---
_id: '438'
abstract:
- lang: eng
text: The MazF toxin sequence-specifically cleaves single-stranded RNA upon various
stressful conditions, and it is activated as a part of the mazEF toxin–antitoxin
module in Escherichia coli. Although autoregulation of mazEF expression through
the MazE antitoxin-dependent transcriptional repression has been biochemically
characterized, less is known about post-transcriptional autoregulation, as well
as how both of these autoregulatory features affect growth of single cells during
conditions that promote MazF production. Here, we demonstrate post-transcriptional
autoregulation of mazF expression dynamics by MazF cleaving its own transcript.
Single-cell analyses of bacterial populations during ectopic MazF production indicated
that two-level autoregulation of mazEF expression influences cell-to-cell growth
rate heterogeneity. The increase in growth rate heterogeneity is governed by the
MazE antitoxin, and tuned by the MazF-dependent mazF mRNA cleavage. Also, both
autoregulatory features grant rapid exit from the stress caused by mazF overexpression.
Time-lapse microscopy revealed that MazF-mediated cleavage of mazF mRNA leads
to increased temporal variability in length of individual cells during ectopic
mazF overexpression, as explained by a stochastic model indicating that mazEF
mRNA cleavage underlies temporal fluctuations in MazF levels during stress.
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Alexandra
full_name: Vandervelde, Alexandra
last_name: Vandervelde
- first_name: Tanino
full_name: Albanese, Tanino
last_name: Albanese
- first_name: Lendert
full_name: Gelens, Lendert
last_name: Gelens
- first_name: Isabella
full_name: Moll, Isabella
last_name: Moll
citation:
ama: Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. Autoregulation
of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic
Acids Research. 2018;46(6):2918-2931. doi:10.1093/nar/gky079
apa: Nikolic, N., Bergmiller, T., Vandervelde, A., Albanese, T., Gelens, L., &
Moll, I. (2018). Autoregulation of mazEF expression underlies growth heterogeneity
in bacterial populations. Nucleic Acids Research. Oxford University Press.
https://doi.org/10.1093/nar/gky079
chicago: Nikolic, Nela, Tobias Bergmiller, Alexandra Vandervelde, Tanino Albanese,
Lendert Gelens, and Isabella Moll. “Autoregulation of MazEF Expression Underlies
Growth Heterogeneity in Bacterial Populations.” Nucleic Acids Research.
Oxford University Press, 2018. https://doi.org/10.1093/nar/gky079.
ieee: N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, and I.
Moll, “Autoregulation of mazEF expression underlies growth heterogeneity in bacterial
populations,” Nucleic Acids Research, vol. 46, no. 6. Oxford University
Press, pp. 2918–2931, 2018.
ista: Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. 2018.
Autoregulation of mazEF expression underlies growth heterogeneity in bacterial
populations. Nucleic Acids Research. 46(6), 2918–2931.
mla: Nikolic, Nela, et al. “Autoregulation of MazEF Expression Underlies Growth
Heterogeneity in Bacterial Populations.” Nucleic Acids Research, vol. 46,
no. 6, Oxford University Press, 2018, pp. 2918–31, doi:10.1093/nar/gky079.
short: N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, I. Moll,
Nucleic Acids Research 46 (2018) 2918–2931.
date_created: 2018-12-11T11:46:29Z
date_published: 2018-04-06T00:00:00Z
date_updated: 2024-02-21T13:44:45Z
day: '06'
ddc:
- '576'
department:
- _id: CaGu
doi: 10.1093/nar/gky079
external_id:
isi:
- '000429009500021'
file:
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checksum: 3ff4f545c27e11a4cd20ccb30778793e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:30Z
date_updated: 2020-07-14T12:46:27Z
file_id: '5151'
file_name: IST-2018-971-v1+1_2018_Nikoloc_Autoregulation_of.pdf
file_size: 5027978
relation: main_file
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issue: '6'
language:
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license: https://creativecommons.org/licenses/by/4.0/
month: '04'
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oa_version: Published Version
page: 2918-2931
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call_identifier: FWF
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publication: Nucleic Acids Research
publication_status: published
publisher: Oxford University Press
pubrep_id: '971'
quality_controlled: '1'
related_material:
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- id: '5569'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Autoregulation of mazEF expression underlies growth heterogeneity in bacterial
populations
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: 46
year: '2018'
...
---
_id: '131'
abstract:
- lang: eng
text: 'XY systems usually show chromosome-wide compensation of X-linked genes, while
in many ZW systems, compensation is restricted to a minority of dosage-sensitive
genes. Why such differences arose is still unclear. Here, we combine comparative
genomics, transcriptomics and proteomics to obtain a complete overview of the
evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare
the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium)
and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary
strata. We use these to assess gene expression evolution following sex-linkage.
The resulting patterns suggest a reduction in expression of Z-linked genes in
females, combined with upregulation of the Z in both sexes, in line with the first
step of Ohno’s classic model of dosage compensation evolution. Quantitative proteomics
suggest that post-transcriptional mechanisms do not play a major role in balancing
the expression of Z-linked genes. '
acknowledgement: We are grateful to Lu Dabing (Soochow University, Suzhou, China)
for providing Schistosoma japonicum samples, to Ariana Macon (IST Austria) and Georgette
Stovall (JLU Giessen) for technical assistance, to IT support at IST Austria for
providing optimal environment to bioinformatic analyses, and to the Vicoso lab for
comments on the manuscript.
article_number: e35684
article_processing_charge: No
article_type: original
author:
- first_name: Marion A
full_name: Picard, Marion A
id: 2C921A7A-F248-11E8-B48F-1D18A9856A87
last_name: Picard
orcid: 0000-0002-8101-2518
- first_name: Celine
full_name: Cosseau, Celine
last_name: Cosseau
- first_name: Sabrina
full_name: Ferré, Sabrina
last_name: Ferré
- first_name: Thomas
full_name: Quack, Thomas
last_name: Quack
- first_name: Christoph
full_name: Grevelding, Christoph
last_name: Grevelding
- first_name: Yohann
full_name: Couté, Yohann
last_name: Couté
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Picard MAL, Cosseau C, Ferré S, et al. Evolution of gene dosage on the Z-chromosome
of schistosome parasites. eLife. 2018;7. doi:10.7554/eLife.35684
apa: Picard, M. A. L., Cosseau, C., Ferré, S., Quack, T., Grevelding, C., Couté,
Y., & Vicoso, B. (2018). Evolution of gene dosage on the Z-chromosome of schistosome
parasites. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.35684
chicago: Picard, Marion A L, Celine Cosseau, Sabrina Ferré, Thomas Quack, Christoph
Grevelding, Yohann Couté, and Beatriz Vicoso. “Evolution of Gene Dosage on the
Z-Chromosome of Schistosome Parasites.” ELife. eLife Sciences Publications,
2018. https://doi.org/10.7554/eLife.35684.
ieee: M. A. L. Picard et al., “Evolution of gene dosage on the Z-chromosome
of schistosome parasites,” eLife, vol. 7. eLife Sciences Publications,
2018.
ista: Picard MAL, Cosseau C, Ferré S, Quack T, Grevelding C, Couté Y, Vicoso B.
2018. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife.
7, e35684.
mla: Picard, Marion A. L., et al. “Evolution of Gene Dosage on the Z-Chromosome
of Schistosome Parasites.” ELife, vol. 7, e35684, eLife Sciences Publications,
2018, doi:10.7554/eLife.35684.
short: M.A.L. Picard, C. Cosseau, S. Ferré, T. Quack, C. Grevelding, Y. Couté, B.
Vicoso, ELife 7 (2018).
date_created: 2018-12-11T11:44:47Z
date_published: 2018-08-13T00:00:00Z
date_updated: 2024-02-21T13:45:12Z
day: '13'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.7554/eLife.35684
external_id:
isi:
- '000441388200001'
file:
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checksum: d6331d4385b1fffd6b47b45d5949d841
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T11:55:05Z
date_updated: 2020-07-14T12:44:43Z
file_id: '5695'
file_name: 2018_eLife_Picard.pdf
file_size: 3158125
relation: main_file
file_date_updated: 2020-07-14T12:44:43Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '7792'
quality_controlled: '1'
related_material:
record:
- id: '5586'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Evolution of gene dosage on the Z-chromosome of schistosome parasites
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: 7
year: '2018'
...
---
_id: '5584'
abstract:
- lang: eng
text: "This package contains data for the publication \"Nonlinear decoding of a
complex movie from the mammalian retina\" by Deny S. et al, PLOS Comput Biol (2018).
\r\n\r\nThe data consists of\r\n(i) 91 spike sorted, isolated rat retinal ganglion
cells that pass stability and quality criteria, recorded on the multi-electrode
array, in response to the presentation of the complex movie with many randomly
moving dark discs. The responses are represented as 648000 x 91 binary matrix,
where the first index indicates the timebin of duration 12.5 ms, and the second
index the neural identity. The matrix entry is 0/1 if the neuron didn't/did spike
in the particular time bin.\r\n(ii) README file and a graphical illustration of
the structure of the experiment, specifying how the 648000 timebins are split
into epochs where 1, 2, 4, or 10 discs were displayed, and which stimulus segments
are exact repeats or unique ball trajectories.\r\n(iii) a 648000 x 400 matrix
of luminance traces for each of the 20 x 20 positions (\"sites\") in the movie
frame, with time that is locked to the recorded raster. The luminance traces are
produced as described in the manuscript by filtering the raw disc movie with a
small gaussian spatial kernel. "
article_processing_charge: No
author:
- first_name: Stephane
full_name: Deny, Stephane
last_name: Deny
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Vicente
full_name: Botella-Soler, Vicente
last_name: Botella-Soler
- first_name: Georg S
full_name: Martius, Georg S
id: 3A276B68-F248-11E8-B48F-1D18A9856A87
last_name: Martius
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. Nonlinear decoding
of a complex movie from the mammalian retina. 2018. doi:10.15479/AT:ISTA:98
apa: Deny, S., Marre, O., Botella-Soler, V., Martius, G. S., & Tkačik, G. (2018).
Nonlinear decoding of a complex movie from the mammalian retina. Institute of
Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:98
chicago: Deny, Stephane, Olivier Marre, Vicente Botella-Soler, Georg S Martius,
and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.”
Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:98.
ieee: S. Deny, O. Marre, V. Botella-Soler, G. S. Martius, and G. Tkačik, “Nonlinear
decoding of a complex movie from the mammalian retina.” Institute of Science and
Technology Austria, 2018.
ista: Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. 2018. Nonlinear decoding
of a complex movie from the mammalian retina, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:98.
mla: Deny, Stephane, et al. Nonlinear Decoding of a Complex Movie from the Mammalian
Retina. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:98.
short: S. Deny, O. Marre, V. Botella-Soler, G.S. Martius, G. Tkačik, (2018).
datarep_id: '98'
date_created: 2018-12-12T12:31:39Z
date_published: 2018-03-29T00:00:00Z
date_updated: 2024-02-21T13:45:26Z
day: '29'
ddc:
- '570'
department:
- _id: ChLa
- _id: GaTk
doi: 10.15479/AT:ISTA:98
file:
- access_level: open_access
checksum: 6808748837b9afbbbabc2a356ca2b88a
content_type: application/octet-stream
creator: system
date_created: 2018-12-12T13:02:24Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5590'
file_name: IST-2018-98-v1+1_BBalls_area2_tile2_20x20.mat
file_size: 1142543971
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content_type: application/pdf
creator: system
date_created: 2018-12-12T13:02:25Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5591'
file_name: IST-2018-98-v1+2_ExperimentStructure.pdf
file_size: 702336
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content_type: application/octet-stream
creator: system
date_created: 2018-12-12T13:02:26Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5592'
file_name: IST-2018-98-v1+3_GoodLocations_area2_20x20.mat
file_size: 432
relation: main_file
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content_type: text/plain
creator: system
date_created: 2018-12-12T13:02:26Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5593'
file_name: IST-2018-98-v1+4_README.txt
file_size: 986
relation: main_file
file_date_updated: 2020-07-14T12:47:07Z
has_accepted_license: '1'
keyword:
- retina
- decoding
- regression
- neural networks
- complex stimulus
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '292'
relation: used_in_publication
status: public
status: public
title: Nonlinear decoding of a complex movie from the mammalian retina
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: '2018'
...
---
_id: '286'
abstract:
- lang: eng
text: 'Pedigree and sibship reconstruction are important methods in quantifying
relationships and fitness of individuals in natural populations. Current methods
employ a Markov chain-based algorithm to explore plausible possible pedigrees
iteratively. This provides accurate results, but is time-consuming. Here, we develop
a method to infer sibship and paternity relationships from half-sibling arrays
of known maternity using hierarchical clustering. Given 50 or more unlinked SNP
markers and empirically derived error rates, the method performs as well as the
widely used package Colony, but is faster by two orders of magnitude. Using simulations,
we show that the method performs well across contrasting mating scenarios, even
when samples are large. We then apply the method to open-pollinated arrays of
the snapdragon Antirrhinum majus and find evidence for a high degree of multiple
mating. Although we focus on diploid SNP data, the method does not depend on marker
type and as such has broad applications in nonmodel systems. '
acknowledgement: 'ERC, Grant/Award Number: 250152'
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- 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: Ellis T, Field D, Barton NH. Efficient inference of paternity and sibship inference
given known maternity via hierarchical clustering. Molecular Ecology Resources.
2018;18(5):988-999. doi:10.1111/1755-0998.12782
apa: Ellis, T., Field, D., & Barton, N. H. (2018). Efficient inference of paternity
and sibship inference given known maternity via hierarchical clustering. Molecular
Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.12782
chicago: Ellis, Thomas, David Field, and Nicholas H Barton. “Efficient Inference
of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.”
Molecular Ecology Resources. Wiley, 2018. https://doi.org/10.1111/1755-0998.12782.
ieee: T. Ellis, D. Field, and N. H. Barton, “Efficient inference of paternity and
sibship inference given known maternity via hierarchical clustering,” Molecular
Ecology Resources, vol. 18, no. 5. Wiley, pp. 988–999, 2018.
ista: Ellis T, Field D, Barton NH. 2018. Efficient inference of paternity and sibship
inference given known maternity via hierarchical clustering. Molecular Ecology
Resources. 18(5), 988–999.
mla: Ellis, Thomas, et al. “Efficient Inference of Paternity and Sibship Inference
given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources,
vol. 18, no. 5, Wiley, 2018, pp. 988–99, doi:10.1111/1755-0998.12782.
short: T. Ellis, D. Field, N.H. Barton, Molecular Ecology Resources 18 (2018) 988–999.
date_created: 2018-12-11T11:45:37Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2024-02-21T13:45:00Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/1755-0998.12782
ec_funded: 1
external_id:
isi:
- '000441753000007'
intvolume: ' 18'
isi: 1
issue: '5'
language:
- iso: eng
month: '09'
oa_version: None
page: 988 - 999
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Molecular Ecology Resources
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '5583'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Efficient inference of paternity and sibship inference given known maternity
via hierarchical clustering
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 18
year: '2018'
...
---
_id: '5586'
abstract:
- lang: eng
text: Input files and scripts from "Evolution of gene dosage on the Z-chromosome
of schistosome parasites" by Picard M.A.L., et al (2018).
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. Input files and scripts from “Evolution of gene dosage on the Z-chromosome
of schistosome parasites” by Picard M.A.L., et al (2018). 2018. doi:10.15479/AT:ISTA:109
apa: Vicoso, B. (2018). Input files and scripts from “Evolution of gene dosage on
the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:109
chicago: Vicoso, Beatriz. “Input Files and Scripts from ‘Evolution of Gene Dosage
on the Z-Chromosome of Schistosome Parasites’ by Picard M.A.L., et Al (2018).”
Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:109.
ieee: B. Vicoso, “Input files and scripts from ‘Evolution of gene dosage on the
Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018).” Institute
of Science and Technology Austria, 2018.
ista: Vicoso B. 2018. Input files and scripts from ‘Evolution of gene dosage on
the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018), Institute
of Science and Technology Austria, 10.15479/AT:ISTA:109.
mla: Vicoso, Beatriz. Input Files and Scripts from “Evolution of Gene Dosage
on the Z-Chromosome of Schistosome Parasites” by Picard M.A.L., et Al (2018).
Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:109.
short: B. Vicoso, (2018).
contributor:
- first_name: Marion A
id: 2C921A7A-F248-11E8-B48F-1D18A9856A87
last_name: Picard
orcid: 0000-0002-8101-2518
datarep_id: '109'
date_created: 2018-12-12T12:31:40Z
date_published: 2018-07-24T00:00:00Z
date_updated: 2024-02-21T13:45:12Z
day: '24'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.15479/AT:ISTA:109
file:
- access_level: open_access
checksum: e60b484bd6f55c08eb66a189cb72c923
content_type: application/zip
creator: system
date_created: 2018-12-12T13:02:35Z
date_updated: 2020-07-14T12:47:08Z
file_id: '5601'
file_name: IST-2018-109-v1+1_SupplementaryMethods.zip
file_size: 11918144
relation: main_file
file_date_updated: 2020-07-14T12:47:08Z
has_accepted_license: '1'
keyword:
- schistosoma
- Z-chromosome
- gene expression
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '131'
relation: research_paper
status: public
status: public
title: Input files and scripts from "Evolution of gene dosage on the Z-chromosome
of schistosome parasites" by Picard M.A.L., et al (2018)
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: '2018'
...
---
_id: '5583'
abstract:
- lang: eng
text: "Data and scripts are provided in support of the manuscript \"Efficient inference
of paternity and sibship inference given known maternity via hierarchical clustering\",
and the associated Python package FAPS, available from www.github.com/ellisztamas/faps.\r\n\r\nSimulation
scripts cover:\r\n1. Performance under different mating scenarios.\r\n2. Comparison
with Colony2.\r\n3. Effect of changing the number of Monte Carlo draws\r\n\r\nThe
final script covers the analysis of half-sib arrays from wild-pollinated seed
in an Antirrhinum majus hybrid zone."
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
citation:
ama: Ellis T. Data and Python scripts supporting Python package FAPS. 2018. doi:10.15479/AT:ISTA:95
apa: Ellis, T. (2018). Data and Python scripts supporting Python package FAPS. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:95
chicago: Ellis, Thomas. “Data and Python Scripts Supporting Python Package FAPS.”
Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:95.
ieee: T. Ellis, “Data and Python scripts supporting Python package FAPS.” Institute
of Science and Technology Austria, 2018.
ista: Ellis T. 2018. Data and Python scripts supporting Python package FAPS, Institute
of Science and Technology Austria, 10.15479/AT:ISTA:95.
mla: Ellis, Thomas. Data and Python Scripts Supporting Python Package FAPS.
Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:95.
short: T. Ellis, (2018).
contributor:
- first_name: David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
- first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
datarep_id: '95'
date_created: 2018-12-12T12:31:39Z
date_published: 2018-02-12T00:00:00Z
date_updated: 2024-02-21T13:45:01Z
day: '12'
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:95
file:
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checksum: fc6aab51439f2622ba6df8632e66fd4f
content_type: text/csv
creator: system
date_created: 2018-12-12T13:02:41Z
date_updated: 2020-07-14T12:47:07Z
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checksum: 92347586ae4f8a6eb7c04354797bf314
content_type: text/csv
creator: system
date_created: 2018-12-12T13:02:42Z
date_updated: 2020-07-14T12:47:07Z
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date_updated: 2020-07-14T12:47:07Z
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checksum: e739fc473567fd8f39438b445fc46147
content_type: application/zip
creator: system
date_created: 2018-12-12T13:02:44Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5609'
file_name: IST-2018-95-v1+4_faps_scripts.zip
file_size: 342090
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file_date_updated: 2020-07-14T12:47:07Z
has_accepted_license: '1'
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '286'
relation: research_paper
status: public
status: public
title: Data and Python scripts supporting Python package FAPS
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: '2018'
...
---
_id: '5569'
abstract:
- lang: eng
text: "Nela Nikolic, Tobias Bergmiller, Alexandra Vandervelde, Tanino G. Albanese,
Lendert Gelens, and Isabella Moll (2018)\r\n“Autoregulation of mazEF expression
underlies growth heterogeneity in bacterial populations” Nucleic Acids Research,
doi: 10.15479/AT:ISTA:74;\r\nmicroscopy experiments by Tobias Bergmiller; image
and data analysis by Nela Nikolic."
article_processing_charge: No
author:
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
citation:
ama: Bergmiller T, Nikolic N. Time-lapse microscopy data. 2018. doi:10.15479/AT:ISTA:74
apa: Bergmiller, T., & Nikolic, N. (2018). Time-lapse microscopy data. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:74
chicago: Bergmiller, Tobias, and Nela Nikolic. “Time-Lapse Microscopy Data.” Institute
of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:74.
ieee: T. Bergmiller and N. Nikolic, “Time-lapse microscopy data.” Institute of Science
and Technology Austria, 2018.
ista: Bergmiller T, Nikolic N. 2018. Time-lapse microscopy data, Institute of Science
and Technology Austria, 10.15479/AT:ISTA:74.
mla: Bergmiller, Tobias, and Nela Nikolic. Time-Lapse Microscopy Data. Institute
of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:74.
short: T. Bergmiller, N. Nikolic, (2018).
datarep_id: '74'
date_created: 2018-12-12T12:31:35Z
date_published: 2018-02-07T00:00:00Z
date_updated: 2024-02-21T13:44:45Z
day: '07'
ddc:
- '579'
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:74
file:
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checksum: 61ebb92213cfffeba3ddbaff984b81af
content_type: application/zip
creator: system
date_created: 2018-12-12T13:04:39Z
date_updated: 2020-07-14T12:47:04Z
file_id: '5637'
file_name: IST-2018-74-v1+2_15-11-05.zip
file_size: 3558703796
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checksum: bf26649af310ef6892d68576515cde6d
content_type: application/zip
creator: system
date_created: 2018-12-12T13:04:55Z
date_updated: 2020-07-14T12:47:04Z
file_id: '5638'
file_name: IST-2018-74-v1+3_15-07-31.zip
file_size: 1830422606
relation: main_file
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checksum: 8e46eedce06f22acb2be1a9b9d3f56bd
content_type: application/zip
creator: system
date_created: 2018-12-12T13:05:11Z
date_updated: 2020-07-14T12:47:04Z
file_id: '5639'
file_name: IST-2018-74-v1+4_Images_for_analysis.zip
file_size: 2140849248
relation: main_file
file_date_updated: 2020-07-14T12:47:04Z
has_accepted_license: '1'
keyword:
- microscopy
- microfluidics
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
publist_id: '7385'
related_material:
record:
- id: '438'
relation: research_paper
status: public
status: public
title: Time-lapse microscopy data
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: '2018'
...
---
_id: '161'
abstract:
- lang: eng
text: 'Which properties of metabolic networks can be derived solely from stoichiometry?
Predictive results have been obtained by flux balance analysis (FBA), by postulating
that cells set metabolic fluxes to maximize growth rate. Here we consider a generalization
of FBA to single-cell level using maximum entropy modeling, which we extend and
test experimentally. Specifically, we define for Escherichia coli metabolism a
flux distribution that yields the experimental growth rate: the model, containing
FBA as a limit, provides a better match to measured fluxes and it makes a wide
range of predictions: on flux variability, regulation, and correlations; on the
relative importance of stoichiometry vs. optimization; on scaling relations for
growth rate distributions. We validate the latter here with single-cell data at
different sub-inhibitory antibiotic concentrations. The model quantifies growth
optimization as emerging from the interplay of competitive dynamics in the population
and regulation of metabolism at the level of single cells.'
article_number: '2988'
article_processing_charge: No
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
- first_name: Andersson Anna
full_name: Mc, Andersson Anna
last_name: Mc
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. Statistical mechanics
for metabolic networks during steady state growth. Nature Communications.
2018;9(1). doi:10.1038/s41467-018-05417-9
apa: De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., & Tkačik, G. (2018).
Statistical mechanics for metabolic networks during steady state growth. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-018-05417-9
chicago: De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet,
and Gašper Tkačik. “Statistical Mechanics for Metabolic Networks during Steady
State Growth.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-05417-9.
ieee: D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical
mechanics for metabolic networks during steady state growth,” Nature Communications,
vol. 9, no. 1. Springer Nature, 2018.
ista: De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. 2018. Statistical mechanics
for metabolic networks during steady state growth. Nature Communications. 9(1),
2988.
mla: De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during
Steady State Growth.” Nature Communications, vol. 9, no. 1, 2988, Springer
Nature, 2018, doi:10.1038/s41467-018-05417-9.
short: D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications
9 (2018).
date_created: 2018-12-11T11:44:57Z
date_published: 2018-07-30T00:00:00Z
date_updated: 2024-02-21T13:45:39Z
day: '30'
ddc:
- '570'
department:
- _id: GaTk
- _id: CaGu
doi: 10.1038/s41467-018-05417-9
ec_funded: 1
external_id:
isi:
- '000440149300021'
file:
- access_level: open_access
checksum: 3ba7ab27b27723c7dcf633e8fc1f8f18
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T16:44:28Z
date_updated: 2020-07-14T12:45:06Z
file_id: '5728'
file_name: 2018_NatureComm_DeMartino.pdf
file_size: 1043205
relation: main_file
file_date_updated: 2020-07-14T12:45:06Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Nature Communications
publication_status: published
publisher: Springer Nature
publist_id: '7760'
quality_controlled: '1'
related_material:
record:
- id: '5587'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Statistical mechanics for metabolic networks during steady state growth
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: 9
year: '2018'
...
---
_id: '5587'
abstract:
- lang: eng
text: "Supporting material to the article \r\nSTATISTICAL MECHANICS FOR METABOLIC
NETWORKS IN STEADY-STATE GROWTH\r\n\r\nboundscoli.dat\r\nFlux Bounds of the E.
coli catabolic core model iAF1260 in a glucose limited minimal medium. \r\n\r\npolcoli.dat\r\nMatrix
enconding the polytope of the E. coli catabolic core model iAF1260 in a glucose
limited minimal medium, \r\nobtained from the soichiometric matrix by standard
linear algebra (reduced row echelon form).\r\n\r\nellis.dat\r\nApproximate Lowner-John
ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in
a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\npoint0.dat\r\nCenter
of the approximate Lowner-John ellipsoid rounding the polytope of the E. coli
catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with
the Lovasz method.\r\n\r\nlovasz.cpp \r\nThis c++ code file receives in input
the polytope of the feasible steady states of a metabolic network, \r\n(matrix
and bounds), and it gives in output an approximate Lowner-John ellipsoid rounding
the polytope\r\nwith the Lovasz method \r\nNB inputs are referred by defaults
to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we
refer to PLoS ONE 10.4 e0122670 (2015).\r\n\r\nsampleHRnew.cpp \r\nThis c++
code file receives in input the polytope of the feasible steady states of a metabolic
network, \r\n(matrix and bounds), the ellipsoid rounding the polytope, a point
inside and \r\nit gives in output a max entropy sampling at fixed average growth
rate \r\nof the steady states by performing an Hit-and-Run Monte Carlo Markov
chain.\r\nNB inputs are referred by defaults to the catabolic core of the E.Coli
network iAF1260. \r\nFor further details we refer to PLoS ONE 10.4 e0122670 (2015)."
article_processing_charge: No
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: De Martino D, Tkačik G. Supporting materials “STATISTICAL MECHANICS FOR METABOLIC
NETWORKS IN STEADY-STATE GROWTH.” 2018. doi:10.15479/AT:ISTA:62
apa: De Martino, D., & Tkačik, G. (2018). Supporting materials “STATISTICAL
MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:62
chicago: De Martino, Daniele, and Gašper Tkačik. “Supporting Materials ‘STATISTICAL
MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science
and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:62.
ieee: D. De Martino and G. Tkačik, “Supporting materials ‘STATISTICAL MECHANICS
FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology
Austria, 2018.
ista: De Martino D, Tkačik G. 2018. Supporting materials ‘STATISTICAL MECHANICS
FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH’, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:62.
mla: De Martino, Daniele, and Gašper Tkačik. Supporting Materials “STATISTICAL
MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science
and Technology Austria, 2018, doi:10.15479/AT:ISTA:62.
short: D. De Martino, G. Tkačik, (2018).
datarep_id: '111'
date_created: 2018-12-12T12:31:41Z
date_published: 2018-09-21T00:00:00Z
date_updated: 2024-02-21T13:45:39Z
day: '21'
ddc:
- '530'
department:
- _id: GaTk
doi: 10.15479/AT:ISTA:62
ec_funded: 1
file:
- access_level: open_access
checksum: 97992e3e8cf8544ec985a48971708726
content_type: application/zip
creator: system
date_created: 2018-12-12T13:05:13Z
date_updated: 2020-07-14T12:47:08Z
file_id: '5641'
file_name: IST-2018-111-v1+1_CODES.zip
file_size: 14376
relation: main_file
file_date_updated: 2020-07-14T12:47:08Z
has_accepted_license: '1'
keyword:
- metabolic networks
- e.coli core
- maximum entropy
- monte carlo markov chain sampling
- ellipsoidal rounding
month: '09'
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: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '161'
relation: research_paper
status: public
status: public
title: Supporting materials "STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE
GROWTH"
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: '2018'
...
---
_id: '542'
abstract:
- lang: eng
text: The t-haplotype, a mouse meiotic driver found on chromosome 17, has been a
model for autosomal segregation distortion for close to a century, but several
questions remain regarding its biology and evolutionary history. A recently published
set of population genomics resources for wild mice includes several individuals
heterozygous for the t-haplotype, which we use to characterize this selfish element
at the genomic and transcriptomic level. Our results show that large sections
of the t-haplotype have been replaced by standard homologous sequences, possibly
due to occasional events of recombination, and that this complicates the inference
of its history. As expected for a long genomic segment of very low recombination,
the t-haplotype carries an excess of fixed nonsynonymous mutations compared to
the standard chromosome. This excess is stronger for regions that have not undergone
recent recombination, suggesting that occasional gene flow between the t and the
standard chromosome may provide a mechanism to regenerate coding sequences that
have accumulated deleterious mutations. Finally, we find that t-complex genes
with altered expression largely overlap with deleted or amplified regions, and
that carrying a t-haplotype alters the testis expression of genes outside of the
t-complex, providing new leads into the pathways involved in the biology of this
segregation distorter.
article_processing_charge: No
article_type: original
author:
- first_name: Réka K
full_name: Kelemen, Réka K
id: 48D3F8DE-F248-11E8-B48F-1D18A9856A87
last_name: Kelemen
orcid: 0000-0002-8489-9281
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Kelemen RK, Vicoso B. Complex history and differentiation patterns of the t-haplotype,
a mouse meiotic driver. Genetics. 2018;208(1):365-375. doi:10.1534/genetics.117.300513
apa: Kelemen, R. K., & Vicoso, B. (2018). Complex history and differentiation
patterns of the t-haplotype, a mouse meiotic driver. Genetics. Genetics
Society of America. https://doi.org/10.1534/genetics.117.300513
chicago: Kelemen, Réka K, and Beatriz Vicoso. “Complex History and Differentiation
Patterns of the T-Haplotype, a Mouse Meiotic Driver.” Genetics. Genetics
Society of America, 2018. https://doi.org/10.1534/genetics.117.300513.
ieee: R. K. Kelemen and B. Vicoso, “Complex history and differentiation patterns
of the t-haplotype, a mouse meiotic driver,” Genetics, vol. 208, no. 1.
Genetics Society of America, pp. 365–375, 2018.
ista: Kelemen RK, Vicoso B. 2018. Complex history and differentiation patterns of
the t-haplotype, a mouse meiotic driver. Genetics. 208(1), 365–375.
mla: Kelemen, Réka K., and Beatriz Vicoso. “Complex History and Differentiation
Patterns of the T-Haplotype, a Mouse Meiotic Driver.” Genetics, vol. 208,
no. 1, Genetics Society of America, 2018, pp. 365–75, doi:10.1534/genetics.117.300513.
short: R.K. Kelemen, B. Vicoso, Genetics 208 (2018) 365–375.
date_created: 2018-12-11T11:47:04Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2024-02-21T13:48:27Z
day: '01'
ddc:
- '576'
department:
- _id: BeVi
doi: 10.1534/genetics.117.300513
ec_funded: 1
external_id:
isi:
- '000419356300024'
file:
- access_level: open_access
checksum: 2123845e7031a0cf043905be160f9e69
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:14Z
date_updated: 2020-07-14T12:46:50Z
file_id: '5132'
file_name: IST-2018-1058-v1+1_365.full__1_.pdf
file_size: 1311661
relation: main_file
file_date_updated: 2020-07-14T12:46:50Z
has_accepted_license: '1'
intvolume: ' 208'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 365 - 375
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '7274'
pubrep_id: '1058'
quality_controlled: '1'
related_material:
record:
- id: '5571'
relation: popular_science
status: public
- id: '5572'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Complex history and differentiation patterns of the t-haplotype, a mouse meiotic
driver
tmp:
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short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 208
year: '2018'
...
---
_id: '5751'
abstract:
- lang: eng
text: 'Because of the intrinsic randomness of the evolutionary process, a mutant
with a fitness advantage has some chance to be selected but no certainty. Any
experiment that searches for advantageous mutants will lose many of them due to
random drift. It is therefore of great interest to find population structures
that improve the odds of advantageous mutants. Such structures are called amplifiers
of natural selection: they increase the probability that advantageous mutants
are selected. Arbitrarily strong amplifiers guarantee the selection of advantageous
mutants, even for very small fitness advantage. Despite intensive research over
the past decade, arbitrarily strong amplifiers have remained rare. Here we show
how to construct a large variety of them. Our amplifiers are so simple that they
could be useful in biotechnology, when optimizing biological molecules, or as
a diagnostic tool, when searching for faster dividing cells or viruses. They could
also occur in natural population structures.'
article_number: '71'
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 A.
full_name: Nowak, Martin A.
last_name: Nowak
citation:
ama: Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. Construction of arbitrarily
strong amplifiers of natural selection using evolutionary graph theory. Communications
Biology. 2018;1(1). doi:10.1038/s42003-018-0078-7
apa: Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. A. (2018). Construction
of arbitrarily strong amplifiers of natural selection using evolutionary graph
theory. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-018-0078-7
chicago: Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin
A. Nowak. “Construction of Arbitrarily Strong Amplifiers of Natural Selection
Using Evolutionary Graph Theory.” Communications Biology. Springer Nature,
2018. https://doi.org/10.1038/s42003-018-0078-7.
ieee: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. A. Nowak, “Construction
of arbitrarily strong amplifiers of natural selection using evolutionary graph
theory,” Communications Biology, vol. 1, no. 1. Springer Nature, 2018.
ista: Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. 2018. Construction of arbitrarily
strong amplifiers of natural selection using evolutionary graph theory. Communications
Biology. 1(1), 71.
mla: Pavlogiannis, Andreas, et al. “Construction of Arbitrarily Strong Amplifiers
of Natural Selection Using Evolutionary Graph Theory.” Communications Biology,
vol. 1, no. 1, 71, Springer Nature, 2018, doi:10.1038/s42003-018-0078-7.
short: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M.A. Nowak, Communications Biology
1 (2018).
date_created: 2018-12-18T13:22:58Z
date_published: 2018-06-14T00:00:00Z
date_updated: 2024-02-21T13:48:42Z
day: '14'
ddc:
- '004'
- '519'
- '576'
department:
- _id: KrCh
doi: 10.1038/s42003-018-0078-7
ec_funded: 1
external_id:
isi:
- '000461126500071'
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date_updated: 2020-07-14T12:47:10Z
file_id: '5752'
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language:
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month: '06'
oa: 1
oa_version: Published Version
project:
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call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
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call_identifier: FWF
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name: Modern Graph Algorithmic Techniques in Formal Verification
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issn:
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publication_status: published
publisher: Springer Nature
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title: Construction of arbitrarily strong amplifiers of natural selection using evolutionary
graph theory
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: 1
year: '2018'
...
---
_id: '5757'
abstract:
- lang: eng
text: "File S1. Variant Calling Format file of the ingroup: 197 haploid sequences
of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference
genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid
sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile
S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous
polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous
divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants
were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions
with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic
sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS;
⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript
in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous
diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (#
of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total
# of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent
sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in
the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous
evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence
data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression
values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized
across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK ,
ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile
S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites,
excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all
covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with
the Eyre-Walker and Keightley method on binned data and using all variants."
article_processing_charge: No
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
citation:
ama: Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection
in Drosophila melanogaster.” 2018. doi:10.15479/at:ista:/5757
apa: Fraisse, C. (2018). Supplementary Files for “Pleiotropy modulates the efficacy
of selection in Drosophila melanogaster.” Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:/5757
chicago: Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the
Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology
Austria, 2018. https://doi.org/10.15479/at:ista:/5757.
ieee: C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of
selection in Drosophila melanogaster.’” Institute of Science and Technology Austria,
2018.
ista: Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy
of selection in Drosophila melanogaster’, Institute of Science and Technology
Austria, 10.15479/at:ista:/5757.
mla: Fraisse, Christelle. Supplementary Files for “Pleiotropy Modulates the Efficacy
of Selection in Drosophila Melanogaster.” Institute of Science and Technology
Austria, 2018, doi:10.15479/at:ista:/5757.
short: C. Fraisse, (2018).
contributor:
- first_name: Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
- first_name: Gemma
id: 33AB266C-F248-11E8-B48F-1D18A9856A87
last_name: Puixeu Sala
- first_name: Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
date_created: 2018-12-19T14:22:35Z
date_published: 2018-12-19T00:00:00Z
date_updated: 2024-02-21T13:59:18Z
day: '19'
ddc:
- '576'
department:
- _id: BeVi
- _id: NiBa
doi: 10.15479/at:ista:/5757
ec_funded: 1
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checksum: aed7ee9ca3f4dc07d8a66945f68e13cd
content_type: application/zip
creator: cfraisse
date_created: 2018-12-19T14:19:52Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5758'
file_name: FileS1.zip
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creator: cfraisse
date_created: 2018-12-19T14:19:49Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5759'
file_name: FileS2.zip
file_size: 84856909
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checksum: c37ac5d5437c457338afc128c1240655
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creator: cfraisse
date_created: 2018-12-19T14:19:49Z
date_updated: 2020-07-14T12:47:11Z
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has_accepted_license: '1'
keyword:
- (mal)adaptation
- pleiotropy
- selective constraint
- evo-devo
- gene expression
- Drosophila melanogaster
month: '12'
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
related_material:
record:
- id: '6089'
relation: research_paper
status: public
status: public
title: Supplementary Files for "Pleiotropy modulates the efficacy of selection in
Drosophila melanogaster"
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '149'
abstract:
- lang: eng
text: The eigenvalue density of many large random matrices is well approximated
by a deterministic measure, the self-consistent density of states. In the present
work, we show this behaviour for several classes of random matrices. In fact,
we establish that, in each of these classes, the self-consistent density of states
approximates the eigenvalue density of the random matrix on all scales slightly
above the typical eigenvalue spacing. For large classes of random matrices, the
self-consistent density of states exhibits several universal features. We prove
that, under suitable assumptions, random Gram matrices and Hermitian random matrices
with decaying correlations have a 1/3-Hölder continuous self-consistent density
of states ρ on R, which is analytic, where it is positive, and has either a square
root edge or a cubic root cusp, where it vanishes. We, thus, extend the validity
of the corresponding result for Wigner-type matrices from [4, 5, 7]. We show that
ρ is determined as the inverse Stieltjes transform of the normalized trace of
the unique solution m(z) to the Dyson equation −m(z) −1 = z − a + S[m(z)] on C
N×N with the constraint Im m(z) ≥ 0. Here, z lies in the complex upper half-plane,
a is a self-adjoint element of C N×N and S is a positivity-preserving operator
on C N×N encoding the first two moments of the random matrix. In order to analyze
a possible limit of ρ for N → ∞ and address some applications in free probability
theory, we also consider the Dyson equation on infinite dimensional von Neumann
algebras. We present two applications to random matrices. We first establish that,
under certain assumptions, large random matrices with independent entries have
a rotationally symmetric self-consistent density of states which is supported
on a centered disk in C. Moreover, it is infinitely often differentiable apart
from a jump on the boundary of this disk. Second, we show edge universality at
all regular (not necessarily extreme) spectral edges for Hermitian random matrices
with decaying correlations.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Johannes
full_name: Alt, Johannes
id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87
last_name: Alt
citation:
ama: Alt J. Dyson equation and eigenvalue statistics of random matrices. 2018. doi:10.15479/AT:ISTA:TH_1040
apa: Alt, J. (2018). Dyson equation and eigenvalue statistics of random matrices.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1040
chicago: Alt, Johannes. “Dyson Equation and Eigenvalue Statistics of Random Matrices.”
Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1040.
ieee: J. Alt, “Dyson equation and eigenvalue statistics of random matrices,” Institute
of Science and Technology Austria, 2018.
ista: Alt J. 2018. Dyson equation and eigenvalue statistics of random matrices.
Institute of Science and Technology Austria.
mla: Alt, Johannes. Dyson Equation and Eigenvalue Statistics of Random Matrices.
Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1040.
short: J. Alt, Dyson Equation and Eigenvalue Statistics of Random Matrices, Institute
of Science and Technology Austria, 2018.
date_created: 2018-12-11T11:44:53Z
date_published: 2018-07-12T00:00:00Z
date_updated: 2024-02-22T14:34:33Z
day: '12'
ddc:
- '515'
- '519'
degree_awarded: PhD
department:
- _id: LaEr
doi: 10.15479/AT:ISTA:TH_1040
ec_funded: 1
file:
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creator: dernst
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file_name: 2018_thesis_Alt_source.zip
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relation: source_file
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language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '456'
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '7772'
pubrep_id: '1040'
related_material:
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- id: '6183'
relation: part_of_dissertation
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- id: '566'
relation: part_of_dissertation
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- id: '1010'
relation: part_of_dissertation
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- id: '6240'
relation: part_of_dissertation
status: public
- id: '6184'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
title: Dyson equation and eigenvalue statistics of random matrices
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '415'
abstract:
- lang: eng
text: Recently it was shown that a molecule rotating in a quantum solvent can be
described in terms of the “angulon” quasiparticle [M. Lemeshko, Phys. Rev. Lett.
118, 095301 (2017)]. Here we extend the angulon theory to the case of molecules
possessing an additional spin-1/2 degree of freedom and study the behavior of
the system in the presence of a static magnetic field. We show that exchange of
angular momentum between the molecule and the solvent can be altered by the field,
even though the solvent itself is non-magnetic. In particular, we demonstrate
a possibility to control resonant emission of phonons with a given angular momentum
using a magnetic field.
acknowledgement: "We acknowledge insightful discussions with Giacomo Bighin, Igor
Cherepanov, Johan Mentink, and Enderalp Yakaboylu. This work was supported by the
Austrian Science Fund (FWF), Project No. P29902-N27. W.R. was supported by the Polish
Ministry of Science and Higher Education Grant No. MNISW/2016/DIR/285/NN and by
the European Union’s Horizon 2020 research and innovation programme under the Marie
Skłodowska-Curie Grant Agreement No. 665385.\r\n"
article_number: '104307'
article_processing_charge: No
article_type: original
author:
- first_name: Wojciech
full_name: Rzadkowski, Wojciech
id: 48C55298-F248-11E8-B48F-1D18A9856A87
last_name: Rzadkowski
orcid: 0000-0002-1106-4419
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Rzadkowski W, Lemeshko M. Effect of a magnetic field on molecule–solvent angular
momentum transfer. The Journal of Chemical Physics. 2018;148(10). doi:10.1063/1.5017591
apa: Rzadkowski, W., & Lemeshko, M. (2018). Effect of a magnetic field on molecule–solvent
angular momentum transfer. The Journal of Chemical Physics. AIP Publishing.
https://doi.org/10.1063/1.5017591
chicago: Rzadkowski, Wojciech, and Mikhail Lemeshko. “Effect of a Magnetic Field
on Molecule–Solvent Angular Momentum Transfer.” The Journal of Chemical Physics.
AIP Publishing, 2018. https://doi.org/10.1063/1.5017591.
ieee: W. Rzadkowski and M. Lemeshko, “Effect of a magnetic field on molecule–solvent
angular momentum transfer,” The Journal of Chemical Physics, vol. 148,
no. 10. AIP Publishing, 2018.
ista: Rzadkowski W, Lemeshko M. 2018. Effect of a magnetic field on molecule–solvent
angular momentum transfer. The Journal of Chemical Physics. 148(10), 104307.
mla: Rzadkowski, Wojciech, and Mikhail Lemeshko. “Effect of a Magnetic Field on
Molecule–Solvent Angular Momentum Transfer.” The Journal of Chemical Physics,
vol. 148, no. 10, 104307, AIP Publishing, 2018, doi:10.1063/1.5017591.
short: W. Rzadkowski, M. Lemeshko, The Journal of Chemical Physics 148 (2018).
date_created: 2018-12-11T11:46:21Z
date_published: 2018-03-14T00:00:00Z
date_updated: 2024-02-28T13:01:59Z
day: '14'
department:
- _id: MiLe
doi: 10.1063/1.5017591
ec_funded: 1
external_id:
arxiv:
- '1711.09904'
isi:
- '000427517200065'
intvolume: ' 148'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1711.09904
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: The Journal of Chemical Physics
publication_status: published
publisher: AIP Publishing
publist_id: '7408'
quality_controlled: '1'
related_material:
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relation: dissertation_contains
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scopus_import: '1'
status: public
title: Effect of a magnetic field on molecule–solvent angular momentum transfer
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 148
year: '2018'
...
---
_id: '134'
abstract:
- lang: eng
text: "The current state of the art in real-time two-dimensional water wave simulation
requires developers to choose between efficient Fourier-based methods, which lack
interactions with moving obstacles, and finite-difference or finite element methods,
which handle environmental interactions but are significantly more expensive.
This paper attempts to bridge this long-standing gap between complexity and performance,
by proposing a new wave simulation method that can faithfully simulate wave interactions
with moving obstacles in real time while simultaneously preserving minute details
and accommodating very large simulation domains.\r\n\r\nPrevious methods for simulating
2D water waves directly compute the change in height of the water surface, a strategy
which imposes limitations based on the CFL condition (fast moving waves require
small time steps) and Nyquist's limit (small wave details require closely-spaced
simulation variables). This paper proposes a novel wavelet transformation that
discretizes the liquid motion in terms of amplitude-like functions that vary over
space, frequency, and direction, effectively generalizing Fourier-based methods
to handle local interactions. Because these new variables change much more slowly
over space than the original water height function, our change of variables drastically
reduces the limitations of the CFL condition and Nyquist limit, allowing us to
simulate highly detailed water waves at very large visual resolutions. Our discretization
is amenable to fast summation and easy to parallelize. We also present basic extensions
like pre-computed wave paths and two-way solid fluid coupling. Finally, we argue
that our discretization provides a convenient set of variables for artistic manipulation,
which we illustrate with a novel wave-painting interface."
acknowledged_ssus:
- _id: ScienComp
alternative_title:
- SIGGRAPH
article_number: '94'
article_processing_charge: No
author:
- first_name: Stefan
full_name: Jeschke, Stefan
id: 44D6411A-F248-11E8-B48F-1D18A9856A87
last_name: Jeschke
- first_name: Tomas
full_name: Skrivan, Tomas
id: 486A5A46-F248-11E8-B48F-1D18A9856A87
last_name: Skrivan
- first_name: Matthias
full_name: Mueller Fischer, Matthias
last_name: Mueller Fischer
- first_name: Nuttapong
full_name: Chentanez, Nuttapong
last_name: Chentanez
- first_name: Miles
full_name: Macklin, Miles
last_name: Macklin
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C.
Water surface wavelets. ACM Transactions on Graphics. 2018;37(4). doi:10.1145/3197517.3201336
apa: Jeschke, S., Skrivan, T., Mueller Fischer, M., Chentanez, N., Macklin, M.,
& Wojtan, C. (2018). Water surface wavelets. ACM Transactions on Graphics.
ACM. https://doi.org/10.1145/3197517.3201336
chicago: Jeschke, Stefan, Tomas Skrivan, Matthias Mueller Fischer, Nuttapong Chentanez,
Miles Macklin, and Chris Wojtan. “Water Surface Wavelets.” ACM Transactions
on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201336.
ieee: S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, and
C. Wojtan, “Water surface wavelets,” ACM Transactions on Graphics, vol.
37, no. 4. ACM, 2018.
ista: Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C.
2018. Water surface wavelets. ACM Transactions on Graphics. 37(4), 94.
mla: Jeschke, Stefan, et al. “Water Surface Wavelets.” ACM Transactions on Graphics,
vol. 37, no. 4, 94, ACM, 2018, doi:10.1145/3197517.3201336.
short: S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, C.
Wojtan, ACM Transactions on Graphics 37 (2018).
date_created: 2018-12-11T11:44:48Z
date_published: 2018-07-30T00:00:00Z
date_updated: 2024-02-28T13:58:51Z
day: '30'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/3197517.3201336
ec_funded: 1
external_id:
isi:
- '000448185000055'
file:
- access_level: open_access
checksum: db75ebabe2ec432bf41389e614d6ef62
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T09:59:23Z
date_updated: 2020-07-14T12:44:45Z
file_id: '5744'
file_name: 2018_ACM_Jeschke.pdf
file_size: 22185016
relation: main_file
file_date_updated: 2020-07-14T12:44:45Z
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '7789'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/new-water-simulation-captures-small-details-even-in-large-scenes/
scopus_import: '1'
status: public
title: Water surface wavelets
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2018'
...
---
_id: '6339'
abstract:
- lang: eng
text: We introduce a diagrammatic Monte Carlo approach to angular momentum properties
of quantum many-particle systems possessing a macroscopic number of degrees of
freedom. The treatment is based on a diagrammatic expansion that merges the usual
Feynman diagrams with the angular momentum diagrams known from atomic and nuclear
structure theory, thereby incorporating the non-Abelian algebra inherent to quantum
rotations. Our approach is applicable at arbitrary coupling, is free of systematic
errors and of finite-size effects, and naturally provides access to the impurity
Green function. We exemplify the technique by obtaining an all-coupling solution
of the angulon model; however, the method is quite general and can be applied
to a broad variety of systems in which particles exchange quantum angular momentum
with their many-body environment.
article_number: '165301'
article_processing_charge: No
author:
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Timur
full_name: Tscherbul, Timur
last_name: Tscherbul
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to angular
momentum in quantum many-particle systems. Physical Review Letters. 2018;121(16).
doi:10.1103/physrevlett.121.165301
apa: Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo
approach to angular momentum in quantum many-particle systems. Physical Review
Letters. American Physical Society. https://doi.org/10.1103/physrevlett.121.165301
chicago: Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo
Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review
Letters. American Physical Society, 2018. https://doi.org/10.1103/physrevlett.121.165301.
ieee: G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach
to angular momentum in quantum many-particle systems,” Physical Review Letters,
vol. 121, no. 16. American Physical Society, 2018.
ista: Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach
to angular momentum in quantum many-particle systems. Physical Review Letters.
121(16), 165301.
mla: Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Angular Momentum
in Quantum Many-Particle Systems.” Physical Review Letters, vol. 121, no.
16, 165301, American Physical Society, 2018, doi:10.1103/physrevlett.121.165301.
short: G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018).
date_created: 2019-04-17T10:53:38Z
date_published: 2018-10-16T00:00:00Z
date_updated: 2024-02-28T13:15:09Z
day: '16'
department:
- _id: MiLe
doi: 10.1103/physrevlett.121.165301
external_id:
arxiv:
- '1803.07990'
isi:
- '000447468400008'
intvolume: ' 121'
isi: 1
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1803.07990
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/description-of-rotating-molecules-made-easy/
scopus_import: '1'
status: public
title: Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle
systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 121
year: '2018'
...
---
_id: '417'
abstract:
- lang: eng
text: 'We introduce a Diagrammatic Monte Carlo (DiagMC) approach to complex molecular
impurities with rotational degrees of freedom interacting with a many-particle
environment. The treatment is based on the diagrammatic expansion that merges
the usual Feynman diagrams with the angular momentum diagrams known from atomic
and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent
to quantum rotations. Our approach works at arbitrary coupling, is free of systematic
errors and of finite size effects, and naturally provides access to the impurity
Green function. We exemplify the technique by obtaining an all-coupling solution
of the angulon model, however, the method is quite general and can be applied
to a broad variety of quantum impurities possessing angular momentum degrees of
freedom. '
article_number: '165301'
article_processing_charge: No
author:
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Timur
full_name: Tscherbul, Timur
last_name: Tscherbul
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to rotating
molecular impurities. Physical Review Letters. 2018;121(16). doi:10.1103/PhysRevLett.121.165301
apa: Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo
approach to rotating molecular impurities. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/PhysRevLett.121.165301
chicago: Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte
Carlo Approach to Rotating Molecular Impurities.” Physical Review Letters.
American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.165301.
ieee: G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach
to rotating molecular impurities,” Physical Review Letters, vol. 121, no.
16. American Physical Society, 2018.
ista: Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach
to rotating molecular impurities. Physical Review Letters. 121(16), 165301.
mla: Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Rotating Molecular
Impurities.” Physical Review Letters, vol. 121, no. 16, 165301, American
Physical Society, 2018, doi:10.1103/PhysRevLett.121.165301.
short: G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018).
date_created: 2018-12-11T11:46:22Z
date_published: 2018-10-16T00:00:00Z
date_updated: 2024-02-28T13:14:53Z
day: '16'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.121.165301
external_id:
arxiv:
- '1803.07990'
intvolume: ' 121'
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1803.07990
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '8025'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diagrammatic Monte Carlo approach to rotating molecular impurities
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 121
year: '2018'
...
---
_id: '412'
abstract:
- lang: eng
text: Clathrin-mediated endocytosis (CME) is a cellular trafficking process in which
cargoes and lipids are internalized from the plasma membrane into vesicles coated
with clathrin and adaptor proteins. CME is essential for many developmental and
physiological processes in plants, but its underlying mechanism is not well characterised
compared to that in yeast and animal systems. Here, we searched for new factors
involved in CME in Arabidopsis thaliana by performing Tandem Affinity Purification
of proteins that interact with clathrin light chain, a principal component of
the clathrin coat. Among the confirmed interactors, we found two putative homologues
of the clathrin-coat uncoating factor auxilin previously described in non-plant
systems. Overexpression of AUXILIN-LIKE1 and AUXILIN-LIKE2 in A. thaliana caused
an arrest of seedling growth and development. This was concomitant with inhibited
endocytosis due to blocking of clathrin recruitment after the initial step of
adaptor protein binding to the plasma membrane. By contrast, auxilin-like(1/2)
loss-of-function lines did not present endocytosis-related developmental or cellular
phenotypes under normal growth conditions. This work contributes to the on-going
characterization of the endocytotic machinery in plants and provides a robust
tool for conditionally and specifically interfering with CME in A. thaliana.
acknowledgement: We thank James Matthew Watson, Monika Borowska, and Peggy Stolt-Bergner
at ProTech Facility of the Vienna Biocenter Core Facilities for the CRISPR/CAS9
construct; Anna Müller for assistance with molecular cloning; Sebastian Bednarek,
Liwen Jiang, and Daniël Van Damme for sharing published material; Matyáš Fendrych,
Daniël Van Damme, and Lindy Abas for valuable discussions; and Martine De Cock for
help with correcting the manuscript. This work was supported by the European Research
Council under the European Union Seventh Framework Programme (FP7/2007-2013)/ERC
Grant 282300 and by the Ministry of Education of the Czech Republic/MŠMT project
NPUI-LO1417.
article_processing_charge: No
article_type: original
author:
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Madhumitha
full_name: Narasimhan, Madhumitha
id: 44BF24D0-F248-11E8-B48F-1D18A9856A87
last_name: Narasimhan
orcid: 0000-0002-8600-0671
- first_name: Urszula
full_name: Kania, Urszula
id: 4AE5C486-F248-11E8-B48F-1D18A9856A87
last_name: Kania
- first_name: Matous
full_name: Glanc, Matous
id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2
last_name: Glanc
orcid: 0000-0003-0619-7783
- first_name: Geert
full_name: De Jaeger, Geert
last_name: De Jaeger
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. A functional
study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis.
The Plant Cell. 2018;30(3):700-716. doi:10.1105/tpc.17.00785
apa: Adamowski, M., Narasimhan, M., Kania, U., Glanc, M., De Jaeger, G., & Friml,
J. (2018). A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating
factors in Arabidopsis. The Plant Cell. American Society of Plant Biologists.
https://doi.org/10.1105/tpc.17.00785
chicago: Adamowski, Maciek, Madhumitha Narasimhan, Urszula Kania, Matous Glanc,
Geert De Jaeger, and Jiří Friml. “A Functional Study of AUXILIN LIKE1 and 2 Two
Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell. American
Society of Plant Biologists, 2018. https://doi.org/10.1105/tpc.17.00785.
ieee: M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, and J. Friml,
“A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors
in Arabidopsis,” The Plant Cell, vol. 30, no. 3. American Society of Plant
Biologists, pp. 700–716, 2018.
ista: Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. 2018. A
functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors
in Arabidopsis. The Plant Cell. 30(3), 700–716.
mla: Adamowski, Maciek, et al. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative
Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell, vol. 30, no.
3, American Society of Plant Biologists, 2018, pp. 700–16, doi:10.1105/tpc.17.00785.
short: M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, J. Friml,
The Plant Cell 30 (2018) 700–716.
date_created: 2018-12-11T11:46:20Z
date_published: 2018-04-09T00:00:00Z
date_updated: 2024-03-27T23:30:06Z
day: '09'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1105/tpc.17.00785
ec_funded: 1
external_id:
isi:
- '000429441400018'
pmid:
- '29511054'
file:
- access_level: open_access
checksum: 4e165e653b67d3f0684697f21aace5a1
content_type: application/pdf
creator: dernst
date_created: 2022-05-23T09:12:38Z
date_updated: 2022-05-23T09:12:38Z
file_id: '11406'
file_name: 2018_PlantCell_Adamowski.pdf
file_size: 4407538
relation: main_file
success: 1
file_date_updated: 2022-05-23T09:12:38Z
has_accepted_license: '1'
intvolume: ' 30'
isi: 1
issue: '3'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 700 - 716
pmid: 1
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: The Plant Cell
publication_identifier:
eissn:
- 1532-298X
issn:
- 1040-4651
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '7417'
quality_controlled: '1'
related_material:
record:
- id: '6269'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors
in Arabidopsis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 30
year: '2018'
...
---
_id: '5914'
abstract:
- lang: eng
text: With the advent of optogenetics, it became possible to change the activity
of a targeted population of neurons in a temporally controlled manner. To combine
the advantages of 60-channel in vivo tetrode recording and laser-based optogenetics,
we have developed a closed-loop recording system that allows for the actual electrophysiological
signal to be used as a trigger for the laser light mediating the optogenetic intervention.
We have optimized the weight, size, and shape of the corresponding implant to
make it compatible with the size, force, and movements of a behaving mouse, and
we have shown that the system can efficiently block sharp wave ripple (SWR) events
using those events themselves as a trigger. To demonstrate the full potential
of the optogenetic recording system we present a pilot study addressing the contribution
of SWR events to learning in a complex behavioral task.
article_number: e0087
article_processing_charge: No
author:
- first_name: Dámaris K
full_name: Rangel Guerrero, Dámaris K
id: 4871BCE6-F248-11E8-B48F-1D18A9856A87
last_name: Rangel Guerrero
orcid: 0000-0002-8602-4374
- first_name: James G.
full_name: Donnett, James G.
last_name: Donnett
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Krisztián
full_name: Kovács, Krisztián
id: 2AB5821E-F248-11E8-B48F-1D18A9856A87
last_name: Kovács
orcid: 0000-0001-6251-1007
citation:
ama: 'Rangel Guerrero DK, Donnett JG, Csicsvari JL, Kovács K. Tetrode recording
from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop
optogenetics: A technique to study the contribution of Hippocampal SWR events
to learning. eNeuro. 2018;5(4). doi:10.1523/ENEURO.0087-18.2018'
apa: 'Rangel Guerrero, D. K., Donnett, J. G., Csicsvari, J. L., & Kovács, K.
(2018). Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation
closed-loop optogenetics: A technique to study the contribution of Hippocampal
SWR events to learning. ENeuro. Society of Neuroscience. https://doi.org/10.1523/ENEURO.0087-18.2018'
chicago: 'Rangel Guerrero, Dámaris K, James G. Donnett, Jozsef L Csicsvari, and
Krisztián Kovács. “Tetrode Recording from the Hippocampus of Behaving Mice Coupled
with Four-Point-Irradiation Closed-Loop Optogenetics: A Technique to Study the
Contribution of Hippocampal SWR Events to Learning.” ENeuro. Society of
Neuroscience, 2018. https://doi.org/10.1523/ENEURO.0087-18.2018.'
ieee: 'D. K. Rangel Guerrero, J. G. Donnett, J. L. Csicsvari, and K. Kovács, “Tetrode
recording from the hippocampus of behaving mice coupled with four-point-irradiation
closed-loop optogenetics: A technique to study the contribution of Hippocampal
SWR events to learning,” eNeuro, vol. 5, no. 4. Society of Neuroscience,
2018.'
ista: 'Rangel Guerrero DK, Donnett JG, Csicsvari JL, Kovács K. 2018. Tetrode recording
from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop
optogenetics: A technique to study the contribution of Hippocampal SWR events
to learning. eNeuro. 5(4), e0087.'
mla: 'Rangel Guerrero, Dámaris K., et al. “Tetrode Recording from the Hippocampus
of Behaving Mice Coupled with Four-Point-Irradiation Closed-Loop Optogenetics:
A Technique to Study the Contribution of Hippocampal SWR Events to Learning.”
ENeuro, vol. 5, no. 4, e0087, Society of Neuroscience, 2018, doi:10.1523/ENEURO.0087-18.2018.'
short: D.K. Rangel Guerrero, J.G. Donnett, J.L. Csicsvari, K. Kovács, ENeuro 5 (2018).
date_created: 2019-02-03T22:59:16Z
date_published: 2018-07-27T00:00:00Z
date_updated: 2024-03-27T23:30:10Z
day: '27'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1523/ENEURO.0087-18.2018
ec_funded: 1
external_id:
isi:
- '000443994700007'
file:
- access_level: open_access
checksum: f4915d45fc7ad4648b7b7a13fdecca01
content_type: application/pdf
creator: dernst
date_created: 2019-02-05T12:48:36Z
date_updated: 2020-07-14T12:47:13Z
file_id: '5921'
file_name: 2018_ENeuro_Guerrero.pdf
file_size: 3746884
relation: main_file
file_date_updated: 2020-07-14T12:47:13Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
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: 257D4372-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I2072-B27
name: Interneuron plasticity during spatial learning
publication: eNeuro
publication_status: published
publisher: Society of Neuroscience
quality_controlled: '1'
related_material:
record:
- id: '6849'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation
closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR
events to learning'
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: 5
year: '2018'
...
---
_id: '402'
abstract:
- lang: eng
text: During metastasis, malignant cells escape the primary tumor, intravasate lymphatic
vessels, and reach draining sentinel lymph nodes before they colonize distant
organs via the blood circulation. Although lymph node metastasis in cancer patients
correlates with poor prognosis, evidence is lacking as to whether and how tumor
cells enter the bloodstream via lymph nodes. To investigate this question, we
delivered carcinoma cells into the lymph nodes of mice by microinfusing the cells
into afferent lymphatic vessels. We found that tumor cells rapidly infiltrated
the lymph node parenchyma, invaded blood vessels, and seeded lung metastases without
involvement of the thoracic duct. These results suggest that the lymph node blood
vessels can serve as an exit route for systemic dissemination of cancer cells
in experimental mouse models. Whether this form of tumor cell spreading occurs
in cancer patients remains to be determined.
acknowledged_ssus:
- _id: Bio
acknowledgement: "M.B. was supported by the Cell Communication in Health and Disease
graduate study program of the Austrian Science Fund (FWF) and the Medical University
of Vienna. M.S. was supported by the European Research Council (grant ERC GA 281556)
and an FWF START award.\r\nWe thank C. Moussion for establishing the intralymphatic
injection at IST Austria and for providing anti-PNAd hybridoma supernatant, R. Förster
and A. Braun for sharing the intralymphatic injection technology, K. Vaahtomeri
for the lentiviral constructs, M. Hons for establishing in vivo multiphoton imaging,
the Sixt lab for intellectual input, M. Schunn for help with the design of the in
vivo experiments, F. Langer for technical assistance with the in vivo experiments,
the bioimaging facility of IST Austria for support, and R. Efferl for providing
the CT26 cell line."
article_processing_charge: No
article_type: original
author:
- first_name: Markus
full_name: Brown, Markus
id: 3DAB9AFC-F248-11E8-B48F-1D18A9856A87
last_name: Brown
- 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: Alexander F
full_name: Leithner, Alexander F
id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87
last_name: Leithner
orcid: 0000-0002-1073-744X
- first_name: Jun
full_name: Abe, Jun
last_name: Abe
- first_name: Helga
full_name: Schachner, Helga
last_name: Schachner
- first_name: Gabriele
full_name: Asfour, Gabriele
last_name: Asfour
- first_name: Zsuzsanna
full_name: Bagó Horváth, Zsuzsanna
last_name: Bagó Horváth
- first_name: Jens
full_name: Stein, Jens
last_name: Stein
- first_name: Pavel
full_name: Uhrin, Pavel
last_name: Uhrin
- 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: Dontscho
full_name: Kerjaschki, Dontscho
last_name: Kerjaschki
citation:
ama: Brown M, Assen FP, Leithner AF, et al. Lymph node blood vessels provide exit
routes for metastatic tumor cell dissemination in mice. Science. 2018;359(6382):1408-1411.
doi:10.1126/science.aal3662
apa: Brown, M., Assen, F. P., Leithner, A. F., Abe, J., Schachner, H., Asfour, G.,
… Kerjaschki, D. (2018). Lymph node blood vessels provide exit routes for metastatic
tumor cell dissemination in mice. Science. American Association for the
Advancement of Science. https://doi.org/10.1126/science.aal3662
chicago: Brown, Markus, Frank P Assen, Alexander F Leithner, Jun Abe, Helga Schachner,
Gabriele Asfour, Zsuzsanna Bagó Horváth, et al. “Lymph Node Blood Vessels Provide
Exit Routes for Metastatic Tumor Cell Dissemination in Mice.” Science.
American Association for the Advancement of Science, 2018. https://doi.org/10.1126/science.aal3662.
ieee: M. Brown et al., “Lymph node blood vessels provide exit routes for
metastatic tumor cell dissemination in mice,” Science, vol. 359, no. 6382.
American Association for the Advancement of Science, pp. 1408–1411, 2018.
ista: Brown M, Assen FP, Leithner AF, Abe J, Schachner H, Asfour G, Bagó Horváth
Z, Stein J, Uhrin P, Sixt MK, Kerjaschki D. 2018. Lymph node blood vessels provide
exit routes for metastatic tumor cell dissemination in mice. Science. 359(6382),
1408–1411.
mla: Brown, Markus, et al. “Lymph Node Blood Vessels Provide Exit Routes for Metastatic
Tumor Cell Dissemination in Mice.” Science, vol. 359, no. 6382, American
Association for the Advancement of Science, 2018, pp. 1408–11, doi:10.1126/science.aal3662.
short: M. Brown, F.P. Assen, A.F. Leithner, J. Abe, H. Schachner, G. Asfour, Z.
Bagó Horváth, J. Stein, P. Uhrin, M.K. Sixt, D. Kerjaschki, Science 359 (2018)
1408–1411.
date_created: 2018-12-11T11:46:16Z
date_published: 2018-03-23T00:00:00Z
date_updated: 2024-03-27T23:30:09Z
day: '23'
department:
- _id: MiSi
doi: 10.1126/science.aal3662
ec_funded: 1
external_id:
isi:
- '000428043600047'
pmid:
- '29567714'
intvolume: ' 359'
isi: 1
issue: '6382'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1126/science.aal3662
month: '03'
oa: 1
oa_version: Published Version
page: 1408 - 1411
pmid: 1
project:
- _id: 25A8E5EA-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y 564-B12
name: Cytoskeletal force generation and transduction of leukocytes (FWF)
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
(EU)
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '7428'
quality_controlled: '1'
related_material:
record:
- id: '6947'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination
in mice
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 359
year: '2018'
...
---
_id: '395'
abstract:
- lang: eng
text: 'Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping
with other neurological conditions. Despite the remarkable number of scientific
breakthroughs of the last 100 years, the treatment of neurodevelopmental disorders
(e.g. autism spectrum disorder, intellectual disability, epilepsy) remains a great
challenge. Recent advancements in geno mics, like whole-exome or whole-genome
sequencing, have enabled scientists to identify numerous mutations underlying
neurodevelopmental disorders. Given the few hundred risk genes that were discovered,
the etiological variability and the heterogeneous phenotypic outcomes, the need
for genotype -along with phenotype- based diagnosis of individual patients becomes
a requisite. Driven by this rationale, in a previous study our group described
mutations, identified via whole - exome sequencing, in the gene BCKDK – encoding
for a key regulator of branched chain amin o acid (BCAA) catabolism - as a cause
of ASD. Following up on the role of BCAAs, in the study described here we show
that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter
localized mainly at the blood brain barrier (BBB), has an essential role in maintaining
normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial
cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation
and severe neurolo gical abnormalities. Additionally, deletion of Slc7a5 from
the neural progenitor cell population leads to microcephaly. Interestingly, we
demonstrate that BCAA intracerebroventricular administration ameliorates abnormal
behaviors in adult mutant mice. Furthermore, whole - exome sequencing of patients
diagnosed with neurological dis o r ders helped us identify several patients with
autistic traits, microcephaly and motor delay carrying deleterious homozygous
mutations in the SLC7A5 gene. In conclusion, our data elucidate a neurological
syndrome defined by SLC7A5 mutations and support an essential role for t he BCAA
s in human bra in function. Together with r ecent studies (described in chapter
two) that have successfully made the transition into clinical practice, our findings
on the role of B CAAs might have a crucial impact on the development of novel
individualized therapeutic strategies for ASD. '
acknowledged_ssus:
- _id: PreCl
- _id: EM-Fac
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Dora-Clara
full_name: Tarlungeanu, Dora-Clara
id: 2ABCE612-F248-11E8-B48F-1D18A9856A87
last_name: Tarlungeanu
citation:
ama: Tarlungeanu D-C. The branched chain amino acids in autism spectrum disorders
. 2018. doi:10.15479/AT:ISTA:th_992
apa: Tarlungeanu, D.-C. (2018). The branched chain amino acids in autism spectrum
disorders . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_992
chicago: Tarlungeanu, Dora-Clara. “The Branched Chain Amino Acids in Autism Spectrum
Disorders .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_992.
ieee: D.-C. Tarlungeanu, “The branched chain amino acids in autism spectrum disorders
,” Institute of Science and Technology Austria, 2018.
ista: Tarlungeanu D-C. 2018. The branched chain amino acids in autism spectrum disorders
. Institute of Science and Technology Austria.
mla: Tarlungeanu, Dora-Clara. The Branched Chain Amino Acids in Autism Spectrum
Disorders . Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_992.
short: D.-C. Tarlungeanu, The Branched Chain Amino Acids in Autism Spectrum Disorders
, Institute of Science and Technology Austria, 2018.
date_created: 2018-12-11T11:46:14Z
date_published: 2018-03-01T00:00:00Z
date_updated: 2023-09-07T12:38:59Z
day: '01'
ddc:
- '570'
- '616'
degree_awarded: PhD
department:
- _id: GaNo
doi: 10.15479/AT:ISTA:th_992
file:
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checksum: 9f5231c96e0ad945040841a8630232da
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date_created: 2019-04-05T09:19:17Z
date_updated: 2021-02-11T23:30:15Z
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file_name: 2018_Thesis_Tarlungeanu_source.docx
file_size: 43684035
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content_type: application/pdf
creator: dernst
date_created: 2019-04-05T09:19:17Z
date_updated: 2021-02-11T11:17:16Z
embargo: 2018-03-15
file_id: '6218'
file_name: 2018_Thesis_Tarlungeanu.pdf
file_size: 30511532
relation: main_file
file_date_updated: 2021-02-11T23:30:15Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '88'
project:
- _id: 25473368-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: F03523
name: Transmembrane Transporters in Health and Disease
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '7434'
pubrep_id: '992'
related_material:
record:
- id: '1183'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
title: 'The branched chain amino acids in autism spectrum disorders '
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '51'
abstract:
- lang: eng
text: Asymmetries have long been known about in the central nervous system. From
gross anatomical differences, such as the presence of the parapineal organ in
only one hemisphere of the developing zebrafish, to more subtle differences in
activity between both hemispheres, as seen in freely roaming animals or human
participants under PET and fMRI imaging analysis. The presence of asymmetries
has been demonstrated to have huge behavioural implications, with their disruption
often leading to the generation of neurological disorders, memory problems, changes
in personality, and in an organism's health and well-being. For my Ph.D. work
I aimed to tackle two important avenues of research. The first being the process
of input-side dependency in the hippocampus, with the goal of finding a key gene
responsible for its development (Gene X). The second project was to do with experience-induced
laterality formation in the hippocampus. Specifically, how laterality in the synapse
density of the CA1 stratum radiatum (s.r.) could be induced purely through environmental
enrichment. Through unilateral tracer injections into the CA3, I was able to selectively
measure the properties of synapses within the CA1 and investigate how they differed
based upon which hemisphere the presynaptic neurone originated. Having found the
existence of a previously unreported reversed (left-isomerism) i.v. mutant, through
morpholocal examination of labelled terminals in the CA1 s.r., I aimed to elucidate
a key gene responsible for the process of left or right determination of inputs
to the CA1 s.r.. This work relates to the previous finding of input-side dependent
asymmetry in the wild-type rodent, where the origin of the projecting neurone
to the CA1 will determine the morphology of a synapse, to a greater degree than
the hemisphere in which the projection terminates. Using left- and right-isomerism
i.v. mice, in combination with whole genome sequence analysis, I highlight Ena/VASP-like
(Evl) as a potential target for Gene X. In relation to this topic, I also highlight
my work in the recently published paper of how knockout of PirB can lead to a
lack of input-side dependency in the murine hippocampus. For the second question,
I show that the environmental enrichment paradigm will lead to an asymmetry in
the synapse densities in the hippocampus of mice. I also highlight that the nature
of the enrichment is of less consequence than the process of enrichment itself.
I demonstrate that the CA3 region will dramatically alter its projection targets,
in relation to environmental stimulation, with the asymmetry in synaptic density,
caused by enrichment, relying heavily on commissural fibres. I also highlight
the vital importance of input-side dependent asymmetry, as a necessary component
of experience-dependent laterality formation in the CA1 s.r.. However, my results
suggest that it isn't the only cause, as there appears to be a CA1 dependent mechanism
also at play. Upon further investigation, I highlight the significant, and highly
important, finding that the changes seen in the CA1 s.r. were predominantly caused
through projections from the left-CA3, with the right-CA3 having less involvement
in this mechanism.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Matthew J
full_name: Case, Matthew J
id: 44B7CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Case
citation:
ama: 'Case MJ. From the left to the right: A tale of asymmetries, environments,
and hippocampal development. 2018. doi:10.15479/AT:ISTA:th_1032'
apa: 'Case, M. J. (2018). From the left to the right: A tale of asymmetries,
environments, and hippocampal development. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:th_1032'
chicago: 'Case, Matthew J. “From the Left to the Right: A Tale of Asymmetries, Environments,
and Hippocampal Development.” Institute of Science and Technology Austria, 2018.
https://doi.org/10.15479/AT:ISTA:th_1032.'
ieee: 'M. J. Case, “From the left to the right: A tale of asymmetries, environments,
and hippocampal development,” Institute of Science and Technology Austria, 2018.'
ista: 'Case MJ. 2018. From the left to the right: A tale of asymmetries, environments,
and hippocampal development. Institute of Science and Technology Austria.'
mla: 'Case, Matthew J. From the Left to the Right: A Tale of Asymmetries, Environments,
and Hippocampal Development. Institute of Science and Technology Austria,
2018, doi:10.15479/AT:ISTA:th_1032.'
short: 'M.J. Case, From the Left to the Right: A Tale of Asymmetries, Environments,
and Hippocampal Development, Institute of Science and Technology Austria, 2018.'
date_created: 2018-12-11T11:44:22Z
date_published: 2018-06-27T00:00:00Z
date_updated: 2023-09-07T12:39:22Z
day: '27'
ddc:
- '571'
- '576'
degree_awarded: PhD
department:
- _id: RySh
doi: 10.15479/AT:ISTA:th_1032
file:
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checksum: dcc7b55619d8509dd62b8e99d6cdee44
content_type: application/msword
creator: dernst
date_created: 2019-04-09T07:16:26Z
date_updated: 2021-02-11T23:30:13Z
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file_id: '6251'
file_name: 2018_Thesis_Case_Source.doc
file_size: 141270528
relation: source_file
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checksum: f69fdd5c8709c4e618aa8c1a1221153d
content_type: application/pdf
creator: dernst
date_created: 2019-04-09T07:16:23Z
date_updated: 2021-02-11T11:17:14Z
embargo: 2019-07-05
file_id: '6252'
file_name: 2018_Thesis_Case.pdf
file_size: 15193621
relation: main_file
file_date_updated: 2021-02-11T23:30:13Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '186'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '8003'
pubrep_id: '1032'
related_material:
record:
- id: '682'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
title: 'From the left to the right: A tale of asymmetries, environments, and hippocampal
development'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '10'
abstract:
- lang: eng
text: Genomic imprinting is an epigenetic process that leads to parent of origin-specific
gene expression in a subset of genes. Imprinted genes are essential for brain
development, and deregulation of imprinting is associated with neurodevelopmental
diseases and the pathogenesis of psychiatric disorders. However, the cell-type
specificity of imprinting at single cell resolution, and how imprinting and thus
gene dosage regulates neuronal circuit assembly is still largely unknown. Here,
MADM (Mosaic Analysis with Double Markers) technology was employed to assess genomic
imprinting at single cell level. By visualizing MADM-induced uniparental disomies
(UPDs) in distinct colors at single cell level in genetic mosaic animals, this
experimental paradigm provides a unique quantitative platform to systematically
assay the UPD-mediated imbalances in imprinted gene expression at unprecedented
resolution. An experimental pipeline based on FACS, RNA-seq and bioinformatics
analysis was established and applied to systematically map cell-type-specific
‘imprintomes’ in the mouse brain. The results revealed that parental-specific
expression of imprinted genes per se is rarely cell-type-specific even at the
individual cell level. Conversely, when we extended the comparison to downstream
responses resulting from imbalanced imprinted gene expression, we discovered an
unexpectedly high degree of cell-type specificity. Furthermore, we determined
a novel function of genomic imprinting in cortical astrocyte production and in
olfactory bulb (OB) granule cell generation. These results suggest important functional
implication of genomic imprinting for generating cell-type diversity in the brain.
In addition, MADM provides a powerful tool to study candidate genes by concomitant
genetic manipulation and fluorescent labelling of single cells. MADM-based candidate
gene approach was utilized to identify potential imprinted genes involved in the
generation of cortical astrocytes and OB granule cells. We investigated p57Kip2,
a maternally expressed gene and known cell cycle regulator. Although we found
that p57Kip2 does not play a role in these processes, we detected an unexpected
function of the paternal allele previously thought to be silent. Finally, we took
advantage of a key property of MADM which is to allow unambiguous investigation
of environmental impact on single cells. The experimental pipeline based on FACS
and RNA-seq analysis of MADM-labeled cells was established to probe the functional
differences of single cell loss of gene function compared to global loss of function
on a transcriptional level. With this method, both common and distinct responses
were isolated due to cell-autonomous and non-autonomous effects acting on genotypically
identical cells. As a result, transcriptional changes were identified which result
solely from the surrounding environment. Using the MADM technology to study genomic
imprinting at single cell resolution, we have identified cell-type-specific gene
expression, novel gene function and the impact of environment on single cell transcriptomes.
Together, these provide important insights to the understanding of mechanisms
regulating cell-type specificity and thus diversity in the brain.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Susanne
full_name: Laukoter, Susanne
id: 2D6B7A9A-F248-11E8-B48F-1D18A9856A87
last_name: Laukoter
orcid: 0000-0002-7903-3010
citation:
ama: Laukoter S. Role of genomic imprinting in cerebral cortex development. 2018:1-139.
doi:10.15479/AT:ISTA:th1057
apa: Laukoter, S. (2018). Role of genomic imprinting in cerebral cortex development.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1057
chicago: Laukoter, Susanne. “Role of Genomic Imprinting in Cerebral Cortex Development.”
Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1057.
ieee: S. Laukoter, “Role of genomic imprinting in cerebral cortex development,”
Institute of Science and Technology Austria, 2018.
ista: Laukoter S. 2018. Role of genomic imprinting in cerebral cortex development.
Institute of Science and Technology Austria.
mla: Laukoter, Susanne. Role of Genomic Imprinting in Cerebral Cortex Development.
Institute of Science and Technology Austria, 2018, pp. 1–139, doi:10.15479/AT:ISTA:th1057.
short: S. Laukoter, Role of Genomic Imprinting in Cerebral Cortex Development, Institute
of Science and Technology Austria, 2018.
date_created: 2018-12-11T11:44:08Z
date_published: 2018-11-21T00:00:00Z
date_updated: 2023-09-07T12:40:44Z
day: '21'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: SiHi
doi: 10.15479/AT:ISTA:th1057
file:
- access_level: closed
checksum: 41fdbf5fdce312802935d88a8ad9932c
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-05-10T07:47:04Z
date_updated: 2019-11-23T23:30:03Z
embargo_to: open_access
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file_name: Thesis_LaukoterSusanne_FINAL.docx
file_size: 17949175
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creator: dernst
date_created: 2019-05-10T07:47:04Z
date_updated: 2021-02-11T11:17:16Z
embargo: 2019-11-21
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file_size: 21187245
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file_date_updated: 2021-02-11T11:17:16Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1 - 139
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '8046'
pubrep_id: '1057'
status: public
supervisor:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
title: Role of genomic imprinting in cerebral cortex development
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '323'
abstract:
- lang: eng
text: 'In the here presented thesis, we explore the role of branched actin networks
in cell migration and antigen presentation, the two most relevant processes in
dendritic cell biology. Branched actin networks construct lamellipodial protrusions
at the leading edge of migrating cells. These are typically seen as adhesive structures,
which mediate force transduction to the extracellular matrix that leads to forward
locomotion. We ablated Arp2/3 nucleation promoting factor WAVE in DCs and found
that the resulting cells lack lamellipodial protrusions. Instead, depending on
the maturation state, one or multiple filopodia were formed. By challenging these
cells in a variety of migration assays we found that lamellipodial protrusions
are dispensable for the locomotion of leukocytes and actually dampen the speed
of migration. However, lamellipodia are critically required to negotiate complex
environments that DCs experience while they travel to the next draining lymph
node. Taken together our results suggest that leukocyte lamellipodia have rather
a sensory- than a force transducing function. Furthermore, we show for the first
time structure and dynamics of dendritic cell F-actin at the immunological synapse
with naïve T cells. Dendritic cell F-actin appears as dynamic foci that are nucleated
by the Arp2/3 complex. WAVE ablated dendritic cells show increased membrane tension,
leading to an altered ultrastructure of the immunological synapse and severe T
cell priming defects. These results point towards a previously unappreciated role
of the cellular mechanics of dendritic cells in T cell activation. Additionally,
we present a novel cell culture based system for the differentiation of dendritic
cells from conditionally immortalized hematopoietic precursors. These precursor
cells are genetically tractable via the CRISPR/Cas9 system while they retain their
ability to differentiate into highly migratory dendritic cells and other immune
cells. This will foster the study of all aspects of dendritic cell biology and
beyond. '
acknowledged_ssus:
- _id: NanoFab
- _id: Bio
- _id: PreCl
- _id: EM-Fac
acknowledgement: "First of all I would like to thank Michael Sixt for giving me the
opportunity to work in \r\nhis group and for his support throughout the years. He
is a truly inspiring person and \r\nthe best boss one can imagine. I would
\ also like to thank all current and past \r\nmembers of the Sixt group for
their help and the great working atmosphere in the lab. \r\nIt is a true privilege
to work with such a bright, funny and friendly group of people and \r\nI’m proud
\ that I could be part of it. Furthermore, I would like to say ‘thank
\ you’ to Daria Siekhaus for all the meetings and discussion we had throughout
the years \r\nand to Federica Benvenuti for being part of my committee.
\ I am also grateful to Jack \r\nMerrin in the nanofabrication facility
\ and all the people working in the bioimaging-\r\n, the electron microscopy-
and the preclinical facilities."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Alexander F
full_name: Leithner, Alexander F
id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87
last_name: Leithner
orcid: 0000-0002-1073-744X
citation:
ama: Leithner AF. Branched actin networks in dendritic cell biology. 2018. doi:10.15479/AT:ISTA:th_998
apa: Leithner, A. F. (2018). Branched actin networks in dendritic cell biology.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_998
chicago: Leithner, Alexander F. “Branched Actin Networks in Dendritic Cell Biology.”
Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_998.
ieee: A. F. Leithner, “Branched actin networks in dendritic cell biology,” Institute
of Science and Technology Austria, 2018.
ista: Leithner AF. 2018. Branched actin networks in dendritic cell biology. Institute
of Science and Technology Austria.
mla: Leithner, Alexander F. Branched Actin Networks in Dendritic Cell Biology.
Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_998.
short: A.F. Leithner, Branched Actin Networks in Dendritic Cell Biology, Institute
of Science and Technology Austria, 2018.
date_created: 2018-12-11T11:45:49Z
date_published: 2018-04-12T00:00:00Z
date_updated: 2023-09-07T12:39:44Z
day: '12'
ddc:
- '571'
- '599'
- '610'
degree_awarded: PhD
department:
- _id: MiSi
doi: 10.15479/AT:ISTA:th_998
file:
- access_level: closed
checksum: d5e3edbac548c26c1fa43a4b37a54a4c
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-04-05T09:23:11Z
date_updated: 2021-02-11T23:30:17Z
embargo_to: open_access
file_id: '6219'
file_name: PhD_thesis_AlexLeithner_final_version.docx
file_size: 29027671
relation: source_file
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checksum: 071f7476db29e41146824ebd0697cb10
content_type: application/pdf
creator: dernst
date_created: 2019-04-05T09:23:11Z
date_updated: 2021-02-11T11:17:16Z
embargo: 2019-04-15
file_id: '6220'
file_name: PhD_thesis_AlexLeithner.pdf
file_size: 66045341
relation: main_file
file_date_updated: 2021-02-11T23:30:17Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '99'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '7542'
pubrep_id: '998'
related_material:
record:
- id: '1321'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
title: Branched actin networks in dendritic cell biology
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '539'
abstract:
- lang: eng
text: The whole life cycle of plants as well as their responses to environmental
stimuli is governed by a complex network of hormonal regulations. A number of
studies have demonstrated an essential role of both auxin and cytokinin in the
regulation of many aspects of plant growth and development including embryogenesis,
postembryonic organogenic processes such as root, and shoot branching, root and
shoot apical meristem activity and phyllotaxis. Over the last decades essential
knowledge on the key molecular factors and pathways that spatio-temporally define
auxin and cytokinin activities in the plant body has accumulated. However, how
both hormonal pathways are interconnected by a complex network of interactions
and feedback circuits that determines the final outcome of the individual hormone
actions is still largely unknown. Root system architecture establishment and in
particular formation of lateral organs is prime example of developmental process
at whose regulation both auxin and cytokinin pathways converge. To dissect convergence
points and pathways that tightly balance auxin - cytokinin antagonistic activities
that determine the root branching pattern transcriptome profiling was applied.
Genome wide expression analyses of the xylem pole pericycle, a tissue giving rise
to lateral roots, led to identification of genes that are highly responsive to
combinatorial auxin and cytokinin treatments and play an essential function in
the auxin-cytokinin regulated root branching. SYNERGISTIC AUXIN CYTOKININ 1 (SYAC1)
gene, which encodes for a protein of unknown function, was detected among the
top candidate genes of which expression was synergistically up-regulated by simultaneous
hormonal treatment. Plants with modulated SYAC1 activity exhibit severe defects
in the root system establishment and attenuate developmental responses to both
auxin and cytokinin. To explore the biological function of the SYAC1, we employed
different strategies including expression pattern analysis, subcellular localization
and phenotypic analyses of the syac1 loss-of-function and gain-of-function transgenic
lines along with the identification of the SYAC1 interaction partners. Detailed
functional characterization revealed that SYAC1 acts as a developmentally specific
regulator of the secretory pathway to control deposition of cell wall components
and thereby rapidly fine tune elongation growth.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Andrej
full_name: Hurny, Andrej
id: 4DC4AF46-F248-11E8-B48F-1D18A9856A87
last_name: Hurny
orcid: 0000-0003-3638-1426
citation:
ama: Hurny A. Identification and characterization of novel auxin-cytokinin cross-talk
components. 2018. doi:10.15479/AT:ISTA:th_930
apa: Hurny, A. (2018). Identification and characterization of novel auxin-cytokinin
cross-talk components. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_930
chicago: Hurny, Andrej. “Identification and Characterization of Novel Auxin-Cytokinin
Cross-Talk Components.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_930.
ieee: A. Hurny, “Identification and characterization of novel auxin-cytokinin cross-talk
components,” Institute of Science and Technology Austria, 2018.
ista: Hurny A. 2018. Identification and characterization of novel auxin-cytokinin
cross-talk components. Institute of Science and Technology Austria.
mla: Hurny, Andrej. Identification and Characterization of Novel Auxin-Cytokinin
Cross-Talk Components. Institute of Science and Technology Austria, 2018,
doi:10.15479/AT:ISTA:th_930.
short: A. Hurny, Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk
Components, Institute of Science and Technology Austria, 2018.
date_created: 2018-12-11T11:47:03Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-09-07T12:41:06Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: EvBe
doi: 10.15479/AT:ISTA:th_930
file:
- access_level: closed
checksum: 0c9d6d1c80d9857e6e545213467bbcb2
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-04-05T09:37:56Z
date_updated: 2020-12-02T23:30:08Z
embargo_to: open_access
file_id: '6226'
file_name: 2018_Hurny_thesis_source.docx
file_size: 28112114
relation: source_file
- access_level: open_access
checksum: ecbe481a1413d270bd501b872c7ed54f
content_type: application/pdf
creator: dernst
date_created: 2019-04-05T09:37:55Z
date_updated: 2020-12-02T09:52:16Z
embargo: 2019-07-10
file_id: '6227'
file_name: 2018_Hurny_thesis.pdf
file_size: 12524427
relation: main_file
file_date_updated: 2020-12-02T23:30:08Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: '147'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '7277'
pubrep_id: '930'
related_material:
record:
- id: '1024'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
title: Identification and characterization of novel auxin-cytokinin cross-talk components
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '48'
abstract:
- lang: eng
text: 'The hippocampus is a key brain region for spatial memory and navigation and
is needed at all stages of memory, including encoding, consolidation, and recall.
Hippocampal place cells selectively discharge at specific locations of the environment
to form a cognitive map of the space. During the rest period and sleep following
spatial navigation and/or learning, the waking activity of the place cells is
reactivated within high synchrony events. This reactivation is thought to be important
for memory consolidation and stabilization of the spatial representations. The
aim of my thesis was to directly test whether the reactivation content encoded
in firing patterns of place cells is important for consolidation of spatial memories.
In particular, I aimed to test whether, in cases when multiple spatial memory
traces are acquired during learning, the specific disruption of the reactivation
of a subset of these memories leads to the selective disruption of the corresponding
memory traces or through memory interference the other learned memories are disrupted
as well. In this thesis, using a modified cheeseboard paradigm and a closed-loop
recording setup with feedback optogenetic stimulation, I examined how the disruption
of the reactivation of specific spiking patterns affects consolidation of the
corresponding memory traces. To obtain multiple distinctive memories, animals
had to perform a spatial task in two distinct cheeseboard environments and the
reactivation of spiking patterns associated with one of the environments (target)
was disrupted after learning during four hours rest period using a real-time decoding
method. This real-time decoding method was capable of selectively affecting the
firing rates and cofiring correlations of the target environment-encoding cells.
The selective disruption led to behavioural impairment in the memory tests after
the rest periods in the target environment but not in the other undisrupted control
environment. In addition, the map of the target environment was less stable in
the impaired memory tests compared to the learning session before than the map
of the control environment. However, when the animal relearned the task, the same
map recurred in the target environment that was present during learning before
the disruption. Altogether my work demonstrated that the reactivation content
is important: assembly-related disruption of reactivation can lead to a selective
memory impairment and deficiency in map stability. These findings indeed suggest
that reactivated assembly patterns reflect processes associated with the consolidation
of memory traces. '
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Igor
full_name: Gridchyn, Igor
id: 4B60654C-F248-11E8-B48F-1D18A9856A87
last_name: Gridchyn
orcid: 0000-0002-1807-1929
citation:
ama: Gridchyn I. Reactivation content is important for consolidation of spatial
memory. 2018. doi:10.15479/AT:ISTA:th_1042
apa: Gridchyn, I. (2018). Reactivation content is important for consolidation
of spatial memory. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1042
chicago: Gridchyn, Igor. “Reactivation Content Is Important for Consolidation of
Spatial Memory.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1042.
ieee: I. Gridchyn, “Reactivation content is important for consolidation of spatial
memory,” Institute of Science and Technology Austria, 2018.
ista: Gridchyn I. 2018. Reactivation content is important for consolidation of spatial
memory. Institute of Science and Technology Austria.
mla: Gridchyn, Igor. Reactivation Content Is Important for Consolidation of Spatial
Memory. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1042.
short: I. Gridchyn, Reactivation Content Is Important for Consolidation of Spatial
Memory, Institute of Science and Technology Austria, 2018.
date_created: 2018-12-11T11:44:21Z
date_published: 2018-08-27T00:00:00Z
date_updated: 2023-09-07T12:42:44Z
day: '27'
ddc:
- '573'
degree_awarded: PhD
department:
- _id: JoCs
doi: 10.15479/AT:ISTA:th_1042
file:
- access_level: closed
checksum: 7db4415e435590fa33542c7b0a0321d7
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-04-08T13:36:01Z
date_updated: 2021-02-11T23:30:22Z
embargo_to: open_access
file_id: '6236'
file_name: 2018_Thesis_Gridchyn_source.docx
file_size: 7666687
relation: source_file
- access_level: open_access
checksum: f96f3fe8979f7b1e6db6acaca962b10c
content_type: application/pdf
creator: dernst
date_created: 2019-04-08T13:36:01Z
date_updated: 2021-02-11T11:17:18Z
embargo: 2019-08-29
file_id: '6237'
file_name: 2018_Thesis_Gridchyn.pdf
file_size: 6034153
relation: main_file
file_date_updated: 2021-02-11T23:30:22Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '104'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '8006'
pubrep_id: '1042'
status: public
supervisor:
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
title: Reactivation content is important for consolidation of spatial memory
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '9'
abstract:
- lang: eng
text: 'Immune cells migrating to the sites of infection navigate through diverse
tissue architectures and switch their migratory mechanisms upon demand. However,
little is known about systemic regulators that could allow the acquisition of
these mechanisms. We performed a genetic screen in Drosophila melanogaster to
identify regulators of germband invasion by embryonic macrophages into the confined
space between the ectoderm and mesoderm. We have found that bZIP circadian transcription
factors (TFs) Kayak (dFos) and Vrille (dNFIL3) have opposite effects on macrophage
germband infiltration: Kayak facilitated and Vrille inhibited it. These TFs are
enriched in the macrophages during migration and genetically interact to control
it. Kayak sets a less coordinated mode of migration of the macrophage group and
increases the probability and length of Levy walks. Intriguingly, the motility
of kayak mutant macrophages was also strongly affected during initial germband
invasion but not along another less confined route. Inhibiting Rho1 signaling
within the tail ectoderm partially rescued the Kayak mutant phenotype, strongly
suggesting that migrating macrophages have to overcome a barrier imposed by the
stiffness of the ectoderm. Also, Kayak appeared to be important for the maintenance
of the round cell shape and the rear edge translocation of the macrophages invading
the germband. Complementary to this, the cortical actin cytoskeleton of Kayak-
deficient macrophages was strongly affected. RNA sequencing revealed the filamin
Cheerio and tetraspanin TM4SF to be downstream of Kayak. Chromatin immunoprecipitation
and immunostaining revealed that the formin Diaphanous is another downstream target
of Kayak. Immunostaining revealed that the formin Diaphanous is another downstream
target of Kayak. Indeed, Cheerio, TM4SF and Diaphanous are required within macrophages
for germband invasion, and expression of constitutively active Diaphanous in macrophages
was able to rescue the kayak mutant phenotype. Moreover, Cher and Diaphanous are
also reduced in the macrophages overexpressing Vrille. We hypothesize that Kayak,
through its targets, increases actin polymerization and cortical tension in macrophages
and thus allows extra force generation necessary for macrophage dissemination
and migration through confined stiff tissues, while Vrille counterbalances it.'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Vera
full_name: Belyaeva, Vera
id: 47F080FE-F248-11E8-B48F-1D18A9856A87
last_name: Belyaeva
citation:
ama: Belyaeva V. Transcriptional regulation of macrophage migration in the Drosophila
melanogaster embryo . 2018. doi:10.15479/AT:ISTA:th1064
apa: Belyaeva, V. (2018). Transcriptional regulation of macrophage migration
in the Drosophila melanogaster embryo . Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:th1064
chicago: Belyaeva, Vera. “Transcriptional Regulation of Macrophage Migration in
the Drosophila Melanogaster Embryo .” Institute of Science and Technology Austria,
2018. https://doi.org/10.15479/AT:ISTA:th1064.
ieee: V. Belyaeva, “Transcriptional regulation of macrophage migration in the Drosophila
melanogaster embryo ,” Institute of Science and Technology Austria, 2018.
ista: Belyaeva V. 2018. Transcriptional regulation of macrophage migration in the
Drosophila melanogaster embryo . Institute of Science and Technology Austria.
mla: Belyaeva, Vera. Transcriptional Regulation of Macrophage Migration in the
Drosophila Melanogaster Embryo . Institute of Science and Technology Austria,
2018, doi:10.15479/AT:ISTA:th1064.
short: V. Belyaeva, Transcriptional Regulation of Macrophage Migration in the Drosophila
Melanogaster Embryo , Institute of Science and Technology Austria, 2018.
date_created: 2018-12-11T11:44:08Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2023-09-07T12:43:10Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: DaSi
doi: 10.15479/AT:ISTA:th1064
file:
- access_level: closed
checksum: d27b2465cb70d0c9678a0381b9b6ced1
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-04-08T14:13:12Z
date_updated: 2020-07-14T12:48:14Z
embargo_to: open_access
file_id: '6243'
file_name: 2018_Thesis_Belyaeva_source.docx
file_size: 102737483
relation: source_file
- access_level: open_access
checksum: a2939b61bde2de7b8ced77bbae0eaaed
content_type: application/pdf
creator: dernst
date_created: 2019-04-08T14:14:08Z
date_updated: 2021-02-11T11:17:16Z
embargo: 2019-11-19
file_id: '6244'
file_name: 2018_Thesis_Belyaeva.pdf
file_size: 88077843
relation: main_file
file_date_updated: 2021-02-11T11:17:16Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '96'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '8047'
pubrep_id: '1064'
status: public
supervisor:
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
title: 'Transcriptional regulation of macrophage migration in the Drosophila melanogaster
embryo '
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '6266'
abstract:
- lang: eng
text: 'A major challenge in neuroscience research is to dissect the circuits that
orchestrate behavior in health and disease. Proteins from a wide range of non-mammalian
species, such as microbial opsins, have been successfully transplanted to specific
neuronal targets to override their natural communication patterns. The goal of
our work is to manipulate synaptic communication in a manner that closely incorporates
the functional intricacies of synapses by preserving temporal encoding (i.e. the
firing pattern of the presynaptic neuron) and connectivity (i.e. target specific
synapses rather than specific neurons). Our strategy to achieve this goal builds
on the use of non-mammalian transplants to create a synthetic synapse. The mode
of modulation comes from pre-synaptic uptake of a synthetic neurotransmitter (SN)
into synaptic vesicles by means of a genetically targeted transporter selective
for the SN. Upon natural vesicular release, exposure of the SN to the synaptic
cleft will modify the post-synaptic potential through an orthogonal ligand gated
ion channel. To achieve this goal we have functionally characterized a mixed cationic
methionine-gated ion channel from Arabidopsis thaliana, designed a method to functionally
characterize a synthetic transporter in isolated synaptic vesicles without the
need for transgenic animals, identified and extracted multiple prokaryotic uptake
systems that are substrate specific for methionine (Met), and established a primary/cell
line co-culture system that would allow future combinatorial testing of this orthogonal
transmitter-transporter-channel trifecta. Synthetic synapses will provide a unique
opportunity to manipulate synaptic communication while maintaining the electrophysiological
integrity of the pre-synaptic cell. In this way, information may be preserved
that was generated in upstream circuits and that could be essential for concerted
function and information processing. '
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Catherine
full_name: Mckenzie, Catherine
id: 3EEDE19A-F248-11E8-B48F-1D18A9856A87
last_name: Mckenzie
citation:
ama: Mckenzie C. Design and characterization of methods and biological components
to realize synthetic neurotransmission . 2018. doi:10.15479/at:ista:th_1055
apa: Mckenzie, C. (2018). Design and characterization of methods and biological
components to realize synthetic neurotransmission . Institute of Science and
Technology Austria. https://doi.org/10.15479/at:ista:th_1055
chicago: Mckenzie, Catherine. “Design and Characterization of Methods and Biological
Components to Realize Synthetic Neurotransmission .” Institute of Science and
Technology Austria, 2018. https://doi.org/10.15479/at:ista:th_1055.
ieee: C. Mckenzie, “Design and characterization of methods and biological components
to realize synthetic neurotransmission ,” Institute of Science and Technology
Austria, 2018.
ista: Mckenzie C. 2018. Design and characterization of methods and biological components
to realize synthetic neurotransmission . Institute of Science and Technology Austria.
mla: Mckenzie, Catherine. Design and Characterization of Methods and Biological
Components to Realize Synthetic Neurotransmission . Institute of Science and
Technology Austria, 2018, doi:10.15479/at:ista:th_1055.
short: C. Mckenzie, Design and Characterization of Methods and Biological Components
to Realize Synthetic Neurotransmission , Institute of Science and Technology Austria,
2018.
date_created: 2019-04-09T14:13:39Z
date_published: 2018-10-31T00:00:00Z
date_updated: 2023-09-07T13:02:37Z
day: '31'
ddc:
- '571'
- '573'
degree_awarded: PhD
department:
- _id: HaJa
doi: 10.15479/at:ista:th_1055
file:
- access_level: open_access
checksum: 9d2c2dca04b00e485470c28b262af59a
content_type: application/pdf
creator: dernst
date_created: 2019-04-09T14:12:40Z
date_updated: 2021-02-11T11:17:16Z
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creator: dernst
date_created: 2019-04-09T14:12:40Z
date_updated: 2020-07-14T12:47:25Z
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language:
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month: '10'
oa: 1
oa_version: Published Version
page: '95'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
pubrep_id: '1055'
related_material:
record:
- id: '7132'
relation: new_edition
status: public
status: public
supervisor:
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
title: 'Design and characterization of methods and biological components to realize
synthetic neurotransmission '
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '50'
abstract:
- lang: eng
text: The Wnt/planar cell polarity (Wnt/PCP) pathway determines planar polarity
of epithelial cells in both vertebrates and invertebrates. The role that Wnt/PCP
signaling plays in mesenchymal contexts, however, is only poorly understood. While
previous studies have demonstrated the capacity of Wnt/PCP signaling to polarize
and guide directed migration of mesenchymal cells, it remains unclear whether
endogenous Wnt/PCP signaling performs these functions instructively, as it does
in epithelial cells. Here we developed a light-switchable version of the Wnt/PCP
receptor Frizzled 7 (Fz7) to unambiguously distinguish between an instructive
and a permissive role of Wnt/PCP signaling for the directional collective migration
of mesendoderm progenitor cells during zebrafish gastrulation. We show that prechordal
plate (ppl) cell migration is defective in maternal-zygotic fz7a and fz7b (MZ
fz7a,b) double mutant embryos, and that Fz7 functions cell-autonomously in this
process by promoting ppl cell protrusion formation and directed migration. We
further show that local activation of Fz7 can direct ppl cell migration both in
vitro and in vivo. Surprisingly, however, uniform Fz7 activation is sufficient
to fully rescue the ppl cell migration defect in MZ fz7a,b mutant embryos, indicating
that Wnt/PCP signaling functions permissively rather than instructively in directed
mesendoderm cell migration during zebrafish gastrulation.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Daniel
full_name: Capek, Daniel
id: 31C42484-F248-11E8-B48F-1D18A9856A87
last_name: Capek
orcid: 0000-0001-5199-9940
citation:
ama: Capek D. Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling
in directed mesenchymal cell migration. 2018. doi:10.15479/AT:ISTA:TH_1031
apa: Capek, D. (2018). Optogenetic Frizzled 7 reveals a permissive function of
Wnt/PCP signaling in directed mesenchymal cell migration. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1031
chicago: Capek, Daniel. “Optogenetic Frizzled 7 Reveals a Permissive Function of
Wnt/PCP Signaling in Directed Mesenchymal Cell Migration.” Institute of Science
and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1031.
ieee: D. Capek, “Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP
signaling in directed mesenchymal cell migration,” Institute of Science and Technology
Austria, 2018.
ista: Capek D. 2018. Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP
signaling in directed mesenchymal cell migration. Institute of Science and Technology
Austria.
mla: Capek, Daniel. Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP
Signaling in Directed Mesenchymal Cell Migration. Institute of Science and
Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1031.
short: D. Capek, Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP
Signaling in Directed Mesenchymal Cell Migration, Institute of Science and Technology
Austria, 2018.
date_created: 2018-12-11T11:44:21Z
date_published: 2018-06-22T00:00:00Z
date_updated: 2023-09-07T12:48:16Z
day: '22'
ddc:
- '570'
- '591'
- '596'
degree_awarded: PhD
department:
- _id: CaHe
doi: 10.15479/AT:ISTA:TH_1031
file:
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content_type: application/pdf
creator: dernst
date_created: 2019-04-08T13:42:26Z
date_updated: 2021-02-11T11:17:17Z
embargo: 2019-06-25
file_id: '6238'
file_name: 2018_Thesis_Capek.pdf
file_size: 31576521
relation: main_file
- access_level: closed
checksum: 876deb14067e638aba65d209668bd821
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-04-08T13:42:27Z
date_updated: 2021-02-11T23:30:21Z
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language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '95'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '8004'
pubrep_id: '1031'
related_material:
record:
- id: '1100'
relation: part_of_dissertation
status: public
- id: '661'
relation: part_of_dissertation
status: public
- id: '676'
relation: part_of_dissertation
status: public
status: public
supervisor:
- 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
title: Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in
directed mesenchymal cell migration
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '26'
abstract:
- lang: eng
text: Expression of genes is a fundamental molecular phenotype that is subject to
evolution by different types of mutations. Both the rate and the effect of mutations
may depend on the DNA sequence context of a particular gene or a particular promoter
sequence. In this thesis I investigate the nature of this dependence using simple
genetic systems in Escherichia coli. With these systems I explore the evolution
of constitutive gene expression from random starting sequences at different loci
on the chromosome and at different locations in sequence space. First, I dissect
chromosomal neighborhood effects that underlie locus-dependent differences in
the potential of a gene under selection to become more highly expressed. Next,
I find that the effects of point mutations in promoter sequences are dependent
on sequence context, and that an existing energy matrix model performs poorly
in predicting relative expression of unrelated sequences. Finally, I show that
a substantial fraction of random sequences contain functional promoters and I
present an extended thermodynamic model that predicts promoter strength in full
sequence space. Taken together, these results provide new insights and guides
on how to integrate information on sequence context to improve our qualitative
and quantitative understanding of bacterial gene expression, with implications
for rapid evolution of drug resistance, de novo evolution of genes, and horizontal
gene transfer.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Magdalena
full_name: Steinrück, Magdalena
id: 2C023F40-F248-11E8-B48F-1D18A9856A87
last_name: Steinrück
orcid: 0000-0003-1229-9719
citation:
ama: Steinrück M. The influence of sequence context on the evolution of bacterial
gene expression. 2018. doi:10.15479/AT:ISTA:th1059
apa: Steinrück, M. (2018). The influence of sequence context on the evolution
of bacterial gene expression. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:th1059
chicago: Steinrück, Magdalena. “The Influence of Sequence Context on the Evolution
of Bacterial Gene Expression.” Institute of Science and Technology Austria, 2018.
https://doi.org/10.15479/AT:ISTA:th1059.
ieee: M. Steinrück, “The influence of sequence context on the evolution of bacterial
gene expression,” Institute of Science and Technology Austria, 2018.
ista: Steinrück M. 2018. The influence of sequence context on the evolution of bacterial
gene expression. Institute of Science and Technology Austria.
mla: Steinrück, Magdalena. The Influence of Sequence Context on the Evolution
of Bacterial Gene Expression. Institute of Science and Technology Austria,
2018, doi:10.15479/AT:ISTA:th1059.
short: M. Steinrück, The Influence of Sequence Context on the Evolution of Bacterial
Gene Expression, Institute of Science and Technology Austria, 2018.
date_created: 2018-12-11T11:44:14Z
date_published: 2018-10-30T00:00:00Z
date_updated: 2023-09-07T12:48:43Z
day: '30'
ddc:
- '576'
- '579'
degree_awarded: PhD
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:th1059
file:
- access_level: closed
checksum: 413cbce1cd1debeae3abe2a25dbc70d1
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-02-08T10:51:22Z
date_updated: 2020-07-14T12:45:43Z
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file_name: Thesis_Steinrueck_final.docx
file_size: 9190845
relation: source_file
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checksum: 3def8b7854c8b42d643597ce0215efac
content_type: application/pdf
creator: dernst
date_created: 2019-02-08T10:51:22Z
date_updated: 2021-02-11T11:17:14Z
embargo: 2019-11-02
file_id: '5942'
file_name: Thesis_Steinrueck_final.pdf
file_size: 7521973
relation: main_file
file_date_updated: 2021-02-11T11:17:14Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '109'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '8029'
pubrep_id: '1059'
related_material:
record:
- id: '704'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
title: The influence of sequence context on the evolution of bacterial gene expression
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '5816'
abstract:
- lang: eng
text: Solid-state qubit manipulation and read-out fidelities are reaching fault-tolerance,
but quantum error correction requires millions of physical qubits and therefore
a scalable quantum computer architecture. To solve signal-line bandwidth and fan-out
problems, microwave sources required for qubit manipulation might be embedded
close to the qubit chip, typically operating at temperatures below 4 K. Here,
we perform the first low temperature measurements of a 130 nm BiCMOS based SiGe
voltage controlled oscillator at cryogenic temperature. We determined the frequency
and output power dependence on temperature and magnetic field up to 5 T and measured
the temperature influence on its noise performance. The device maintains its full
functionality from 300 K to 4 K. The carrier frequency at 4 K increases by 3%
with respect to the carrier frequency at 300 K, and the output power at 4 K increases
by 10 dB relative to the output power at 300 K. The frequency tuning range of
approximately 20% remains unchanged between 300 K and 4 K. In an in-plane magnetic
field of 5 T, the carrier frequency shifts by only 0.02% compared to the frequency
at zero magnetic field.
article_number: '114701'
article_processing_charge: No
author:
- first_name: Arne
full_name: Hollmann, Arne
last_name: Hollmann
- first_name: Daniel
full_name: Jirovec, Daniel
id: 4C473F58-F248-11E8-B48F-1D18A9856A87
last_name: Jirovec
orcid: 0000-0002-7197-4801
- first_name: Maciej
full_name: Kucharski, Maciej
last_name: Kucharski
- first_name: Dietmar
full_name: Kissinger, Dietmar
last_name: Kissinger
- first_name: Gunter
full_name: Fischer, Gunter
last_name: Fischer
- first_name: Lars R.
full_name: Schreiber, Lars R.
last_name: Schreiber
citation:
ama: Hollmann A, Jirovec D, Kucharski M, Kissinger D, Fischer G, Schreiber LR. 30
GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments.
2018;89(11). doi:10.1063/1.5038258
apa: Hollmann, A., Jirovec, D., Kucharski, M., Kissinger, D., Fischer, G., &
Schreiber, L. R. (2018). 30 GHz-voltage controlled oscillator operating at 4 K.
Review of Scientific Instruments. AIP Publishing. https://doi.org/10.1063/1.5038258
chicago: Hollmann, Arne, Daniel Jirovec, Maciej Kucharski, Dietmar Kissinger, Gunter
Fischer, and Lars R. Schreiber. “30 GHz-Voltage Controlled Oscillator Operating
at 4 K.” Review of Scientific Instruments. AIP Publishing, 2018. https://doi.org/10.1063/1.5038258.
ieee: A. Hollmann, D. Jirovec, M. Kucharski, D. Kissinger, G. Fischer, and L. R.
Schreiber, “30 GHz-voltage controlled oscillator operating at 4 K,” Review
of Scientific Instruments, vol. 89, no. 11. AIP Publishing, 2018.
ista: Hollmann A, Jirovec D, Kucharski M, Kissinger D, Fischer G, Schreiber LR.
2018. 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific
Instruments. 89(11), 114701.
mla: Hollmann, Arne, et al. “30 GHz-Voltage Controlled Oscillator Operating at 4
K.” Review of Scientific Instruments, vol. 89, no. 11, 114701, AIP Publishing,
2018, doi:10.1063/1.5038258.
short: A. Hollmann, D. Jirovec, M. Kucharski, D. Kissinger, G. Fischer, L.R. Schreiber,
Review of Scientific Instruments 89 (2018).
date_created: 2019-01-10T14:22:23Z
date_published: 2018-11-01T00:00:00Z
date_updated: 2024-03-27T23:30:26Z
day: '01'
department:
- _id: GeKa
doi: 10.1063/1.5038258
external_id:
arxiv:
- '1804.09522'
isi:
- '000451735700054'
intvolume: ' 89'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.09522
month: '11'
oa: 1
oa_version: Preprint
publication: Review of Scientific Instruments
publication_identifier:
issn:
- '00346748'
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
record:
- id: '10058'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 30 GHz-voltage controlled oscillator operating at 4 K
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 89
year: '2018'
...
---
_id: '6263'
abstract:
- lang: eng
text: 'Antibiotic resistance can emerge spontaneously through genomic mutation and render
treatment ineffective. To counteract this process, in addition to the discovery and
description of resistance mechanisms,a deeper understanding of resistanceevolvabilityand
its determinantsis needed. To address this challenge, this thesisuncoversnew genetic
determinants of resistance evolvability using a customized robotic setup,
exploressystematic ways in which resistance evolution is perturbed due to
dose-responsecharacteristics of drugs and mutation rate differences,and mathematically investigates
the evolutionary fate of one specific type of evolvability modifier -a stress-induced
mutagenesis allele.We find severalgenes which strongly inhibit or potentiate resistance evolution. In order
to identify them, we first developedan automated high-throughput feedback-controlled
protocol whichkeeps the population size and selection pressure approximately constant
for hundreds of cultures by dynamically re-diluting the cultures and adjusting the antibiotic
concentration. We implementedthis protocol on a customized liquid handling robot and
propagated 100 different gene deletion strains of Escherichia coliin triplicate for over 100
generations in tetracycline and in chloramphenicol, and comparedtheir adaptation rates.We find a diminishing returns pattern, where initially sensitive strains adapted more
compared to less sensitive ones. Our data uncover that deletions of certain genes
which do not affect mutation rate,including efflux pump components, a chaperone and
severalstructural and regulatory genes can strongly and reproducibly alterresistance evolution.
Sequencing analysis of evolved populations indicates that epistasis with resistance
mutations is the most likelyexplanation. This work could inspire treatment strategies in
which targeted inhibitors of evolvability mechanisms will be given alongside antibiotics to
slow down resistance evolution and extend theefficacy of antibiotics.We implemented astochasticpopulation genetics model,
toverifyways in which general properties, namely, dose-response characteristics of drugs and mutation rates, influence
evolutionary dynamics. In particular, under the exposure to antibiotics with shallow dose-response curves,bacteria have narrower distributions of fitness effects of new mutations.
We show that in silicothis also leads to slower resistance evolution. We
see and confirm with experiments that increased mutation rates, apart from speeding
up evolution, also leadto high reproducibility of phenotypic adaptation in a context
of continually strong selection pressure.Knowledge of these patterns can aid in predicting the dynamics of antibiotic
resistance evolutionand adapting treatment schemes accordingly.Focusing on a previously described type of evolvability modifier
–a stress-induced mutagenesis allele –we find conditions under which it can persist in a population under
periodic selectionakin to clinical treatment. We set up a deterministic
infinite populationcontinuous time model tracking the frequencies of a mutator and resistance allele and
evaluate various treatment schemes in how well they maintain a stress-induced
mutator allele. In particular,a high diversity of stresses is crucial for the persistence
of the mutator allele. This leads to a general trade-off where exactly those
diversifying treatment schemes which are likely to decrease levels of resistance could lead to stronger selection of highly
evolvable genotypes.In the long run, this work will lead to a deeper understanding of the genetic and cellular
mechanisms involved in antibiotic resistance evolution and could inspire new strategies
for slowing down its rate. '
acknowledged_ssus:
- _id: M-Shop
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
citation:
ama: Lukacisinova M. Genetic determinants of antibiotic resistance evolution. 2018.
doi:10.15479/AT:ISTA:th1072
apa: Lukacisinova, M. (2018). Genetic determinants of antibiotic resistance evolution.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1072
chicago: Lukacisinova, Marta. “Genetic Determinants of Antibiotic Resistance Evolution.”
Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1072.
ieee: M. Lukacisinova, “Genetic determinants of antibiotic resistance evolution,”
Institute of Science and Technology Austria, 2018.
ista: Lukacisinova M. 2018. Genetic determinants of antibiotic resistance evolution.
Institute of Science and Technology Austria.
mla: Lukacisinova, Marta. Genetic Determinants of Antibiotic Resistance Evolution.
Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1072.
short: M. Lukacisinova, Genetic Determinants of Antibiotic Resistance Evolution,
Institute of Science and Technology Austria, 2018.
date_created: 2019-04-09T13:57:15Z
date_published: 2018-12-28T00:00:00Z
date_updated: 2023-09-22T09:20:37Z
day: '28'
ddc:
- '570'
- '576'
- '579'
degree_awarded: PhD
department:
- _id: ToBo
doi: 10.15479/AT:ISTA:th1072
file:
- access_level: open_access
checksum: fc60585c9eaad868ac007004ef130908
content_type: application/pdf
creator: dernst
date_created: 2019-04-09T13:49:24Z
date_updated: 2021-02-11T11:17:17Z
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creator: dernst
date_created: 2019-04-09T13:49:23Z
date_updated: 2020-07-14T12:47:25Z
embargo_to: open_access
file_id: '6265'
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relation: source_file
file_date_updated: 2021-02-11T11:17:17Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '91'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1619'
relation: part_of_dissertation
status: public
- id: '696'
relation: part_of_dissertation
status: public
- id: '1027'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
title: Genetic determinants of antibiotic resistance evolution
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '544'
abstract:
- lang: eng
text: Drosophila melanogaster plasmatocytes, the phagocytic cells among hemocytes,
are essential for immune responses, but also play key roles from early development
to death through their interactions with other cell types. They regulate homeostasis
and signaling during development, stem cell proliferation, metabolism, cancer,
wound responses and aging, displaying intriguing molecular and functional conservation
with vertebrate macrophages. Given the relative ease of genetics in Drosophila
compared to vertebrates, tools permitting visualization and genetic manipulation
of plasmatocytes and surrounding tissues independently at all stages would greatly
aid in fully understanding these processes, but are lacking. Here we describe
a comprehensive set of transgenic lines that allow this. These include extremely
brightly fluorescing mCherry-based lines that allow GAL4-independent visualization
of plasmatocyte nuclei, cytoplasm or actin cytoskeleton from embryonic Stage 8
through adulthood in both live and fixed samples even as heterozygotes, greatly
facilitating screening. These lines allow live visualization and tracking of embryonic
plasmatocytes, as well as larval plasmatocytes residing at the body wall or flowing
with the surrounding hemolymph. With confocal imaging, interactions of plasmatocytes
and inner tissues can be seen in live or fixed embryos, larvae and adults. They
permit efficient GAL4-independent FACS analysis/sorting of plasmatocytes throughout
life. To facilitate genetic analysis of reciprocal signaling, we have also made
a plasmatocyte-expressing QF2 line that in combination with extant GAL4 drivers
allows independent genetic manipulation of both plasmatocytes and surrounding
tissues, and a GAL80 line that blocks GAL4 drivers from affecting plasmatocytes,
both of which function from the early embryo to the adult.
acknowledged_ssus:
- _id: LifeSc
acknowledgement: ' A. Ratheesh also by Marie Curie IIF GA-2012-32950BB:DICJI, Marko
Roblek by the provincial government of Lower Austria, K. Valoskova and S. Wachner
by DOC Fellowships from the Austrian Academy of Sciences, '
article_processing_charge: No
author:
- first_name: Attila
full_name: György, Attila
id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87
last_name: György
orcid: 0000-0002-1819-198X
- first_name: Marko
full_name: Roblek, Marko
id: 3047D808-F248-11E8-B48F-1D18A9856A87
last_name: Roblek
orcid: 0000-0001-9588-1389
- first_name: Aparna
full_name: Ratheesh, Aparna
id: 2F064CFE-F248-11E8-B48F-1D18A9856A87
last_name: Ratheesh
orcid: 0000-0001-7190-0776
- first_name: Katarina
full_name: Valosková, Katarina
id: 46F146FC-F248-11E8-B48F-1D18A9856A87
last_name: Valosková
- first_name: Vera
full_name: Belyaeva, Vera
id: 47F080FE-F248-11E8-B48F-1D18A9856A87
last_name: Belyaeva
- first_name: Stephanie
full_name: Wachner, Stephanie
id: 2A95E7B0-F248-11E8-B48F-1D18A9856A87
last_name: Wachner
- first_name: Yutaka
full_name: Matsubayashi, Yutaka
last_name: Matsubayashi
- first_name: Besaiz
full_name: Sanchez Sanchez, Besaiz
last_name: Sanchez Sanchez
- first_name: Brian
full_name: Stramer, Brian
last_name: Stramer
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
citation:
ama: 'György A, Roblek M, Ratheesh A, et al. Tools allowing independent visualization
and genetic manipulation of Drosophila melanogaster macrophages and surrounding
tissues. G3: Genes, Genomes, Genetics. 2018;8(3):845-857. doi:10.1534/g3.117.300452'
apa: 'György, A., Roblek, M., Ratheesh, A., Valosková, K., Belyaeva, V., Wachner,
S., … Siekhaus, D. E. (2018). Tools allowing independent visualization and genetic
manipulation of Drosophila melanogaster macrophages and surrounding tissues. G3:
Genes, Genomes, Genetics. Genetics Society of America. https://doi.org/10.1534/g3.117.300452'
chicago: 'György, Attila, Marko Roblek, Aparna Ratheesh, Katarina Valosková, Vera
Belyaeva, Stephanie Wachner, Yutaka Matsubayashi, Besaiz Sanchez Sanchez, Brian
Stramer, and Daria E Siekhaus. “Tools Allowing Independent Visualization and Genetic
Manipulation of Drosophila Melanogaster Macrophages and Surrounding Tissues.”
G3: Genes, Genomes, Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/g3.117.300452.'
ieee: 'A. György et al., “Tools allowing independent visualization and genetic
manipulation of Drosophila melanogaster macrophages and surrounding tissues,”
G3: Genes, Genomes, Genetics, vol. 8, no. 3. Genetics Society of America,
pp. 845–857, 2018.'
ista: 'György A, Roblek M, Ratheesh A, Valosková K, Belyaeva V, Wachner S, Matsubayashi
Y, Sanchez Sanchez B, Stramer B, Siekhaus DE. 2018. Tools allowing independent
visualization and genetic manipulation of Drosophila melanogaster macrophages
and surrounding tissues. G3: Genes, Genomes, Genetics. 8(3), 845–857.'
mla: 'György, Attila, et al. “Tools Allowing Independent Visualization and Genetic
Manipulation of Drosophila Melanogaster Macrophages and Surrounding Tissues.”
G3: Genes, Genomes, Genetics, vol. 8, no. 3, Genetics Society of America,
2018, pp. 845–57, doi:10.1534/g3.117.300452.'
short: 'A. György, M. Roblek, A. Ratheesh, K. Valosková, V. Belyaeva, S. Wachner,
Y. Matsubayashi, B. Sanchez Sanchez, B. Stramer, D.E. Siekhaus, G3: Genes, Genomes,
Genetics 8 (2018) 845–857.'
date_created: 2018-12-11T11:47:05Z
date_published: 2018-03-01T00:00:00Z
date_updated: 2024-03-27T23:30:29Z
day: '01'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.1534/g3.117.300452
ec_funded: 1
external_id:
isi:
- '000426693300011'
file:
- access_level: open_access
checksum: 7d9d28b915159078a4ca7add568010e8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:48Z
date_updated: 2020-07-14T12:46:56Z
file_id: '4905'
file_name: IST-2018-990-v1+1_2018_Gyoergy_Tools_allowing.pdf
file_size: 2251222
relation: main_file
file_date_updated: 2020-07-14T12:46:56Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 845 - 857
project:
- _id: 253B6E48-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29638
name: Drosophila TNFa´s Funktion in Immunzellen
- _id: 253B6E48-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29638
name: The role of Drosophila TNF alpha in immune cell invasion
- _id: 2637E9C0-B435-11E9-9278-68D0E5697425
grant_number: 'LSC16-021 '
name: Investigating the role of the novel major superfamily facilitator transporter
family member MFSD1 in metastasis
- _id: 2536F660-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '334077'
name: Investigating the role of transporters in invasive migration through junctions
publication: 'G3: Genes, Genomes, Genetics'
publication_status: published
publisher: Genetics Society of America
publist_id: '7271'
pubrep_id: '990'
quality_controlled: '1'
related_material:
record:
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relation: research_paper
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relation: research_paper
- id: '11193'
relation: dissertation_contains
status: public
- id: '6546'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Tools allowing independent visualization and genetic manipulation of Drosophila
melanogaster macrophages and surrounding tissues
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: 8
year: '2018'
...
---
_id: '612'
abstract:
- lang: eng
text: Metabotropic GABAB receptors mediate slow inhibitory effects presynaptically
and postsynaptically through the modulation of different effector signalling pathways.
Here, we analysed the distribution of GABAB receptors using highly sensitive SDS-digested
freeze-fracture replica labelling in mouse cerebellar Purkinje cells. Immunoreactivity
for GABAB1 was observed on presynaptic and, more abundantly, on postsynaptic compartments,
showing both scattered and clustered distribution patterns. Quantitative analysis
of immunoparticles revealed a somato-dendritic gradient, with the density of immunoparticles
increasing 26-fold from somata to dendritic spines. To understand the spatial
relationship of GABAB receptors with two key effector ion channels, the G protein-gated
inwardly rectifying K+ (GIRK/Kir3) channel and the voltage-dependent Ca2+ channel,
biochemical and immunohistochemical approaches were performed. Co-immunoprecipitation
analysis demonstrated that GABAB receptors co-assembled with GIRK and CaV2.1 channels
in the cerebellum. Using double-labelling immunoelectron microscopic techniques,
co-clustering between GABAB1 and GIRK2 was detected in dendritic spines, whereas
they were mainly segregated in the dendritic shafts. In contrast, co-clustering
of GABAB1 and CaV2.1 was detected in dendritic shafts but not spines. Presynaptically,
although no significant co-clustering of GABAB1 and GIRK2 or CaV2.1 channels was
detected, inter-cluster distance for GABAB1 and GIRK2 was significantly smaller
in the active zone than in the dendritic shafts, and that for GABAB1 and CaV2.1
was significantly smaller in the active zone than in the dendritic shafts and
spines. Thus, GABAB receptors are associated with GIRK and CaV2.1 channels in
different subcellular compartments. These data provide a better framework for
understanding the different roles played by GABAB receptors and their effector
ion channels in the cerebellar network.
article_processing_charge: No
article_type: original
author:
- first_name: Rafael
full_name: Luján, Rafael
last_name: Luján
- first_name: Carolina
full_name: Aguado, Carolina
last_name: Aguado
- first_name: Francisco
full_name: Ciruela, Francisco
last_name: Ciruela
- first_name: Javier
full_name: Cózar, Javier
last_name: Cózar
- first_name: David
full_name: Kleindienst, David
id: 42E121A4-F248-11E8-B48F-1D18A9856A87
last_name: Kleindienst
- first_name: Luis
full_name: De La Ossa, Luis
last_name: De La Ossa
- first_name: Bernhard
full_name: Bettler, Bernhard
last_name: Bettler
- first_name: Kevin
full_name: Wickman, Kevin
last_name: Wickman
- first_name: Masahiko
full_name: Watanabe, Masahiko
last_name: Watanabe
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Yugo
full_name: Fukazawa, Yugo
last_name: Fukazawa
citation:
ama: Luján R, Aguado C, Ciruela F, et al. Differential association of GABAB receptors
with their effector ion channels in Purkinje cells. Brain Structure and Function.
2018;223(3):1565-1587. doi:10.1007/s00429-017-1568-y
apa: Luján, R., Aguado, C., Ciruela, F., Cózar, J., Kleindienst, D., De La Ossa,
L., … Fukazawa, Y. (2018). Differential association of GABAB receptors with their
effector ion channels in Purkinje cells. Brain Structure and Function.
Springer. https://doi.org/10.1007/s00429-017-1568-y
chicago: Luján, Rafael, Carolina Aguado, Francisco Ciruela, Javier Cózar, David
Kleindienst, Luis De La Ossa, Bernhard Bettler, et al. “Differential Association
of GABAB Receptors with Their Effector Ion Channels in Purkinje Cells.” Brain
Structure and Function. Springer, 2018. https://doi.org/10.1007/s00429-017-1568-y.
ieee: R. Luján et al., “Differential association of GABAB receptors with
their effector ion channels in Purkinje cells,” Brain Structure and Function,
vol. 223, no. 3. Springer, pp. 1565–1587, 2018.
ista: Luján R, Aguado C, Ciruela F, Cózar J, Kleindienst D, De La Ossa L, Bettler
B, Wickman K, Watanabe M, Shigemoto R, Fukazawa Y. 2018. Differential association
of GABAB receptors with their effector ion channels in Purkinje cells. Brain Structure
and Function. 223(3), 1565–1587.
mla: Luján, Rafael, et al. “Differential Association of GABAB Receptors with Their
Effector Ion Channels in Purkinje Cells.” Brain Structure and Function,
vol. 223, no. 3, Springer, 2018, pp. 1565–87, doi:10.1007/s00429-017-1568-y.
short: R. Luján, C. Aguado, F. Ciruela, J. Cózar, D. Kleindienst, L. De La Ossa,
B. Bettler, K. Wickman, M. Watanabe, R. Shigemoto, Y. Fukazawa, Brain Structure
and Function 223 (2018) 1565–1587.
date_created: 2018-12-11T11:47:29Z
date_published: 2018-04-01T00:00:00Z
date_updated: 2024-03-27T23:30:30Z
day: '01'
ddc:
- '571'
department:
- _id: RySh
doi: 10.1007/s00429-017-1568-y
ec_funded: 1
external_id:
isi:
- '000428419500030'
file:
- access_level: open_access
checksum: a55b3103476ecb5f4f983d8801807e8b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:36Z
date_updated: 2020-07-14T12:47:20Z
file_id: '5157'
file_name: IST-2018-1013-v1+1_2018_Kleindienst_Differential.pdf
file_size: 5542926
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has_accepted_license: '1'
intvolume: ' 223'
isi: 1
issue: '3'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1565 - 1587
project:
- _id: 25CBA828-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '720270'
name: Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Brain Structure and Function
publication_status: published
publisher: Springer
publist_id: '7192'
pubrep_id: '1013'
quality_controlled: '1'
related_material:
record:
- id: '9562'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Differential association of GABAB receptors with their effector ion channels
in Purkinje cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 223
year: '2018'
...
---
_id: '21'
abstract:
- lang: eng
text: Parvalbumin-positive (PV+) GABAergic interneurons in hippocampal microcircuits
are thought to play a key role in several higher network functions, such as feedforward
and feedback inhibition, network oscillations, and pattern separation. Fast lateral
inhibition mediated by GABAergic interneurons may implement a winner-takes-all
mechanism in the hippocampal input layer. However, it is not clear whether the
functional connectivity rules of granule cells (GCs) and interneurons in the dentate
gyrus are consistent with such a mechanism. Using simultaneous patch-clamp recordings
from up to seven GCs and up to four PV+ interneurons in the dentate gyrus, we
find that connectivity is structured in space, synapse-specific, and enriched
in specific disynaptic motifs. In contrast to the neocortex, lateral inhibition
in the dentate gyrus (in which a GC inhibits neighboring GCs via a PV+ interneuron)
is ~ 10-times more abundant than recurrent inhibition (in which a GC inhibits
itself). Thus, unique connectivity rules may enable the dentate gyrus to perform
specific higher-order computations
acknowledgement: This project received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement No 692692) and the Fond zur Förderung der Wissenschaftlichen Forschung
(Z 312-B27, Wittgenstein award), both to P.J..
article_number: '4605'
article_processing_charge: No
article_type: original
author:
- first_name: 'Claudia '
full_name: 'Espinoza Martinez, Claudia '
id: 31FFEE2E-F248-11E8-B48F-1D18A9856A87
last_name: Espinoza Martinez
orcid: 0000-0003-4710-2082
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
orcid: 0000-0003-2209-5242
- first_name: Xiaomin
full_name: Zhang, Xiaomin
id: 423EC9C2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Espinoza Martinez C, Guzmán J, Zhang X, Jonas PM. Parvalbumin+ interneurons
obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit
in dentate gyrus. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-06899-3
apa: Espinoza Martinez, C., Guzmán, J., Zhang, X., & Jonas, P. M. (2018). Parvalbumin+
interneurons obey unique connectivity rules and establish a powerful lateral-inhibition
microcircuit in dentate gyrus. Nature Communications. Nature Publishing
Group. https://doi.org/10.1038/s41467-018-06899-3
chicago: Espinoza Martinez, Claudia , José Guzmán, Xiaomin Zhang, and Peter M Jonas.
“Parvalbumin+ Interneurons Obey Unique Connectivity Rules and Establish a Powerful
Lateral-Inhibition Microcircuit in Dentate Gyrus.” Nature Communications.
Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-018-06899-3.
ieee: C. Espinoza Martinez, J. Guzmán, X. Zhang, and P. M. Jonas, “Parvalbumin+
interneurons obey unique connectivity rules and establish a powerful lateral-inhibition
microcircuit in dentate gyrus,” Nature Communications, vol. 9, no. 1. Nature
Publishing Group, 2018.
ista: Espinoza Martinez C, Guzmán J, Zhang X, Jonas PM. 2018. Parvalbumin+ interneurons
obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit
in dentate gyrus. Nature Communications. 9(1), 4605.
mla: Espinoza Martinez, Claudia, et al. “Parvalbumin+ Interneurons Obey Unique Connectivity
Rules and Establish a Powerful Lateral-Inhibition Microcircuit in Dentate Gyrus.”
Nature Communications, vol. 9, no. 1, 4605, Nature Publishing Group, 2018,
doi:10.1038/s41467-018-06899-3.
short: C. Espinoza Martinez, J. Guzmán, X. Zhang, P.M. Jonas, Nature Communications
9 (2018).
date_created: 2018-12-11T11:44:12Z
date_published: 2018-11-02T00:00:00Z
date_updated: 2024-03-27T23:30:31Z
day: '02'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1038/s41467-018-06899-3
ec_funded: 1
external_id:
isi:
- '000449069700009'
file:
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checksum: 9fe2a63bd95a5067d896c087d07998f3
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T15:41:57Z
date_updated: 2020-07-14T12:45:28Z
file_id: '5715'
file_name: 2018_NatureComm_Espinoza.pdf
file_size: 4651930
relation: main_file
file_date_updated: 2020-07-14T12:45:28Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '8034'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/lateral-inhibition-keeps-similar-memories-apart/
record:
- id: '6363'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful
lateral-inhibition microcircuit in dentate gyrus
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: 9
year: '2018'
...
---
_id: '66'
abstract:
- lang: eng
text: 'Crypto-currencies are digital assets designed to work as a medium of exchange,
e.g., Bitcoin, but they are susceptible to attacks (dishonest behavior of participants).
A framework for the analysis of attacks in crypto-currencies requires (a) modeling
of game-theoretic aspects to analyze incentives for deviation from honest behavior;
(b) concurrent interactions between participants; and (c) analysis of long-term
monetary gains. Traditional game-theoretic approaches for the analysis of security
protocols consider either qualitative temporal properties such as safety and termination,
or the very special class of one-shot (stateless) games. However, to analyze general
attacks on protocols for crypto-currencies, both stateful analysis and quantitative
objectives are necessary. In this work our main contributions are as follows:
(a) we show how a class of concurrent mean-payo games, namely ergodic games, can
model various attacks that arise naturally in crypto-currencies; (b) we present
the first practical implementation of algorithms for ergodic games that scales
to model realistic problems for crypto-currencies; and (c) we present experimental
results showing that our framework can handle games with thousands of states and
millions of transitions.'
alternative_title:
- LIPIcs
article_number: '11'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir
full_name: Goharshady, Amir
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Yaron
full_name: Velner, Yaron
last_name: Velner
citation:
ama: 'Chatterjee K, Goharshady AK, Ibsen-Jensen R, Velner Y. Ergodic mean-payoff
games for the analysis of attacks in crypto-currencies. In: Vol 118. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.CONCUR.2018.11'
apa: 'Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., & Velner, Y. (2018).
Ergodic mean-payoff games for the analysis of attacks in crypto-currencies (Vol.
118). Presented at the CONCUR: Conference on Concurrency Theory, Beijing, China:
Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2018.11'
chicago: Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen,
and Yaron Velner. “Ergodic Mean-Payoff Games for the Analysis of Attacks in Crypto-Currencies,”
Vol. 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.CONCUR.2018.11.
ieee: 'K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and Y. Velner, “Ergodic
mean-payoff games for the analysis of attacks in crypto-currencies,” presented
at the CONCUR: Conference on Concurrency Theory, Beijing, China, 2018, vol. 118.'
ista: 'Chatterjee K, Goharshady AK, Ibsen-Jensen R, Velner Y. 2018. Ergodic mean-payoff
games for the analysis of attacks in crypto-currencies. CONCUR: Conference on
Concurrency Theory, LIPIcs, vol. 118, 11.'
mla: Chatterjee, Krishnendu, et al. Ergodic Mean-Payoff Games for the Analysis
of Attacks in Crypto-Currencies. Vol. 118, 11, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2018, doi:10.4230/LIPIcs.CONCUR.2018.11.
short: K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, Y. Velner, in:, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2018.
conference:
end_date: 2018-09-07
location: Beijing, China
name: 'CONCUR: Conference on Concurrency Theory'
start_date: 2018-09-04
date_created: 2018-12-11T11:44:27Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2024-03-27T23:30:33Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.CONCUR.2018.11
ec_funded: 1
external_id:
arxiv:
- '1806.03108'
file:
- access_level: open_access
checksum: 68a055b1aaa241cc38375083cf832a7d
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:08:00Z
date_updated: 2020-07-14T12:47:34Z
file_id: '5696'
file_name: 2018_CONCUR_Chatterjee.pdf
file_size: 1078309
relation: main_file
file_date_updated: 2020-07-14T12:47:34Z
has_accepted_license: '1'
intvolume: ' 118'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 266EEEC0-B435-11E9-9278-68D0E5697425
name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart
Contracts
publication_identifier:
isbn:
- 978-3-95977-087-3
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '7988'
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Ergodic mean-payoff games for the analysis of attacks in crypto-currencies
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2018'
...
---
_id: '311'
abstract:
- lang: eng
text: 'Smart contracts are computer programs that are executed by a network of mutually
distrusting agents, without the need of an external trusted authority. Smart contracts
handle and transfer assets of considerable value (in the form of crypto-currency
like Bitcoin). Hence, it is crucial that their implementation is bug-free. We
identify the utility (or expected payoff) of interacting with such smart contracts
as the basic and canonical quantitative property for such contracts. We present
a framework for such quantitative analysis of smart contracts. Such a formal framework
poses new and novel research challenges in programming languages, as it requires
modeling of game-theoretic aspects to analyze incentives for deviation from honest
behavior and modeling utilities which are not specified as standard temporal properties
such as safety and termination. While game-theoretic incentives have been analyzed
in the security community, their analysis has been restricted to the very special
case of stateless games. However, to analyze smart contracts, stateful analysis
is required as it must account for the different program states of the protocol.
Our main contributions are as follows: we present (i)~a simplified programming
language for smart contracts; (ii)~an automatic translation of the programs to
state-based games; (iii)~an abstraction-refinement approach to solve such games;
and (iv)~experimental results on real-world-inspired smart contracts.'
acknowledgement: 'The research was partially supported by Vienna Science and Technology
Fund (WWTF) Project ICT15-003, Austrian Science Fund (FWF) NFN Grant No S11407-N23
(RiSE/SHiNE), and ERC Starting grant (279307: Graph Games).'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir
full_name: Goharshady, Amir
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Yaron
full_name: Velner, Yaron
last_name: Velner
citation:
ama: 'Chatterjee K, Goharshady AK, Velner Y. Quantitative analysis of smart contracts.
In: Vol 10801. Springer; 2018:739-767. doi:10.1007/978-3-319-89884-1_26'
apa: 'Chatterjee, K., Goharshady, A. K., & Velner, Y. (2018). Quantitative analysis
of smart contracts (Vol. 10801, pp. 739–767). Presented at the ESOP: European
Symposium on Programming, Thessaloniki, Greece: Springer. https://doi.org/10.1007/978-3-319-89884-1_26'
chicago: Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Yaron Velner. “Quantitative
Analysis of Smart Contracts,” 10801:739–67. Springer, 2018. https://doi.org/10.1007/978-3-319-89884-1_26.
ieee: 'K. Chatterjee, A. K. Goharshady, and Y. Velner, “Quantitative analysis of
smart contracts,” presented at the ESOP: European Symposium on Programming, Thessaloniki,
Greece, 2018, vol. 10801, pp. 739–767.'
ista: 'Chatterjee K, Goharshady AK, Velner Y. 2018. Quantitative analysis of smart
contracts. ESOP: European Symposium on Programming, LNCS, vol. 10801, 739–767.'
mla: Chatterjee, Krishnendu, et al. Quantitative Analysis of Smart Contracts.
Vol. 10801, Springer, 2018, pp. 739–67, doi:10.1007/978-3-319-89884-1_26.
short: K. Chatterjee, A.K. Goharshady, Y. Velner, in:, Springer, 2018, pp. 739–767.
conference:
end_date: 2018-04-19
location: Thessaloniki, Greece
name: 'ESOP: European Symposium on Programming'
start_date: 2018-04-16
date_created: 2018-12-11T11:45:45Z
date_published: 2018-04-01T00:00:00Z
date_updated: 2024-03-27T23:30:33Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-319-89884-1_26
ec_funded: 1
file:
- access_level: open_access
checksum: 9c8a8338c571903b599b6ca93abd2cce
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T15:45:49Z
date_updated: 2020-07-14T12:46:00Z
file_id: '5716'
file_name: 2018_ESOP_Chatterjee.pdf
file_size: 1394993
relation: main_file
file_date_updated: 2020-07-14T12:46:00Z
has_accepted_license: '1'
intvolume: ' 10801'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 739 - 767
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_status: published
publisher: Springer
publist_id: '7554'
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Quantitative analysis of smart contracts
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10801
year: '2018'
...
---
_id: '6340'
abstract:
- lang: eng
text: We present a secure approach for maintaining andreporting credit history records on the Blockchain. Our ap-proach removes third-parties such as credit reporting agen-cies from the lending process and replaces them with smartcontracts. This allows customers to interact directly with thelenders or banks while ensuring the integrity, unmalleabilityand privacy of their credit data. Additionally, each customerhas full control over complete or selective disclosure of hercredit
records, eliminating the risk of privacy violations or databreaches. Moreover,
our approach provides strong guaranteesfor the lenders as well. A lender can check
both correctness andcompleteness of the credit data disclosed to her. This is
the firstapproach that can perform all credit reporting tasks withouta central authority or changing the financial mechanisms*.
article_processing_charge: No
author:
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Ali
full_name: Behrouz, Ali
last_name: Behrouz
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Goharshady AK, Behrouz A, Chatterjee K. Secure Credit Reporting on the Blockchain.
In: Proceedings of the IEEE International Conference on Blockchain. IEEE;
2018:1343-1348. doi:10.1109/Cybermatics_2018.2018.00231'
apa: 'Goharshady, A. K., Behrouz, A., & Chatterjee, K. (2018). Secure Credit
Reporting on the Blockchain. In Proceedings of the IEEE International Conference
on Blockchain (pp. 1343–1348). Halifax, Canada: IEEE. https://doi.org/10.1109/Cybermatics_2018.2018.00231'
chicago: Goharshady, Amir Kafshdar, Ali Behrouz, and Krishnendu Chatterjee. “Secure
Credit Reporting on the Blockchain.” In Proceedings of the IEEE International
Conference on Blockchain, 1343–48. IEEE, 2018. https://doi.org/10.1109/Cybermatics_2018.2018.00231.
ieee: A. K. Goharshady, A. Behrouz, and K. Chatterjee, “Secure Credit Reporting
on the Blockchain,” in Proceedings of the IEEE International Conference on
Blockchain, Halifax, Canada, 2018, pp. 1343–1348.
ista: Goharshady AK, Behrouz A, Chatterjee K. 2018. Secure Credit Reporting on the
Blockchain. Proceedings of the IEEE International Conference on Blockchain. IEEE
International Conference on Blockchain, 1343–1348.
mla: Goharshady, Amir Kafshdar, et al. “Secure Credit Reporting on the Blockchain.”
Proceedings of the IEEE International Conference on Blockchain, IEEE, 2018,
pp. 1343–48, doi:10.1109/Cybermatics_2018.2018.00231.
short: A.K. Goharshady, A. Behrouz, K. Chatterjee, in:, Proceedings of the IEEE
International Conference on Blockchain, IEEE, 2018, pp. 1343–1348.
conference:
end_date: 2018-08-03
location: Halifax, Canada
name: IEEE International Conference on Blockchain
start_date: 2018-07-30
date_created: 2019-04-18T10:37:35Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2024-03-27T23:30:34Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1109/Cybermatics_2018.2018.00231
ec_funded: 1
external_id:
arxiv:
- '1805.09104'
isi:
- '000481634500196'
file:
- access_level: open_access
checksum: b25c9bb7cf6e7e6634e692d26d41ead8
content_type: application/pdf
creator: akafshda
date_created: 2019-04-18T10:36:39Z
date_updated: 2020-07-14T12:47:27Z
file_id: '6341'
file_name: blockchain2018.pdf
file_size: 624338
relation: main_file
file_date_updated: 2020-07-14T12:47:27Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '09'
oa: 1
oa_version: Submitted Version
page: 1343-1348
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 266EEEC0-B435-11E9-9278-68D0E5697425
name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart
Contracts
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: Proceedings of the IEEE International Conference on Blockchain
publication_identifier:
isbn:
- '978-1-5386-7975-3 '
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Secure Credit Reporting on the Blockchain
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '6009'
abstract:
- lang: eng
text: "We study algorithmic questions wrt algebraic path properties in concurrent
systems, where the transitions of the system are labeled from a complete, closed
semiring. The algebraic path properties can model dataflow analysis problems,
the shortest path problem, and many other natural problems that arise in program
analysis. We consider that each component of the concurrent system is a graph
with constant treewidth, a property satisfied by the controlflow graphs of most
programs. We allow for multiple possible queries, which arise naturally in demand
driven dataflow analysis. The study of multiple queries allows us to consider
the tradeoff between the resource usage of the one-time preprocessing and for
each individual query. The traditional approach constructs the product graph of
all components and applies the best-known graph algorithm on the product. In this
approach, even the answer to a single query requires the transitive closure (i.e.,
the results of all possible queries), which provides no room for tradeoff between
preprocessing and query time.\r\nOur main contributions are algorithms that significantly
improve the worst-case running time of the traditional approach, and provide various
tradeoffs depending on the number of queries. For example, in a concurrent system
of two components, the traditional approach requires hexic time in the worst case
for answering one query as well as computing the transitive closure, whereas we
show that with one-time preprocessing in almost cubic time, each subsequent query
can be answered in at most linear time, and even the transitive closure can be
computed in almost quartic time. Furthermore, we establish conditional optimality
results showing that the worst-case running time of our algorithms cannot be improved
without achieving major breakthroughs in graph algorithms (i.e., improving the
worst-case bound for the shortest path problem in general graphs). Preliminary
experimental results show that our algorithms perform favorably on several benchmarks.\r\n"
article_number: '9'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. Algorithms for
algebraic path properties in concurrent systems of constant treewidth components.
ACM Transactions on Programming Languages and Systems. 2018;40(3). doi:10.1145/3210257
apa: Chatterjee, K., Ibsen-Jensen, R., Goharshady, A. K., & Pavlogiannis, A.
(2018). Algorithms for algebraic path properties in concurrent systems of constant
treewidth components. ACM Transactions on Programming Languages and Systems.
Association for Computing Machinery (ACM). https://doi.org/10.1145/3210257
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Amir Kafshdar Goharshady,
and Andreas Pavlogiannis. “Algorithms for Algebraic Path Properties in Concurrent
Systems of Constant Treewidth Components.” ACM Transactions on Programming
Languages and Systems. Association for Computing Machinery (ACM), 2018. https://doi.org/10.1145/3210257.
ieee: K. Chatterjee, R. Ibsen-Jensen, A. K. Goharshady, and A. Pavlogiannis, “Algorithms
for algebraic path properties in concurrent systems of constant treewidth components,”
ACM Transactions on Programming Languages and Systems, vol. 40, no. 3.
Association for Computing Machinery (ACM), 2018.
ista: Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. 2018. Algorithms
for algebraic path properties in concurrent systems of constant treewidth components.
ACM Transactions on Programming Languages and Systems. 40(3), 9.
mla: Chatterjee, Krishnendu, et al. “Algorithms for Algebraic Path Properties in
Concurrent Systems of Constant Treewidth Components.” ACM Transactions on Programming
Languages and Systems, vol. 40, no. 3, 9, Association for Computing Machinery
(ACM), 2018, doi:10.1145/3210257.
short: K. Chatterjee, R. Ibsen-Jensen, A.K. Goharshady, A. Pavlogiannis, ACM Transactions
on Programming Languages and Systems 40 (2018).
date_created: 2019-02-14T14:31:52Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2024-03-27T23:30:34Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3210257
ec_funded: 1
external_id:
arxiv:
- '1510.07565'
isi:
- '000444694800001'
intvolume: ' 40'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1510.07565
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: ACM Transactions on Programming Languages and Systems
publication_identifier:
issn:
- 0164-0925
publication_status: published
publisher: Association for Computing Machinery (ACM)
quality_controlled: '1'
related_material:
record:
- id: '1437'
relation: earlier_version
status: public
- id: '5441'
relation: earlier_version
status: public
- id: '5442'
relation: earlier_version
status: public
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Algorithms for algebraic path properties in concurrent systems of constant
treewidth components
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 40
year: '2018'
...
---
_id: '5977'
abstract:
- lang: eng
text: 'We consider the stochastic shortest path (SSP)problem for succinct Markov
decision processes(MDPs), where the MDP consists of a set of vari-ables, and a
set of nondeterministic rules that up-date the variables. First, we show that
several ex-amples from the AI literature can be modeled assuccinct MDPs. Then
we present computationalapproaches for upper and lower bounds for theSSP problem:
(a) for computing upper bounds, ourmethod is polynomial-time in the implicit descrip-tion
of the MDP; (b) for lower bounds, we present apolynomial-time (in the size of
the implicit descrip-tion) reduction to quadratic programming. Our ap-proach is
applicable even to infinite-state MDPs.Finally, we present experimental results
to demon-strate the effectiveness of our approach on severalclassical examples
from the AI literature.'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Hongfei
full_name: Fu, Hongfei
id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87
last_name: Fu
- first_name: Amir
full_name: Goharshady, Amir
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Nastaran
full_name: Okati, Nastaran
last_name: Okati
citation:
ama: 'Chatterjee K, Fu H, Goharshady AK, Okati N. Computational approaches for stochastic
shortest path on succinct MDPs. In: Proceedings of the Twenty-Seventh International
Joint Conference on Artificial Intelligence. Vol 2018. IJCAI; 2018:4700-4707.
doi:10.24963/ijcai.2018/653'
apa: 'Chatterjee, K., Fu, H., Goharshady, A. K., & Okati, N. (2018). Computational
approaches for stochastic shortest path on succinct MDPs. In Proceedings of
the Twenty-Seventh International Joint Conference on Artificial Intelligence
(Vol. 2018, pp. 4700–4707). Stockholm, Sweden: IJCAI. https://doi.org/10.24963/ijcai.2018/653'
chicago: Chatterjee, Krishnendu, Hongfei Fu, Amir Kafshdar Goharshady, and Nastaran
Okati. “Computational Approaches for Stochastic Shortest Path on Succinct MDPs.”
In Proceedings of the Twenty-Seventh International Joint Conference on Artificial
Intelligence, 2018:4700–4707. IJCAI, 2018. https://doi.org/10.24963/ijcai.2018/653.
ieee: K. Chatterjee, H. Fu, A. K. Goharshady, and N. Okati, “Computational approaches
for stochastic shortest path on succinct MDPs,” in Proceedings of the Twenty-Seventh
International Joint Conference on Artificial Intelligence, Stockholm, Sweden,
2018, vol. 2018, pp. 4700–4707.
ista: 'Chatterjee K, Fu H, Goharshady AK, Okati N. 2018. Computational approaches
for stochastic shortest path on succinct MDPs. Proceedings of the Twenty-Seventh
International Joint Conference on Artificial Intelligence. IJCAI: International
Joint Conference on Artificial Intelligence vol. 2018, 4700–4707.'
mla: Chatterjee, Krishnendu, et al. “Computational Approaches for Stochastic Shortest
Path on Succinct MDPs.” Proceedings of the Twenty-Seventh International Joint
Conference on Artificial Intelligence, vol. 2018, IJCAI, 2018, pp. 4700–07,
doi:10.24963/ijcai.2018/653.
short: K. Chatterjee, H. Fu, A.K. Goharshady, N. Okati, in:, Proceedings of the
Twenty-Seventh International Joint Conference on Artificial Intelligence, IJCAI,
2018, pp. 4700–4707.
conference:
end_date: 2018-07-19
location: Stockholm, Sweden
name: 'IJCAI: International Joint Conference on Artificial Intelligence'
start_date: 2018-07-13
date_created: 2019-02-13T13:26:27Z
date_published: 2018-07-17T00:00:00Z
date_updated: 2024-03-27T23:30:34Z
day: '17'
department:
- _id: KrCh
doi: 10.24963/ijcai.2018/653
ec_funded: 1
external_id:
arxiv:
- '1804.08984'
isi:
- '000764175404118'
intvolume: ' 2018'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.08984
month: '07'
oa: 1
oa_version: Preprint
page: 4700-4707
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Proceedings of the Twenty-Seventh International Joint Conference on Artificial
Intelligence
publication_identifier:
isbn:
- 978-099924112-7
issn:
- '10450823'
publication_status: published
publisher: IJCAI
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Computational approaches for stochastic shortest path on succinct MDPs
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018
year: '2018'
...
---
_id: '422'
abstract:
- lang: eng
text: We show that a rather simple, steady modification of the streamwise velocity
profile in a pipe can lead to a complete collapse of turbulence and the flow fully
relaminarizes. Two different devices, a stationary obstacle (inset) and a device
which injects fluid through an annular gap close to the wall, are used to control
the flow. Both devices modify the streamwise velocity profile such that the flow
in the center of the pipe is decelerated and the flow in the near wall region
is accelerated. We present measurements with stereoscopic particle image velocimetry
to investigate and capture the development of the relaminarizing flow downstream
these devices and the specific circumstances responsible for relaminarization.
We find total relaminarization up to Reynolds numbers of 6000, where the skin
friction in the far downstream distance is reduced by a factor of 3.4 due to relaminarization.
In a smooth straight pipe the flow remains completely laminar downstream of the
control. Furthermore, we show that transient (temporary) relaminarization in a
spatially confined region right downstream the devices occurs also at much higher
Reynolds numbers, accompanied by a significant local skin friction drag reduction.
The underlying physical mechanism of relaminarization is attributed to a weakening
of the near-wall turbulence production cycle.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Jakob
full_name: Kühnen, Jakob
id: 3A47AE32-F248-11E8-B48F-1D18A9856A87
last_name: Kühnen
orcid: 0000-0003-4312-0179
- first_name: Davide
full_name: Scarselli, Davide
id: 40315C30-F248-11E8-B48F-1D18A9856A87
last_name: Scarselli
orcid: 0000-0001-5227-4271
- first_name: Markus
full_name: Schaner, Markus
id: 316CE034-F248-11E8-B48F-1D18A9856A87
last_name: Schaner
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Kühnen J, Scarselli D, Schaner M, Hof B. Relaminarization by steady modification
of the streamwise velocity profile in a pipe. Flow Turbulence and Combustion.
2018;100(4):919-942. doi:10.1007/s10494-018-9896-4
apa: Kühnen, J., Scarselli, D., Schaner, M., & Hof, B. (2018). Relaminarization
by steady modification of the streamwise velocity profile in a pipe. Flow Turbulence
and Combustion. Springer. https://doi.org/10.1007/s10494-018-9896-4
chicago: Kühnen, Jakob, Davide Scarselli, Markus Schaner, and Björn Hof. “Relaminarization
by Steady Modification of the Streamwise Velocity Profile in a Pipe.” Flow
Turbulence and Combustion. Springer, 2018. https://doi.org/10.1007/s10494-018-9896-4.
ieee: J. Kühnen, D. Scarselli, M. Schaner, and B. Hof, “Relaminarization by steady
modification of the streamwise velocity profile in a pipe,” Flow Turbulence
and Combustion, vol. 100, no. 4. Springer, pp. 919–942, 2018.
ista: Kühnen J, Scarselli D, Schaner M, Hof B. 2018. Relaminarization by steady
modification of the streamwise velocity profile in a pipe. Flow Turbulence and
Combustion. 100(4), 919–942.
mla: Kühnen, Jakob, et al. “Relaminarization by Steady Modification of the Streamwise
Velocity Profile in a Pipe.” Flow Turbulence and Combustion, vol. 100,
no. 4, Springer, 2018, pp. 919–42, doi:10.1007/s10494-018-9896-4.
short: J. Kühnen, D. Scarselli, M. Schaner, B. Hof, Flow Turbulence and Combustion
100 (2018) 919–942.
date_created: 2018-12-11T11:46:23Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2024-03-27T23:30:36Z
day: '01'
ddc:
- '530'
department:
- _id: BjHo
doi: 10.1007/s10494-018-9896-4
ec_funded: 1
external_id:
isi:
- '000433113900004'
file:
- access_level: open_access
checksum: d7c0bade150faabca150b0a9986e60ca
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T15:52:37Z
date_updated: 2020-07-14T12:46:25Z
file_id: '5717'
file_name: 2018_FlowTurbulenceCombust_Kuehnen.pdf
file_size: 2210020
relation: main_file
file_date_updated: 2020-07-14T12:46:25Z
has_accepted_license: '1'
intvolume: ' 100'
isi: 1
issue: '4'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 919 - 942
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
publication: Flow Turbulence and Combustion
publication_status: published
publisher: Springer
publist_id: '7401'
quality_controlled: '1'
related_material:
record:
- id: '7258'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Relaminarization by steady modification of the streamwise velocity profile
in a pipe
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: 100
year: '2018'
...
---
_id: '461'
abstract:
- lang: eng
text: Turbulence is the major cause of friction losses in transport processes and
it is responsible for a drastic drag increase in flows over bounding surfaces.
While much effort is invested into developing ways to control and reduce turbulence
intensities, so far no methods exist to altogether eliminate turbulence if velocities
are sufficiently large. We demonstrate for pipe flow that appropriate distortions
to the velocity profile lead to a complete collapse of turbulence and subsequently
friction losses are reduced by as much as 90%. Counterintuitively, the return
to laminar motion is accomplished by initially increasing turbulence intensities
or by transiently amplifying wall shear. Since neither the Reynolds number nor
the shear stresses decrease (the latter often increase), these measures are not
indicative of turbulence collapse. Instead, an amplification mechanism measuring
the interaction between eddies and the mean shear is found to set a threshold
below which turbulence is suppressed beyond recovery.
acknowledgement: We acknowledge the European Research Council under the European Union’s
Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement 306589, the European
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
programme (grant agreement no. 737549) and the Deutsche Forschungsgemeinschaft (Project
No. FOR 1182) for financial support. We thank our technician P. Maier for providing
highly valuable ideas and greatly supporting us in all technical aspects. We thank
M. Schaner for technical drawings, construction and design. We thank M. Schwegel
for a Matlab code to post-process experimental data.
article_processing_charge: No
author:
- first_name: Jakob
full_name: Kühnen, Jakob
id: 3A47AE32-F248-11E8-B48F-1D18A9856A87
last_name: Kühnen
orcid: 0000-0003-4312-0179
- first_name: Baofang
full_name: Song, Baofang
last_name: Song
- first_name: Davide
full_name: Scarselli, Davide
id: 40315C30-F248-11E8-B48F-1D18A9856A87
last_name: Scarselli
orcid: 0000-0001-5227-4271
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
- first_name: Michael
full_name: Riedl, Michael
id: 3BE60946-F248-11E8-B48F-1D18A9856A87
last_name: Riedl
orcid: 0000-0003-4844-6311
- first_name: Ashley
full_name: Willis, Ashley
last_name: Willis
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Kühnen J, Song B, Scarselli D, et al. Destabilizing turbulence in pipe flow.
Nature Physics. 2018;14:386-390. doi:10.1038/s41567-017-0018-3
apa: Kühnen, J., Song, B., Scarselli, D., Budanur, N. B., Riedl, M., Willis, A.,
… Hof, B. (2018). Destabilizing turbulence in pipe flow. Nature Physics.
Nature Publishing Group. https://doi.org/10.1038/s41567-017-0018-3
chicago: Kühnen, Jakob, Baofang Song, Davide Scarselli, Nazmi B Budanur, Michael
Riedl, Ashley Willis, Marc Avila, and Björn Hof. “Destabilizing Turbulence in
Pipe Flow.” Nature Physics. Nature Publishing Group, 2018. https://doi.org/10.1038/s41567-017-0018-3.
ieee: J. Kühnen et al., “Destabilizing turbulence in pipe flow,” Nature
Physics, vol. 14. Nature Publishing Group, pp. 386–390, 2018.
ista: Kühnen J, Song B, Scarselli D, Budanur NB, Riedl M, Willis A, Avila M, Hof
B. 2018. Destabilizing turbulence in pipe flow. Nature Physics. 14, 386–390.
mla: Kühnen, Jakob, et al. “Destabilizing Turbulence in Pipe Flow.” Nature Physics,
vol. 14, Nature Publishing Group, 2018, pp. 386–90, doi:10.1038/s41567-017-0018-3.
short: J. Kühnen, B. Song, D. Scarselli, N.B. Budanur, M. Riedl, A. Willis, M. Avila,
B. Hof, Nature Physics 14 (2018) 386–390.
date_created: 2018-12-11T11:46:36Z
date_published: 2018-01-08T00:00:00Z
date_updated: 2024-03-27T23:30:36Z
day: '08'
department:
- _id: BjHo
doi: 10.1038/s41567-017-0018-3
ec_funded: 1
external_id:
isi:
- '000429434100020'
intvolume: ' 14'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1711.06543
month: '01'
oa: 1
oa_version: Preprint
page: 386-390
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
- _id: 25104D44-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '737549'
name: Eliminating turbulence in oil pipelines
publication: Nature Physics
publication_status: published
publisher: Nature Publishing Group
publist_id: '7360'
quality_controlled: '1'
related_material:
record:
- id: '12726'
relation: dissertation_contains
status: public
- id: '14530'
relation: dissertation_contains
status: public
- id: '7258'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Destabilizing turbulence in pipe flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 14
year: '2018'
...
---
_id: '449'
abstract:
- lang: eng
text: Auxin is unique among plant hormones due to its directional transport that
is mediated by the polarly distributed PIN auxin transporters at the plasma membrane.
The canalization hypothesis proposes that the auxin feedback on its polar flow
is a crucial, plant-specific mechanism mediating multiple self-organizing developmental
processes. Here, we used the auxin effect on the PIN polar localization in Arabidopsis
thaliana roots as a proxy for the auxin feedback on the PIN polarity during canalization.
We performed microarray experiments to find regulators of this process that act
downstream of auxin. We identified genes that were transcriptionally regulated
by auxin in an AXR3/IAA17- and ARF7/ARF19-dependent manner. Besides the known
components of the PIN polarity, such as PID and PIP5K kinases, a number of potential
new regulators were detected, among which the WRKY23 transcription factor, which
was characterized in more detail. Gain- and loss-of-function mutants confirmed
a role for WRKY23 in mediating the auxin effect on the PIN polarity. Accordingly,
processes requiring auxin-mediated PIN polarity rearrangements, such as vascular
tissue development during leaf venation, showed a higher WRKY23 expression and
required the WRKY23 activity. Our results provide initial insights into the auxin
transcriptional network acting upstream of PIN polarization and, potentially,
canalization-mediated plant development.
article_processing_charge: Yes
author:
- first_name: Tomas
full_name: Prat, Tomas
id: 3DA3BFEE-F248-11E8-B48F-1D18A9856A87
last_name: Prat
- first_name: Jakub
full_name: Hajny, Jakub
id: 4800CC20-F248-11E8-B48F-1D18A9856A87
last_name: Hajny
orcid: 0000-0003-2140-7195
- first_name: Wim
full_name: Grunewald, Wim
last_name: Grunewald
- first_name: Mina K
full_name: Vasileva, Mina K
id: 3407EB18-F248-11E8-B48F-1D18A9856A87
last_name: Vasileva
- first_name: Gergely
full_name: Molnar, Gergely
id: 34F1AF46-F248-11E8-B48F-1D18A9856A87
last_name: Molnar
- first_name: Ricardo
full_name: Tejos, Ricardo
last_name: Tejos
- first_name: Markus
full_name: Schmid, Markus
last_name: Schmid
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Prat T, Hajny J, Grunewald W, et al. WRKY23 is a component of the transcriptional
network mediating auxin feedback on PIN polarity. PLoS Genetics. 2018;14(1).
doi:10.1371/journal.pgen.1007177
apa: Prat, T., Hajny, J., Grunewald, W., Vasileva, M. K., Molnar, G., Tejos, R.,
… Friml, J. (2018). WRKY23 is a component of the transcriptional network mediating
auxin feedback on PIN polarity. PLoS Genetics. Public Library of Science.
https://doi.org/10.1371/journal.pgen.1007177
chicago: Prat, Tomas, Jakub Hajny, Wim Grunewald, Mina K Vasileva, Gergely Molnar,
Ricardo Tejos, Markus Schmid, Michael Sauer, and Jiří Friml. “WRKY23 Is a Component
of the Transcriptional Network Mediating Auxin Feedback on PIN Polarity.” PLoS
Genetics. Public Library of Science, 2018. https://doi.org/10.1371/journal.pgen.1007177.
ieee: T. Prat et al., “WRKY23 is a component of the transcriptional network
mediating auxin feedback on PIN polarity,” PLoS Genetics, vol. 14, no.
1. Public Library of Science, 2018.
ista: Prat T, Hajny J, Grunewald W, Vasileva MK, Molnar G, Tejos R, Schmid M, Sauer
M, Friml J. 2018. WRKY23 is a component of the transcriptional network mediating
auxin feedback on PIN polarity. PLoS Genetics. 14(1).
mla: Prat, Tomas, et al. “WRKY23 Is a Component of the Transcriptional Network Mediating
Auxin Feedback on PIN Polarity.” PLoS Genetics, vol. 14, no. 1, Public
Library of Science, 2018, doi:10.1371/journal.pgen.1007177.
short: T. Prat, J. Hajny, W. Grunewald, M.K. Vasileva, G. Molnar, R. Tejos, M. Schmid,
M. Sauer, J. Friml, PLoS Genetics 14 (2018).
date_created: 2018-12-11T11:46:32Z
date_published: 2018-01-29T00:00:00Z
date_updated: 2024-03-27T23:30:37Z
day: '29'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1371/journal.pgen.1007177
ec_funded: 1
external_id:
isi:
- '000423718600034'
file:
- access_level: open_access
checksum: 0276d66788ec076f4924164a39e6a712
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:52Z
date_updated: 2020-07-14T12:46:30Z
file_id: '4843'
file_name: IST-2018-967-v1+1_journal.pgen.1007177.pdf
file_size: 24709062
relation: main_file
file_date_updated: 2020-07-14T12:46:30Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '7373'
pubrep_id: '967'
quality_controlled: '1'
related_material:
record:
- id: '1127'
relation: dissertation_contains
status: public
- id: '7172'
relation: dissertation_contains
status: public
- id: '8822'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: WRKY23 is a component of the transcriptional network mediating auxin feedback
on PIN polarity
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: 14
year: '2018'
...
---
_id: '191'
abstract:
- lang: eng
text: Intercellular distribution of the plant hormone auxin largely depends on the
polar subcellular distribution of the plasma membrane PIN-FORMED (PIN) auxin transporters.
PIN polarity switches in response to different developmental and environmental
signals have been shown to redirect auxin fluxes mediating certain developmental
responses. PIN phosphorylation at different sites and by different kinases is
crucial for PIN function. Here we investigate the role of PIN phosphorylation
during gravitropic response. Loss- and gain-of-function mutants in PINOID and
related kinases but not in D6PK kinase as well as mutations mimicking constitutive
dephosphorylated or phosphorylated status of two clusters of predicted phosphorylation
sites partially disrupted PIN3 phosphorylation and caused defects in gravitropic
bending in roots and hypocotyls. In particular, they impacted PIN3 polarity rearrangements
in response to gravity and during feed-back regulation by auxin itself. Thus PIN
phosphorylation, besides regulating transport activity and apical-basal targeting,
is also important for the rapid polarity switches in response to environmental
and endogenous signals.
article_number: '10279'
article_processing_charge: No
author:
- first_name: Peter
full_name: Grones, Peter
id: 399876EC-F248-11E8-B48F-1D18A9856A87
last_name: Grones
- first_name: Melinda F
full_name: Abas, Melinda F
id: 3CFB3B1C-F248-11E8-B48F-1D18A9856A87
last_name: Abas
- first_name: Jakub
full_name: Hajny, Jakub
id: 4800CC20-F248-11E8-B48F-1D18A9856A87
last_name: Hajny
orcid: 0000-0003-2140-7195
- first_name: Angharad
full_name: Jones, Angharad
last_name: Jones
- first_name: Sascha
full_name: Waidmann, Sascha
last_name: Waidmann
- first_name: Jürgen
full_name: Kleine Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Grones P, Abas MF, Hajny J, et al. PID/WAG-mediated phosphorylation of the
Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism.
Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-28188-1
apa: Grones, P., Abas, M. F., Hajny, J., Jones, A., Waidmann, S., Kleine Vehn, J.,
& Friml, J. (2018). PID/WAG-mediated phosphorylation of the Arabidopsis PIN3
auxin transporter mediates polarity switches during gravitropism. Scientific
Reports. Springer. https://doi.org/10.1038/s41598-018-28188-1
chicago: Grones, Peter, Melinda F Abas, Jakub Hajny, Angharad Jones, Sascha Waidmann,
Jürgen Kleine Vehn, and Jiří Friml. “PID/WAG-Mediated Phosphorylation of the Arabidopsis
PIN3 Auxin Transporter Mediates Polarity Switches during Gravitropism.” Scientific
Reports. Springer, 2018. https://doi.org/10.1038/s41598-018-28188-1.
ieee: P. Grones et al., “PID/WAG-mediated phosphorylation of the Arabidopsis
PIN3 auxin transporter mediates polarity switches during gravitropism,” Scientific
Reports, vol. 8, no. 1. Springer, 2018.
ista: Grones P, Abas MF, Hajny J, Jones A, Waidmann S, Kleine Vehn J, Friml J. 2018.
PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates
polarity switches during gravitropism. Scientific Reports. 8(1), 10279.
mla: Grones, Peter, et al. “PID/WAG-Mediated Phosphorylation of the Arabidopsis
PIN3 Auxin Transporter Mediates Polarity Switches during Gravitropism.” Scientific
Reports, vol. 8, no. 1, 10279, Springer, 2018, doi:10.1038/s41598-018-28188-1.
short: P. Grones, M.F. Abas, J. Hajny, A. Jones, S. Waidmann, J. Kleine Vehn, J.
Friml, Scientific Reports 8 (2018).
date_created: 2018-12-11T11:45:06Z
date_published: 2018-07-06T00:00:00Z
date_updated: 2024-03-27T23:30:37Z
day: '06'
ddc:
- '581'
department:
- _id: JiFr
- _id: EvBe
doi: 10.1038/s41598-018-28188-1
ec_funded: 1
external_id:
isi:
- '000437673200053'
file:
- access_level: open_access
checksum: 266b03f4fb8198e83141617aaa99dcab
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T15:38:56Z
date_updated: 2020-07-14T12:45:20Z
file_id: '5714'
file_name: 2018_ScientificReports_Grones.pdf
file_size: 2413876
relation: main_file
file_date_updated: 2020-07-14T12:45:20Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Scientific Reports
publication_status: published
publisher: Springer
publist_id: '7729'
quality_controlled: '1'
related_material:
record:
- id: '8822'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter
mediates polarity switches during gravitropism
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: 8
year: '2018'
...
---
_id: '47'
abstract:
- lang: eng
text: Plant hormones as signalling molecules play an essential role in the control
of plant growth and development. Typically, sites of hormonal action are usually
distant from the site of biosynthesis thus relying on efficient transport mechanisms.
Over the last decades, molecular identification of proteins and protein complexes
involved in hormonal transport has started. Advanced screens for genes involved
in hormonal transport in combination with transport assays using heterologous
systems such as yeast, insect, or tobacco BY2 cells or Xenopus oocytes provided
important insights into mechanisms underlying distribution of hormones in plant
body and led to identification of principal transporters for each hormone. This
review gives a short overview of the mechanisms of hormonal transport and transporters
identified in Arabidopsis thaliana.
article_processing_charge: No
author:
- first_name: Rashed
full_name: Abualia, Rashed
id: 4827E134-F248-11E8-B48F-1D18A9856A87
last_name: Abualia
orcid: 0000-0002-9357-9415
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Benoît
full_name: Lacombe, Benoît
last_name: Lacombe
citation:
ama: Abualia R, Benková E, Lacombe B. Transporters and mechanisms of hormone transport
in arabidopsis. Advances in Botanical Research. 2018;87:115-138. doi:10.1016/bs.abr.2018.09.007
apa: Abualia, R., Benková, E., & Lacombe, B. (2018). Transporters and mechanisms
of hormone transport in arabidopsis. Advances in Botanical Research. Elsevier.
https://doi.org/10.1016/bs.abr.2018.09.007
chicago: Abualia, Rashed, Eva Benková, and Benoît Lacombe. “Transporters and Mechanisms
of Hormone Transport in Arabidopsis.” Advances in Botanical Research. Elsevier,
2018. https://doi.org/10.1016/bs.abr.2018.09.007.
ieee: R. Abualia, E. Benková, and B. Lacombe, “Transporters and mechanisms of hormone
transport in arabidopsis,” Advances in Botanical Research, vol. 87. Elsevier,
pp. 115–138, 2018.
ista: Abualia R, Benková E, Lacombe B. 2018. Transporters and mechanisms of hormone
transport in arabidopsis. Advances in Botanical Research. 87, 115–138.
mla: Abualia, Rashed, et al. “Transporters and Mechanisms of Hormone Transport in
Arabidopsis.” Advances in Botanical Research, vol. 87, Elsevier, 2018,
pp. 115–38, doi:10.1016/bs.abr.2018.09.007.
short: R. Abualia, E. Benková, B. Lacombe, Advances in Botanical Research 87 (2018)
115–138.
date_created: 2018-12-11T11:44:20Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2024-03-27T23:30:39Z
day: '01'
department:
- _id: EvBe
doi: 10.1016/bs.abr.2018.09.007
external_id:
isi:
- '000453657800006'
intvolume: ' 87'
isi: 1
language:
- iso: eng
month: '01'
oa_version: None
page: 115 - 138
publication: Advances in Botanical Research
publication_status: published
publisher: Elsevier
publist_id: '8007'
quality_controlled: '1'
related_material:
record:
- id: '10303'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Transporters and mechanisms of hormone transport in arabidopsis
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 87
year: '2018'
...
---
_id: '15'
abstract:
- lang: eng
text: Although much is known about the physiological framework of T cell motility,
and numerous rate-limiting molecules have been identified through loss-of-function
approaches, an integrated functional concept of T cell motility is lacking. Here,
we used in vivo precision morphometry together with analysis of cytoskeletal dynamics
in vitro to deconstruct the basic mechanisms of T cell migration within lymphatic
organs. We show that the contributions of the integrin LFA-1 and the chemokine
receptor CCR7 are complementary rather than positioned in a linear pathway, as
they are during leukocyte extravasation from the blood vasculature. Our data demonstrate
that CCR7 controls cortical actin flows, whereas integrins mediate substrate friction
that is sufficient to drive locomotion in the absence of considerable surface
adhesions and plasma membrane flux.
acknowledged_ssus:
- _id: SSU
acknowledgement: This work was funded by grants from the European Research Council
(ERC StG 281556 and CoG 724373) and the Austrian Science Foundation (FWF) to M.S.
and by Swiss National Foundation (SNF) project grants 31003A_135649, 31003A_153457
and CR23I3_156234 to J.V.S. F.G. received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement
no. 747687, and J.R. was funded by an EMBO long-term fellowship (ALTF 1396-2014).
article_processing_charge: No
author:
- first_name: Miroslav
full_name: Hons, Miroslav
id: 4167FE56-F248-11E8-B48F-1D18A9856A87
last_name: Hons
orcid: 0000-0002-6625-3348
- first_name: Aglaja
full_name: Kopf, Aglaja
id: 31DAC7B6-F248-11E8-B48F-1D18A9856A87
last_name: Kopf
orcid: 0000-0002-2187-6656
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Alexander F
full_name: Leithner, Alexander F
id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87
last_name: Leithner
orcid: 0000-0002-1073-744X
- first_name: Florian R
full_name: Gärtner, Florian R
id: 397A88EE-F248-11E8-B48F-1D18A9856A87
last_name: Gärtner
orcid: 0000-0001-6120-3723
- first_name: Jun
full_name: Abe, Jun
last_name: Abe
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Jens
full_name: Stein, Jens
last_name: Stein
- 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: Hons M, Kopf A, Hauschild R, et al. Chemokines and integrins independently
tune actin flow and substrate friction during intranodal migration of T cells.
Nature Immunology. 2018;19(6):606-616. doi:10.1038/s41590-018-0109-z
apa: Hons, M., Kopf, A., Hauschild, R., Leithner, A. F., Gärtner, F. R., Abe, J.,
… Sixt, M. K. (2018). Chemokines and integrins independently tune actin flow and
substrate friction during intranodal migration of T cells. Nature Immunology.
Nature Publishing Group. https://doi.org/10.1038/s41590-018-0109-z
chicago: Hons, Miroslav, Aglaja Kopf, Robert Hauschild, Alexander F Leithner, Florian
R Gärtner, Jun Abe, Jörg Renkawitz, Jens Stein, and Michael K Sixt. “Chemokines
and Integrins Independently Tune Actin Flow and Substrate Friction during Intranodal
Migration of T Cells.” Nature Immunology. Nature Publishing Group, 2018.
https://doi.org/10.1038/s41590-018-0109-z.
ieee: M. Hons et al., “Chemokines and integrins independently tune actin
flow and substrate friction during intranodal migration of T cells,” Nature
Immunology, vol. 19, no. 6. Nature Publishing Group, pp. 606–616, 2018.
ista: Hons M, Kopf A, Hauschild R, Leithner AF, Gärtner FR, Abe J, Renkawitz J,
Stein J, Sixt MK. 2018. Chemokines and integrins independently tune actin flow
and substrate friction during intranodal migration of T cells. Nature Immunology.
19(6), 606–616.
mla: Hons, Miroslav, et al. “Chemokines and Integrins Independently Tune Actin Flow
and Substrate Friction during Intranodal Migration of T Cells.” Nature Immunology,
vol. 19, no. 6, Nature Publishing Group, 2018, pp. 606–16, doi:10.1038/s41590-018-0109-z.
short: M. Hons, A. Kopf, R. Hauschild, A.F. Leithner, F.R. Gärtner, J. Abe, J. Renkawitz,
J. Stein, M.K. Sixt, Nature Immunology 19 (2018) 606–616.
date_created: 2018-12-11T11:44:10Z
date_published: 2018-05-18T00:00:00Z
date_updated: 2024-03-27T23:30:39Z
day: '18'
department:
- _id: MiSi
- _id: Bio
doi: 10.1038/s41590-018-0109-z
ec_funded: 1
external_id:
isi:
- '000433041500026'
pmid:
- '29777221'
intvolume: ' 19'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/29777221
month: '05'
oa: 1
oa_version: Published Version
page: 606 - 616
pmid: 1
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular navigation along spatial gradients
- _id: 260AA4E2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '747687'
name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells
- _id: 25A48D24-B435-11E9-9278-68D0E5697425
grant_number: ALTF 1396-2014
name: Molecular and system level view of immune cell migration
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
(EU)
publication: Nature Immunology
publication_status: published
publisher: Nature Publishing Group
publist_id: '8040'
quality_controlled: '1'
related_material:
record:
- id: '6891'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Chemokines and integrins independently tune actin flow and substrate friction
during intranodal migration of T cells
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 19
year: '2018'
...
---
_id: '28'
abstract:
- lang: eng
text: 'This scientific commentary refers to ‘NEGR1 and FGFR2 cooperatively regulate
cortical development and core behaviours related to autism disorders in mice’
by Szczurkowska et al. '
article_processing_charge: No
author:
- first_name: Ximena
full_name: Contreras, Ximena
id: 475990FE-F248-11E8-B48F-1D18A9856A87
last_name: Contreras
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Contreras X, Hippenmeyer S. Incorrect trafficking route leads to autism. Brain
a journal of neurology. 2018;141(9):2542-2544. doi:10.1093/brain/awy218
apa: Contreras, X., & Hippenmeyer, S. (2018). Incorrect trafficking route leads
to autism. Brain a Journal of Neurology. Oxford University Press. https://doi.org/10.1093/brain/awy218
chicago: Contreras, Ximena, and Simon Hippenmeyer. “Incorrect Trafficking Route
Leads to Autism.” Brain a Journal of Neurology. Oxford University Press,
2018. https://doi.org/10.1093/brain/awy218.
ieee: X. Contreras and S. Hippenmeyer, “Incorrect trafficking route leads to autism,”
Brain a journal of neurology, vol. 141, no. 9. Oxford University Press,
pp. 2542–2544, 2018.
ista: Contreras X, Hippenmeyer S. 2018. Incorrect trafficking route leads to autism.
Brain a journal of neurology. 141(9), 2542–2544.
mla: Contreras, Ximena, and Simon Hippenmeyer. “Incorrect Trafficking Route Leads
to Autism.” Brain a Journal of Neurology, vol. 141, no. 9, Oxford University
Press, 2018, pp. 2542–44, doi:10.1093/brain/awy218.
short: X. Contreras, S. Hippenmeyer, Brain a Journal of Neurology 141 (2018) 2542–2544.
date_created: 2018-12-11T11:44:14Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2024-03-27T23:30:41Z
day: '01'
department:
- _id: SiHi
doi: 10.1093/brain/awy218
external_id:
isi:
- '000446548100012'
intvolume: ' 141'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa_version: None
page: 2542 - 2544
publication: Brain a journal of neurology
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '7902'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Incorrect trafficking route leads to autism
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 141
year: '2018'
...
---
_id: '442'
abstract:
- lang: eng
text: The rapid auxin-triggered growth of the Arabidopsis hypocotyls involves the
nuclear TIR1/AFB-Aux/IAA signaling and is accompanied by acidification of the
apoplast and cell walls (Fendrych et al., 2016). Here, we describe in detail the
method for analysis of the elongation and the TIR1/AFB-Aux/IAA-dependent auxin
response in hypocotyl segments as well as the determination of relative values
of the cell wall pH.
acknowledgement: 'This protocol was adapted from Fendrych et al., 2016. This project
has received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 665385, and Austrian
Science Fund (FWF) [M 2128-B21]. '
article_processing_charge: No
article_type: original
author:
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Li L, Krens G, Fendrych M, Friml J. Real-time analysis of auxin response, cell
wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-protocol.
2018;8(1). doi:10.21769/BioProtoc.2685
apa: Li, L., Krens, G., Fendrych, M., & Friml, J. (2018). Real-time analysis
of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls.
Bio-Protocol. Bio-protocol. https://doi.org/10.21769/BioProtoc.2685
chicago: Li, Lanxin, Gabriel Krens, Matyas Fendrych, and Jiří Friml. “Real-Time
Analysis of Auxin Response, Cell Wall PH and Elongation in Arabidopsis Thaliana
Hypocotyls.” Bio-Protocol. Bio-protocol, 2018. https://doi.org/10.21769/BioProtoc.2685.
ieee: L. Li, G. Krens, M. Fendrych, and J. Friml, “Real-time analysis of auxin response,
cell wall pH and elongation in Arabidopsis thaliana Hypocotyls,” Bio-protocol,
vol. 8, no. 1. Bio-protocol, 2018.
ista: Li L, Krens G, Fendrych M, Friml J. 2018. Real-time analysis of auxin response,
cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-protocol.
8(1).
mla: Li, Lanxin, et al. “Real-Time Analysis of Auxin Response, Cell Wall PH and
Elongation in Arabidopsis Thaliana Hypocotyls.” Bio-Protocol, vol. 8, no.
1, Bio-protocol, 2018, doi:10.21769/BioProtoc.2685.
short: L. Li, G. Krens, M. Fendrych, J. Friml, Bio-Protocol 8 (2018).
date_created: 2018-12-11T11:46:30Z
date_published: 2018-01-05T00:00:00Z
date_updated: 2024-03-27T23:30:42Z
day: '05'
ddc:
- '576'
- '581'
department:
- _id: JiFr
- _id: Bio
doi: 10.21769/BioProtoc.2685
ec_funded: 1
file:
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content_type: application/pdf
creator: system
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date_updated: 2020-07-14T12:46:29Z
file_id: '5299'
file_name: IST-2018-970-v1+1_2018_Lanxin_Real-time_analysis.pdf
file_size: 11352389
relation: main_file
file_date_updated: 2020-07-14T12:46:29Z
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intvolume: ' 8'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Bio-protocol
publication_identifier:
eissn:
- 2331-8325
publication_status: published
publisher: Bio-protocol
publist_id: '7381'
pubrep_id: '970'
quality_controlled: '1'
related_material:
record:
- id: '10083'
relation: dissertation_contains
status: public
status: public
title: Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis
thaliana Hypocotyls
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: '2018'
...
---
_id: '3'
abstract:
- lang: eng
text: SETD5 gene mutations have been identified as a frequent cause of idiopathic
intellectual disability. Here we show that Setd5-haploinsufficient mice present
developmental defects such as abnormal brain-to-body weight ratios and neural
crest defect-associated phenotypes. Furthermore, Setd5-mutant mice show impairments
in cognitive tasks, enhanced long-term potentiation, delayed ontogenetic profile
of ultrasonic vocalization, and behavioral inflexibility. Behavioral issues are
accompanied by abnormal expression of postsynaptic density proteins previously
associated with cognition. Our data additionally indicate that Setd5 regulates
RNA polymerase II dynamics and gene transcription via its interaction with the
Hdac3 and Paf1 complexes, findings potentially explaining the gene expression
defects observed in Setd5-haploinsufficient mice. Our results emphasize the decisive
role of Setd5 in a biological pathway found to be disrupted in humans with intellectual
disability and autism spectrum disorder.
acknowledged_ssus:
- _id: M-Shop
- _id: PreCl
acknowledgement: This work was supported by the Simons Foundation Autism Research
Initiative (grant 401299) to G.N. and the DFG (SPP1738 grant NO 1249) to K.-M.N.
article_processing_charge: No
article_type: original
author:
- first_name: Elena
full_name: Deliu, Elena
id: 37A40D7E-F248-11E8-B48F-1D18A9856A87
last_name: Deliu
orcid: 0000-0002-7370-5293
- first_name: Niccoló
full_name: Arecco, Niccoló
last_name: Arecco
- first_name: Jasmin
full_name: Morandell, Jasmin
id: 4739D480-F248-11E8-B48F-1D18A9856A87
last_name: Morandell
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
orcid: 0000-0002-9033-9096
- first_name: Ximena
full_name: Contreras, Ximena
id: 475990FE-F248-11E8-B48F-1D18A9856A87
last_name: Contreras
- first_name: Charles
full_name: Girardot, Charles
last_name: Girardot
- first_name: Eva
full_name: Käsper, Eva
last_name: Käsper
- first_name: Alena
full_name: Kozlova, Alena
id: C50A9596-02D0-11E9-976E-E38CFE5CBC1D
last_name: Kozlova
- first_name: Kasumi
full_name: Kishi, Kasumi
id: 3065DFC4-F248-11E8-B48F-1D18A9856A87
last_name: Kishi
- first_name: Ilaria
full_name: Chiaradia, Ilaria
id: B6467F20-02D0-11E9-BDA5-E960C241894A
last_name: Chiaradia
orcid: 0000-0002-9529-4464
- first_name: Kyung
full_name: Noh, Kyung
last_name: Noh
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Deliu E, Arecco N, Morandell J, et al. Haploinsufficiency of the intellectual
disability gene SETD5 disturbs developmental gene expression and cognition. Nature
Neuroscience. 2018;21(12):1717-1727. doi:10.1038/s41593-018-0266-2
apa: Deliu, E., Arecco, N., Morandell, J., Dotter, C., Contreras, X., Girardot,
C., … Novarino, G. (2018). Haploinsufficiency of the intellectual disability gene
SETD5 disturbs developmental gene expression and cognition. Nature Neuroscience.
Nature Publishing Group. https://doi.org/10.1038/s41593-018-0266-2
chicago: Deliu, Elena, Niccoló Arecco, Jasmin Morandell, Christoph Dotter, Ximena
Contreras, Charles Girardot, Eva Käsper, et al. “Haploinsufficiency of the Intellectual
Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” Nature
Neuroscience. Nature Publishing Group, 2018. https://doi.org/10.1038/s41593-018-0266-2.
ieee: E. Deliu et al., “Haploinsufficiency of the intellectual disability
gene SETD5 disturbs developmental gene expression and cognition,” Nature Neuroscience,
vol. 21, no. 12. Nature Publishing Group, pp. 1717–1727, 2018.
ista: Deliu E, Arecco N, Morandell J, Dotter C, Contreras X, Girardot C, Käsper
E, Kozlova A, Kishi K, Chiaradia I, Noh K, Novarino G. 2018. Haploinsufficiency
of the intellectual disability gene SETD5 disturbs developmental gene expression
and cognition. Nature Neuroscience. 21(12), 1717–1727.
mla: Deliu, Elena, et al. “Haploinsufficiency of the Intellectual Disability Gene
SETD5 Disturbs Developmental Gene Expression and Cognition.” Nature Neuroscience,
vol. 21, no. 12, Nature Publishing Group, 2018, pp. 1717–27, doi:10.1038/s41593-018-0266-2.
short: E. Deliu, N. Arecco, J. Morandell, C. Dotter, X. Contreras, C. Girardot,
E. Käsper, A. Kozlova, K. Kishi, I. Chiaradia, K. Noh, G. Novarino, Nature Neuroscience
21 (2018) 1717–1727.
date_created: 2018-12-11T11:44:05Z
date_published: 2018-11-19T00:00:00Z
date_updated: 2024-03-27T23:30:44Z
day: '19'
ddc:
- '570'
department:
- _id: GaNo
- _id: EdHa
doi: 10.1038/s41593-018-0266-2
external_id:
isi:
- '000451324700010'
file:
- access_level: open_access
checksum: 60abd0f05b7cdc08a6b0ec460884084f
content_type: application/pdf
creator: dernst
date_created: 2019-04-09T07:41:57Z
date_updated: 2020-07-14T12:45:58Z
file_id: '6255'
file_name: 2017_NatureNeuroscience_Deliu.pdf
file_size: 8167169
relation: main_file
file_date_updated: 2020-07-14T12:45:58Z
has_accepted_license: '1'
intvolume: ' 21'
isi: 1
issue: '12'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 1717 - 1727
project:
- _id: 254BA948-B435-11E9-9278-68D0E5697425
grant_number: '401299'
name: Probing development and reversibility of autism spectrum disorders
publication: Nature Neuroscience
publication_status: published
publisher: Nature Publishing Group
publist_id: '8054'
pubrep_id: '1071'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/mutation-that-causes-autism-and-intellectual-disability-makes-brain-less-flexible/
record:
- id: '6074'
relation: popular_science
status: public
- id: '12364'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental
gene expression and cognition
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 21
year: '2018'
...
---
_id: '2'
abstract:
- lang: eng
text: Indirect reciprocity explores how humans act when their reputation is at stake,
and which social norms they use to assess the actions of others. A crucial question
in indirect reciprocity is which social norms can maintain stable cooperation
in a society. Past research has highlighted eight such norms, called “leading-eight”
strategies. This past research, however, is based on the assumption that all relevant
information about other population members is publicly available and that everyone
agrees on who is good or bad. Instead, here we explore the reputation dynamics
when information is private and noisy. We show that under these conditions, most
leading-eight strategies fail to evolve. Those leading-eight strategies that do
evolve are unable to sustain full cooperation.Indirect reciprocity is a mechanism
for cooperation based on shared moral systems and individual reputations. It assumes
that members of a community routinely observe and assess each other and that they
use this information to decide who is good or bad, and who deserves cooperation.
When information is transmitted publicly, such that all community members agree
on each other’s reputation, previous research has highlighted eight crucial moral
systems. These “leading-eight” strategies can maintain cooperation and resist
invasion by defectors. However, in real populations individuals often hold their
own private views of others. Once two individuals disagree about their opinion
of some third party, they may also see its subsequent actions in a different light.
Their opinions may further diverge over time. Herein, we explore indirect reciprocity
when information transmission is private and noisy. We find that in the presence
of perception errors, most leading-eight strategies cease to be stable. Even if
a leading-eight strategy evolves, cooperation rates may drop considerably when
errors are common. Our research highlights the role of reliable information and
synchronized reputations to maintain stable moral systems.
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: Laura
full_name: Schmid, Laura
id: 38B437DE-F248-11E8-B48F-1D18A9856A87
last_name: Schmid
orcid: 0000-0002-6978-7329
- 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: Hilbe C, Schmid L, Tkadlec J, Chatterjee K, Nowak M. Indirect reciprocity with
private, noisy, and incomplete information. PNAS. 2018;115(48):12241-12246.
doi:10.1073/pnas.1810565115
apa: Hilbe, C., Schmid, L., Tkadlec, J., Chatterjee, K., & Nowak, M. (2018).
Indirect reciprocity with private, noisy, and incomplete information. PNAS.
National Academy of Sciences. https://doi.org/10.1073/pnas.1810565115
chicago: Hilbe, Christian, Laura Schmid, Josef Tkadlec, Krishnendu Chatterjee, and
Martin Nowak. “Indirect Reciprocity with Private, Noisy, and Incomplete Information.”
PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1810565115.
ieee: C. Hilbe, L. Schmid, J. Tkadlec, K. Chatterjee, and M. Nowak, “Indirect reciprocity
with private, noisy, and incomplete information,” PNAS, vol. 115, no. 48.
National Academy of Sciences, pp. 12241–12246, 2018.
ista: Hilbe C, Schmid L, Tkadlec J, Chatterjee K, Nowak M. 2018. Indirect reciprocity
with private, noisy, and incomplete information. PNAS. 115(48), 12241–12246.
mla: Hilbe, Christian, et al. “Indirect Reciprocity with Private, Noisy, and Incomplete
Information.” PNAS, vol. 115, no. 48, National Academy of Sciences, 2018,
pp. 12241–46, doi:10.1073/pnas.1810565115.
short: C. Hilbe, L. Schmid, J. Tkadlec, K. Chatterjee, M. Nowak, PNAS 115 (2018)
12241–12246.
date_created: 2018-12-11T11:44:05Z
date_published: 2018-11-27T00:00:00Z
date_updated: 2024-03-27T23:30:44Z
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title: Indirect reciprocity with private, noisy, and incomplete information
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...