---
_id: '6230'
abstract:
- lang: eng
text: Great care is needed when interpreting claims about the genetic basis of human
variation based on data from genome-wide association studies.
article_number: e45380
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Joachim
full_name: Hermisson, Joachim
last_name: Hermisson
- first_name: Magnus
full_name: Nordborg, Magnus
last_name: Nordborg
citation:
ama: Barton NH, Hermisson J, Nordborg M. Why structure matters. eLife. 2019;8.
doi:10.7554/eLife.45380
apa: Barton, N. H., Hermisson, J., & Nordborg, M. (2019). Why structure matters.
ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.45380
chicago: Barton, Nicholas H, Joachim Hermisson, and Magnus Nordborg. “Why Structure
Matters.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.45380.
ieee: N. H. Barton, J. Hermisson, and M. Nordborg, “Why structure matters,” eLife,
vol. 8. eLife Sciences Publications, 2019.
ista: Barton NH, Hermisson J, Nordborg M. 2019. Why structure matters. eLife. 8,
e45380.
mla: Barton, Nicholas H., et al. “Why Structure Matters.” ELife, vol. 8,
e45380, eLife Sciences Publications, 2019, doi:10.7554/eLife.45380.
short: N.H. Barton, J. Hermisson, M. Nordborg, ELife 8 (2019).
date_created: 2019-04-07T21:59:15Z
date_published: 2019-03-21T00:00:00Z
date_updated: 2023-08-25T08:59:38Z
day: '21'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.7554/eLife.45380
external_id:
isi:
- '000461988300001'
file:
- access_level: open_access
checksum: 130d7544b57df4a6787e1263c2d7ea43
content_type: application/pdf
creator: dernst
date_created: 2019-04-11T11:43:38Z
date_updated: 2020-07-14T12:47:24Z
file_id: '6293'
file_name: 2019_eLife_Barton.pdf
file_size: 298466
relation: main_file
file_date_updated: 2020-07-14T12:47:24Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
eissn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/body-height-bmi-disease-risk-co/
scopus_import: '1'
status: public
title: Why structure matters
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: 8
year: '2019'
...
---
_id: '6232'
abstract:
- lang: eng
text: 'The boundary behaviour of solutions of stochastic PDEs with Dirichlet boundary
conditions can be surprisingly—and in a sense, arbitrarily—bad: as shown by Krylov[
SIAM J. Math. Anal.34(2003) 1167–1182], for any α>0 one can find a simple 1-dimensional
constant coefficient linear equation whose solution at the boundary is not α-Hölder
continuous.We obtain a positive counterpart of this: under some mild regularity
assumptions on the coefficients, solutions of semilinear SPDEs on C1 domains are
proved to be α-Hölder continuous up to the boundary with some α>0.'
article_processing_charge: No
arxiv: 1
author:
- first_name: Mate
full_name: Gerencser, Mate
id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87
last_name: Gerencser
citation:
ama: Gerencser M. Boundary regularity of stochastic PDEs. Annals of Probability.
2019;47(2):804-834. doi:10.1214/18-AOP1272
apa: Gerencser, M. (2019). Boundary regularity of stochastic PDEs. Annals of
Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AOP1272
chicago: Gerencser, Mate. “Boundary Regularity of Stochastic PDEs.” Annals of
Probability. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-AOP1272.
ieee: M. Gerencser, “Boundary regularity of stochastic PDEs,” Annals of Probability,
vol. 47, no. 2. Institute of Mathematical Statistics, pp. 804–834, 2019.
ista: Gerencser M. 2019. Boundary regularity of stochastic PDEs. Annals of Probability.
47(2), 804–834.
mla: Gerencser, Mate. “Boundary Regularity of Stochastic PDEs.” Annals of Probability,
vol. 47, no. 2, Institute of Mathematical Statistics, 2019, pp. 804–34, doi:10.1214/18-AOP1272.
short: M. Gerencser, Annals of Probability 47 (2019) 804–834.
date_created: 2019-04-07T21:59:15Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2023-08-25T08:59:11Z
day: '01'
department:
- _id: JaMa
doi: 10.1214/18-AOP1272
external_id:
arxiv:
- '1705.05364'
isi:
- '000459681900005'
intvolume: ' 47'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.05364
month: '03'
oa: 1
oa_version: Preprint
page: 804-834
publication: Annals of Probability
publication_identifier:
issn:
- '00911798'
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Boundary regularity of stochastic PDEs
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 47
year: '2019'
...
---
_id: '6240'
abstract:
- lang: eng
text: For a general class of large non-Hermitian random block matrices X we prove
that there are no eigenvalues away from a deterministic set with very high probability.
This set is obtained from the Dyson equation of the Hermitization of X as the
self-consistent approximation of the pseudospectrum. We demonstrate that the analysis
of the matrix Dyson equation from (Probab. Theory Related Fields (2018)) offers
a unified treatment of many structured matrix ensembles.
article_processing_charge: No
arxiv: 1
author:
- first_name: Johannes
full_name: Alt, Johannes
id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87
last_name: Alt
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
- first_name: Yuriy
full_name: Nemish, Yuriy
id: 4D902E6A-F248-11E8-B48F-1D18A9856A87
last_name: Nemish
orcid: 0000-0002-7327-856X
citation:
ama: Alt J, Erdös L, Krüger TH, Nemish Y. Location of the spectrum of Kronecker
random matrices. Annales de l’institut Henri Poincare. 2019;55(2):661-696.
doi:10.1214/18-AIHP894
apa: Alt, J., Erdös, L., Krüger, T. H., & Nemish, Y. (2019). Location of the
spectrum of Kronecker random matrices. Annales de l’institut Henri Poincare.
Institut Henri Poincaré. https://doi.org/10.1214/18-AIHP894
chicago: Alt, Johannes, László Erdös, Torben H Krüger, and Yuriy Nemish. “Location
of the Spectrum of Kronecker Random Matrices.” Annales de l’institut Henri
Poincare. Institut Henri Poincaré, 2019. https://doi.org/10.1214/18-AIHP894.
ieee: J. Alt, L. Erdös, T. H. Krüger, and Y. Nemish, “Location of the spectrum of
Kronecker random matrices,” Annales de l’institut Henri Poincare, vol.
55, no. 2. Institut Henri Poincaré, pp. 661–696, 2019.
ista: Alt J, Erdös L, Krüger TH, Nemish Y. 2019. Location of the spectrum of Kronecker
random matrices. Annales de l’institut Henri Poincare. 55(2), 661–696.
mla: Alt, Johannes, et al. “Location of the Spectrum of Kronecker Random Matrices.”
Annales de l’institut Henri Poincare, vol. 55, no. 2, Institut Henri Poincaré,
2019, pp. 661–96, doi:10.1214/18-AIHP894.
short: J. Alt, L. Erdös, T.H. Krüger, Y. Nemish, Annales de l’institut Henri Poincare
55 (2019) 661–696.
date_created: 2019-04-08T14:05:04Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2023-10-17T12:20:20Z
day: '01'
department:
- _id: LaEr
doi: 10.1214/18-AIHP894
ec_funded: 1
external_id:
arxiv:
- '1706.08343'
isi:
- '000467793600003'
intvolume: ' 55'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1706.08343
month: '05'
oa: 1
oa_version: Preprint
page: 661-696
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Annales de l'institut Henri Poincare
publication_identifier:
issn:
- 0246-0203
publication_status: published
publisher: Institut Henri Poincaré
quality_controlled: '1'
related_material:
record:
- id: '149'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Location of the spectrum of Kronecker random matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2019'
...
---
_id: '6259'
abstract:
- lang: eng
text: The plant hormone auxin has crucial roles in almost all aspects of plant growth
and development. Concentrations of auxin vary across different tissues, mediating
distinct developmental outcomes and contributing to the functional diversity of
auxin. However, the mechanisms that underlie these activities are poorly understood.
Here we identify an auxin signalling mechanism, which acts in parallel to the
canonical auxin pathway based on the transport inhibitor response1 (TIR1) and
other auxin receptor F-box (AFB) family proteins (TIR1/AFB receptors)1,2, that
translates levels of cellular auxin to mediate differential growth during apical-hook
development. This signalling mechanism operates at the concave side of the apical
hook, and involves auxin-mediated C-terminal cleavage of transmembrane kinase
1 (TMK1). The cytosolic and nucleus-translocated C terminus of TMK1 specifically
interacts with and phosphorylates two non-canonical transcriptional repressors
of the auxin or indole-3-acetic acid (Aux/IAA) family (IAA32 and IAA34), thereby
regulating ARF transcription factors. In contrast to the degradation of Aux/IAA
transcriptional repressors in the canonical pathway, the newly identified mechanism
stabilizes the non-canonical IAA32 and IAA34 transcriptional repressors to regulate
gene expression and ultimately inhibit growth. The auxin–TMK1 signalling pathway
originates at the cell surface, is triggered by high levels of auxin and shares
a partially overlapping set of transcription factors with the TIR1/AFB signalling
pathway. This allows distinct interpretations of different concentrations of cellular
auxin, and thus enables this versatile signalling molecule to mediate complex
developmental outcomes.
article_processing_charge: No
article_type: original
author:
- first_name: Min
full_name: Cao, Min
last_name: Cao
- first_name: Rong
full_name: Chen, Rong
last_name: Chen
- first_name: Pan
full_name: Li, Pan
last_name: Li
- first_name: Yongqiang
full_name: Yu, Yongqiang
last_name: Yu
- first_name: Rui
full_name: Zheng, Rui
last_name: Zheng
- first_name: Danfeng
full_name: Ge, Danfeng
last_name: Ge
- first_name: Wei
full_name: Zheng, Wei
last_name: Zheng
- first_name: Xuhui
full_name: Wang, Xuhui
last_name: Wang
- first_name: Yangtao
full_name: Gu, Yangtao
last_name: Gu
- first_name: Zuzana
full_name: Gelová, Zuzana
id: 0AE74790-0E0B-11E9-ABC7-1ACFE5697425
last_name: Gelová
orcid: 0000-0003-4783-1752
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Heng
full_name: Zhang, Heng
last_name: Zhang
- first_name: Renyi
full_name: Liu, Renyi
last_name: Liu
- first_name: Jun
full_name: He, Jun
last_name: He
- first_name: Tongda
full_name: Xu, Tongda
last_name: Xu
citation:
ama: Cao M, Chen R, Li P, et al. TMK1-mediated auxin signalling regulates differential
growth of the apical hook. Nature. 2019;568:240-243. doi:10.1038/s41586-019-1069-7
apa: Cao, M., Chen, R., Li, P., Yu, Y., Zheng, R., Ge, D., … Xu, T. (2019). TMK1-mediated
auxin signalling regulates differential growth of the apical hook. Nature.
Springer Nature. https://doi.org/10.1038/s41586-019-1069-7
chicago: Cao, Min, Rong Chen, Pan Li, Yongqiang Yu, Rui Zheng, Danfeng Ge, Wei Zheng,
et al. “TMK1-Mediated Auxin Signalling Regulates Differential Growth of the Apical
Hook.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1069-7.
ieee: M. Cao et al., “TMK1-mediated auxin signalling regulates differential
growth of the apical hook,” Nature, vol. 568. Springer Nature, pp. 240–243,
2019.
ista: Cao M, Chen R, Li P, Yu Y, Zheng R, Ge D, Zheng W, Wang X, Gu Y, Gelová Z,
Friml J, Zhang H, Liu R, He J, Xu T. 2019. TMK1-mediated auxin signalling regulates
differential growth of the apical hook. Nature. 568, 240–243.
mla: Cao, Min, et al. “TMK1-Mediated Auxin Signalling Regulates Differential Growth
of the Apical Hook.” Nature, vol. 568, Springer Nature, 2019, pp. 240–43,
doi:10.1038/s41586-019-1069-7.
short: M. Cao, R. Chen, P. Li, Y. Yu, R. Zheng, D. Ge, W. Zheng, X. Wang, Y. Gu,
Z. Gelová, J. Friml, H. Zhang, R. Liu, J. He, T. Xu, Nature 568 (2019) 240–243.
date_created: 2019-04-09T08:37:05Z
date_published: 2019-04-11T00:00:00Z
date_updated: 2023-09-05T14:58:41Z
day: '11'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41586-019-1069-7
ec_funded: 1
external_id:
isi:
- '000464412700050'
pmid:
- '30944466'
file:
- access_level: open_access
checksum: 6b84ab602a34382cf0340a37a1378c75
content_type: application/pdf
creator: dernst
date_created: 2020-11-13T07:37:41Z
date_updated: 2020-11-13T07:37:41Z
file_id: '8751'
file_name: 2019_Nature _Cao_accepted.pdf
file_size: 4321328
relation: main_file
success: 1
file_date_updated: 2020-11-13T07:37:41Z
has_accepted_license: '1'
intvolume: ' 568'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 240-243
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
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/newly-discovered-mechanism-of-plant-hormone-auxin-acts-the-opposite-way/
scopus_import: '1'
status: public
title: TMK1-mediated auxin signalling regulates differential growth of the apical
hook
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 568
year: '2019'
...
---
_id: '6260'
abstract:
- lang: eng
text: Polar auxin transport plays a pivotal role in plant growth and development.
PIN auxin efflux carriers regulate directional auxin movement by establishing
local auxin maxima, minima, and gradients that drive multiple developmental processes
and responses to environmental signals. Auxin has been proposed to modulate its
own transport by regulating subcellular PIN trafficking via processes such as
clathrin-mediated PIN endocytosis and constitutive recycling. Here, we further
investigated the mechanisms by which auxin affects PIN trafficking by screening
auxin analogs and identified pinstatic acid (PISA) as a positive modulator of
polar auxin transport in Arabidopsis thaliana. PISA had an auxin-like effect on
hypocotyl elongation and adventitious root formation via positive regulation of
auxin transport. PISA did not activate SCFTIR1/AFB signaling and yet induced PIN
accumulation at the cell surface by inhibiting PIN internalization from the plasma
membrane. This work demonstrates PISA to be a promising chemical tool to dissect
the regulatory mechanisms behind subcellular PIN trafficking and auxin transport.
acknowledgement: "We thank Dr. H. Fukaki (University of Kobe), Dr. R. Offringa (Leiden
University), Dr. Jianwei Pan (Zhejiang Normal University), and Dr. M. Estelle (University
of California at San Diego) for providing mutants and transgenic line seeds.\r\nThis
work was supported by the Ministry of Education, Culture, Sports, Science, and Technology
(Grant-in-Aid for Scientific Research no. JP25114518 to K.H.), the Biotechnology
and Biological Sciences Research Council (award no. BB/L009366/1 to R.N. and S.K.),
and the European Union’s Horizon2020 program (European Research Council grant agreement
no. 742985 to J.F.)."
article_processing_charge: No
article_type: original
author:
- first_name: A
full_name: Oochi, A
last_name: Oochi
- first_name: Jakub
full_name: Hajny, Jakub
id: 4800CC20-F248-11E8-B48F-1D18A9856A87
last_name: Hajny
orcid: 0000-0003-2140-7195
- first_name: K
full_name: Fukui, K
last_name: Fukui
- first_name: Y
full_name: Nakao, Y
last_name: Nakao
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- first_name: M
full_name: Quareshy, M
last_name: Quareshy
- first_name: K
full_name: Takahashi, K
last_name: Takahashi
- first_name: T
full_name: Kinoshita, T
last_name: Kinoshita
- first_name: SR
full_name: Harborough, SR
last_name: Harborough
- first_name: S
full_name: Kepinski, S
last_name: Kepinski
- first_name: H
full_name: Kasahara, H
last_name: Kasahara
- first_name: RM
full_name: Napier, RM
last_name: Napier
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: KI
full_name: Hayashi, KI
last_name: Hayashi
citation:
ama: Oochi A, Hajny J, Fukui K, et al. Pinstatic acid promotes auxin transport by
inhibiting PIN internalization. Plant Physiology. 2019;180(2):1152-1165.
doi:10.1104/pp.19.00201
apa: Oochi, A., Hajny, J., Fukui, K., Nakao, Y., Gallei, M. C., Quareshy, M., …
Hayashi, K. (2019). Pinstatic acid promotes auxin transport by inhibiting PIN
internalization. Plant Physiology. ASPB. https://doi.org/10.1104/pp.19.00201
chicago: Oochi, A, Jakub Hajny, K Fukui, Y Nakao, Michelle C Gallei, M Quareshy,
K Takahashi, et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN
Internalization.” Plant Physiology. ASPB, 2019. https://doi.org/10.1104/pp.19.00201.
ieee: A. Oochi et al., “Pinstatic acid promotes auxin transport by inhibiting
PIN internalization,” Plant Physiology, vol. 180, no. 2. ASPB, pp. 1152–1165,
2019.
ista: Oochi A, Hajny J, Fukui K, Nakao Y, Gallei MC, Quareshy M, Takahashi K, Kinoshita
T, Harborough S, Kepinski S, Kasahara H, Napier R, Friml J, Hayashi K. 2019. Pinstatic
acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology.
180(2), 1152–1165.
mla: Oochi, A., et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN
Internalization.” Plant Physiology, vol. 180, no. 2, ASPB, 2019, pp. 1152–65,
doi:10.1104/pp.19.00201.
short: A. Oochi, J. Hajny, K. Fukui, Y. Nakao, M.C. Gallei, M. Quareshy, K. Takahashi,
T. Kinoshita, S. Harborough, S. Kepinski, H. Kasahara, R. Napier, J. Friml, K.
Hayashi, Plant Physiology 180 (2019) 1152–1165.
date_created: 2019-04-09T08:38:20Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2024-03-25T23:30:21Z
day: '01'
department:
- _id: JiFr
doi: 10.1104/pp.19.00201
ec_funded: 1
external_id:
isi:
- '000470086100045'
pmid:
- '30936248'
intvolume: ' 180'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1104/pp.19.00201
month: '06'
oa: 1
oa_version: Published Version
page: 1152-1165
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Plant Physiology
publication_identifier:
eissn:
- 1532-2548
issn:
- 0032-0889
publication_status: published
publisher: ASPB
quality_controlled: '1'
related_material:
record:
- id: '11626'
relation: dissertation_contains
status: public
- id: '8822'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Pinstatic acid promotes auxin transport by inhibiting PIN internalization
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 180
year: '2019'
...
---
_id: '6261'
abstract:
- lang: eng
text: Nitrate regulation of root stem cell activity is auxin-dependent.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Y
full_name: Wang, Y
last_name: Wang
- first_name: Z
full_name: Gong, Z
last_name: Gong
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: J
full_name: Zhang, J
last_name: Zhang
citation:
ama: Wang Y, Gong Z, Friml J, Zhang J. Nitrate modulates the differentiation of
root distal stem cells. Plant Physiology. 2019;180(1):22-25. doi:10.1104/pp.18.01305
apa: Wang, Y., Gong, Z., Friml, J., & Zhang, J. (2019). Nitrate modulates the
differentiation of root distal stem cells. Plant Physiology. ASPB. https://doi.org/10.1104/pp.18.01305
chicago: Wang, Y, Z Gong, Jiří Friml, and J Zhang. “Nitrate Modulates the Differentiation
of Root Distal Stem Cells.” Plant Physiology. ASPB, 2019. https://doi.org/10.1104/pp.18.01305.
ieee: Y. Wang, Z. Gong, J. Friml, and J. Zhang, “Nitrate modulates the differentiation
of root distal stem cells,” Plant Physiology, vol. 180, no. 1. ASPB, pp.
22–25, 2019.
ista: Wang Y, Gong Z, Friml J, Zhang J. 2019. Nitrate modulates the differentiation
of root distal stem cells. Plant Physiology. 180(1), 22–25.
mla: Wang, Y., et al. “Nitrate Modulates the Differentiation of Root Distal Stem
Cells.” Plant Physiology, vol. 180, no. 1, ASPB, 2019, pp. 22–25, doi:10.1104/pp.18.01305.
short: Y. Wang, Z. Gong, J. Friml, J. Zhang, Plant Physiology 180 (2019) 22–25.
date_created: 2019-04-09T08:46:17Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2023-08-25T10:10:23Z
day: '01'
department:
- _id: JiFr
doi: 10.1104/pp.18.01305
external_id:
isi:
- '000466860800010'
pmid:
- '30787134'
intvolume: ' 180'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1104/pp.18.01305
month: '05'
oa: 1
oa_version: Published Version
page: 22-25
pmid: 1
publication: Plant Physiology
publication_identifier:
eissn:
- 1532-2548
issn:
- 0032-0889
publication_status: published
publisher: ASPB
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nitrate modulates the differentiation of root distal stem cells
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 180
year: '2019'
...
---
_id: '6262'
abstract:
- lang: eng
text: "Gravitropism is an adaptive response that orients plant growth parallel to
the gravity vector. Asymmetric\r\ndistribution of the phytohormone auxin is a
necessary prerequisite to the tropic bending both in roots and\r\nshoots. During
hypocotyl gravitropic response, the PIN3 auxin transporter polarizes within gravity-sensing\r\ncells
to redirect intercellular auxin fluxes. First gravity-induced PIN3 polarization
to the bottom cell mem-\r\nbranes leads to the auxin accumulation at the lower
side of the organ, initiating bending and, later, auxin\r\nfeedback-mediated repolarization
restores symmetric auxin distribution to terminate bending. Here, we per-\r\nformed
a forward genetic screen to identify regulators of both PIN3 polarization events
during gravitropic\r\nresponse. We searched for mutants with defective PIN3 polarizations
based on easy-to-score morphological\r\noutputs of decreased or increased gravity-induced
hypocotyl bending. We identified the number of\r\nhypocotyl reduced bending (hrb)
and hypocotyl hyperbending (hhb) mutants, revealing that reduced bending corre-\r\nlated
typically with defective gravity-induced PIN3 relocation whereas all analyzed
hhb mutants showed\r\ndefects in the second, auxin-mediated PIN3 relocation. Next-generation
sequencing-aided mutation map-\r\nping identified several candidate genes, including
SCARECROW and ACTIN2, revealing roles of endodermis\r\nspecification and actin
cytoskeleton in the respective gravity- and auxin-induced PIN polarization events.\r\nThe
hypocotyl gravitropism screen thus promises to provide novel insights into mechanisms
underlying cell\r\npolarity and plant adaptive development."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Hana
full_name: Rakusová, Hana
last_name: Rakusová
- first_name: Huibin
full_name: Han, Huibin
id: 31435098-F248-11E8-B48F-1D18A9856A87
last_name: Han
- first_name: Petr
full_name: Valošek, Petr
id: 3CDB6F94-F248-11E8-B48F-1D18A9856A87
last_name: Valošek
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Rakusová H, Han H, Valošek P, Friml J. Genetic screen for factors mediating
PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. The Plant
Journal. 2019;98(6):1048-1059. doi:10.1111/tpj.14301
apa: Rakusová, H., Han, H., Valošek, P., & Friml, J. (2019). Genetic screen
for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana
hypocotyls. The Plant Journal. Wiley. https://doi.org/10.1111/tpj.14301
chicago: Rakusová, Hana, Huibin Han, Petr Valošek, and Jiří Friml. “Genetic Screen
for Factors Mediating PIN Polarization in Gravistimulated Arabidopsis Thaliana
Hypocotyls.” The Plant Journal. Wiley, 2019. https://doi.org/10.1111/tpj.14301.
ieee: H. Rakusová, H. Han, P. Valošek, and J. Friml, “Genetic screen for factors
mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls,”
The Plant Journal, vol. 98, no. 6. Wiley, pp. 1048–1059, 2019.
ista: Rakusová H, Han H, Valošek P, Friml J. 2019. Genetic screen for factors mediating
PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. The Plant
Journal. 98(6), 1048–1059.
mla: Rakusová, Hana, et al. “Genetic Screen for Factors Mediating PIN Polarization
in Gravistimulated Arabidopsis Thaliana Hypocotyls.” The Plant Journal,
vol. 98, no. 6, Wiley, 2019, pp. 1048–59, doi:10.1111/tpj.14301.
short: H. Rakusová, H. Han, P. Valošek, J. Friml, The Plant Journal 98 (2019) 1048–1059.
date_created: 2019-04-09T08:46:44Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2025-05-07T11:12:30Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/tpj.14301
ec_funded: 1
external_id:
isi:
- '000473644100008'
pmid:
- '30821050'
file:
- access_level: open_access
checksum: ad3b5e270b67ba2a45f894ce3be27920
content_type: application/pdf
creator: dernst
date_created: 2019-04-15T09:38:43Z
date_updated: 2020-07-14T12:47:25Z
file_id: '6304'
file_name: 2019_PlantJournal_Rakusov.pdf
file_size: 1383100
relation: main_file
file_date_updated: 2020-07-14T12:47:25Z
has_accepted_license: '1'
intvolume: ' 98'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1048-1059
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 Journal
publication_identifier:
eissn:
- 1365-313x
issn:
- 0960-7412
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetic screen for factors mediating PIN polarization in gravistimulated 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 98
year: '2019'
...
---
_id: '6269'
abstract:
- lang: eng
text: 'Clathrin-Mediated Endocytosis (CME) is an aspect of cellular trafficking
that is constantly regulated for mediating developmental and physiological responses.
The main aim of my thesis is to decipher the basic mechanisms of CME and post-endocytic
trafficking in the whole multicellular organ systems of Arabidopsis. The first
chapter of my thesis describes the search for new components involved in CME.
Tandem affinity purification was conducted using CLC and its interacting partners
were identified. Amongst the identified proteins were the Auxilin-likes1 and 2
(Axl1/2), putative uncoating factors, for which we made a full functional analysis.
Over-expression of Axl1/2 causes extreme modifications in the dynamics of the
machinery proteins and inhibition of endocytosis altogether. However the loss
of function of the axl1/2 did not present any cellular or physiological phenotype,
meaning Auxilin-likes do not form the major uncoating machinery. The second chapter
of my thesis describes the establishment/utilisation of techniques to capture
the dynamicity and the complexity of CME and post-endocytic trafficking. We have
studied the development of endocytic pits at the PM – specifically, the mode of
membrane remodeling during pit development and the role of actin in it, given
plant cells possess high turgor pressure. Utilizing the improved z-resolution
of TIRF and VAEM techniques, we captured the time-lapse of the endocytic events
at the plasma membrane; and using particle detection software, we quantitatively
analysed all the endocytic trajectories in an unbiased way to obtain the endocytic
rate of the system. This together with the direct analysis of cargo internalisation
from the PM provided an estimate on the endocytic potential of the cell. We also
developed a methodology for ultrastructural analysis of different populations
of Clathrin-Coated Structures (CCSs) in both PM and endomembranes in unroofed
protoplasts. Structural analysis, together with the intensity profile of CCSs
at the PM show that the mode of CCP development at the PM follows ‘Constant curvature
model’; meaning that clathrin polymerisation energy is a major contributing factor
of membrane remodeling. In addition, other analyses clearly show that actin is
not required for membrane remodeling during invagination or any other step of
CCP development, despite the prevalent high turgor pressure. However, actin is
essential in orchestrating the post-endocytic trafficking of CCVs facilitating
the EE formation. We also observed that the uncoating process post-endocytosis
is not immediate; an alternative mechanism of uncoating – Sequential multi-step
process – functions in the cell. Finally we also looked at one of the important
physiological stimuli modulating the process – hormone, auxin. auxin has been
known to influence CME before. We have made a detailed study on the concentration-time
based effect of auxin on the machinery proteins, CCP development, and the specificity
of cargoes endocytosed. To this end, we saw no general effect of auxin on CME
at earlier time points. However, very low concentration of IAA, such as 50nM,
accelerates endocytosis of specifically PIN2 through CME. Such a tight regulatory
control with high specificity to PIN2 could be essential in modulating its polarity. '
acknowledged_ssus:
- _id: Bio
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Madhumitha
full_name: Narasimhan, Madhumitha
id: 44BF24D0-F248-11E8-B48F-1D18A9856A87
last_name: Narasimhan
orcid: 0000-0002-8600-0671
citation:
ama: Narasimhan M. Clathrin-Mediated endocytosis, post-endocytic trafficking and
their regulatory controls in plants . 2019. doi:10.15479/at:ista:th1075
apa: Narasimhan, M. (2019). Clathrin-Mediated endocytosis, post-endocytic trafficking
and their regulatory controls in plants . Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:th1075
chicago: Narasimhan, Madhumitha. “Clathrin-Mediated Endocytosis, Post-Endocytic
Trafficking and Their Regulatory Controls in Plants .” Institute of Science and
Technology Austria, 2019. https://doi.org/10.15479/at:ista:th1075.
ieee: M. Narasimhan, “Clathrin-Mediated endocytosis, post-endocytic trafficking
and their regulatory controls in plants ,” Institute of Science and Technology
Austria, 2019.
ista: Narasimhan M. 2019. Clathrin-Mediated endocytosis, post-endocytic trafficking
and their regulatory controls in plants . Institute of Science and Technology
Austria.
mla: Narasimhan, Madhumitha. Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking
and Their Regulatory Controls in Plants . Institute of Science and Technology
Austria, 2019, doi:10.15479/at:ista:th1075.
short: M. Narasimhan, Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking
and Their Regulatory Controls in Plants , Institute of Science and Technology
Austria, 2019.
date_created: 2019-04-09T14:37:06Z
date_published: 2019-02-04T00:00:00Z
date_updated: 2025-05-07T11:12:27Z
day: '04'
ddc:
- '575'
degree_awarded: PhD
department:
- _id: JiFr
doi: 10.15479/at:ista:th1075
file:
- access_level: open_access
checksum: c958f27dd752712886e7e2638b847a3c
content_type: video/x-msvideo
creator: dernst
date_created: 2019-04-09T14:35:18Z
date_updated: 2021-02-11T23:30:15Z
embargo: 2020-02-11
file_id: '6270'
file_name: Supplementary_movie_1.avi
file_size: 5402078
relation: main_file
- access_level: open_access
checksum: 8786fdc29c62987c0aad3c866a4d3691
content_type: video/x-msvideo
creator: dernst
date_created: 2019-04-09T14:35:18Z
date_updated: 2021-02-11T23:30:15Z
embargo: 2020-02-11
file_id: '6271'
file_name: 3.7_supplementary_movie_10.avi
file_size: 5927736
relation: main_file
- access_level: open_access
checksum: 25f784c5159d6f4d966b2f9b371ebaf6
content_type: video/x-msvideo
creator: dernst
date_created: 2019-04-09T14:35:18Z
date_updated: 2021-02-11T23:30:15Z
embargo: 2020-02-11
file_id: '6272'
file_name: 3.7_supplementary_movie_9.avi
file_size: 9570210
relation: main_file
- access_level: open_access
checksum: 917069272a7a08d1f38224d5e12765d6
content_type: video/x-msvideo
creator: dernst
date_created: 2019-04-09T14:35:18Z
date_updated: 2021-02-11T23:30:15Z
embargo: 2020-02-11
file_id: '6273'
file_name: 3.7_supplementary_movie_8.avi
file_size: 2827360
relation: main_file
- access_level: open_access
checksum: 81e74f5ca0ad70050504f18192236dc0
content_type: video/x-msvideo
creator: dernst
date_created: 2019-04-09T14:35:18Z
date_updated: 2021-02-11T23:30:15Z
embargo: 2020-02-11
file_id: '6274'
file_name: 3.7_supplementary_movie_7.avi
file_size: 5771410
relation: main_file
- access_level: open_access
checksum: 47eb37b27a2930252713924307ea8c6f
content_type: video/x-msvideo
creator: dernst
date_created: 2019-04-09T14:35:18Z
date_updated: 2021-02-11T23:30:15Z
embargo: 2020-02-11
file_id: '6275'
file_name: 3.7_supplementary_movie_6.avi
file_size: 1113486
relation: main_file
- access_level: open_access
checksum: f68f66721041ce84e331959c9a5779c3
content_type: video/x-msvideo
creator: dernst
date_created: 2019-04-09T14:35:18Z
date_updated: 2021-02-11T23:30:15Z
embargo: 2020-02-11
file_id: '6276'
file_name: 3.7_supplementary_movie_5.avi
file_size: 1057232
relation: main_file
- access_level: open_access
checksum: 67c01cefab51b363c5e214fe4cd671f3
content_type: video/x-msvideo
creator: dernst
date_created: 2019-04-09T14:35:23Z
date_updated: 2021-02-11T23:30:15Z
embargo: 2020-02-11
file_id: '6277'
file_name: 3.7_supplementary_movie_3.avi
file_size: 127472916
relation: main_file
- access_level: open_access
checksum: e5a397edbee05b8821e2b19b3c1a9260
content_type: video/x-msvideo
creator: dernst
date_created: 2019-04-09T14:35:19Z
date_updated: 2021-02-11T23:30:15Z
embargo: 2020-02-11
file_id: '6278'
file_name: 3.7_supplementary_movie_4.avi
file_size: 3181238
relation: main_file
- access_level: open_access
checksum: 32d92b2a9277f956fdb0b42351d07c0b
content_type: video/x-msvideo
creator: dernst
date_created: 2019-04-09T14:35:19Z
date_updated: 2021-02-11T23:30:15Z
embargo: 2020-02-11
file_id: '6279'
file_name: 3.7_supplementary_movie_2.avi
file_size: 5970952
relation: main_file
- access_level: open_access
checksum: efe7001f5d9a8c61e631e12d5f324ade
content_type: video/x-msvideo
creator: dernst
date_created: 2019-04-09T14:35:21Z
date_updated: 2021-02-11T23:30:15Z
embargo: 2020-02-11
file_id: '6280'
file_name: 3.7_Supplementary_movie_1.avi
file_size: 39835236
relation: main_file
- access_level: open_access
checksum: eeb0a5603c6449c5f34eacd5ff0b3a16
content_type: video/x-msvideo
creator: dernst
date_created: 2019-04-09T14:35:21Z
date_updated: 2021-02-11T23:30:15Z
embargo: 2020-02-11
file_id: '6281'
file_name: 2.5_Suppl_Movie_4_AP2A1_TagRFP.avi
file_size: 3696740
relation: main_file
- access_level: open_access
checksum: 8e7c00ef6223bf0e177deb168338af13
content_type: video/x-msvideo
creator: dernst
date_created: 2019-04-09T14:35:21Z
date_updated: 2021-02-11T23:30:15Z
embargo: 2020-02-11
file_id: '6282'
file_name: 2.5_Suppl_Movie_3_TPLATE_GFP.avi
file_size: 6741232
relation: main_file
- access_level: open_access
checksum: 3636006a7cb709a7543d6581e359b28d
content_type: video/x-msvideo
creator: dernst
date_created: 2019-04-09T14:35:22Z
date_updated: 2021-02-11T23:30:15Z
embargo: 2020-02-11
file_id: '6283'
file_name: 2.5_Suppl_Movie_2_CLC_GFP.avi
file_size: 2445946
relation: main_file
- access_level: open_access
checksum: 39ca5519a6e9a38356e7b3704004fea7
content_type: video/x-msvideo
creator: dernst
date_created: 2019-04-09T14:35:22Z
date_updated: 2021-02-11T23:30:15Z
embargo: 2020-02-11
file_id: '6284'
file_name: 2.5_Suppl_Movie_1_CLC_GFPxAxl1_mcherry.avi
file_size: 58594
relation: main_file
- access_level: open_access
checksum: 4fcdaa3a6c645514a3b3205f0f69dc76
content_type: application/pdf
creator: dernst
date_created: 2019-04-09T14:35:33Z
date_updated: 2021-02-11T11:17:15Z
embargo: 2020-02-11
file_id: '6285'
file_name: 2019_Thesis_Narasimhan.pdf
file_size: 10553937
relation: main_file
- access_level: closed
checksum: 268f0b6bad21d5f0d671e5d4b88104a7
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-04-09T14:35:36Z
date_updated: 2020-07-14T12:47:26Z
embargo_to: open_access
file_id: '6286'
file_name: 2019_Thesis_Narasimhan_source.docx
file_size: 135291990
relation: source_file
file_date_updated: 2021-02-11T23:30:15Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '138'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '412'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: 'Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory
controls in plants '
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: '2019'
...
---
_id: '6297'
abstract:
- lang: eng
text: Cell-cell and cell-glycocalyx interactions under flow are important for the
behaviour of circulating cells in blood and lymphatic vessels. However, such interactions
are not well understood due in part to a lack of tools to study them in defined
environments. Here, we develop a versatile in vitro platform for the study of
cell-glycocalyx interactions in well-defined physical and chemical settings under
flow. Our approach is demonstrated with the interaction between hyaluronan (HA,
a key component of the endothelial glycocalyx) and its cell receptor CD44. We
generate HA brushes in situ within a microfluidic device, and demonstrate the
tuning of their physical (thickness and softness) and chemical (density of CD44
binding sites) properties using characterisation with reflection interference
contrast microscopy (RICM) and application of polymer theory. We highlight the
interactions of HA brushes with CD44-displaying beads and cells under flow. Observations
of CD44+ beads on a HA brush with RICM enabled the 3-dimensional trajectories
to be generated, and revealed interactions in the form of stop and go phases with
reduced rolling velocity and reduced distance between the bead and the HA brush,
compared to uncoated beads. Combined RICM and bright-field microscopy of CD44+
AKR1 T-lymphocytes revealed complementary information about the dynamics of cell
rolling and cell morphology, and highlighted the formation of tethers and slings,
as they interacted with a HA brush under flow. This platform can readily incorporate
more complex models of the glycocalyx, and should permit the study of how mechanical
and biochemical factors are orchestrated to enable highly selective blood cell-vessel
wall interactions under flow.
article_processing_charge: No
article_type: original
author:
- first_name: Heather S.
full_name: Davies, Heather S.
last_name: Davies
- first_name: Natalia S.
full_name: Baranova, Natalia S.
id: 38661662-F248-11E8-B48F-1D18A9856A87
last_name: Baranova
orcid: 0000-0002-3086-9124
- first_name: Nouha
full_name: El Amri, Nouha
last_name: El Amri
- first_name: Liliane
full_name: Coche-Guérente, Liliane
last_name: Coche-Guérente
- first_name: Claude
full_name: Verdier, Claude
last_name: Verdier
- first_name: Lionel
full_name: Bureau, Lionel
last_name: Bureau
- first_name: Ralf P.
full_name: Richter, Ralf P.
last_name: Richter
- first_name: Delphine
full_name: Débarre, Delphine
last_name: Débarre
citation:
ama: Davies HS, Baranova NS, El Amri N, et al. An integrated assay to probe endothelial
glycocalyx-blood cell interactions under flow in mechanically and biochemically
well-defined environments. Matrix Biology. 2019;78-79:47-59. doi:10.1016/j.matbio.2018.12.002
apa: Davies, H. S., Baranova, N. S., El Amri, N., Coche-Guérente, L., Verdier, C.,
Bureau, L., … Débarre, D. (2019). An integrated assay to probe endothelial glycocalyx-blood
cell interactions under flow in mechanically and biochemically well-defined environments.
Matrix Biology. Elsevier. https://doi.org/10.1016/j.matbio.2018.12.002
chicago: Davies, Heather S., Natalia S. Baranova, Nouha El Amri, Liliane Coche-Guérente,
Claude Verdier, Lionel Bureau, Ralf P. Richter, and Delphine Débarre. “An Integrated
Assay to Probe Endothelial Glycocalyx-Blood Cell Interactions under Flow in Mechanically
and Biochemically Well-Defined Environments.” Matrix Biology. Elsevier,
2019. https://doi.org/10.1016/j.matbio.2018.12.002.
ieee: H. S. Davies et al., “An integrated assay to probe endothelial glycocalyx-blood
cell interactions under flow in mechanically and biochemically well-defined environments,”
Matrix Biology, vol. 78–79. Elsevier, pp. 47–59, 2019.
ista: Davies HS, Baranova NS, El Amri N, Coche-Guérente L, Verdier C, Bureau L,
Richter RP, Débarre D. 2019. An integrated assay to probe endothelial glycocalyx-blood
cell interactions under flow in mechanically and biochemically well-defined environments.
Matrix Biology. 78–79, 47–59.
mla: Davies, Heather S., et al. “An Integrated Assay to Probe Endothelial Glycocalyx-Blood
Cell Interactions under Flow in Mechanically and Biochemically Well-Defined Environments.”
Matrix Biology, vol. 78–79, Elsevier, 2019, pp. 47–59, doi:10.1016/j.matbio.2018.12.002.
short: H.S. Davies, N.S. Baranova, N. El Amri, L. Coche-Guérente, C. Verdier, L.
Bureau, R.P. Richter, D. Débarre, Matrix Biology 78–79 (2019) 47–59.
date_created: 2019-04-11T20:55:01Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2023-08-25T10:11:28Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1016/j.matbio.2018.12.002
external_id:
isi:
- '000468707600005'
file:
- access_level: open_access
checksum: 790878cd78bfc54a147ddcc7c8f286a0
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T09:02:07Z
date_updated: 2020-07-14T12:47:27Z
file_id: '7825'
file_name: 2018_MatrixBiology_Davies.pdf
file_size: 4444339
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: '05'
oa: 1
oa_version: Submitted Version
page: 47-59
publication: Matrix Biology
publication_identifier:
issn:
- 0945-053X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: An integrated assay to probe endothelial glycocalyx-blood cell interactions
under flow in mechanically and biochemically well-defined environments
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: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 78-79
year: '2019'
...
---
_id: '6310'
abstract:
- lang: eng
text: An asymptotic formula is established for the number of rational points of
bounded anticanonical height which lie on a certain Zariskiopen subset of an arbitrary
smooth biquadratic hypersurface in sufficiently many variables. The proof uses
the Hardy–Littlewood circle method.
article_processing_charge: No
arxiv: 1
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: L.Q.
full_name: Hu, L.Q.
last_name: Hu
citation:
ama: Browning TD, Hu LQ. Counting rational points on biquadratic hypersurfaces.
Advances in Mathematics. 2019;349:920-940. doi:10.1016/j.aim.2019.04.031
apa: Browning, T. D., & Hu, L. Q. (2019). Counting rational points on biquadratic
hypersurfaces. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2019.04.031
chicago: Browning, Timothy D, and L.Q. Hu. “Counting Rational Points on Biquadratic
Hypersurfaces.” Advances in Mathematics. Elsevier, 2019. https://doi.org/10.1016/j.aim.2019.04.031.
ieee: T. D. Browning and L. Q. Hu, “Counting rational points on biquadratic hypersurfaces,”
Advances in Mathematics, vol. 349. Elsevier, pp. 920–940, 2019.
ista: Browning TD, Hu LQ. 2019. Counting rational points on biquadratic hypersurfaces.
Advances in Mathematics. 349, 920–940.
mla: Browning, Timothy D., and L. Q. Hu. “Counting Rational Points on Biquadratic
Hypersurfaces.” Advances in Mathematics, vol. 349, Elsevier, 2019, pp.
920–40, doi:10.1016/j.aim.2019.04.031.
short: T.D. Browning, L.Q. Hu, Advances in Mathematics 349 (2019) 920–940.
date_created: 2019-04-16T09:13:25Z
date_published: 2019-06-20T00:00:00Z
date_updated: 2023-08-25T10:11:55Z
day: '20'
ddc:
- '512'
department:
- _id: TiBr
doi: 10.1016/j.aim.2019.04.031
external_id:
arxiv:
- '1810.08426'
isi:
- '000468857300025'
file:
- access_level: open_access
checksum: a63594a3a91b4ba6e2a1b78b0720b3d0
content_type: application/pdf
creator: tbrownin
date_created: 2019-04-16T09:12:20Z
date_updated: 2020-07-14T12:47:27Z
file_id: '6311'
file_name: wliqun.pdf
file_size: 379158
relation: main_file
file_date_updated: 2020-07-14T12:47:27Z
has_accepted_license: '1'
intvolume: ' 349'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 920-940
publication: Advances in Mathematics
publication_identifier:
eissn:
- '10902082'
issn:
- '00018708'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Counting rational points on biquadratic hypersurfaces
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 349
year: '2019'
...
---
_id: '6328'
abstract:
- lang: eng
text: During metazoan development, immune surveillance and cancer dissemination,
cells migrate in complex three-dimensional microenvironments1,2,3. These spaces
are crowded by cells and extracellular matrix, generating mazes with differently
sized gaps that are typically smaller than the diameter of the migrating cell4,5.
Most mesenchymal and epithelial cells and some—but not all—cancer cells actively
generate their migratory path using pericellular tissue proteolysis6. By contrast,
amoeboid cells such as leukocytes use non-destructive strategies of locomotion7,
raising the question how these extremely fast cells navigate through dense tissues.
Here we reveal that leukocytes sample their immediate vicinity for large pore
sizes, and are thereby able to choose the path of least resistance. This allows
them to circumnavigate local obstacles while effectively following global directional
cues such as chemotactic gradients. Pore-size discrimination is facilitated by
frontward positioning of the nucleus, which enables the cells to use their bulkiest
compartment as a mechanical gauge. Once the nucleus and the closely associated
microtubule organizing centre pass the largest pore, cytoplasmic protrusions still
lingering in smaller pores are retracted. These retractions are coordinated by
dynamic microtubules; when microtubules are disrupted, migrating cells lose coherence
and frequently fragment into migratory cytoplasmic pieces. As nuclear positioning
in front of the microtubule organizing centre is a typical feature of amoeboid
migration, our findings link the fundamental organization of cellular polarity
to the strategy of locomotion.
acknowledged_ssus:
- _id: SSU
article_processing_charge: No
article_type: letter_note
author:
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Aglaja
full_name: Kopf, Aglaja
id: 31DAC7B6-F248-11E8-B48F-1D18A9856A87
last_name: Kopf
orcid: 0000-0002-2187-6656
- first_name: Julian A
full_name: Stopp, Julian A
id: 489E3F00-F248-11E8-B48F-1D18A9856A87
last_name: Stopp
- first_name: Ingrid
full_name: de Vries, Ingrid
id: 4C7D837E-F248-11E8-B48F-1D18A9856A87
last_name: de Vries
- first_name: Meghan K.
full_name: Driscoll, Meghan K.
last_name: Driscoll
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Erik S.
full_name: Welf, Erik S.
last_name: Welf
- first_name: Gaudenz
full_name: Danuser, Gaudenz
last_name: Danuser
- first_name: Reto
full_name: Fiolka, Reto
last_name: Fiolka
- 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: Renkawitz J, Kopf A, Stopp JA, et al. Nuclear positioning facilitates amoeboid
migration along the path of least resistance. Nature. 2019;568:546-550.
doi:10.1038/s41586-019-1087-5
apa: Renkawitz, J., Kopf, A., Stopp, J. A., de Vries, I., Driscoll, M. K., Merrin,
J., … Sixt, M. K. (2019). Nuclear positioning facilitates amoeboid migration along
the path of least resistance. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1087-5
chicago: Renkawitz, Jörg, Aglaja Kopf, Julian A Stopp, Ingrid de Vries, Meghan K.
Driscoll, Jack Merrin, Robert Hauschild, et al. “Nuclear Positioning Facilitates
Amoeboid Migration along the Path of Least Resistance.” Nature. Springer
Nature, 2019. https://doi.org/10.1038/s41586-019-1087-5.
ieee: J. Renkawitz et al., “Nuclear positioning facilitates amoeboid migration
along the path of least resistance,” Nature, vol. 568. Springer Nature,
pp. 546–550, 2019.
ista: Renkawitz J, Kopf A, Stopp JA, de Vries I, Driscoll MK, Merrin J, Hauschild
R, Welf ES, Danuser G, Fiolka R, Sixt MK. 2019. Nuclear positioning facilitates
amoeboid migration along the path of least resistance. Nature. 568, 546–550.
mla: Renkawitz, Jörg, et al. “Nuclear Positioning Facilitates Amoeboid Migration
along the Path of Least Resistance.” Nature, vol. 568, Springer Nature,
2019, pp. 546–50, doi:10.1038/s41586-019-1087-5.
short: J. Renkawitz, A. Kopf, J.A. Stopp, I. de Vries, M.K. Driscoll, J. Merrin,
R. Hauschild, E.S. Welf, G. Danuser, R. Fiolka, M.K. Sixt, Nature 568 (2019) 546–550.
date_created: 2019-04-17T06:52:28Z
date_published: 2019-04-25T00:00:00Z
date_updated: 2024-03-25T23:30:22Z
day: '25'
department:
- _id: MiSi
- _id: NanoFab
- _id: Bio
doi: 10.1038/s41586-019-1087-5
ec_funded: 1
external_id:
isi:
- '000465594200050'
pmid:
- '30944468'
intvolume: ' 568'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217284/
month: '04'
oa: 1
oa_version: Submitted Version
page: 546-550
pmid: 1
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
(EU)
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular navigation along spatial gradients
- _id: 265FAEBA-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W01250-B20
name: Nano-Analytics of Cellular Systems
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25A48D24-B435-11E9-9278-68D0E5697425
grant_number: ALTF 1396-2014
name: Molecular and system level view of immune cell migration
publication: Nature
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/leukocytes-use-their-nucleus-as-a-ruler-to-choose-path-of-least-resistance/
record:
- id: '14697'
relation: dissertation_contains
status: public
- id: '6891'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Nuclear positioning facilitates amoeboid migration along the path of least
resistance
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 568
year: '2019'
...
---
_id: '6338'
abstract:
- lang: eng
text: Hippocampal activity patterns representing movement trajectories are reactivated
in immobility and sleep periods, a process associated with memory recall, consolidation,
and decision making. It is thought that only fixed, behaviorally relevant patterns
can be reactivated, which are stored across hippocampal synaptic connections.
To test whether some generalized rules govern reactivation, we examined trajectory
reactivation following non-stereotypical exploration of familiar open-field environments.
We found that random trajectories of varying lengths and timescales were reactivated,
resembling that of Brownian motion of particles. The animals’ behavioral trajectory
did not follow Brownian diffusion demonstrating that the exact behavioral experience
is not reactivated. Therefore, hippocampal circuits are able to generate random
trajectories of any recently active map by following diffusion dynamics. This
ability of hippocampal circuits to generate representations of all behavioral
outcome combinations, experienced or not, may underlie a wide variety of hippocampal-dependent
cognitive functions such as learning, generalization, and planning.
article_processing_charge: No
article_type: original
author:
- first_name: Federico
full_name: Stella, Federico
id: 39AF1E74-F248-11E8-B48F-1D18A9856A87
last_name: Stella
orcid: 0000-0001-9439-3148
- first_name: Peter
full_name: Baracskay, Peter
id: 361CC00E-F248-11E8-B48F-1D18A9856A87
last_name: Baracskay
- first_name: Joseph
full_name: O'Neill, Joseph
id: 426376DC-F248-11E8-B48F-1D18A9856A87
last_name: O'Neill
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Stella F, Baracskay P, O’Neill J, Csicsvari JL. Hippocampal reactivation of
random trajectories resembling Brownian diffusion. Neuron. 2019;102:450-461.
doi:10.1016/j.neuron.2019.01.052
apa: Stella, F., Baracskay, P., O’Neill, J., & Csicsvari, J. L. (2019). Hippocampal
reactivation of random trajectories resembling Brownian diffusion. Neuron.
Elsevier. https://doi.org/10.1016/j.neuron.2019.01.052
chicago: Stella, Federico, Peter Baracskay, Joseph O’Neill, and Jozsef L Csicsvari.
“Hippocampal Reactivation of Random Trajectories Resembling Brownian Diffusion.”
Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.01.052.
ieee: F. Stella, P. Baracskay, J. O’Neill, and J. L. Csicsvari, “Hippocampal reactivation
of random trajectories resembling Brownian diffusion,” Neuron, vol. 102.
Elsevier, pp. 450–461, 2019.
ista: Stella F, Baracskay P, O’Neill J, Csicsvari JL. 2019. Hippocampal reactivation
of random trajectories resembling Brownian diffusion. Neuron. 102, 450–461.
mla: Stella, Federico, et al. “Hippocampal Reactivation of Random Trajectories Resembling
Brownian Diffusion.” Neuron, vol. 102, Elsevier, 2019, pp. 450–61, doi:10.1016/j.neuron.2019.01.052.
short: F. Stella, P. Baracskay, J. O’Neill, J.L. Csicsvari, Neuron 102 (2019) 450–461.
date_created: 2019-04-17T08:28:59Z
date_published: 2019-04-17T00:00:00Z
date_updated: 2023-08-25T10:13:07Z
day: '17'
department:
- _id: JoCs
doi: 10.1016/j.neuron.2019.01.052
ec_funded: 1
external_id:
isi:
- '000465169700017'
pmid:
- '30819547'
intvolume: ' 102'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.neuron.2019.01.052
month: '04'
oa: 1
oa_version: Published Version
page: 450-461
pmid: 1
project:
- _id: 257A4776-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281511'
name: Memory-related information processing in neuronal circuits of the hippocampus
and entorhinal cortex
- _id: 2654F984-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03713
name: Interneuro Plasticity During Spatial Learning
publication: Neuron
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/memories-of-movement-are-replayed-randomly-during-sleep/
scopus_import: '1'
status: public
title: Hippocampal reactivation of random trajectories resembling Brownian diffusion
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 102
year: '2019'
...
---
_id: '6348'
abstract:
- lang: eng
text: 'High-speed optical telecommunication is enabled by wavelength-division multiplexing,
whereby hundreds of individually stabilized lasers encode information within a
single-mode optical fibre. Higher bandwidths require higher total optical power,
but the power sent into the fibre is limited by optical nonlinearities within
the fibre, and energy consumption by the light sources starts to become a substantial
cost factor1. Optical frequency combs have been suggested to remedy this problem
by generating numerous discrete, equidistant laser lines within a monolithic device;
however, at present their stability and coherence allow them to operate only within
small parameter ranges2,3,4. Here we show that a broadband frequency comb realized
through the electro-optic effect within a high-quality whispering-gallery-mode
resonator can operate at low microwave and optical powers. Unlike the usual third-order
Kerr nonlinear optical frequency combs, our combs rely on the second-order nonlinear
effect, which is much more efficient. Our result uses a fixed microwave signal
that is mixed with an optical-pump signal to generate a coherent frequency comb
with a precisely determined carrier separation. The resonant enhancement enables
us to work with microwave powers that are three orders of magnitude lower than
those in commercially available devices. We emphasize the practical relevance
of our results to high rates of data communication. To circumvent the limitations
imposed by nonlinear effects in optical communication fibres, one has to solve
two problems: to provide a compact and fully integrated, yet high-quality and
coherent, frequency comb generator; and to calculate nonlinear signal propagation
in real time5. We report a solution to the first problem.'
article_processing_charge: No
arxiv: 1
author:
- first_name: Alfredo R
full_name: Rueda Sanchez, Alfredo R
id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87
last_name: Rueda Sanchez
orcid: 0000-0001-6249-5860
- first_name: Florian
full_name: Sedlmeir, Florian
last_name: Sedlmeir
- first_name: Madhuri
full_name: Kumari, Madhuri
last_name: Kumari
- first_name: Gerd
full_name: Leuchs, Gerd
last_name: Leuchs
- first_name: Harald G.L.
full_name: Schwefel, Harald G.L.
last_name: Schwefel
citation:
ama: Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. Resonant electro-optic
frequency comb. Nature. 2019;568(7752):378-381. doi:10.1038/s41586-019-1110-x
apa: Rueda Sanchez, A. R., Sedlmeir, F., Kumari, M., Leuchs, G., & Schwefel,
H. G. L. (2019). Resonant electro-optic frequency comb. Nature. Springer
Nature. https://doi.org/10.1038/s41586-019-1110-x
chicago: Rueda Sanchez, Alfredo R, Florian Sedlmeir, Madhuri Kumari, Gerd Leuchs,
and Harald G.L. Schwefel. “Resonant Electro-Optic Frequency Comb.” Nature.
Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1110-x.
ieee: A. R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, and H. G. L. Schwefel,
“Resonant electro-optic frequency comb,” Nature, vol. 568, no. 7752. Springer
Nature, pp. 378–381, 2019.
ista: Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. 2019. Resonant
electro-optic frequency comb. Nature. 568(7752), 378–381.
mla: Rueda Sanchez, Alfredo R., et al. “Resonant Electro-Optic Frequency Comb.”
Nature, vol. 568, no. 7752, Springer Nature, 2019, pp. 378–81, doi:10.1038/s41586-019-1110-x.
short: A.R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, H.G.L. Schwefel, Nature
568 (2019) 378–381.
date_created: 2019-04-28T21:59:13Z
date_published: 2019-04-18T00:00:00Z
date_updated: 2023-08-25T10:15:25Z
day: '18'
department:
- _id: JoFi
doi: 10.1038/s41586-019-1110-x
external_id:
arxiv:
- '1808.10608'
isi:
- '000464950700053'
intvolume: ' 568'
isi: 1
issue: '7752'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1808.10608
month: '04'
oa: 1
oa_version: Preprint
page: 378-381
publication: Nature
publication_identifier:
eissn:
- '14764687'
issn:
- '00280836'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41586-019-1220-5
scopus_import: '1'
status: public
title: Resonant electro-optic frequency comb
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 568
year: '2019'
...
---
_id: '6351'
abstract:
- lang: eng
text: "A process of restorative patterning in plant roots correctly replaces eliminated
cells to heal local injuries despite the absence of cell migration, which underpins
wound healing in animals. \r\n\r\nPatterning in plants relies on oriented cell
divisions and acquisition of specific cell identities. Plants regularly endure
wounds caused by abiotic or biotic environmental stimuli and have developed extraordinary
abilities to restore their tissues after injuries. Here, we provide insight into
a mechanism of restorative patterning that repairs tissues after wounding. Laser-assisted
elimination of different cells in Arabidopsis root combined with live-imaging
tracking during vertical growth allowed analysis of the regeneration processes
in vivo. Specifically, the cells adjacent to the inner side of the injury re-activated
their stem cell transcriptional programs. They accelerated their progression through
cell cycle, coordinately changed the cell division orientation, and ultimately
acquired de novo the correct cell fates to replace missing cells. These observations
highlight existence of unknown intercellular positional signaling and demonstrate
the capability of specified cells to re-acquire stem cell programs as a crucial
part of the plant-specific mechanism of wound healing."
acknowledged_ssus:
- _id: Bio
article_processing_charge: No
author:
- first_name: Petra
full_name: Marhavá, Petra
id: 44E59624-F248-11E8-B48F-1D18A9856A87
last_name: Marhavá
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
orcid: 0000-0001-8295-2926
- first_name: Saiko
full_name: Yoshida, Saiko
id: 2E46069C-F248-11E8-B48F-1D18A9856A87
last_name: Yoshida
- first_name: Peter
full_name: Marhavy, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. Re-activation
of stem cell pathways for pattern restoration in plant wound healing. Cell.
2019;177(4):957-969.e13. doi:10.1016/j.cell.2019.04.015
apa: Marhavá, P., Hörmayer, L., Yoshida, S., Marhavý, P., Benková, E., & Friml,
J. (2019). Re-activation of stem cell pathways for pattern restoration in plant
wound healing. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.04.015
chicago: Marhavá, Petra, Lukas Hörmayer, Saiko Yoshida, Peter Marhavý, Eva Benková,
and Jiří Friml. “Re-Activation of Stem Cell Pathways for Pattern Restoration in
Plant Wound Healing.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.04.015.
ieee: P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, and J. Friml,
“Re-activation of stem cell pathways for pattern restoration in plant wound healing,”
Cell, vol. 177, no. 4. Elsevier, p. 957–969.e13, 2019.
ista: Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. 2019. Re-activation
of stem cell pathways for pattern restoration in plant wound healing. Cell. 177(4),
957–969.e13.
mla: Marhavá, Petra, et al. “Re-Activation of Stem Cell Pathways for Pattern Restoration
in Plant Wound Healing.” Cell, vol. 177, no. 4, Elsevier, 2019, p. 957–969.e13,
doi:10.1016/j.cell.2019.04.015.
short: P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, J. Friml, Cell
177 (2019) 957–969.e13.
date_created: 2019-04-28T21:59:14Z
date_published: 2019-05-02T00:00:00Z
date_updated: 2024-03-25T23:30:06Z
day: '02'
ddc:
- '570'
department:
- _id: JiFr
- _id: EvBe
doi: 10.1016/j.cell.2019.04.015
ec_funded: 1
external_id:
isi:
- '000466843000015'
pmid:
- '31051107'
file:
- access_level: open_access
checksum: 4ceba04a96a74f5092ec3ce2c579a0c7
content_type: application/pdf
creator: dernst
date_created: 2019-05-13T06:12:45Z
date_updated: 2020-07-14T12:47:28Z
file_id: '6411'
file_name: 2019_Cell_Marhava.pdf
file_size: 10272032
relation: main_file
file_date_updated: 2020-07-14T12:47:28Z
has_accepted_license: '1'
intvolume: ' 177'
isi: 1
issue: '4'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 957-969.e13
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Cell
publication_identifier:
eissn:
- '10974172'
issn:
- '00928674'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/specialized-plant-cells-regain-stem-cell-features-to-heal-wounds/
record:
- id: '9992'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Re-activation of stem cell pathways for pattern restoration in plant wound
healing
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: 177
year: '2019'
...
---
_id: '6352'
abstract:
- lang: eng
text: Chronic overuse of common pharmaceuticals, e.g. acetaminophen (paracetamol),
often leads to the development of acute liver failure (ALF). This study aimed
to elucidate the effect of cultured mesenchymal stem cells (MSCs) proteome on
the onset of liver damage and regeneration dynamics in animals with ALF induced
by acetaminophen, to test the liver protective efficacy of MSCs proteome depending
on the oxygen tension in cell culture, and to blueprint protein components responsible
for the effect. Protein compositions prepared from MSCs cultured in mild hypoxic
(5% and 10% O2) and normal (21% O2) conditions were used to treat ALF induced
in mice by injection of acetaminophen. To test the effect of reduced oxygen tension
in cell culture on resulting MSCs proteome content we applied a combination of
high performance liquid chromatography and mass-spectrometry (LC–MS/MS) for the
identification of proteins in lysates of MSCs cultured at different O2 levels.
The treatment of acetaminophen-administered animals with proteins released from
cultured MSCs resulted in the inhibition of inflammatory reactions in damaged
liver; the area of hepatocyte necrosis being reduced in the first 24 h. Compositions
obtained from MSCs cultured at lower O2 level were shown to be more potent than
a composition prepared from normoxic cells. A comparative characterization of
protein pattern and identification of individual components done by a cytokine
assay and proteomics analysis of protein compositions revealed that even moderate
hypoxia produces discrete changes in the expression of various subsets of proteins
responsible for intracellular respiration and cell signaling. The application
of proteins prepared from MSCs grown in vitro at reduced oxygen tension significantly
accelerates healing process in damaged liver tissue. The proteomics data obtained
for different preparations offer new information about the potential candidates
in the MSCs protein repertoire sensitive to oxygen tension in culture medium,
which can be involved in the generalized mechanisms the cells use to respond to
acute liver failure.
acknowledgement: The studies were supported by the Austrian Federal Ministry of Economy,
Family and Youth through the initiative “Laura Bassi Centres of Expertise” funding
the Center of Optimized Structural Stud-ies, grant No. 253275
article_processing_charge: Yes (via OA deal)
author:
- first_name: Andrey Alexandrovich
full_name: Temnov, Andrey Alexandrovich
last_name: Temnov
- first_name: Konstantin Arkadevich
full_name: Rogov, Konstantin Arkadevich
last_name: Rogov
- first_name: Alla Nikolaevna
full_name: Sklifas, Alla Nikolaevna
last_name: Sklifas
- first_name: Elena Valerievna
full_name: Klychnikova, Elena Valerievna
last_name: Klychnikova
- first_name: Markus
full_name: Hartl, Markus
last_name: Hartl
- first_name: Kristina
full_name: Djinovic-Carugo, Kristina
last_name: Djinovic-Carugo
- first_name: Alexej
full_name: Charnagalov, Alexej
id: 49F06DBA-F248-11E8-B48F-1D18A9856A87
last_name: Charnagalov
citation:
ama: Temnov AA, Rogov KA, Sklifas AN, et al. Protective properties of the cultured
stem cell proteome studied in an animal model of acetaminophen-induced acute liver
failure. Molecular Biology Reports. 2019. doi:10.1007/s11033-019-04765-z
apa: Temnov, A. A., Rogov, K. A., Sklifas, A. N., Klychnikova, E. V., Hartl, M.,
Djinovic-Carugo, K., & Charnagalov, A. (2019). Protective properties of the
cultured stem cell proteome studied in an animal model of acetaminophen-induced
acute liver failure. Molecular Biology Reports. Springer. https://doi.org/10.1007/s11033-019-04765-z
chicago: Temnov, Andrey Alexandrovich, Konstantin Arkadevich Rogov, Alla Nikolaevna
Sklifas, Elena Valerievna Klychnikova, Markus Hartl, Kristina Djinovic-Carugo,
and Alexej Charnagalov. “Protective Properties of the Cultured Stem Cell Proteome
Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” Molecular
Biology Reports. Springer, 2019. https://doi.org/10.1007/s11033-019-04765-z.
ieee: A. A. Temnov et al., “Protective properties of the cultured stem cell
proteome studied in an animal model of acetaminophen-induced acute liver failure,”
Molecular Biology Reports. Springer, 2019.
ista: Temnov AA, Rogov KA, Sklifas AN, Klychnikova EV, Hartl M, Djinovic-Carugo
K, Charnagalov A. 2019. Protective properties of the cultured stem cell proteome
studied in an animal model of acetaminophen-induced acute liver failure. Molecular
Biology Reports.
mla: Temnov, Andrey Alexandrovich, et al. “Protective Properties of the Cultured
Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver
Failure.” Molecular Biology Reports, Springer, 2019, doi:10.1007/s11033-019-04765-z.
short: A.A. Temnov, K.A. Rogov, A.N. Sklifas, E.V. Klychnikova, M. Hartl, K. Djinovic-Carugo,
A. Charnagalov, Molecular Biology Reports (2019).
date_created: 2019-04-28T21:59:14Z
date_published: 2019-04-12T00:00:00Z
date_updated: 2023-08-25T10:14:26Z
day: '12'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1007/s11033-019-04765-z
external_id:
isi:
- '000470332600049'
file:
- access_level: open_access
checksum: 45bf040bbce1cea274f6013fa18ba21b
content_type: application/pdf
creator: dernst
date_created: 2019-04-30T09:52:36Z
date_updated: 2020-07-14T12:47:28Z
file_id: '6362'
file_name: 2019_MolecularBioReport_Temnov.pdf
file_size: 1948014
relation: main_file
file_date_updated: 2020-07-14T12:47:28Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Molecular Biology Reports
publication_identifier:
eissn:
- '15734978'
issn:
- '03014851'
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Protective properties of the cultured stem cell proteome studied in an animal
model of acetaminophen-induced acute liver failure
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
year: '2019'
...
---
_id: '6363'
abstract:
- lang: eng
text: "Distinguishing between similar experiences is achieved by the brain
\ in a process called pattern separation. In the hippocampus, pattern
\ separation reduces the interference of memories and increases the storage
capacity by decorrelating similar inputs patterns of neuronal activity into
\ non-overlapping output firing patterns. Winners-take-all (WTA) mechanism
\ is a theoretical model for pattern separation in which a \"winner\"
\ cell suppresses the activity of the neighboring neurons through feedback
inhibition. However, if the network properties of the dentate gyrus support WTA
as a biologically conceivable model remains unknown. Here, we showed that the
connectivity rules of PV+interneurons and their synaptic properties are optimizedfor
efficient pattern separation. We found using multiple whole-cell in vitrorecordings
that PV+interneurons mainly connect to granule cells (GC) through lateral inhibition,
a form of feedback inhibition in which a GC inhibits other GCs but not
\ itself through the activation of PV+interneurons. Thus, lateral inhibition
between GC–PV+interneurons was ~10 times more abundant than recurrent connections.
Furthermore, the GC–PV+interneuron connectivity was more spatially confined
\ but less abundant than PV+interneurons–GC connectivity, leading to an
\ asymmetrical distribution of excitatory and inhibitory connectivity. Our
network model of the dentate gyrus with incorporated real connectivity rules efficiently
decorrelates neuronal activity patterns using WTA as the primary mechanism.
\ This process relied on lateral inhibition, fast-signaling properties of
\ PV+interneurons and the asymmetrical distribution of excitatory and inhibitory
connectivity. Finally, we found that silencing the activity of PV+interneurons
in vivoleads to acute deficits in discrimination between similar environments,
suggesting that PV+interneuron networks are necessary for behavioral relevant
computations. Our results demonstrate that PV+interneurons possess unique
connectivity and fast signaling properties that confer to the dentate
\ gyrus network properties that allow the emergence of pattern separation. Thus,
our results contribute to the knowledge of how specific forms of network organization
underlie sophisticated types of information processing. \r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: 'Claudia '
full_name: 'Espinoza Martinez, Claudia '
id: 31FFEE2E-F248-11E8-B48F-1D18A9856A87
last_name: Espinoza Martinez
orcid: 0000-0003-4710-2082
citation:
ama: Espinoza Martinez C. Parvalbumin+ interneurons enable efficient pattern separation
in hippocampal microcircuits. 2019. doi:10.15479/AT:ISTA:6363
apa: Espinoza Martinez, C. (2019). Parvalbumin+ interneurons enable efficient
pattern separation in hippocampal microcircuits. Institute of Science and
Technology Austria. https://doi.org/10.15479/AT:ISTA:6363
chicago: Espinoza Martinez, Claudia . “Parvalbumin+ Interneurons Enable Efficient
Pattern Separation in Hippocampal Microcircuits.” Institute of Science and Technology
Austria, 2019. https://doi.org/10.15479/AT:ISTA:6363.
ieee: C. Espinoza Martinez, “Parvalbumin+ interneurons enable efficient pattern
separation in hippocampal microcircuits,” Institute of Science and Technology
Austria, 2019.
ista: Espinoza Martinez C. 2019. Parvalbumin+ interneurons enable efficient pattern
separation in hippocampal microcircuits. Institute of Science and Technology Austria.
mla: Espinoza Martinez, Claudia. Parvalbumin+ Interneurons Enable Efficient Pattern
Separation in Hippocampal Microcircuits. Institute of Science and Technology
Austria, 2019, doi:10.15479/AT:ISTA:6363.
short: C. Espinoza Martinez, Parvalbumin+ Interneurons Enable Efficient Pattern
Separation in Hippocampal Microcircuits, Institute of Science and Technology Austria,
2019.
date_created: 2019-04-30T11:56:10Z
date_published: 2019-04-30T00:00:00Z
date_updated: 2023-09-15T12:03:48Z
day: '30'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: PeJo
doi: 10.15479/AT:ISTA:6363
file:
- access_level: open_access
checksum: 77c6c05cfe8b58c8abcf1b854375d084
content_type: application/pdf
creator: cespinoza
date_created: 2019-05-07T16:00:39Z
date_updated: 2021-02-11T11:17:15Z
embargo: 2020-05-09
file_id: '6389'
file_name: Espinozathesis_all2.pdf
file_size: 13966891
relation: main_file
- access_level: closed
checksum: f6aa819f127691a2b0fc21c76eb09746
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: cespinoza
date_created: 2019-05-07T16:00:48Z
date_updated: 2020-07-14T12:47:28Z
embargo_to: open_access
file_id: '6390'
file_name: Espinoza_Thesis.docx
file_size: 11159900
relation: source_file
file_date_updated: 2021-02-11T11:17:15Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '140'
publication_identifier:
isbn:
- 978-3-99078-000-8
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '21'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
title: Parvalbumin+ interneurons enable efficient pattern separation in hippocampal
microcircuits
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6366'
abstract:
- lang: eng
text: Plants have a remarkable capacity to adjust their growth and development to
elevated ambient temperatures. Increased elongation growth of roots, hypocotyls
and petioles in warm temperatures are hallmarks of seedling thermomorphogenesis.
In the last decade, significant progress has been made to identify the molecular
signaling components regulating these growth responses. Increased ambient temperature
utilizes diverse components of the light sensing and signal transduction network
to trigger growth adjustments. However, it remains unknown whether temperature
sensing and responses are universal processes that occur uniformly in all plant
organs. Alternatively, temperature sensing may be confined to specific tissues
or organs, which would require a systemic signal that mediates responses in distal
parts of the plant. Here we show that Arabidopsis (Arabidopsis thaliana) seedlings
show organ-specific transcriptome responses to elevated temperatures, and that
thermomorphogenesis involves both autonomous and organ-interdependent temperature
sensing and signaling. Seedling roots can sense and respond to temperature in
a shoot-independent manner, whereas shoot temperature responses require both local
and systemic processes. The induction of cell elongation in hypocotyls requires
temperature sensing in cotyledons, followed by generation of a mobile auxin signal.
Subsequently, auxin travels to the hypocotyl where it triggers local brassinosteroid-induced
cell elongation in seedling stems, which depends upon a distinct, permissive temperature
sensor in the hypocotyl.
article_processing_charge: No
article_type: original
author:
- first_name: Julia
full_name: Bellstaedt, Julia
last_name: Bellstaedt
- first_name: Jana
full_name: Trenner, Jana
last_name: Trenner
- first_name: Rebecca
full_name: Lippmann, Rebecca
last_name: Lippmann
- first_name: Yvonne
full_name: Poeschl, Yvonne
last_name: Poeschl
- first_name: Xixi
full_name: Zhang, Xixi
id: 61A66458-47E9-11EA-85BA-8AEAAF14E49A
last_name: Zhang
orcid: 0000-0001-7048-4627
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Marcel
full_name: Quint, Marcel
last_name: Quint
- first_name: Carolin
full_name: Delker, Carolin
last_name: Delker
citation:
ama: Bellstaedt J, Trenner J, Lippmann R, et al. A mobile auxin signal connects
temperature sensing in cotyledons with growth responses in hypocotyls. Plant
Physiology. 2019;180(2):757-766. doi:10.1104/pp.18.01377
apa: Bellstaedt, J., Trenner, J., Lippmann, R., Poeschl, Y., Zhang, X., Friml, J.,
… Delker, C. (2019). A mobile auxin signal connects temperature sensing in cotyledons
with growth responses in hypocotyls. Plant Physiology. ASPB. https://doi.org/10.1104/pp.18.01377
chicago: Bellstaedt, Julia, Jana Trenner, Rebecca Lippmann, Yvonne Poeschl, Xixi
Zhang, Jiří Friml, Marcel Quint, and Carolin Delker. “A Mobile Auxin Signal Connects
Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.” Plant
Physiology. ASPB, 2019. https://doi.org/10.1104/pp.18.01377.
ieee: J. Bellstaedt et al., “A mobile auxin signal connects temperature sensing
in cotyledons with growth responses in hypocotyls,” Plant Physiology, vol.
180, no. 2. ASPB, pp. 757–766, 2019.
ista: Bellstaedt J, Trenner J, Lippmann R, Poeschl Y, Zhang X, Friml J, Quint M,
Delker C. 2019. A mobile auxin signal connects temperature sensing in cotyledons
with growth responses in hypocotyls. Plant Physiology. 180(2), 757–766.
mla: Bellstaedt, Julia, et al. “A Mobile Auxin Signal Connects Temperature Sensing
in Cotyledons with Growth Responses in Hypocotyls.” Plant Physiology, vol.
180, no. 2, ASPB, 2019, pp. 757–66, doi:10.1104/pp.18.01377.
short: J. Bellstaedt, J. Trenner, R. Lippmann, Y. Poeschl, X. Zhang, J. Friml, M.
Quint, C. Delker, Plant Physiology 180 (2019) 757–766.
date_created: 2019-04-30T15:24:22Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-09-05T12:25:19Z
day: '01'
department:
- _id: JiFr
doi: 10.1104/pp.18.01377
external_id:
isi:
- '000470086100019'
pmid:
- '31000634'
intvolume: ' 180'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: www.doi.org/10.1104/pp.18.01377
month: '06'
oa: 1
oa_version: Published Version
page: 757-766
pmid: 1
publication: Plant Physiology
publication_identifier:
eissn:
- 1532-2548
issn:
- 0032-0889
publication_status: published
publisher: ASPB
quality_controlled: '1'
scopus_import: '1'
status: public
title: A mobile auxin signal connects temperature sensing in cotyledons with growth
responses in hypocotyls
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 180
year: '2019'
...
---
_id: '6371'
abstract:
- lang: eng
text: "Decades of studies have revealed the mechanisms of gene regulation in molecular
detail. We make use of such well-described regulatory systems to explore how the
molecular mechanisms of protein-protein and protein-DNA interactions shape the
dynamics and evolution of gene regulation. \r\n\r\ni) We uncover how the biophysics
of protein-DNA binding determines the potential of regulatory networks to evolve
and adapt, which can be captured using a simple mathematical model. \r\nii) The
evolution of regulatory connections can lead to a significant amount of crosstalk
between binding proteins. We explore the effect of crosstalk on gene expression
from a target promoter, which seems to be modulated through binding competition
at non-specific DNA sites. \r\niii) We investigate how the very same biophysical
characteristics as in i) can generate significant fitness costs for cells through
global crosstalk, meaning non-specific DNA binding across the genomic background.
\r\niv) Binding competition between proteins at a target promoter is a prevailing
regulatory feature due to the prevalence of co-regulation at bacterial promoters.
However, the dynamics of these systems are not always straightforward to determine
even if the molecular mechanisms of regulation are known. A detailed model of
the biophysical interactions reveals that interference between the regulatory
proteins can constitute a new, generic form of system memory that records the
history of the input signals at the promoter. \r\n\r\nWe demonstrate how the biophysics
of protein-DNA binding can be harnessed to investigate the principles that shape
and ultimately limit cellular gene regulation. These results provide a basis for
studies of higher-level functionality, which arises from the underlying regulation.
\ \r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Claudia
full_name: Igler, Claudia
id: 46613666-F248-11E8-B48F-1D18A9856A87
last_name: Igler
citation:
ama: Igler C. On the nature of gene regulatory design - The biophysics of transcription
factor binding shapes gene regulation. 2019. doi:10.15479/AT:ISTA:6371
apa: Igler, C. (2019). On the nature of gene regulatory design - The biophysics
of transcription factor binding shapes gene regulation. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:6371
chicago: Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics
of Transcription Factor Binding Shapes Gene Regulation.” Institute of Science
and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6371.
ieee: C. Igler, “On the nature of gene regulatory design - The biophysics of transcription
factor binding shapes gene regulation,” Institute of Science and Technology Austria,
2019.
ista: Igler C. 2019. On the nature of gene regulatory design - The biophysics of
transcription factor binding shapes gene regulation. Institute of Science and
Technology Austria.
mla: Igler, Claudia. On the Nature of Gene Regulatory Design - The Biophysics
of Transcription Factor Binding Shapes Gene Regulation. Institute of Science
and Technology Austria, 2019, doi:10.15479/AT:ISTA:6371.
short: C. Igler, On the Nature of Gene Regulatory Design - The Biophysics of Transcription
Factor Binding Shapes Gene Regulation, Institute of Science and Technology Austria,
2019.
date_created: 2019-05-03T11:55:51Z
date_published: 2019-05-03T00:00:00Z
date_updated: 2024-02-21T13:45:52Z
day: '03'
ddc:
- '576'
- '579'
degree_awarded: PhD
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:6371
file:
- access_level: open_access
checksum: c0085d47c58c9cbcab1b0a783480f6da
content_type: application/pdf
creator: cigler
date_created: 2019-05-03T11:54:52Z
date_updated: 2021-02-11T11:17:13Z
embargo: 2020-05-02
file_id: '6373'
file_name: IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf
file_size: 12597663
relation: main_file
- access_level: closed
checksum: 2eac954de1c8bbf7e6fb35ed0221ae8c
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: cigler
date_created: 2019-05-03T11:54:54Z
date_updated: 2020-07-14T12:47:28Z
embargo_to: open_access
file_id: '6374'
file_name: IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx
file_size: 34644426
relation: source_file
file_date_updated: 2021-02-11T11:17:13Z
has_accepted_license: '1'
keyword:
- gene regulation
- biophysics
- transcription factor binding
- bacteria
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '152'
project:
- _id: 251EE76E-B435-11E9-9278-68D0E5697425
grant_number: '24573'
name: Design principles underlying genetic switch architecture (DOC Fellowship)
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '67'
relation: part_of_dissertation
status: public
- id: '5585'
relation: popular_science
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: On the nature of gene regulatory design - The biophysics of transcription factor
binding shapes gene regulation
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6378'
abstract:
- lang: eng
text: 'In today''s cryptocurrencies, Hashcash proof of work is the most commonly-adopted
approach to mining. In Hashcash, when a miner decides to add a block to the chain,
she has to solve the difficult computational puzzle of inverting a hash function.
While Hashcash has been successfully adopted in both Bitcoin and Ethereum, it
has attracted significant and harsh criticism due to its massive waste of electricity,
its carbon footprint and environmental effects, and the inherent lack of usefulness
in inverting a hash function. Various other mining protocols have been suggested,
including proof of stake, in which a miner''s chance of adding the next block
is proportional to her current balance. However, such protocols lead to a higher
entry cost for new miners who might not still have any stake in the cryptocurrency,
and can in the worst case lead to an oligopoly, where the rich have complete control
over mining. In this paper, we propose Hybrid Mining: a new mining protocol that
combines solving real-world useful problems with Hashcash. Our protocol allows
new miners to join the network by taking part in Hashcash mining without having
to own an initial stake. It also allows nodes of the network to submit hard computational
problems whose solutions are of interest in the real world, e.g.~protein folding
problems. Then, miners can choose to compete in solving these problems, in lieu
of Hashcash, for adding a new block. Hence, Hybrid Mining incentivizes miners
to solve useful problems, such as hard computational problems arising in biology,
in a distributed manner. It also gives researchers in other areas an easy-to-use
tool to outsource their hard computations to the blockchain network, which has
enormous computational power, by paying a reward to the miner who solves the problem
for them. Moreover, our protocol provides strong security guarantees and is at
least as resilient to double spending as Bitcoin.'
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 Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Arash
full_name: Pourdamghani, Arash
last_name: Pourdamghani
citation:
ama: 'Chatterjee K, Goharshady AK, Pourdamghani A. Hybrid Mining: Exploiting blockchain’s
computational power for distributed problem solving. In: Proceedings of the
34th ACM Symposium on Applied Computing. Vol Part F147772. ACM; 2019:374-381.
doi:10.1145/3297280.3297319'
apa: 'Chatterjee, K., Goharshady, A. K., & Pourdamghani, A. (2019). Hybrid Mining:
Exploiting blockchain’s computational power for distributed problem solving. In
Proceedings of the 34th ACM Symposium on Applied Computing (Vol. Part F147772,
pp. 374–381). Limassol, Cyprus: ACM. https://doi.org/10.1145/3297280.3297319'
chicago: 'Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Arash Pourdamghani.
“Hybrid Mining: Exploiting Blockchain’s Computational Power for Distributed Problem
Solving.” In Proceedings of the 34th ACM Symposium on Applied Computing,
Part F147772:374–81. ACM, 2019. https://doi.org/10.1145/3297280.3297319.'
ieee: 'K. Chatterjee, A. K. Goharshady, and A. Pourdamghani, “Hybrid Mining: Exploiting
blockchain’s computational power for distributed problem solving,” in Proceedings
of the 34th ACM Symposium on Applied Computing, Limassol, Cyprus, 2019, vol.
Part F147772, pp. 374–381.'
ista: 'Chatterjee K, Goharshady AK, Pourdamghani A. 2019. Hybrid Mining: Exploiting
blockchain’s computational power for distributed problem solving. Proceedings
of the 34th ACM Symposium on Applied Computing. ACM Symposium on Applied Computing
vol. Part F147772, 374–381.'
mla: 'Chatterjee, Krishnendu, et al. “Hybrid Mining: Exploiting Blockchain’s Computational
Power for Distributed Problem Solving.” Proceedings of the 34th ACM Symposium
on Applied Computing, vol. Part F147772, ACM, 2019, pp. 374–81, doi:10.1145/3297280.3297319.'
short: K. Chatterjee, A.K. Goharshady, A. Pourdamghani, in:, Proceedings of the
34th ACM Symposium on Applied Computing, ACM, 2019, pp. 374–381.
conference:
end_date: 2019-04-12
location: Limassol, Cyprus
name: ACM Symposium on Applied Computing
start_date: 2019-04-08
date_created: 2019-05-06T12:11:36Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2025-06-02T08:53:46Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.1145/3297280.3297319
ec_funded: 1
external_id:
isi:
- '000474685800049'
file:
- access_level: open_access
checksum: fbfbcd5a0c7a743862bfc3045539a614
content_type: application/pdf
creator: dernst
date_created: 2019-05-06T12:09:27Z
date_updated: 2020-07-14T12:47:29Z
file_id: '6379'
file_name: 2019_ACM_Chatterjee.pdf
file_size: 1023934
relation: main_file
file_date_updated: 2020-07-14T12:47:29Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 374-381
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _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
publication: Proceedings of the 34th ACM Symposium on Applied Computing
publication_identifier:
isbn:
- '9781450359337'
publication_status: published
publisher: ACM
pubrep_id: '1069'
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Hybrid Mining: Exploiting blockchain’s computational power for distributed
problem solving'
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: Part F147772
year: '2019'
...
---
_id: '6380'
abstract:
- lang: eng
text: 'There is a huge gap between the speeds of modern caches and main memories,
and therefore cache misses account for a considerable loss of efficiency in programs.
The predominant technique to address this issue has been Data Packing: data elements
that are frequently accessed within time proximity are packed into the same cache
block, thereby minimizing accesses to the main memory. We consider the algorithmic
problem of Data Packing on a two-level memory system. Given a reference sequence
R of accesses to data elements, the task is to partition the elements into cache
blocks such that the number of cache misses on R is minimized. The problem is
notoriously difficult: it is NP-hard even when the cache has size 1, and is hard
to approximate for any cache size larger than 4. Therefore, all existing techniques
for Data Packing are based on heuristics and lack theoretical guarantees. In this
work, we present the first positive theoretical results for Data Packing, along
with new and stronger negative results. We consider the problem under the lens
of the underlying access hypergraphs, which are hypergraphs of affinities between
the data elements, where the order of an access hypergraph corresponds to the
size of the affinity group. We study the problem parameterized by the treewidth
of access hypergraphs, which is a standard notion in graph theory to measure the
closeness of a graph to a tree. Our main results are as follows: We show there
is a number q* depending on the cache parameters such that (a) if the access hypergraph
of order q* has constant treewidth, then there is a linear-time algorithm for
Data Packing; (b)the Data Packing problem remains NP-hard even if the access hypergraph
of order q*-1 has constant treewidth. Thus, we establish a fine-grained dichotomy
depending on a single parameter, namely, the highest order among access hypegraphs
that have constant treewidth; and establish the optimal value q* of this parameter.
Finally, we present an experimental evaluation of a prototype implementation of
our algorithm. Our results demonstrate that, in practice, access hypergraphs of
many commonly-used algorithms have small treewidth. We compare our approach with
several state-of-the-art heuristic-based algorithms and show that our algorithm
leads to significantly fewer cache-misses. '
article_number: '53'
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 Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Nastaran
full_name: Okati, Nastaran
last_name: Okati
- 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, Goharshady AK, Okati N, Pavlogiannis A. Efficient parameterized
algorithms for data packing. Proceedings of the ACM on Programming Languages.
2019;3(POPL). doi:10.1145/3290366
apa: Chatterjee, K., Goharshady, A. K., Okati, N., & Pavlogiannis, A. (2019).
Efficient parameterized algorithms for data packing. Proceedings of the ACM
on Programming Languages. ACM. https://doi.org/10.1145/3290366
chicago: Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Nastaran Okati, and Andreas
Pavlogiannis. “Efficient Parameterized Algorithms for Data Packing.” Proceedings
of the ACM on Programming Languages. ACM, 2019. https://doi.org/10.1145/3290366.
ieee: K. Chatterjee, A. K. Goharshady, N. Okati, and A. Pavlogiannis, “Efficient
parameterized algorithms for data packing,” Proceedings of the ACM on Programming
Languages, vol. 3, no. POPL. ACM, 2019.
ista: Chatterjee K, Goharshady AK, Okati N, Pavlogiannis A. 2019. Efficient parameterized
algorithms for data packing. Proceedings of the ACM on Programming Languages.
3(POPL), 53.
mla: Chatterjee, Krishnendu, et al. “Efficient Parameterized Algorithms for Data
Packing.” Proceedings of the ACM on Programming Languages, vol. 3, no.
POPL, 53, ACM, 2019, doi:10.1145/3290366.
short: K. Chatterjee, A.K. Goharshady, N. Okati, A. Pavlogiannis, Proceedings of
the ACM on Programming Languages 3 (2019).
date_created: 2019-05-06T12:18:17Z
date_published: 2019-01-01T00:00:00Z
date_updated: 2024-03-25T23:30:18Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.1145/3290366
ec_funded: 1
file:
- access_level: open_access
checksum: c157752f96877b36685ad7063ada4524
content_type: application/pdf
creator: dernst
date_created: 2019-05-06T12:23:11Z
date_updated: 2020-07-14T12:47:29Z
file_id: '6381'
file_name: 2019_ACM_POPL_Chatterjee.pdf
file_size: 1294962
relation: main_file
file_date_updated: 2020-07-14T12:47:29Z
has_accepted_license: '1'
intvolume: ' 3'
issue: POPL
language:
- iso: eng
month: '01'
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: 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 ACM on Programming Languages
publication_identifier:
issn:
- 2475-1421
publication_status: published
publisher: ACM
pubrep_id: '1056'
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
status: public
title: Efficient parameterized algorithms for data packing
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2019'
...