---
_id: '9710'
abstract:
- lang: eng
text: Much of quantitative genetics is based on the ‘infinitesimal model’, under
which selection has a negligible effect on the genetic variance. This is typically
justified by assuming a very large number of loci with additive effects. However,
it applies even when genes interact, provided that the number of loci is large
enough that selection on each of them is weak relative to random drift. In the
long term, directional selection will change allele frequencies, but even then,
the effects of epistasis on the ultimate change in trait mean due to selection
may be modest. Stabilising selection can maintain many traits close to their optima,
even when the underlying alleles are weakly selected. However, the number of traits
that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this
is hard to reconcile with the apparent complexity of many organisms. Just as for
the mutation load, this limit can be evaded by a particular form of negative epistasis.
A more robust limit is set by the variance in reproductive success. This suggests
that selection accumulates information most efficiently in the infinitesimal regime,
when selection on individual alleles is weak, and comparable with random drift.
A review of evidence on selection strength suggests that although most variance
in fitness may be because of alleles with large Nes, substantial amounts of adaptation
may be because of alleles in the infinitesimal regime, in which epistasis has
modest effects.
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Data from: How does epistasis influence the response to selection?
2016. doi:10.5061/dryad.s5s7r'
apa: 'Barton, N. H. (2016). Data from: How does epistasis influence the response
to selection? Dryad. https://doi.org/10.5061/dryad.s5s7r'
chicago: 'Barton, Nicholas H. “Data from: How Does Epistasis Influence the Response
to Selection?” Dryad, 2016. https://doi.org/10.5061/dryad.s5s7r.'
ieee: 'N. H. Barton, “Data from: How does epistasis influence the response to selection?”
Dryad, 2016.'
ista: 'Barton NH. 2016. Data from: How does epistasis influence the response to
selection?, Dryad, 10.5061/dryad.s5s7r.'
mla: 'Barton, Nicholas H. Data from: How Does Epistasis Influence the Response
to Selection? Dryad, 2016, doi:10.5061/dryad.s5s7r.'
short: N.H. Barton, (2016).
date_created: 2021-07-23T11:45:47Z
date_published: 2016-09-23T00:00:00Z
date_updated: 2025-05-28T11:57:03Z
day: '23'
department:
- _id: NiBa
doi: 10.5061/dryad.s5s7r
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.s5s7r
month: '09'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1199'
relation: used_in_publication
status: public
status: public
title: 'Data from: How does epistasis influence the response to selection?'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9720'
abstract:
- lang: eng
text: 'Summary: Declining populations of bee pollinators are a cause of concern,
with major repercussions for biodiversity loss and food security. RNA viruses
associated with honeybees represent a potential threat to other insect pollinators,
but the extent of this threat is poorly understood. This study aims to attain
a detailed understanding of the current and ongoing risk of emerging infectious
disease (EID) transmission between managed and wild pollinator species across
a wide range of RNA viruses. Within a structured large-scale national survey across
26 independent sites, we quantify the prevalence and pathogen loads of multiple
RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee
(Bombus spp.) populations. We then construct models that compare virus prevalence
between wild and managed pollinators. Multiple RNA viruses associated with honeybees
are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees
is a significant predictor of virus prevalence in bumblebees, but we remain cautious
in speculating over the principle direction of pathogen transmission. We demonstrate
species-specific differences in prevalence, indicating significant variation in
disease susceptibility or tolerance. Pathogen loads within individual bumblebees
may be high and in the case of at least one RNA virus, prevalence is higher in
wild bumblebees than in managed honeybee populations. Our findings indicate widespread
transmission of RNA viruses between managed and wild bee pollinators, pointing
to an interconnected network of potential disease pressures within and among pollinator
species. In the context of the biodiversity crisis, our study emphasizes the importance
of targeting a wide range of pathogens and defining host associations when considering
potential drivers of population decline.'
article_processing_charge: No
author:
- first_name: Dino
full_name: Mcmahon, Dino
last_name: Mcmahon
- first_name: Matthias
full_name: Fürst, Matthias
id: 393B1196-F248-11E8-B48F-1D18A9856A87
last_name: Fürst
orcid: 0000-0002-3712-925X
- first_name: Jesicca
full_name: Caspar, Jesicca
last_name: Caspar
- first_name: Panagiotis
full_name: Theodorou, Panagiotis
last_name: Theodorou
- first_name: Mark
full_name: Brown, Mark
last_name: Brown
- first_name: Robert
full_name: Paxton, Robert
last_name: Paxton
citation:
ama: 'Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. Data from: A
sting in the spit: widespread cross-infection of multiple RNA viruses across wild
and managed bees. 2016. doi:10.5061/dryad.4b565'
apa: 'Mcmahon, D., Fürst, M., Caspar, J., Theodorou, P., Brown, M., & Paxton,
R. (2016). Data from: A sting in the spit: widespread cross-infection of multiple
RNA viruses across wild and managed bees. Dryad. https://doi.org/10.5061/dryad.4b565'
chicago: 'Mcmahon, Dino, Matthias Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark
Brown, and Robert Paxton. “Data from: A Sting in the Spit: Widespread Cross-Infection
of Multiple RNA Viruses across Wild and Managed Bees.” Dryad, 2016. https://doi.org/10.5061/dryad.4b565.'
ieee: 'D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, and R. Paxton, “Data
from: A sting in the spit: widespread cross-infection of multiple RNA viruses
across wild and managed bees.” Dryad, 2016.'
ista: 'Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. 2016. Data
from: A sting in the spit: widespread cross-infection of multiple RNA viruses
across wild and managed bees, Dryad, 10.5061/dryad.4b565.'
mla: 'Mcmahon, Dino, et al. Data from: A Sting in the Spit: Widespread Cross-Infection
of Multiple RNA Viruses across Wild and Managed Bees. Dryad, 2016, doi:10.5061/dryad.4b565.'
short: D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, (2016).
date_created: 2021-07-26T09:14:19Z
date_published: 2016-01-22T00:00:00Z
date_updated: 2023-02-23T10:17:25Z
day: '22'
department:
- _id: SyCr
doi: 10.5061/dryad.4b565
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.4b565
month: '01'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1855'
relation: used_in_publication
status: public
status: public
title: 'Data from: A sting in the spit: widespread cross-infection of multiple RNA
viruses across wild and managed bees'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9862'
article_processing_charge: No
author:
- first_name: Camille
full_name: Roux, Camille
last_name: Roux
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Jonathan
full_name: Romiguier, Jonathan
last_name: Romiguier
- first_name: Youann
full_name: Anciaux, Youann
last_name: Anciaux
- first_name: Nicolas
full_name: Galtier, Nicolas
last_name: Galtier
- first_name: Nicolas
full_name: Bierne, Nicolas
last_name: Bierne
citation:
ama: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Simulation
study to test the robustness of ABC in face of recent times of divergence. 2016.
doi:10.1371/journal.pbio.2000234.s016
apa: Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne,
N. (2016). Simulation study to test the robustness of ABC in face of recent times
of divergence. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234.s016
chicago: Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux,
Nicolas Galtier, and Nicolas Bierne. “Simulation Study to Test the Robustness
of ABC in Face of Recent Times of Divergence.” Public Library of Science, 2016.
https://doi.org/10.1371/journal.pbio.2000234.s016.
ieee: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne,
“Simulation study to test the robustness of ABC in face of recent times of divergence.”
Public Library of Science, 2016.
ista: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Simulation
study to test the robustness of ABC in face of recent times of divergence, Public
Library of Science, 10.1371/journal.pbio.2000234.s016.
mla: Roux, Camille, et al. Simulation Study to Test the Robustness of ABC in
Face of Recent Times of Divergence. Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.s016.
short: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).
date_created: 2021-08-10T08:20:17Z
date_updated: 2023-02-21T16:21:20Z
day: '27'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1371/journal.pbio.2000234.s016
month: '12'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1158'
relation: used_in_publication
status: public
status: public
title: Simulation study to test the robustness of ABC in face of recent times of divergence
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9863'
article_processing_charge: No
author:
- first_name: Camille
full_name: Roux, Camille
last_name: Roux
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Jonathan
full_name: Romiguier, Jonathan
last_name: Romiguier
- first_name: Youann
full_name: Anciaux, Youann
last_name: Anciaux
- first_name: Nicolas
full_name: Galtier, Nicolas
last_name: Galtier
- first_name: Nicolas
full_name: Bierne, Nicolas
last_name: Bierne
citation:
ama: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Accessions
of surveyed individuals, geographic locations and summary statistics. 2016. doi:10.1371/journal.pbio.2000234.s017
apa: Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne,
N. (2016). Accessions of surveyed individuals, geographic locations and summary
statistics. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234.s017
chicago: Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux,
Nicolas Galtier, and Nicolas Bierne. “Accessions of Surveyed Individuals, Geographic
Locations and Summary Statistics.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.s017.
ieee: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne,
“Accessions of surveyed individuals, geographic locations and summary statistics.”
Public Library of Science, 2016.
ista: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Accessions
of surveyed individuals, geographic locations and summary statistics, Public Library
of Science, 10.1371/journal.pbio.2000234.s017.
mla: Roux, Camille, et al. Accessions of Surveyed Individuals, Geographic Locations
and Summary Statistics. Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.s017.
short: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).
date_created: 2021-08-10T08:22:52Z
date_updated: 2023-02-21T16:21:20Z
day: '27'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1371/journal.pbio.2000234.s017
month: '12'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1158'
relation: used_in_publication
status: public
status: public
title: Accessions of surveyed individuals, geographic locations and summary statistics
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9864'
abstract:
- lang: eng
text: Viral capsids are structurally constrained by interactions among the amino
acids (AAs) of their constituent proteins. Therefore, epistasis is expected to
evolve among physically interacting sites and to influence the rates of substitution.
To study the evolution of epistasis, we focused on the major structural protein
of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences
of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction
differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each
ancestral haplotype and the extant species, we estimated, in silico, the distribution
of free energies and epistasis of the capsid structure. We found that free energy
has not significantly increased but epistasis has. We decomposed epistasis up
to fifth order and found that higher-order epistasis sometimes compensates pairwise
interactions making the free energy seem additive. The dN/dS ratio is low, suggesting
strong purifying selection, and that structure is under stabilizing selection.
We synthesized phages carrying ancestral haplotypes of the coat protein gene and
measured their fitness experimentally. Our findings indicate that stabilizing
mutations can have higher fitness, and that fitness optima do not necessarily
coincide with energy minima.
article_processing_charge: No
author:
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
- first_name: Tomasz
full_name: Włodarski, Tomasz
last_name: Włodarski
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary
interplay between structure, energy and epistasis in the coat protein of the ϕX174
phage family. 2016. doi:10.6084/m9.figshare.4315652.v1
apa: Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J.
P. (2016). Data from evolutionary interplay between structure, energy and epistasis
in the coat protein of the ϕX174 phage family. The Royal Society. https://doi.org/10.6084/m9.figshare.4315652.v1
chicago: Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan
P Bollback. “Data from Evolutionary Interplay between Structure, Energy and Epistasis
in the Coat Protein of the ΦX174 Phage Family.” The Royal Society, 2016. https://doi.org/10.6084/m9.figshare.4315652.v1.
ieee: R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Data
from evolutionary interplay between structure, energy and epistasis in the coat
protein of the ϕX174 phage family.” The Royal Society, 2016.
ista: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2016. Data from
evolutionary interplay between structure, energy and epistasis in the coat protein
of the ϕX174 phage family, The Royal Society, 10.6084/m9.figshare.4315652.v1.
mla: Fernandes Redondo, Rodrigo A., et al. Data from Evolutionary Interplay between
Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.
The Royal Society, 2016, doi:10.6084/m9.figshare.4315652.v1.
short: R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016).
date_created: 2021-08-10T08:29:47Z
date_published: 2016-12-14T00:00:00Z
date_updated: 2025-05-28T11:57:06Z
day: '14'
department:
- _id: NiBa
- _id: JoBo
doi: 10.6084/m9.figshare.4315652.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.4315652.v1
month: '12'
oa: 1
oa_version: Published Version
publisher: The Royal Society
related_material:
record:
- id: '1077'
relation: used_in_publication
status: public
status: public
title: Data from evolutionary interplay between structure, energy and epistasis in
the coat protein of the ϕX174 phage family
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9866'
article_processing_charge: No
author:
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
- first_name: Zdzisław
full_name: Burda, Zdzisław
last_name: Burda
- first_name: Bartłomiej
full_name: Wacław, Bartłomiej
last_name: Wacław
citation:
ama: Zagórski MP, Burda Z, Wacław B. ZIP-archived directory containing all data
and computer programs. 2016. doi:10.1371/journal.pcbi.1005218.s009
apa: Zagórski, M. P., Burda, Z., & Wacław, B. (2016). ZIP-archived directory
containing all data and computer programs. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005218.s009
chicago: Zagórski, Marcin P, Zdzisław Burda, and Bartłomiej Wacław. “ZIP-Archived
Directory Containing All Data and Computer Programs.” Public Library of Science,
2016. https://doi.org/10.1371/journal.pcbi.1005218.s009.
ieee: M. P. Zagórski, Z. Burda, and B. Wacław, “ZIP-archived directory containing
all data and computer programs.” Public Library of Science, 2016.
ista: Zagórski MP, Burda Z, Wacław B. 2016. ZIP-archived directory containing all
data and computer programs, Public Library of Science, 10.1371/journal.pcbi.1005218.s009.
mla: Zagórski, Marcin P., et al. ZIP-Archived Directory Containing All Data and
Computer Programs. Public Library of Science, 2016, doi:10.1371/journal.pcbi.1005218.s009.
short: M.P. Zagórski, Z. Burda, B. Wacław, (2016).
date_created: 2021-08-10T08:37:20Z
date_published: 2016-12-09T00:00:00Z
date_updated: 2023-02-21T16:24:29Z
day: '09'
department:
- _id: AnKi
doi: 10.1371/journal.pcbi.1005218.s009
month: '12'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1167'
relation: used_in_publication
status: public
status: public
title: ZIP-archived directory containing all data and computer programs
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9867'
abstract:
- lang: eng
text: In the beginning of our experiment, subjects were asked to read a few pages
on their computer screens that would explain the rules of the subsequent game.
Here, we provide these instructions, translated from German.
article_processing_charge: No
author:
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Kristin
full_name: Hagel, Kristin
last_name: Hagel
- first_name: Manfred
full_name: Milinski, Manfred
last_name: Milinski
citation:
ama: Hilbe C, Hagel K, Milinski M. Experimental game instructions. 2016. doi:10.1371/journal.pone.0163867.s008
apa: Hilbe, C., Hagel, K., & Milinski, M. (2016). Experimental game instructions.
Public Library of Science. https://doi.org/10.1371/journal.pone.0163867.s008
chicago: Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Experimental Game
Instructions.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163867.s008.
ieee: C. Hilbe, K. Hagel, and M. Milinski, “Experimental game instructions.” Public
Library of Science, 2016.
ista: Hilbe C, Hagel K, Milinski M. 2016. Experimental game instructions, Public
Library of Science, 10.1371/journal.pone.0163867.s008.
mla: Hilbe, Christian, et al. Experimental Game Instructions. Public Library
of Science, 2016, doi:10.1371/journal.pone.0163867.s008.
short: C. Hilbe, K. Hagel, M. Milinski, (2016).
date_created: 2021-08-10T08:42:00Z
date_updated: 2023-02-21T16:59:01Z
day: '04'
department:
- _id: KrCh
doi: 10.1371/journal.pone.0163867.s008
month: '10'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1322'
relation: used_in_publication
status: public
status: public
title: Experimental game instructions
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9868'
abstract:
- lang: eng
text: The raw data file containing the experimental decisions of all our study subjects.
article_processing_charge: No
author:
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Kristin
full_name: Hagel, Kristin
last_name: Hagel
- first_name: Manfred
full_name: Milinski, Manfred
last_name: Milinski
citation:
ama: Hilbe C, Hagel K, Milinski M. Experimental data. 2016. doi:10.1371/journal.pone.0163867.s009
apa: Hilbe, C., Hagel, K., & Milinski, M. (2016). Experimental data. Public
Library of Science. https://doi.org/10.1371/journal.pone.0163867.s009
chicago: Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Experimental Data.”
Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163867.s009.
ieee: C. Hilbe, K. Hagel, and M. Milinski, “Experimental data.” Public Library of
Science, 2016.
ista: Hilbe C, Hagel K, Milinski M. 2016. Experimental data, Public Library of Science,
10.1371/journal.pone.0163867.s009.
mla: Hilbe, Christian, et al. Experimental Data. Public Library of Science,
2016, doi:10.1371/journal.pone.0163867.s009.
short: C. Hilbe, K. Hagel, M. Milinski, (2016).
date_created: 2021-08-10T08:45:00Z
date_published: 2016-10-04T00:00:00Z
date_updated: 2023-02-21T16:59:01Z
day: '04'
department:
- _id: KrCh
doi: 10.1371/journal.pone.0163867.s009
month: '10'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1322'
relation: used_in_publication
status: public
status: public
title: Experimental data
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9869'
abstract:
- lang: eng
text: A lower bound on the error of a positional estimator with limited positional
information is derived.
article_processing_charge: No
author:
- first_name: Patrick
full_name: Hillenbrand, Patrick
last_name: Hillenbrand
- first_name: Ulrich
full_name: Gerland, Ulrich
last_name: Gerland
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Hillenbrand P, Gerland U, Tkačik G. Error bound on an estimator of position.
2016. doi:10.1371/journal.pone.0163628.s001
apa: Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Error bound on an estimator
of position. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628.s001
chicago: Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Error Bound on
an Estimator of Position.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.s001.
ieee: P. Hillenbrand, U. Gerland, and G. Tkačik, “Error bound on an estimator of
position.” Public Library of Science, 2016.
ista: Hillenbrand P, Gerland U, Tkačik G. 2016. Error bound on an estimator of position,
Public Library of Science, 10.1371/journal.pone.0163628.s001.
mla: Hillenbrand, Patrick, et al. Error Bound on an Estimator of Position.
Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s001.
short: P. Hillenbrand, U. Gerland, G. Tkačik, (2016).
date_created: 2021-08-10T08:53:48Z
date_published: 2016-09-27T00:00:00Z
date_updated: 2023-02-21T16:56:40Z
day: '27'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0163628.s001
month: '09'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1270'
relation: used_in_publication
status: public
status: public
title: Error bound on an estimator of position
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9870'
abstract:
- lang: eng
text: The effect of noise in the input field on an Ising model is approximated.
Furthermore, methods to compute positional information in an Ising model by transfer
matrices and Monte Carlo sampling are outlined.
article_processing_charge: No
author:
- first_name: Patrick
full_name: Hillenbrand, Patrick
last_name: Hillenbrand
- first_name: Ulrich
full_name: Gerland, Ulrich
last_name: Gerland
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in
an Ising model. 2016. doi:10.1371/journal.pone.0163628.s002
apa: Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Computation of positional
information in an Ising model. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628.s002
chicago: Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of
Positional Information in an Ising Model.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.s002.
ieee: P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information
in an Ising model.” Public Library of Science, 2016.
ista: Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information
in an Ising model, Public Library of Science, 10.1371/journal.pone.0163628.s002.
mla: Hillenbrand, Patrick, et al. Computation of Positional Information in an
Ising Model. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s002.
short: P. Hillenbrand, U. Gerland, G. Tkačik, (2016).
date_created: 2021-08-10T09:23:45Z
date_published: 2016-09-27T00:00:00Z
date_updated: 2023-02-21T16:56:40Z
day: '27'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0163628.s002
month: '09'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1270'
relation: used_in_publication
status: public
status: public
title: Computation of positional information in an Ising model
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9871'
abstract:
- lang: eng
text: The positional information in a discrete morphogen field with Gaussian noise
is computed.
article_processing_charge: No
author:
- first_name: Patrick
full_name: Hillenbrand, Patrick
last_name: Hillenbrand
- first_name: Ulrich
full_name: Gerland, Ulrich
last_name: Gerland
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in
a discrete morphogen field. 2016. doi:10.1371/journal.pone.0163628.s003
apa: Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Computation of positional
information in a discrete morphogen field. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628.s003
chicago: Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of
Positional Information in a Discrete Morphogen Field.” Public Library of Science,
2016. https://doi.org/10.1371/journal.pone.0163628.s003.
ieee: P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information
in a discrete morphogen field.” Public Library of Science, 2016.
ista: Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information
in a discrete morphogen field, Public Library of Science, 10.1371/journal.pone.0163628.s003.
mla: Hillenbrand, Patrick, et al. Computation of Positional Information in a
Discrete Morphogen Field. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s003.
short: P. Hillenbrand, U. Gerland, G. Tkačik, (2016).
date_created: 2021-08-10T09:27:35Z
date_updated: 2023-02-21T16:56:40Z
day: '27'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0163628.s003
month: '09'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1270'
relation: used_in_publication
status: public
status: public
title: Computation of positional information in a discrete morphogen field
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9873'
article_processing_charge: No
author:
- first_name: Alex
full_name: Boehm, Alex
last_name: Boehm
- first_name: Markus
full_name: Arnoldini, Markus
last_name: Arnoldini
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Thomas
full_name: Röösli, Thomas
last_name: Röösli
- first_name: Colette
full_name: Bigosch, Colette
last_name: Bigosch
- first_name: Martin
full_name: Ackermann, Martin
last_name: Ackermann
citation:
ama: Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. Quantification
of the growth rate reduction as a consequence of age-specific mortality. 2016.
doi:10.1371/journal.pgen.1005974.s015
apa: Boehm, A., Arnoldini, M., Bergmiller, T., Röösli, T., Bigosch, C., & Ackermann,
M. (2016). Quantification of the growth rate reduction as a consequence of age-specific
mortality. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005974.s015
chicago: Boehm, Alex, Markus Arnoldini, Tobias Bergmiller, Thomas Röösli, Colette
Bigosch, and Martin Ackermann. “Quantification of the Growth Rate Reduction as
a Consequence of Age-Specific Mortality.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pgen.1005974.s015.
ieee: A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, and M. Ackermann,
“Quantification of the growth rate reduction as a consequence of age-specific
mortality.” Public Library of Science, 2016.
ista: Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. 2016.
Quantification of the growth rate reduction as a consequence of age-specific mortality,
Public Library of Science, 10.1371/journal.pgen.1005974.s015.
mla: Boehm, Alex, et al. Quantification of the Growth Rate Reduction as a Consequence
of Age-Specific Mortality. Public Library of Science, 2016, doi:10.1371/journal.pgen.1005974.s015.
short: A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, M. Ackermann,
(2016).
date_created: 2021-08-10T09:42:34Z
date_updated: 2023-02-21T16:50:13Z
day: '19'
department:
- _id: CaGu
doi: 10.1371/journal.pgen.1005974.s015
month: '04'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1250'
relation: used_in_publication
status: public
status: public
title: Quantification of the growth rate reduction as a consequence of age-specific
mortality
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '10794'
abstract:
- lang: eng
text: Mathematical models are of fundamental importance in the understanding of
complex population dynamics. For instance, they can be used to predict the population
evolution starting from different initial conditions or to test how a system responds
to external perturbations. For this analysis to be meaningful in real applications,
however, it is of paramount importance to choose an appropriate model structure
and to infer the model parameters from measured data. While many parameter inference
methods are available for models based on deterministic ordinary differential
equations, the same does not hold for more detailed individual-based models. Here
we consider, in particular, stochastic models in which the time evolution of the
species abundances is described by a continuous-time Markov chain. These models
are governed by a master equation that is typically difficult to solve. Consequently,
traditional inference methods that rely on iterative evaluation of parameter likelihoods
are computationally intractable. The aim of this paper is to present recent advances
in parameter inference for continuous-time Markov chain models, based on a moment
closure approximation of the parameter likelihood, and to investigate how these
results can help in understanding, and ultimately controlling, complex systems
in ecology. Specifically, we illustrate through an agricultural pest case study
how parameters of a stochastic individual-based model can be identified from measured
data and how the resulting model can be used to solve an optimal control problem
in a stochastic setting. In particular, we show how the matter of determining
the optimal combination of two different pest control methods can be formulated
as a chance constrained optimization problem where the control action is modeled
as a state reset, leading to a hybrid system formulation.
acknowledgement: "The authors would like to acknowledge contributions from Baptiste
Mottet who performed preliminary analysis regarding parameter inference for the
considered case study in a student project (Mottet, 2014/2015).\r\nThe research
leading to these results has received funding from the People Programme (Marie Curie
Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under
REA grant agreement No. [291734] and from SystemsX under the project SignalX."
article_number: '42'
article_processing_charge: No
article_type: original
author:
- first_name: Francesca
full_name: Parise, Francesca
last_name: Parise
- first_name: John
full_name: Lygeros, John
last_name: Lygeros
- first_name: Jakob
full_name: Ruess, Jakob
id: 4A245D00-F248-11E8-B48F-1D18A9856A87
last_name: Ruess
orcid: 0000-0003-1615-3282
citation:
ama: 'Parise F, Lygeros J, Ruess J. Bayesian inference for stochastic individual-based
models of ecological systems: a pest control simulation study. Frontiers in
Environmental Science. 2015;3. doi:10.3389/fenvs.2015.00042'
apa: 'Parise, F., Lygeros, J., & Ruess, J. (2015). Bayesian inference for stochastic
individual-based models of ecological systems: a pest control simulation study.
Frontiers in Environmental Science. Frontiers. https://doi.org/10.3389/fenvs.2015.00042'
chicago: 'Parise, Francesca, John Lygeros, and Jakob Ruess. “Bayesian Inference
for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation
Study.” Frontiers in Environmental Science. Frontiers, 2015. https://doi.org/10.3389/fenvs.2015.00042.'
ieee: 'F. Parise, J. Lygeros, and J. Ruess, “Bayesian inference for stochastic individual-based
models of ecological systems: a pest control simulation study,” Frontiers in
Environmental Science, vol. 3. Frontiers, 2015.'
ista: 'Parise F, Lygeros J, Ruess J. 2015. Bayesian inference for stochastic individual-based
models of ecological systems: a pest control simulation study. Frontiers in Environmental
Science. 3, 42.'
mla: 'Parise, Francesca, et al. “Bayesian Inference for Stochastic Individual-Based
Models of Ecological Systems: A Pest Control Simulation Study.” Frontiers in
Environmental Science, vol. 3, 42, Frontiers, 2015, doi:10.3389/fenvs.2015.00042.'
short: F. Parise, J. Lygeros, J. Ruess, Frontiers in Environmental Science 3 (2015).
date_created: 2022-02-25T11:42:25Z
date_published: 2015-06-10T00:00:00Z
date_updated: 2022-02-25T11:59:23Z
day: '10'
ddc:
- '000'
- '570'
department:
- _id: ToHe
- _id: GaTk
doi: 10.3389/fenvs.2015.00042
ec_funded: 1
file:
- access_level: open_access
checksum: 26c222487564e1be02a11d688d6f769d
content_type: application/pdf
creator: dernst
date_created: 2022-02-25T11:55:26Z
date_updated: 2022-02-25T11:55:26Z
file_id: '10795'
file_name: 2015_FrontiersEnvironmScience_Parise.pdf
file_size: 1371201
relation: main_file
success: 1
file_date_updated: 2022-02-25T11:55:26Z
has_accepted_license: '1'
intvolume: ' 3'
keyword:
- General Environmental Science
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Frontiers in Environmental Science
publication_identifier:
issn:
- 2296-665X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Bayesian inference for stochastic individual-based models of ecological systems:
a pest control simulation study'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2015'
...
---
_id: '10796'
abstract:
- lang: eng
text: 'We consider concurrent mean-payoff games, a very well-studied class of two-player
(player 1 vs player 2) zero-sum games on finite-state graphs where every transition
is assigned a reward between 0 and 1, and the payoff function is the long-run
average of the rewards. The value is the maximal expected payoff that player 1
can guarantee against all strategies of player 2. We consider the computation
of the set of states with value 1 under finite-memory strategies for player 1,
and our main results for the problem are as follows: (1) we present a polynomial-time
algorithm; (2) we show that whenever there is a finite-memory strategy, there
is a stationary strategy that does not need memory at all; and (3) we present
an optimal bound (which is double exponential) on the patience of stationary strategies
(where patience of a distribution is the inverse of the smallest positive probability
and represents a complexity measure of a stationary strategy).'
acknowledgement: "The research was partly supported by FWF Grant No P 23499-N23, FWF
NFN Grant\r\nNo S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft
faculty fellows award."
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: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
citation:
ama: 'Chatterjee K, Ibsen-Jensen R. The value 1 problem under finite-memory strategies
for concurrent mean-payoff games. In: Proceedings of the Twenty-Sixth Annual
ACM-SIAM Symposium on Discrete Algorithms. Vol 2015. SIAM; 2015:1018-1029.
doi:10.1137/1.9781611973730.69'
apa: 'Chatterjee, K., & Ibsen-Jensen, R. (2015). The value 1 problem under finite-memory
strategies for concurrent mean-payoff games. In Proceedings of the Twenty-Sixth
Annual ACM-SIAM Symposium on Discrete Algorithms (Vol. 2015, pp. 1018–1029).
San Diego, CA, United States: SIAM. https://doi.org/10.1137/1.9781611973730.69'
chicago: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under
Finite-Memory Strategies for Concurrent Mean-Payoff Games.” In Proceedings
of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, 2015:1018–29.
SIAM, 2015. https://doi.org/10.1137/1.9781611973730.69.
ieee: K. Chatterjee and R. Ibsen-Jensen, “The value 1 problem under finite-memory
strategies for concurrent mean-payoff games,” in Proceedings of the Twenty-Sixth
Annual ACM-SIAM Symposium on Discrete Algorithms, San Diego, CA, United States,
2015, vol. 2015, no. 1, pp. 1018–1029.
ista: 'Chatterjee K, Ibsen-Jensen R. 2015. The value 1 problem under finite-memory
strategies for concurrent mean-payoff games. Proceedings of the Twenty-Sixth Annual
ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms
vol. 2015, 1018–1029.'
mla: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under
Finite-Memory Strategies for Concurrent Mean-Payoff Games.” Proceedings of
the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, vol. 2015,
no. 1, SIAM, 2015, pp. 1018–29, doi:10.1137/1.9781611973730.69.
short: K. Chatterjee, R. Ibsen-Jensen, in:, Proceedings of the Twenty-Sixth Annual
ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2015, pp. 1018–1029.
conference:
end_date: 2015-01-06
location: San Diego, CA, United States
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2015-01-04
date_created: 2022-02-25T12:18:43Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2022-02-25T12:33:32Z
day: '01'
department:
- _id: KrCh
doi: 10.1137/1.9781611973730.69
ec_funded: 1
external_id:
arxiv:
- '1409.6690'
intvolume: ' 2015'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: Preprint
page: 1018-1029
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _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'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete
Algorithms
publication_identifier:
isbn:
- 978-161197374-7
publication_status: published
publisher: SIAM
quality_controlled: '1'
scopus_import: '1'
status: public
title: The value 1 problem under finite-memory strategies for concurrent mean-payoff
games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015
year: '2015'
...
---
_id: '802'
abstract:
- lang: eng
text: Glycoinositolphosphoceramides (GIPCs) are complex sphingolipids present at
the plasma membrane of various eukaryotes with the important exception of mammals.
In fungi, these glycosphingolipids commonly contain an alpha-mannose residue (Man)
linked at position 2 of the inositol. However, several pathogenic fungi additionally
synthesize zwitterionic GIPCs carrying an alpha-glucosamine residue (GlcN) at
this position. In the human pathogen Aspergillus fumigatus, the GlcNalpha1,2IPC
core (where IPC is inositolphosphoceramide) is elongated to Manalpha1,3Manalpha1,6GlcNalpha1,2IPC,
which is the most abundant GIPC synthesized by this fungus. In this study, we
identified an A. fumigatus N-acetylglucosaminyltransferase, named GntA, and demonstrate
its involvement in the initiation of zwitterionic GIPC biosynthesis. Targeted
deletion of the gene encoding GntA in A. fumigatus resulted in complete absence
of zwitterionic GIPC; a phenotype that could be reverted by episomal expression
of GntA in the mutant. The N-acetylhexosaminyltransferase activity of GntA was
substantiated by production of N-acetylhexosamine-IPC in the yeast Saccharomyces
cerevisiae upon GntA expression. Using an in vitro assay, GntA was furthermore
shown to use UDP-N-acetylglucosamine as donor substrate to generate a glycolipid
product resistant to saponification and to digestion by phosphatidylinositol-phospholipase
C as expected for GlcNAcalpha1,2IPC. Finally, as the enzymes involved in mannosylation
of IPC, GntA was localized to the Golgi apparatus, the site of IPC synthesis.
author:
- first_name: Jakob
full_name: Engel, Jakob
last_name: Engel
- first_name: Philipp S
full_name: Schmalhorst, Philipp S
id: 309D50DA-F248-11E8-B48F-1D18A9856A87
last_name: Schmalhorst
orcid: 0000-0002-5795-0133
- first_name: Anke
full_name: Kruger, Anke
last_name: Kruger
- first_name: Christina
full_name: Muller, Christina
last_name: Muller
- first_name: Falk
full_name: Buettner, Falk
last_name: Buettner
- first_name: Françoise
full_name: Routier, Françoise
last_name: Routier
citation:
ama: Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. Characterization
of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic
glycoinositolphosphoceramide biosynthesis. Glycobiology. 2015;25(12):1423-1430.
doi:10.1093/glycob/cwv059
apa: Engel, J., Schmalhorst, P. S., Kruger, A., Muller, C., Buettner, F., &
Routier, F. (2015). Characterization of an N-acetylglucosaminyltransferase involved
in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis.
Glycobiology. Oxford University Press. https://doi.org/10.1093/glycob/cwv059
chicago: Engel, Jakob, Philipp S Schmalhorst, Anke Kruger, Christina Muller, Falk
Buettner, and Françoise Routier. “Characterization of an N-Acetylglucosaminyltransferase
Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.”
Glycobiology. Oxford University Press, 2015. https://doi.org/10.1093/glycob/cwv059.
ieee: J. Engel, P. S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, and F. Routier,
“Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus
fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis,” Glycobiology,
vol. 25, no. 12. Oxford University Press, pp. 1423–1430, 2015.
ista: Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. 2015.
Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus
fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. Glycobiology.
25(12), 1423–1430.
mla: Engel, Jakob, et al. “Characterization of an N-Acetylglucosaminyltransferase
Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.”
Glycobiology, vol. 25, no. 12, Oxford University Press, 2015, pp. 1423–30,
doi:10.1093/glycob/cwv059.
short: J. Engel, P.S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, F. Routier,
Glycobiology 25 (2015) 1423–1430.
date_created: 2018-12-11T11:48:35Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2021-01-12T08:16:33Z
day: '01'
department:
- _id: CaHe
doi: 10.1093/glycob/cwv059
external_id:
pmid:
- '26306635'
intvolume: ' 25'
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
page: 1423 - 1430
pmid: 1
publication: Glycobiology
publication_status: published
publisher: Oxford University Press
publist_id: '6851'
quality_controlled: '1'
scopus_import: 1
status: public
title: Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus
fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2015'
...
---
_id: '8183'
abstract:
- lang: eng
text: "We study conditions under which a finite simplicial complex $K$ can be mapped
to $\\mathbb R^d$ without higher-multiplicity intersections. An almost $r$-embedding
is a map $f: K\\to \\mathbb R^d$ such that the images of any $r$\r\npairwise disjoint
simplices of $K$ do not have a common point. We show that if $r$ is not a prime
power and $d\\geq 2r+1$, then there is a counterexample to the topological Tverberg
conjecture, i.e., there is an almost $r$-embedding of\r\nthe $(d+1)(r-1)$-simplex
in $\\mathbb R^d$. This improves on previous constructions of counterexamples
(for $d\\geq 3r$) based on a series of papers by M. \\\"Ozaydin, M. Gromov, P.
Blagojevi\\'c, F. Frick, G. Ziegler, and the second and fourth present authors.
The counterexamples are obtained by proving the following algebraic criterion
in codimension 2: If $r\\ge3$ and if $K$ is a finite $2(r-1)$-complex then there
exists an almost $r$-embedding $K\\to \\mathbb R^{2r}$ if and only if there exists
a general position PL map $f:K\\to \\mathbb R^{2r}$ such that the algebraic intersection
number of the $f$-images of any $r$ pairwise disjoint simplices of $K$ is zero.
This result can be restated in terms of cohomological obstructions or equivariant
maps, and extends an analogous codimension 3 criterion by the second and fourth
authors. As another application we classify ornaments $f:S^3 \\sqcup S^3\\sqcup
S^3\\to \\mathbb R^5$ up to ornament\r\nconcordance. It follows from work of M.
Freedman, V. Krushkal and P. Teichner that the analogous criterion for $r=2$ is
false. We prove a lemma on singular higher-dimensional Borromean rings, yielding
an elementary proof of the counterexample."
acknowledgement: We would like to thank A. Klyachko, V. Krushkal, S. Melikhov, M.
Tancer, P. Teichner and anonymous referees for helpful discussions.
article_number: '1511.03501'
article_processing_charge: No
arxiv: 1
author:
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
- first_name: Isaac
full_name: Mabillard, Isaac
id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87
last_name: Mabillard
- first_name: A.
full_name: Skopenkov, A.
last_name: Skopenkov
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity
intersections, III. Codimension 2. arXiv.
apa: Avvakumov, S., Mabillard, I., Skopenkov, A., & Wagner, U. (n.d.). Eliminating
higher-multiplicity intersections, III. Codimension 2. arXiv.
chicago: Avvakumov, Sergey, Isaac Mabillard, A. Skopenkov, and Uli Wagner. “Eliminating
Higher-Multiplicity Intersections, III. Codimension 2.” ArXiv, n.d.
ieee: S. Avvakumov, I. Mabillard, A. Skopenkov, and U. Wagner, “Eliminating higher-multiplicity
intersections, III. Codimension 2,” arXiv. .
ista: Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity
intersections, III. Codimension 2. arXiv, 1511.03501.
mla: Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections, III.
Codimension 2.” ArXiv, 1511.03501.
short: S. Avvakumov, I. Mabillard, A. Skopenkov, U. Wagner, ArXiv (n.d.).
date_created: 2020-07-30T10:45:19Z
date_published: 2015-11-15T00:00:00Z
date_updated: 2023-09-07T13:12:17Z
day: '15'
department:
- _id: UlWa
external_id:
arxiv:
- '1511.03501'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1511.03501
month: '11'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
related_material:
record:
- id: '9308'
relation: later_version
status: public
- id: '10220'
relation: later_version
status: public
- id: '8156'
relation: dissertation_contains
status: public
status: public
title: Eliminating higher-multiplicity intersections, III. Codimension 2
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1615'
abstract:
- lang: eng
text: Loss-of-function mutations in the synaptic adhesion protein Neuroligin-4 are
among the most common genetic abnormalities associated with autism spectrum disorders,
but little is known about the function of Neuroligin-4 and the consequences of
its loss. We assessed synaptic and network characteristics in Neuroligin-4 knockout
mice, focusing on the hippocampus as a model brain region with a critical role
in cognition and memory, and found that Neuroligin-4 deletion causes subtle defects
of the protein composition and function of GABAergic synapses in the hippocampal
CA3 region. Interestingly, these subtle synaptic changes are accompanied by pronounced
perturbations of γ-oscillatory network activity, which has been implicated in
cognitive function and is altered in multiple psychiatric and neurodevelopmental
disorders. Our data provide important insights into the mechanisms by which Neuroligin-4-dependent
GABAergic synapses may contribute to autism phenotypes and indicate new strategies
for therapeutic approaches.
acknowledgement: This work was supported by the Max Planck Society (N.B. and H.E.),
the European Commission (EU-AIMS FP7-115300, N.B. and H.E.; Marie Curie IRG, D.K.-B.),
the German Research Foundation (CNMPB, N.B., H.E., and F.V.), the Alexander von
Humboldt-Foundation (D.K.-B.), and the Austrian Fond zur Förderung der Wissenschaftlichen
Forschung (P 24909-B24, P.J.). M.H. was a student of the doctoral program Molecular
Physiology of the Brain. Dr. J.-M. Fritschy generously provided the GABAARγ2 antibody.
We thank F. Benseler, I. Thanhäuser, D. Schwerdtfeger, A. Ronnenberg, and D. Winkler
for valuable advice and excellent technical support. We are grateful to the staff
at the animal facility of the Max Planck Institute of Experimental Medicine for
mouse husbandry.
author:
- first_name: Matthieu
full_name: Hammer, Matthieu
last_name: Hammer
- first_name: Dilja
full_name: Krueger Burg, Dilja
last_name: Krueger Burg
- first_name: Liam
full_name: Tuffy, Liam
last_name: Tuffy
- first_name: Benjamin
full_name: Cooper, Benjamin
last_name: Cooper
- first_name: Holger
full_name: Taschenberger, Holger
last_name: Taschenberger
- first_name: Sarit
full_name: Goswami, Sarit
id: 3A578F32-F248-11E8-B48F-1D18A9856A87
last_name: Goswami
- first_name: Hannelore
full_name: Ehrenreich, Hannelore
last_name: Ehrenreich
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Frederique
full_name: Varoqueaux, Frederique
last_name: Varoqueaux
- first_name: Jeong
full_name: Rhee, Jeong
last_name: Rhee
- first_name: Nils
full_name: Brose, Nils
last_name: Brose
citation:
ama: Hammer M, Krueger Burg D, Tuffy L, et al. Perturbed hippocampal synaptic inhibition
and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports.
2015;13(3):516-523. doi:10.1016/j.celrep.2015.09.011
apa: Hammer, M., Krueger Burg, D., Tuffy, L., Cooper, B., Taschenberger, H., Goswami,
S., … Brose, N. (2015). Perturbed hippocampal synaptic inhibition and γ-oscillations
in a neuroligin-4 knockout mouse model of autism. Cell Reports. Cell Press.
https://doi.org/10.1016/j.celrep.2015.09.011
chicago: Hammer, Matthieu, Dilja Krueger Burg, Liam Tuffy, Benjamin Cooper, Holger
Taschenberger, Sarit Goswami, Hannelore Ehrenreich, et al. “Perturbed Hippocampal
Synaptic Inhibition and γ-Oscillations in a Neuroligin-4 Knockout Mouse Model
of Autism.” Cell Reports. Cell Press, 2015. https://doi.org/10.1016/j.celrep.2015.09.011.
ieee: M. Hammer et al., “Perturbed hippocampal synaptic inhibition and γ-oscillations
in a neuroligin-4 knockout mouse model of autism,” Cell Reports, vol. 13,
no. 3. Cell Press, pp. 516–523, 2015.
ista: Hammer M, Krueger Burg D, Tuffy L, Cooper B, Taschenberger H, Goswami S, Ehrenreich
H, Jonas PM, Varoqueaux F, Rhee J, Brose N. 2015. Perturbed hippocampal synaptic
inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism.
Cell Reports. 13(3), 516–523.
mla: Hammer, Matthieu, et al. “Perturbed Hippocampal Synaptic Inhibition and γ-Oscillations
in a Neuroligin-4 Knockout Mouse Model of Autism.” Cell Reports, vol. 13,
no. 3, Cell Press, 2015, pp. 516–23, doi:10.1016/j.celrep.2015.09.011.
short: M. Hammer, D. Krueger Burg, L. Tuffy, B. Cooper, H. Taschenberger, S. Goswami,
H. Ehrenreich, P.M. Jonas, F. Varoqueaux, J. Rhee, N. Brose, Cell Reports 13 (2015)
516–523.
date_created: 2018-12-11T11:53:02Z
date_published: 2015-10-20T00:00:00Z
date_updated: 2021-01-12T06:52:01Z
day: '20'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1016/j.celrep.2015.09.011
file:
- access_level: open_access
checksum: 44d30fbb543774b076b4938bd36af9d7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:23Z
date_updated: 2020-07-14T12:45:07Z
file_id: '5005'
file_name: IST-2016-470-v1+1_1-s2.0-S2211124715010220-main.pdf
file_size: 2314406
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '3'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 516 - 523
publication: Cell Reports
publication_status: published
publisher: Cell Press
publist_id: '5551'
pubrep_id: '470'
quality_controlled: '1'
scopus_import: 1
status: public
title: Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4
knockout mouse model of autism
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2015'
...
---
_id: '1618'
abstract:
- lang: eng
text: CCL19 and CCL21 are chemokines involved in the trafficking of immune cells,
particularly within the lymphatic system, through activation of CCR7. Concurrent
expression of PSGL-1 and CCR7 in naive T-cells enhances recruitment of these cells
to secondary lymphoid organs by CCL19 and CCL21. Here the solution structure of
CCL19 is reported. It contains a canonical chemokine domain. Chemical shift mapping
shows the N-termini of PSGL-1 and CCR7 have overlapping binding sites for CCL19
and binding is competitive. Implications for the mechanism of PSGL-1's enhancement
of resting T-cell recruitment are discussed.
article_processing_charge: No
author:
- first_name: Christopher
full_name: Veldkamp, Christopher
last_name: Veldkamp
- first_name: Eva
full_name: Kiermaier, Eva
id: 3EB04B78-F248-11E8-B48F-1D18A9856A87
last_name: Kiermaier
orcid: 0000-0001-6165-5738
- first_name: Skylar
full_name: Gabel Eissens, Skylar
last_name: Gabel Eissens
- first_name: Miranda
full_name: Gillitzer, Miranda
last_name: Gillitzer
- first_name: David
full_name: Lippner, David
last_name: Lippner
- first_name: Frank
full_name: Disilvio, Frank
last_name: Disilvio
- first_name: Casey
full_name: Mueller, Casey
last_name: Mueller
- first_name: Paeton
full_name: Wantuch, Paeton
last_name: Wantuch
- first_name: Gary
full_name: Chaffee, Gary
last_name: Chaffee
- first_name: Michael
full_name: Famiglietti, Michael
last_name: Famiglietti
- first_name: Danielle
full_name: Zgoba, Danielle
last_name: Zgoba
- first_name: Asha
full_name: Bailey, Asha
last_name: Bailey
- first_name: Yaya
full_name: Bah, Yaya
last_name: Bah
- first_name: Samantha
full_name: Engebretson, Samantha
last_name: Engebretson
- first_name: David
full_name: Graupner, David
last_name: Graupner
- first_name: Emily
full_name: Lackner, Emily
last_name: Lackner
- first_name: Vincent
full_name: Larosa, Vincent
last_name: Larosa
- first_name: Tysha
full_name: Medeiros, Tysha
last_name: Medeiros
- first_name: Michael
full_name: Olson, Michael
last_name: Olson
- first_name: Andrew
full_name: Phillips, Andrew
last_name: Phillips
- first_name: Harley
full_name: Pyles, Harley
last_name: Pyles
- first_name: Amanda
full_name: Richard, Amanda
last_name: Richard
- first_name: Scott
full_name: Schoeller, Scott
last_name: Schoeller
- first_name: Boris
full_name: Touzeau, Boris
last_name: Touzeau
- first_name: Larry
full_name: Williams, Larry
last_name: Williams
- 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: Francis
full_name: Peterson, Francis
last_name: Peterson
citation:
ama: Veldkamp C, Kiermaier E, Gabel Eissens S, et al. Solution structure of CCL19
and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry.
2015;54(27):4163-4166. doi:10.1021/acs.biochem.5b00560
apa: Veldkamp, C., Kiermaier, E., Gabel Eissens, S., Gillitzer, M., Lippner, D.,
Disilvio, F., … Peterson, F. (2015). Solution structure of CCL19 and identification
of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. American Chemical
Society. https://doi.org/10.1021/acs.biochem.5b00560
chicago: Veldkamp, Christopher, Eva Kiermaier, Skylar Gabel Eissens, Miranda Gillitzer,
David Lippner, Frank Disilvio, Casey Mueller, et al. “Solution Structure of CCL19
and Identification of Overlapping CCR7 and PSGL-1 Binding Sites.” Biochemistry.
American Chemical Society, 2015. https://doi.org/10.1021/acs.biochem.5b00560.
ieee: C. Veldkamp et al., “Solution structure of CCL19 and identification
of overlapping CCR7 and PSGL-1 binding sites,” Biochemistry, vol. 54, no.
27. American Chemical Society, pp. 4163–4166, 2015.
ista: Veldkamp C, Kiermaier E, Gabel Eissens S, Gillitzer M, Lippner D, Disilvio
F, Mueller C, Wantuch P, Chaffee G, Famiglietti M, Zgoba D, Bailey A, Bah Y, Engebretson
S, Graupner D, Lackner E, Larosa V, Medeiros T, Olson M, Phillips A, Pyles H,
Richard A, Schoeller S, Touzeau B, Williams L, Sixt MK, Peterson F. 2015. Solution
structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites.
Biochemistry. 54(27), 4163–4166.
mla: Veldkamp, Christopher, et al. “Solution Structure of CCL19 and Identification
of Overlapping CCR7 and PSGL-1 Binding Sites.” Biochemistry, vol. 54, no.
27, American Chemical Society, 2015, pp. 4163–66, doi:10.1021/acs.biochem.5b00560.
short: C. Veldkamp, E. Kiermaier, S. Gabel Eissens, M. Gillitzer, D. Lippner, F.
Disilvio, C. Mueller, P. Wantuch, G. Chaffee, M. Famiglietti, D. Zgoba, A. Bailey,
Y. Bah, S. Engebretson, D. Graupner, E. Lackner, V. Larosa, T. Medeiros, M. Olson,
A. Phillips, H. Pyles, A. Richard, S. Schoeller, B. Touzeau, L. Williams, M.K.
Sixt, F. Peterson, Biochemistry 54 (2015) 4163–4166.
date_created: 2018-12-11T11:53:03Z
date_published: 2015-06-26T00:00:00Z
date_updated: 2023-03-30T11:32:57Z
day: '26'
department:
- _id: MiSi
doi: 10.1021/acs.biochem.5b00560
ec_funded: 1
external_id:
pmid:
- '26115234'
intvolume: ' 54'
issue: '27'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4809050/
month: '06'
oa: 1
oa_version: Submitted Version
page: 4163 - 4166
pmid: 1
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
(EU)
publication: Biochemistry
publication_status: published
publisher: American Chemical Society
publist_id: '5548'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1
binding sites
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2015'
...
---
_id: '1619'
abstract:
- lang: eng
text: The emergence of drug resistant pathogens is a serious public health problem.
It is a long-standing goal to predict rates of resistance evolution and design
optimal treatment strategies accordingly. To this end, it is crucial to reveal
the underlying causes of drug-specific differences in the evolutionary dynamics
leading to resistance. However, it remains largely unknown why the rates of resistance
evolution via spontaneous mutations and the diversity of mutational paths vary
substantially between drugs. Here we comprehensively quantify the distribution
of fitness effects (DFE) of mutations, a key determinant of evolutionary dynamics,
in the presence of eight antibiotics representing the main modes of action. Using
precise high-throughput fitness measurements for genome-wide Escherichia coli
gene deletion strains, we find that the width of the DFE varies dramatically between
antibiotics and, contrary to conventional wisdom, for some drugs the DFE width
is lower than in the absence of stress. We show that this previously underappreciated
divergence in DFE width among antibiotics is largely caused by their distinct
drug-specific dose-response characteristics. Unlike the DFE, the magnitude of
the changes in tolerated drug concentration resulting from genome-wide mutations
is similar for most drugs but exceptionally small for the antibiotic nitrofurantoin,
i.e., mutations generally have considerably smaller resistance effects for nitrofurantoin
than for other drugs. A population genetics model predicts that resistance evolution
for drugs with this property is severely limited and confined to reproducible
mutational paths. We tested this prediction in laboratory evolution experiments
using the “morbidostat”, a device for evolving bacteria in well-controlled drug
environments. Nitrofurantoin resistance indeed evolved extremely slowly via reproducible
mutations—an almost paradoxical behavior since this drug causes DNA damage and
increases the mutation rate. Overall, we identified novel quantitative characteristics
of the evolutionary landscape that provide the conceptual foundation for predicting
the dynamics of drug resistance evolution.
article_number: e1002299
author:
- first_name: Guillaume
full_name: Chevereau, Guillaume
id: 424D78A0-F248-11E8-B48F-1D18A9856A87
last_name: Chevereau
- first_name: Marta
full_name: Dravecka, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Dravecka
orcid: 0000-0002-2519-8004
- first_name: Tugce
full_name: Batur, Tugce
last_name: Batur
- first_name: Aysegul
full_name: Guvenek, Aysegul
last_name: Guvenek
- first_name: Dilay
full_name: Ayhan, Dilay
last_name: Ayhan
- first_name: Erdal
full_name: Toprak, Erdal
last_name: Toprak
- 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: Chevereau G, Lukacisinova M, Batur T, et al. Quantifying the determinants of
evolutionary dynamics leading to drug resistance. PLoS Biology. 2015;13(11).
doi:10.1371/journal.pbio.1002299
apa: Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D., Toprak,
E., & Bollenbach, M. T. (2015). Quantifying the determinants of evolutionary
dynamics leading to drug resistance. PLoS Biology. Public Library of Science.
https://doi.org/10.1371/journal.pbio.1002299
chicago: Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek,
Dilay Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Quantifying the Determinants
of Evolutionary Dynamics Leading to Drug Resistance.” PLoS Biology. Public
Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.
ieee: G. Chevereau et al., “Quantifying the determinants of evolutionary
dynamics leading to drug resistance,” PLoS Biology, vol. 13, no. 11. Public
Library of Science, 2015.
ista: Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan D, Toprak E, Bollenbach
MT. 2015. Quantifying the determinants of evolutionary dynamics leading to drug
resistance. PLoS Biology. 13(11), e1002299.
mla: Chevereau, Guillaume, et al. “Quantifying the Determinants of Evolutionary
Dynamics Leading to Drug Resistance.” PLoS Biology, vol. 13, no. 11, e1002299,
Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299.
short: G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D. Ayhan, E. Toprak,
M.T. Bollenbach, PLoS Biology 13 (2015).
date_created: 2018-12-11T11:53:04Z
date_published: 2015-11-18T00:00:00Z
date_updated: 2024-03-25T23:30:14Z
day: '18'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.1371/journal.pbio.1002299
ec_funded: 1
file:
- access_level: open_access
checksum: 0e82e3279f50b15c6c170c042627802b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:00Z
date_updated: 2020-07-14T12:45:07Z
file_id: '4723'
file_name: IST-2016-468-v1+1_journal.pbio.1002299.pdf
file_size: 1387760
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25EB3A80-B435-11E9-9278-68D0E5697425
grant_number: RGP0042/2013
name: Revealing the fundamental limits of cell growth
- _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
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5547'
pubrep_id: '468'
quality_controlled: '1'
related_material:
record:
- id: '9711'
relation: research_data
status: public
- id: '9765'
relation: research_data
status: public
- id: '6263'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Quantifying the determinants of evolutionary dynamics leading to drug resistance
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2015'
...
---
_id: '1623'
abstract:
- lang: eng
text: "Background\r\nPhotosynthetic cyanobacteria are attractive for a range of
biotechnological applications including biofuel production. However, due to slow
growth, screening of mutant libraries using microtiter plates is not feasible.\r\nResults\r\nWe
present a method for high-throughput, single-cell analysis and sorting of genetically
engineered l-lactate-producing strains of Synechocystis sp. PCC6803. A microfluidic
device is used to encapsulate single cells in picoliter droplets, assay the droplets
for l-lactate production, and sort strains with high productivity. We demonstrate
the separation of low- and high-producing reference strains, as well as enrichment
of a more productive l-lactate-synthesizing population after UV-induced mutagenesis.
The droplet platform also revealed population heterogeneity in photosynthetic
growth and lactate production, as well as the presence of metabolically stalled
cells.\r\nConclusions\r\nThe workflow will facilitate metabolic engineering and
directed evolution studies and will be useful in studies of cyanobacteria biochemistry
and physiology.\r\n"
article_number: '193'
author:
- first_name: Petter
full_name: Hammar, Petter
last_name: Hammar
- first_name: Andreas
full_name: Angermayr, Andreas
id: 4677C796-F248-11E8-B48F-1D18A9856A87
last_name: Angermayr
orcid: 0000-0001-8619-2223
- first_name: Staffan
full_name: Sjostrom, Staffan
last_name: Sjostrom
- first_name: Josefin
full_name: Van Der Meer, Josefin
last_name: Van Der Meer
- first_name: Klaas
full_name: Hellingwerf, Klaas
last_name: Hellingwerf
- first_name: Elton
full_name: Hudson, Elton
last_name: Hudson
- first_name: Hakaan
full_name: Joensson, Hakaan
last_name: Joensson
citation:
ama: Hammar P, Angermayr A, Sjostrom S, et al. Single-cell screening of photosynthetic
growth and lactate production by cyanobacteria. Biotechnology for Biofuels.
2015;8(1). doi:10.1186/s13068-015-0380-2
apa: Hammar, P., Angermayr, A., Sjostrom, S., Van Der Meer, J., Hellingwerf, K.,
Hudson, E., & Joensson, H. (2015). Single-cell screening of photosynthetic
growth and lactate production by cyanobacteria. Biotechnology for Biofuels.
BioMed Central. https://doi.org/10.1186/s13068-015-0380-2
chicago: Hammar, Petter, Andreas Angermayr, Staffan Sjostrom, Josefin Van Der Meer,
Klaas Hellingwerf, Elton Hudson, and Hakaan Joensson. “Single-Cell Screening of
Photosynthetic Growth and Lactate Production by Cyanobacteria.” Biotechnology
for Biofuels. BioMed Central, 2015. https://doi.org/10.1186/s13068-015-0380-2.
ieee: P. Hammar et al., “Single-cell screening of photosynthetic growth and
lactate production by cyanobacteria,” Biotechnology for Biofuels, vol.
8, no. 1. BioMed Central, 2015.
ista: Hammar P, Angermayr A, Sjostrom S, Van Der Meer J, Hellingwerf K, Hudson E,
Joensson H. 2015. Single-cell screening of photosynthetic growth and lactate production
by cyanobacteria. Biotechnology for Biofuels. 8(1), 193.
mla: Hammar, Petter, et al. “Single-Cell Screening of Photosynthetic Growth and
Lactate Production by Cyanobacteria.” Biotechnology for Biofuels, vol.
8, no. 1, 193, BioMed Central, 2015, doi:10.1186/s13068-015-0380-2.
short: P. Hammar, A. Angermayr, S. Sjostrom, J. Van Der Meer, K. Hellingwerf, E.
Hudson, H. Joensson, Biotechnology for Biofuels 8 (2015).
date_created: 2018-12-11T11:53:05Z
date_published: 2015-11-25T00:00:00Z
date_updated: 2021-01-12T06:52:04Z
day: '25'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.1186/s13068-015-0380-2
file:
- access_level: open_access
checksum: 172b0b6f4eb2e5c22b7cec1d57dc0107
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:11Z
date_updated: 2020-07-14T12:45:07Z
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file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '1'
language:
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month: '11'
oa: 1
oa_version: Published Version
publication: Biotechnology for Biofuels
publication_status: published
publisher: BioMed Central
publist_id: '5537'
pubrep_id: '467'
quality_controlled: '1'
scopus_import: 1
status: public
title: Single-cell screening of photosynthetic growth and lactate production by cyanobacteria
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2015'
...