---
_id: '9652'
abstract:
- lang: eng
text: In 1998 Burago and Kleiner and (independently) McMullen gave examples of separated
nets in Euclidean space which are non-bilipschitz equivalent to the integer lattice.
We study weaker notions of equivalence of separated nets and demonstrate that
such notions also give rise to distinct equivalence classes. Put differently,
we find occurrences of particularly strong divergence of separated nets from the
integer lattice. Our approach generalises that of Burago and Kleiner and McMullen
which takes place largely in a continuous setting. Existence of irregular separated
nets is verified via the existence of non-realisable density functions ρ:[0,1]d→(0,∞).
In the present work we obtain stronger types of non-realisable densities.
acknowledgement: 'This work was done while both authors were employed at the University
of Innsbruck and enjoyed the full support of Austrian Science Fund (FWF): P 30902-N35.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Michael
full_name: Dymond, Michael
last_name: Dymond
- first_name: Vojtech
full_name: Kaluza, Vojtech
id: 21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E
last_name: Kaluza
orcid: 0000-0002-2512-8698
citation:
ama: Dymond M, Kaluza V. Highly irregular separated nets. Israel Journal of Mathematics.
2023;253:501-554. doi:10.1007/s11856-022-2448-6
apa: Dymond, M., & Kaluza, V. (2023). Highly irregular separated nets. Israel
Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s11856-022-2448-6
chicago: Dymond, Michael, and Vojtech Kaluza. “Highly Irregular Separated Nets.”
Israel Journal of Mathematics. Springer Nature, 2023. https://doi.org/10.1007/s11856-022-2448-6.
ieee: M. Dymond and V. Kaluza, “Highly irregular separated nets,” Israel Journal
of Mathematics, vol. 253. Springer Nature, pp. 501–554, 2023.
ista: Dymond M, Kaluza V. 2023. Highly irregular separated nets. Israel Journal
of Mathematics. 253, 501–554.
mla: Dymond, Michael, and Vojtech Kaluza. “Highly Irregular Separated Nets.” Israel
Journal of Mathematics, vol. 253, Springer Nature, 2023, pp. 501–54, doi:10.1007/s11856-022-2448-6.
short: M. Dymond, V. Kaluza, Israel Journal of Mathematics 253 (2023) 501–554.
date_created: 2021-07-14T07:01:28Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-14T11:26:34Z
day: '01'
ddc:
- '515'
- '516'
department:
- _id: UlWa
doi: 10.1007/s11856-022-2448-6
external_id:
arxiv:
- '1903.05923'
isi:
- '000904950300003'
file:
- access_level: open_access
checksum: 6fa0a3207dd1d6467c309fd1bcc867d1
content_type: application/pdf
creator: vkaluza
date_created: 2021-07-14T07:41:50Z
date_updated: 2021-07-14T07:41:50Z
file_id: '9653'
file_name: separated_nets.pdf
file_size: 900422
relation: main_file
file_date_updated: 2021-07-14T07:41:50Z
has_accepted_license: '1'
intvolume: ' 253'
isi: 1
keyword:
- Lipschitz
- bilipschitz
- bounded displacement
- modulus of continuity
- separated net
- non-realisable density
- Burago--Kleiner construction
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 501-554
publication: Israel Journal of Mathematics
publication_identifier:
eissn:
- 1565-8511
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Highly irregular separated nets
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 253
year: '2023'
...
---
_id: '10583'
abstract:
- lang: eng
text: The synthetic strigolactone (SL) analog, rac-GR24, has been instrumental in
studying the role of SLs as well as karrikins because it activates the receptors
DWARF14 (D14) and KARRIKIN INSENSITIVE 2 (KAI2) of their signaling pathways, respectively.
Treatment with rac-GR24 modifies the root architecture at different levels, such
as decreasing the lateral root density (LRD), while promoting root hair elongation
or flavonol accumulation. Previously, we have shown that the flavonol biosynthesis
is transcriptionally activated in the root by rac-GR24 treatment, but, thus far,
the molecular players involved in that response have remained unknown. To get
an in-depth insight into the changes that occur after the compound is perceived
by the roots, we compared the root transcriptomes of the wild type and the more
axillary growth2 (max2) mutant, affected in both SL and karrikin signaling pathways,
with and without rac-GR24 treatment. Quantitative reverse transcription (qRT)-PCR,
reporter line analysis and mutant phenotyping indicated that the flavonol response
and the root hair elongation are controlled by the ELONGATED HYPOCOTYL 5 (HY5)
and MYB12 transcription factors, but HY5, in contrast to MYB12, affects the LRD
as well. Furthermore, we identified the transcription factors TARGET OF MONOPTEROS
5 (TMO5) and TMO5 LIKE1 as negative and the Mediator complex as positive regulators
of the rac-GR24 effect on LRD. Altogether, hereby, we get closer toward understanding
the molecular mechanisms that underlay the rac-GR24 responses in the root.
acknowledgement: The authors thank Ralf Stracke (Bielefeld University, Bielefeld,
Germany) for providing the myb mutants and their colleagues Bert De Rybel for the
tmo5t;mo5l1 double mutant, Boris Parizot for tips on the RNA-seq analysis, Veronique
Storme for statistical help on both the RNA-seq and lateral root density, and Martine
De Cock for help in preparing the manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Sylwia
full_name: Struk, Sylwia
last_name: Struk
- first_name: Lukas
full_name: Braem, Lukas
last_name: Braem
- first_name: Cedrick
full_name: Matthys, Cedrick
last_name: Matthys
- first_name: Alan
full_name: Walton, Alan
last_name: Walton
- first_name: Nick
full_name: Vangheluwe, Nick
last_name: Vangheluwe
- first_name: Stan
full_name: Van Praet, Stan
last_name: Van Praet
- first_name: Lingxiang
full_name: Jiang, Lingxiang
last_name: Jiang
- first_name: Pawel
full_name: Baster, Pawel
id: 3028BD74-F248-11E8-B48F-1D18A9856A87
last_name: Baster
- first_name: Carolien
full_name: De Cuyper, Carolien
last_name: De Cuyper
- first_name: Francois-Didier
full_name: Boyer, Francois-Didier
last_name: Boyer
- first_name: Elisabeth
full_name: Stes, Elisabeth
last_name: Stes
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Kris
full_name: Gevaert, Kris
last_name: Gevaert
- first_name: Sofie
full_name: Goormachtig, Sofie
last_name: Goormachtig
citation:
ama: Struk S, Braem L, Matthys C, et al. Transcriptional analysis in the Arabidopsis
roots reveals new regulators that link rac-GR24 treatment with changes in flavonol
accumulation, root hair elongation and lateral root density. Plant & Cell
Physiology. 2022;63(1):104-119. doi:10.1093/pcp/pcab149
apa: Struk, S., Braem, L., Matthys, C., Walton, A., Vangheluwe, N., Van Praet, S.,
… Goormachtig, S. (2022). Transcriptional analysis in the Arabidopsis roots reveals
new regulators that link rac-GR24 treatment with changes in flavonol accumulation,
root hair elongation and lateral root density. Plant & Cell Physiology.
Oxford University Press. https://doi.org/10.1093/pcp/pcab149
chicago: Struk, Sylwia, Lukas Braem, Cedrick Matthys, Alan Walton, Nick Vangheluwe,
Stan Van Praet, Lingxiang Jiang, et al. “Transcriptional Analysis in the Arabidopsis
Roots Reveals New Regulators That Link Rac-GR24 Treatment with Changes in Flavonol
Accumulation, Root Hair Elongation and Lateral Root Density.” Plant & Cell
Physiology. Oxford University Press, 2022. https://doi.org/10.1093/pcp/pcab149.
ieee: S. Struk et al., “Transcriptional analysis in the Arabidopsis roots
reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation,
root hair elongation and lateral root density,” Plant & Cell Physiology,
vol. 63, no. 1. Oxford University Press, pp. 104–119, 2022.
ista: Struk S, Braem L, Matthys C, Walton A, Vangheluwe N, Van Praet S, Jiang L,
Baster P, De Cuyper C, Boyer F-D, Stes E, Beeckman T, Friml J, Gevaert K, Goormachtig
S. 2022. Transcriptional analysis in the Arabidopsis roots reveals new regulators
that link rac-GR24 treatment with changes in flavonol accumulation, root hair
elongation and lateral root density. Plant & Cell Physiology. 63(1), 104–119.
mla: Struk, Sylwia, et al. “Transcriptional Analysis in the Arabidopsis Roots Reveals
New Regulators That Link Rac-GR24 Treatment with Changes in Flavonol Accumulation,
Root Hair Elongation and Lateral Root Density.” Plant & Cell Physiology,
vol. 63, no. 1, Oxford University Press, 2022, pp. 104–19, doi:10.1093/pcp/pcab149.
short: S. Struk, L. Braem, C. Matthys, A. Walton, N. Vangheluwe, S. Van Praet, L.
Jiang, P. Baster, C. De Cuyper, F.-D. Boyer, E. Stes, T. Beeckman, J. Friml, K.
Gevaert, S. Goormachtig, Plant & Cell Physiology 63 (2022) 104–119.
date_created: 2021-12-28T11:44:18Z
date_published: 2022-01-21T00:00:00Z
date_updated: 2023-08-02T13:40:43Z
day: '21'
department:
- _id: JiFr
doi: 10.1093/pcp/pcab149
external_id:
isi:
- '000877899400009'
pmid:
- '34791413'
intvolume: ' 63'
isi: 1
issue: '1'
keyword:
- flavonols
- MAX2
- rac-Gr24
- RNA-seq
- root development
- transcriptional regulation
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/pcp/pcab149
month: '01'
oa: 1
oa_version: Published Version
page: 104-119
pmid: 1
publication: Plant & Cell Physiology
publication_identifier:
eissn:
- 1471-9053
issn:
- 0032-0781
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Transcriptional analysis in the Arabidopsis roots reveals new regulators that
link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation
and lateral root density
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 63
year: '2022'
...
---
_id: '5556'
abstract:
- lang: eng
text: "MATLAB code and processed datasets available for reproducing the results
in: \r\nLukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic
Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking
in Yeast.\r\n*equal contributions"
article_processing_charge: No
author:
- first_name: Martin
full_name: Lukacisin, Martin
id: 298FFE8C-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisin
orcid: 0000-0001-6549-4177
- first_name: Matthieu
full_name: Landon, Matthieu
last_name: Landon
- first_name: Rishi
full_name: Jajoo, Rishi
last_name: Jajoo
citation:
ama: Lukacisin M, Landon M, Jajoo R. MATLAB analysis code for “Sequence-Specific
Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing
and Backtracking in Yeast.” 2016. doi:10.15479/AT:ISTA:45
apa: Lukacisin, M., Landon, M., & Jajoo, R. (2016). MATLAB analysis code for
“Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional
Pausing and Backtracking in Yeast.” Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:45
chicago: Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “MATLAB Analysis Code
for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both
Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and
Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:45.
ieee: M. Lukacisin, M. Landon, and R. Jajoo, “MATLAB analysis code for ‘Sequence-Specific
Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing
and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2016.
ista: Lukacisin M, Landon M, Jajoo R. 2016. MATLAB analysis code for ‘Sequence-Specific
Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing
and Backtracking in Yeast’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:45.
mla: Lukacisin, Martin, et al. MATLAB Analysis Code for “Sequence-Specific Thermodynamic
Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking
in Yeast.” Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:45.
short: M. Lukacisin, M. Landon, R. Jajoo, (2016).
datarep_id: '45'
date_created: 2018-12-12T12:31:31Z
date_published: 2016-08-25T00:00:00Z
date_updated: 2024-02-21T13:51:53Z
day: '25'
ddc:
- '571'
department:
- _id: ToBo
doi: 10.15479/AT:ISTA:45
file:
- access_level: open_access
checksum: ee697f2b1ade4dc14d6ac0334dd832ab
content_type: application/zip
creator: system
date_created: 2018-12-12T13:02:58Z
date_updated: 2020-07-14T12:47:02Z
file_id: '5616'
file_name: IST-2016-45-v1+1_PaperCode.zip
file_size: 296722548
relation: main_file
file_date_updated: 2020-07-14T12:47:02Z
has_accepted_license: '1'
keyword:
- transcription
- pausing
- backtracking
- polymerase
- RNA
- NET-seq
- nucleosome
- basepairing
license: https://creativecommons.org/licenses/by-sa/4.0/
month: '08'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8431'
relation: used_in_publication
status: deleted
- id: '1029'
relation: research_paper
status: public
status: public
title: MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic
Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...