---
_id: '1081'
abstract:
- lang: eng
text: The asymmetric localization of proteins in the plasma membrane domains of
eukaryotic cells is a fundamental manifestation of cell polarity that is central
to multicellular organization and developmental patterning. In plants, the mechanisms
underlying the polar localization of cargo proteins are still largely unknown
and appear to be fundamentally distinct from those operating in mammals. Here,
we present a systematic, quantitative comparative analysis of the polar delivery
and subcellular localization of proteins that characterize distinct polar plasma
membrane domains in plant cells. The combination of microscopic analyses and computational
modeling revealed a mechanistic framework common to diverse polar cargos and underlying
the establishment and maintenance of apical, basal, and lateral polar domains
in plant cells. This mechanism depends on the polar secretion, constitutive endocytic
recycling, and restricted lateral diffusion of cargos within the plasma membrane.
Moreover, our observations suggest that polar cargo distribution involves the
individual protein potential to form clusters within the plasma membrane and interact
with the extracellular matrix. Our observations provide insights into the shared
cellular mechanisms of polar cargo delivery and polarity maintenance in plant
cells.
acknowledgement: "We thank Bonnie Bartel, Jenny Russinova and Niko Geldner\r\nfor
sharing published material, Martine de Cock and Annick\r\nBleys for help in preparing
the manuscript. This work was\r\nsupported by the European Research Council (project\r\nERC-2011-StG-20101109-PSDP);
Czech Science Foundation\r\nGAČR (GA13-40637S); project CEITEC—Central European\r\nInstitute
of Technology (CZ.1.05/1.1.00/02.0068). SV is a\r\npostdoctoral fellow of the Research
Foundation-Flanders.\r\nSN is a Project Assistant Professor supported by the Japanese\r\nSociety
for the Promotion of Science (JSPS; 30612022 to SN),\r\nthe NC-CARP project of the
Ministry of Education, Culture,\r\nSports, Science and Technology in Japan to SN."
article_number: '16018'
author:
- first_name: Łukasz
full_name: Łangowski, Łukasz
last_name: Łangowski
- first_name: Krzysztof T
full_name: Wabnik, Krzysztof T
id: 4DE369A4-F248-11E8-B48F-1D18A9856A87
last_name: Wabnik
orcid: 0000-0001-7263-0560
- first_name: Hongjiang
full_name: Li, Hongjiang
id: 33CA54A6-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0001-5039-9660
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Hirokazu
full_name: Tanaka, Hirokazu
last_name: Tanaka
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Łangowski Ł, Wabnik KT, Li H, et al. Cellular mechanisms for cargo delivery
and polarity maintenance at different polar domains in plant cells. Cell Discovery.
2016;2. doi:10.1038/celldisc.2016.18
apa: Łangowski, Ł., Wabnik, K. T., Li, H., Vanneste, S., Naramoto, S., Tanaka, H.,
& Friml, J. (2016). Cellular mechanisms for cargo delivery and polarity maintenance
at different polar domains in plant cells. Cell Discovery. Nature Publishing
Group. https://doi.org/10.1038/celldisc.2016.18
chicago: Łangowski, Łukasz, Krzysztof T Wabnik, Hongjiang Li, Steffen Vanneste,
Satoshi Naramoto, Hirokazu Tanaka, and Jiří Friml. “Cellular Mechanisms for Cargo
Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells.”
Cell Discovery. Nature Publishing Group, 2016. https://doi.org/10.1038/celldisc.2016.18.
ieee: Ł. Łangowski et al., “Cellular mechanisms for cargo delivery and polarity
maintenance at different polar domains in plant cells,” Cell Discovery,
vol. 2. Nature Publishing Group, 2016.
ista: Łangowski Ł, Wabnik KT, Li H, Vanneste S, Naramoto S, Tanaka H, Friml J. 2016.
Cellular mechanisms for cargo delivery and polarity maintenance at different polar
domains in plant cells. Cell Discovery. 2, 16018.
mla: Łangowski, Łukasz, et al. “Cellular Mechanisms for Cargo Delivery and Polarity
Maintenance at Different Polar Domains in Plant Cells.” Cell Discovery,
vol. 2, 16018, Nature Publishing Group, 2016, doi:10.1038/celldisc.2016.18.
short: Ł. Łangowski, K.T. Wabnik, H. Li, S. Vanneste, S. Naramoto, H. Tanaka, J.
Friml, Cell Discovery 2 (2016).
date_created: 2018-12-11T11:50:02Z
date_published: 2016-07-19T00:00:00Z
date_updated: 2021-01-12T06:48:08Z
day: '19'
ddc:
- '580'
department:
- _id: EvBe
- _id: JiFr
doi: 10.1038/celldisc.2016.18
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:33Z
date_updated: 2018-12-12T10:13:33Z
file_id: '5017'
file_name: IST-2017-757-v1+1_celldisc201618.pdf
file_size: 5261671
relation: main_file
file_date_updated: 2018-12-12T10:13:33Z
has_accepted_license: '1'
intvolume: ' 2'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Cell Discovery
publication_status: published
publisher: Nature Publishing Group
publist_id: '6299'
pubrep_id: '757'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cellular mechanisms for cargo delivery and polarity maintenance at different
polar domains in plant cells
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2016'
...
---
_id: '10810'
abstract:
- lang: eng
text: "The main goal of the SCP-ECG standard is to address ECG data and related
metadata structuring, semantics and syntax, with the objective of facilitating
interoperability and thus supporting and promoting the exchange of the relevant
information for unary and serial ECG diagnosis. Starting with version V3.0, the
standard now also provides support for the storage of continuous, long-term ECG
recordings and affords a repository for selected ECG sequences and the related
metadata to accommodate stress tests, drug trials and protocol-based ECG recordings.
The global and per-lead measurements sections have been extended and three new
sections have been introduced for storing beat-by-beat and/or spike-by-spike measurements\r\nand
annotations. The used terminology and the provided measurements and annotations
have been harmonized with the ISO/IEEE 11073-10102 Annotated ECG standard. Emphasis
has also been put on harmonizing the Universal Statement Codes with the CDISC
and the categorized AHA statement codes and similarly the drug and implanted devices
codes with the ATC and NASPE/BPEG codes. "
acknowledgement: The authors are thankful to Drs. Roger Abaecherli, Nikus Kjell, Paul
Kligfield, Jay Mason, Patrice Nony, Vito Starc, Anders Thurin and the late Galen
Wagner for their in depth review and constructive comments.
article_processing_charge: No
author:
- first_name: Paul
full_name: Rubel, Paul
last_name: Rubel
- first_name: Danilo
full_name: Pani, Danilo
last_name: Pani
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Jocelyne
full_name: Fayn, Jocelyne
last_name: Fayn
- first_name: Fabio
full_name: Badilini, Fabio
last_name: Badilini
- first_name: Peter
full_name: Macfarlane, Peter
last_name: Macfarlane
- first_name: Alpo
full_name: Varri, Alpo
last_name: Varri
citation:
ama: 'Rubel P, Pani D, Schlögl A, et al. SCP-ECG V3.0: An enhanced standard communication
protocol for computer-assisted electrocardiography. In: 2016 Computing in Cardiology
Conference. Vol 43. Computing in Cardiology; 2016:309-312. doi:10.22489/cinc.2016.090-500'
apa: 'Rubel, P., Pani, D., Schlögl, A., Fayn, J., Badilini, F., Macfarlane, P.,
& Varri, A. (2016). SCP-ECG V3.0: An enhanced standard communication protocol
for computer-assisted electrocardiography. In 2016 Computing in Cardiology
Conference (Vol. 43, pp. 309–312). Vancouver, Canada: Computing in Cardiology.
https://doi.org/10.22489/cinc.2016.090-500'
chicago: 'Rubel, Paul, Danilo Pani, Alois Schlögl, Jocelyne Fayn, Fabio Badilini,
Peter Macfarlane, and Alpo Varri. “SCP-ECG V3.0: An Enhanced Standard Communication
Protocol for Computer-Assisted Electrocardiography.” In 2016 Computing in Cardiology
Conference, 43:309–12. Computing in Cardiology, 2016. https://doi.org/10.22489/cinc.2016.090-500.'
ieee: 'P. Rubel et al., “SCP-ECG V3.0: An enhanced standard communication
protocol for computer-assisted electrocardiography,” in 2016 Computing in Cardiology
Conference, Vancouver, Canada, 2016, vol. 43, pp. 309–312.'
ista: 'Rubel P, Pani D, Schlögl A, Fayn J, Badilini F, Macfarlane P, Varri A. 2016.
SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted
electrocardiography. 2016 Computing in Cardiology Conference. CinC: Computing
in Cardiology vol. 43, 309–312.'
mla: 'Rubel, Paul, et al. “SCP-ECG V3.0: An Enhanced Standard Communication Protocol
for Computer-Assisted Electrocardiography.” 2016 Computing in Cardiology Conference,
vol. 43, Computing in Cardiology, 2016, pp. 309–12, doi:10.22489/cinc.2016.090-500.'
short: P. Rubel, D. Pani, A. Schlögl, J. Fayn, F. Badilini, P. Macfarlane, A. Varri,
in:, 2016 Computing in Cardiology Conference, Computing in Cardiology, 2016, pp.
309–312.
conference:
end_date: 2016-09-14
location: Vancouver, Canada
name: 'CinC: Computing in Cardiology'
start_date: 2016-09-11
date_created: 2022-03-03T10:43:10Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2022-03-04T07:34:45Z
day: '01'
department:
- _id: CampIT
doi: 10.22489/cinc.2016.090-500
intvolume: ' 43'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.22489/cinc.2016.090-500
month: '03'
oa: 1
oa_version: Published Version
page: 309-312
publication: 2016 Computing in Cardiology Conference
publication_identifier:
issn:
- 2325-887X
publication_status: published
publisher: Computing in Cardiology
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted
electrocardiography'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
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'
...
---
_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'
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'
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: '948'
abstract:
- lang: eng
text: Experience constantly shapes neural circuits through a variety of plasticity
mechanisms. While the functional roles of some plasticity mechanisms are well-understood,
it remains unclear how changes in neural excitability contribute to learning.
Here, we develop a normative interpretation of intrinsic plasticity (IP) as a
key component of unsupervised learning. We introduce a novel generative mixture
model that accounts for the class-specific statistics of stimulus intensities,
and we derive a neural circuit that learns the input classes and their intensities.
We will analytically show that inference and learning for our generative model
can be achieved by a neural circuit with intensity-sensitive neurons equipped
with a specific form of IP. Numerical experiments verify our analytical derivations
and show robust behavior for artificial and natural stimuli. Our results link
IP to non-trivial input statistics, in particular the statistics of stimulus intensities
for classes to which a neuron is sensitive. More generally, our work paves the
way toward new classification algorithms that are robust to intensity variations.
acknowledgement: DFG Cluster of Excellence EXC 1077/1 (Hearing4all) and LU 1196/5-1
(JL and TM), People Programme (Marie Curie Actions) FP7/2007-2013 grant agreement
no. 291734 (CS)
alternative_title:
- Advances in Neural Information Processing Systems
author:
- first_name: Travis
full_name: Monk, Travis
last_name: Monk
- first_name: Cristina
full_name: Savin, Cristina
id: 3933349E-F248-11E8-B48F-1D18A9856A87
last_name: Savin
- first_name: Jörg
full_name: Lücke, Jörg
last_name: Lücke
citation:
ama: 'Monk T, Savin C, Lücke J. Neurons equipped with intrinsic plasticity learn
stimulus intensity statistics. In: Vol 29. Neural Information Processing Systems;
2016:4285-4293.'
apa: 'Monk, T., Savin, C., & Lücke, J. (2016). Neurons equipped with intrinsic
plasticity learn stimulus intensity statistics (Vol. 29, pp. 4285–4293). Presented
at the NIPS: Neural Information Processing Systems, Barcelona, Spaine: Neural
Information Processing Systems.'
chicago: Monk, Travis, Cristina Savin, and Jörg Lücke. “Neurons Equipped with Intrinsic
Plasticity Learn Stimulus Intensity Statistics,” 29:4285–93. Neural Information
Processing Systems, 2016.
ieee: 'T. Monk, C. Savin, and J. Lücke, “Neurons equipped with intrinsic plasticity
learn stimulus intensity statistics,” presented at the NIPS: Neural Information
Processing Systems, Barcelona, Spaine, 2016, vol. 29, pp. 4285–4293.'
ista: 'Monk T, Savin C, Lücke J. 2016. Neurons equipped with intrinsic plasticity
learn stimulus intensity statistics. NIPS: Neural Information Processing Systems,
Advances in Neural Information Processing Systems, vol. 29, 4285–4293.'
mla: Monk, Travis, et al. Neurons Equipped with Intrinsic Plasticity Learn Stimulus
Intensity Statistics. Vol. 29, Neural Information Processing Systems, 2016,
pp. 4285–93.
short: T. Monk, C. Savin, J. Lücke, in:, Neural Information Processing Systems,
2016, pp. 4285–4293.
conference:
end_date: 2016-12-10
location: Barcelona, Spaine
name: 'NIPS: Neural Information Processing Systems'
start_date: 2016-12-05
date_created: 2018-12-11T11:49:21Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T08:22:08Z
day: '01'
department:
- _id: GaTk
ec_funded: 1
intvolume: ' 29'
language:
- iso: eng
main_file_link:
- url: https://papers.nips.cc/paper/6582-neurons-equipped-with-intrinsic-plasticity-learn-stimulus-intensity-statistics
month: '01'
oa_version: None
page: 4285 - 4293
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '6469'
quality_controlled: '1'
scopus_import: 1
status: public
title: Neurons equipped with intrinsic plasticity learn stimulus intensity statistics
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 29
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'
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'
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'
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: '9704'
abstract:
- lang: eng
text: Emerging infectious diseases (EIDs) have contributed significantly to the
current biodiversity crisis, leading to widespread epidemics and population loss.
Owing to genetic variation in pathogen virulence, a complete understanding of
species decline requires the accurate identification and characterization of EIDs.
We explore this issue in the Western honeybee, where increasing mortality of populations
in the Northern Hemisphere has caused major concern. Specifically, we investigate
the importance of genetic identity of the main suspect in mortality, deformed
wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a
systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B)
is more virulent than the established DWV genotype (DWV-A) and is widespread in
the landscape. Furthermore, we show in a simple model that colonies infected with
DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential
for rapid DWV evolution by revealing extensive genome-wide recombination in vivo.
The emergence of DWV-B in naive honeybee populations, including via recombination
with DWV-A, could be of significant ecological and economic importance. Our findings
emphasize that knowledge of pathogen genetic identity and diversity is critical
to understanding drivers of species decline.
article_processing_charge: No
author:
- first_name: Dino
full_name: Mcmahon, Dino
last_name: Mcmahon
- first_name: Myrsini
full_name: Natsopoulou, Myrsini
last_name: Natsopoulou
- first_name: Vincent
full_name: Doublet, Vincent
last_name: Doublet
- first_name: Matthias
full_name: Fürst, Matthias
id: 393B1196-F248-11E8-B48F-1D18A9856A87
last_name: Fürst
orcid: 0000-0002-3712-925X
- first_name: Silvio
full_name: Weging, Silvio
last_name: Weging
- first_name: Mark
full_name: Brown, Mark
last_name: Brown
- first_name: Andreas
full_name: Gogol Döring, Andreas
last_name: Gogol Döring
- first_name: Robert
full_name: Paxton, Robert
last_name: Paxton
citation:
ama: 'Mcmahon D, Natsopoulou M, Doublet V, et al. Data from: Elevated virulence
of an emerging viral genotype as a driver of honeybee loss. 2016. doi:10.5061/dryad.cq7t1'
apa: 'Mcmahon, D., Natsopoulou, M., Doublet, V., Fürst, M., Weging, S., Brown, M.,
… Paxton, R. (2016). Data from: Elevated virulence of an emerging viral genotype
as a driver of honeybee loss. Dryad. https://doi.org/10.5061/dryad.cq7t1'
chicago: 'Mcmahon, Dino, Myrsini Natsopoulou, Vincent Doublet, Matthias Fürst, Silvio
Weging, Mark Brown, Andreas Gogol Döring, and Robert Paxton. “Data from: Elevated
Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” Dryad,
2016. https://doi.org/10.5061/dryad.cq7t1.'
ieee: 'D. Mcmahon et al., “Data from: Elevated virulence of an emerging viral
genotype as a driver of honeybee loss.” Dryad, 2016.'
ista: 'Mcmahon D, Natsopoulou M, Doublet V, Fürst M, Weging S, Brown M, Gogol Döring
A, Paxton R. 2016. Data from: Elevated virulence of an emerging viral genotype
as a driver of honeybee loss, Dryad, 10.5061/dryad.cq7t1.'
mla: 'Mcmahon, Dino, et al. Data from: Elevated Virulence of an Emerging Viral
Genotype as a Driver of Honeybee Loss. Dryad, 2016, doi:10.5061/dryad.cq7t1.'
short: D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A.
Gogol Döring, R. Paxton, (2016).
date_created: 2021-07-23T08:30:38Z
date_published: 2016-05-06T00:00:00Z
date_updated: 2023-02-21T16:54:31Z
day: '06'
department:
- _id: SyCr
doi: 10.5061/dryad.cq7t1
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.cq7t1
month: '05'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1262'
relation: used_in_publication
status: public
status: public
title: 'Data from: Elevated virulence of an emerging viral genotype as a driver of
honeybee loss'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
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: 2025-05-28T11:57:03Z
day: '23'
department:
- _id: NiBa
doi: 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: 2023-02-23T10:17:25Z
day: '22'
department:
- _id: SyCr
doi: 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'
...
---
_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.
author:
- first_name: Andrew
full_name: Potter, Andrew C
last_name: Potter
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Ashvin
full_name: Vishwanath, Ashvin K
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: 2021-01-12T08:22:25Z
day: '01'
doi: 10.1103/PhysRevX.6.031026
extern: 1
intvolume: ' 6'
issue: '3'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1512.06852
month: '01'
oa: 1
publication: Physical Review X
publication_status: published
publisher: American Physical Society
publist_id: '6417'
quality_controlled: 0
status: public
title: Thermoelectric transport signatures of Dirac composite fermions in the half-filled
Landau level
type: journal_article
volume: 6
year: '2016'
...
---
_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.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Alexios
full_name: Alexios Michailidis
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
- first_name: Dmitry
full_name: Abanin, Dmitry A
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).
mla: Serbyn, Maksym, et al. “Power-Law Entanglement Spectrum in Many-Body Localized
Phases.” Physical Review Letters, vol. 117, no. 16, 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: 2016-10-16T00:00:00Z
date_updated: 2021-01-12T08:22:25Z
day: '16'
doi: 10.1103/PhysRevLett.117.160601
extern: 1
intvolume: ' 117'
issue: '16'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1605.05737
month: '10'
oa: 1
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6414'
quality_controlled: 0
status: public
title: Power-law entanglement spectrum in many-body localized phases
type: journal_article
volume: 117
year: '2016'
...
---
_id: '985'
abstract:
- lang: eng
text: We report on magnetotransport studies of dual-gated, Bernal-stacked trilayer
graphene (TLG) encapsulated in boron nitride crystals. We observe a quantum Hall
effect staircase which indicates a complete lifting of the 12-fold degeneracy
of the zeroth Landau level. As a function of perpendicular electric field, our
data exhibit a sequence of phase transitions between all integer quantum Hall
states in the filling factor interval -8<ν<0. We develop a theoretical model
and argue that, in contrast to monolayer and bilayer graphene, the observed Landau
level splittings and quantum Hall phase transitions can be understood within a
single-particle picture, but imply the presence of a charge density imbalance
between the inner and outer layers of TLG, even at charge neutrality and zero
transverse electric field. Our results indicate the importance of a previously
unaccounted band structure parameter which, together with a more accurate estimate
of the other tight-binding parameters, results in a significantly improved determination
of the electronic and Landau level structure of TLG.
acknowledgement: This work has been primarily supported by the National Science Foundation
(DMR-1405221) for device fabrication and transport, and partly by ONR Young Investigator
Award N00014-13-1-0610 for data analysis.
author:
- first_name: Leonardo
full_name: Campos, Leonardo C
last_name: Campos
- first_name: Thiti
full_name: Taychatanapat, Thiti
last_name: Taychatanapat
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Kawin
full_name: Surakitbovorn, Kawin N
last_name: Surakitbovorn
- first_name: Kenji
full_name: Watanabe, Kenji
last_name: Watanabe
- first_name: Takashi
full_name: Taniguchi, Takashi
last_name: Taniguchi
- first_name: Dmitry
full_name: Abanin, Dmitry A
last_name: Abanin
- first_name: Pablo
full_name: Jarillo-Herrero, Pablo
last_name: Jarillo Herrero
citation:
ama: Campos L, Taychatanapat T, Serbyn M, et al. Landau Level Splittings, Phase
Transitions, and Nonuniform Charge Distribution in Trilayer Graphene. Physical
Review Letters. 2016;117(6). doi:10.1103/PhysRevLett.117.066601
apa: Campos, L., Taychatanapat, T., Serbyn, M., Surakitbovorn, K., Watanabe, K.,
Taniguchi, T., … Jarillo Herrero, P. (2016). Landau Level Splittings, Phase Transitions,
and Nonuniform Charge Distribution in Trilayer Graphene. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.117.066601
chicago: Campos, Leonardo, Thiti Taychatanapat, Maksym Serbyn, Kawin Surakitbovorn,
Kenji Watanabe, Takashi Taniguchi, Dmitry Abanin, and Pablo Jarillo Herrero. “Landau
Level Splittings, Phase Transitions, and Nonuniform Charge Distribution in Trilayer
Graphene.” Physical Review Letters. American Physical Society, 2016. https://doi.org/10.1103/PhysRevLett.117.066601.
ieee: L. Campos et al., “Landau Level Splittings, Phase Transitions, and
Nonuniform Charge Distribution in Trilayer Graphene,” Physical Review Letters,
vol. 117, no. 6. American Physical Society, 2016.
ista: Campos L, Taychatanapat T, Serbyn M, Surakitbovorn K, Watanabe K, Taniguchi
T, Abanin D, Jarillo Herrero P. 2016. Landau Level Splittings, Phase Transitions,
and Nonuniform Charge Distribution in Trilayer Graphene. Physical Review Letters.
117(6).
mla: Campos, Leonardo, et al. “Landau Level Splittings, Phase Transitions, and Nonuniform
Charge Distribution in Trilayer Graphene.” Physical Review Letters, vol.
117, no. 6, American Physical Society, 2016, doi:10.1103/PhysRevLett.117.066601.
short: L. Campos, T. Taychatanapat, M. Serbyn, K. Surakitbovorn, K. Watanabe, T.
Taniguchi, D. Abanin, P. Jarillo Herrero, Physical Review Letters 117 (2016).
date_created: 2018-12-11T11:49:33Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-01-12T08:22:26Z
day: '01'
doi: 10.1103/PhysRevLett.117.066601
extern: 1
intvolume: ' 117'
issue: '6'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1607.00784
month: '04'
oa: 1
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6415'
quality_controlled: 0
status: public
title: Landau Level Splittings, Phase Transitions, and Nonuniform Charge Distribution
in Trilayer Graphene
type: journal_article
volume: 117
year: '2016'
...
---
_id: '986'
abstract:
- lang: eng
text: The many-body localization transition (MBLT) between ergodic and many-body
localized phases in disordered interacting systems is a subject of much recent
interest. The statistics of eigenenergies is known to be a powerful probe of crossovers
between ergodic and integrable systems in simpler examples of quantum chaos. We
consider the evolution of the spectral statistics across the MBLT, starting with
mapping to a Brownian motion process that analytically relates the spectral properties
to the statistics of matrix elements. We demonstrate that the flow from Wigner-Dyson
to Poisson statistics is a two-stage process. First, a fractal enhancement of
matrix elements upon approaching the MBLT from the delocalized side produces an
effective power-law interaction between energy levels, and leads to a plasma model
for level statistics. At the second stage, the gas of eigenvalues has local interactions
and the level statistics belongs to a semi-Poisson universality class. We verify
our findings numerically on the XXZ spin chain. We provide a microscopic understanding
of the level statistics across the MBLT and discuss implications for the transition
that are strong constraints on possible theories.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Joel
full_name: Moore, Joel E
last_name: Moore
citation:
ama: Serbyn M, Moore J. Spectral statistics across the many-body localization transition.
Physical Review B - Condensed Matter and Materials Physics. 2016;93(4).
doi:10.1103/PhysRevB.93.041424
apa: Serbyn, M., & Moore, J. (2016). Spectral statistics across the many-body
localization transition. Physical Review B - Condensed Matter and Materials
Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.93.041424
chicago: Serbyn, Maksym, and Joel Moore. “Spectral Statistics across the Many-Body
Localization Transition.” Physical Review B - Condensed Matter and Materials
Physics. American Physical Society, 2016. https://doi.org/10.1103/PhysRevB.93.041424.
ieee: M. Serbyn and J. Moore, “Spectral statistics across the many-body localization
transition,” Physical Review B - Condensed Matter and Materials Physics,
vol. 93, no. 4. American Physical Society, 2016.
ista: Serbyn M, Moore J. 2016. Spectral statistics across the many-body localization
transition. Physical Review B - Condensed Matter and Materials Physics. 93(4).
mla: Serbyn, Maksym, and Joel Moore. “Spectral Statistics across the Many-Body Localization
Transition.” Physical Review B - Condensed Matter and Materials Physics,
vol. 93, no. 4, American Physical Society, 2016, doi:10.1103/PhysRevB.93.041424.
short: M. Serbyn, J. Moore, Physical Review B - Condensed Matter and Materials Physics
93 (2016).
date_created: 2018-12-11T11:49:33Z
date_published: 2016-01-29T00:00:00Z
date_updated: 2021-01-12T08:22:26Z
day: '29'
doi: 10.1103/PhysRevB.93.041424
extern: 1
intvolume: ' 93'
issue: '4'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1508.07293
month: '01'
oa: 1
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '6416'
quality_controlled: 0
status: public
title: Spectral statistics across the many-body localization transition
type: journal_article
volume: 93
year: '2016'
...
---
_id: '9862'
article_processing_charge: No
author:
- first_name: Camille
full_name: Roux, Camille
last_name: Roux
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Jonathan
full_name: Romiguier, Jonathan
last_name: Romiguier
- first_name: Youann
full_name: Anciaux, Youann
last_name: Anciaux
- first_name: Nicolas
full_name: Galtier, Nicolas
last_name: Galtier
- first_name: Nicolas
full_name: Bierne, Nicolas
last_name: Bierne
citation:
ama: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Simulation
study to test the robustness of ABC in face of recent times of divergence. 2016.
doi:10.1371/journal.pbio.2000234.s016
apa: Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne,
N. (2016). Simulation study to test the robustness of ABC in face of recent times
of divergence. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234.s016
chicago: Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux,
Nicolas Galtier, and Nicolas Bierne. “Simulation Study to Test the Robustness
of ABC in Face of Recent Times of Divergence.” Public Library of Science, 2016.
https://doi.org/10.1371/journal.pbio.2000234.s016.
ieee: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne,
“Simulation study to test the robustness of ABC in face of recent times of divergence.”
Public Library of Science, 2016.
ista: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Simulation
study to test the robustness of ABC in face of recent times of divergence, Public
Library of Science, 10.1371/journal.pbio.2000234.s016.
mla: Roux, Camille, et al. Simulation Study to Test the Robustness of ABC in
Face of Recent Times of Divergence. Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.s016.
short: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).
date_created: 2021-08-10T08:20:17Z
date_updated: 2023-02-21T16:21:20Z
day: '27'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1371/journal.pbio.2000234.s016
month: '12'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1158'
relation: used_in_publication
status: public
status: public
title: Simulation study to test the robustness of ABC in face of recent times of divergence
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9863'
article_processing_charge: No
author:
- first_name: Camille
full_name: Roux, Camille
last_name: Roux
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Jonathan
full_name: Romiguier, Jonathan
last_name: Romiguier
- first_name: Youann
full_name: Anciaux, Youann
last_name: Anciaux
- first_name: Nicolas
full_name: Galtier, Nicolas
last_name: Galtier
- first_name: Nicolas
full_name: Bierne, Nicolas
last_name: Bierne
citation:
ama: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Accessions
of surveyed individuals, geographic locations and summary statistics. 2016. doi:10.1371/journal.pbio.2000234.s017
apa: Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne,
N. (2016). Accessions of surveyed individuals, geographic locations and summary
statistics. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234.s017
chicago: Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux,
Nicolas Galtier, and Nicolas Bierne. “Accessions of Surveyed Individuals, Geographic
Locations and Summary Statistics.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.s017.
ieee: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne,
“Accessions of surveyed individuals, geographic locations and summary statistics.”
Public Library of Science, 2016.
ista: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Accessions
of surveyed individuals, geographic locations and summary statistics, Public Library
of Science, 10.1371/journal.pbio.2000234.s017.
mla: Roux, Camille, et al. Accessions of Surveyed Individuals, Geographic Locations
and Summary Statistics. Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.s017.
short: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).
date_created: 2021-08-10T08:22:52Z
date_updated: 2023-02-21T16:21:20Z
day: '27'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1371/journal.pbio.2000234.s017
month: '12'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1158'
relation: used_in_publication
status: public
status: public
title: Accessions of surveyed individuals, geographic locations and summary statistics
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9864'
abstract:
- lang: eng
text: Viral capsids are structurally constrained by interactions among the amino
acids (AAs) of their constituent proteins. Therefore, epistasis is expected to
evolve among physically interacting sites and to influence the rates of substitution.
To study the evolution of epistasis, we focused on the major structural protein
of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences
of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction
differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each
ancestral haplotype and the extant species, we estimated, in silico, the distribution
of free energies and epistasis of the capsid structure. We found that free energy
has not significantly increased but epistasis has. We decomposed epistasis up
to fifth order and found that higher-order epistasis sometimes compensates pairwise
interactions making the free energy seem additive. The dN/dS ratio is low, suggesting
strong purifying selection, and that structure is under stabilizing selection.
We synthesized phages carrying ancestral haplotypes of the coat protein gene and
measured their fitness experimentally. Our findings indicate that stabilizing
mutations can have higher fitness, and that fitness optima do not necessarily
coincide with energy minima.
article_processing_charge: No
author:
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
- first_name: Tomasz
full_name: Włodarski, Tomasz
last_name: Włodarski
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary
interplay between structure, energy and epistasis in the coat protein of the ϕX174
phage family. 2016. doi:10.6084/m9.figshare.4315652.v1
apa: Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J.
P. (2016). Data from evolutionary interplay between structure, energy and epistasis
in the coat protein of the ϕX174 phage family. The Royal Society. https://doi.org/10.6084/m9.figshare.4315652.v1
chicago: Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan
P Bollback. “Data from Evolutionary Interplay between Structure, Energy and Epistasis
in the Coat Protein of the ΦX174 Phage Family.” The Royal Society, 2016. https://doi.org/10.6084/m9.figshare.4315652.v1.
ieee: R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Data
from evolutionary interplay between structure, energy and epistasis in the coat
protein of the ϕX174 phage family.” The Royal Society, 2016.
ista: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2016. Data from
evolutionary interplay between structure, energy and epistasis in the coat protein
of the ϕX174 phage family, The Royal Society, 10.6084/m9.figshare.4315652.v1.
mla: Fernandes Redondo, Rodrigo A., et al. Data from Evolutionary Interplay between
Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.
The Royal Society, 2016, doi:10.6084/m9.figshare.4315652.v1.
short: R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016).
date_created: 2021-08-10T08:29:47Z
date_published: 2016-12-14T00:00:00Z
date_updated: 2025-05-28T11:57:06Z
day: '14'
department:
- _id: NiBa
- _id: JoBo
doi: 10.6084/m9.figshare.4315652.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.4315652.v1
month: '12'
oa: 1
oa_version: Published Version
publisher: The Royal Society
related_material:
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status: public
title: Data from evolutionary interplay between structure, energy and epistasis in
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type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
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...
---
_id: '9866'
article_processing_charge: No
author:
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
- first_name: Zdzisław
full_name: Burda, Zdzisław
last_name: Burda
- first_name: Bartłomiej
full_name: Wacław, Bartłomiej
last_name: Wacław
citation:
ama: Zagórski MP, Burda Z, Wacław B. ZIP-archived directory containing all data
and computer programs. 2016. doi:10.1371/journal.pcbi.1005218.s009
apa: Zagórski, M. P., Burda, Z., & Wacław, B. (2016). ZIP-archived directory
containing all data and computer programs. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005218.s009
chicago: Zagórski, Marcin P, Zdzisław Burda, and Bartłomiej Wacław. “ZIP-Archived
Directory Containing All Data and Computer Programs.” Public Library of Science,
2016. https://doi.org/10.1371/journal.pcbi.1005218.s009.
ieee: M. P. Zagórski, Z. Burda, and B. Wacław, “ZIP-archived directory containing
all data and computer programs.” Public Library of Science, 2016.
ista: Zagórski MP, Burda Z, Wacław B. 2016. ZIP-archived directory containing all
data and computer programs, Public Library of Science, 10.1371/journal.pcbi.1005218.s009.
mla: Zagórski, Marcin P., et al. ZIP-Archived Directory Containing All Data and
Computer Programs. Public Library of Science, 2016, doi:10.1371/journal.pcbi.1005218.s009.
short: M.P. Zagórski, Z. Burda, B. Wacław, (2016).
date_created: 2021-08-10T08:37:20Z
date_published: 2016-12-09T00:00:00Z
date_updated: 2023-02-21T16:24:29Z
day: '09'
department:
- _id: AnKi
doi: 10.1371/journal.pcbi.1005218.s009
month: '12'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
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relation: used_in_publication
status: public
status: public
title: ZIP-archived directory containing all data and computer programs
type: research_data_reference
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...