---
_id: '696'
abstract:
- lang: eng
text: Mutator strains are expected to evolve when the availability and effect of
beneficial mutations are high enough to counteract the disadvantage from deleterious
mutations that will inevitably accumulate. As the population becomes more adapted
to its environment, both availability and effect of beneficial mutations necessarily
decrease and mutation rates are predicted to decrease. It has been shown that
certain molecular mechanisms can lead to increased mutation rates when the organism
finds itself in a stressful environment. While this may be a correlated response
to other functions, it could also be an adaptive mechanism, raising mutation rates
only when it is most advantageous. Here, we use a mathematical model to investigate
the plausibility of the adaptive hypothesis. We show that such a mechanism can
be mantained if the population is subjected to diverse stresses. By simulating
various antibiotic treatment schemes, we find that combination treatments can
reduce the effectiveness of second-order selection on stress-induced mutagenesis.
We discuss the implications of our results to strategies of antibiotic therapy.
article_number: e1005609
article_processing_charge: No
article_type: original
author:
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
orcid: 0000-0002-2519-824X
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: 'Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity
facilitates the persistence of mutator genes. PLoS Computational Biology.
2017;13(7). doi:10.1371/journal.pcbi.1005609'
apa: 'Lukacisinova, M., Novak, S., & Paixao, T. (2017). Stress induced mutagenesis:
Stress diversity facilitates the persistence of mutator genes. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609'
chicago: 'Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced
Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” PLoS
Computational Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.'
ieee: 'M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress
diversity facilitates the persistence of mutator genes,” PLoS Computational
Biology, vol. 13, no. 7. Public Library of Science, 2017.'
ista: 'Lukacisinova M, Novak S, Paixao T. 2017. Stress induced mutagenesis: Stress
diversity facilitates the persistence of mutator genes. PLoS Computational Biology.
13(7), e1005609.'
mla: 'Lukacisinova, Marta, et al. “Stress Induced Mutagenesis: Stress Diversity
Facilitates the Persistence of Mutator Genes.” PLoS Computational Biology,
vol. 13, no. 7, e1005609, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.'
short: M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017).
corr_author: '1'
date_created: 2018-12-11T11:47:58Z
date_published: 2017-07-18T00:00:00Z
date_updated: 2026-04-23T22:30:47Z
day: '18'
ddc:
- '576'
department:
- _id: ToBo
- _id: NiBa
- _id: CaGu
doi: 10.1371/journal.pcbi.1005609
ec_funded: 1
external_id:
isi:
- '000406619800014'
file:
- access_level: open_access
checksum: 9143c290fa6458ed2563bff4b295554a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:01Z
date_updated: 2020-07-14T12:47:46Z
file_id: '5117'
file_name: IST-2017-894-v1+1_journal.pcbi.1005609.pdf
file_size: 3775716
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: PLoS Computational Biology
publication_identifier:
issn:
- 1553-734X
publication_status: published
publisher: Public Library of Science
publist_id: '7004'
pubrep_id: '894'
quality_controlled: '1'
related_material:
record:
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relation: research_data
status: public
- id: '9850'
relation: research_data
status: public
- id: '9851'
relation: research_data
status: public
- id: '9852'
relation: research_data
status: public
- id: '6263'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Stress induced mutagenesis: Stress diversity facilitates the persistence of
mutator genes'
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 13
year: '2017'
...
---
_id: '682'
abstract:
- lang: eng
text: Left-right asymmetry is a fundamental feature of higher-order brain structure;
however, the molecular basis of brain asymmetry remains unclear. We recently identified
structural and functional asymmetries in mouse hippocampal circuitry that result
from the asymmetrical distribution of two distinct populations of pyramidal cell
synapses that differ in the density of the NMDA receptor subunit GluRε2 (also
known as NR2B, GRIN2B or GluN2B). By examining the synaptic distribution of ε2
subunits, we previously found that β2-microglobulin-deficient mice, which lack
cell surface expression of the vast majority of major histocompatibility complex
class I (MHCI) proteins, do not exhibit circuit asymmetry. In the present study,
we conducted electrophysiological and anatomical analyses on the hippocampal circuitry
of mice with a knockout of the paired immunoglobulin-like receptor B (PirB), an
MHCI receptor. As in β2-microglobulin-deficient mice, the PirB-deficient hippocampus
lacked circuit asymmetries. This finding that MHCI loss-of-function mice and PirB
knockout mice have identical phenotypes suggests that MHCI signals that produce
hippocampal asymmetries are transduced through PirB. Our results provide evidence
for a critical role of the MHCI/PirB signaling system in the generation of asymmetries
in hippocampal circuitry.
article_number: e0179377
article_processing_charge: No
article_type: original
author:
- first_name: Hikari
full_name: Ukai, Hikari
last_name: Ukai
- first_name: Aiko
full_name: Kawahara, Aiko
last_name: Kawahara
- first_name: Keiko
full_name: Hirayama, Keiko
last_name: Hirayama
- first_name: Matthew J
full_name: Case, Matthew J
id: 44B7CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Case
- first_name: Shotaro
full_name: Aino, Shotaro
last_name: Aino
- first_name: Masahiro
full_name: Miyabe, Masahiro
last_name: Miyabe
- first_name: Ken
full_name: Wakita, Ken
last_name: Wakita
- first_name: Ryohei
full_name: Oogi, Ryohei
last_name: Oogi
- first_name: Michiyo
full_name: Kasayuki, Michiyo
last_name: Kasayuki
- first_name: Shihomi
full_name: Kawashima, Shihomi
last_name: Kawashima
- first_name: Shunichi
full_name: Sugimoto, Shunichi
last_name: Sugimoto
- first_name: Kanako
full_name: Chikamatsu, Kanako
last_name: Chikamatsu
- first_name: Noritaka
full_name: Nitta, Noritaka
last_name: Nitta
- first_name: Tsuneyuki
full_name: Koga, Tsuneyuki
last_name: Koga
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Toshiyuki
full_name: Takai, Toshiyuki
last_name: Takai
- first_name: Isao
full_name: Ito, Isao
last_name: Ito
citation:
ama: Ukai H, Kawahara A, Hirayama K, et al. PirB regulates asymmetries in hippocampal
circuitry. PLoS One. 2017;12(6). doi:10.1371/journal.pone.0179377
apa: Ukai, H., Kawahara, A., Hirayama, K., Case, M. J., Aino, S., Miyabe, M., …
Ito, I. (2017). PirB regulates asymmetries in hippocampal circuitry. PLoS One.
Public Library of Science. https://doi.org/10.1371/journal.pone.0179377
chicago: Ukai, Hikari, Aiko Kawahara, Keiko Hirayama, Matthew J Case, Shotaro Aino,
Masahiro Miyabe, Ken Wakita, et al. “PirB Regulates Asymmetries in Hippocampal
Circuitry.” PLoS One. Public Library of Science, 2017. https://doi.org/10.1371/journal.pone.0179377.
ieee: H. Ukai et al., “PirB regulates asymmetries in hippocampal circuitry,”
PLoS One, vol. 12, no. 6. Public Library of Science, 2017.
ista: Ukai H, Kawahara A, Hirayama K, Case MJ, Aino S, Miyabe M, Wakita K, Oogi
R, Kasayuki M, Kawashima S, Sugimoto S, Chikamatsu K, Nitta N, Koga T, Shigemoto
R, Takai T, Ito I. 2017. PirB regulates asymmetries in hippocampal circuitry.
PLoS One. 12(6), e0179377.
mla: Ukai, Hikari, et al. “PirB Regulates Asymmetries in Hippocampal Circuitry.”
PLoS One, vol. 12, no. 6, e0179377, Public Library of Science, 2017, doi:10.1371/journal.pone.0179377.
short: H. Ukai, A. Kawahara, K. Hirayama, M.J. Case, S. Aino, M. Miyabe, K. Wakita,
R. Oogi, M. Kasayuki, S. Kawashima, S. Sugimoto, K. Chikamatsu, N. Nitta, T. Koga,
R. Shigemoto, T. Takai, I. Ito, PLoS One 12 (2017).
date_created: 2018-12-11T11:47:54Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2026-04-23T22:30:48Z
day: '01'
ddc:
- '571'
department:
- _id: RySh
doi: 10.1371/journal.pone.0179377
external_id:
isi:
- '000402923200125'
file:
- access_level: open_access
checksum: 24dd19c46fb1c761b0bcbbcd1025a3a8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:16Z
date_updated: 2020-07-14T12:47:40Z
file_id: '4934'
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isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_identifier:
issn:
- 1932-6203
publication_status: published
publisher: Public Library of Science
publist_id: '7034'
pubrep_id: '897'
quality_controlled: '1'
related_material:
record:
- id: '51'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: PirB regulates asymmetries in hippocampal circuitry
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 12
year: '2017'
...
---
_id: '1027'
abstract:
- lang: eng
text: The rising prevalence of antibiotic resistant bacteria is an increasingly
serious public health challenge. To address this problem, recent work ranging
from clinical studies to theoretical modeling has provided valuable insights into
the mechanisms of resistance, its emergence and spread, and ways to counteract
it. A deeper understanding of the underlying dynamics of resistance evolution
will require a combination of experimental and theoretical expertise from different
disciplines and new technology for studying evolution in the laboratory. Here,
we review recent advances in the quantitative understanding of the mechanisms
and evolution of antibiotic resistance. We focus on key theoretical concepts and
new technology that enables well-controlled experiments. We further highlight
key challenges that can be met in the near future to ultimately develop effective
strategies for combating resistance.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Lukacisinova M, Bollenbach MT. Toward a quantitative understanding of antibiotic
resistance evolution. Current Opinion in Biotechnology. 2017;46:90-97.
doi:10.1016/j.copbio.2017.02.013
apa: Lukacisinova, M., & Bollenbach, M. T. (2017). Toward a quantitative understanding
of antibiotic resistance evolution. Current Opinion in Biotechnology. Elsevier.
https://doi.org/10.1016/j.copbio.2017.02.013
chicago: Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative
Understanding of Antibiotic Resistance Evolution.” Current Opinion in Biotechnology.
Elsevier, 2017. https://doi.org/10.1016/j.copbio.2017.02.013.
ieee: M. Lukacisinova and M. T. Bollenbach, “Toward a quantitative understanding
of antibiotic resistance evolution,” Current Opinion in Biotechnology,
vol. 46. Elsevier, pp. 90–97, 2017.
ista: Lukacisinova M, Bollenbach MT. 2017. Toward a quantitative understanding of
antibiotic resistance evolution. Current Opinion in Biotechnology. 46, 90–97.
mla: Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative Understanding
of Antibiotic Resistance Evolution.” Current Opinion in Biotechnology,
vol. 46, Elsevier, 2017, pp. 90–97, doi:10.1016/j.copbio.2017.02.013.
short: M. Lukacisinova, M.T. Bollenbach, Current Opinion in Biotechnology 46 (2017)
90–97.
corr_author: '1'
date_created: 2018-12-11T11:49:45Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2026-04-23T22:30:47Z
day: '01'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.1016/j.copbio.2017.02.013
ec_funded: 1
external_id:
isi:
- '000408077400015'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T09:57:57Z
date_updated: 2019-01-18T09:57:57Z
file_id: '5846'
file_name: 2017_CurrentOpinion_Lukaciinova.pdf
file_size: 858338
relation: main_file
success: 1
file_date_updated: 2019-01-18T09:57:57Z
has_accepted_license: '1'
intvolume: ' 46'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 90 - 97
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303507'
name: Optimality principles in responses to antibiotics
- _id: 25EB3A80-B435-11E9-9278-68D0E5697425
grant_number: RGP0042/2013
name: Revealing the fundamental limits of cell growth
publication: Current Opinion in Biotechnology
publication_status: published
publisher: Elsevier
publist_id: '6364'
pubrep_id: '801'
quality_controlled: '1'
related_material:
record:
- id: '6263'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Toward a quantitative understanding of antibiotic resistance evolution
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 46
year: '2017'
...
---
_id: '704'
abstract:
- lang: eng
text: 'How the organization of genes on a chromosome shapes adaptation is essential
for understanding evolutionary paths. Here, we investigate how adaptation to rapidly
increasing levels of antibiotic depends on the chromosomal neighborhood of a drug-resistance
gene inserted at different positions of the Escherichia coli chromosome. Using
a dual-fluorescence reporter that allows us to distinguish gene amplifications
from other up-mutations, we track in real-time adaptive changes in expression
of the drug-resistance gene. We find that the relative contribution of several
mutation types differs systematically between loci due to properties of neighboring
genes: essentiality, expression, orientation, termination, and presence of duplicates.
These properties determine rate and fitness effects of gene amplification, deletions,
and mutations compromising transcriptional termination. Thus, the adaptive potential
of a gene under selection is a system-property with a complex genetic basis that
is specific for each chromosomal locus, and it can be inferred from detailed functional
and genomic data.'
article_number: e25100
article_processing_charge: No
author:
- first_name: Magdalena
full_name: Steinrück, Magdalena
id: 2C023F40-F248-11E8-B48F-1D18A9856A87
last_name: Steinrück
orcid: 0000-0003-1229-9719
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Steinrück M, Guet CC. Complex chromosomal neighborhood effects determine the
adaptive potential of a gene under selection. eLife. 2017;6. doi:10.7554/eLife.25100
apa: Steinrück, M., & Guet, C. C. (2017). Complex chromosomal neighborhood effects
determine the adaptive potential of a gene under selection. ELife. eLife
Sciences Publications. https://doi.org/10.7554/eLife.25100
chicago: Steinrück, Magdalena, and Calin C Guet. “Complex Chromosomal Neighborhood
Effects Determine the Adaptive Potential of a Gene under Selection.” ELife.
eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25100.
ieee: M. Steinrück and C. C. Guet, “Complex chromosomal neighborhood effects determine
the adaptive potential of a gene under selection,” eLife, vol. 6. eLife
Sciences Publications, 2017.
ista: Steinrück M, Guet CC. 2017. Complex chromosomal neighborhood effects determine
the adaptive potential of a gene under selection. eLife. 6, e25100.
mla: Steinrück, Magdalena, and Calin C. Guet. “Complex Chromosomal Neighborhood
Effects Determine the Adaptive Potential of a Gene under Selection.” ELife,
vol. 6, e25100, eLife Sciences Publications, 2017, doi:10.7554/eLife.25100.
short: M. Steinrück, C.C. Guet, ELife 6 (2017).
corr_author: '1'
date_created: 2018-12-11T11:48:01Z
date_published: 2017-07-25T00:00:00Z
date_updated: 2026-04-23T22:30:50Z
day: '25'
ddc:
- '576'
department:
- _id: CaGu
doi: 10.7554/eLife.25100
external_id:
isi:
- '000406183700001'
file:
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creator: system
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oa_version: Published Version
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
publist_id: '6990'
pubrep_id: '890'
quality_controlled: '1'
related_material:
record:
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relation: popular_science
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Complex chromosomal neighborhood effects determine the adaptive potential of
a gene under selection
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 6
year: '2017'
...
---
_id: '1024'
abstract:
- lang: eng
text: The history of auxin and cytokinin biology including the initial discoveries
by father–son duo Charles Darwin and Francis Darwin (1880), and Gottlieb Haberlandt
(1919) is a beautiful demonstration of unceasing continuity of research. Novel
findings are integrated into existing hypotheses and models and deepen our understanding
of biological principles. At the same time new questions are triggered and hand
to hand with this new methodologies are developed to address these new challenges.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Andrej
full_name: Hurny, Andrej
id: 4DC4AF46-F248-11E8-B48F-1D18A9856A87
last_name: Hurny
orcid: 0000-0003-3638-1426
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Hurny A, Benková E. Methodological advances in auxin and cytokinin biology.
Auxins and Cytokinins in Plant Biology. 2017;1569:1-29. doi:10.1007/978-1-4939-6831-2_1
apa: Hurny, A., & Benková, E. (2017). Methodological advances in auxin and cytokinin
biology. Auxins and Cytokinins in Plant Biology. Springer. https://doi.org/10.1007/978-1-4939-6831-2_1
chicago: Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin
Biology.” Auxins and Cytokinins in Plant Biology. Springer, 2017. https://doi.org/10.1007/978-1-4939-6831-2_1.
ieee: A. Hurny and E. Benková, “Methodological advances in auxin and cytokinin biology,”
Auxins and Cytokinins in Plant Biology, vol. 1569. Springer, pp. 1–29,
2017.
ista: Hurny A, Benková E. 2017. Methodological advances in auxin and cytokinin biology.
Auxins and Cytokinins in Plant Biology. 1569, 1–29.
mla: Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin
Biology.” Auxins and Cytokinins in Plant Biology, vol. 1569, Springer,
2017, pp. 1–29, doi:10.1007/978-1-4939-6831-2_1.
short: A. Hurny, E. Benková, Auxins and Cytokinins in Plant Biology 1569 (2017)
1–29.
corr_author: '1'
date_created: 2018-12-11T11:49:45Z
date_published: 2017-03-17T00:00:00Z
date_updated: 2026-04-23T22:30:49Z
day: '17'
ddc:
- '575'
department:
- _id: EvBe
doi: 10.1007/978-1-4939-6831-2_1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:18Z
date_updated: 2019-10-15T07:47:05Z
file_id: '5068'
file_name: IST-2018-1019-v1+1_Hurny_MethodsMolBiol_2017.pdf
file_size: 840646
relation: main_file
file_date_updated: 2019-10-15T07:47:05Z
has_accepted_license: '1'
intvolume: ' 1569'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 1 - 29
project:
- _id: 2542D156-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 1774-B16
name: Hormone cross-talk drives nutrient dependent plant development
publication: Auxins and Cytokinins in Plant Biology
publication_identifier:
issn:
- 1064-3745
publication_status: published
publisher: Springer
publist_id: '6369'
pubrep_id: '1019'
quality_controlled: '1'
related_material:
record:
- id: '539'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Methodological advances in auxin and cytokinin biology
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1569
year: '2017'
...
---
_id: '679'
abstract:
- lang: eng
text: Protective responses against pathogens require a rapid mobilization of resting
neutrophils and the timely removal of activated ones. Neutrophils are exceptionally
short-lived leukocytes, yet it remains unclear whether the lifespan of pathogen-engaged
neutrophils is regulated differently from that in the circulating steady-state
pool. Here, we have found that under homeostatic conditions, the mRNA-destabilizing
protein tristetraprolin (TTP) regulates apoptosis and the numbers of activated
infiltrating murine neutrophils but not neutrophil cellularity. Activated TTP-deficient
neutrophils exhibited decreased apoptosis and enhanced accumulation at the infection
site. In the context of myeloid-specific deletion of Ttp, the potentiation of
neutrophil deployment protected mice against lethal soft tissue infection with
Streptococcus pyogenes and prevented bacterial dissemination. Neutrophil transcriptome
analysis revealed that decreased apoptosis of TTP-deficient neutrophils was specifically
associated with elevated expression of myeloid cell leukemia 1 (Mcl1) but not
other antiapoptotic B cell leukemia/ lymphoma 2 (Bcl2) family members. Higher
Mcl1 expression resulted from stabilization of Mcl1 mRNA in the absence of TTP.
The low apoptosis rate of infiltrating TTP-deficient neutrophils was comparable
to that of transgenic Mcl1-overexpressing neutrophils. Our study demonstrates
that posttranscriptional gene regulation by TTP schedules the termination of the
antimicrobial engagement of neutrophils. The balancing role of TTP comes at the
cost of an increased risk of bacterial infections.
acknowledgement: This work was supported by grants from the Austrian Science Fund
(FWF) (P27538-B21, I1621-B22, and SFB 43, to PK); by funding from the European Union
Seventh Framework Programme Marie Curie Initial Training Networks (FP7-PEOPLE-2012-ITN)
for the project INBIONET (INfection BIOlogy Training NETwork under grant agreement
PITN-GA-2012-316682; and by a joint research cluster initiative of the University
of Vienna and the Medical University of Vienna.
article_processing_charge: No
author:
- first_name: Florian
full_name: Ebner, Florian
last_name: Ebner
- first_name: Vitaly
full_name: Sedlyarov, Vitaly
last_name: Sedlyarov
- first_name: Saren
full_name: Tasciyan, Saren
id: 4323B49C-F248-11E8-B48F-1D18A9856A87
last_name: Tasciyan
orcid: 0000-0003-1671-393X
- first_name: Masa
full_name: Ivin, Masa
last_name: Ivin
- first_name: Franz
full_name: Kratochvill, Franz
last_name: Kratochvill
- first_name: Nina
full_name: Gratz, Nina
last_name: Gratz
- first_name: Lukas
full_name: Kenner, Lukas
last_name: Kenner
- first_name: Andreas
full_name: Villunger, Andreas
last_name: Villunger
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Pavel
full_name: Kovarik, Pavel
last_name: Kovarik
citation:
ama: Ebner F, Sedlyarov V, Tasciyan S, et al. The RNA-binding protein tristetraprolin
schedules apoptosis of pathogen-engaged neutrophils during bacterial infection.
The Journal of Clinical Investigation. 2017;127(6):2051-2065. doi:10.1172/JCI80631
apa: Ebner, F., Sedlyarov, V., Tasciyan, S., Ivin, M., Kratochvill, F., Gratz, N.,
… Kovarik, P. (2017). The RNA-binding protein tristetraprolin schedules apoptosis
of pathogen-engaged neutrophils during bacterial infection. The Journal of
Clinical Investigation. American Society for Clinical Investigation. https://doi.org/10.1172/JCI80631
chicago: Ebner, Florian, Vitaly Sedlyarov, Saren Tasciyan, Masa Ivin, Franz Kratochvill,
Nina Gratz, Lukas Kenner, Andreas Villunger, Michael K Sixt, and Pavel Kovarik.
“The RNA-Binding Protein Tristetraprolin Schedules Apoptosis of Pathogen-Engaged
Neutrophils during Bacterial Infection.” The Journal of Clinical Investigation.
American Society for Clinical Investigation, 2017. https://doi.org/10.1172/JCI80631.
ieee: F. Ebner et al., “The RNA-binding protein tristetraprolin schedules
apoptosis of pathogen-engaged neutrophils during bacterial infection,” The
Journal of Clinical Investigation, vol. 127, no. 6. American Society for Clinical
Investigation, pp. 2051–2065, 2017.
ista: Ebner F, Sedlyarov V, Tasciyan S, Ivin M, Kratochvill F, Gratz N, Kenner L,
Villunger A, Sixt MK, Kovarik P. 2017. The RNA-binding protein tristetraprolin
schedules apoptosis of pathogen-engaged neutrophils during bacterial infection.
The Journal of Clinical Investigation. 127(6), 2051–2065.
mla: Ebner, Florian, et al. “The RNA-Binding Protein Tristetraprolin Schedules Apoptosis
of Pathogen-Engaged Neutrophils during Bacterial Infection.” The Journal of
Clinical Investigation, vol. 127, no. 6, American Society for Clinical Investigation,
2017, pp. 2051–65, doi:10.1172/JCI80631.
short: F. Ebner, V. Sedlyarov, S. Tasciyan, M. Ivin, F. Kratochvill, N. Gratz, L.
Kenner, A. Villunger, M.K. Sixt, P. Kovarik, The Journal of Clinical Investigation
127 (2017) 2051–2065.
date_created: 2018-12-11T11:47:53Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2026-04-23T22:30:51Z
day: '01'
department:
- _id: MiSi
doi: 10.1172/JCI80631
external_id:
isi:
- '000402620800008'
pmid:
- '28504646'
intvolume: ' 127'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451238/
month: '06'
oa: 1
oa_version: Submitted Version
page: 2051 - 2065
pmid: 1
project:
- _id: 25985A36-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: T00817-B21
name: The biochemical basis of PAR polarization
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
publication: The Journal of Clinical Investigation
publication_identifier:
issn:
- 0021-9738
publication_status: published
publisher: American Society for Clinical Investigation
publist_id: '7038'
quality_controlled: '1'
related_material:
record:
- id: '12401'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged
neutrophils during bacterial infection
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 127
year: '2017'
...
---
_id: '676'
abstract:
- lang: eng
text: The segregation of different cell types into distinct tissues is a fundamental
process in metazoan development. Differences in cell adhesion and cortex tension
are commonly thought to drive cell sorting by regulating tissue surface tension
(TST). However, the role that differential TST plays in cell segregation within
the developing embryo is as yet unclear. Here, we have analyzed the role of differential
TST for germ layer progenitor cell segregation during zebrafish gastrulation.
Contrary to previous observations that differential TST drives germ layer progenitor
cell segregation in vitro, we show that germ layers display indistinguishable
TST within the gastrulating embryo, arguing against differential TST driving germ
layer progenitor cell segregation in vivo. We further show that the osmolarity
of the interstitial fluid (IF) is an important factor that influences germ layer
TST in vivo, and that lower osmolarity of the IF compared with standard cell culture
medium can explain why germ layers display differential TST in culture but not
in vivo. Finally, we show that directed migration of mesendoderm progenitors is
required for germ layer progenitor cell segregation and germ layer formation.
article_processing_charge: No
article_type: original
author:
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Jim
full_name: Veldhuis, Jim
last_name: Veldhuis
- first_name: Vanessa
full_name: Barone, Vanessa
id: 419EECCC-F248-11E8-B48F-1D18A9856A87
last_name: Barone
orcid: 0000-0003-2676-3367
- first_name: Daniel
full_name: Capek, Daniel
id: 31C42484-F248-11E8-B48F-1D18A9856A87
last_name: Capek
orcid: 0000-0001-5199-9940
- first_name: Jean-Léon
full_name: Maître, Jean-Léon
id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87
last_name: Maître
orcid: 0000-0002-3688-1474
- first_name: Wayne
full_name: Brodland, Wayne
last_name: Brodland
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Krens G, Veldhuis J, Barone V, et al. Interstitial fluid osmolarity modulates
the action of differential tissue surface tension in progenitor cell segregation
during gastrulation. Development. 2017;144(10):1798-1806. doi:10.1242/dev.144964
apa: Krens, G., Veldhuis, J., Barone, V., Capek, D., Maître, J.-L., Brodland, W.,
& Heisenberg, C.-P. J. (2017). Interstitial fluid osmolarity modulates the
action of differential tissue surface tension in progenitor cell segregation during
gastrulation. Development. Company of Biologists. https://doi.org/10.1242/dev.144964
chicago: Krens, Gabriel, Jim Veldhuis, Vanessa Barone, Daniel Capek, Jean-Léon Maître,
Wayne Brodland, and Carl-Philipp J Heisenberg. “Interstitial Fluid Osmolarity
Modulates the Action of Differential Tissue Surface Tension in Progenitor Cell
Segregation during Gastrulation.” Development. Company of Biologists, 2017.
https://doi.org/10.1242/dev.144964.
ieee: G. Krens et al., “Interstitial fluid osmolarity modulates the action
of differential tissue surface tension in progenitor cell segregation during gastrulation,”
Development, vol. 144, no. 10. Company of Biologists, pp. 1798–1806, 2017.
ista: Krens G, Veldhuis J, Barone V, Capek D, Maître J-L, Brodland W, Heisenberg
C-PJ. 2017. Interstitial fluid osmolarity modulates the action of differential
tissue surface tension in progenitor cell segregation during gastrulation. Development.
144(10), 1798–1806.
mla: Krens, Gabriel, et al. “Interstitial Fluid Osmolarity Modulates the Action
of Differential Tissue Surface Tension in Progenitor Cell Segregation during Gastrulation.”
Development, vol. 144, no. 10, Company of Biologists, 2017, pp. 1798–806,
doi:10.1242/dev.144964.
short: G. Krens, J. Veldhuis, V. Barone, D. Capek, J.-L. Maître, W. Brodland, C.-P.J.
Heisenberg, Development 144 (2017) 1798–1806.
corr_author: '1'
date_created: 2018-12-11T11:47:52Z
date_published: 2017-05-15T00:00:00Z
date_updated: 2026-04-23T22:30:55Z
day: '15'
ddc:
- '570'
department:
- _id: Bio
- _id: CaHe
doi: 10.1242/dev.144964
external_id:
isi:
- '000402275900007'
pmid:
- '28512197'
file:
- access_level: open_access
checksum: bc25125fb664706cdf180e061429f91d
content_type: application/pdf
creator: dernst
date_created: 2019-09-24T06:56:22Z
date_updated: 2020-07-14T12:47:39Z
file_id: '6905'
file_name: 2017_Development_Krens.pdf
file_size: 8194516
relation: main_file
file_date_updated: 2020-07-14T12:47:39Z
has_accepted_license: '1'
intvolume: ' 144'
isi: 1
issue: '10'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1798 - 1806
pmid: 1
publication: Development
publication_identifier:
issn:
- 0950-1991
publication_status: published
publisher: Company of Biologists
publist_id: '7047'
quality_controlled: '1'
related_material:
record:
- id: '961'
relation: dissertation_contains
status: public
- id: '50'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Interstitial fluid osmolarity modulates the action of differential tissue surface
tension in progenitor cell segregation during gastrulation
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: 144
year: '2017'
...
---
_id: '661'
abstract:
- lang: eng
text: During embryonic development, mechanical forces are essential for cellular
rearrangements driving tissue morphogenesis. Here, we show that in the early zebrafish
embryo, friction forces are generated at the interface between anterior axial
mesoderm (prechordal plate, ppl) progenitors migrating towards the animal pole
and neurectoderm progenitors moving in the opposite direction towards the vegetal
pole of the embryo. These friction forces lead to global rearrangement of cells
within the neurectoderm and determine the position of the neural anlage. Using
a combination of experiments and simulations, we show that this process depends
on hydrodynamic coupling between neurectoderm and ppl as a result of E-cadherin-mediated
adhesion between those tissues. Our data thus establish the emergence of friction
forces at the interface between moving tissues as a critical force-generating
process shaping the embryo.
acknowledged_ssus:
- _id: SSU
article_processing_charge: No
author:
- first_name: Michael
full_name: Smutny, Michael
id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87
last_name: Smutny
orcid: 0000-0002-5920-9090
- first_name: Zsuzsa
full_name: Ákos, Zsuzsa
last_name: Ákos
- first_name: Silvia
full_name: Grigolon, Silvia
last_name: Grigolon
- first_name: Shayan
full_name: Shamipour, Shayan
id: 40B34FE2-F248-11E8-B48F-1D18A9856A87
last_name: Shamipour
- first_name: Verena
full_name: Ruprecht, Verena
last_name: Ruprecht
- first_name: Daniel
full_name: Capek, Daniel
id: 31C42484-F248-11E8-B48F-1D18A9856A87
last_name: Capek
orcid: 0000-0001-5199-9940
- first_name: Martin
full_name: Behrndt, Martin
id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87
last_name: Behrndt
- first_name: Ekaterina
full_name: Papusheva, Ekaterina
id: 41DB591E-F248-11E8-B48F-1D18A9856A87
last_name: Papusheva
- first_name: Masazumi
full_name: Tada, Masazumi
last_name: Tada
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Tamás
full_name: Vicsek, Tamás
last_name: Vicsek
- first_name: Guillaume
full_name: Salbreux, Guillaume
last_name: Salbreux
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Smutny M, Ákos Z, Grigolon S, et al. Friction forces position the neural anlage.
Nature Cell Biology. 2017;19:306-317. doi:10.1038/ncb3492
apa: Smutny, M., Ákos, Z., Grigolon, S., Shamipour, S., Ruprecht, V., Capek, D.,
… Heisenberg, C.-P. J. (2017). Friction forces position the neural anlage. Nature
Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3492
chicago: Smutny, Michael, Zsuzsa Ákos, Silvia Grigolon, Shayan Shamipour, Verena
Ruprecht, Daniel Capek, Martin Behrndt, et al. “Friction Forces Position the Neural
Anlage.” Nature Cell Biology. Nature Publishing Group, 2017. https://doi.org/10.1038/ncb3492.
ieee: M. Smutny et al., “Friction forces position the neural anlage,” Nature
Cell Biology, vol. 19. Nature Publishing Group, pp. 306–317, 2017.
ista: Smutny M, Ákos Z, Grigolon S, Shamipour S, Ruprecht V, Capek D, Behrndt M,
Papusheva E, Tada M, Hof B, Vicsek T, Salbreux G, Heisenberg C-PJ. 2017. Friction
forces position the neural anlage. Nature Cell Biology. 19, 306–317.
mla: Smutny, Michael, et al. “Friction Forces Position the Neural Anlage.” Nature
Cell Biology, vol. 19, Nature Publishing Group, 2017, pp. 306–17, doi:10.1038/ncb3492.
short: M. Smutny, Z. Ákos, S. Grigolon, S. Shamipour, V. Ruprecht, D. Capek, M.
Behrndt, E. Papusheva, M. Tada, B. Hof, T. Vicsek, G. Salbreux, C.-P.J. Heisenberg,
Nature Cell Biology 19 (2017) 306–317.
corr_author: '1'
date_created: 2018-12-11T11:47:46Z
date_published: 2017-03-27T00:00:00Z
date_updated: 2026-04-23T22:30:55Z
day: '27'
department:
- _id: CaHe
- _id: BjHo
- _id: Bio
doi: 10.1038/ncb3492
ec_funded: 1
external_id:
isi:
- '000397917000009'
pmid:
- '28346437'
intvolume: ' 19'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://europepmc.org/articles/pmc5635970
month: '03'
oa: 1
oa_version: Submitted Version
page: 306 - 317
pmid: 1
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
- _id: 252ABD0A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I930-B20
name: Control of Epithelial Cell Layer Spreading in Zebrafish
publication: Nature Cell Biology
publication_identifier:
issn:
- 1465-7392
publication_status: published
publisher: Nature Publishing Group
publist_id: '7074'
quality_controlled: '1'
related_material:
record:
- id: '8350'
relation: dissertation_contains
status: public
- id: '50'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Friction forces position the neural anlage
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 19
year: '2017'
...
---
_id: '639'
abstract:
- lang: eng
text: We study the problem of developing efficient approaches for proving worst-case
bounds of non-deterministic recursive programs. Ranking functions are sound and
complete for proving termination and worst-case bounds of non-recursive programs.
First, we apply ranking functions to recursion, resulting in measure functions,
and show that they provide a sound and complete approach to prove worst-case bounds
of non-deterministic recursive programs. Our second contribution is the synthesis
of measure functions in non-polynomial forms. We show that non-polynomial measure
functions with logarithm and exponentiation can be synthesized through abstraction
of logarithmic or exponentiation terms, Farkas’ Lemma, and Handelman’s Theorem
using linear programming. While previous methods obtain worst-case polynomial
bounds, our approach can synthesize bounds of the form O(n log n) as well as O(nr)
where r is not an integer. We present experimental results to demonstrate that
our approach can efficiently obtain worst-case bounds of classical recursive algorithms
such as Merge-Sort, Closest-Pair, Karatsuba’s algorithm and Strassen’s algorithm.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Hongfei
full_name: Fu, Hongfei
last_name: Fu
- first_name: Amir
full_name: Goharshady, Amir
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
citation:
ama: 'Chatterjee K, Fu H, Goharshady AK. Non-polynomial worst case analysis of recursive
programs. In: Majumdar R, Kunčak V, eds. Vol 10427. Springer; 2017:41-63. doi:10.1007/978-3-319-63390-9_3'
apa: 'Chatterjee, K., Fu, H., & Goharshady, A. K. (2017). Non-polynomial worst
case analysis of recursive programs. In R. Majumdar & V. Kunčak (Eds.) (Vol.
10427, pp. 41–63). Presented at the CAV: Computer Aided Verification, Heidelberg,
Germany: Springer. https://doi.org/10.1007/978-3-319-63390-9_3'
chicago: Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Non-Polynomial
Worst Case Analysis of Recursive Programs.” edited by Rupak Majumdar and Viktor
Kunčak, 10427:41–63. Springer, 2017. https://doi.org/10.1007/978-3-319-63390-9_3.
ieee: 'K. Chatterjee, H. Fu, and A. K. Goharshady, “Non-polynomial worst case analysis
of recursive programs,” presented at the CAV: Computer Aided Verification, Heidelberg,
Germany, 2017, vol. 10427, pp. 41–63.'
ista: 'Chatterjee K, Fu H, Goharshady AK. 2017. Non-polynomial worst case analysis
of recursive programs. CAV: Computer Aided Verification, LNCS, vol. 10427, 41–63.'
mla: Chatterjee, Krishnendu, et al. Non-Polynomial Worst Case Analysis of Recursive
Programs. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10427, Springer,
2017, pp. 41–63, doi:10.1007/978-3-319-63390-9_3.
short: K. Chatterjee, H. Fu, A.K. Goharshady, in:, R. Majumdar, V. Kunčak (Eds.),
Springer, 2017, pp. 41–63.
conference:
end_date: 2017-07-28
location: Heidelberg, Germany
name: 'CAV: Computer Aided Verification'
start_date: 2017-07-24
date_created: 2018-12-11T11:47:39Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2026-04-23T22:30:58Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-319-63390-9_3
ec_funded: 1
editor:
- first_name: Rupak
full_name: Majumdar, Rupak
last_name: Majumdar
- first_name: Viktor
full_name: Kunčak, Viktor
last_name: Kunčak
external_id:
arxiv:
- '1705.00317'
isi:
- '000431900900003'
intvolume: ' 10427'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.00317
month: '01'
oa: 1
oa_version: Submitted Version
page: 41 - 63
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_identifier:
isbn:
- 978-331963389-3
publication_status: published
publisher: Springer
publist_id: '7149'
quality_controlled: '1'
related_material:
record:
- id: '7014'
relation: later_version
status: public
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Non-polynomial worst case analysis of recursive programs
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 10427
year: '2017'
...
---
_id: '949'
abstract:
- lang: eng
text: The notion of treewidth of graphs has been exploited for faster algorithms
for several problems arising in verification and program analysis. Moreover, various
notions of balanced tree decompositions have been used for improved algorithms
supporting dynamic updates and analysis of concurrent programs. In this work,
we present a tool for constructing tree-decompositions of CFGs obtained from Java
methods, which is implemented as an extension to the widely used Soot framework.
The experimental results show that our implementation on real-world Java benchmarks
is very efficient. Our tool also provides the first implementation for balancing
tree-decompositions. In summary, we present the first tool support for exploiting
treewidth in the static analysis problems on Java programs.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir
full_name: Goharshady, Amir
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: 'Chatterjee K, Goharshady AK, Pavlogiannis A. JTDec: A tool for tree decompositions
in soot. In: D’Souza D, ed. Vol 10482. Springer; 2017:59-66. doi:10.1007/978-3-319-68167-2_4'
apa: 'Chatterjee, K., Goharshady, A. K., & Pavlogiannis, A. (2017). JTDec: A
tool for tree decompositions in soot. In D. D’Souza (Ed.) (Vol. 10482, pp. 59–66).
Presented at the ATVA: Automated Technology for Verification and Analysis, Pune,
India: Springer. https://doi.org/10.1007/978-3-319-68167-2_4'
chicago: 'Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Andreas Pavlogiannis.
“JTDec: A Tool for Tree Decompositions in Soot.” edited by Deepak D’Souza, 10482:59–66.
Springer, 2017. https://doi.org/10.1007/978-3-319-68167-2_4.'
ieee: 'K. Chatterjee, A. K. Goharshady, and A. Pavlogiannis, “JTDec: A tool for
tree decompositions in soot,” presented at the ATVA: Automated Technology for
Verification and Analysis, Pune, India, 2017, vol. 10482, pp. 59–66.'
ista: 'Chatterjee K, Goharshady AK, Pavlogiannis A. 2017. JTDec: A tool for tree
decompositions in soot. ATVA: Automated Technology for Verification and Analysis,
LNCS, vol. 10482, 59–66.'
mla: 'Chatterjee, Krishnendu, et al. JTDec: A Tool for Tree Decompositions in
Soot. Edited by Deepak D’Souza, vol. 10482, Springer, 2017, pp. 59–66, doi:10.1007/978-3-319-68167-2_4.'
short: K. Chatterjee, A.K. Goharshady, A. Pavlogiannis, in:, D. D’Souza (Ed.), Springer,
2017, pp. 59–66.
conference:
end_date: 2017-10-06
location: Pune, India
name: 'ATVA: Automated Technology for Verification and Analysis'
start_date: 2017-10-03
corr_author: '1'
date_created: 2018-12-11T11:49:22Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2026-04-23T22:30:58Z
day: '01'
ddc:
- '005'
department:
- _id: KrCh
doi: 10.1007/978-3-319-68167-2_4
ec_funded: 1
editor:
- first_name: Deepak
full_name: D'Souza, Deepak
last_name: D'Souza
external_id:
isi:
- '000723567800004'
file:
- access_level: open_access
checksum: a0d9f5f94dc594c4e71e78525c9942f1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:45Z
date_updated: 2020-07-14T12:48:16Z
file_id: '4835'
file_name: IST-2017-845-v1+1_2017_Chatterjee_JTDec.pdf
file_size: 948514
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
has_accepted_license: '1'
intvolume: ' 10482'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 59 - 66
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_identifier:
issn:
- 0302-9743
publication_status: published
publisher: Springer
publist_id: '6468'
pubrep_id: '845'
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'JTDec: A tool for tree decompositions in soot'
type: conference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 10482
year: '2017'
...
---
_id: '1145'
abstract:
- lang: eng
text: Auxin directs plant ontogenesis via differential accumulation within tissues
depending largely on the activity of PIN proteins that mediate auxin efflux from
cells and its directional cell-to-cell transport. Regardless of the developmental
importance of PINs, the structure of these transporters is poorly characterized.
Here, we present experimental data concerning protein topology of plasma membrane-localized
PINs. Utilizing approaches based on pH-dependent quenching of fluorescent reporters
combined with immunolocalization techniques, we mapped the membrane topology of
PINs and further cross-validated our results using available topology modeling
software. We delineated the topology of PIN1 with two transmembrane (TM) bundles
of five α-helices linked by a large intracellular loop and a C-terminus positioned
outside the cytoplasm. Using constraints derived from our experimental data, we
also provide an updated position of helical regions generating a verisimilitude
model of PIN1. Since the canonical long PINs show a high degree of conservation
in TM domains and auxin transport capacity has been demonstrated for Arabidopsis
representatives of this group, this empirically enhanced topological model of
PIN1 will be an important starting point for further studies on PIN structure–function
relationships. In addition, we have established protocols that can be used to
probe the topology of other plasma membrane proteins in plants. © 2016 The Authors
acknowledgement: This research has been financially supported by the Ministry of Education,
Youth and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) (T.N.,
M.Z., M.P., J.H.), Czech Science Foundation (13-40637S [J.F., M.Z.], 13-39982S [J.H.]);
Research Foundation Flanders (Grant number FWO09/PDO/196) (S.V.) and the European
Research Council (project ERC-2011-StG-20101109-PSDP) (J.F.). We thank David G.
Robinson and Ranjan Swarup for sharing published material; Maria Šimášková, Mamoona
Khan, Eva Benková for technical assistance; and R. Tejos, J. Kleine-Vehn, and E.
Feraru for helpful discussions.
article_processing_charge: No
author:
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Marta
full_name: Zwiewka, Marta
last_name: Zwiewka
- first_name: Markéta
full_name: Pernisová, Markéta
last_name: Pernisová
- first_name: Jan
full_name: Hejátko, Jan
last_name: Hejátko
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. Enquiry
into the topology of plasma membrane localized PIN auxin transport components.
Molecular Plant. 2016;9(11):1504-1519. doi:10.1016/j.molp.2016.08.010
apa: Nodzyński, T., Vanneste, S., Zwiewka, M., Pernisová, M., Hejátko, J., &
Friml, J. (2016). Enquiry into the topology of plasma membrane localized PIN auxin
transport components. Molecular Plant. Cell Press. https://doi.org/10.1016/j.molp.2016.08.010
chicago: Nodzyński, Tomasz, Steffen Vanneste, Marta Zwiewka, Markéta Pernisová,
Jan Hejátko, and Jiří Friml. “Enquiry into the Topology of Plasma Membrane Localized
PIN Auxin Transport Components.” Molecular Plant. Cell Press, 2016. https://doi.org/10.1016/j.molp.2016.08.010.
ieee: T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, and J. Friml,
“Enquiry into the topology of plasma membrane localized PIN auxin transport components,”
Molecular Plant, vol. 9, no. 11. Cell Press, pp. 1504–1519, 2016.
ista: Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. 2016.
Enquiry into the topology of plasma membrane localized PIN auxin transport components.
Molecular Plant. 9(11), 1504–1519.
mla: Nodzyński, Tomasz, et al. “Enquiry into the Topology of Plasma Membrane Localized
PIN Auxin Transport Components.” Molecular Plant, vol. 9, no. 11, Cell
Press, 2016, pp. 1504–19, doi:10.1016/j.molp.2016.08.010.
short: T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, J. Friml,
Molecular Plant 9 (2016) 1504–1519.
date_created: 2018-12-11T11:50:23Z
date_published: 2016-11-07T00:00:00Z
date_updated: 2025-09-22T14:08:07Z
day: '07'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1016/j.molp.2016.08.010
ec_funded: 1
external_id:
isi:
- '000389594100008'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:22Z
date_updated: 2018-12-12T10:13:22Z
file_id: '5004'
file_name: IST-2017-746-v1+1_1-s2.0-S1674205216301915-main.pdf
file_size: 5005876
relation: main_file
file_date_updated: 2018-12-12T10:13:22Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1504 - 1519
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Molecular Plant
publication_status: published
publisher: Cell Press
publist_id: '6213'
pubrep_id: '746'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Enquiry into the topology of plasma membrane localized PIN auxin transport
components
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 9
year: '2016'
...
---
_id: '1147'
abstract:
- lang: eng
text: Apical dominance is one of the fundamental developmental phenomena in plant
biology, which determines the overall architecture of aerial plant parts. Here
we show apex decapitation activated competition for dominance in adjacent upper
and lower axillary buds. A two-nodal-bud pea (Pisum sativum L.) was used as a
model system to monitor and assess auxin flow, auxin transport channels, and dormancy
and initiation status of axillary buds. Auxin flow was manipulated by lateral
stem wounds or chemically by auxin efflux inhibitors 2,3,5-triiodobenzoic acid
(TIBA), 1-N-naphtylphtalamic acid (NPA), or protein synthesis inhibitor cycloheximide
(CHX) treatments, which served to interfere with axillary bud competition. Redirecting
auxin flow to different points influenced which bud formed the outgrowing and
dominant shoot. The obtained results proved that competition between upper and
lower axillary buds as secondary auxin sources is based on the same auxin canalization
principle that operates between the shoot apex and axillary bud. © The Author(s)
2016.
acknowledgement: This research was carried out under the project CEITEC 2020 (LQ1601)
with financial support from the Ministry of Education, Youth and Sports of the Czech
Republic under the National Sustainability Programme II., supported by the project
“CEITEC–Central European Institute of Technology” (CZ.1.05/1.1.00/02.0068) and the
Agronomy faculty grant from Mendel University “IGA AF MENDELU” (IP 14/2013).
article_number: '35955'
article_processing_charge: No
author:
- first_name: Jozef
full_name: Balla, Jozef
last_name: Balla
- first_name: Zuzana
full_name: Medved'Ová, Zuzana
last_name: Medved'Ová
- first_name: Petr
full_name: Kalousek, Petr
last_name: Kalousek
- first_name: Natálie
full_name: Matiješčuková, Natálie
last_name: Matiješčuková
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Vilém
full_name: Reinöhl, Vilém
last_name: Reinöhl
- first_name: Stanislav
full_name: Procházka, Stanislav
last_name: Procházka
citation:
ama: Balla J, Medved’Ová Z, Kalousek P, et al. Auxin flow mediated competition between
axillary buds to restore apical dominance. Scientific Reports. 2016;6.
doi:10.1038/srep35955
apa: Balla, J., Medved’Ová, Z., Kalousek, P., Matiješčuková, N., Friml, J., Reinöhl,
V., & Procházka, S. (2016). Auxin flow mediated competition between axillary
buds to restore apical dominance. Scientific Reports. Nature Publishing
Group. https://doi.org/10.1038/srep35955
chicago: Balla, Jozef, Zuzana Medved’Ová, Petr Kalousek, Natálie Matiješčuková,
Jiří Friml, Vilém Reinöhl, and Stanislav Procházka. “Auxin Flow Mediated Competition
between Axillary Buds to Restore Apical Dominance.” Scientific Reports.
Nature Publishing Group, 2016. https://doi.org/10.1038/srep35955.
ieee: J. Balla et al., “Auxin flow mediated competition between axillary
buds to restore apical dominance,” Scientific Reports, vol. 6. Nature Publishing
Group, 2016.
ista: Balla J, Medved’Ová Z, Kalousek P, Matiješčuková N, Friml J, Reinöhl V, Procházka
S. 2016. Auxin flow mediated competition between axillary buds to restore apical
dominance. Scientific Reports. 6, 35955.
mla: Balla, Jozef, et al. “Auxin Flow Mediated Competition between Axillary Buds
to Restore Apical Dominance.” Scientific Reports, vol. 6, 35955, Nature
Publishing Group, 2016, doi:10.1038/srep35955.
short: J. Balla, Z. Medved’Ová, P. Kalousek, N. Matiješčuková, J. Friml, V. Reinöhl,
S. Procházka, Scientific Reports 6 (2016).
date_created: 2018-12-11T11:50:24Z
date_published: 2016-11-08T00:00:00Z
date_updated: 2025-09-22T09:59:19Z
day: '08'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1038/srep35955
external_id:
isi:
- '000387284700001'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:28Z
date_updated: 2018-12-12T10:09:28Z
file_id: '4752'
file_name: IST-2017-745-v1+1_srep35955.pdf
file_size: 1587544
relation: main_file
file_date_updated: 2018-12-12T10:09:28Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6211'
pubrep_id: '745'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Auxin flow mediated competition between axillary buds to restore apical dominance
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 6
year: '2016'
...
---
_id: '1148'
abstract:
- lang: eng
text: Continuous-time Markov chain (CTMC) models have become a central tool for
understanding the dynamics of complex reaction networks and the importance of
stochasticity in the underlying biochemical processes. When such models are employed
to answer questions in applications, in order to ensure that the model provides
a sufficiently accurate representation of the real system, it is of vital importance
that the model parameters are inferred from real measured data. This, however,
is often a formidable task and all of the existing methods fail in one case or
the other, usually because the underlying CTMC model is high-dimensional and computationally
difficult to analyze. The parameter inference methods that tend to scale best
in the dimension of the CTMC are based on so-called moment closure approximations.
However, there exists a large number of different moment closure approximations
and it is typically hard to say a priori which of the approximations is the most
suitable for the inference procedure. Here, we propose a moment-based parameter
inference method that automatically chooses the most appropriate moment closure
method. Accordingly, contrary to existing methods, the user is not required to
be experienced in moment closure techniques. In addition to that, our method adaptively
changes the approximation during the parameter inference to ensure that always
the best approximation is used, even in cases where different approximations are
best in different regions of the parameter space. © 2016 Elsevier Ireland Ltd
acknowledgement: This work is based on the CMSB 2015 paper “Adaptive moment closure
for parameter inference of biochemical reaction networks” (Bogomolov et al., 2015).
The work was partly supported by the German Research Foundation (DFG) as part of
the Transregional Collaborative Research Center “Automatic Verification and Analysis
of Complex Systems” (SFB/TR 14 AVACS1), by the European Research Council (ERC) under
grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23
(RiSE) and Z211-N23 (Wittgenstein Award). J.R. acknowledges support from the People
Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme
(FP7/2007-2013) under REA grant agreement no. 291734.
article_processing_charge: No
author:
- first_name: Christian
full_name: Schilling, Christian
last_name: Schilling
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Andreas
full_name: Podelski, Andreas
last_name: Podelski
- first_name: Jakob
full_name: Ruess, Jakob
id: 4A245D00-F248-11E8-B48F-1D18A9856A87
last_name: Ruess
orcid: 0000-0003-1615-3282
citation:
ama: Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. Adaptive moment
closure for parameter inference of biochemical reaction networks. Biosystems.
2016;149:15-25. doi:10.1016/j.biosystems.2016.07.005
apa: Schilling, C., Bogomolov, S., Henzinger, T. A., Podelski, A., & Ruess,
J. (2016). Adaptive moment closure for parameter inference of biochemical reaction
networks. Biosystems. Elsevier. https://doi.org/10.1016/j.biosystems.2016.07.005
chicago: Schilling, Christian, Sergiy Bogomolov, Thomas A Henzinger, Andreas Podelski,
and Jakob Ruess. “Adaptive Moment Closure for Parameter Inference of Biochemical
Reaction Networks.” Biosystems. Elsevier, 2016. https://doi.org/10.1016/j.biosystems.2016.07.005.
ieee: C. Schilling, S. Bogomolov, T. A. Henzinger, A. Podelski, and J. Ruess, “Adaptive
moment closure for parameter inference of biochemical reaction networks,” Biosystems,
vol. 149. Elsevier, pp. 15–25, 2016.
ista: Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. 2016. Adaptive
moment closure for parameter inference of biochemical reaction networks. Biosystems.
149, 15–25.
mla: Schilling, Christian, et al. “Adaptive Moment Closure for Parameter Inference
of Biochemical Reaction Networks.” Biosystems, vol. 149, Elsevier, 2016,
pp. 15–25, doi:10.1016/j.biosystems.2016.07.005.
short: C. Schilling, S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, Biosystems
149 (2016) 15–25.
date_created: 2018-12-11T11:50:24Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2025-09-23T07:44:57Z
day: '01'
department:
- _id: ToHe
- _id: GaTk
doi: 10.1016/j.biosystems.2016.07.005
ec_funded: 1
external_id:
isi:
- '000390743600003'
intvolume: ' 149'
isi: 1
language:
- iso: eng
month: '11'
oa_version: None
page: 15 - 25
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Biosystems
publication_status: published
publisher: Elsevier
publist_id: '6210'
quality_controlled: '1'
related_material:
record:
- id: '1658'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Adaptive moment closure for parameter inference of biochemical reaction networks
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 149
year: '2016'
...
---
_id: '1149'
abstract:
- lang: eng
text: 'We study the usefulness of two most prominent publicly available rigorous
ODE integrators: one provided by the CAPD group (capd.ii.uj.edu.pl), the other
based on the COSY Infinity project (cosyinfinity.org). Both integrators are capable
of handling entire sets of initial conditions and provide tight rigorous outer
enclosures of the images under a time-T map. We conduct extensive benchmark computations
using the well-known Lorenz system, and compare the computation time against the
final accuracy achieved. We also discuss the effect of a few technical parameters,
such as the order of the numerical integration method, the value of T, and the
phase space resolution. We conclude that COSY may provide more precise results
due to its ability of avoiding the variable dependency problem. However, the overall
cost of computations conducted using CAPD is typically lower, especially when
intervals of parameters are involved. Moreover, access to COSY is limited (registration
required) and the rigorous ODE integrators are not publicly available, while CAPD
is an open source free software project. Therefore, we recommend the latter integrator
for this kind of computations. Nevertheless, proper choice of the various integration
parameters turns out to be of even greater importance than the choice of the integrator
itself. © 2016 IMACS. Published by Elsevier B.V. All rights reserved.'
acknowledgement: "MG was partially supported by FAPESP grants 2013/07460-7 and 2010/00875-9,
and by CNPq grants 305860/2013-5 and 306453/2009-6, Brazil. The work of HK was partially
supported by Grant-in-Aid for Scientific Research (Nos.24654022, 25287029), Ministry
of Education, Science, Technology, Culture and Sports, Japan. KM was supported by
NSF grants NSF-DMS-0835621, 0915019, 1125174, 1248071, and contracts from AFOSR
and DARPA. TM was supported by Grant-in-Aid for JSPS Fellows No. 245312. A part
of the research of TM and HK was also supported by JST, CREST.\r\n\r\nResearch conducted
by PP has received funding from Fundo Europeu de Desenvolvimento Regional (FEDER)
through COMPETE – Programa Operacional Factores de Competitividade (POFC) and from
the Portuguese national funds through Fundação para a Ciência e a Tecnologia (FCT)
in the framework of the research project FCOMP-01-0124-FEDER-010645 (Ref. FCT PTDC/MAT/098871/2008);
from the People Programme (Marie Curie Actions) of the European Union's Seventh
Framework Programme (FP7/2007-2013) under REA grant agreement No. 622033; and from
the same sources as HK.\r\n\r\nThe authors express their gratitude to the Department
of Mathematics of Kyoto University for making their server available for conducting
the computations described in the paper, and to the reviewers for helpful comments
that contributed towards increasing the quality of the paper."
article_processing_charge: No
author:
- first_name: Tomoyuki
full_name: Miyaji, Tomoyuki
last_name: Miyaji
- first_name: Pawel
full_name: Pilarczyk, Pawel
id: 3768D56A-F248-11E8-B48F-1D18A9856A87
last_name: Pilarczyk
- first_name: Marcio
full_name: Gameiro, Marcio
last_name: Gameiro
- first_name: Hiroshi
full_name: Kokubu, Hiroshi
last_name: Kokubu
- first_name: Konstantin
full_name: Mischaikow, Konstantin
last_name: Mischaikow
citation:
ama: Miyaji T, Pilarczyk P, Gameiro M, Kokubu H, Mischaikow K. A study of rigorous
ODE integrators for multi scale set oriented computations. Applied Numerical
Mathematics. 2016;107:34-47. doi:10.1016/j.apnum.2016.04.005
apa: Miyaji, T., Pilarczyk, P., Gameiro, M., Kokubu, H., & Mischaikow, K. (2016).
A study of rigorous ODE integrators for multi scale set oriented computations.
Applied Numerical Mathematics. Elsevier. https://doi.org/10.1016/j.apnum.2016.04.005
chicago: Miyaji, Tomoyuki, Pawel Pilarczyk, Marcio Gameiro, Hiroshi Kokubu, and
Konstantin Mischaikow. “A Study of Rigorous ODE Integrators for Multi Scale Set
Oriented Computations.” Applied Numerical Mathematics. Elsevier, 2016.
https://doi.org/10.1016/j.apnum.2016.04.005.
ieee: T. Miyaji, P. Pilarczyk, M. Gameiro, H. Kokubu, and K. Mischaikow, “A study
of rigorous ODE integrators for multi scale set oriented computations,” Applied
Numerical Mathematics, vol. 107. Elsevier, pp. 34–47, 2016.
ista: Miyaji T, Pilarczyk P, Gameiro M, Kokubu H, Mischaikow K. 2016. A study of
rigorous ODE integrators for multi scale set oriented computations. Applied Numerical
Mathematics. 107, 34–47.
mla: Miyaji, Tomoyuki, et al. “A Study of Rigorous ODE Integrators for Multi Scale
Set Oriented Computations.” Applied Numerical Mathematics, vol. 107, Elsevier,
2016, pp. 34–47, doi:10.1016/j.apnum.2016.04.005.
short: T. Miyaji, P. Pilarczyk, M. Gameiro, H. Kokubu, K. Mischaikow, Applied Numerical
Mathematics 107 (2016) 34–47.
date_created: 2018-12-11T11:50:25Z
date_published: 2016-09-01T00:00:00Z
date_updated: 2025-09-22T09:58:16Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.apnum.2016.04.005
ec_funded: 1
external_id:
isi:
- '000378447000003'
intvolume: ' 107'
isi: 1
language:
- iso: eng
month: '09'
oa_version: None
page: 34 - 47
project:
- _id: 255F06BE-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '622033'
name: Persistent Homology - Images, Data and Maps
publication: Applied Numerical Mathematics
publication_status: published
publisher: Elsevier
publist_id: '6209'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A study of rigorous ODE integrators for multi scale set oriented computations
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 107
year: '2016'
...
---
_id: '1150'
abstract:
- lang: eng
text: When neutrophils infiltrate a site of inflammation, they have to stop at the
right place to exert their effector function. In this issue of Developmental Cell,
Wang et al. (2016) show that neutrophils sense reactive oxygen species via the
TRPM2 channel to arrest migration at their target site. © 2016 Elsevier Inc.
article_processing_charge: No
author:
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Renkawitz J, Sixt MK. A Radical Break Restraining Neutrophil Migration. Developmental
Cell. 2016;38(5):448-450. doi:10.1016/j.devcel.2016.08.017
apa: Renkawitz, J., & Sixt, M. K. (2016). A Radical Break Restraining Neutrophil
Migration. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2016.08.017
chicago: Renkawitz, Jörg, and Michael K Sixt. “A Radical Break Restraining Neutrophil
Migration.” Developmental Cell. Cell Press, 2016. https://doi.org/10.1016/j.devcel.2016.08.017.
ieee: J. Renkawitz and M. K. Sixt, “A Radical Break Restraining Neutrophil Migration,”
Developmental Cell, vol. 38, no. 5. Cell Press, pp. 448–450, 2016.
ista: Renkawitz J, Sixt MK. 2016. A Radical Break Restraining Neutrophil Migration.
Developmental Cell. 38(5), 448–450.
mla: Renkawitz, Jörg, and Michael K. Sixt. “A Radical Break Restraining Neutrophil
Migration.” Developmental Cell, vol. 38, no. 5, Cell Press, 2016, pp. 448–50,
doi:10.1016/j.devcel.2016.08.017.
short: J. Renkawitz, M.K. Sixt, Developmental Cell 38 (2016) 448–450.
date_created: 2018-12-11T11:50:25Z
date_published: 2016-09-12T00:00:00Z
date_updated: 2025-09-22T09:57:46Z
day: '12'
department:
- _id: MiSi
doi: 10.1016/j.devcel.2016.08.017
external_id:
isi:
- '000383413000003'
intvolume: ' 38'
isi: 1
issue: '5'
language:
- iso: eng
month: '09'
oa_version: None
page: 448 - 450
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '6208'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A Radical Break Restraining Neutrophil Migration
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 38
year: '2016'
...
---
_id: '1151'
abstract:
- lang: eng
text: Tissue patterning in multicellular organisms is the output of precise spatio–temporal
regulation of gene expression coupled with changes in hormone dynamics. In plants,
the hormone auxin regulates growth and development at every stage of a plant’s
life cycle. Auxin signaling occurs through binding of the auxin molecule to a
TIR1/AFB F-box ubiquitin ligase, allowing interaction with Aux/IAA transcriptional
repressor proteins. These are subsequently ubiquitinated and degraded via the
26S proteasome, leading to derepression of auxin response factors (ARFs). How
auxin is able to elicit such a diverse range of developmental responses through
a single signaling module has not yet been resolved. Here we present an alternative
auxin-sensing mechanism in which the ARF ARF3/ETTIN controls gene expression through
interactions with process-specific transcription factors. This noncanonical hormonesensing
mechanism exhibits strong preference for the naturally occurring auxin indole
3-acetic acid (IAA) and is important for coordinating growth and patterning in
diverse developmental contexts such as gynoecium morphogenesis, lateral root emergence,
ovule development, and primary branch formation. Disrupting this IAA-sensing ability
induces morphological aberrations with consequences for plant fitness. Therefore,
our findings introduce a novel transcription factor-based mechanism of hormone
perception in plants. © 2016 Simonini et al.
acknowledgement: "We thank Norwich Research Park Bioimaging, Grant Calder, Roy\r\nDunford,
Caroline Smith, Paul Thomas, and Mark Youles for\r\ntechnical support; Charlie Scutt,
Alejandro Ferrando, and George\r\nLomonossoff for plasmids; Toshiro Ito for seeds;
Brendan Davies\r\nand Barry Causier for the REGIA library; and Mark Buttner,\r\nSimona
Masiero, Fabio Rossi, Doris Wagner, and Jun Xiao for\r\nhelp and material. We are
also grateful to Stefano Bencivenga,\r\nMarie Brüser, Friederike Jantzen, Lukasz
Langowski, Xinran Li,\r\nand Nicola Stacey for discussions and helpful comments
on the\r\nmanuscript. This work was supported by grants BB/M004112/1\r\nand BB/I017232/1
(Crop Improvement Research Club) to L.Ø.\r\nfrom the Biotechnological and Biological
Sciences Research\r\nCouncil, and Institute Strategic Programme grant (BB/J004553/\r\n1)
to the John Innes Centre. S.S., J.D., and L.Ø conceived the ex-\r\nperiments. "
article_processing_charge: No
author:
- first_name: Sara
full_name: Simonini, Sara
last_name: Simonini
- first_name: Joyita
full_name: Deb, Joyita
last_name: Deb
- first_name: Laila
full_name: Moubayidin, Laila
last_name: Moubayidin
- first_name: Pauline
full_name: Stephenson, Pauline
last_name: Stephenson
- first_name: Manoj
full_name: Valluru, Manoj
last_name: Valluru
- first_name: Alejandra
full_name: Freire Rios, Alejandra
last_name: Freire Rios
- first_name: Karim
full_name: Sorefan, Karim
last_name: Sorefan
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Lars
full_name: Östergaard, Lars
last_name: Östergaard
citation:
ama: Simonini S, Deb J, Moubayidin L, et al. A noncanonical auxin sensing mechanism
is required for organ morphogenesis in arabidopsis. Genes and Development.
2016;30(20):2286-2296. doi:10.1101/gad.285361.116
apa: Simonini, S., Deb, J., Moubayidin, L., Stephenson, P., Valluru, M., Freire
Rios, A., … Östergaard, L. (2016). A noncanonical auxin sensing mechanism is required
for organ morphogenesis in arabidopsis. Genes and Development. Cold Spring
Harbor Laboratory Press. https://doi.org/10.1101/gad.285361.116
chicago: Simonini, Sara, Joyita Deb, Laila Moubayidin, Pauline Stephenson, Manoj
Valluru, Alejandra Freire Rios, Karim Sorefan, Dolf Weijers, Jiří Friml, and Lars
Östergaard. “A Noncanonical Auxin Sensing Mechanism Is Required for Organ Morphogenesis
in Arabidopsis.” Genes and Development. Cold Spring Harbor Laboratory Press,
2016. https://doi.org/10.1101/gad.285361.116.
ieee: S. Simonini et al., “A noncanonical auxin sensing mechanism is required
for organ morphogenesis in arabidopsis,” Genes and Development, vol. 30,
no. 20. Cold Spring Harbor Laboratory Press, pp. 2286–2296, 2016.
ista: Simonini S, Deb J, Moubayidin L, Stephenson P, Valluru M, Freire Rios A, Sorefan
K, Weijers D, Friml J, Östergaard L. 2016. A noncanonical auxin sensing mechanism
is required for organ morphogenesis in arabidopsis. Genes and Development. 30(20),
2286–2296.
mla: Simonini, Sara, et al. “A Noncanonical Auxin Sensing Mechanism Is Required
for Organ Morphogenesis in Arabidopsis.” Genes and Development, vol. 30,
no. 20, Cold Spring Harbor Laboratory Press, 2016, pp. 2286–96, doi:10.1101/gad.285361.116.
short: S. Simonini, J. Deb, L. Moubayidin, P. Stephenson, M. Valluru, A. Freire
Rios, K. Sorefan, D. Weijers, J. Friml, L. Östergaard, Genes and Development 30
(2016) 2286–2296.
date_created: 2018-12-11T11:50:25Z
date_published: 2016-10-15T00:00:00Z
date_updated: 2025-09-22T09:57:16Z
day: '15'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1101/gad.285361.116
external_id:
isi:
- '000387814000005'
pmid:
- '27898393'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-01-25T09:32:55Z
date_updated: 2019-01-25T09:32:55Z
file_id: '5882'
file_name: 2016_GeneDev_Simonini.pdf
file_size: 1419263
relation: main_file
success: 1
file_date_updated: 2019-01-25T09:32:55Z
has_accepted_license: '1'
intvolume: ' 30'
isi: 1
issue: '20'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 2286 - 2296
pmid: 1
publication: Genes and Development
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '6207'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A noncanonical auxin sensing mechanism is required for organ morphogenesis
in arabidopsis
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 30
year: '2016'
...
---
_id: '1153'
abstract:
- lang: eng
text: Differential cell growth enables flexible organ bending in the presence of
environmental signals such as light or gravity. A prominent example of the developmental
processes based on differential cell growth is the formation of the apical hook
that protects the fragile shoot apical meristem when it breaks through the soil
during germination. Here, we combined in silico and in vivo approaches to identify
a minimal mechanism producing auxin gradient-guided differential growth during
the establishment of the apical hook in the model plant Arabidopsis thaliana.
Computer simulation models based on experimental data demonstrate that asymmetric
expression of the PIN-FORMED auxin efflux carrier at the concave (inner) versus
convex (outer) side of the hook suffices to establish an auxin maximum in the
epidermis at the concave side of the apical hook. Furthermore, we propose a mechanism
that translates this maximum into differential growth, and thus curvature, of
the apical hook. Through a combination of experimental and in silico computational
approaches, we have identified the individual contributions of differential cell
elongation and proliferation to defining the apical hook and reveal the role of
auxin-ethylene crosstalk in balancing these two processes. © 2016 American Society
of Plant Biologists. All rights reserved.
acknowledgement: "We thank Martine De Cock and Annick Bleys for help in preparing
the manuscript, Daniel Van Damme for sharing material and stimulating discussion,
and Rudiger Simon for support during revision of the manuscript.\r\nThis work was
supported by grants from the European Research Council (StartingIndependentResearchGrantERC-2007-Stg-207362-HCPO)and
the Czech Science Foundation (GACR CZ.1.07/2.3.00/20.0043) to E.B.\r\nand Natural
Sciences and Engineering Research Council of Canada Discovery Grant 2014-05325 to
P.P. K.W. acknowledges funding from a Human Frontier Science Program Long-Term Fellowship
(LT-000209-2014)."
article_processing_charge: No
author:
- first_name: Petra
full_name: Žádníková, Petra
last_name: Žádníková
- 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: Anas
full_name: Abuzeineh, Anas
last_name: Abuzeineh
- first_name: Marçal
full_name: Gallemí, Marçal
last_name: Gallemí
- first_name: Dominique
full_name: Van Der Straeten, Dominique
last_name: Van Der Straeten
- first_name: Richard
full_name: Smith, Richard
last_name: Smith
- first_name: Dirk
full_name: Inze, Dirk
last_name: Inze
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Przemysław
full_name: Prusinkiewicz, Przemysław
last_name: Prusinkiewicz
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Žádníková P, Wabnik KT, Abuzeineh A, et al. A model of differential growth
guided apical hook formation in plants. Plant Cell. 2016;28(10):2464-2477.
doi:10.1105/tpc.15.00569
apa: Žádníková, P., Wabnik, K. T., Abuzeineh, A., Gallemí, M., Van Der Straeten,
D., Smith, R., … Benková, E. (2016). A model of differential growth guided apical
hook formation in plants. Plant Cell. American Society of Plant Biologists.
https://doi.org/10.1105/tpc.15.00569
chicago: Žádníková, Petra, Krzysztof T Wabnik, Anas Abuzeineh, Marçal Gallemí, Dominique
Van Der Straeten, Richard Smith, Dirk Inze, Jiří Friml, Przemysław Prusinkiewicz,
and Eva Benková. “A Model of Differential Growth Guided Apical Hook Formation
in Plants.” Plant Cell. American Society of Plant Biologists, 2016. https://doi.org/10.1105/tpc.15.00569.
ieee: P. Žádníková et al., “A model of differential growth guided apical
hook formation in plants,” Plant Cell, vol. 28, no. 10. American Society
of Plant Biologists, pp. 2464–2477, 2016.
ista: Žádníková P, Wabnik KT, Abuzeineh A, Gallemí M, Van Der Straeten D, Smith
R, Inze D, Friml J, Prusinkiewicz P, Benková E. 2016. A model of differential
growth guided apical hook formation in plants. Plant Cell. 28(10), 2464–2477.
mla: Žádníková, Petra, et al. “A Model of Differential Growth Guided Apical Hook
Formation in Plants.” Plant Cell, vol. 28, no. 10, American Society of
Plant Biologists, 2016, pp. 2464–77, doi:10.1105/tpc.15.00569.
short: P. Žádníková, K.T. Wabnik, A. Abuzeineh, M. Gallemí, D. Van Der Straeten,
R. Smith, D. Inze, J. Friml, P. Prusinkiewicz, E. Benková, Plant Cell 28 (2016)
2464–2477.
corr_author: '1'
date_created: 2018-12-11T11:50:26Z
date_published: 2016-10-01T00:00:00Z
date_updated: 2025-09-22T09:56:45Z
day: '01'
department:
- _id: EvBe
- _id: JiFr
doi: 10.1105/tpc.15.00569
ec_funded: 1
external_id:
isi:
- '000390135400013'
intvolume: ' 28'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5134968/
month: '10'
oa: 1
oa_version: Submitted Version
page: 2464 - 2477
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '6205'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A model of differential growth guided apical hook formation in plants
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 28
year: '2016'
...
---
_id: '1154'
abstract:
- lang: eng
text: "Cellular locomotion is a central hallmark of eukaryotic life. It is governed
by cell-extrinsic molecular factors, which can either emerge in the soluble phase
or as immobilized, often adhesive ligands. To encode for direction, every cue
must be present as a spatial or temporal gradient. Here, we developed a microfluidic
chamber that allows measurement of cell migration in combined response to surface
immobilized and soluble molecular gradients. As a proof of principle we study
the response of dendritic cells to their major guidance cues, chemokines. The
majority of data on chemokine gradient sensing is based on in vitro studies employing
soluble gradients. Despite evidence suggesting that in vivo chemokines are often
immobilized to sugar residues, limited information is available how cells respond
to immobilized chemokines. We tracked migration of dendritic cells towards immobilized
gradients of the chemokine CCL21 and varying superimposed soluble gradients of
CCL19. Differential migratory patterns illustrate the potential of our setup to
quantitatively study the competitive response to both types of gradients. Beyond
chemokines our approach is broadly applicable to alternative systems of chemo-
and haptotaxis such as cells migrating along gradients of adhesion receptor ligands
vs. any soluble cue. \r\n"
acknowledgement: 'This work was supported by the Swiss National Science Foundation
(Ambizione fellowship; PZ00P3-154733 to M.M.), the Swiss Multiple Sclerosis Society
(research support to M.M.), a fellowship from the Boehringer Ingelheim Fonds (BIF)
to J.S., the European Research Council (grant ERC GA 281556) and a START award from
the Austrian Science Foundation (FWF) to M.S. #BioimagingFacility'
article_number: '36440'
article_processing_charge: No
author:
- first_name: Jan
full_name: Schwarz, Jan
id: 346C1EC6-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Veronika
full_name: Bierbaum, Veronika
id: 3FD04378-F248-11E8-B48F-1D18A9856A87
last_name: Bierbaum
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Tino
full_name: Frank, Tino
last_name: Frank
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
- first_name: Savaş
full_name: Tay, Savaş
last_name: Tay
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Matthias
full_name: Mehling, Matthias
id: 3C23B994-F248-11E8-B48F-1D18A9856A87
last_name: Mehling
orcid: 0000-0001-8599-1226
citation:
ama: Schwarz J, Bierbaum V, Merrin J, et al. A microfluidic device for measuring
cell migration towards substrate bound and soluble chemokine gradients. Scientific
Reports. 2016;6. doi:10.1038/srep36440
apa: Schwarz, J., Bierbaum, V., Merrin, J., Frank, T., Hauschild, R., Bollenbach,
M. T., … Mehling, M. (2016). A microfluidic device for measuring cell migration
towards substrate bound and soluble chemokine gradients. Scientific Reports.
Nature Publishing Group. https://doi.org/10.1038/srep36440
chicago: Schwarz, Jan, Veronika Bierbaum, Jack Merrin, Tino Frank, Robert Hauschild,
Mark Tobias Bollenbach, Savaş Tay, Michael K Sixt, and Matthias Mehling. “A Microfluidic
Device for Measuring Cell Migration towards Substrate Bound and Soluble Chemokine
Gradients.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep36440.
ieee: J. Schwarz et al., “A microfluidic device for measuring cell migration
towards substrate bound and soluble chemokine gradients,” Scientific Reports,
vol. 6. Nature Publishing Group, 2016.
ista: Schwarz J, Bierbaum V, Merrin J, Frank T, Hauschild R, Bollenbach MT, Tay
S, Sixt MK, Mehling M. 2016. A microfluidic device for measuring cell migration
towards substrate bound and soluble chemokine gradients. Scientific Reports. 6,
36440.
mla: Schwarz, Jan, et al. “A Microfluidic Device for Measuring Cell Migration towards
Substrate Bound and Soluble Chemokine Gradients.” Scientific Reports, vol.
6, 36440, Nature Publishing Group, 2016, doi:10.1038/srep36440.
short: J. Schwarz, V. Bierbaum, J. Merrin, T. Frank, R. Hauschild, M.T. Bollenbach,
S. Tay, M.K. Sixt, M. Mehling, Scientific Reports 6 (2016).
date_created: 2018-12-11T11:50:27Z
date_published: 2016-11-07T00:00:00Z
date_updated: 2025-09-22T09:56:13Z
day: '07'
ddc:
- '579'
department:
- _id: MiSi
- _id: NanoFab
- _id: Bio
- _id: ToBo
doi: 10.1038/srep36440
ec_funded: 1
external_id:
isi:
- '000387118300001'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:32Z
date_updated: 2018-12-12T10:09:32Z
file_id: '4756'
file_name: IST-2017-744-v1+1_srep36440.pdf
file_size: 2353456
relation: main_file
file_date_updated: 2018-12-12T10:09:32Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
- _id: 25A8E5EA-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y 564-B12
name: Cytoskeletal force generation and force transduction of migrating leukocytes
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6204'
pubrep_id: '744'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A microfluidic device for measuring cell migration towards substrate bound
and soluble chemokine gradients
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 6
year: '2016'
...
---
_id: '1157'
abstract:
- lang: eng
text: We consider sample covariance matrices of the form Q = ( σ1/2X)(σ1/2X)∗, where
the sample X is an M ×N random matrix whose entries are real independent random
variables with variance 1/N and whereσ is an M × M positive-definite deterministic
matrix. We analyze the asymptotic fluctuations of the largest rescaled eigenvalue
of Q when both M and N tend to infinity with N/M →d ϵ (0,∞). For a large class
of populations σ in the sub-critical regime, we show that the distribution of
the largest rescaled eigenvalue of Q is given by the type-1 Tracy-Widom distribution
under the additional assumptions that (1) either the entries of X are i.i.d. Gaussians
or (2) that σ is diagonal and that the entries of X have a sub-exponential decay.
acknowledgement: "We thank Horng-Tzer Yau for numerous discussions and remarks. We
are grateful to Ben Adlam, Jinho Baik, Zhigang Bao, Paul Bourgade, László Erd ̋os,
Iain Johnstone and Antti Knowles for comments. We are also grate-\r\nful to the
anonymous referee for carefully reading our manuscript and suggesting several improvements."
article_processing_charge: No
arxiv: 1
author:
- first_name: Ji
full_name: Lee, Ji
last_name: Lee
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
citation:
ama: Lee J, Schnelli K. Tracy-widom distribution for the largest eigenvalue of real
sample covariance matrices with general population. Annals of Applied Probability.
2016;26(6):3786-3839. doi:10.1214/16-AAP1193
apa: Lee, J., & Schnelli, K. (2016). Tracy-widom distribution for the largest
eigenvalue of real sample covariance matrices with general population. Annals
of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/16-AAP1193
chicago: Lee, Ji, and Kevin Schnelli. “Tracy-Widom Distribution for the Largest
Eigenvalue of Real Sample Covariance Matrices with General Population.” Annals
of Applied Probability. Institute of Mathematical Statistics, 2016. https://doi.org/10.1214/16-AAP1193.
ieee: J. Lee and K. Schnelli, “Tracy-widom distribution for the largest eigenvalue
of real sample covariance matrices with general population,” Annals of Applied
Probability, vol. 26, no. 6. Institute of Mathematical Statistics, pp. 3786–3839,
2016.
ista: Lee J, Schnelli K. 2016. Tracy-widom distribution for the largest eigenvalue
of real sample covariance matrices with general population. Annals of Applied
Probability. 26(6), 3786–3839.
mla: Lee, Ji, and Kevin Schnelli. “Tracy-Widom Distribution for the Largest Eigenvalue
of Real Sample Covariance Matrices with General Population.” Annals of Applied
Probability, vol. 26, no. 6, Institute of Mathematical Statistics, 2016, pp.
3786–839, doi:10.1214/16-AAP1193.
short: J. Lee, K. Schnelli, Annals of Applied Probability 26 (2016) 3786–3839.
date_created: 2018-12-11T11:50:27Z
date_published: 2016-12-15T00:00:00Z
date_updated: 2025-09-22T09:55:43Z
day: '15'
department:
- _id: LaEr
doi: 10.1214/16-AAP1193
ec_funded: 1
external_id:
arxiv:
- '1409.4979'
isi:
- '000391240100016'
intvolume: ' 26'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1409.4979
month: '12'
oa: 1
oa_version: Preprint
page: 3786 - 3839
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Annals of Applied Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '6201'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tracy-widom distribution for the largest eigenvalue of real sample covariance
matrices with general population
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 26
year: '2016'
...
---
_id: '1158'
abstract:
- lang: eng
text: Speciation results from the progressive accumulation of mutations that decrease
the probability of mating between parental populations or reduce the fitness of
hybrids—the so-called species barriers. The speciation genomic literature, however,
is mainly a collection of case studies, each with its own approach and specificities,
such that a global view of the gradual process of evolution from one to two species
is currently lacking. Of primary importance is the prevalence of gene flow between
diverging entities, which is central in most species concepts and has been widely
discussed in recent years. Here, we explore the continuum of speciation thanks
to a comparative analysis of genomic data from 61 pairs of populations/species
of animals with variable levels of divergence. Gene flow between diverging gene
pools is assessed under an approximate Bayesian computation (ABC) framework. We
show that the intermediate "grey zone" of speciation, in which taxonomy
is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective
of species life history traits or ecology. Thanks to appropriate modeling of among-locus
variation in genetic drift and introgression rate, we clarify the status of the
majority of ambiguous cases and uncover a number of cryptic species. Our analysis
also reveals the high incidence in animals of semi-isolated species (when some
but not all loci are affected by barriers to gene flow) and highlights the intrinsic
difficulty, both statistical and conceptual, of delineating species in the grey
zone of speciation.
acknowledgement: "European Research Council (ERC) https://erc.europa.eu/ (grant number
ERC grant 232971). PopPhyl project. The funder had no role in study design, data
collection and analysis, decision to publish, or preparation of the manuscript.
French National Research Agency (ANR) http://www.agence-nationale-recherche.fr/en/project-based-funding-to-advance-french-research/
(grant number ANR-12-BSV7- 0011). HYSEA project.\r\nWe thank Aude Darracq, Vincent
Castric, Pierre-Alexandre Gagnaire, Xavier Vekemans, and John Welch for insightful
discussions. The computations were performed at the Vital-IT (http://www.vital-it.ch)
Center for high-performance computing of the SIB Swiss Institute of Bioinformatics
and the ISEM computing cluster at the platform Montpellier Bioinformatique et Biodiversité."
article_number: e2000234
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. Shedding light
on the grey zone of speciation along a continuum of genomic divergence. PLoS
Biology. 2016;14(12). doi:10.1371/journal.pbio.2000234
apa: Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne,
N. (2016). Shedding light on the grey zone of speciation along a continuum of
genomic divergence. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234
chicago: Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux,
Nicolas Galtier, and Nicolas Bierne. “Shedding Light on the Grey Zone of Speciation
along a Continuum of Genomic Divergence.” PLoS Biology. Public Library
of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.
ieee: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne,
“Shedding light on the grey zone of speciation along a continuum of genomic divergence,”
PLoS Biology, vol. 14, no. 12. Public Library of Science, 2016.
ista: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Shedding
light on the grey zone of speciation along a continuum of genomic divergence.
PLoS Biology. 14(12), e2000234.
mla: Roux, Camille, et al. “Shedding Light on the Grey Zone of Speciation along
a Continuum of Genomic Divergence.” PLoS Biology, vol. 14, no. 12, e2000234,
Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.
short: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS
Biology 14 (2016).
date_created: 2018-12-11T11:50:28Z
date_published: 2016-12-27T00:00:00Z
date_updated: 2025-09-22T09:55:10Z
day: '27'
ddc:
- '576'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1371/journal.pbio.2000234
external_id:
isi:
- '000392120100008'
file:
- access_level: open_access
checksum: 2bab63b068a9840efd532b9ae583f9bb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:42Z
date_updated: 2020-07-14T12:44:36Z
file_id: '5164'
file_name: IST-2017-742-v1+1_journal.pbio.2000234.pdf
file_size: 2494348
relation: main_file
file_date_updated: 2020-07-14T12:44:36Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '6200'
pubrep_id: '742'
quality_controlled: '1'
related_material:
record:
- id: '9862'
relation: research_data
status: public
- id: '9863'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Shedding light on the grey zone of speciation along a continuum of genomic
divergence
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 14
year: '2016'
...