---
_id: '665'
abstract:
- lang: eng
text: The molecular mechanisms underlying phenotypic variation in isogenic bacterial
populations remain poorly understood.We report that AcrAB-TolC, the main multidrug
efflux pump of Escherichia coli, exhibits a strong partitioning bias for old cell
poles by a segregation mechanism that is mediated by ternary AcrAB-TolC complex
formation. Mother cells inheriting old poles are phenotypically distinct and display
increased drug efflux activity relative to daughters. Consequently, we find systematic
and long-lived growth differences between mother and daughter cells in the presence
of subinhibitory drug concentrations. A simple model for biased partitioning predicts
a population structure of long-lived and highly heterogeneous phenotypes. This
straightforward mechanism of generating sustained growth rate differences at subinhibitory
antibiotic concentrations has implications for understanding the emergence of
multidrug resistance in bacteria.
article_processing_charge: No
article_type: original
author:
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Anna M
full_name: Andersson, Anna M
id: 2B8A40DA-F248-11E8-B48F-1D18A9856A87
last_name: Andersson
orcid: 0000-0003-2912-6769
- first_name: Kathrin
full_name: Tomasek, Kathrin
id: 3AEC8556-F248-11E8-B48F-1D18A9856A87
last_name: Tomasek
orcid: 0000-0003-3768-877X
- first_name: Enrique
full_name: Balleza, Enrique
last_name: Balleza
- first_name: Daniel
full_name: Kiviet, Daniel
last_name: Kiviet
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- 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: Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multidrug
efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science.
2017;356(6335):311-315. doi:10.1126/science.aaf4762
apa: Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild,
R., … Guet, C. C. (2017). Biased partitioning of the multidrug efflux pump AcrAB
TolC underlies long lived phenotypic heterogeneity. Science. American Association
for the Advancement of Science. https://doi.org/10.1126/science.aaf4762
chicago: Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza,
Daniel Kiviet, Robert Hauschild, Gašper Tkačik, and Calin C Guet. “Biased Partitioning
of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.”
Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aaf4762.
ieee: T. Bergmiller et al., “Biased partitioning of the multidrug efflux
pump AcrAB TolC underlies long lived phenotypic heterogeneity,” Science,
vol. 356, no. 6335. American Association for the Advancement of Science, pp. 311–315,
2017.
ista: Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkačik
G, Guet CC. 2017. Biased partitioning of the multidrug efflux pump AcrAB TolC
underlies long lived phenotypic heterogeneity. Science. 356(6335), 311–315.
mla: Bergmiller, Tobias, et al. “Biased Partitioning of the Multidrug Efflux Pump
AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” Science, vol.
356, no. 6335, American Association for the Advancement of Science, 2017, pp.
311–15, doi:10.1126/science.aaf4762.
short: T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild,
G. Tkačik, C.C. Guet, Science 356 (2017) 311–315.
date_created: 2018-12-11T11:47:48Z
date_published: 2017-04-21T00:00:00Z
date_updated: 2024-02-21T13:49:00Z
day: '21'
department:
- _id: CaGu
- _id: GaTk
- _id: Bio
doi: 10.1126/science.aaf4762
intvolume: ' 356'
issue: '6335'
language:
- iso: eng
month: '04'
oa_version: None
page: 311 - 315
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Science
publication_identifier:
issn:
- '00368075'
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '7064'
quality_controlled: '1'
related_material:
record:
- id: '5560'
relation: popular_science
status: public
scopus_import: 1
status: public
title: Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long
lived phenotypic heterogeneity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 356
year: '2017'
...
---
_id: '5571'
abstract:
- lang: eng
text: "This folder contains all the data used in each of the main figures of \"The
genomic characterization of the t-haplotype, a mouse meiotic driver, highlights
its complex history and specialized biology\" (Kelemen, R., Vicoso, B.), as well
as in the supplementary figures. \r\n"
article_processing_charge: No
author:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Vicoso B. Data for “The genomic characterization of the t-haplotype, a mouse
meiotic driver, highlights its complex history and specialized biology.” 2017.
doi:10.15479/AT:ISTA:78
apa: Vicoso, B. (2017). Data for “The genomic characterization of the t-haplotype,
a mouse meiotic driver, highlights its complex history and specialized biology.”
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:78
chicago: Vicoso, Beatriz. “Data for ‘The Genomic Characterization of the t-Haplotype,
a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.’”
Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:78.
ieee: B. Vicoso, “Data for ‘The genomic characterization of the t-haplotype, a mouse
meiotic driver, highlights its complex history and specialized biology.’” Institute
of Science and Technology Austria, 2017.
ista: Vicoso B. 2017. Data for ‘The genomic characterization of the t-haplotype,
a mouse meiotic driver, highlights its complex history and specialized biology’,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:78.
mla: Vicoso, Beatriz. Data for “The Genomic Characterization of the t-Haplotype,
a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.”
Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:78.
short: B. Vicoso, (2017).
contributor:
- contributor_type: contact_person
first_name: Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
datarep_id: '78'
date_created: 2018-12-12T12:31:36Z
date_published: 2017-11-06T00:00:00Z
date_updated: 2024-02-21T13:48:16Z
day: '06'
ddc:
- '576'
department:
- _id: BeVi
doi: 10.15479/AT:ISTA:78
file:
- access_level: open_access
checksum: 4520eb2b8379417ee916995719158f16
content_type: application/zip
creator: system
date_created: 2018-12-12T13:03:00Z
date_updated: 2020-07-14T12:47:04Z
file_id: '5618'
file_name: IST-2017-78-v1+1_Data.zip
file_size: 143697895
relation: main_file
file_date_updated: 2020-07-14T12:47:04Z
has_accepted_license: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '11'
oa: 1
oa_version: Submitted Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '542'
relation: research_paper
status: public
status: public
title: Data for "The genomic characterization of the t-haplotype, a mouse meiotic
driver, highlights its complex history and specialized biology"
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '5559'
abstract:
- lang: eng
text: Strong amplifiers of natural selection
article_processing_charge: No
author:
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak , Martin
last_name: 'Nowak '
citation:
ama: Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Strong amplifiers of natural
selection. 2017. doi:10.15479/AT:ISTA:51
apa: Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak , M. (2017). Strong
amplifiers of natural selection. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:51
chicago: Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin
Nowak . “Strong Amplifiers of Natural Selection.” Institute of Science and Technology
Austria, 2017. https://doi.org/10.15479/AT:ISTA:51.
ieee: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak , “Strong amplifiers
of natural selection.” Institute of Science and Technology Austria, 2017.
ista: Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2017. Strong amplifiers
of natural selection, Institute of Science and Technology Austria, 10.15479/AT:ISTA:51.
mla: Pavlogiannis, Andreas, et al. Strong Amplifiers of Natural Selection.
Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:51.
short: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak , (2017).
datarep_id: '51'
date_created: 2018-12-12T12:31:32Z
date_published: 2017-01-02T00:00:00Z
date_updated: 2024-02-21T13:48:42Z
day: '02'
ddc:
- '519'
department:
- _id: KrCh
doi: 10.15479/AT:ISTA:51
ec_funded: 1
file:
- access_level: open_access
checksum: b427dd46a30096a1911b245640c47af8
content_type: video/mp4
creator: system
date_created: 2018-12-12T13:05:18Z
date_updated: 2020-07-14T12:47:02Z
file_id: '5644'
file_name: IST-2017-51-v1+2_illustration.mp4
file_size: 32987015
relation: main_file
file_date_updated: 2020-07-14T12:47:02Z
has_accepted_license: '1'
keyword:
- natural selection
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '5452'
relation: research_paper
status: public
- id: '5751'
relation: research_paper
status: public
status: public
title: Strong amplifiers of natural selection
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '5572'
abstract:
- lang: eng
text: Code described in the Supplementary Methods of "The genomic characterization
of the t-haplotype, a mouse meiotic driver, highlights its complex history and
specialized biology" (Kelemen, R., Vicoso, B.)
article_processing_charge: No
author:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Vicoso B. Code for “The genomic characterization of the t-haplotype, a mouse
meiotic driver, highlights its complex history and specialized biology.” 2017.
doi:10.15479/AT:ISTA:79
apa: Vicoso, B. (2017). Code for “The genomic characterization of the t-haplotype,
a mouse meiotic driver, highlights its complex history and specialized biology.”
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:79
chicago: Vicoso, Beatriz. “Code for ‘The Genomic Characterization of the t-Haplotype,
a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.’”
Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:79 .
ieee: B. Vicoso, “Code for ‘The genomic characterization of the t-haplotype, a mouse
meiotic driver, highlights its complex history and specialized biology.’” Institute
of Science and Technology Austria, 2017.
ista: Vicoso B. 2017. Code for ‘The genomic characterization of the t-haplotype,
a mouse meiotic driver, highlights its complex history and specialized biology’,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:79 .
mla: Vicoso, Beatriz. Code for “The Genomic Characterization of the t-Haplotype,
a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.”
Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:79 .
short: B. Vicoso, (2017).
datarep_id: '79'
date_created: 2018-12-12T12:31:36Z
date_published: 2017-11-06T00:00:00Z
date_updated: 2024-02-21T13:48:28Z
day: '06'
ddc:
- '576'
department:
- _id: BeVi
doi: '10.15479/AT:ISTA:79 '
file:
- access_level: open_access
checksum: 3e70a7bcd6ff0c38b79e4c8a7d137034
content_type: application/zip
creator: system
date_created: 2018-12-12T13:05:15Z
date_updated: 2020-07-14T12:47:05Z
file_id: '5643'
file_name: IST-2017-79-v1+1_Code.zip
file_size: 49823
relation: main_file
file_date_updated: 2020-07-14T12:47:05Z
has_accepted_license: '1'
month: '11'
oa: 1
oa_version: Submitted Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '542'
relation: research_paper
status: public
status: public
title: Code for "The genomic characterization of the t-haplotype, a mouse meiotic
driver, highlights its complex history and specialized biology"
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '946'
abstract:
- lang: eng
text: Roots navigate through soil integrating environmental signals to orient their
growth. The Arabidopsis root is a widely used model for developmental, physiological
and cell biological studies. Live imaging greatly aids these efforts, but the
horizontal sample position and continuous root tip displacement present significant
difficulties. Here, we develop a confocal microscope setup for vertical sample
mounting and integrated directional illumination. We present TipTracker – a custom
software for automatic tracking of diverse moving objects usable on various microscope
setups. Combined, this enables observation of root tips growing along the natural
gravity vector over prolonged periods of time, as well as the ability to induce
rapid gravity or light stimulation. We also track migrating cells in the developing
zebrafish embryo, demonstrating the utility of this system in the acquisition
of high-resolution data sets of dynamic samples. We provide detailed descriptions
of the tools enabling the easy implementation on other microscopes.
acknowledged_ssus:
- _id: M-Shop
- _id: Bio
acknowledgement: "Funding: Marie Curie Actions (FP7/2007-2013 no 291734) to Daniel
von Wangenheim; Austrian Science Fund (M 2128-B21) to Matyáš Fendrych; Austrian
Science Fund (FWF01_I1774S) to Eva Benková; European Research Council (FP7/2007-2013
no 282300) to Jiří Friml. \r\nThe authors are grateful to the Miba Machine Shop
at IST Austria for their contribution to the microscope setup and to Yvonne Kemper
for reading, understanding and correcting the manuscript.\r\n#BioimagingFacility"
article_number: e26792
article_processing_charge: Yes
author:
- first_name: Daniel
full_name: Von Wangenheim, Daniel
id: 49E91952-F248-11E8-B48F-1D18A9856A87
last_name: Von Wangenheim
orcid: 0000-0002-6862-1247
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Vanessa
full_name: Barone, Vanessa
id: 419EECCC-F248-11E8-B48F-1D18A9856A87
last_name: Barone
orcid: 0000-0003-2676-3367
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. Live
tracking of moving samples in confocal microscopy for vertically grown roots.
eLife. 2017;6. doi:10.7554/eLife.26792
apa: von Wangenheim, D., Hauschild, R., Fendrych, M., Barone, V., Benková, E., &
Friml, J. (2017). Live tracking of moving samples in confocal microscopy for vertically
grown roots. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.26792
chicago: Wangenheim, Daniel von, Robert Hauschild, Matyas Fendrych, Vanessa Barone,
Eva Benková, and Jiří Friml. “Live Tracking of Moving Samples in Confocal Microscopy
for Vertically Grown Roots.” ELife. eLife Sciences Publications, 2017.
https://doi.org/10.7554/eLife.26792.
ieee: D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, and J.
Friml, “Live tracking of moving samples in confocal microscopy for vertically
grown roots,” eLife, vol. 6. eLife Sciences Publications, 2017.
ista: von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. 2017.
Live tracking of moving samples in confocal microscopy for vertically grown roots.
eLife. 6, e26792.
mla: von Wangenheim, Daniel, et al. “Live Tracking of Moving Samples in Confocal
Microscopy for Vertically Grown Roots.” ELife, vol. 6, e26792, eLife Sciences
Publications, 2017, doi:10.7554/eLife.26792.
short: D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, J. Friml,
ELife 6 (2017).
date_created: 2018-12-11T11:49:21Z
date_published: 2017-06-19T00:00:00Z
date_updated: 2024-02-21T13:49:34Z
day: '19'
ddc:
- '570'
department:
- _id: JiFr
- _id: Bio
- _id: CaHe
- _id: EvBe
doi: 10.7554/eLife.26792
ec_funded: 1
external_id:
isi:
- '000404728300001'
file:
- access_level: open_access
checksum: 9af3398cb0d81f99d79016a616df22e9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:57Z
date_updated: 2020-07-14T12:48:15Z
file_id: '5315'
file_name: IST-2017-847-v1+1_elife-26792-v2.pdf
file_size: 19581847
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
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
- _id: 2572ED28-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02128
name: Molecular basis of root growth inhibition by auxin
- _id: 2542D156-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 1774-B16
name: Hormone cross-talk drives nutrient dependent plant development
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '6471'
pubrep_id: '847'
quality_controlled: '1'
related_material:
record:
- id: '5566'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Live tracking of moving samples in confocal microscopy for vertically grown
roots
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 6
year: '2017'
...
---
_id: '1078'
abstract:
- lang: eng
text: 'One of the key questions in understanding plant development is how single
cells behave in a larger context of the tissue. Therefore, it requires the observation
of the whole organ with a high spatial- as well as temporal resolution over prolonged
periods of time, which may cause photo-toxic effects. This protocol shows a plant
sample preparation method for light-sheet microscopy, which is characterized by
mounting the plant vertically on the surface of a gel. The plant is mounted in
such a way that the roots are submerged in a liquid medium while the leaves remain
in the air. In order to ensure photosynthetic activity of the plant, a custom-made
lighting system illuminates the leaves. To keep the roots in darkness the water
surface is covered with sheets of black plastic foil. This method allows long-term
imaging of plant organ development in standardized conditions. '
acknowledged_ssus:
- _id: M-Shop
- _id: Bio
article_number: e55044
article_processing_charge: No
author:
- first_name: Daniel
full_name: Von Wangenheim, Daniel
id: 49E91952-F248-11E8-B48F-1D18A9856A87
last_name: Von Wangenheim
orcid: 0000-0002-6862-1247
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: von Wangenheim D, Hauschild R, Friml J. Light sheet fluorescence microscopy
of plant roots growing on the surface of a gel. Journal of visualized experiments
JoVE. 2017;2017(119). doi:10.3791/55044
apa: von Wangenheim, D., Hauschild, R., & Friml, J. (2017). Light sheet fluorescence
microscopy of plant roots growing on the surface of a gel. Journal of Visualized
Experiments JoVE. Journal of Visualized Experiments. https://doi.org/10.3791/55044
chicago: Wangenheim, Daniel von, Robert Hauschild, and Jiří Friml. “Light Sheet
Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” Journal
of Visualized Experiments JoVE. Journal of Visualized Experiments, 2017. https://doi.org/10.3791/55044.
ieee: D. von Wangenheim, R. Hauschild, and J. Friml, “Light sheet fluorescence microscopy
of plant roots growing on the surface of a gel,” Journal of visualized experiments
JoVE, vol. 2017, no. 119. Journal of Visualized Experiments, 2017.
ista: von Wangenheim D, Hauschild R, Friml J. 2017. Light sheet fluorescence microscopy
of plant roots growing on the surface of a gel. Journal of visualized experiments
JoVE. 2017(119), e55044.
mla: von Wangenheim, Daniel, et al. “Light Sheet Fluorescence Microscopy of Plant
Roots Growing on the Surface of a Gel.” Journal of Visualized Experiments JoVE,
vol. 2017, no. 119, e55044, Journal of Visualized Experiments, 2017, doi:10.3791/55044.
short: D. von Wangenheim, R. Hauschild, J. Friml, Journal of Visualized Experiments
JoVE 2017 (2017).
date_created: 2018-12-11T11:50:01Z
date_published: 2017-01-18T00:00:00Z
date_updated: 2024-02-21T13:49:12Z
day: '18'
ddc:
- '580'
department:
- _id: JiFr
- _id: Bio
doi: 10.3791/55044
ec_funded: 1
external_id:
isi:
- '000397847200041'
file:
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content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:31Z
date_updated: 2018-12-12T10:16:31Z
file_id: '5219'
file_name: IST-2017-808-v1+1_2017_VWangenheim_list.pdf
file_size: 57678
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content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:32Z
date_updated: 2018-12-12T10:16:32Z
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file_size: 1317820
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has_accepted_license: '1'
intvolume: ' 2017'
isi: 1
issue: '119'
language:
- iso: eng
month: '01'
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
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Journal of visualized experiments JoVE
publication_status: published
publisher: Journal of Visualized Experiments
publist_id: '6302'
pubrep_id: '808'
related_material:
record:
- id: '5565'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Light sheet fluorescence microscopy of plant roots growing on the surface of
a gel
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2017
year: '2017'
...
---
_id: '5565'
abstract:
- lang: eng
text: "One of the key questions in understanding plant development is how single
cells behave in a larger context of the tissue. Therefore, it requires the observation
of the whole organ with a high spatial- as well as temporal resolution over prolonged
periods of time, which may cause photo-toxic effects. This protocol shows a plant
sample preparation method for light-sheet microscopy, which is characterized by
mounting the plant vertically on the surface of a gel. The plant is mounted in
such a way that the roots are submerged in a liquid medium while the leaves remain
in the air. In order to ensure photosynthetic activity of the plant, a custom-made
lighting system illuminates the leaves. To keep the roots in darkness the water
surface is covered with sheets of black plastic foil. This method allows long-term
imaging of plant organ development in standardized conditions. \r\nThe Video is
licensed under a CC BY NC ND license. "
acknowledgement: 'fund: FP7-ERC 0101109'
article_processing_charge: No
author:
- first_name: Daniel
full_name: Von Wangenheim, Daniel
id: 49E91952-F248-11E8-B48F-1D18A9856A87
last_name: Von Wangenheim
orcid: 0000-0002-6862-1247
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: von Wangenheim D, Hauschild R, Friml J. Light Sheet Fluorescence microscopy
of plant roots growing on the surface of a gel. 2017. doi:10.15479/AT:ISTA:66
apa: von Wangenheim, D., Hauschild, R., & Friml, J. (2017). Light Sheet Fluorescence
microscopy of plant roots growing on the surface of a gel. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:66
chicago: Wangenheim, Daniel von, Robert Hauschild, and Jiří Friml. “Light Sheet
Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” Institute
of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:66.
ieee: D. von Wangenheim, R. Hauschild, and J. Friml, “Light Sheet Fluorescence microscopy
of plant roots growing on the surface of a gel.” Institute of Science and Technology
Austria, 2017.
ista: von Wangenheim D, Hauschild R, Friml J. 2017. Light Sheet Fluorescence microscopy
of plant roots growing on the surface of a gel, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:66.
mla: von Wangenheim, Daniel, et al. Light Sheet Fluorescence Microscopy of Plant
Roots Growing on the Surface of a Gel. Institute of Science and Technology
Austria, 2017, doi:10.15479/AT:ISTA:66.
short: D. von Wangenheim, R. Hauschild, J. Friml, (2017).
datarep_id: '66'
date_created: 2018-12-12T12:31:34Z
date_published: 2017-04-10T00:00:00Z
date_updated: 2024-02-21T13:49:13Z
day: '10'
ddc:
- '580'
department:
- _id: JiFr
- _id: Bio
doi: 10.15479/AT:ISTA:66
ec_funded: 1
file:
- access_level: open_access
checksum: b7552fc23540a85dc5a22fd4484eae71
content_type: video/mp4
creator: system
date_created: 2018-12-12T13:02:33Z
date_updated: 2020-07-14T12:47:03Z
file_id: '5599'
file_name: IST-2017-66-v1+1_WangenheimHighResolution55044-NEW_1.mp4
file_size: 101497758
relation: main_file
file_date_updated: 2020-07-14T12:47:03Z
has_accepted_license: '1'
month: '04'
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
publisher: Institute of Science and Technology Austria
publist_id: '6302'
related_material:
record:
- id: '1078'
relation: research_paper
status: public
status: public
title: Light Sheet Fluorescence microscopy of plant roots growing on the surface of
a gel
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '5566'
abstract:
- lang: eng
text: Current minimal version of TipTracker
article_processing_charge: No
author:
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
citation:
ama: Hauschild R. Live tracking of moving samples in confocal microscopy for vertically
grown roots. 2017. doi:10.15479/AT:ISTA:69
apa: Hauschild, R. (2017). Live tracking of moving samples in confocal microscopy
for vertically grown roots. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:69
chicago: Hauschild, Robert. “Live Tracking of Moving Samples in Confocal Microscopy
for Vertically Grown Roots.” Institute of Science and Technology Austria, 2017.
https://doi.org/10.15479/AT:ISTA:69.
ieee: R. Hauschild, “Live tracking of moving samples in confocal microscopy for
vertically grown roots.” Institute of Science and Technology Austria, 2017.
ista: Hauschild R. 2017. Live tracking of moving samples in confocal microscopy
for vertically grown roots, Institute of Science and Technology Austria, 10.15479/AT:ISTA:69.
mla: Hauschild, Robert. Live Tracking of Moving Samples in Confocal Microscopy
for Vertically Grown Roots. Institute of Science and Technology Austria, 2017,
doi:10.15479/AT:ISTA:69.
short: R. Hauschild, (2017).
datarep_id: '69'
date_created: 2018-12-12T12:31:34Z
date_published: 2017-07-21T00:00:00Z
date_updated: 2024-02-21T13:49:34Z
day: '21'
ddc:
- '570'
department:
- _id: Bio
doi: 10.15479/AT:ISTA:69
file:
- access_level: open_access
checksum: a976000e6715106724a271cc9422be4a
content_type: application/zip
creator: system
date_created: 2018-12-12T13:04:12Z
date_updated: 2020-07-14T12:47:04Z
file_id: '5636'
file_name: IST-2017-69-v1+2_TipTrackerZeissLSM700.zip
file_size: 1587986
relation: main_file
file_date_updated: 2020-07-14T12:47:04Z
has_accepted_license: '1'
keyword:
- tool
- tracking
- confocal microscopy
license: https://creativecommons.org/licenses/by-sa/4.0/
month: '07'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '946'
relation: research_paper
status: public
status: public
title: Live tracking of moving samples in confocal microscopy for vertically grown
roots
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '424'
abstract:
- lang: eng
text: 'We show that very weak topological assumptions are enough to ensure the existence
of a Helly-type theorem. More precisely, we show that for any non-negative integers
b and d there exists an integer h(b, d) such that the following holds. If F is
a finite family of subsets of Rd such that βi(∩G)≤b for any G⊊F and every 0 ≤
i ≤ [d/2]-1 then F has Helly number at most h(b, d). Here βi denotes the reduced
Z2-Betti numbers (with singular homology). These topological conditions are sharp:
not controlling any of these [d/2] first Betti numbers allow for families with
unbounded Helly number. Our proofs combine homological non-embeddability results
with a Ramsey-based approach to build, given an arbitrary simplicial complex K,
some well-behaved chain map C*(K)→C*(Rd).'
author:
- first_name: Xavier
full_name: Goaoc, Xavier
last_name: Goaoc
- first_name: Pavel
full_name: Paták, Pavel
last_name: Paták
- first_name: Zuzana
full_name: Patakova, Zuzana
last_name: Patakova
orcid: 0000-0002-3975-1683
- first_name: Martin
full_name: Tancer, Martin
last_name: Tancer
orcid: 0000-0002-1191-6714
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Bounding helly numbers via
betti numbers. In: Loebl M, Nešetřil J, Thomas R, eds. A Journey through Discrete
Mathematics: A Tribute to Jiri Matousek. A Journey Through Discrete Mathematics.
Springer; 2017:407-447. doi:10.1007/978-3-319-44479-6_17'
apa: 'Goaoc, X., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2017). Bounding
helly numbers via betti numbers. In M. Loebl, J. Nešetřil, & R. Thomas (Eds.),
A Journey through Discrete Mathematics: A Tribute to Jiri Matousek (pp.
407–447). Springer. https://doi.org/10.1007/978-3-319-44479-6_17'
chicago: 'Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner.
“Bounding Helly Numbers via Betti Numbers.” In A Journey through Discrete Mathematics:
A Tribute to Jiri Matousek, edited by Martin Loebl, Jaroslav Nešetřil, and
Robin Thomas, 407–47. A Journey Through Discrete Mathematics. Springer, 2017.
https://doi.org/10.1007/978-3-319-44479-6_17.'
ieee: 'X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Bounding helly
numbers via betti numbers,” in A Journey through Discrete Mathematics: A Tribute
to Jiri Matousek, M. Loebl, J. Nešetřil, and R. Thomas, Eds. Springer, 2017,
pp. 407–447.'
ista: 'Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2017.Bounding helly numbers
via betti numbers. In: A Journey through Discrete Mathematics: A Tribute to Jiri
Matousek. , 407–447.'
mla: 'Goaoc, Xavier, et al. “Bounding Helly Numbers via Betti Numbers.” A Journey
through Discrete Mathematics: A Tribute to Jiri Matousek, edited by Martin
Loebl et al., Springer, 2017, pp. 407–47, doi:10.1007/978-3-319-44479-6_17.'
short: 'X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, M. Loebl, J.
Nešetřil, R. Thomas (Eds.), A Journey through Discrete Mathematics: A Tribute
to Jiri Matousek, Springer, 2017, pp. 407–447.'
date_created: 2018-12-11T11:46:24Z
date_published: 2017-10-06T00:00:00Z
date_updated: 2024-02-28T12:59:37Z
day: '06'
department:
- _id: UlWa
doi: 10.1007/978-3-319-44479-6_17
editor:
- first_name: Martin
full_name: Loebl, Martin
last_name: Loebl
- first_name: Jaroslav
full_name: Nešetřil, Jaroslav
last_name: Nešetřil
- first_name: Robin
full_name: Thomas, Robin
last_name: Thomas
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1310.4613v3
month: '10'
oa: 1
oa_version: Published Version
page: 407 - 447
publication: 'A Journey through Discrete Mathematics: A Tribute to Jiri Matousek'
publication_identifier:
isbn:
- 978-331944479-6
publication_status: published
publisher: Springer
publist_id: '7399'
quality_controlled: '1'
related_material:
record:
- id: '1512'
relation: earlier_version
status: public
scopus_import: 1
series_title: A Journey Through Discrete Mathematics
status: public
title: Bounding helly numbers via betti numbers
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '463'
abstract:
- lang: eng
text: We investigate transient behaviors induced by magnetic fields on the dynamics
of the flow of a ferrofluid in the gap between two concentric, independently rotating
cylinders. Without applying any magnetic fields, we uncover emergence of flow
states constituted by a combination of a localized spiral state (SPIl) in the
top and bottom of the annulus and different multi-cell flow states (SPI2v, SPI3v)
with toroidally closed vortices in the interior of the bulk (SPIl+2v = SPIl +
SPI2v and SPIl+3v = SPIl + SPI3v). However, when a magnetic field is presented,
we observe the transient behaviors between multi-cell states passing through two
critical thresholds in a strength of an axial (transverse) magnetic field. Before
the first critical threshold of a magnetic field strength, multi-stable states
with different number of cells could be observed. After the first critical threshold,
we find the transient behavior between the three- and two-cell flow states. For
more strength of magnetic field or after the second critical threshold, we discover
that multi-cell states are disappeared and a localized spiral state remains to
be stimulated. The studied transient behavior could be understood by the investigation
of various quantities including a modal kinetic energy, a mode amplitude of the
radial velocity, wavenumber, angular momentum, and torque. In addition, the emergence
of new flow states and the transient behavior between their states in ferrofluidic
flows indicate that richer and potentially controllable dynamics through magnetic
fields could be possible in ferrofluic flow.
article_number: '113112'
article_processing_charge: No
article_type: original
author:
- first_name: Sebastian
full_name: Altmeyer, Sebastian
id: 2EE67FDC-F248-11E8-B48F-1D18A9856A87
last_name: Altmeyer
orcid: 0000-0001-5964-0203
- first_name: Younghae
full_name: Do, Younghae
last_name: Do
- first_name: Soorok
full_name: Ryu, Soorok
last_name: Ryu
citation:
ama: Altmeyer S, Do Y, Ryu S. Transient behavior between multi-cell flow states
in ferrofluidic Taylor-Couette flow. Chaos. 2017;27(11). doi:10.1063/1.5002771
apa: Altmeyer, S., Do, Y., & Ryu, S. (2017). Transient behavior between multi-cell
flow states in ferrofluidic Taylor-Couette flow. Chaos. AIP Publishing.
https://doi.org/10.1063/1.5002771
chicago: Altmeyer, Sebastian, Younghae Do, and Soorok Ryu. “Transient Behavior between
Multi-Cell Flow States in Ferrofluidic Taylor-Couette Flow.” Chaos. AIP
Publishing, 2017. https://doi.org/10.1063/1.5002771.
ieee: S. Altmeyer, Y. Do, and S. Ryu, “Transient behavior between multi-cell flow
states in ferrofluidic Taylor-Couette flow,” Chaos, vol. 27, no. 11. AIP
Publishing, 2017.
ista: Altmeyer S, Do Y, Ryu S. 2017. Transient behavior between multi-cell flow
states in ferrofluidic Taylor-Couette flow. Chaos. 27(11), 113112.
mla: Altmeyer, Sebastian, et al. “Transient Behavior between Multi-Cell Flow States
in Ferrofluidic Taylor-Couette Flow.” Chaos, vol. 27, no. 11, 113112, AIP
Publishing, 2017, doi:10.1063/1.5002771.
short: S. Altmeyer, Y. Do, S. Ryu, Chaos 27 (2017).
date_created: 2018-12-11T11:46:37Z
date_published: 2017-11-01T00:00:00Z
date_updated: 2024-02-28T13:02:12Z
day: '01'
ddc:
- '530'
department:
- _id: BjHo
doi: 10.1063/1.5002771
file:
- access_level: open_access
checksum: 0731f9d416760c1062db258ca51f8bdc
content_type: application/pdf
creator: dernst
date_created: 2019-10-24T15:14:30Z
date_updated: 2020-07-14T12:46:32Z
file_id: '6970'
file_name: 2017_Chaos_Altmeyer.pdf
file_size: 7714020
relation: main_file
file_date_updated: 2020-07-14T12:46:32Z
has_accepted_license: '1'
intvolume: ' 27'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Chaos
publication_identifier:
issn:
- '10541500'
publication_status: published
publisher: AIP Publishing
publist_id: '7358'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Transient behavior between multi-cell flow states in ferrofluidic Taylor-Couette
flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2017'
...
---
_id: '996'
abstract:
- lang: eng
text: 'Iodine (I 2 ) molecules embedded in He nanodroplets are aligned by a 160
ps long laser pulse. The highest degree of alignment, occurring at the peak of
the pulse and quantified by ⟨cos 2 θ 2D ⟩ , is measured as a function of the laser
intensity. The results are well described by ⟨cos 2 θ 2D ⟩ calculated for a gas
of isolated molecules each with an effective rotational constant of 0.6 times
the gas-phase value, and at a temperature of 0.4 K. Theoretical analysis using
the angulon quasiparticle to describe rotating molecules in superfluid helium
rationalizes why the alignment mechanism is similar to that of isolated molecules
with an effective rotational constant. A major advantage of molecules in He droplets
is that their 0.4 K temperature leads to stronger alignment than what can generally
be achieved for gas phase molecules -- here demonstrated by a direct comparison
of the droplet results to measurements on a ∼ 1 K supersonic beam of isolated
molecules. This point is further illustrated for more complex system by measurements
on 1,4-diiodobenzene and 1,4-dibromobenzene. For all three molecular species studied
the highest values of ⟨cos 2 θ 2D ⟩ achieved in He droplets exceed 0.96. '
article_number: '013946'
article_processing_charge: No
author:
- first_name: Benjamin
full_name: Shepperson, Benjamin
last_name: Shepperson
- first_name: Adam
full_name: Chatterley, Adam
last_name: Chatterley
- first_name: Anders
full_name: Søndergaard, Anders
last_name: Søndergaard
- first_name: Lars
full_name: Christiansen, Lars
last_name: Christiansen
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Henrik
full_name: Stapelfeldt, Henrik
last_name: Stapelfeldt
citation:
ama: Shepperson B, Chatterley A, Søndergaard A, Christiansen L, Lemeshko M, Stapelfeldt
H. Strongly aligned molecules inside helium droplets in the near-adiabatic regime.
The Journal of Chemical Physics. 2017;147(1). doi:10.1063/1.4983703
apa: Shepperson, B., Chatterley, A., Søndergaard, A., Christiansen, L., Lemeshko,
M., & Stapelfeldt, H. (2017). Strongly aligned molecules inside helium droplets
in the near-adiabatic regime. The Journal of Chemical Physics. AIP Publishing.
https://doi.org/10.1063/1.4983703
chicago: Shepperson, Benjamin, Adam Chatterley, Anders Søndergaard, Lars Christiansen,
Mikhail Lemeshko, and Henrik Stapelfeldt. “Strongly Aligned Molecules inside Helium
Droplets in the Near-Adiabatic Regime.” The Journal of Chemical Physics.
AIP Publishing, 2017. https://doi.org/10.1063/1.4983703.
ieee: B. Shepperson, A. Chatterley, A. Søndergaard, L. Christiansen, M. Lemeshko,
and H. Stapelfeldt, “Strongly aligned molecules inside helium droplets in the
near-adiabatic regime,” The Journal of Chemical Physics, vol. 147, no.
1. AIP Publishing, 2017.
ista: Shepperson B, Chatterley A, Søndergaard A, Christiansen L, Lemeshko M, Stapelfeldt
H. 2017. Strongly aligned molecules inside helium droplets in the near-adiabatic
regime. The Journal of Chemical Physics. 147(1), 013946.
mla: Shepperson, Benjamin, et al. “Strongly Aligned Molecules inside Helium Droplets
in the Near-Adiabatic Regime.” The Journal of Chemical Physics, vol. 147,
no. 1, 013946, AIP Publishing, 2017, doi:10.1063/1.4983703.
short: B. Shepperson, A. Chatterley, A. Søndergaard, L. Christiansen, M. Lemeshko,
H. Stapelfeldt, The Journal of Chemical Physics 147 (2017).
date_created: 2018-12-11T11:49:36Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2024-02-28T13:02:26Z
day: '01'
department:
- _id: MiLe
doi: 10.1063/1.4983703
external_id:
isi:
- '000405089400047'
intvolume: ' 147'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.03684
month: '06'
oa: 1
oa_version: Submitted Version
publication: The Journal of Chemical Physics
publication_identifier:
issn:
- '00219606'
publication_status: published
publisher: AIP Publishing
publist_id: '6403'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strongly aligned molecules inside helium droplets in the near-adiabatic regime
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 147
year: '2017'
...
---
_id: '912'
abstract:
- lang: eng
text: "We consider a many-body system of fermionic atoms interacting via a local
pair potential and subject to an external potential within the framework of Bardeen-Cooper-Schrieffer
(BCS) theory. We measure the free energy of the whole sample with respect to the
free energy of a reference state which allows us to define a BCS functional with
boundary conditions at infinity. Our main result is a lower bound for this energy
functional in terms of expressions that typically appear in Ginzburg-Landau functionals.\r\n"
article_number: '081901'
article_processing_charge: No
author:
- first_name: Andreas
full_name: Deuchert, Andreas
id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87
last_name: Deuchert
orcid: 0000-0003-3146-6746
citation:
ama: Deuchert A. A lower bound for the BCS functional with boundary conditions at
infinity. Journal of Mathematical Physics. 2017;58(8). doi:10.1063/1.4996580
apa: Deuchert, A. (2017). A lower bound for the BCS functional with boundary conditions
at infinity. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/1.4996580
chicago: Deuchert, Andreas. “A Lower Bound for the BCS Functional with Boundary
Conditions at Infinity.” Journal of Mathematical Physics. AIP Publishing,
2017. https://doi.org/10.1063/1.4996580.
ieee: A. Deuchert, “A lower bound for the BCS functional with boundary conditions
at infinity,” Journal of Mathematical Physics, vol. 58, no. 8. AIP Publishing,
2017.
ista: Deuchert A. 2017. A lower bound for the BCS functional with boundary conditions
at infinity. Journal of Mathematical Physics. 58(8), 081901.
mla: Deuchert, Andreas. “A Lower Bound for the BCS Functional with Boundary Conditions
at Infinity.” Journal of Mathematical Physics, vol. 58, no. 8, 081901,
AIP Publishing, 2017, doi:10.1063/1.4996580.
short: A. Deuchert, Journal of Mathematical Physics 58 (2017).
date_created: 2018-12-11T11:49:10Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2024-02-28T13:07:56Z
day: '01'
department:
- _id: RoSe
doi: 10.1063/1.4996580
ec_funded: 1
external_id:
isi:
- '000409197200015'
intvolume: ' 58'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
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url: https://arxiv.org/abs/1703.04616
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: ' Journal of Mathematical Physics'
publication_identifier:
issn:
- '00222488'
publication_status: published
publisher: AIP Publishing
publist_id: '6531'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A lower bound for the BCS functional with boundary conditions at infinity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 58
year: '2017'
...
---
_id: '1029'
abstract:
- lang: eng
text: RNA Polymerase II pauses and backtracks during transcription, with many consequences
for gene expression and cellular physiology. Here, we show that the energy required
to melt double-stranded nucleic acids in the transcription bubble predicts pausing
in Saccharomyces cerevisiae far more accurately than nucleosome roadblocks do.
In addition, the same energy difference also determines when the RNA polymerase
backtracks instead of continuing to move forward. This data-driven model corroborates—in
a genome wide and quantitative manner—previous evidence that sequence-dependent
thermodynamic features of nucleic acids influence both transcriptional pausing
and backtracking.
article_number: e0174066
article_processing_charge: Yes
author:
- first_name: Martin
full_name: Lukacisin, Martin
id: 298FFE8C-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisin
orcid: 0000-0001-6549-4177
- first_name: Matthieu
full_name: Landon, Matthieu
last_name: Landon
- first_name: Rishi
full_name: Jajoo, Rishi
last_name: Jajoo
citation:
ama: Lukacisin M, Landon M, Jajoo R. Sequence-specific thermodynamic properties
of nucleic acids influence both transcriptional pausing and backtracking in yeast.
PLoS One. 2017;12(3). doi:10.1371/journal.pone.0174066
apa: Lukacisin, M., Landon, M., & Jajoo, R. (2017). Sequence-specific thermodynamic
properties of nucleic acids influence both transcriptional pausing and backtracking
in yeast. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0174066
chicago: Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “Sequence-Specific
Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing
and Backtracking in Yeast.” PLoS One. Public Library of Science, 2017.
https://doi.org/10.1371/journal.pone.0174066.
ieee: M. Lukacisin, M. Landon, and R. Jajoo, “Sequence-specific thermodynamic properties
of nucleic acids influence both transcriptional pausing and backtracking in yeast,”
PLoS One, vol. 12, no. 3. Public Library of Science, 2017.
ista: Lukacisin M, Landon M, Jajoo R. 2017. Sequence-specific thermodynamic properties
of nucleic acids influence both transcriptional pausing and backtracking in yeast.
PLoS One. 12(3), e0174066.
mla: Lukacisin, Martin, et al. “Sequence-Specific Thermodynamic Properties of Nucleic
Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” PLoS
One, vol. 12, no. 3, e0174066, Public Library of Science, 2017, doi:10.1371/journal.pone.0174066.
short: M. Lukacisin, M. Landon, R. Jajoo, PLoS One 12 (2017).
date_created: 2018-12-11T11:49:46Z
date_published: 2017-03-16T00:00:00Z
date_updated: 2024-03-27T23:30:05Z
day: '16'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.1371/journal.pone.0174066
external_id:
isi:
- '000396318300121'
file:
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content_type: application/pdf
creator: system
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date_updated: 2018-12-12T10:09:47Z
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issue: '3'
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oa: 1
oa_version: Published Version
publication: PLoS One
publication_identifier:
issn:
- '19326203'
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publisher: Public Library of Science
publist_id: '6361'
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related_material:
record:
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Sequence-specific thermodynamic properties of nucleic acids influence both
transcriptional pausing and backtracking in yeast
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 12
year: '2017'
...
---
_id: '664'
abstract:
- lang: eng
text: Immune cells communicate using cytokine signals, but the quantitative rules
of this communication aren't clear. In this issue of Immunity, Oyler-Yaniv et
al. (2017) suggest that the distribution of a cytokine within a lymphatic organ
is primarily governed by the local density of cells consuming it.
author:
- first_name: Frank P
full_name: Assen, Frank P
id: 3A8E7F24-F248-11E8-B48F-1D18A9856A87
last_name: Assen
orcid: 0000-0003-3470-6119
- 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: Assen FP, Sixt MK. The dynamic cytokine niche. Immunity. 2017;46(4):519-520.
doi:10.1016/j.immuni.2017.04.006
apa: Assen, F. P., & Sixt, M. K. (2017). The dynamic cytokine niche. Immunity.
Cell Press. https://doi.org/10.1016/j.immuni.2017.04.006
chicago: Assen, Frank P, and Michael K Sixt. “The Dynamic Cytokine Niche.” Immunity.
Cell Press, 2017. https://doi.org/10.1016/j.immuni.2017.04.006.
ieee: F. P. Assen and M. K. Sixt, “The dynamic cytokine niche,” Immunity,
vol. 46, no. 4. Cell Press, pp. 519–520, 2017.
ista: Assen FP, Sixt MK. 2017. The dynamic cytokine niche. Immunity. 46(4), 519–520.
mla: Assen, Frank P., and Michael K. Sixt. “The Dynamic Cytokine Niche.” Immunity,
vol. 46, no. 4, Cell Press, 2017, pp. 519–20, doi:10.1016/j.immuni.2017.04.006.
short: F.P. Assen, M.K. Sixt, Immunity 46 (2017) 519–520.
date_created: 2018-12-11T11:47:47Z
date_published: 2017-04-18T00:00:00Z
date_updated: 2024-03-27T23:30:09Z
day: '18'
department:
- _id: MiSi
doi: 10.1016/j.immuni.2017.04.006
intvolume: ' 46'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 519 - 520
publication: Immunity
publication_identifier:
issn:
- '10747613'
publication_status: published
publisher: Cell Press
publist_id: '7065'
quality_controlled: '1'
related_material:
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scopus_import: 1
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title: The dynamic cytokine niche
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 46
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_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: 2024-03-27T23:30:12Z
day: '01'
ddc:
- '571'
department:
- _id: RySh
doi: 10.1371/journal.pone.0179377
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checksum: 24dd19c46fb1c761b0bcbbcd1025a3a8
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publication: PLoS One
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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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2017'
...
---
_id: '1028'
abstract:
- lang: eng
text: Optogenetics and photopharmacology provide spatiotemporally precise control
over protein interactions and protein function in cells and animals. Optogenetic
methods that are sensitive to green light and can be used to break protein complexes
are not broadly available but would enable multichromatic experiments with previously
inaccessible biological targets. Herein, we repurposed cobalamin (vitamin B12)
binding domains of bacterial CarH transcription factors for green-light-induced
receptor dissociation. In cultured cells, we observed oligomerization-induced
cell signaling for the fibroblast growth factor receptor 1 fused to cobalamin-binding
domains in the dark that was rapidly eliminated upon illumination. In zebrafish
embryos expressing fusion receptors, green light endowed control over aberrant
fibroblast growth factor signaling during development. Green-light-induced domain
dissociation and light-inactivated receptors will critically expand the optogenetic
toolbox for control of biological processes.
acknowledgement: "This work was supported by a grant from the European Union\U0010FC1Ds
Seventh Framework Programme (CIG-303564). E.R. was supported by the graduate program
MolecularDrugTargets (Austrian Science Fund (FWF), W1232) and a FemTech fellowship
(Austrian Research Promotion Agency, 3580812)"
article_processing_charge: No
author:
- first_name: Stephanie
full_name: Kainrath, Stephanie
id: 32CFBA64-F248-11E8-B48F-1D18A9856A87
last_name: Kainrath
- first_name: Manuela
full_name: Stadler, Manuela
last_name: Stadler
- first_name: Eva
full_name: Gschaider-Reichhart, Eva
id: 3FEE232A-F248-11E8-B48F-1D18A9856A87
last_name: Gschaider-Reichhart
orcid: 0000-0002-7218-7738
- first_name: Martin
full_name: Distel, Martin
last_name: Distel
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Green-light-induced
inactivation of receptor signaling using cobalamin-binding domains. Angewandte
Chemie - International Edition. 2017;56(16):4608-4611. doi:10.1002/anie.201611998
apa: Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak,
H. L. (2017). Green-light-induced inactivation of receptor signaling using cobalamin-binding
domains. Angewandte Chemie - International Edition. Wiley-Blackwell. https://doi.org/10.1002/anie.201611998
chicago: Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel,
and Harald L Janovjak. “Green-Light-Induced Inactivation of Receptor Signaling
Using Cobalamin-Binding Domains.” Angewandte Chemie - International Edition.
Wiley-Blackwell, 2017. https://doi.org/10.1002/anie.201611998.
ieee: S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak,
“Green-light-induced inactivation of receptor signaling using cobalamin-binding
domains,” Angewandte Chemie - International Edition, vol. 56, no. 16. Wiley-Blackwell,
pp. 4608–4611, 2017.
ista: Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017.
Green-light-induced inactivation of receptor signaling using cobalamin-binding
domains. Angewandte Chemie - International Edition. 56(16), 4608–4611.
mla: Kainrath, Stephanie, et al. “Green-Light-Induced Inactivation of Receptor Signaling
Using Cobalamin-Binding Domains.” Angewandte Chemie - International Edition,
vol. 56, no. 16, Wiley-Blackwell, 2017, pp. 4608–11, doi:10.1002/anie.201611998.
short: S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak,
Angewandte Chemie - International Edition 56 (2017) 4608–4611.
date_created: 2018-12-11T11:49:46Z
date_published: 2017-03-20T00:00:00Z
date_updated: 2024-03-27T23:30:13Z
day: '20'
ddc:
- '540'
department:
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- _id: HaJa
doi: 10.1002/anie.201611998
ec_funded: 1
external_id:
isi:
- '000398154000038'
file:
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content_type: application/pdf
creator: dernst
date_created: 2019-01-18T09:39:55Z
date_updated: 2019-01-18T09:39:55Z
file_id: '5845'
file_name: 2017_communications_Kainrath.pdf
file_size: 2614942
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intvolume: ' 56'
isi: 1
issue: '16'
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oa: 1
oa_version: Published Version
page: 4608-4611
project:
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call_identifier: FP7
grant_number: '303564'
name: Microbial Ion Channels for Synthetic Neurobiology
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets [do not use to be deleted]
publication: Angewandte Chemie - International Edition
publication_identifier:
issn:
- '14337851'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6362'
quality_controlled: '1'
related_material:
record:
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relation: dissertation_contains
status: public
- id: '7680'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Green-light-induced inactivation of receptor signaling using cobalamin-binding
domains
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 56
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
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.
date_created: 2018-12-11T11:49:45Z
date_published: 2017-03-17T00:00:00Z
date_updated: 2024-03-27T23:30:17Z
day: '17'
ddc:
- '575'
department:
- _id: EvBe
doi: 10.1007/978-1-4939-6831-2_1
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creator: system
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file_name: IST-2018-1019-v1+1_Hurny_MethodsMolBiol_2017.pdf
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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:
- '10643745'
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.
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: 2024-03-27T23:30:23Z
day: '01'
department:
- _id: MiSi
doi: 10.1172/JCI80631
external_id:
pmid:
- '28504646'
intvolume: ' 127'
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:
- '00219738'
publication_status: published
publisher: American Society for Clinical Investigation
publist_id: '7038'
quality_controlled: '1'
related_material:
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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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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.
date_created: 2018-12-11T11:47:52Z
date_published: 2017-05-15T00:00:00Z
date_updated: 2024-03-27T23:30:25Z
day: '15'
ddc:
- '570'
department:
- _id: Bio
- _id: CaHe
doi: 10.1242/dev.144964
external_id:
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- '28512197'
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oa_version: Published Version
page: 1798 - 1806
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publication: Development
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issn:
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publication_status: published
publisher: Company of Biologists
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scopus_import: 1
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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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 144
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
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).
date_created: 2018-12-11T11:48:01Z
date_published: 2017-07-25T00:00:00Z
date_updated: 2024-03-27T23:30:27Z
day: '25'
ddc:
- '576'
department:
- _id: CaGu
doi: 10.7554/eLife.25100
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publication: eLife
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scopus_import: 1
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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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2017'
...