---
_id: '1934'
abstract:
- lang: eng
text: The plant hormones auxin and cytokinin mutually coordinate their activities
to control various aspects of development [1-9], and their crosstalk occurs at
multiple levels [10, 11]. Cytokinin-mediated modulation of auxin transport provides
an efficient means to regulate auxin distribution in plant organs. Here, we demonstrate
that cytokinin does not merely control the overall auxin flow capacity, but might
also act as a polarizing cue and control the auxin stream directionality during
plant organogenesis. Cytokinin enhances the PIN-FORMED1 (PIN1) auxin transporter
depletion at specific polar domains, thus rearranging the cellular PIN polarities
and directly regulating the auxin flow direction. This selective cytokinin sensitivity
correlates with the PIN protein phosphorylation degree. PIN1 phosphomimicking
mutations, as well as enhanced phosphorylation in plants with modulated activities
of PIN-specific kinases and phosphatases, desensitize PIN1 to cytokinin. Our results
reveal conceptually novel, cytokinin-driven polarization mechanism that operates
in developmental processes involving rapid auxin stream redirection, such as lateral
root organogenesis, in which a gradual PIN polarity switch defines the growth
axis of the newly formed organ.
author:
- first_name: Peter
full_name: Marhavy, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Jérôme
full_name: Duclercq, Jérôme
last_name: Duclercq
- first_name: Benjamin
full_name: Weller, Benjamin
last_name: Weller
- first_name: Elena
full_name: Feraru, Elena
last_name: Feraru
- first_name: Agnieszka
full_name: Bielach, Agnieszka
last_name: Bielach
- first_name: Remko
full_name: Offringa, Remko
last_name: Offringa
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Claus
full_name: Schwechheimer, Claus
last_name: Schwechheimer
- first_name: Angus
full_name: Murphy, Angus
last_name: Murphy
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Marhavý P, Duclercq J, Weller B, et al. Cytokinin controls polarity of PIN1-dependent
Auxin transport during lateral root organogenesis. Current Biology. 2014;24(9):1031-1037.
doi:10.1016/j.cub.2014.04.002
apa: Marhavý, P., Duclercq, J., Weller, B., Feraru, E., Bielach, A., Offringa, R.,
… Benková, E. (2014). Cytokinin controls polarity of PIN1-dependent Auxin transport
during lateral root organogenesis. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2014.04.002
chicago: Marhavý, Peter, Jérôme Duclercq, Benjamin Weller, Elena Feraru, Agnieszka
Bielach, Remko Offringa, Jiří Friml, Claus Schwechheimer, Angus Murphy, and Eva
Benková. “Cytokinin Controls Polarity of PIN1-Dependent Auxin Transport during
Lateral Root Organogenesis.” Current Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2014.04.002.
ieee: P. Marhavý et al., “Cytokinin controls polarity of PIN1-dependent Auxin
transport during lateral root organogenesis,” Current Biology, vol. 24,
no. 9. Cell Press, pp. 1031–1037, 2014.
ista: Marhavý P, Duclercq J, Weller B, Feraru E, Bielach A, Offringa R, Friml J,
Schwechheimer C, Murphy A, Benková E. 2014. Cytokinin controls polarity of PIN1-dependent
Auxin transport during lateral root organogenesis. Current Biology. 24(9), 1031–1037.
mla: Marhavý, Peter, et al. “Cytokinin Controls Polarity of PIN1-Dependent Auxin
Transport during Lateral Root Organogenesis.” Current Biology, vol. 24,
no. 9, Cell Press, 2014, pp. 1031–37, doi:10.1016/j.cub.2014.04.002.
short: P. Marhavý, J. Duclercq, B. Weller, E. Feraru, A. Bielach, R. Offringa, J.
Friml, C. Schwechheimer, A. Murphy, E. Benková, Current Biology 24 (2014) 1031–1037.
date_created: 2018-12-11T11:54:48Z
date_published: 2014-05-05T00:00:00Z
date_updated: 2021-01-12T06:54:10Z
day: '05'
department:
- _id: EvBe
- _id: JiFr
doi: 10.1016/j.cub.2014.04.002
ec_funded: 1
intvolume: ' 24'
issue: '9'
language:
- iso: eng
month: '05'
oa_version: None
page: 1031 - 1037
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '5160'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral
root organogenesis
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2014'
...
---
_id: '1932'
abstract:
- lang: eng
text: The existence of complex (multiple-step) genetic adaptations that are "irreducible"
(i.e., all partial combinations are less fit than the original genotype) is one
of the longest standing problems in evolutionary biology. In standard genetics
parlance, these adaptations require the crossing of a wide adaptive valley of
deleterious intermediate stages. Here, we demonstrate, using a simple model, that
evolution can cross wide valleys to produce "irreducibly complex" adaptations
by making use of previously cryptic mutations. When revealed by an evolutionary
capacitor, previously cryptic mutants have higher initial frequencies than do
new mutations, bringing them closer to a valley-crossing saddle in allele frequency
space. Moreover, simple combinatorics implies an enormous number of candidate
combinations exist within available cryptic genetic variation. We model the dynamics
of crossing of a wide adaptive valley after a capacitance event using both numerical
simulations and analytical approximations. Although individual valley crossing
events become less likely as valleys widen, by taking the combinatorics of genotype
space into account, we see that revealing cryptic variation can cause the frequent
evolution of complex adaptations.
acknowledgement: "Funded by National Institutes of Health. Grant Numbers: R01GM076041,
R01GM104040 \r\n\r\nSimons Foundation\r\n\r\n"
author:
- first_name: Meredith
full_name: Trotter, Meredith
last_name: Trotter
- first_name: Daniel
full_name: Weissman, Daniel
id: 2D0CE020-F248-11E8-B48F-1D18A9856A87
last_name: Weissman
- first_name: Grant
full_name: Peterson, Grant
last_name: Peterson
- first_name: Kayla
full_name: Peck, Kayla
last_name: Peck
- first_name: Joanna
full_name: Masel, Joanna
last_name: Masel
citation:
ama: Trotter M, Weissman D, Peterson G, Peck K, Masel J. Cryptic genetic variation
can make "irreducible complexity" a common mode of adaptation
in sexual populations. Evolution. 2014;68(12):3357-3367. doi:10.1111/evo.12517
apa: Trotter, M., Weissman, D., Peterson, G., Peck, K., & Masel, J. (2014).
Cryptic genetic variation can make "irreducible complexity"
a common mode of adaptation in sexual populations. Evolution. Wiley-Blackwell.
https://doi.org/10.1111/evo.12517
chicago: Trotter, Meredith, Daniel Weissman, Grant Peterson, Kayla Peck, and Joanna
Masel. “Cryptic Genetic Variation Can Make "Irreducible Complexity"
a Common Mode of Adaptation in Sexual Populations.” Evolution. Wiley-Blackwell,
2014. https://doi.org/10.1111/evo.12517.
ieee: M. Trotter, D. Weissman, G. Peterson, K. Peck, and J. Masel, “Cryptic genetic
variation can make "irreducible complexity" a common mode of
adaptation in sexual populations,” Evolution, vol. 68, no. 12. Wiley-Blackwell,
pp. 3357–3367, 2014.
ista: Trotter M, Weissman D, Peterson G, Peck K, Masel J. 2014. Cryptic genetic
variation can make "irreducible complexity" a common mode of
adaptation in sexual populations. Evolution. 68(12), 3357–3367.
mla: Trotter, Meredith, et al. “Cryptic Genetic Variation Can Make "Irreducible
Complexity" a Common Mode of Adaptation in Sexual Populations.” Evolution,
vol. 68, no. 12, Wiley-Blackwell, 2014, pp. 3357–67, doi:10.1111/evo.12517.
short: M. Trotter, D. Weissman, G. Peterson, K. Peck, J. Masel, Evolution 68 (2014)
3357–3367.
date_created: 2018-12-11T11:54:47Z
date_published: 2014-12-01T00:00:00Z
date_updated: 2021-01-12T06:54:10Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/evo.12517
ec_funded: 1
intvolume: ' 68'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1310.6077
month: '12'
oa: 1
oa_version: Submitted Version
page: 3357 - 3367
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5162'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cryptic genetic variation can make "irreducible complexity" a common
mode of adaptation in sexual populations
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 68
year: '2014'
...
---
_id: '1930'
abstract:
- lang: eng
text: (Figure Presented) Data acquisition, numerical inaccuracies, and sampling
often introduce noise in measurements and simulations. Removing this noise is
often necessary for efficient analysis and visualization of this data, yet many
denoising techniques change the minima and maxima of a scalar field. For example,
the extrema can appear or disappear, spatially move, and change their value. This
can lead to wrong interpretations of the data, e.g., when the maximum temperature
over an area is falsely reported being a few degrees cooler because the denoising
method is unaware of these features. Recently, a topological denoising technique
based on a global energy optimization was proposed, which allows the topology-controlled
denoising of 2D scalar fields. While this method preserves the minima and maxima,
it is constrained by the size of the data. We extend this work to large 2D data
and medium-sized 3D data by introducing a novel domain decomposition approach.
It allows processing small patches of the domain independently while still avoiding
the introduction of new critical points. Furthermore, we propose an iterative
refinement of the solution, which decreases the optimization energy compared to
the previous approach and therefore gives smoother results that are closer to
the input. We illustrate our technique on synthetic and real-world 2D and 3D data
sets that highlight potential applications.
acknowledgement: RTRA Digiteoproject; ERC grant; SNF award; Intel Doctoral Fellowship;
MPC-VCC
author:
- first_name: David
full_name: Günther, David
last_name: Günther
- first_name: Alec
full_name: Jacobson, Alec
last_name: Jacobson
- first_name: Jan
full_name: Reininghaus, Jan
id: 4505473A-F248-11E8-B48F-1D18A9856A87
last_name: Reininghaus
- first_name: Hans
full_name: Seidel, Hans
last_name: Seidel
- first_name: Olga
full_name: Sorkine Hornung, Olga
last_name: Sorkine Hornung
- first_name: Tino
full_name: Weinkauf, Tino
last_name: Weinkauf
citation:
ama: Günther D, Jacobson A, Reininghaus J, Seidel H, Sorkine Hornung O, Weinkauf
T. Fast and memory-efficient topological denoising of 2D and 3D scalar fields.
IEEE Transactions on Visualization and Computer Graphics. 2014;20(12):2585-2594.
doi:10.1109/TVCG.2014.2346432
apa: Günther, D., Jacobson, A., Reininghaus, J., Seidel, H., Sorkine Hornung, O.,
& Weinkauf, T. (2014). Fast and memory-efficient topological denoising of
2D and 3D scalar fields. IEEE Transactions on Visualization and Computer Graphics.
IEEE. https://doi.org/10.1109/TVCG.2014.2346432
chicago: Günther, David, Alec Jacobson, Jan Reininghaus, Hans Seidel, Olga Sorkine
Hornung, and Tino Weinkauf. “Fast and Memory-Efficient Topological Denoising of
2D and 3D Scalar Fields.” IEEE Transactions on Visualization and Computer Graphics.
IEEE, 2014. https://doi.org/10.1109/TVCG.2014.2346432.
ieee: D. Günther, A. Jacobson, J. Reininghaus, H. Seidel, O. Sorkine Hornung, and
T. Weinkauf, “Fast and memory-efficient topological denoising of 2D and 3D scalar
fields,” IEEE Transactions on Visualization and Computer Graphics, vol.
20, no. 12. IEEE, pp. 2585–2594, 2014.
ista: Günther D, Jacobson A, Reininghaus J, Seidel H, Sorkine Hornung O, Weinkauf
T. 2014. Fast and memory-efficient topological denoising of 2D and 3D scalar fields.
IEEE Transactions on Visualization and Computer Graphics. 20(12), 2585–2594.
mla: Günther, David, et al. “Fast and Memory-Efficient Topological Denoising of
2D and 3D Scalar Fields.” IEEE Transactions on Visualization and Computer Graphics,
vol. 20, no. 12, IEEE, 2014, pp. 2585–94, doi:10.1109/TVCG.2014.2346432.
short: D. Günther, A. Jacobson, J. Reininghaus, H. Seidel, O. Sorkine Hornung, T.
Weinkauf, IEEE Transactions on Visualization and Computer Graphics 20 (2014) 2585–2594.
date_created: 2018-12-11T11:54:46Z
date_published: 2014-12-31T00:00:00Z
date_updated: 2021-01-12T06:54:09Z
day: '31'
department:
- _id: HeEd
doi: 10.1109/TVCG.2014.2346432
intvolume: ' 20'
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
page: 2585 - 2594
publication: IEEE Transactions on Visualization and Computer Graphics
publication_status: published
publisher: IEEE
publist_id: '5164'
quality_controlled: '1'
scopus_import: 1
status: public
title: Fast and memory-efficient topological denoising of 2D and 3D scalar fields
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2014'
...
---
_id: '1933'
abstract:
- lang: eng
text: The development of the vertebrate brain requires an exquisite balance between
proliferation and differentiation of neural progenitors. Notch signaling plays
a pivotal role in regulating this balance, yet the interaction between signaling
and receiving cells remains poorly understood. We have found that numerous nascent
neurons and/or intermediate neurogenic progenitors expressing the ligand of Notch
retain apical endfeet transiently at the ventricular lumen that form adherens
junctions (AJs) with the endfeet of progenitors. Forced detachment of the apical
endfeet of those differentiating cells by disrupting AJs resulted in precocious
neurogenesis that was preceded by the downregulation of Notch signaling. Both
Notch1 and its ligand Dll1 are distributed around AJs in the apical endfeet, and
these proteins physically interact with ZO-1, a constituent of the AJ. Furthermore,
live imaging of a fluorescently tagged Notch1 demonstrated its trafficking from
the apical endfoot to the nucleus upon cleavage. Our results identified the apical
endfoot as the central site of active Notch signaling to securely prohibit inappropriate
differentiation of neural progenitors.
author:
- first_name: Jun
full_name: Hatakeyama, Jun
last_name: Hatakeyama
- first_name: Yoshio
full_name: Wakamatsu, Yoshio
last_name: Wakamatsu
- first_name: Akira
full_name: Nagafuchi, Akira
last_name: Nagafuchi
- first_name: Ryoichiro
full_name: Kageyama, Ryoichiro
last_name: Kageyama
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Kenji
full_name: Shimamura, Kenji
last_name: Shimamura
citation:
ama: Hatakeyama J, Wakamatsu Y, Nagafuchi A, Kageyama R, Shigemoto R, Shimamura
K. Cadherin-based adhesions in the apical endfoot are required for active Notch
signaling to control neurogenesis in vertebrates. Development. 2014;141(8):1671-1682.
doi:10.1242/dev.102988
apa: Hatakeyama, J., Wakamatsu, Y., Nagafuchi, A., Kageyama, R., Shigemoto, R.,
& Shimamura, K. (2014). Cadherin-based adhesions in the apical endfoot are
required for active Notch signaling to control neurogenesis in vertebrates. Development.
Company of Biologists. https://doi.org/10.1242/dev.102988
chicago: Hatakeyama, Jun, Yoshio Wakamatsu, Akira Nagafuchi, Ryoichiro Kageyama,
Ryuichi Shigemoto, and Kenji Shimamura. “Cadherin-Based Adhesions in the Apical
Endfoot Are Required for Active Notch Signaling to Control Neurogenesis in Vertebrates.”
Development. Company of Biologists, 2014. https://doi.org/10.1242/dev.102988.
ieee: J. Hatakeyama, Y. Wakamatsu, A. Nagafuchi, R. Kageyama, R. Shigemoto, and
K. Shimamura, “Cadherin-based adhesions in the apical endfoot are required for
active Notch signaling to control neurogenesis in vertebrates,” Development,
vol. 141, no. 8. Company of Biologists, pp. 1671–1682, 2014.
ista: Hatakeyama J, Wakamatsu Y, Nagafuchi A, Kageyama R, Shigemoto R, Shimamura
K. 2014. Cadherin-based adhesions in the apical endfoot are required for active
Notch signaling to control neurogenesis in vertebrates. Development. 141(8), 1671–1682.
mla: Hatakeyama, Jun, et al. “Cadherin-Based Adhesions in the Apical Endfoot Are
Required for Active Notch Signaling to Control Neurogenesis in Vertebrates.” Development,
vol. 141, no. 8, Company of Biologists, 2014, pp. 1671–82, doi:10.1242/dev.102988.
short: J. Hatakeyama, Y. Wakamatsu, A. Nagafuchi, R. Kageyama, R. Shigemoto, K.
Shimamura, Development 141 (2014) 1671–1682.
date_created: 2018-12-11T11:54:47Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T06:54:10Z
day: '01'
department:
- _id: RySh
doi: 10.1242/dev.102988
intvolume: ' 141'
issue: '8'
language:
- iso: eng
month: '04'
oa_version: None
page: 1671 - 1682
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '5161'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cadherin-based adhesions in the apical endfoot are required for active Notch
signaling to control neurogenesis in vertebrates
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 141
year: '2014'
...
---
_id: '1931'
abstract:
- lang: eng
text: A wealth of experimental evidence suggests that working memory circuits preferentially
represent information that is behaviorally relevant. Still, we are missing a mechanistic
account of how these representations come about. Here we provide a simple explanation
for a range of experimental findings, in light of prefrontal circuits adapting
to task constraints by reward-dependent learning. In particular, we model a neural
network shaped by reward-modulated spike-timing dependent plasticity (r-STDP)
and homeostatic plasticity (intrinsic excitability and synaptic scaling). We show
that the experimentally-observed neural representations naturally emerge in an
initially unstructured circuit as it learns to solve several working memory tasks.
These results point to a critical, and previously unappreciated, role for reward-dependent
learning in shaping prefrontal cortex activity.
acknowledgement: Supported in part by EC MEXT project PLICON and the LOEWE-Program
“Neuronal Coordination Research Focus Frankfurt” (NeFF). Jochen Triesch was supported
by the Quandt foundation.
article_number: '57'
author:
- first_name: Cristina
full_name: Savin, Cristina
id: 3933349E-F248-11E8-B48F-1D18A9856A87
last_name: Savin
- first_name: Jochen
full_name: Triesch, Jochen
last_name: Triesch
citation:
ama: Savin C, Triesch J. Emergence of task-dependent representations in working
memory circuits. Frontiers in Computational Neuroscience. 2014;8(MAY).
doi:10.3389/fncom.2014.00057
apa: Savin, C., & Triesch, J. (2014). Emergence of task-dependent representations
in working memory circuits. Frontiers in Computational Neuroscience. Frontiers
Research Foundation. https://doi.org/10.3389/fncom.2014.00057
chicago: Savin, Cristina, and Jochen Triesch. “Emergence of Task-Dependent Representations
in Working Memory Circuits.” Frontiers in Computational Neuroscience. Frontiers
Research Foundation, 2014. https://doi.org/10.3389/fncom.2014.00057.
ieee: C. Savin and J. Triesch, “Emergence of task-dependent representations in working
memory circuits,” Frontiers in Computational Neuroscience, vol. 8, no.
MAY. Frontiers Research Foundation, 2014.
ista: Savin C, Triesch J. 2014. Emergence of task-dependent representations in working
memory circuits. Frontiers in Computational Neuroscience. 8(MAY), 57.
mla: Savin, Cristina, and Jochen Triesch. “Emergence of Task-Dependent Representations
in Working Memory Circuits.” Frontiers in Computational Neuroscience, vol.
8, no. MAY, 57, Frontiers Research Foundation, 2014, doi:10.3389/fncom.2014.00057.
short: C. Savin, J. Triesch, Frontiers in Computational Neuroscience 8 (2014).
date_created: 2018-12-11T11:54:46Z
date_published: 2014-05-28T00:00:00Z
date_updated: 2021-01-12T06:54:09Z
day: '28'
department:
- _id: GaTk
doi: 10.3389/fncom.2014.00057
intvolume: ' 8'
issue: MAY
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035833/
month: '05'
oa: 1
oa_version: Submitted Version
publication: Frontiers in Computational Neuroscience
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '5163'
quality_controlled: '1'
scopus_import: 1
status: public
title: Emergence of task-dependent representations in working memory circuits
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2014'
...