---
_id: '2443'
abstract:
- lang: eng
text: The mode of action of auxin is based on its non-uniform distribution within
tissues and organs. Despite the wide use of several auxin analogues in research
and agriculture, little is known about the specificity of different auxin-related
transport and signalling processes towards these compounds. Using seedlings of
Arabidopsis thaliana and suspension-cultured cells of Nicotiana tabacum (BY-2),
the physiological activity of several auxin analogues was investigated, together
with their capacity to induce auxin-dependent gene expression, to inhibit endocytosis
and to be transported across the plasma membrane. This study shows that the specificity
criteria for different auxin-related processes vary widely. Notably, the special
behaviour of some synthetic auxin analogues suggests that they might be useful
tools in investigations of the molecular mechanism of auxin action. Thus, due
to their differential stimulatory effects on DR5 expression, indole-3-propionic
(IPA) and 2,4,5-trichlorophenoxy acetic (2,4,5-T) acids can serve in studies of
TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALLING F-BOX (TIR1/AFB)-mediated auxin
signalling, and 5-fluoroindole-3-acetic acid (5-F-IAA) can help to discriminate
between transcriptional and non-transcriptional pathways of auxin signalling.
The results demonstrate that the major determinants for the auxin-like physiological
potential of a particular compound are very complex and involve its chemical and
metabolic stability, its ability to distribute in tissues in a polar manner and
its activity towards auxin signalling machinery.
acknowledgement: The authors thank Dr Christian Luschnig (University of Natural Resources
and Life Sciences (BOKU), Vienna, Austria) for the anti-PIN2 antibody, Professor
Mark Estelle (University of California, San Diego, CA, USA) for tir1-1 mutant seeds
and, last but not least, to Dr David Morris for critical reading of the manuscript.
We also thank Markéta Pařezová and Jana Stýblová for excellent technical assistance.
This work was supported by the Grant Agency of the Czech Republic (P305/11/0797
to E.Z. and 13-40637S to J.F.), the Central European Institute of Technology project
CZ.1.05/1.1.00/02.0068 from the European Regional Development Fund and by a European
Research Council starting independent research grant ERC-2011-StG-20101109-PSDP
(to J.F.).
article_processing_charge: No
article_type: original
author:
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Martin
full_name: Kubeš, Martin
last_name: Kubeš
- first_name: Pawel
full_name: Baster, Pawel
id: 3028BD74-F248-11E8-B48F-1D18A9856A87
last_name: Baster
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Petre
full_name: Dobrev, Petre
last_name: Dobrev
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
citation:
ama: 'Simon S, Kubeš M, Baster P, et al. Defining the selectivity of processes along
the auxin response chain: A study using auxin analogues. New Phytologist.
2013;200(4):1034-1048. doi:10.1111/nph.12437'
apa: 'Simon, S., Kubeš, M., Baster, P., Robert, S., Dobrev, P., Friml, J., … Zažímalová,
E. (2013). Defining the selectivity of processes along the auxin response chain:
A study using auxin analogues. New Phytologist. Wiley. https://doi.org/10.1111/nph.12437'
chicago: 'Simon, Sibu, Martin Kubeš, Pawel Baster, Stéphanie Robert, Petre Dobrev,
Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Defining the Selectivity of Processes
along the Auxin Response Chain: A Study Using Auxin Analogues.” New Phytologist.
Wiley, 2013. https://doi.org/10.1111/nph.12437.'
ieee: 'S. Simon et al., “Defining the selectivity of processes along the
auxin response chain: A study using auxin analogues,” New Phytologist,
vol. 200, no. 4. Wiley, pp. 1034–1048, 2013.'
ista: 'Simon S, Kubeš M, Baster P, Robert S, Dobrev P, Friml J, Petrášek J, Zažímalová
E. 2013. Defining the selectivity of processes along the auxin response chain:
A study using auxin analogues. New Phytologist. 200(4), 1034–1048.'
mla: 'Simon, Sibu, et al. “Defining the Selectivity of Processes along the Auxin
Response Chain: A Study Using Auxin Analogues.” New Phytologist, vol. 200,
no. 4, Wiley, 2013, pp. 1034–48, doi:10.1111/nph.12437.'
short: S. Simon, M. Kubeš, P. Baster, S. Robert, P. Dobrev, J. Friml, J. Petrášek,
E. Zažímalová, New Phytologist 200 (2013) 1034–1048.
date_created: 2018-12-11T11:57:41Z
date_published: 2013-12-01T00:00:00Z
date_updated: 2025-09-29T14:15:18Z
day: '01'
department:
- _id: JiFr
doi: 10.1111/nph.12437
ec_funded: 1
external_id:
isi:
- '000330955300012'
intvolume: ' 200'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/nph.12437
month: '12'
oa: 1
oa_version: Published Version
page: 1034 - 1048
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: New Phytologist
publication_status: published
publisher: Wiley
publist_id: '4460'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Defining the selectivity of processes along the auxin response chain: A study
using auxin analogues'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 200
year: '2013'
...
---
_id: '2444'
abstract:
- lang: eng
text: 'We consider two core algorithmic problems for probabilistic verification:
the maximal end-component decomposition and the almost-sure reachability set computation
for Markov decision processes (MDPs). For MDPs with treewidth k, we present two
improved static algorithms for both the problems that run in time O(n·k 2.38·2k
) and O(m·logn· k), respectively, where n is the number of states and m is the
number of edges, significantly improving the previous known O(n·k·√n· k) bound
for low treewidth. We also present decremental algorithms for both problems for
MDPs with constant treewidth that run in amortized logarithmic time, which is
a huge improvement over the previously known algorithms that require amortized
linear time.'
alternative_title:
- LNCS
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Jakub
full_name: Ła̧Cki, Jakub
last_name: Ła̧Cki
citation:
ama: Chatterjee K, Ła̧Cki J. Faster algorithms for Markov decision processes with
low treewidth. 2013;8044:543-558. doi:10.1007/978-3-642-39799-8_36
apa: 'Chatterjee, K., & Ła̧Cki, J. (2013). Faster algorithms for Markov decision
processes with low treewidth. Presented at the CAV: Computer Aided Verification,
St. Petersburg, Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_36'
chicago: Chatterjee, Krishnendu, and Jakub Ła̧Cki. “Faster Algorithms for Markov
Decision Processes with Low Treewidth.” Lecture Notes in Computer Science. Springer,
2013. https://doi.org/10.1007/978-3-642-39799-8_36.
ieee: K. Chatterjee and J. Ła̧Cki, “Faster algorithms for Markov decision processes
with low treewidth,” vol. 8044. Springer, pp. 543–558, 2013.
ista: Chatterjee K, Ła̧Cki J. 2013. Faster algorithms for Markov decision processes
with low treewidth. 8044, 543–558.
mla: Chatterjee, Krishnendu, and Jakub Ła̧Cki. Faster Algorithms for Markov Decision
Processes with Low Treewidth. Vol. 8044, Springer, 2013, pp. 543–58, doi:10.1007/978-3-642-39799-8_36.
short: K. Chatterjee, J. Ła̧Cki, 8044 (2013) 543–558.
conference:
end_date: 2013-07-19
location: St. Petersburg, Russia
name: 'CAV: Computer Aided Verification'
start_date: 2013-07-13
date_created: 2018-12-11T11:57:42Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2020-08-11T10:09:47Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-642-39799-8_36
ec_funded: 1
external_id:
arxiv:
- '1304.0084'
intvolume: ' 8044'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1304.0084
month: '07'
oa: 1
oa_version: Preprint
page: 543 - 558
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Springer
publist_id: '4459'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Faster algorithms for Markov decision processes with low treewidth
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8044
year: '2013'
...
---
_id: '2446'
abstract:
- lang: eng
text: The model-checking problem for probabilistic systems crucially relies on the
translation of LTL to deterministic Rabin automata (DRW). Our recent Safraless
translation [KE12, GKE12] for the LTL(F,G) fragment produces smaller automata
as compared to the traditional approach. In this work, instead of DRW we consider
deterministic automata with acceptance condition given as disjunction of generalized
Rabin pairs (DGRW). The Safraless translation of LTL(F,G) formulas to DGRW results
in smaller automata as compared to DRW. We present algorithms for probabilistic
model-checking as well as game solving for DGRW conditions. Our new algorithms
lead to improvement both in terms of theoretical bounds as well as practical evaluation.
We compare PRISM with and without our new translation, and show that the new translation
leads to significant improvements.
alternative_title:
- LNCS
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Gaiser, Andreas
last_name: Gaiser
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
citation:
ama: Chatterjee K, Gaiser A, Kretinsky J. Automata with generalized Rabin pairs
for probabilistic model checking and LTL synthesis. 2013;8044:559-575. doi:10.1007/978-3-642-39799-8_37
apa: 'Chatterjee, K., Gaiser, A., & Kretinsky, J. (2013). Automata with generalized
Rabin pairs for probabilistic model checking and LTL synthesis. Presented at the
CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_37'
chicago: Chatterjee, Krishnendu, Andreas Gaiser, and Jan Kretinsky. “Automata with
Generalized Rabin Pairs for Probabilistic Model Checking and LTL Synthesis.” Lecture
Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-39799-8_37.
ieee: K. Chatterjee, A. Gaiser, and J. Kretinsky, “Automata with generalized Rabin
pairs for probabilistic model checking and LTL synthesis,” vol. 8044. Springer,
pp. 559–575, 2013.
ista: Chatterjee K, Gaiser A, Kretinsky J. 2013. Automata with generalized Rabin
pairs for probabilistic model checking and LTL synthesis. 8044, 559–575.
mla: Chatterjee, Krishnendu, et al. Automata with Generalized Rabin Pairs for
Probabilistic Model Checking and LTL Synthesis. Vol. 8044, Springer, 2013,
pp. 559–75, doi:10.1007/978-3-642-39799-8_37.
short: K. Chatterjee, A. Gaiser, J. Kretinsky, 8044 (2013) 559–575.
conference:
end_date: 2013-07-19
location: St. Petersburg, Russia
name: 'CAV: Computer Aided Verification'
start_date: 2013-07-13
date_created: 2018-12-11T11:57:42Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2020-08-11T10:09:47Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-642-39799-8_37
ec_funded: 1
external_id:
arxiv:
- '1304.5281'
intvolume: ' 8044'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1304.5281
month: '07'
oa: 1
oa_version: Preprint
page: 559 - 575
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Springer
publist_id: '4457'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Automata with generalized Rabin pairs for probabilistic model checking and
LTL synthesis
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8044
year: '2013'
...
---
_id: '2447'
abstract:
- lang: eng
text: "Separation logic (SL) has gained widespread popularity because of its ability
to succinctly express complex invariants of a program’s heap configurations. Several
specialized provers have been developed for decidable SL fragments. However, these
provers cannot be easily extended or combined with solvers for other theories
that are important in program verification, e.g., linear arithmetic. In this paper,
we present a reduction of decidable SL fragments to a decidable first-order theory
that fits well into the satisfiability modulo theories (SMT) framework. We show
how to use this reduction to automate satisfiability, entailment, frame inference,
and abduction problems for separation logic using SMT solvers. Our approach provides
a simple method of integrating separation logic into existing verification tools
that provide SMT backends, and an elegant way of combining SL fragments with other
decidable first-order theories. We implemented this approach in a verification
tool and applied it to heap-manipulating programs whose verification involves
reasoning in theory combinations.\r\n"
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Ruzica
full_name: Piskac, Ruzica
last_name: Piskac
- first_name: Thomas
full_name: Wies, Thomas
id: 447BFB88-F248-11E8-B48F-1D18A9856A87
last_name: Wies
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
citation:
ama: Piskac R, Wies T, Zufferey D. Automating separation logic using SMT. 2013;8044:773-789.
doi:10.1007/978-3-642-39799-8_54
apa: 'Piskac, R., Wies, T., & Zufferey, D. (2013). Automating separation logic
using SMT. Presented at the CAV: Computer Aided Verification, St. Petersburg,
Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_54'
chicago: Piskac, Ruzica, Thomas Wies, and Damien Zufferey. “Automating Separation
Logic Using SMT.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-39799-8_54.
ieee: R. Piskac, T. Wies, and D. Zufferey, “Automating separation logic using SMT,”
vol. 8044. Springer, pp. 773–789, 2013.
ista: Piskac R, Wies T, Zufferey D. 2013. Automating separation logic using SMT.
8044, 773–789.
mla: Piskac, Ruzica, et al. Automating Separation Logic Using SMT. Vol. 8044,
Springer, 2013, pp. 773–89, doi:10.1007/978-3-642-39799-8_54.
short: R. Piskac, T. Wies, D. Zufferey, 8044 (2013) 773–789.
conference:
end_date: 2013-07-19
location: St. Petersburg, Russia
name: 'CAV: Computer Aided Verification'
start_date: 2013-07-13
date_created: 2018-12-11T11:57:43Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2020-08-11T10:09:47Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-642-39799-8_54
file:
- access_level: open_access
checksum: 2e866932ab688f47ecd504acb4d5c7d4
content_type: application/pdf
creator: dernst
date_created: 2020-05-15T11:13:01Z
date_updated: 2020-07-14T12:45:41Z
file_id: '7859'
file_name: 2013_CAV_Piskac.pdf
file_size: 309182
relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 8044'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 773 - 789
publication_status: published
publisher: Springer
publist_id: '4456'
quality_controlled: '1'
scopus_import: 1
series_title: Lecture Notes in Computer Science
status: public
title: Automating separation logic using SMT
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8044
year: '2013'
...
---
_id: '2448'
abstract:
- lang: eng
text: Cell-to-cell directional flow of the phytohormone auxin is primarily established
by polar localization of the PIN auxin transporters, a process tightly regulated
at multiple levels by auxin itself. We recently reported that, in the context
of strong auxin flows, activity of the vacuolar ZIFL1.1 transporter is required
for fine-tuning of polar auxin transport rates in the Arabidopsis root. In particular,
ZIFL1.1 function protects plasma-membrane stability of the PIN2 carrier in epidermal
root tip cells under conditions normally triggering PIN2 degradation. Here, we
show that ZIFL1.1 activity at the root tip also promotes PIN1 plasma-membrane
abundance in central cylinder cells, thus supporting the notion that ZIFL1.1 acts
as a general positive modulator of polar auxin transport in roots.
article_number: e25688
article_processing_charge: No
article_type: original
author:
- first_name: Estelle
full_name: Remy, Estelle
last_name: Remy
- first_name: Pawel
full_name: Baster, Pawel
id: 3028BD74-F248-11E8-B48F-1D18A9856A87
last_name: Baster
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Paula
full_name: Duque, Paula
last_name: Duque
citation:
ama: Remy E, Baster P, Friml J, Duque P. ZIFL1.1 transporter modulates polar auxin
transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root
tip. Plant Signaling & Behavior. 2013;8(10). doi:10.4161/psb.25688
apa: Remy, E., Baster, P., Friml, J., & Duque, P. (2013). ZIFL1.1 transporter
modulates polar auxin transport by stabilizing membrane abundance of multiple
PINs in Arabidopsis root tip. Plant Signaling & Behavior. Taylor &
Francis. https://doi.org/10.4161/psb.25688
chicago: Remy, Estelle, Pawel Baster, Jiří Friml, and Paula Duque. “ZIFL1.1 Transporter
Modulates Polar Auxin Transport by Stabilizing Membrane Abundance of Multiple
PINs in Arabidopsis Root Tip.” Plant Signaling & Behavior. Taylor &
Francis, 2013. https://doi.org/10.4161/psb.25688.
ieee: E. Remy, P. Baster, J. Friml, and P. Duque, “ZIFL1.1 transporter modulates
polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis
root tip,” Plant Signaling & Behavior, vol. 8, no. 10. Taylor &
Francis, 2013.
ista: Remy E, Baster P, Friml J, Duque P. 2013. ZIFL1.1 transporter modulates polar
auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis
root tip. Plant Signaling & Behavior. 8(10), e25688.
mla: Remy, Estelle, et al. “ZIFL1.1 Transporter Modulates Polar Auxin Transport
by Stabilizing Membrane Abundance of Multiple PINs in Arabidopsis Root Tip.” Plant
Signaling & Behavior, vol. 8, no. 10, e25688, Taylor & Francis, 2013,
doi:10.4161/psb.25688.
short: E. Remy, P. Baster, J. Friml, P. Duque, Plant Signaling & Behavior 8
(2013).
date_created: 2018-12-11T11:57:43Z
date_published: 2013-07-10T00:00:00Z
date_updated: 2025-04-15T07:48:02Z
day: '10'
department:
- _id: JiFr
doi: 10.4161/psb.25688
ec_funded: 1
external_id:
pmid:
- '23857365'
intvolume: ' 8'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4091088/
month: '07'
oa: 1
oa_version: Submitted Version
pmid: 1
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Plant Signaling & Behavior
publication_status: published
publisher: Taylor & Francis
publist_id: '4455'
quality_controlled: '1'
scopus_import: '1'
status: public
title: ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane
abundance of multiple PINs in Arabidopsis root tip
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2013'
...
---
_id: '2449'
abstract:
- lang: eng
text: 'Intracellular protein routing is mediated by vesicular transport which is
tightly regulated in eukaryotes. The protein and lipid homeostasis depends on
coordinated delivery of de novo synthesized or recycled cargoes to the plasma
membrane by exocytosis and their subsequent removal by rerouting them for recycling
or degradation. Here, we report the characterization of protein affected trafficking
3 (pat3) mutant that we identified by an epifluorescence-based forward genetic
screen for mutants defective in subcellular distribution of Arabidopsis auxin
transporter PIN1–GFP. While pat3 displays largely normal plant morphology and
development in nutrient-rich conditions, it shows strong ectopic intracellular
accumulations of different plasma membrane cargoes in structures that resemble
prevacuolar compartments (PVC) with an aberrant morphology. Genetic mapping revealed
that pat3 is defective in vacuolar protein sorting 35A (VPS35A), a putative subunit
of the retromer complex that mediates retrograde trafficking between the PVC and
trans-Golgi network. Similarly, a mutant defective in another retromer subunit,
vps29, shows comparable subcellular defects in PVC morphology and protein accumulation.
Thus, our data provide evidence that the retromer components VPS35A and VPS29
are essential for normal PVC morphology and normal trafficking of plasma membrane
proteins in plants. In addition, we show that, out of the three VPS35 retromer
subunits present in Arabidopsis thaliana genome, the VPS35 homolog A plays a prevailing
role in trafficking to the lytic vacuole, presenting another level of complexity
in the retromer-dependent vacuolar sorting. '
article_processing_charge: No
author:
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Murguel
full_name: Feraru, Murguel
last_name: Feraru
- first_name: Sibylle
full_name: Hirsch, Sibylle
last_name: Hirsch
- first_name: Riet
full_name: De Rycke, Riet
last_name: De Rycke
- first_name: Claudiu
full_name: Nicuales, Claudiu
last_name: Nicuales
- first_name: Jelle
full_name: Van Leene, Jelle
last_name: Van Leene
- first_name: Geert
full_name: De Jaeger, Geert
last_name: De Jaeger
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Nodzyński T, Feraru M, Hirsch S, et al. Retromer subunits VPS35A and VPS29
mediate prevacuolar compartment (PVC) function in Arabidopsis. Molecular Plant.
2013;6(6):1849-1862. doi:10.1093/mp/sst044
apa: Nodzyński, T., Feraru, M., Hirsch, S., De Rycke, R., Nicuales, C., Van Leene,
J., … Friml, J. (2013). Retromer subunits VPS35A and VPS29 mediate prevacuolar
compartment (PVC) function in Arabidopsis. Molecular Plant. Cell Press.
https://doi.org/10.1093/mp/sst044
chicago: Nodzyński, Tomasz, Murguel Feraru, Sibylle Hirsch, Riet De Rycke, Claudiu
Nicuales, Jelle Van Leene, Geert De Jaeger, Steffen Vanneste, and Jiří Friml.
“Retromer Subunits VPS35A and VPS29 Mediate Prevacuolar Compartment (PVC) Function
in Arabidopsis.” Molecular Plant. Cell Press, 2013. https://doi.org/10.1093/mp/sst044.
ieee: T. Nodzyński et al., “Retromer subunits VPS35A and VPS29 mediate prevacuolar
compartment (PVC) function in Arabidopsis,” Molecular Plant, vol. 6, no.
6. Cell Press, pp. 1849–1862, 2013.
ista: Nodzyński T, Feraru M, Hirsch S, De Rycke R, Nicuales C, Van Leene J, De Jaeger
G, Vanneste S, Friml J. 2013. Retromer subunits VPS35A and VPS29 mediate prevacuolar
compartment (PVC) function in Arabidopsis. Molecular Plant. 6(6), 1849–1862.
mla: Nodzyński, Tomasz, et al. “Retromer Subunits VPS35A and VPS29 Mediate Prevacuolar
Compartment (PVC) Function in Arabidopsis.” Molecular Plant, vol. 6, no.
6, Cell Press, 2013, pp. 1849–62, doi:10.1093/mp/sst044.
short: T. Nodzyński, M. Feraru, S. Hirsch, R. De Rycke, C. Nicuales, J. Van Leene,
G. De Jaeger, S. Vanneste, J. Friml, Molecular Plant 6 (2013) 1849–1862.
corr_author: '1'
date_created: 2018-12-11T11:57:44Z
date_published: 2013-11-01T00:00:00Z
date_updated: 2025-09-29T14:14:22Z
day: '01'
department:
- _id: JiFr
doi: 10.1093/mp/sst044
external_id:
isi:
- '000327541200010'
intvolume: ' 6'
isi: 1
issue: '6'
language:
- iso: eng
month: '11'
oa_version: None
page: 1849 - 1862
publication: Molecular Plant
publication_status: published
publisher: Cell Press
publist_id: '4454'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function
in Arabidopsis
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 6
year: '2013'
...
---
_id: '245'
abstract:
- lang: eng
text: For given non-zero integers a, b, q we investigate the density of solutions
(x; y) ∈ ℤ2 to the binary cubic congruence ax2 + by3 ≡ 0 mod q, and use it to
establish the Manin conjecture for a singular del Pezzo surface of degree 2 defined
over ℚ.
author:
- first_name: Stephan
full_name: Baier, Stephan
last_name: Baier
- first_name: Timothy D
full_name: Timothy Browning
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
citation:
ama: Baier S, Browning TD. Inhomogeneous cubic congruences and rational points on
del Pezzo surfaces. Journal fur die Reine und Angewandte Mathematik. 2013;(680):69-151.
doi:10.1515/crelle.2012.039
apa: Baier, S., & Browning, T. D. (2013). Inhomogeneous cubic congruences and
rational points on del Pezzo surfaces. Journal Fur Die Reine Und Angewandte
Mathematik. Walter de Gruyter. https://doi.org/10.1515/crelle.2012.039
chicago: Baier, Stephan, and Timothy D Browning. “Inhomogeneous Cubic Congruences
and Rational Points on Del Pezzo Surfaces.” Journal Fur Die Reine Und Angewandte
Mathematik. Walter de Gruyter, 2013. https://doi.org/10.1515/crelle.2012.039.
ieee: S. Baier and T. D. Browning, “Inhomogeneous cubic congruences and rational
points on del Pezzo surfaces,” Journal fur die Reine und Angewandte Mathematik,
no. 680. Walter de Gruyter, pp. 69–151, 2013.
ista: Baier S, Browning TD. 2013. Inhomogeneous cubic congruences and rational points
on del Pezzo surfaces. Journal fur die Reine und Angewandte Mathematik. (680),
69–151.
mla: Baier, Stephan, and Timothy D. Browning. “Inhomogeneous Cubic Congruences and
Rational Points on Del Pezzo Surfaces.” Journal Fur Die Reine Und Angewandte
Mathematik, no. 680, Walter de Gruyter, 2013, pp. 69–151, doi:10.1515/crelle.2012.039.
short: S. Baier, T.D. Browning, Journal Fur Die Reine Und Angewandte Mathematik
(2013) 69–151.
date_created: 2018-12-11T11:45:24Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2021-01-12T06:57:33Z
day: '01'
doi: 10.1515/crelle.2012.039
extern: 1
issue: '680'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1011.3434
month: '07'
oa: 1
page: 69 - 151
publication: Journal fur die Reine und Angewandte Mathematik
publication_status: published
publisher: Walter de Gruyter
publist_id: '7659'
quality_controlled: 0
status: public
title: Inhomogeneous cubic congruences and rational points on del Pezzo surfaces
type: journal_article
year: '2013'
...
---
_id: '2450'
abstract:
- lang: eng
text: 'Understanding how hormones and genes interact to coordinate plant growth
is a major challenge in developmental biology. The activities of auxin, ethylene,
and cytokinin depend on cellular context and exhibit either synergistic or antagonistic
interactions. Here we use experimentation and network construction to elucidate
the role of the interaction of the POLARIS peptide (PLS) and the auxin efflux
carrier PIN proteins in the crosstalk of three hormones (auxin, ethylene, and
cytokinin) in Arabidopsis root development. In ethylene hypersignaling mutants
such as polaris (pls), we show experimentally that expression of both PIN1 and
PIN2 significantly increases. This relationship is analyzed in the context of
the crosstalk between auxin, ethylene, and cytokinin: in pls, endogenous auxin,
ethylene and cytokinin concentration decreases, approximately remains unchanged
and increases, respectively. Experimental data are integrated into a hormonal
crosstalk network through combination with information in literature. Network
construction reveals that the regulation of both PIN1 and PIN2 is predominantly
via ethylene signaling. In addition, it is deduced that the relationship between
cytokinin and PIN1 and PIN2 levels implies a regulatory role of cytokinin in addition
to its regulation to auxin, ethylene, and PLS levels. We discuss how the network
of hormones and genes coordinates plant growth by simultaneously regulating the
activities of auxin, ethylene, and cytokinin signaling pathways.hormonal crosstalk,
root development, auxin flux, PIN proteins, PLS protein, signaling network'
author:
- first_name: Junli
full_name: Liu, Junli
last_name: Liu
- first_name: Saher
full_name: Menhi, Saher
last_name: Menhi
- first_name: Jennifer
full_name: Topping, Jennifer
last_name: Topping
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Keith
full_name: Lindsey, Keith
last_name: Lindsey
citation:
ama: Liu J, Menhi S, Topping J, Friml J, Lindsey K. Interaction of PLS and PIN and
hormonal crosstalk in Arabidopsis root development. Frontiers in Plant Science.
2013;4(75). doi:10.3389/fpls.2013.00075
apa: Liu, J., Menhi, S., Topping, J., Friml, J., & Lindsey, K. (2013). Interaction
of PLS and PIN and hormonal crosstalk in Arabidopsis root development. Frontiers
in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2013.00075
chicago: Liu, Junli, Saher Menhi, Jennifer Topping, Jiří Friml, and Keith Lindsey.
“Interaction of PLS and PIN and Hormonal Crosstalk in Arabidopsis Root Development.”
Frontiers in Plant Science. Frontiers Research Foundation, 2013. https://doi.org/10.3389/fpls.2013.00075.
ieee: J. Liu, S. Menhi, J. Topping, J. Friml, and K. Lindsey, “Interaction of PLS
and PIN and hormonal crosstalk in Arabidopsis root development,” Frontiers
in Plant Science, vol. 4, no. 75. Frontiers Research Foundation, 2013.
ista: Liu J, Menhi S, Topping J, Friml J, Lindsey K. 2013. Interaction of PLS and
PIN and hormonal crosstalk in Arabidopsis root development. Frontiers in Plant
Science. 4(75).
mla: Liu, Junli, et al. “Interaction of PLS and PIN and Hormonal Crosstalk in Arabidopsis
Root Development.” Frontiers in Plant Science, vol. 4, no. 75, Frontiers
Research Foundation, 2013, doi:10.3389/fpls.2013.00075.
short: J. Liu, S. Menhi, J. Topping, J. Friml, K. Lindsey, Frontiers in Plant Science
4 (2013).
date_created: 2018-12-11T11:57:44Z
date_published: 2013-04-01T00:00:00Z
date_updated: 2021-01-12T06:57:34Z
day: '01'
doi: 10.3389/fpls.2013.00075
extern: 1
intvolume: ' 4'
issue: '75'
month: '04'
publication: Frontiers in Plant Science
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '4453'
quality_controlled: 0
status: public
title: Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development
type: journal_article
volume: 4
year: '2013'
...
---
_id: '2452'
abstract:
- lang: eng
text: 'Background: Abundance and distribution of the plant hormone auxin play important
roles in plant development. Besides other metabolic processes, various auxin carriers
control the cellular level of active auxin and, hence, are major regulators of
cellular auxin homeostasis. Despite the developmental importance of auxin transporters,
a simple medium-to-high throughput approach to assess carrier activities is still
missing. Here we show that carrier driven depletion of cellular auxin correlates
with reduced nuclear auxin signaling in tobacco Bright Yellow-2 (BY-2) cell cultures.Results:
We developed an easy to use transient single-cell-based system to detect carrier
activity. We use the relative changes in signaling output of the auxin responsive
promoter element DR5 to indirectly visualize auxin carrier activity. The feasibility
of the transient approach was demonstrated by pharmacological and genetic interference
with auxin signaling and transport. As a proof of concept, we provide visual evidence
that the prominent auxin transport proteins PIN-FORMED (PIN)2 and PIN5 regulate
cellular auxin homeostasis at the plasma membrane and endoplasmic reticulum (ER),
respectively. Our data suggest that PIN2 and PIN5 have different sensitivities
to the auxin transport inhibitor 1-naphthylphthalamic acid (NPA). Also the putative
PIN-LIKES (PILS) auxin carrier activity at the ER is insensitive to NPA in our
system, indicating that NPA blocks intercellular, but not intracellular auxin
transport.Conclusions: This single-cell-based system is a useful tool by which
the activity of putative auxin carriers, such as PINs, PILS and WALLS ARE THIN1
(WAT1), can be indirectly visualized in a medium-to-high throughput manner. Moreover,
our single cell system might be useful to investigate also other hormonal signaling
pathways, such as cytokinin.'
author:
- first_name: Elke
full_name: Barbez, Elke
last_name: Barbez
- first_name: Martina
full_name: Laňková, Martina
last_name: Laňková
- first_name: Markéta
full_name: Pařezová, Markéta
last_name: Pařezová
- first_name: Alexis
full_name: Maizel, Alexis
last_name: Maizel
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
citation:
ama: Barbez E, Laňková M, Pařezová M, et al. Single-cell-based system to monitor
carrier driven cellular auxin homeostasis. BMC Plant Biology. 2013;13(1).
doi:10.1186/1471-2229-13-20
apa: Barbez, E., Laňková, M., Pařezová, M., Maizel, A., Zažímalová, E., Petrášek,
J., … Kleine Vehn, J. (2013). Single-cell-based system to monitor carrier driven
cellular auxin homeostasis. BMC Plant Biology. BioMed Central. https://doi.org/10.1186/1471-2229-13-20
chicago: Barbez, Elke, Martina Laňková, Markéta Pařezová, Alexis Maizel, Eva Zažímalová,
Jan Petrášek, Jiří Friml, and Jürgen Kleine Vehn. “Single-Cell-Based System to
Monitor Carrier Driven Cellular Auxin Homeostasis.” BMC Plant Biology.
BioMed Central, 2013. https://doi.org/10.1186/1471-2229-13-20.
ieee: E. Barbez et al., “Single-cell-based system to monitor carrier driven
cellular auxin homeostasis,” BMC Plant Biology, vol. 13, no. 1. BioMed
Central, 2013.
ista: Barbez E, Laňková M, Pařezová M, Maizel A, Zažímalová E, Petrášek J, Friml
J, Kleine Vehn J. 2013. Single-cell-based system to monitor carrier driven cellular
auxin homeostasis. BMC Plant Biology. 13(1).
mla: Barbez, Elke, et al. “Single-Cell-Based System to Monitor Carrier Driven Cellular
Auxin Homeostasis.” BMC Plant Biology, vol. 13, no. 1, BioMed Central,
2013, doi:10.1186/1471-2229-13-20.
short: E. Barbez, M. Laňková, M. Pařezová, A. Maizel, E. Zažímalová, J. Petrášek,
J. Friml, J. Kleine Vehn, BMC Plant Biology 13 (2013).
date_created: 2018-12-11T11:57:45Z
date_published: 2013-02-01T00:00:00Z
date_updated: 2021-01-12T06:57:34Z
day: '01'
doi: 10.1186/1471-2229-13-20
extern: 1
intvolume: ' 13'
issue: '1'
month: '02'
publication: BMC Plant Biology
publication_status: published
publisher: BioMed Central
publist_id: '4451'
quality_controlled: 0
status: public
title: Single-cell-based system to monitor carrier driven cellular auxin homeostasis
type: journal_article
volume: 13
year: '2013'
...
---
_id: '2457'
author:
- first_name: Tom
full_name: Viaene, Tom
last_name: Viaene
- first_name: Charles
full_name: Delwiche, Charles
last_name: Delwiche
- first_name: Stefan
full_name: Rensing, Stefan
last_name: Rensing
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Viaene T, Delwiche C, Rensing S, Friml J. Origin and evolution of PIN auxin
transporters in the green lineage. Trends in Plant Science. 2013;18(1):5-10.
doi:10.1016/j.tplants.2012.08.009
apa: Viaene, T., Delwiche, C., Rensing, S., & Friml, J. (2013). Origin and evolution
of PIN auxin transporters in the green lineage. Trends in Plant Science.
Cell Press. https://doi.org/10.1016/j.tplants.2012.08.009
chicago: Viaene, Tom, Charles Delwiche, Stefan Rensing, and Jiří Friml. “Origin
and Evolution of PIN Auxin Transporters in the Green Lineage.” Trends in Plant
Science. Cell Press, 2013. https://doi.org/10.1016/j.tplants.2012.08.009.
ieee: T. Viaene, C. Delwiche, S. Rensing, and J. Friml, “Origin and evolution of
PIN auxin transporters in the green lineage,” Trends in Plant Science,
vol. 18, no. 1. Cell Press, pp. 5–10, 2013.
ista: Viaene T, Delwiche C, Rensing S, Friml J. 2013. Origin and evolution of PIN
auxin transporters in the green lineage. Trends in Plant Science. 18(1), 5–10.
mla: Viaene, Tom, et al. “Origin and Evolution of PIN Auxin Transporters in the
Green Lineage.” Trends in Plant Science, vol. 18, no. 1, Cell Press, 2013,
pp. 5–10, doi:10.1016/j.tplants.2012.08.009.
short: T. Viaene, C. Delwiche, S. Rensing, J. Friml, Trends in Plant Science 18
(2013) 5–10.
date_created: 2018-12-11T11:57:46Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T06:57:36Z
day: '01'
doi: 10.1016/j.tplants.2012.08.009
extern: '1'
intvolume: ' 18'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 5 - 10
publication: Trends in Plant Science
publication_status: published
publisher: Cell Press
publist_id: '4446'
quality_controlled: '1'
status: public
title: Origin and evolution of PIN auxin transporters in the green lineage
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2013'
...
---
_id: '246'
abstract:
- lang: eng
text: Given an intersection of two quadrics X Pm1, with m > 9, the quantitative
arithmetic of the set X(Q) is investigated under the assumption that the singular
locus of X consists of a pair of conjugate singular points defined over Q(i).
acknowledgement: "EP/E053262/1\tEngineering and Physical Sciences Research Council"
author:
- first_name: Timothy D
full_name: Timothy Browning
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Ritabrata
full_name: Munshi, Ritabrata
last_name: Munshi
citation:
ama: Browning TD, Munshi R. Rational points on singular intersections of quadrics.
Compositio Mathematica. 2013;149(9):1457-1494. doi:10.1112/S0010437X13007185
apa: Browning, T. D., & Munshi, R. (2013). Rational points on singular intersections
of quadrics. Compositio Mathematica. Cambridge University Press. https://doi.org/10.1112/S0010437X13007185
chicago: Browning, Timothy D, and Ritabrata Munshi. “Rational Points on Singular
Intersections of Quadrics.” Compositio Mathematica. Cambridge University
Press, 2013. https://doi.org/10.1112/S0010437X13007185.
ieee: T. D. Browning and R. Munshi, “Rational points on singular intersections of
quadrics,” Compositio Mathematica, vol. 149, no. 9. Cambridge University
Press, pp. 1457–1494, 2013.
ista: Browning TD, Munshi R. 2013. Rational points on singular intersections of
quadrics. Compositio Mathematica. 149(9), 1457–1494.
mla: Browning, Timothy D., and Ritabrata Munshi. “Rational Points on Singular Intersections
of Quadrics.” Compositio Mathematica, vol. 149, no. 9, Cambridge University
Press, 2013, pp. 1457–94, doi:10.1112/S0010437X13007185.
short: T.D. Browning, R. Munshi, Compositio Mathematica 149 (2013) 1457–1494.
date_created: 2018-12-11T11:45:25Z
date_published: 2013-09-01T00:00:00Z
date_updated: 2021-01-12T06:57:37Z
day: '01'
doi: 10.1112/S0010437X13007185
extern: 1
intvolume: ' 149'
issue: '9'
month: '09'
page: 1457 - 1494
publication: Compositio Mathematica
publication_status: published
publisher: Cambridge University Press
publist_id: '7658'
quality_controlled: 0
status: public
title: Rational points on singular intersections of quadrics
type: journal_article
volume: 149
year: '2013'
...
---
_id: '2466'
abstract:
- lang: eng
text: 'We introduce a new method for efficiently simulating liquid with extreme
amounts of spatial adaptivity. Our method combines several key components to drastically
speed up the simulation of large-scale fluid phenomena: We leverage an alternative
Eulerian tetrahedral mesh discretization to significantly reduce the complexity
of the pressure solve while increasing the robustness with respect to element
quality and removing the possibility of locking. Next, we enable subtle free-surface
phenomena by deriving novel second-order boundary conditions consistent with our
discretization. We couple this discretization with a spatially adaptive Fluid-Implicit
Particle (FLIP) method, enabling efficient, robust, minimally-dissipative simulations
that can undergo sharp changes in spatial resolution while minimizing artifacts.
Along the way, we provide a new method for generating a smooth and detailed surface
from a set of particles with variable sizes. Finally, we explore several new sizing
functions for determining spatially adaptive simulation resolutions, and we show
how to couple them to our simulator. We combine each of these elements to produce
a simulation algorithm that is capable of creating animations at high maximum
resolutions while avoiding common pitfalls like inaccurate boundary conditions
and inefficient computation.'
article_number: '103'
article_processing_charge: No
author:
- first_name: Ryoichi
full_name: Ando, Ryoichi
last_name: Ando
- first_name: Nils
full_name: Thuerey, Nils
last_name: Thuerey
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Ando R, Thuerey N, Wojtan C. Highly adaptive liquid simulations on tetrahedral
meshes. ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2461982
apa: Ando, R., Thuerey, N., & Wojtan, C. (2013). Highly adaptive liquid simulations
on tetrahedral meshes. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2461982
chicago: Ando, Ryoichi, Nils Thuerey, and Chris Wojtan. “Highly Adaptive Liquid
Simulations on Tetrahedral Meshes.” ACM Transactions on Graphics. ACM,
2013. https://doi.org/10.1145/2461912.2461982.
ieee: R. Ando, N. Thuerey, and C. Wojtan, “Highly adaptive liquid simulations on
tetrahedral meshes,” ACM Transactions on Graphics, vol. 32, no. 4. ACM,
2013.
ista: Ando R, Thuerey N, Wojtan C. 2013. Highly adaptive liquid simulations on tetrahedral
meshes. ACM Transactions on Graphics. 32(4), 103.
mla: Ando, Ryoichi, et al. “Highly Adaptive Liquid Simulations on Tetrahedral Meshes.”
ACM Transactions on Graphics, vol. 32, no. 4, 103, ACM, 2013, doi:10.1145/2461912.2461982.
short: R. Ando, N. Thuerey, C. Wojtan, ACM Transactions on Graphics 32 (2013).
date_created: 2018-12-11T11:57:50Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2025-09-29T14:13:52Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2461912.2461982
external_id:
isi:
- '000321840100072'
file:
- access_level: open_access
checksum: aeea6b0ff2b27c695aeb8408c7d2fc50
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:25Z
date_updated: 2020-07-14T12:45:41Z
file_id: '5279'
file_name: IST-2016-605-v1+1_tetflip_fixed.pdf
file_size: 8601561
relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '4436'
pubrep_id: '605'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Highly adaptive liquid simulations on tetrahedral meshes
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 32
year: '2013'
...
---
_id: '2467'
abstract:
- lang: eng
text: This paper presents a method for computing topology changes for triangle meshes
in an interactive geometric modeling environment. Most triangle meshes in practice
do not exhibit desirable geometric properties, so we develop a solution that is
independent of standard assumptions and robust to geometric errors. Specifically,
we provide the first method for topology change applicable to arbitrary non-solid,
non-manifold, non-closed, self-intersecting surfaces. We prove that this new method
for topology change produces the expected conventional results when applied to
solid (closed, manifold, non-self-intersecting) surfaces---that is, we prove a
backwards-compatibility property relative to prior work. Beyond solid surfaces,
we present empirical evidence that our method remains tolerant to a variety of
surface aberrations through the incorporation of a novel error correction scheme.
Finally, we demonstrate how topology change applied to non-solid objects enables
wholly new and useful behaviors.
article_number: '34'
article_processing_charge: No
author:
- first_name: Gilbert
full_name: Bernstein, Gilbert
last_name: Bernstein
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: 'Bernstein G, Wojtan C. Putting holes in holey geometry: Topology change for
arbitrary surfaces. ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2462027'
apa: 'Bernstein, G., & Wojtan, C. (2013). Putting holes in holey geometry: Topology
change for arbitrary surfaces. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2462027'
chicago: 'Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry:
Topology Change for Arbitrary Surfaces.” ACM Transactions on Graphics.
ACM, 2013. https://doi.org/10.1145/2461912.2462027.'
ieee: 'G. Bernstein and C. Wojtan, “Putting holes in holey geometry: Topology change
for arbitrary surfaces,” ACM Transactions on Graphics, vol. 32, no. 4.
ACM, 2013.'
ista: 'Bernstein G, Wojtan C. 2013. Putting holes in holey geometry: Topology change
for arbitrary surfaces. ACM Transactions on Graphics. 32(4), 34.'
mla: 'Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry: Topology
Change for Arbitrary Surfaces.” ACM Transactions on Graphics, vol. 32,
no. 4, 34, ACM, 2013, doi:10.1145/2461912.2462027.'
short: G. Bernstein, C. Wojtan, ACM Transactions on Graphics 32 (2013).
date_created: 2018-12-11T11:57:50Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2025-09-29T14:13:25Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2461912.2462027
external_id:
isi:
- '000321840100003'
file:
- access_level: open_access
checksum: 9c8425d62246996ca632c5a01870515b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:43Z
date_updated: 2020-07-14T12:45:41Z
file_id: '4768'
file_name: IST-2016-604-v1+1_toptop2013.pdf
file_size: 3514674
relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '4435'
pubrep_id: '604'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Putting holes in holey geometry: Topology change for arbitrary surfaces'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 32
year: '2013'
...
---
_id: '2468'
abstract:
- lang: eng
text: Our work concerns the combination of an Eulerian liquid simulation with a
high-resolution surface tracker (e.g. the level set method or a Lagrangian triangle
mesh). The naive application of a high-resolution surface tracker to a low-resolution
velocity field can produce many visually disturbing physical and topological artifacts
that limit their use in practice. We address these problems by defining an error
function which compares the current state of the surface tracker to the set of
physically valid surface states. By reducing this error with a gradient descent
technique, we introduce a novel physics-based surface fairing method. Similarly,
by treating this error function as a potential energy, we derive a new surface
correction force that mimics the vortex sheet equations. We demonstrate our results
with both level set and mesh-based surface trackers.
article_number: '68'
article_processing_charge: No
author:
- first_name: Morten
full_name: Bojsen-Hansen, Morten
id: 439F0C8C-F248-11E8-B48F-1D18A9856A87
last_name: Bojsen-Hansen
orcid: 0000-0002-4417-3224
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Bojsen-Hansen M, Wojtan C. Liquid surface tracking with error compensation.
ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2461991
apa: Bojsen-Hansen, M., & Wojtan, C. (2013). Liquid surface tracking with error
compensation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2461991
chicago: Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with
Error Compensation.” ACM Transactions on Graphics. ACM, 2013. https://doi.org/10.1145/2461912.2461991.
ieee: M. Bojsen-Hansen and C. Wojtan, “Liquid surface tracking with error compensation,”
ACM Transactions on Graphics, vol. 32, no. 4. ACM, 2013.
ista: Bojsen-Hansen M, Wojtan C. 2013. Liquid surface tracking with error compensation.
ACM Transactions on Graphics. 32(4), 68.
mla: Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with Error
Compensation.” ACM Transactions on Graphics, vol. 32, no. 4, 68, ACM, 2013,
doi:10.1145/2461912.2461991.
short: M. Bojsen-Hansen, C. Wojtan, ACM Transactions on Graphics 32 (2013).
corr_author: '1'
date_created: 2018-12-11T11:57:50Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2025-09-29T14:12:53Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2461912.2461991
external_id:
isi:
- '000321840100037'
file:
- access_level: open_access
checksum: 53d905e0180e23ef3e813b969ffed4e1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:37Z
date_updated: 2020-07-14T12:45:41Z
file_id: '4761'
file_name: IST-2016-603-v1+1_liquidError_web.pdf
file_size: 5813685
relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '4434'
pubrep_id: '603'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Liquid surface tracking with error compensation
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 32
year: '2013'
...
---
_id: '2469'
abstract:
- lang: eng
text: Cadherins are transmembrane proteins that mediate cell–cell adhesion in animals.
By regulating contact formation and stability, cadherins play a crucial role in
tissue morphogenesis and homeostasis. Here, we review the three major unctions
of cadherins in cell–cell contact formation and stability. Two of those functions
lead to a decrease in interfacial ension at the forming cell–cell contact, thereby
promoting contact expansion — first, by providing adhesion tension that lowers
interfacial tension at the cell–cell contact, and second, by signaling to the
actomyosin cytoskeleton in order to reduce cortex tension and thus interfacial
tension at the contact. The third function of cadherins in cell–cell contact formation
is to stabilize the contact by resisting mechanical forces that pull on the contact.
article_processing_charge: No
author:
- first_name: Jean-Léon
full_name: Maître, Jean-Léon
id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87
last_name: Maître
orcid: 0000-0002-3688-1474
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Maître J-L, Heisenberg C-PJ. Three functions of cadherins in cell adhesion.
Current Biology. 2013;23(14):R626-R633. doi:10.1016/j.cub.2013.06.019
apa: Maître, J.-L., & Heisenberg, C.-P. J. (2013). Three functions of cadherins
in cell adhesion. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.06.019
chicago: Maître, Jean-Léon, and Carl-Philipp J Heisenberg. “Three Functions of Cadherins
in Cell Adhesion.” Current Biology. Cell Press, 2013. https://doi.org/10.1016/j.cub.2013.06.019.
ieee: J.-L. Maître and C.-P. J. Heisenberg, “Three functions of cadherins in cell
adhesion,” Current Biology, vol. 23, no. 14. Cell Press, pp. R626–R633,
2013.
ista: Maître J-L, Heisenberg C-PJ. 2013. Three functions of cadherins in cell adhesion.
Current Biology. 23(14), R626–R633.
mla: Maître, Jean-Léon, and Carl-Philipp J. Heisenberg. “Three Functions of Cadherins
in Cell Adhesion.” Current Biology, vol. 23, no. 14, Cell Press, 2013,
pp. R626–33, doi:10.1016/j.cub.2013.06.019.
short: J.-L. Maître, C.-P.J. Heisenberg, Current Biology 23 (2013) R626–R633.
corr_author: '1'
date_created: 2018-12-11T11:57:51Z
date_published: 2013-07-22T00:00:00Z
date_updated: 2025-09-29T14:12:25Z
day: '22'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1016/j.cub.2013.06.019
external_id:
isi:
- '000322414200018'
pmid:
- '23885883'
file:
- access_level: open_access
checksum: 6a424b2f007b41d4955a9135793b2162
content_type: application/pdf
creator: dernst
date_created: 2019-01-24T15:40:22Z
date_updated: 2020-07-14T12:45:41Z
file_id: '5881'
file_name: 2013_CurrentBiology_Maitre.pdf
file_size: 247320
relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
issue: '14'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '07'
oa: 1
oa_version: Published Version
page: R626 - R633
pmid: 1
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '4433'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Three functions of cadherins in cell adhesion
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 23
year: '2013'
...
---
_id: '247'
abstract:
- lang: eng
text: An improved estimate is provided for the number of Fq-rational points on a
geometrically irreducible, projective, cubic hypersurface that is not equal to
a cone.
acknowledgement: "EP/E053262/1\tEngineering and Physical Sciences Research Council"
author:
- first_name: Timothy D
full_name: Timothy Browning
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
citation:
ama: Browning TD. The Lang-Weil estimate for cubic hypersurfaces. Canadian Mathematical
Bulletin. 2013;56(3):500-502. doi:10.4153/CMB-2011-177-4
apa: Browning, T. D. (2013). The Lang-Weil estimate for cubic hypersurfaces. Canadian
Mathematical Bulletin. Unknown. https://doi.org/10.4153/CMB-2011-177-4
chicago: Browning, Timothy D. “The Lang-Weil Estimate for Cubic Hypersurfaces.”
Canadian Mathematical Bulletin. Unknown, 2013. https://doi.org/10.4153/CMB-2011-177-4.
ieee: T. D. Browning, “The Lang-Weil estimate for cubic hypersurfaces,” Canadian
Mathematical Bulletin, vol. 56, no. 3. Unknown, pp. 500–502, 2013.
ista: Browning TD. 2013. The Lang-Weil estimate for cubic hypersurfaces. Canadian
Mathematical Bulletin. 56(3), 500–502.
mla: Browning, Timothy D. “The Lang-Weil Estimate for Cubic Hypersurfaces.” Canadian
Mathematical Bulletin, vol. 56, no. 3, Unknown, 2013, pp. 500–02, doi:10.4153/CMB-2011-177-4.
short: T.D. Browning, Canadian Mathematical Bulletin 56 (2013) 500–502.
date_created: 2018-12-11T11:45:25Z
date_published: 2013-08-31T00:00:00Z
date_updated: 2021-01-12T06:57:40Z
day: '31'
doi: 10.4153/CMB-2011-177-4
extern: 1
intvolume: ' 56'
issue: '3'
month: '08'
page: 500 - 502
publication: Canadian Mathematical Bulletin
publication_status: published
publisher: Unknown
publist_id: '7657'
quality_controlled: 0
status: public
title: The Lang-Weil estimate for cubic hypersurfaces
type: journal_article
volume: 56
year: '2013'
...
---
_id: '2470'
abstract:
- lang: eng
text: Background:Auxin binding protein 1 (ABP1) is a putative auxin receptor and
its function is indispensable for plant growth and development. ABP1 has been
shown to be involved in auxin-dependent regulation of cell division and expansion,
in plasma-membrane-related processes such as changes in transmembrane potential,
and in the regulation of clathrin-dependent endocytosis. However, the ABP1-regulated
downstream pathway remains elusive.Methodology/Principal Findings:Using auxin
transport assays and quantitative analysis of cellular morphology we show that
ABP1 regulates auxin efflux from tobacco BY-2 cells. The overexpression of ABP1can
counterbalance increased auxin efflux and auxin starvation phenotypes caused by
the overexpression of PIN auxin efflux carrier. Relevant mechanism involves the
ABP1-controlled vesicle trafficking processes, including positive regulation of
endocytosis of PIN auxin efflux carriers, as indicated by fluorescence recovery
after photobleaching (FRAP) and pharmacological manipulations.Conclusions/Significance:The
findings indicate the involvement of ABP1 in control of rate of auxin transport
across plasma membrane emphasizing the role of ABP1 in regulation of PIN activity
at the plasma membrane, and highlighting the relevance of ABP1 for the formation
of developmentally important, PIN-dependent auxin gradients.
article_number: e70050
article_processing_charge: No
author:
- first_name: Milada
full_name: Čovanová, Milada
last_name: Čovanová
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Jan
full_name: Rychtář, Jan
last_name: Rychtář
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
citation:
ama: Čovanová M, Sauer M, Rychtář J, Friml J, Petrášek J, Zažímalová E. Overexpression
of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco
cells. PLoS One. 2013;8(7). doi:10.1371/journal.pone.0070050
apa: Čovanová, M., Sauer, M., Rychtář, J., Friml, J., Petrášek, J., & Zažímalová,
E. (2013). Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent
auxin transport in tobacco cells. PLoS One. Public Library of Science.
https://doi.org/10.1371/journal.pone.0070050
chicago: Čovanová, Milada, Michael Sauer, Jan Rychtář, Jiří Friml, Jan Petrášek,
and Eva Zažímalová. “Overexpression of the Auxin Binding PROTEIN1 Modulates PIN-Dependent
Auxin Transport in Tobacco Cells.” PLoS One. Public Library of Science,
2013. https://doi.org/10.1371/journal.pone.0070050.
ieee: M. Čovanová, M. Sauer, J. Rychtář, J. Friml, J. Petrášek, and E. Zažímalová,
“Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport
in tobacco cells,” PLoS One, vol. 8, no. 7. Public Library of Science,
2013.
ista: Čovanová M, Sauer M, Rychtář J, Friml J, Petrášek J, Zažímalová E. 2013. Overexpression
of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco
cells. PLoS One. 8(7), e70050.
mla: Čovanová, Milada, et al. “Overexpression of the Auxin Binding PROTEIN1 Modulates
PIN-Dependent Auxin Transport in Tobacco Cells.” PLoS One, vol. 8, no.
7, e70050, Public Library of Science, 2013, doi:10.1371/journal.pone.0070050.
short: M. Čovanová, M. Sauer, J. Rychtář, J. Friml, J. Petrášek, E. Zažímalová,
PLoS One 8 (2013).
date_created: 2018-12-11T11:57:51Z
date_published: 2013-07-23T00:00:00Z
date_updated: 2025-09-29T14:11:54Z
day: '23'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1371/journal.pone.0070050
external_id:
isi:
- '000325211000181'
file:
- access_level: open_access
checksum: 2d47ef47616ef4de1d517d146548184e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:21Z
date_updated: 2020-07-14T12:45:41Z
file_id: '4681'
file_name: IST-2016-413-v1+1_journal.pone.0070050.pdf
file_size: 2294955
relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '4432'
pubrep_id: '413'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin
transport in tobacco cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 8
year: '2013'
...
---
_id: '2471'
abstract:
- lang: eng
text: The impact of disulfide bonds on protein stability goes beyond simple equilibrium
thermodynamics effects associated with the conformational entropy of the unfolded
state. Indeed, disulfide crosslinks may play a role in the prevention of dysfunctional
association and strongly affect the rates of irreversible enzyme inactivation,
highly relevant in biotechnological applications. While these kinetic-stability
effects remain poorly understood, by analogy with proposed mechanisms for processes
of protein aggregation and fibrillogenesis, we propose that they may be determined
by the properties of sparsely-populated, partially-unfolded intermediates. Here
we report the successful design, on the basis of high temperature molecular-dynamics
simulations, of six thermodynamically and kinetically stabilized variants of phytase
from Citrobacter braakii (a biotechnologically important enzyme) with one, two
or three engineered disulfides. Activity measurements and 3D crystal structure
determination demonstrate that the engineered crosslinks do not cause dramatic
alterations in the native structure. The inactivation kinetics for all the variants
displays a strongly non-Arrhenius temperature dependence, with the time-scale
for the irreversible denaturation process reaching a minimum at a given temperature
within the range of the denaturation transition. We show this striking feature
to be a signature of a key role played by a partially unfolded, intermediate state/ensemble.
Energetic and mutational analyses confirm that the intermediate is highly unfolded
(akin to a proposed critical intermediate in the misfolding of the prion protein),
a result that explains the observed kinetic stabilization. Our results provide
a rationale for the kinetic-stability consequences of disulfide-crosslink engineering
and an experimental methodology to arrive at energetic/structural descriptions
of the sparsely populated and elusive intermediates that play key roles in irreversible
protein denaturation.
article_number: e70013
article_processing_charge: No
author:
- first_name: Inmaculada
full_name: Sanchez Romero, Inmaculada
id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87
last_name: Sanchez Romero
- first_name: Antonio
full_name: Ariza, Antonio
last_name: Ariza
- first_name: Keith
full_name: Wilson, Keith
last_name: Wilson
- first_name: Michael
full_name: Skjøt, Michael
last_name: Skjøt
- first_name: Jesper
full_name: Vind, Jesper
last_name: Vind
- first_name: Leonardo
full_name: De Maria, Leonardo
last_name: De Maria
- first_name: Lars
full_name: Skov, Lars
last_name: Skov
- first_name: Jose
full_name: Sánchez Ruiz, Jose
last_name: Sánchez Ruiz
citation:
ama: Sanchez-Romero I, Ariza A, Wilson K, et al. Mechanism of protein kinetic stabilization
by engineered disulfide crosslinks. PLoS One. 2013;8(7). doi:10.1371/journal.pone.0070013
apa: Sanchez-Romero, I., Ariza, A., Wilson, K., Skjøt, M., Vind, J., De Maria, L.,
… Sánchez Ruiz, J. (2013). Mechanism of protein kinetic stabilization by engineered
disulfide crosslinks. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0070013
chicago: Sanchez-Romero, Inmaculada, Antonio Ariza, Keith Wilson, Michael Skjøt,
Jesper Vind, Leonardo De Maria, Lars Skov, and Jose Sánchez Ruiz. “Mechanism of
Protein Kinetic Stabilization by Engineered Disulfide Crosslinks.” PLoS One.
Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0070013.
ieee: I. Sanchez-Romero et al., “Mechanism of protein kinetic stabilization
by engineered disulfide crosslinks,” PLoS One, vol. 8, no. 7. Public Library
of Science, 2013.
ista: Sanchez-Romero I, Ariza A, Wilson K, Skjøt M, Vind J, De Maria L, Skov L,
Sánchez Ruiz J. 2013. Mechanism of protein kinetic stabilization by engineered
disulfide crosslinks. PLoS One. 8(7), e70013.
mla: Sanchez-Romero, Inmaculada, et al. “Mechanism of Protein Kinetic Stabilization
by Engineered Disulfide Crosslinks.” PLoS One, vol. 8, no. 7, e70013, Public
Library of Science, 2013, doi:10.1371/journal.pone.0070013.
short: I. Sanchez-Romero, A. Ariza, K. Wilson, M. Skjøt, J. Vind, L. De Maria, L.
Skov, J. Sánchez Ruiz, PLoS One 8 (2013).
date_created: 2018-12-11T11:57:51Z
date_published: 2013-07-30T00:00:00Z
date_updated: 2025-09-29T14:10:56Z
day: '30'
ddc:
- '570'
department:
- _id: HaJa
doi: 10.1371/journal.pone.0070013
external_id:
isi:
- '000323114200054'
file:
- access_level: open_access
checksum: c0c96cc76ed7ef0d036a31a7e33c9a37
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:07Z
date_updated: 2020-07-14T12:45:41Z
file_id: '5124'
file_name: IST-2016-414-v1+1_journal.pone.0070013.pdf
file_size: 1323666
relation: main_file
file_date_updated: 2020-07-14T12:45:41Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '4430'
pubrep_id: '414'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanism of protein kinetic stabilization by engineered disulfide crosslinks
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 8
year: '2013'
...
---
_id: '2472'
abstract:
- lang: eng
text: Plant-specific PIN-formed (PIN) efflux transporters for the plant hormone
auxin are required for tissue-specific directional auxin transport and cellular
auxin homeostasis. The Arabidopsis PIN protein family has been shown to play important
roles in developmental processes such as embryogenesis, organogenesis, vascular
tissue differentiation, root meristem patterning and tropic growth. Here we analyzed
roles of the less characterised Arabidopsis PIN6 auxin transporter. PIN6 is auxin-inducible
and is expressed during multiple auxin-regulated developmental processes. Loss
of pin6 function interfered with primary root growth and lateral root development.
Misexpression of PIN6 affected auxin transport and interfered with auxin homeostasis
in other growth processes such as shoot apical dominance, lateral root primordia
development, adventitious root formation, root hair outgrowth and root waving.
These changes in auxin-regulated growth correlated with a reduction in total auxin
transport as well as with an altered activity of DR5-GUS auxin response reporter.
Overall, the data indicate that PIN6 regulates auxin homeostasis during plant
development.
article_number: e70069
article_processing_charge: No
author:
- first_name: Christopher
full_name: Cazzonelli, Christopher
last_name: Cazzonelli
- first_name: Marleen
full_name: Vanstraelen, Marleen
last_name: Vanstraelen
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Kuide
full_name: Yin, Kuide
last_name: Yin
- first_name: Ashley
full_name: Carron Arthur, Ashley
last_name: Carron Arthur
- first_name: Nazia
full_name: Nisar, Nazia
last_name: Nisar
- first_name: Gauri
full_name: Tarle, Gauri
last_name: Tarle
- first_name: Abby
full_name: Cuttriss, Abby
last_name: Cuttriss
- first_name: Iain
full_name: Searle, Iain
last_name: Searle
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Ulrike
full_name: Mathesius, Ulrike
last_name: Mathesius
- first_name: Josette
full_name: Masle, Josette
last_name: Masle
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Barry
full_name: Pogson, Barry
last_name: Pogson
citation:
ama: Cazzonelli C, Vanstraelen M, Simon S, et al. Role of the Arabidopsis PIN6 auxin
transporter in auxin homeostasis and auxin-mediated development. PLoS One.
2013;8(7). doi:10.1371/journal.pone.0070069
apa: Cazzonelli, C., Vanstraelen, M., Simon, S., Yin, K., Carron Arthur, A., Nisar,
N., … Pogson, B. (2013). Role of the Arabidopsis PIN6 auxin transporter in auxin
homeostasis and auxin-mediated development. PLoS One. Public Library of
Science. https://doi.org/10.1371/journal.pone.0070069
chicago: Cazzonelli, Christopher, Marleen Vanstraelen, Sibu Simon, Kuide Yin, Ashley
Carron Arthur, Nazia Nisar, Gauri Tarle, et al. “Role of the Arabidopsis PIN6
Auxin Transporter in Auxin Homeostasis and Auxin-Mediated Development.” PLoS
One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0070069.
ieee: C. Cazzonelli et al., “Role of the Arabidopsis PIN6 auxin transporter
in auxin homeostasis and auxin-mediated development,” PLoS One, vol. 8,
no. 7. Public Library of Science, 2013.
ista: Cazzonelli C, Vanstraelen M, Simon S, Yin K, Carron Arthur A, Nisar N, Tarle
G, Cuttriss A, Searle I, Benková E, Mathesius U, Masle J, Friml J, Pogson B. 2013.
Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated
development. PLoS One. 8(7), e70069.
mla: Cazzonelli, Christopher, et al. “Role of the Arabidopsis PIN6 Auxin Transporter
in Auxin Homeostasis and Auxin-Mediated Development.” PLoS One, vol. 8,
no. 7, e70069, Public Library of Science, 2013, doi:10.1371/journal.pone.0070069.
short: C. Cazzonelli, M. Vanstraelen, S. Simon, K. Yin, A. Carron Arthur, N. Nisar,
G. Tarle, A. Cuttriss, I. Searle, E. Benková, U. Mathesius, J. Masle, J. Friml,
B. Pogson, PLoS One 8 (2013).
date_created: 2018-12-11T11:57:52Z
date_published: 2013-07-29T00:00:00Z
date_updated: 2025-09-29T14:11:25Z
day: '29'
ddc:
- '580'
- '570'
department:
- _id: JiFr
- _id: EvBe
doi: 10.1371/journal.pone.0070069
ec_funded: 1
external_id:
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oa: 1
oa_version: Published Version
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '4431'
pubrep_id: '393'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated
development
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 8
year: '2013'
...
---
_id: '2473'
abstract:
- lang: eng
text: 'When a mutation with selective advantage s spreads through a panmictic population,
it may cause two lineages at a linked locus to coalesce; the probability of coalescence
is exp(−2rT), where T∼log(2Ns)/s is the time to fixation, N is the number of haploid
individuals, and r is the recombination rate. Population structure delays fixation,
and so weakens the effect of a selective sweep. However, favourable alleles spread
through a spatially continuous population behind a narrow wavefront; ancestral
lineages are confined at the tip of this front, and so coalesce rapidly. In extremely
dense populations, coalescence is dominated by rare fluctuations ahead of the
front. However, we show that for moderate densities, a simple quasi-deterministic
approximation applies: the rate of coalescence within the front is λ∼2g(η)/(ρℓ),
where ρ is the population density and is the characteristic scale of the wavefront;
g(η) depends only on the strength of random drift, . The net effect of a sweep
on coalescence also depends crucially on whether two lineages are ever both within
the wavefront at the same time: even in the extreme case when coalescence within
the front is instantaneous, the net rate of coalescence may be lower than in a
single panmictic population. Sweeps can also have a substantial impact on the
rate of gene flow. A single lineage will jump to a new location when it is hit
by a sweep, with mean square displacement ; this can be substantial if the species’
range, L, is large, even if the species-wide rate of sweeps per map length, Λ/R,
is small. This effect is half as strong in two dimensions. In contrast, the rate
of coalescence between lineages, at random locations in space and on the genetic
map, is proportional to (c/L)(Λ/R), where c is the wavespeed: thus, on average,
one-dimensional structure is likely to reduce coalescence due to sweeps, relative
to panmixis. In two dimensions, genes must move along the front before they can
coalesce; this process is rapid, being dominated by rare fluctuations. This leads
to a dramatically higher rate of coalescence within the wavefront than if lineages
simply diffused along the front. Nevertheless, the net rate of coalescence due
to a sweep through a two-dimensional population is likely to be lower than it
would be with panmixis.'
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: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Jerome
full_name: Kelleher, Jerome
last_name: Kelleher
- first_name: Amandine
full_name: Véber, Amandine
last_name: Véber
citation:
ama: Barton NH, Etheridge A, Kelleher J, Véber A. Genetic hitch-hiking in spatially
extended populations. Theoretical Population Biology. 2013;87(8):75-89.
doi:10.1016/j.tpb.2012.12.001
apa: Barton, N. H., Etheridge, A., Kelleher, J., & Véber, A. (2013). Genetic
hitch-hiking in spatially extended populations. Theoretical Population Biology.
Elsevier. https://doi.org/10.1016/j.tpb.2012.12.001
chicago: Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber.
“Genetic Hitch-Hiking in Spatially Extended Populations.” Theoretical Population
Biology. Elsevier, 2013. https://doi.org/10.1016/j.tpb.2012.12.001.
ieee: N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Genetic hitch-hiking
in spatially extended populations,” Theoretical Population Biology, vol.
87, no. 8. Elsevier, pp. 75–89, 2013.
ista: Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Genetic hitch-hiking in
spatially extended populations. Theoretical Population Biology. 87(8), 75–89.
mla: Barton, Nicholas H., et al. “Genetic Hitch-Hiking in Spatially Extended Populations.”
Theoretical Population Biology, vol. 87, no. 8, Elsevier, 2013, pp. 75–89,
doi:10.1016/j.tpb.2012.12.001.
short: N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population
Biology 87 (2013) 75–89.
corr_author: '1'
date_created: 2018-12-11T11:57:52Z
date_published: 2013-01-03T00:00:00Z
date_updated: 2025-09-29T14:10:28Z
day: '03'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2012.12.001
ec_funded: 1
external_id:
isi:
- '000322688800008'
file:
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checksum: 4274ec1f433b838a7d5b941cc9684ca7
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creator: system
date_created: 2018-12-12T10:18:54Z
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file_name: IST-2013-118-v1+1_bartonetalRevision.pdf
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has_accepted_license: '1'
intvolume: ' 87'
isi: 1
issue: '8'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 75 - 89
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Theoretical Population Biology
publication_status: published
publisher: Elsevier
publist_id: '4428'
pubrep_id: '118'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetic hitch-hiking in spatially extended populations
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 87
year: '2013'
...