrew P Higginbotham, et al. “Relating the Structure
of Geminal Amido Esters to Their Molecular Hyperpolarizability.” Journal of
Physical Chemistry C. American Chemical Society, 2016. https://doi.org/10.1021/acs.jpcc.6b10724.
ieee: J. Cole et al., “Relating the structure of geminal Amido Esters to
their molecular hyperpolarizability,” Journal of Physical Chemistry C,
vol. 120, no. 51. American Chemical Society, pp. 29439–29448, 2016.
ista: Cole J, Lin T, Ashcroft C, Pérez Moreno J, Tan Y, Venkatesan P, Higginbotham
AP, Pattison P, Edwards A, Piltz R, Clays K, Ilangovan A. 2016. Relating the structure
of geminal Amido Esters to their molecular hyperpolarizability. Journal of Physical
Chemistry C. 120(51), 29439–29448.
mla: Cole, Jaqueline, et al. “Relating the Structure of Geminal Amido Esters to
Their Molecular Hyperpolarizability.” Journal of Physical Chemistry C,
vol. 120, no. 51, American Chemical Society, 2016, pp. 29439–48, doi:10.1021/acs.jpcc.6b10724.
short: J. Cole, T. Lin, C. Ashcroft, J. Pérez Moreno, Y. Tan, P. Venkatesan, A.P.
Higginbotham, P. Pattison, A. Edwards, R. Piltz, K. Clays, A. Ilangovan, Journal
of Physical Chemistry C 120 (2016) 29439–29448.
date_created: 2018-12-11T11:44:35Z
date_published: 2016-12-05T00:00:00Z
date_updated: 2021-01-12T08:21:55Z
day: '05'
doi: 10.1021/acs.jpcc.6b10724
extern: '1'
intvolume: ' 120'
issue: '51'
language:
- iso: eng
month: '12'
oa_version: None
page: 29439 - 29448
publication: Journal of Physical Chemistry C
publication_status: published
publisher: American Chemical Society
publist_id: '7962'
quality_controlled: '1'
status: public
title: Relating the structure of geminal Amido Esters to their molecular hyperpolarizability
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 120
year: '2016'
...
---
_id: '930'
abstract:
- lang: eng
text: The changes in cell dynamics after oncogenic mutation that lead to the development
of tumours are currently unknown. Here, using skin epidermis as a model, we assessed
the effect of oncogenic hedgehog signalling in distinct cell populations and their
capacity to induce basal cell carcinoma, the most frequent cancer in humans. We
found that only stem cells, and not progenitors, initiated tumour formation upon
oncogenic hedgehog signalling. This difference was due to the hierarchical organization
of tumour growth in oncogene-targeted stem cells, characterized by an increase
in symmetric self-renewing divisions and a higher p53-dependent resistance to
apoptosis, leading to rapid clonal expansion and progression into invasive tumours.
Our work reveals that the capacity of oncogene-targeted cells to induce tumour
formation is dependent not only on their long-term survival and expansion, but
also on the specific clonal dynamics of the cancer cell of origin.
acknowledgement: We would like to thank J.-M. Vanderwinden and the LiMiF for the help
with confocal microscopy. C.B. is an investigator of WELBIO. A.S.-D. and J.C.L.
are supported by a fellowship of the FNRS and FRIA respectively. B.D.S. and E.H.
are supported by the Wellcome Trust (grant numbers 098357/Z/12/Z and 110326/Z/15/Z).
E.H. is supported by a fellowship from Trinity College, Cambridge. This work was
supported by the FNRS, the IUAP program, the Fondation contre le Cancer, the ULB
fondation, the foundation Bettencourt Schueller, the foundation Baillet Latour,
a consolidator grant of the European Research Council.
article_processing_charge: No
author:
- first_name: Adriana
full_name: Sánchez Danés, Adriana
last_name: Sánchez Danés
- 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: Jean
full_name: Larsimont, Jean
last_name: Larsimont
- first_name: Mélanie
full_name: Liagre, Mélanie
last_name: Liagre
- first_name: Khalil
full_name: Youssef, Khalil
last_name: Youssef
- first_name: Benjamin
full_name: Simons, Benjamin
last_name: Simons
- first_name: Cédric
full_name: Blanpain, Cédric
last_name: Blanpain
citation:
ama: Sánchez Danés A, Hannezo EB, Larsimont J, et al. Defining the clonal dynamics
leading to mouse skin tumour initiation. Nature. 2016;536(7616):298-303.
doi:10.1038/nature19069
apa: Sánchez Danés, A., Hannezo, E. B., Larsimont, J., Liagre, M., Youssef, K.,
Simons, B., & Blanpain, C. (2016). Defining the clonal dynamics leading to
mouse skin tumour initiation. Nature. Nature Publishing Group. https://doi.org/10.1038/nature19069
chicago: Sánchez Danés, Adriana, Edouard B Hannezo, Jean Larsimont, Mélanie Liagre,
Khalil Youssef, Benjamin Simons, and Cédric Blanpain. “Defining the Clonal Dynamics
Leading to Mouse Skin Tumour Initiation.” Nature. Nature Publishing Group,
2016. https://doi.org/10.1038/nature19069.
ieee: A. Sánchez Danés et al., “Defining the clonal dynamics leading to mouse
skin tumour initiation,” Nature, vol. 536, no. 7616. Nature Publishing
Group, pp. 298–303, 2016.
ista: Sánchez Danés A, Hannezo EB, Larsimont J, Liagre M, Youssef K, Simons B, Blanpain
C. 2016. Defining the clonal dynamics leading to mouse skin tumour initiation.
Nature. 536(7616), 298–303.
mla: Sánchez Danés, Adriana, et al. “Defining the Clonal Dynamics Leading to Mouse
Skin Tumour Initiation.” Nature, vol. 536, no. 7616, Nature Publishing
Group, 2016, pp. 298–303, doi:10.1038/nature19069.
short: A. Sánchez Danés, E.B. Hannezo, J. Larsimont, M. Liagre, K. Youssef, B. Simons,
C. Blanpain, Nature 536 (2016) 298–303.
date_created: 2018-12-11T11:49:15Z
date_published: 2016-07-08T00:00:00Z
date_updated: 2021-01-12T08:21:59Z
day: '08'
doi: 10.1038/nature19069
extern: '1'
intvolume: ' 536'
issue: '7616'
language:
- iso: eng
month: '07'
oa_version: None
page: 298 - 303
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6508'
status: public
title: Defining the clonal dynamics leading to mouse skin tumour initiation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 536
year: '2016'
...
---
_id: '931'
abstract:
- lang: eng
text: 'In many adult tissues, stem cells and differentiated cells are not homogeneously
distributed: stem cells are arranged in periodic "niches," and differentiated
cells are constantly produced and migrate out of these niches. In this article,
we provide a general theoretical framework to study mixtures of dividing and actively
migrating particles, which we apply to biological tissues. We show in particular
that the interplay between the stresses arising from active cell migration and
stem cell division give rise to robust stem cell patterns. The instability of
the tissue leads to spatial patterns which are either steady or oscillating in
time. The wavelength of the instability has an order of magnitude consistent with
the biological observations. We also discuss the implications of these results
for future in vitro and in vivo experiments.'
acknowledgement: The authors thank Jacques Prost and Pierre Recho for helpful discussions,
as well as the Labex CelTisPhyBio and all its members. E.H. acknowledges for funding
a Young Researcher Prize from the Bettencourt-Schueller Fondation, and a Junior
Research Fellowship from Trinity College, Cambridge.
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: Alice
full_name: Coucke, Alice
last_name: Coucke
- first_name: Jean
full_name: Joanny, Jean
last_name: Joanny
citation:
ama: Hannezo EB, Coucke A, Joanny J. Interplay of migratory and division forces
as a generic mechanism for stem cell patterns. Physical Review E Statistical
Nonlinear and Soft Matter Physics. 2016;93(2). doi:10.1103/PhysRevE.93.022405
apa: Hannezo, E. B., Coucke, A., & Joanny, J. (2016). Interplay of migratory
and division forces as a generic mechanism for stem cell patterns. Physical
Review E Statistical Nonlinear and Soft Matter Physics. American Institute
of Physics. https://doi.org/10.1103/PhysRevE.93.022405
chicago: Hannezo, Edouard B, Alice Coucke, and Jean Joanny. “Interplay of Migratory
and Division Forces as a Generic Mechanism for Stem Cell Patterns.” Physical
Review E Statistical Nonlinear and Soft Matter Physics. American Institute
of Physics, 2016. https://doi.org/10.1103/PhysRevE.93.022405.
ieee: E. B. Hannezo, A. Coucke, and J. Joanny, “Interplay of migratory and division
forces as a generic mechanism for stem cell patterns,” Physical Review E Statistical
Nonlinear and Soft Matter Physics, vol. 93, no. 2. American Institute of Physics,
2016.
ista: Hannezo EB, Coucke A, Joanny J. 2016. Interplay of migratory and division
forces as a generic mechanism for stem cell patterns. Physical Review E Statistical
Nonlinear and Soft Matter Physics. 93(2).
mla: Hannezo, Edouard B., et al. “Interplay of Migratory and Division Forces as
a Generic Mechanism for Stem Cell Patterns.” Physical Review E Statistical
Nonlinear and Soft Matter Physics, vol. 93, no. 2, American Institute of Physics,
2016, doi:10.1103/PhysRevE.93.022405.
short: E.B. Hannezo, A. Coucke, J. Joanny, Physical Review E Statistical Nonlinear
and Soft Matter Physics 93 (2016).
date_created: 2018-12-11T11:49:16Z
date_published: 2016-02-28T00:00:00Z
date_updated: 2021-01-12T08:22:00Z
day: '28'
doi: 10.1103/PhysRevE.93.022405
extern: '1'
intvolume: ' 93'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '6509'
status: public
title: Interplay of migratory and division forces as a generic mechanism for stem
cell patterns
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 93
year: '2016'
...
---
_id: '932'
abstract:
- lang: eng
text: Epithelial sheets are crucial components of all metazoan animals, enclosing
organs and protecting the animal from its environment. Epithelial homeostasis
poses unique challenges, as addition of new cells and loss of old cells must be
achieved without disrupting the fluid-tight barrier and apicobasal polarity of
the epithelium. Several studies have identified cell biological mechanisms underlying
extrusion of cells from epithelia, but far less is known of the converse mechanism
by which new cells are added. Here, we combine molecular, pharmacological, and
laser-dissection experiments with theoretical modeling to characterize forces
driving emergence of an apical surface as single nascent cells are added to a
vertebrate epithelium in vivo. We find that this process involves the interplay
between cell-autonomous actin-generated pushing forces in the emerging cell and
mechanical properties of neighboring cells. Our findings define the forces driving
this cell behavior, contributing to a more comprehensive understanding of epithelial
homeostasis.
acknowledgement: We thank J. Bear, B. Goldstein, A. Ewald, and D. Soroldoni for critical
reading. This work was funded by an EMBO Long Term Fellowship to J.S., a Research
Fellowship from Trinity College, Cambridge and a Bettencourt-Schueller Foundation
Young Researcher Prize to E.H., a Cancer Institute NSW Early Career Researcher fellowship
(13/ECF/1–25) and a Cancer Australia/Cure Cancer Australia Foundation project grant
(1070498) to M.B., and grants from the NHLBI (HL117164) and NIGMS (GM074104) to
J.B.W. J.B.W. was an early career scientist of the Howard Hughes Medical Institute.
This work was initiated at the New Quantitative Approaches to Morphogenesis Workshop
at UCSB, which is funded in part by the National Science Foundation (PHY11-25915)
and the NIGMS (GM067110-05).
article_processing_charge: No
author:
- first_name: Jakub
full_name: Sedzinski, Jakub
last_name: Sedzinski
- 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: Fan
full_name: Tu, Fan
last_name: Tu
- first_name: Maté
full_name: Biro, Maté
last_name: Biro
- first_name: John
full_name: Wallingford, John
last_name: Wallingford
citation:
ama: Sedzinski J, Hannezo EB, Tu F, Biro M, Wallingford J. Emergence of an Apical
Epithelial Cell Surface In Vivo. Developmental Cell. 2016;36(1):24-35.
doi:10.1016/j.devcel.2015.12.013
apa: Sedzinski, J., Hannezo, E. B., Tu, F., Biro, M., & Wallingford, J. (2016).
Emergence of an Apical Epithelial Cell Surface In Vivo. Developmental Cell.
Cell Press. https://doi.org/10.1016/j.devcel.2015.12.013
chicago: Sedzinski, Jakub, Edouard B Hannezo, Fan Tu, Maté Biro, and John Wallingford.
“Emergence of an Apical Epithelial Cell Surface In Vivo.” Developmental Cell.
Cell Press, 2016. https://doi.org/10.1016/j.devcel.2015.12.013.
ieee: J. Sedzinski, E. B. Hannezo, F. Tu, M. Biro, and J. Wallingford, “Emergence
of an Apical Epithelial Cell Surface In Vivo,” Developmental Cell, vol.
36, no. 1. Cell Press, pp. 24–35, 2016.
ista: Sedzinski J, Hannezo EB, Tu F, Biro M, Wallingford J. 2016. Emergence of an
Apical Epithelial Cell Surface In Vivo. Developmental Cell. 36(1), 24–35.
mla: Sedzinski, Jakub, et al. “Emergence of an Apical Epithelial Cell Surface In
Vivo.” Developmental Cell, vol. 36, no. 1, Cell Press, 2016, pp. 24–35,
doi:10.1016/j.devcel.2015.12.013.
short: J. Sedzinski, E.B. Hannezo, F. Tu, M. Biro, J. Wallingford, Developmental
Cell 36 (2016) 24–35.
date_created: 2018-12-11T11:49:16Z
date_published: 2016-01-12T00:00:00Z
date_updated: 2021-01-12T08:22:00Z
day: '12'
doi: 10.1016/j.devcel.2015.12.013
extern: '1'
intvolume: ' 36'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 24 - 35
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '6510'
status: public
title: Emergence of an Apical Epithelial Cell Surface In Vivo
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2016'
...
---
_id: '9456'
abstract:
- lang: eng
text: The discovery of introns four decades ago was one of the most unexpected findings
in molecular biology. Introns are sequences interrupting genes that must be removed
as part of messenger RNA production. Genome sequencing projects have shown that
most eukaryotic genes contain at least one intron, and frequently many. Comparison
of these genomes reveals a history of long evolutionary periods during which few
introns were gained, punctuated by episodes of rapid, extensive gain. However,
although several detailed mechanisms for such episodic intron generation have
been proposed, none has been empirically supported on a genomic scale. Here we
show how short, non-autonomous DNA transposons independently generated hundreds
to thousands of introns in the prasinophyte Micromonas pusilla and the pelagophyte
Aureococcus anophagefferens. Each transposon carries one splice site. The other
splice site is co-opted from the gene sequence that is duplicated upon transposon
insertion, allowing perfect splicing out of the RNA. The distributions of sequences
that can be co-opted are biased with respect to codons, and phasing of transposon-generated
introns is similarly biased. These transposons insert between pre-existing nucleosomes,
so that multiple nearby insertions generate nucleosome-sized intervening segments.
Thus, transposon insertion and sequence co-option may explain the intron phase
biases and prevalence of nucleosome-sized exons observed in eukaryotes. Overall,
the two independent examples of proliferating elements illustrate a general DNA
transposon mechanism that can plausibly account for episodes of rapid, extensive
intron gain during eukaryotic evolution.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Jason T.
full_name: Huff, Jason T.
last_name: Huff
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Scott W.
full_name: Roy, Scott W.
last_name: Roy
citation:
ama: Huff JT, Zilberman D, Roy SW. Mechanism for DNA transposons to generate introns
on genomic scales. Nature. 2016;538(7626):533-536. doi:10.1038/nature20110
apa: Huff, J. T., Zilberman, D., & Roy, S. W. (2016). Mechanism for DNA transposons
to generate introns on genomic scales. Nature. Springer Nature . https://doi.org/10.1038/nature20110
chicago: Huff, Jason T., Daniel Zilberman, and Scott W. Roy. “Mechanism for DNA
Transposons to Generate Introns on Genomic Scales.” Nature. Springer Nature
, 2016. https://doi.org/10.1038/nature20110.
ieee: J. T. Huff, D. Zilberman, and S. W. Roy, “Mechanism for DNA transposons to
generate introns on genomic scales,” Nature, vol. 538, no. 7626. Springer
Nature , pp. 533–536, 2016.
ista: Huff JT, Zilberman D, Roy SW. 2016. Mechanism for DNA transposons to generate
introns on genomic scales. Nature. 538(7626), 533–536.
mla: Huff, Jason T., et al. “Mechanism for DNA Transposons to Generate Introns on
Genomic Scales.” Nature, vol. 538, no. 7626, Springer Nature , 2016, pp.
533–36, doi:10.1038/nature20110.
short: J.T. Huff, D. Zilberman, S.W. Roy, Nature 538 (2016) 533–536.
date_created: 2021-06-04T11:34:55Z
date_published: 2016-10-27T00:00:00Z
date_updated: 2021-12-14T07:55:30Z
day: '27'
department:
- _id: DaZi
doi: 10.1038/nature20110
extern: '1'
external_id:
pmid:
- '27760113'
intvolume: ' 538'
issue: '7626'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5684705/
month: '10'
oa: 1
oa_version: Submitted Version
page: 533-536
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: 'Springer Nature '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanism for DNA transposons to generate introns on genomic scales
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 538
year: '2016'
...