---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_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.
article_processing_charge: No
article_type: original
author:
- first_name: Elizaveta
full_name: Rivkina, Elizaveta
last_name: Rivkina
- first_name: Lada
full_name: Petrovskaya, Lada
last_name: Petrovskaya
- first_name: Tatiana
full_name: Vishnivetskaya, Tatiana
last_name: Vishnivetskaya
- first_name: Kirill
full_name: Krivushin, Kirill
last_name: Krivushin
- first_name: Lyubov
full_name: Shmakova, Lyubov
last_name: Shmakova
- first_name: Maria
full_name: Tutukina, Maria
last_name: Tutukina
- first_name: Arthur
full_name: Meyers, Arthur
last_name: Meyers
- first_name: Fyodor
full_name: Kondrashov, Fyodor
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: 2016-04-15T00:00:00Z
date_updated: 2026-05-20T08:59:47Z
day: '15'
doi: 10.5194/bg-13-2207-2016
extern: '1'
fulldoi: https://doi.org/10.5194/bg-13-2207-2016
intvolume: ' 13'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.5194/bg-13-2207-2016
month: '04'
oa: 1
oa_version: Published Version
page: 2207 - 2219
publication: Biogeosciences
publication_identifier:
eissn:
- 1726-4189
issn:
- 1726-4170
publication_status: published
publisher: European Geosciences Union
publist_id: '6793'
quality_controlled: '1'
scopus_import: '1'
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
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 13
year: '2016'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_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.
article_number: ' 160009'
article_processing_charge: No
article_type: original
author:
- first_name: Kerstin
full_name: Howe, Kerstin
last_name: Howe
- first_name: Philipp
full_name: Schiffer, Philipp
last_name: Schiffer
- first_name: Julia
full_name: Zielinski, Julia
last_name: Zielinski
- first_name: Thomas
full_name: Wiehe, Thomas
last_name: Wiehe
- first_name: Gavin
full_name: Laird, Gavin
last_name: Laird
- first_name: John
full_name: Marioni, John
last_name: Marioni
- first_name: Onuralp
full_name: Soylemez, Onuralp
last_name: Soylemez
- first_name: Fyodor
full_name: Kondrashov, Fyodor
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), 160009.
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, 160009,
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: 2016-04-01T00:00:00Z
date_updated: 2026-05-20T09:09:18Z
day: '01'
doi: 10.1098/rsob.160009
extern: '1'
external_id:
pmid:
- '27248802'
fulldoi: https://doi.org/10.1098/rsob.160009
intvolume: ' 6'
issue: '4'
keyword:
- NACHT
- B30
- SPRY
- Gene conversion
- Innate immune system
- Genome evolution
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1098/rsob.160009
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Open Biology
publication_identifier:
eissn:
- 2046-2441
publication_status: published
publisher: Royal Society, The
publist_id: '6754'
quality_controlled: '1'
scopus_import: '1'
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
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
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
fulldoi: https://doi.org/10.1016/j.crci.2015.12.004
has_accepted_license: '1'
intvolume: ' 19'
issue: 1-2
keyword:
- General Chemistry
- General Chemical Engineering
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
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'
fulldoi: https://doi.org/10.1039/c5sm03127c
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'
fulldoi: https://doi.org/10.1039/c6sm01163b
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'
fulldoi: https://doi.org/10.1002/2015jd023497
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'
fulldoi: https://doi.org/10.1021/acs.jpcc.6b10724
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'
...
---
OA_type: closed access
_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
article_type: original
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;536:298-303. 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. Springer Nature. 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. Springer Nature, 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. Springer Nature, 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, 298–303.
mla: Sánchez Danés, Adriana, et al. “Defining the Clonal Dynamics Leading to Mouse
Skin Tumour Initiation.” Nature, vol. 536, Springer Nature, 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: 2016-08-18T00:00:00Z
date_updated: 2026-05-20T09:22:23Z
day: '18'
doi: 10.1038/nature19069
extern: '1'
external_id:
pmid:
- '27459053'
fulldoi: https://doi.org/10.1038/nature19069
intvolume: ' 536'
language:
- iso: eng
month: '08'
oa_version: None
page: 298 - 303
pmid: 1
publication: Nature
publication_identifier:
issn:
- 0028-0836
unknown:
- 1476-4687
publication_status: published
publisher: Springer Nature
publist_id: '6508'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Defining the clonal dynamics leading to mouse skin tumour initiation
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 536
year: '2016'
...
---
OA_place: repository
OA_type: green
_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_number: '022405'
article_processing_charge: No
article_type: original
arxiv: 1
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 . 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 . 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 . 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 ,
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 . 93(2),
022405.
mla: Hannezo, Edouard B., et al. “Interplay of Migratory and Division Forces as
a Generic Mechanism for Stem Cell Patterns.” Physical Review E , vol. 93,
no. 2, 022405, American Institute of Physics, 2016, doi:10.1103/PhysRevE.93.022405.
short: E.B. Hannezo, A. Coucke, J. Joanny, Physical Review E 93 (2016).
date_created: 2018-12-11T11:49:16Z
date_published: 2016-02-08T00:00:00Z
date_updated: 2026-05-20T09:18:55Z
day: '08'
doi: 10.1103/PhysRevE.93.022405
extern: '1'
external_id:
arxiv:
- '1512.05896'
pmid:
- '26986360'
fulldoi: https://doi.org/10.1103/PhysRevE.93.022405
intvolume: ' 93'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.1512.05896'
month: '02'
oa: 1
oa_version: Preprint
pmid: 1
publication: 'Physical Review E '
publication_identifier:
eissn:
- 2470-0053
issn:
- 2470-0045
publication_status: published
publisher: American Institute of Physics
publist_id: '6509'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interplay of migratory and division forces as a generic mechanism for stem
cell patterns
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 93
year: '2016'
...
---
OA_place: publisher
OA_type: free access
_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
article_type: original
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.
Elsevier. 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.
Elsevier, 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. Elsevier, 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, Elsevier, 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: 2026-05-20T09:14:43Z
day: '12'
doi: 10.1016/j.devcel.2015.12.013
extern: '1'
external_id:
pmid:
- '26766441'
fulldoi: https://doi.org/10.1016/j.devcel.2015.12.013
intvolume: ' 36'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.devcel.2015.12.013
month: '01'
oa: 1
oa_version: Published Version
page: 24 - 35
pmid: 1
publication: Developmental Cell
publication_identifier:
eissn:
- 1878-1551
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
publist_id: '6510'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Emergence of an Apical Epithelial Cell Surface In Vivo
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
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'
fulldoi: https://doi.org/10.1038/nature20110
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'
...
---
_id: '9473'
abstract:
- lang: eng
text: Cytosine DNA methylation regulates the expression of eukaryotic genes and
transposons. Methylation is copied by methyltransferases after DNA replication,
which results in faithful transmission of methylation patterns during cell division
and, at least in flowering plants, across generations. Transgenerational inheritance
is mediated by a small group of cells that includes gametes and their progenitors.
However, methylation is usually analyzed in somatic tissues that do not contribute
to the next generation, and the mechanisms of transgenerational inheritance are
inferred from such studies. To gain a better understanding of how DNA methylation
is inherited, we analyzed purified Arabidopsis thaliana sperm and vegetative cells-the
cell types that comprise pollen-with mutations in the DRM, CMT2, and CMT3 methyltransferases.
We find that DNA methylation dependency on these enzymes is similar in sperm,
vegetative cells, and somatic tissues, although DRM activity extends into heterochromatin
in vegetative cells, likely reflecting transcription of heterochromatic transposons
in this cell type. We also show that lack of histone H1, which elevates heterochromatic
DNA methylation in somatic tissues, does not have this effect in pollen. Instead,
levels of CG methylation in wild-type sperm and vegetative cells, as well as in
wild-type microspores from which both pollen cell types originate, are substantially
higher than in wild-type somatic tissues and similar to those of H1-depleted roots.
Our results demonstrate that the mechanisms of methylation maintenance are similar
between pollen and somatic cells, but the efficiency of CG methylation is higher
in pollen, allowing methylation patterns to be accurately inherited across generations.
article_processing_charge: No
article_type: original
author:
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Toby
full_name: Buttress, Toby
last_name: Buttress
- first_name: Hongbo
full_name: Gao, Hongbo
last_name: Gao
- first_name: Matthew
full_name: Couchman, Matthew
last_name: Couchman
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: Hsieh P-H, He S, Buttress T, et al. Arabidopsis male sexual lineage exhibits
more robust maintenance of CG methylation than somatic tissues. Proceedings
of the National Academy of Sciences. 2016;113(52):15132-15137. doi:10.1073/pnas.1619074114
apa: Hsieh, P.-H., He, S., Buttress, T., Gao, H., Couchman, M., Fischer, R. L.,
… Feng, X. (2016). Arabidopsis male sexual lineage exhibits more robust maintenance
of CG methylation than somatic tissues. Proceedings of the National Academy
of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1619074114
chicago: Hsieh, Ping-Hung, Shengbo He, Toby Buttress, Hongbo Gao, Matthew Couchman,
Robert L. Fischer, Daniel Zilberman, and Xiaoqi Feng. “Arabidopsis Male Sexual
Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.”
Proceedings of the National Academy of Sciences. National Academy of Sciences,
2016. https://doi.org/10.1073/pnas.1619074114.
ieee: P.-H. Hsieh et al., “Arabidopsis male sexual lineage exhibits more
robust maintenance of CG methylation than somatic tissues,” Proceedings of
the National Academy of Sciences, vol. 113, no. 52. National Academy of Sciences,
pp. 15132–15137, 2016.
ista: Hsieh P-H, He S, Buttress T, Gao H, Couchman M, Fischer RL, Zilberman D, Feng
X. 2016. Arabidopsis male sexual lineage exhibits more robust maintenance of CG
methylation than somatic tissues. Proceedings of the National Academy of Sciences.
113(52), 15132–15137.
mla: Hsieh, Ping-Hung, et al. “Arabidopsis Male Sexual Lineage Exhibits More Robust
Maintenance of CG Methylation than Somatic Tissues.” Proceedings of the National
Academy of Sciences, vol. 113, no. 52, National Academy of Sciences, 2016,
pp. 15132–37, doi:10.1073/pnas.1619074114.
short: P.-H. Hsieh, S. He, T. Buttress, H. Gao, M. Couchman, R.L. Fischer, D. Zilberman,
X. Feng, Proceedings of the National Academy of Sciences 113 (2016) 15132–15137.
date_created: 2021-06-07T06:21:39Z
date_published: 2016-12-27T00:00:00Z
date_updated: 2023-05-08T11:00:40Z
day: '27'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1073/pnas.1619074114
extern: '1'
external_id:
pmid:
- '27956643'
fulldoi: https://doi.org/10.1073/pnas.1619074114
intvolume: ' 113'
issue: '52'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1619074114
month: '12'
oa: 1
oa_version: Published Version
page: 15132-15137
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation
than somatic tissues
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '9477'
abstract:
- lang: eng
text: Cytosine methylation is a DNA modification with important regulatory functions
in eukaryotes. In flowering plants, sexual reproduction is accompanied by extensive
DNA demethylation, which is required for proper gene expression in the endosperm,
a nutritive extraembryonic seed tissue. Endosperm arises from a fusion of a sperm
cell carried in the pollen and a female central cell. Endosperm DNA demethylation
is observed specifically on the chromosomes inherited from the central cell in
Arabidopsis thaliana, rice, and maize, and requires the DEMETER DNA demethylase
in Arabidopsis. DEMETER is expressed in the central cell before fertilization,
suggesting that endosperm demethylation patterns are inherited from the central
cell. Down-regulation of the MET1 DNA methyltransferase has also been proposed
to contribute to central cell demethylation. However, with the exception of three
maize genes, central cell DNA methylation has not been directly measured, leaving
the origin and mechanism of endosperm demethylation uncertain. Here, we report
genome-wide analysis of DNA methylation in the central cells of Arabidopsis and
rice—species that diverged 150 million years ago—as well as in rice egg cells.
We find that DNA demethylation in both species is initiated in central cells,
which requires DEMETER in Arabidopsis. However, we do not observe a global reduction
of CG methylation that would be indicative of lowered MET1 activity; on the contrary,
CG methylation efficiency is elevated in female gametes compared with nonsexual
tissues. Our results demonstrate that locus-specific, active DNA demethylation
in the central cell is the origin of maternal chromosome hypomethylation in the
endosperm.
article_processing_charge: No
article_type: original
author:
- first_name: Kyunghyuk
full_name: Park, Kyunghyuk
last_name: Park
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: Jin-Sup
full_name: Park, Jin-Sup
last_name: Park
- first_name: Youbong
full_name: Hyun, Youbong
last_name: Hyun
- first_name: Takashi
full_name: Okamoto, Takashi
last_name: Okamoto
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Yeonhee
full_name: Choi, Yeonhee
last_name: Choi
- first_name: Stefan
full_name: Scholten, Stefan
last_name: Scholten
citation:
ama: Park K, Kim MY, Vickers M, et al. DNA demethylation is initiated in the central
cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences.
2016;113(52):15138-15143. doi:10.1073/pnas.1619047114
apa: Park, K., Kim, M. Y., Vickers, M., Park, J.-S., Hyun, Y., Okamoto, T., … Scholten,
S. (2016). DNA demethylation is initiated in the central cells of Arabidopsis
and rice. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.1619047114
chicago: Park, Kyunghyuk, M. Yvonne Kim, Martin Vickers, Jin-Sup Park, Youbong Hyun,
Takashi Okamoto, Daniel Zilberman, et al. “DNA Demethylation Is Initiated in the
Central Cells of Arabidopsis and Rice.” Proceedings of the National Academy
of Sciences. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1619047114.
ieee: K. Park et al., “DNA demethylation is initiated in the central cells
of Arabidopsis and rice,” Proceedings of the National Academy of Sciences,
vol. 113, no. 52. National Academy of Sciences, pp. 15138–15143, 2016.
ista: Park K, Kim MY, Vickers M, Park J-S, Hyun Y, Okamoto T, Zilberman D, Fischer
RL, Feng X, Choi Y, Scholten S. 2016. DNA demethylation is initiated in the central
cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences.
113(52), 15138–15143.
mla: Park, Kyunghyuk, et al. “DNA Demethylation Is Initiated in the Central Cells
of Arabidopsis and Rice.” Proceedings of the National Academy of Sciences,
vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15138–43, doi:10.1073/pnas.1619047114.
short: K. Park, M.Y. Kim, M. Vickers, J.-S. Park, Y. Hyun, T. Okamoto, D. Zilberman,
R.L. Fischer, X. Feng, Y. Choi, S. Scholten, Proceedings of the National Academy
of Sciences 113 (2016) 15138–15143.
date_created: 2021-06-07T07:10:59Z
date_published: 2016-12-27T00:00:00Z
date_updated: 2023-05-08T11:00:07Z
day: '27'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1073/pnas.1619047114
extern: '1'
external_id:
pmid:
- '27956642'
fulldoi: https://doi.org/10.1073/pnas.1619047114
intvolume: ' 113'
issue: '52'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1619047114
month: '12'
oa: 1
oa_version: Published Version
page: 15138-15143
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA demethylation is initiated in the central cells of Arabidopsis and rice
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '9591'
abstract:
- lang: eng
text: We give several results showing that different discrete structures typically
gain certain spanning substructures (in particular, Hamilton cycles) after a modest
random perturbation. First, we prove that adding linearly many random edges to
a dense k-uniform hypergraph ensures the (asymptotically almost sure) existence
of a perfect matching or a loose Hamilton cycle. The proof involves an interesting
application of Szemerédi's Regularity Lemma, which might be independently useful.
We next prove that digraphs with certain strong expansion properties are pancyclic,
and use this to show that adding a linear number of random edges typically makes
a dense digraph pancyclic. Finally, we prove that perturbing a certain (minimum-degree-dependent)
number of random edges in a tournament typically ensures the existence of multiple
edge-disjoint Hamilton cycles. All our results are tight.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Michael
full_name: Krivelevich, Michael
last_name: Krivelevich
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Benny
full_name: Sudakov, Benny
last_name: Sudakov
citation:
ama: Krivelevich M, Kwan MA, Sudakov B. Cycles and matchings in randomly perturbed
digraphs and hypergraphs. Combinatorics, Probability and Computing. 2016;25(6):909-927.
doi:10.1017/s0963548316000079
apa: Krivelevich, M., Kwan, M. A., & Sudakov, B. (2016). Cycles and matchings
in randomly perturbed digraphs and hypergraphs. Combinatorics, Probability
and Computing. Cambridge University Press. https://doi.org/10.1017/s0963548316000079
chicago: Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Cycles and
Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Combinatorics, Probability
and Computing. Cambridge University Press, 2016. https://doi.org/10.1017/s0963548316000079.
ieee: M. Krivelevich, M. A. Kwan, and B. Sudakov, “Cycles and matchings in randomly
perturbed digraphs and hypergraphs,” Combinatorics, Probability and Computing,
vol. 25, no. 6. Cambridge University Press, pp. 909–927, 2016.
ista: Krivelevich M, Kwan MA, Sudakov B. 2016. Cycles and matchings in randomly
perturbed digraphs and hypergraphs. Combinatorics, Probability and Computing.
25(6), 909–927.
mla: Krivelevich, Michael, et al. “Cycles and Matchings in Randomly Perturbed Digraphs
and Hypergraphs.” Combinatorics, Probability and Computing, vol. 25, no.
6, Cambridge University Press, 2016, pp. 909–27, doi:10.1017/s0963548316000079.
short: M. Krivelevich, M.A. Kwan, B. Sudakov, Combinatorics, Probability and Computing
25 (2016) 909–927.
date_created: 2021-06-22T12:35:13Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2023-02-23T14:02:07Z
day: '01'
doi: 10.1017/s0963548316000079
extern: '1'
external_id:
arxiv:
- '1501.04816'
fulldoi: https://doi.org/10.1017/s0963548316000079
intvolume: ' 25'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1501.04816
month: '11'
oa: 1
oa_version: Preprint
page: 909-927
publication: Combinatorics, Probability and Computing
publication_identifier:
eissn:
- 1469-2163
issn:
- 0963-5483
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cycles and matchings in randomly perturbed digraphs and hypergraphs
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 25
year: '2016'
...
---
_id: '9654'
abstract:
- lang: eng
text: RNA polymerase I (Pol I) is a highly processive enzyme that transcribes ribosomal
DNA (rDNA) and regulates growth of eukaryotic cells. Crystal structures of free
Pol I from the yeast Saccharomyces cerevisiae have revealed dimers of the enzyme
stabilized by a 'connector' element and an expanded cleft containing the active
centre in an inactive conformation. The central bridge helix was unfolded and
a Pol-I-specific 'expander' element occupied the DNA-template-binding site. The
structure of Pol I in its active transcribing conformation has yet to be determined,
whereas structures of Pol II and Pol III have been solved with bound DNA template
and RNA transcript. Here we report structures of active transcribing Pol I from
yeast solved by two different cryo-electron microscopy approaches. A single-particle
structure at 3.8 Å resolution reveals a contracted active centre cleft with bound
DNA and RNA, and a narrowed pore beneath the active site that no longer holds
the RNA-cleavage-stimulating domain of subunit A12.2. A structure at 29 Å resolution
that was determined from cryo-electron tomograms of Pol I enzymes transcribing
cellular rDNA confirms contraction of the cleft and reveals that incoming and
exiting rDNA enclose an angle of around 150°. The structures suggest a model for
the regulation of transcription elongation in which contracted and expanded polymerase
conformations are associated with active and inactive states, respectively.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Simon
full_name: Neyer, Simon
last_name: Neyer
- first_name: Michael
full_name: Kunz, Michael
last_name: Kunz
- first_name: Christian
full_name: Geiss, Christian
last_name: Geiss
- first_name: Merle
full_name: Hantsche, Merle
last_name: Hantsche
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: Anja
full_name: Seybert, Anja
last_name: Seybert
- first_name: Christoph
full_name: Engel, Christoph
last_name: Engel
- first_name: Margot P.
full_name: Scheffer, Margot P.
last_name: Scheffer
- first_name: Patrick
full_name: Cramer, Patrick
last_name: Cramer
- first_name: Achilleas S.
full_name: Frangakis, Achilleas S.
last_name: Frangakis
citation:
ama: Neyer S, Kunz M, Geiss C, et al. Structure of RNA polymerase I transcribing
ribosomal DNA genes. Nature. 2016;540(7634):607-610. doi:10.1038/nature20561
apa: Neyer, S., Kunz, M., Geiss, C., Hantsche, M., Hodirnau, V.-V., Seybert, A.,
… Frangakis, A. S. (2016). Structure of RNA polymerase I transcribing ribosomal
DNA genes. Nature. Springer Nature. https://doi.org/10.1038/nature20561
chicago: Neyer, Simon, Michael Kunz, Christian Geiss, Merle Hantsche, Victor-Valentin
Hodirnau, Anja Seybert, Christoph Engel, Margot P. Scheffer, Patrick Cramer, and
Achilleas S. Frangakis. “Structure of RNA Polymerase I Transcribing Ribosomal
DNA Genes.” Nature. Springer Nature, 2016. https://doi.org/10.1038/nature20561.
ieee: S. Neyer et al., “Structure of RNA polymerase I transcribing ribosomal
DNA genes,” Nature, vol. 540, no. 7634. Springer Nature, pp. 607–610, 2016.
ista: Neyer S, Kunz M, Geiss C, Hantsche M, Hodirnau V-V, Seybert A, Engel C, Scheffer
MP, Cramer P, Frangakis AS. 2016. Structure of RNA polymerase I transcribing ribosomal
DNA genes. Nature. 540(7634), 607–610.
mla: Neyer, Simon, et al. “Structure of RNA Polymerase I Transcribing Ribosomal
DNA Genes.” Nature, vol. 540, no. 7634, Springer Nature, 2016, pp. 607–10,
doi:10.1038/nature20561.
short: S. Neyer, M. Kunz, C. Geiss, M. Hantsche, V.-V. Hodirnau, A. Seybert, C.
Engel, M.P. Scheffer, P. Cramer, A.S. Frangakis, Nature 540 (2016) 607–610.
date_created: 2021-07-14T09:04:24Z
date_published: 2016-12-22T00:00:00Z
date_updated: 2021-07-22T09:22:20Z
day: '22'
doi: 10.1038/nature20561
extern: '1'
external_id:
pmid:
- '27842382'
fulldoi: https://doi.org/10.1038/nature20561
intvolume: ' 540'
issue: '7634'
language:
- iso: eng
month: '12'
oa_version: None
page: 607-610
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: Structure of RNA polymerase I transcribing ribosomal DNA genes
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 540
year: '2016'
...
---
_id: '9681'
abstract:
- lang: eng
text: One of the most prominent consequences of the quantum nature of light atomic
nuclei is that their kinetic energy does not follow a Maxwell–Boltzmann distribution.
Deep inelastic neutron scattering (DINS) experiments can measure this effect.
Thus, the nuclear quantum kinetic energy can be probed directly in both ordered
and disordered samples. However, the relation between the quantum kinetic energy
and the atomic environment is a very indirect one, and cross-validation with theoretical
modeling is therefore urgently needed. Here, we use state of the art path integral
molecular dynamics techniques to compute the kinetic energy of hydrogen and oxygen
nuclei in liquid, solid, and gas-phase water close to the triple point, comparing
three different interatomic potentials and validating our results against equilibrium
isotope fractionation measurements. We will then show how accurate simulations
can draw a link between extremely precise fractionation experiments and DINS,
therefore establishing a reliable benchmark for future measurements and providing
key insights to increase further the accuracy of interatomic potentials for water.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Jörg
full_name: Behler, Jörg
last_name: Behler
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: 'Cheng B, Behler J, Ceriotti M. Nuclear quantum effects in water at the triple
point: Using theory as a link between experiments. The Journal of Physical
Chemistry Letters. 2016;7(12):2210-2215. doi:10.1021/acs.jpclett.6b00729'
apa: 'Cheng, B., Behler, J., & Ceriotti, M. (2016). Nuclear quantum effects
in water at the triple point: Using theory as a link between experiments. The
Journal of Physical Chemistry Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.6b00729'
chicago: 'Cheng, Bingqing, Jörg Behler, and Michele Ceriotti. “Nuclear Quantum Effects
in Water at the Triple Point: Using Theory as a Link between Experiments.” The
Journal of Physical Chemistry Letters. American Chemical Society, 2016. https://doi.org/10.1021/acs.jpclett.6b00729.'
ieee: 'B. Cheng, J. Behler, and M. Ceriotti, “Nuclear quantum effects in water at
the triple point: Using theory as a link between experiments,” The Journal
of Physical Chemistry Letters, vol. 7, no. 12. American Chemical Society,
pp. 2210–2215, 2016.'
ista: 'Cheng B, Behler J, Ceriotti M. 2016. Nuclear quantum effects in water at
the triple point: Using theory as a link between experiments. The Journal of Physical
Chemistry Letters. 7(12), 2210–2215.'
mla: 'Cheng, Bingqing, et al. “Nuclear Quantum Effects in Water at the Triple Point:
Using Theory as a Link between Experiments.” The Journal of Physical Chemistry
Letters, vol. 7, no. 12, American Chemical Society, 2016, pp. 2210–15, doi:10.1021/acs.jpclett.6b00729.'
short: B. Cheng, J. Behler, M. Ceriotti, The Journal of Physical Chemistry Letters
7 (2016) 2210–2215.
date_created: 2021-07-19T08:57:32Z
date_published: 2016-06-16T00:00:00Z
date_updated: 2023-02-23T14:04:49Z
day: '16'
doi: 10.1021/acs.jpclett.6b00729
extern: '1'
external_id:
pmid:
- '27203358'
fulldoi: https://doi.org/10.1021/acs.jpclett.6b00729
intvolume: ' 7'
issue: '12'
language:
- iso: eng
month: '06'
oa_version: None
page: 2210-2215
pmid: 1
publication: The Journal of Physical Chemistry Letters
publication_identifier:
eissn:
- 1948-7185
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Nuclear quantum effects in water at the triple point: Using theory as a link
between experiments'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 7
year: '2016'
...
---
_id: '9710'
abstract:
- lang: eng
text: Much of quantitative genetics is based on the ‘infinitesimal model’, under
which selection has a negligible effect on the genetic variance. This is typically
justified by assuming a very large number of loci with additive effects. However,
it applies even when genes interact, provided that the number of loci is large
enough that selection on each of them is weak relative to random drift. In the
long term, directional selection will change allele frequencies, but even then,
the effects of epistasis on the ultimate change in trait mean due to selection
may be modest. Stabilising selection can maintain many traits close to their optima,
even when the underlying alleles are weakly selected. However, the number of traits
that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this
is hard to reconcile with the apparent complexity of many organisms. Just as for
the mutation load, this limit can be evaded by a particular form of negative epistasis.
A more robust limit is set by the variance in reproductive success. This suggests
that selection accumulates information most efficiently in the infinitesimal regime,
when selection on individual alleles is weak, and comparable with random drift.
A review of evidence on selection strength suggests that although most variance
in fitness may be because of alleles with large Nes, substantial amounts of adaptation
may be because of alleles in the infinitesimal regime, in which epistasis has
modest effects.
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Data from: How does epistasis influence the response to selection?
2016. doi:10.5061/dryad.s5s7r'
apa: 'Barton, N. H. (2016). Data from: How does epistasis influence the response
to selection? Dryad. https://doi.org/10.5061/dryad.s5s7r'
chicago: 'Barton, Nicholas H. “Data from: How Does Epistasis Influence the Response
to Selection?” Dryad, 2016. https://doi.org/10.5061/dryad.s5s7r.'
ieee: 'N. H. Barton, “Data from: How does epistasis influence the response to selection?”
Dryad, 2016.'
ista: 'Barton NH. 2016. Data from: How does epistasis influence the response to
selection?, Dryad, 10.5061/dryad.s5s7r.'
mla: 'Barton, Nicholas H. Data from: How Does Epistasis Influence the Response
to Selection? Dryad, 2016, doi:10.5061/dryad.s5s7r.'
short: N.H. Barton, (2016).
date_created: 2021-07-23T11:45:47Z
date_published: 2016-09-23T00:00:00Z
date_updated: 2025-04-15T07:11:02Z
day: '23'
department:
- _id: NiBa
doi: 10.5061/dryad.s5s7r
fulldoi: https://doi.org/10.5061/dryad.s5s7r
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.s5s7r
month: '09'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1199'
relation: used_in_publication
status: public
status: public
title: 'Data from: How does epistasis influence the response to selection?'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9720'
abstract:
- lang: eng
text: 'Summary: Declining populations of bee pollinators are a cause of concern,
with major repercussions for biodiversity loss and food security. RNA viruses
associated with honeybees represent a potential threat to other insect pollinators,
but the extent of this threat is poorly understood. This study aims to attain
a detailed understanding of the current and ongoing risk of emerging infectious
disease (EID) transmission between managed and wild pollinator species across
a wide range of RNA viruses. Within a structured large-scale national survey across
26 independent sites, we quantify the prevalence and pathogen loads of multiple
RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee
(Bombus spp.) populations. We then construct models that compare virus prevalence
between wild and managed pollinators. Multiple RNA viruses associated with honeybees
are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees
is a significant predictor of virus prevalence in bumblebees, but we remain cautious
in speculating over the principle direction of pathogen transmission. We demonstrate
species-specific differences in prevalence, indicating significant variation in
disease susceptibility or tolerance. Pathogen loads within individual bumblebees
may be high and in the case of at least one RNA virus, prevalence is higher in
wild bumblebees than in managed honeybee populations. Our findings indicate widespread
transmission of RNA viruses between managed and wild bee pollinators, pointing
to an interconnected network of potential disease pressures within and among pollinator
species. In the context of the biodiversity crisis, our study emphasizes the importance
of targeting a wide range of pathogens and defining host associations when considering
potential drivers of population decline.'
article_processing_charge: No
author:
- first_name: Dino
full_name: Mcmahon, Dino
last_name: Mcmahon
- first_name: Matthias
full_name: Fürst, Matthias
id: 393B1196-F248-11E8-B48F-1D18A9856A87
last_name: Fürst
orcid: 0000-0002-3712-925X
- first_name: Jesicca
full_name: Caspar, Jesicca
last_name: Caspar
- first_name: Panagiotis
full_name: Theodorou, Panagiotis
last_name: Theodorou
- first_name: Mark
full_name: Brown, Mark
last_name: Brown
- first_name: Robert
full_name: Paxton, Robert
last_name: Paxton
citation:
ama: 'Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. Data from: A
sting in the spit: widespread cross-infection of multiple RNA viruses across wild
and managed bees. 2016. doi:10.5061/dryad.4b565'
apa: 'Mcmahon, D., Fürst, M., Caspar, J., Theodorou, P., Brown, M., & Paxton,
R. (2016). Data from: A sting in the spit: widespread cross-infection of multiple
RNA viruses across wild and managed bees. Dryad. https://doi.org/10.5061/dryad.4b565'
chicago: 'Mcmahon, Dino, Matthias Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark
Brown, and Robert Paxton. “Data from: A Sting in the Spit: Widespread Cross-Infection
of Multiple RNA Viruses across Wild and Managed Bees.” Dryad, 2016. https://doi.org/10.5061/dryad.4b565.'
ieee: 'D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, and R. Paxton, “Data
from: A sting in the spit: widespread cross-infection of multiple RNA viruses
across wild and managed bees.” Dryad, 2016.'
ista: 'Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. 2016. Data
from: A sting in the spit: widespread cross-infection of multiple RNA viruses
across wild and managed bees, Dryad, 10.5061/dryad.4b565.'
mla: 'Mcmahon, Dino, et al. Data from: A Sting in the Spit: Widespread Cross-Infection
of Multiple RNA Viruses across Wild and Managed Bees. Dryad, 2016, doi:10.5061/dryad.4b565.'
short: D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, (2016).
date_created: 2021-07-26T09:14:19Z
date_published: 2016-01-22T00:00:00Z
date_updated: 2025-09-23T07:26:23Z
day: '22'
department:
- _id: SyCr
doi: 10.5061/dryad.4b565
fulldoi: https://doi.org/10.5061/dryad.4b565
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.4b565
month: '01'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1855'
relation: used_in_publication
status: public
status: public
title: 'Data from: A sting in the spit: widespread cross-infection of multiple RNA
viruses across wild and managed bees'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '983'
abstract:
- lang: eng
text: The half-filled Landau level is expected to be approximately particle-hole
symmetric, which requires an extension of the Halperin-Lee-Read (HLR) theory of
the compressible state observed at this filling. Recent work indicates that, when
particle-hole symmetry is preserved, the composite fermions experience a quantized
π-Berry phase upon winding around the composite Fermi surface, analogous to Dirac
fermions at the surface of a 3D topological insulator. In contrast, the effective
low-energy theory of the composite fermion liquid originally proposed by HLR lacks
particle-hole symmetry and has vanishing Berry phase. In this paper, we explain
how thermoelectric transport measurements can be used to test the Dirac nature
of the composite fermions by quantitatively extracting this Berry phase. First,
we point out that longitudinal thermopower (Seebeck effect) is nonvanishing because
of the unusual nature of particle-hole symmetry in this context and is not sensitive
to the Berry phase. In contrast, we find that off-diagonal thermopower (Nernst
effect) is directly related to the topological structure of the composite Fermi
surface, vanishing for zero Berry phase and taking its maximal value for π Berry
phase. In contrast, in purely electrical transport signatures, the Berry phase
contributions appear as small corrections to a large background signal, making
the Nernst effect a promising diagnostic of the Dirac nature of composite fermions.
acknowledgement: We thank B. I. Halperin, N. Cooper, C. Wang, J. Alicea, and M. Zaletel
for insightful conversations. A. C. P. and M. S. were supported by the Gordon and
Betty Moore Foundation’s EPiQS Initiative through Grant No. GBMF4307. A. V. was
supported by a Simons Investigator grant.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Andrew
full_name: Potter, Andrew
last_name: Potter
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Ashvin
full_name: Vishwanath, Ashvin
last_name: Vishwanath
citation:
ama: Potter A, Serbyn M, Vishwanath A. Thermoelectric transport signatures of Dirac
composite fermions in the half-filled Landau level. Physical Review X.
2016;6(3). doi:10.1103/PhysRevX.6.031026
apa: Potter, A., Serbyn, M., & Vishwanath, A. (2016). Thermoelectric transport
signatures of Dirac composite fermions in the half-filled Landau level. Physical
Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.6.031026
chicago: Potter, Andrew, Maksym Serbyn, and Ashvin Vishwanath. “Thermoelectric Transport
Signatures of Dirac Composite Fermions in the Half-Filled Landau Level.” Physical
Review X. American Physical Society, 2016. https://doi.org/10.1103/PhysRevX.6.031026.
ieee: A. Potter, M. Serbyn, and A. Vishwanath, “Thermoelectric transport signatures
of Dirac composite fermions in the half-filled Landau level,” Physical Review
X, vol. 6, no. 3. American Physical Society, 2016.
ista: Potter A, Serbyn M, Vishwanath A. 2016. Thermoelectric transport signatures
of Dirac composite fermions in the half-filled Landau level. Physical Review X.
6(3).
mla: Potter, Andrew, et al. “Thermoelectric Transport Signatures of Dirac Composite
Fermions in the Half-Filled Landau Level.” Physical Review X, vol. 6, no.
3, American Physical Society, 2016, doi:10.1103/PhysRevX.6.031026.
short: A. Potter, M. Serbyn, A. Vishwanath, Physical Review X 6 (2016).
date_created: 2018-12-11T11:49:32Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2026-05-20T13:03:47Z
day: '01'
doi: 10.1103/PhysRevX.6.031026
extern: '1'
external_id:
arxiv:
- '1512.06852'
fulldoi: https://doi.org/10.1103/PhysRevX.6.031026
intvolume: ' 6'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1103/PhysRevX.6.031026
month: '01'
oa: 1
oa_version: Published Version
publication: Physical Review X
publication_identifier:
eissn:
- 2160-3308
publication_status: published
publisher: American Physical Society
publist_id: '6417'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Thermoelectric transport signatures of Dirac composite fermions in the half-filled
Landau level
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 6
year: '2016'
...
---
OA_place: repository
OA_type: green
_id: '984'
abstract:
- lang: eng
text: The entanglement spectrum of the reduced density matrix contains information
beyond the von Neumann entropy and provides unique insights into exotic orders
or critical behavior of quantum systems. Here, we show that strongly disordered
systems in the many-body localized phase have power-law entanglement spectra,
arising from the presence of extensively many local integrals of motion. The power-law
entanglement spectrum distinguishes many-body localized systems from ergodic systems,
as well as from ground states of gapped integrable models or free systems in the
vicinity of scale-invariant critical points. We confirm our results using large-scale
exact diagonalization. In addition, we develop a matrix-product state algorithm
which allows us to access the eigenstates of large systems close to the localization
transition, and discuss general implications of our results for variational studies
of highly excited eigenstates in many-body localized systems.
acknowledgement: We thank M. Stoudenmire and C. Turner for useful discussions. M.
S. was supported by Gordon and Betty Moore Foundation's EPiQS Initiative through
Grant No. GBMF4307. This research was supported in part by the National Science
Foundation under Grant No. NSF PHY11-25915, and by the Swiss National Science Foundation
and Alfred Sloan Foundation (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.
article_number: '160601'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
- first_name: Dmitry
full_name: Abanin, Dmitry
last_name: Abanin
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
citation:
ama: Serbyn M, Michailidis A, Abanin D, Papić Z. Power-law entanglement spectrum
in many-body localized phases. Physical Review Letters. 2016;117(16). doi:10.1103/PhysRevLett.117.160601
apa: Serbyn, M., Michailidis, A., Abanin, D., & Papić, Z. (2016). Power-law
entanglement spectrum in many-body localized phases. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.117.160601
chicago: Serbyn, Maksym, Alexios Michailidis, Dmitry Abanin, and Zlatko Papić. “Power-Law
Entanglement Spectrum in Many-Body Localized Phases.” Physical Review Letters.
American Physical Society, 2016. https://doi.org/10.1103/PhysRevLett.117.160601.
ieee: M. Serbyn, A. Michailidis, D. Abanin, and Z. Papić, “Power-law entanglement
spectrum in many-body localized phases,” Physical Review Letters, vol.
117, no. 16. American Physical Society, 2016.
ista: Serbyn M, Michailidis A, Abanin D, Papić Z. 2016. Power-law entanglement spectrum
in many-body localized phases. Physical Review Letters. 117(16), 160601.
mla: Serbyn, Maksym, et al. “Power-Law Entanglement Spectrum in Many-Body Localized
Phases.” Physical Review Letters, vol. 117, no. 16, 160601, American Physical
Society, 2016, doi:10.1103/PhysRevLett.117.160601.
short: M. Serbyn, A. Michailidis, D. Abanin, Z. Papić, Physical Review Letters 117
(2016).
date_created: 2018-12-11T11:49:32Z
date_published: 2016-10-14T00:00:00Z
date_updated: 2026-05-20T13:46:33Z
day: '14'
doi: 10.1103/PhysRevLett.117.160601
extern: '1'
external_id:
arxiv:
- '1605.05737'
pmid:
- '27792374'
fulldoi: https://doi.org/10.1103/PhysRevLett.117.160601
intvolume: ' 117'
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.1605.05737'
month: '10'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- ' 1079-7114'
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
publist_id: '6414'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Power-law entanglement spectrum in many-body localized phases
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 117
year: '2016'
...