---
_id: '12333'
abstract:
- lang: eng
text: Together, copy-number and point mutations form the basis for most evolutionary
novelty, through the process of gene duplication and divergence. While a plethora
of genomic data reveals the long-term fate of diverging coding sequences and their
cis-regulatory elements, little is known about the early dynamics around the duplication
event itself. In microorganisms, selection for increased gene expression often
drives the expansion of gene copy-number mutations, which serves as a crude adaptation,
prior to divergence through refining point mutations. Using a simple synthetic
genetic reporter system that can distinguish between copy-number and point mutations,
we study their early and transient adaptive dynamics in real time in Escherichia
coli. We find two qualitatively different routes of adaptation, depending on the
level of functional improvement needed. In conditions of high gene expression
demand, the two mutation types occur as a combination. However, under low gene
expression demand, copy-number and point mutations are mutually exclusive; here,
owing to their higher frequency, adaptation is dominated by copy-number mutations,
in a process we term amplification hindrance. Ultimately, due to high reversal
rates and pleiotropic cost, copy-number mutations may not only serve as a crude
and transient adaptation, but also constrain sequence divergence over evolutionary
time scales.
acknowledgement: "We are grateful to N Barton, F Kondrashov, M Lagator, M Pleska,
R Roemhild, D Siekhaus, and G\r\nTkacik for input on the manuscript and to K Tomasek
for help with flow cytometry."
article_number: e82240
article_processing_charge: No
article_type: original
author:
- first_name: Isabella
full_name: Tomanek, Isabella
id: 3981F020-F248-11E8-B48F-1D18A9856A87
last_name: Tomanek
orcid: 0000-0001-6197-363X
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Tomanek I, Guet CC. Adaptation dynamics between copynumber and point mutations.
eLife. 2022;11. doi:10.7554/ELIFE.82240
apa: Tomanek, I., & Guet, C. C. (2022). Adaptation dynamics between copynumber
and point mutations. ELife. eLife Sciences Publications. https://doi.org/10.7554/ELIFE.82240
chicago: Tomanek, Isabella, and Calin C Guet. “Adaptation Dynamics between Copynumber
and Point Mutations.” ELife. eLife Sciences Publications, 2022. https://doi.org/10.7554/ELIFE.82240.
ieee: I. Tomanek and C. C. Guet, “Adaptation dynamics between copynumber and point
mutations,” eLife, vol. 11. eLife Sciences Publications, 2022.
ista: Tomanek I, Guet CC. 2022. Adaptation dynamics between copynumber and point
mutations. eLife. 11, e82240.
mla: Tomanek, Isabella, and Calin C. Guet. “Adaptation Dynamics between Copynumber
and Point Mutations.” ELife, vol. 11, e82240, eLife Sciences Publications,
2022, doi:10.7554/ELIFE.82240.
short: I. Tomanek, C.C. Guet, ELife 11 (2022).
date_created: 2023-01-22T23:00:55Z
date_published: 2022-12-22T00:00:00Z
date_updated: 2023-08-03T14:23:07Z
day: '22'
ddc:
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department:
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doi: 10.7554/ELIFE.82240
external_id:
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title: Adaptation dynamics between copynumber and point mutations
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2022'
...
---
_id: '12339'
abstract:
- lang: eng
text: 'Copy-number and point mutations form the basis for most evolutionary novelty
through the process of gene duplication and divergence. While a plethora of genomic
sequence data reveals the long-term fate of diverging coding sequences and their
cis-regulatory elements, little is known about the early dynamics around the duplication
event itself. In microorganisms, selection for increased gene expression often
drives the expansion of gene copy-number mutations, which serves as a crude adaptation,
prior to divergence through refining point mutations. Using a simple synthetic
genetic system that allows us to distinguish copy-number and point mutations,
we study their early and transient adaptive dynamics in real-time in Escherichia
coli. We find two qualitatively different routes of adaptation depending on the
level of functional improvement selected for: In conditions of high gene expression
demand, the two types of mutations occur as a combination. Under low gene expression
demand, negative epistasis between the two types of mutations renders them mutually
exclusive. Thus, owing to their higher frequency, adaptation is dominated by copy-number
mutations. Ultimately, due to high rates of reversal and pleiotropic cost, copy-number
mutations may not only serve as a crude and transient adaptation but also constrain
sequence divergence over evolutionary time scales.'
article_processing_charge: No
author:
- first_name: Isabella
full_name: Tomanek, Isabella
id: 3981F020-F248-11E8-B48F-1D18A9856A87
last_name: Tomanek
orcid: 0000-0001-6197-363X
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Tomanek I, Guet CC. Flow cytometry YFP and CFP data and deep sequencing data
of populations evolving in galactose. 2022. doi:10.5061/dryad.rfj6q57ds
apa: Tomanek, I., & Guet, C. C. (2022). Flow cytometry YFP and CFP data and
deep sequencing data of populations evolving in galactose. Dryad. https://doi.org/10.5061/dryad.rfj6q57ds
chicago: Tomanek, Isabella, and Calin C Guet. “Flow Cytometry YFP and CFP Data and
Deep Sequencing Data of Populations Evolving in Galactose.” Dryad, 2022. https://doi.org/10.5061/dryad.rfj6q57ds.
ieee: I. Tomanek and C. C. Guet, “Flow cytometry YFP and CFP data and deep sequencing
data of populations evolving in galactose.” Dryad, 2022.
ista: Tomanek I, Guet CC. 2022. Flow cytometry YFP and CFP data and deep sequencing
data of populations evolving in galactose, Dryad, 10.5061/dryad.rfj6q57ds.
mla: Tomanek, Isabella, and Calin C. Guet. Flow Cytometry YFP and CFP Data and
Deep Sequencing Data of Populations Evolving in Galactose. Dryad, 2022, doi:10.5061/dryad.rfj6q57ds.
short: I. Tomanek, C.C. Guet, (2022).
date_created: 2023-01-23T09:00:37Z
date_published: 2022-12-23T00:00:00Z
date_updated: 2023-08-03T14:23:06Z
day: '23'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.5061/dryad.rfj6q57ds
main_file_link:
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url: https://doi.org/10.5061/dryad.rfj6q57ds
month: '12'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '12333'
relation: used_in_publication
status: public
status: public
title: Flow cytometry YFP and CFP data and deep sequencing data of populations evolving
in galactose
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '8151'
abstract:
- lang: eng
text: The main idea behind the Core Project is to teach first year students at IST
scientific communication skills and let them practice by presenting their research
within an interdisciplinary environment. Over the course of the first semester,
students participated in seminars, where they shared their results with the colleagues
from other fields and took part in discussions on relevant subjects. The main
focus during this sessions was on delivering the information in a simplified and
comprehensible way, going into the very basics of a subject if necessary. At the
end, the students were asked to present their research in the written form to
exercise their writing skills. The reports were gathered in this document. All
of them were reviewed by the teaching assistants and write-ups illustrating unique
stylistic features and, in general, an outstanding level of writing skills, were
honorably mentioned in the section "Selected Reports".
article_processing_charge: No
author:
- first_name: Mikhail
full_name: Maslov, Mikhail
id: 2E65BB0E-F248-11E8-B48F-1D18A9856A87
last_name: Maslov
orcid: 0000-0003-4074-2570
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Christina
full_name: Artner, Christina
id: 45DF286A-F248-11E8-B48F-1D18A9856A87
last_name: Artner
- first_name: Mike
full_name: Hennessey-Wesen, Mike
id: 3F338C72-F248-11E8-B48F-1D18A9856A87
last_name: Hennessey-Wesen
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
- first_name: Nick N
full_name: Machnik, Nick N
id: 3591A0AA-F248-11E8-B48F-1D18A9856A87
last_name: Machnik
- first_name: Roshan K
full_name: Satapathy, Roshan K
id: 46046B7A-F248-11E8-B48F-1D18A9856A87
last_name: Satapathy
- first_name: Isabella
full_name: Tomanek, Isabella
id: 3981F020-F248-11E8-B48F-1D18A9856A87
last_name: Tomanek
orcid: 0000-0001-6197-363X
citation:
ama: Maslov M, Kondrashov F, Artner C, et al. Core Project Proceedings. IST
Austria; 2020.
apa: Maslov, M., Kondrashov, F., Artner, C., Hennessey-Wesen, M., Kavcic, B., Machnik,
N. N., … Tomanek, I. (2020). Core Project Proceedings. IST Austria.
chicago: Maslov, Mikhail, Fyodor Kondrashov, Christina Artner, Mike Hennessey-Wesen,
Bor Kavcic, Nick N Machnik, Roshan K Satapathy, and Isabella Tomanek. Core
Project Proceedings. IST Austria, 2020.
ieee: M. Maslov et al., Core Project Proceedings. IST Austria, 2020.
ista: Maslov M, Kondrashov F, Artner C, Hennessey-Wesen M, Kavcic B, Machnik NN,
Satapathy RK, Tomanek I. 2020. Core Project Proceedings, IST Austria, 425p.
mla: Maslov, Mikhail, et al. Core Project Proceedings. IST Austria, 2020.
short: M. Maslov, F. Kondrashov, C. Artner, M. Hennessey-Wesen, B. Kavcic, N.N.
Machnik, R.K. Satapathy, I. Tomanek, Core Project Proceedings, IST Austria, 2020.
date_created: 2020-07-22T14:48:14Z
date_published: 2020-06-01T00:00:00Z
date_updated: 2023-02-23T13:26:00Z
day: '01'
ddc:
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extern: '1'
file:
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content_type: application/pdf
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date_created: 2020-07-22T14:45:07Z
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month: '06'
oa_version: None
page: '425'
publication_status: published
publisher: IST Austria
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title: Core Project Proceedings
type: report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8653'
abstract:
- lang: eng
text: "Mutations are the raw material of evolution and come in many different flavors.
Point mutations change a single letter in the DNA sequence, while copy number
mutations like duplications or deletions add or remove many letters of the DNA
sequence simultaneously. Each type of mutation exhibits specific properties like
its rate of formation and reversal. \r\nGene expression is a fundamental phenotype
that can be altered by both, point and copy number mutations. The following thesis
is concerned with the dynamics of gene expression evolution and how it is affected
by the properties exhibited by point and copy number mutations. Specifically,
we are considering i) copy number mutations during adaptation to fluctuating environments
and ii) the interaction of copy number and point mutations during adaptation to
constant environments. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Isabella
full_name: Tomanek, Isabella
id: 3981F020-F248-11E8-B48F-1D18A9856A87
last_name: Tomanek
orcid: 0000-0001-6197-363X
citation:
ama: Tomanek I. The evolution of gene expression by copy number and point mutations.
2020. doi:10.15479/AT:ISTA:8653
apa: Tomanek, I. (2020). The evolution of gene expression by copy number and
point mutations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8653
chicago: Tomanek, Isabella. “The Evolution of Gene Expression by Copy Number and
Point Mutations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8653.
ieee: I. Tomanek, “The evolution of gene expression by copy number and point mutations,”
Institute of Science and Technology Austria, 2020.
ista: Tomanek I. 2020. The evolution of gene expression by copy number and point
mutations. Institute of Science and Technology Austria.
mla: Tomanek, Isabella. The Evolution of Gene Expression by Copy Number and Point
Mutations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8653.
short: I. Tomanek, The Evolution of Gene Expression by Copy Number and Point Mutations,
Institute of Science and Technology Austria, 2020.
date_created: 2020-10-13T13:02:33Z
date_published: 2020-10-13T00:00:00Z
date_updated: 2023-09-07T13:22:42Z
day: '13'
ddc:
- '576'
degree_awarded: PhD
department:
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creator: itomanek
date_created: 2020-10-16T12:14:21Z
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keyword:
- duplication
- amplification
- promoter
- CNV
- AMGET
- experimental evolution
- Escherichia coli
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '117'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
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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 evolution of gene expression by copy number and point mutations
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '7652'
abstract:
- lang: eng
text: Organisms cope with change by taking advantage of transcriptional regulators.
However, when faced with rare environments, the evolution of transcriptional regulators
and their promoters may be too slow. Here, we investigate whether the intrinsic
instability of gene duplication and amplification provides a generic alternative
to canonical gene regulation. Using real-time monitoring of gene-copy-number mutations
in Escherichia coli, we show that gene duplications and amplifications enable
adaptation to fluctuating environments by rapidly generating copy-number and,
therefore, expression-level polymorphisms. This amplification-mediated gene expression
tuning (AMGET) occurs on timescales that are similar to canonical gene regulation
and can respond to rapid environmental changes. Mathematical modelling shows that
amplifications also tune gene expression in stochastic environments in which transcription-factor-based
schemes are hard to evolve or maintain. The fleeting nature of gene amplifications
gives rise to a generic population-level mechanism that relies on genetic heterogeneity
to rapidly tune the expression of any gene, without leaving any genomic signature.
acknowledgement: We thank L. Hurst, N. Barton, M. Pleska, M. Steinrück, B. Kavcic
and A. Staron for input on the manuscript, and To. Bergmiller and R. Chait for help
with microfluidics experiments. I.T. is a recipient the OMV fellowship. R.G. is
a recipient of a DOC (Doctoral Fellowship Programme of the Austrian Academy of Sciences)
Fellowship of the Austrian Academy of Sciences.
article_processing_charge: No
article_type: original
author:
- first_name: Isabella
full_name: Tomanek, Isabella
id: 3981F020-F248-11E8-B48F-1D18A9856A87
last_name: Tomanek
orcid: 0000-0001-6197-363X
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
- first_name: M.
full_name: Lagator, M.
last_name: Lagator
- first_name: A. M. C.
full_name: Andersson, A. M. C.
last_name: Andersson
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Tomanek I, Grah R, Lagator M, et al. Gene amplification as a form of population-level
gene expression regulation. Nature Ecology & Evolution. 2020;4(4):612-625.
doi:10.1038/s41559-020-1132-7
apa: Tomanek, I., Grah, R., Lagator, M., Andersson, A. M. C., Bollback, J. P., Tkačik,
G., & Guet, C. C. (2020). Gene amplification as a form of population-level
gene expression regulation. Nature Ecology & Evolution. Springer Nature.
https://doi.org/10.1038/s41559-020-1132-7
chicago: Tomanek, Isabella, Rok Grah, M. Lagator, A. M. C. Andersson, Jonathan P
Bollback, Gašper Tkačik, and Calin C Guet. “Gene Amplification as a Form of Population-Level
Gene Expression Regulation.” Nature Ecology & Evolution. Springer Nature,
2020. https://doi.org/10.1038/s41559-020-1132-7.
ieee: I. Tomanek et al., “Gene amplification as a form of population-level
gene expression regulation,” Nature Ecology & Evolution, vol. 4, no.
4. Springer Nature, pp. 612–625, 2020.
ista: Tomanek I, Grah R, Lagator M, Andersson AMC, Bollback JP, Tkačik G, Guet CC.
2020. Gene amplification as a form of population-level gene expression regulation.
Nature Ecology & Evolution. 4(4), 612–625.
mla: Tomanek, Isabella, et al. “Gene Amplification as a Form of Population-Level
Gene Expression Regulation.” Nature Ecology & Evolution, vol. 4, no.
4, Springer Nature, 2020, pp. 612–25, doi:10.1038/s41559-020-1132-7.
short: I. Tomanek, R. Grah, M. Lagator, A.M.C. Andersson, J.P. Bollback, G. Tkačik,
C.C. Guet, Nature Ecology & Evolution 4 (2020) 612–625.
date_created: 2020-04-08T15:20:53Z
date_published: 2020-04-01T00:00:00Z
date_updated: 2024-03-25T23:30:20Z
day: '01'
ddc:
- '570'
department:
- _id: GaTk
- _id: CaGu
doi: 10.1038/s41559-020-1132-7
external_id:
isi:
- '000519008300005'
file:
- access_level: open_access
checksum: ef3bbf42023e30b2c24a6278025d2040
content_type: application/pdf
creator: dernst
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file_name: 2020_NatureEcolEvo_Tomanek.pdf
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intvolume: ' 4'
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language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 612-625
project:
- _id: 267C84F4-B435-11E9-9278-68D0E5697425
name: Biophysically realistic genotype-phenotype maps for regulatory networks
publication: Nature Ecology & Evolution
publication_identifier:
issn:
- 2397-334X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/how-to-thrive-without-gene-regulation/
record:
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relation: dissertation_contains
status: public
- id: '7383'
relation: research_data
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relation: used_in_publication
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scopus_import: '1'
status: public
title: Gene amplification as a form of population-level gene expression regulation
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 4
year: '2020'
...
---
_id: '7016'
abstract:
- lang: eng
text: Organisms cope with change by employing transcriptional regulators. However,
when faced with rare environments, the evolution of transcriptional regulators
and their promoters may be too slow. We ask whether the intrinsic instability
of gene duplication and amplification provides a generic alternative to canonical
gene regulation. By real-time monitoring of gene copy number mutations in E. coli,
we show that gene duplications and amplifications enable adaptation to fluctuating
environments by rapidly generating copy number, and hence expression level, polymorphism.
This ‘amplification-mediated gene expression tuning’ occurs on timescales similar
to canonical gene regulation and can deal with rapid environmental changes. Mathematical
modeling shows that amplifications also tune gene expression in stochastic environments
where transcription factor-based schemes are hard to evolve or maintain. The fleeting
nature of gene amplifications gives rise to a generic population-level mechanism
that relies on genetic heterogeneity to rapidly tune expression of any gene, without
leaving any genomic signature.
article_processing_charge: No
author:
- first_name: Isabella
full_name: Tomanek, Isabella
id: 3981F020-F248-11E8-B48F-1D18A9856A87
last_name: Tomanek
orcid: 0000-0001-6197-363X
citation:
ama: Tomanek I. Data for the paper “Gene amplification as a form of population-level
gene expression regulation.” 2019. doi:10.15479/AT:ISTA:7016
apa: Tomanek, I. (2019). Data for the paper “Gene amplification as a form of population-level
gene expression regulation.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7016
chicago: Tomanek, Isabella. “Data for the Paper ‘Gene Amplification as a Form of
Population-Level Gene Expression Regulation.’” Institute of Science and Technology
Austria, 2019. https://doi.org/10.15479/AT:ISTA:7016.
ieee: I. Tomanek, “Data for the paper ‘Gene amplification as a form of population-level
gene expression regulation.’” Institute of Science and Technology Austria, 2019.
ista: Tomanek I. 2019. Data for the paper ‘Gene amplification as a form of population-level
gene expression regulation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7016.
mla: Tomanek, Isabella. Data for the Paper “Gene Amplification as a Form of Population-Level
Gene Expression Regulation.” Institute of Science and Technology Austria,
2019, doi:10.15479/AT:ISTA:7016.
short: I. Tomanek, (2019).
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date_created: 2019-11-13T09:07:31Z
date_published: 2019-11-13T00:00:00Z
date_updated: 2024-02-21T12:45:25Z
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- gene amplification
- galactose
- DOG
- experimental evolution
- Illumina sequence data
- FACS data
- microfluidics data
month: '11'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
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status: public
status: public
title: Data for the paper "Gene amplification as a form of population-level gene expression
regulation"
type: research_data
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...