---
_id: '1560'
abstract:
- lang: eng
text: Stromal cells in the subcapsular sinus of the lymph node 'decide' which cells
and molecules are allowed access to the deeper parenchyma. The glycoprotein PLVAP
is a crucial component of this selector function.
author:
- first_name: Miroslav
full_name: Hons, Miroslav
id: 4167FE56-F248-11E8-B48F-1D18A9856A87
last_name: Hons
orcid: 0000-0002-6625-3348
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Hons M, Sixt MK. The lymph node filter revealed. Nature Immunology.
2015;16(4):338-340. doi:10.1038/ni.3126
apa: Hons, M., & Sixt, M. K. (2015). The lymph node filter revealed. Nature
Immunology. Nature Publishing Group. https://doi.org/10.1038/ni.3126
chicago: Hons, Miroslav, and Michael K Sixt. “The Lymph Node Filter Revealed.” Nature
Immunology. Nature Publishing Group, 2015. https://doi.org/10.1038/ni.3126.
ieee: M. Hons and M. K. Sixt, “The lymph node filter revealed,” Nature Immunology,
vol. 16, no. 4. Nature Publishing Group, pp. 338–340, 2015.
ista: Hons M, Sixt MK. 2015. The lymph node filter revealed. Nature Immunology.
16(4), 338–340.
mla: Hons, Miroslav, and Michael K. Sixt. “The Lymph Node Filter Revealed.” Nature
Immunology, vol. 16, no. 4, Nature Publishing Group, 2015, pp. 338–40, doi:10.1038/ni.3126.
short: M. Hons, M.K. Sixt, Nature Immunology 16 (2015) 338–340.
date_created: 2018-12-11T11:52:43Z
date_published: 2015-03-19T00:00:00Z
date_updated: 2021-01-12T06:51:36Z
day: '19'
department:
- _id: MiSi
doi: 10.1038/ni.3126
intvolume: ' 16'
issue: '4'
language:
- iso: eng
month: '03'
oa_version: None
page: 338 - 340
publication: Nature Immunology
publication_status: published
publisher: Nature Publishing Group
publist_id: '5611'
quality_controlled: '1'
scopus_import: 1
status: public
title: The lymph node filter revealed
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2015'
...
---
_id: '1561'
abstract:
- lang: eng
text: Replication-deficient recombinant adenoviruses are potent vectors for the
efficient transient expression of exogenous genes in resting immune cells. However,
most leukocytes are refractory to efficient adenoviral transduction as they lack
expression of the coxsackie/adenovirus receptor (CAR). To circumvent this obstacle,
we generated the R26/CAG-CARΔ1StopF (where R26 is ROSA26 and CAG is CMV early
enhancer/chicken β actin promoter) knock-in mouse line. This strain allows monitoring
of in situ Cre recombinase activity through expression of CARΔ1. Simultaneously,
CARΔ1 expression permits selective and highly efficient adenoviral transduction
of immune cell populations, such as mast cells or T cells, directly ex vivo in
bulk cultures without prior cell purification or activation. Furthermore, we show
that CARΔ1 expression dramatically improves adenoviral infection of in vitro differentiated
conventional and plasmacytoid dendritic cells (DCs), basophils, mast cells, as
well as Hoxb8-immortalized hematopoietic progenitor cells. This novel dual function
mouse strain will hence be a valuable tool to rapidly dissect the function of
specific genes in leukocyte physiology.
author:
- first_name: Klaus
full_name: Heger, Klaus
last_name: Heger
- first_name: Maike
full_name: Kober, Maike
last_name: Kober
- first_name: David
full_name: Rieß, David
last_name: Rieß
- first_name: Christoph
full_name: Drees, Christoph
last_name: Drees
- first_name: Ingrid
full_name: De Vries, Ingrid
id: 4C7D837E-F248-11E8-B48F-1D18A9856A87
last_name: De Vries
- first_name: Arianna
full_name: Bertossi, Arianna
last_name: Bertossi
- first_name: Axel
full_name: Roers, Axel
last_name: Roers
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Marc
full_name: Schmidt Supprian, Marc
last_name: Schmidt Supprian
citation:
ama: Heger K, Kober M, Rieß D, et al. A novel Cre recombinase reporter mouse strain
facilitates selective and efficient infection of primary immune cells with adenoviral
vectors. European Journal of Immunology. 2015;45(6):1614-1620. doi:10.1002/eji.201545457
apa: Heger, K., Kober, M., Rieß, D., Drees, C., de Vries, I., Bertossi, A., … Schmidt
Supprian, M. (2015). A novel Cre recombinase reporter mouse strain facilitates
selective and efficient infection of primary immune cells with adenoviral vectors.
European Journal of Immunology. Wiley. https://doi.org/10.1002/eji.201545457
chicago: Heger, Klaus, Maike Kober, David Rieß, Christoph Drees, Ingrid de Vries,
Arianna Bertossi, Axel Roers, Michael K Sixt, and Marc Schmidt Supprian. “A Novel
Cre Recombinase Reporter Mouse Strain Facilitates Selective and Efficient Infection
of Primary Immune Cells with Adenoviral Vectors.” European Journal of Immunology.
Wiley, 2015. https://doi.org/10.1002/eji.201545457.
ieee: K. Heger et al., “A novel Cre recombinase reporter mouse strain facilitates
selective and efficient infection of primary immune cells with adenoviral vectors,”
European Journal of Immunology, vol. 45, no. 6. Wiley, pp. 1614–1620, 2015.
ista: Heger K, Kober M, Rieß D, Drees C, de Vries I, Bertossi A, Roers A, Sixt MK,
Schmidt Supprian M. 2015. A novel Cre recombinase reporter mouse strain facilitates
selective and efficient infection of primary immune cells with adenoviral vectors.
European Journal of Immunology. 45(6), 1614–1620.
mla: Heger, Klaus, et al. “A Novel Cre Recombinase Reporter Mouse Strain Facilitates
Selective and Efficient Infection of Primary Immune Cells with Adenoviral Vectors.”
European Journal of Immunology, vol. 45, no. 6, Wiley, 2015, pp. 1614–20,
doi:10.1002/eji.201545457.
short: K. Heger, M. Kober, D. Rieß, C. Drees, I. de Vries, A. Bertossi, A. Roers,
M.K. Sixt, M. Schmidt Supprian, European Journal of Immunology 45 (2015) 1614–1620.
date_created: 2018-12-11T11:52:44Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2021-01-12T06:51:36Z
day: '01'
department:
- _id: MiSi
doi: 10.1002/eji.201545457
intvolume: ' 45'
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 1614 - 1620
publication: European Journal of Immunology
publication_status: published
publisher: Wiley
publist_id: '5610'
quality_controlled: '1'
scopus_import: 1
status: public
title: A novel Cre recombinase reporter mouse strain facilitates selective and efficient
infection of primary immune cells with adenoviral vectors
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2015'
...
---
_id: '1562'
abstract:
- lang: eng
text: The plant hormone auxin is a key regulator of plant growth and development.
Auxin levels are sensed and interpreted by distinct receptor systems that activate
a broad range of cellular responses. The Auxin-Binding Protein1 (ABP1) that has
been identified based on its ability to bind auxin with high affinity is a prime
candidate for the extracellular receptor responsible for mediating a range of
auxin effects, in particular, the fast non-transcriptional ones. Contradictory
genetic studies suggested prominent or no importance of ABP1 in many developmental
processes. However, how crucial the role of auxin binding to ABP1 is for its functions
has not been addressed. Here, we show that the auxin-binding pocket of ABP1 is
essential for its gain-of-function cellular and developmental roles. In total,
16 different abp1 mutants were prepared that possessed substitutions in the metal
core or in the hydrophobic amino acids of the auxin-binding pocket as well as
neutral mutations. Their analysis revealed that an intact auxin-binding pocket
is a prerequisite for ABP1 to activate downstream components of the ABP1 signalling
pathway, such as Rho of Plants (ROPs) and to mediate the clathrin association
with membranes for endocytosis regulation. In planta analyses demonstrated the
importance of the auxin binding pocket for all known ABP1-mediated postembryonic
developmental processes, including morphology of leaf epidermal cells, root growth
and root meristem activity, and vascular tissue differentiation. Taken together,
these findings suggest that auxin binding to ABP1 is central to its function,
supporting the role of ABP1 as auxin receptor.
acknowledgement: This work was supported by ERC Independent Research grant (ERC-2011-StG-
20101109-PSDP to JF); the European Social Fund and the state budget of the Czech
Republic [the project ‘Employment of Newly Graduated Doctors of Science for Scientific
Excellence’ (CZ.1.07/2.3.00/30.0009) to TN]; the Czech Science Foundation (GACR)
[project 13-40637S to JF].
article_type: original
author:
- first_name: Peter
full_name: Grones, Peter
id: 399876EC-F248-11E8-B48F-1D18A9856A87
last_name: Grones
- first_name: Xu
full_name: Chen, Xu
id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Riet
full_name: De Rycke, Riet
last_name: De Rycke
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Grones P, Chen X, Simon S, et al. Auxin-binding pocket of ABP1 is crucial for
its gain-of-function cellular and developmental roles. Journal of Experimental
Botany. 2015;66(16):5055-5065. doi:10.1093/jxb/erv177
apa: Grones, P., Chen, X., Simon, S., Kaufmann, W., De Rycke, R., Nodzyński, T.,
… Friml, J. (2015). Auxin-binding pocket of ABP1 is crucial for its gain-of-function
cellular and developmental roles. Journal of Experimental Botany. Oxford
University Press. https://doi.org/10.1093/jxb/erv177
chicago: Grones, Peter, Xu Chen, Sibu Simon, Walter Kaufmann, Riet De Rycke, Tomasz
Nodzyński, Eva Zažímalová, and Jiří Friml. “Auxin-Binding Pocket of ABP1 Is Crucial
for Its Gain-of-Function Cellular and Developmental Roles.” Journal of Experimental
Botany. Oxford University Press, 2015. https://doi.org/10.1093/jxb/erv177.
ieee: P. Grones et al., “Auxin-binding pocket of ABP1 is crucial for its
gain-of-function cellular and developmental roles,” Journal of Experimental
Botany, vol. 66, no. 16. Oxford University Press, pp. 5055–5065, 2015.
ista: Grones P, Chen X, Simon S, Kaufmann W, De Rycke R, Nodzyński T, Zažímalová
E, Friml J. 2015. Auxin-binding pocket of ABP1 is crucial for its gain-of-function
cellular and developmental roles. Journal of Experimental Botany. 66(16), 5055–5065.
mla: Grones, Peter, et al. “Auxin-Binding Pocket of ABP1 Is Crucial for Its Gain-of-Function
Cellular and Developmental Roles.” Journal of Experimental Botany, vol.
66, no. 16, Oxford University Press, 2015, pp. 5055–65, doi:10.1093/jxb/erv177.
short: P. Grones, X. Chen, S. Simon, W. Kaufmann, R. De Rycke, T. Nodzyński, E.
Zažímalová, J. Friml, Journal of Experimental Botany 66 (2015) 5055–5065.
date_created: 2018-12-11T11:52:44Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2023-02-23T10:04:26Z
day: '01'
department:
- _id: JiFr
- _id: EM-Fac
doi: 10.1093/jxb/erv177
ec_funded: 1
intvolume: ' 66'
issue: '16'
language:
- iso: eng
month: '08'
oa_version: None
page: 5055 - 5065
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Journal of Experimental Botany
publication_status: published
publisher: Oxford University Press
publist_id: '5609'
quality_controlled: '1'
scopus_import: 1
status: public
title: Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and
developmental roles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 66
year: '2015'
...
---
_id: '1563'
abstract:
- lang: eng
text: For a given self-map $f$ of $M$, a closed smooth connected and simply-connected
manifold of dimension $m\geq 4$, we provide an algorithm for estimating the values
of the topological invariant $D^m_r[f]$, which equals the minimal number of $r$-periodic
points in the smooth homotopy class of $f$. Our results are based on the combinatorial
scheme for computing $D^m_r[f]$ introduced by G. Graff and J. Jezierski [J. Fixed
Point Theory Appl. 13 (2013), 63-84]. An open-source implementation of the algorithm
programmed in C++ is publicly available at {\tt http://www.pawelpilarczyk.com/combtop/}.
author:
- first_name: Grzegorz
full_name: Graff, Grzegorz
last_name: Graff
- first_name: Pawel
full_name: Pilarczyk, Pawel
id: 3768D56A-F248-11E8-B48F-1D18A9856A87
last_name: Pilarczyk
citation:
ama: Graff G, Pilarczyk P. An algorithmic approach to estimating the minimal number
of periodic points for smooth self-maps of simply-connected manifolds. Topological
Methods in Nonlinear Analysis. 2015;45(1):273-286. doi:10.12775/TMNA.2015.014
apa: Graff, G., & Pilarczyk, P. (2015). An algorithmic approach to estimating
the minimal number of periodic points for smooth self-maps of simply-connected
manifolds. Topological Methods in Nonlinear Analysis. Juliusz Schauder
Center for Nonlinear Studies. https://doi.org/10.12775/TMNA.2015.014
chicago: Graff, Grzegorz, and Pawel Pilarczyk. “An Algorithmic Approach to Estimating
the Minimal Number of Periodic Points for Smooth Self-Maps of Simply-Connected
Manifolds.” Topological Methods in Nonlinear Analysis. Juliusz Schauder
Center for Nonlinear Studies, 2015. https://doi.org/10.12775/TMNA.2015.014.
ieee: G. Graff and P. Pilarczyk, “An algorithmic approach to estimating the minimal
number of periodic points for smooth self-maps of simply-connected manifolds,”
Topological Methods in Nonlinear Analysis, vol. 45, no. 1. Juliusz Schauder
Center for Nonlinear Studies, pp. 273–286, 2015.
ista: Graff G, Pilarczyk P. 2015. An algorithmic approach to estimating the minimal
number of periodic points for smooth self-maps of simply-connected manifolds.
Topological Methods in Nonlinear Analysis. 45(1), 273–286.
mla: Graff, Grzegorz, and Pawel Pilarczyk. “An Algorithmic Approach to Estimating
the Minimal Number of Periodic Points for Smooth Self-Maps of Simply-Connected
Manifolds.” Topological Methods in Nonlinear Analysis, vol. 45, no. 1,
Juliusz Schauder Center for Nonlinear Studies, 2015, pp. 273–86, doi:10.12775/TMNA.2015.014.
short: G. Graff, P. Pilarczyk, Topological Methods in Nonlinear Analysis 45 (2015)
273–286.
date_created: 2018-12-11T11:52:44Z
date_published: 2015-03-01T00:00:00Z
date_updated: 2021-01-12T06:51:37Z
day: '01'
department:
- _id: HeEd
doi: 10.12775/TMNA.2015.014
intvolume: ' 45'
issue: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: 273 - 286
publication: Topological Methods in Nonlinear Analysis
publication_status: published
publisher: Juliusz Schauder Center for Nonlinear Studies
publist_id: '5608'
quality_controlled: '1'
scopus_import: 1
status: public
title: An algorithmic approach to estimating the minimal number of periodic points
for smooth self-maps of simply-connected manifolds
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2015'
...
---
_id: '1564'
article_number: '145'
author:
- first_name: Matthieu
full_name: Gilson, Matthieu
last_name: Gilson
- first_name: Cristina
full_name: Savin, Cristina
id: 3933349E-F248-11E8-B48F-1D18A9856A87
last_name: Savin
- first_name: Friedemann
full_name: Zenke, Friedemann
last_name: Zenke
citation:
ama: 'Gilson M, Savin C, Zenke F. Editorial: Emergent neural computation from the
interaction of different forms of plasticity. Frontiers in Computational Neuroscience.
2015;9(11). doi:10.3389/fncom.2015.00145'
apa: 'Gilson, M., Savin, C., & Zenke, F. (2015). Editorial: Emergent neural
computation from the interaction of different forms of plasticity. Frontiers
in Computational Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncom.2015.00145'
chicago: 'Gilson, Matthieu, Cristina Savin, and Friedemann Zenke. “Editorial: Emergent
Neural Computation from the Interaction of Different Forms of Plasticity.” Frontiers
in Computational Neuroscience. Frontiers Research Foundation, 2015. https://doi.org/10.3389/fncom.2015.00145.'
ieee: 'M. Gilson, C. Savin, and F. Zenke, “Editorial: Emergent neural computation
from the interaction of different forms of plasticity,” Frontiers in Computational
Neuroscience, vol. 9, no. 11. Frontiers Research Foundation, 2015.'
ista: 'Gilson M, Savin C, Zenke F. 2015. Editorial: Emergent neural computation
from the interaction of different forms of plasticity. Frontiers in Computational
Neuroscience. 9(11), 145.'
mla: 'Gilson, Matthieu, et al. “Editorial: Emergent Neural Computation from the
Interaction of Different Forms of Plasticity.” Frontiers in Computational Neuroscience,
vol. 9, no. 11, 145, Frontiers Research Foundation, 2015, doi:10.3389/fncom.2015.00145.'
short: M. Gilson, C. Savin, F. Zenke, Frontiers in Computational Neuroscience 9
(2015).
date_created: 2018-12-11T11:52:45Z
date_published: 2015-11-30T00:00:00Z
date_updated: 2021-01-12T06:51:37Z
day: '30'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.3389/fncom.2015.00145
ec_funded: 1
file:
- access_level: open_access
checksum: cea73b6d3ef1579f32da10b82f4de4fd
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:09Z
date_updated: 2020-07-14T12:45:02Z
file_id: '4927'
file_name: IST-2016-479-v1+1_fncom-09-00145.pdf
file_size: 187038
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Frontiers in Computational Neuroscience
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '5607'
pubrep_id: '479'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Editorial: Emergent neural computation from the interaction of different forms
of plasticity'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2015'
...
---
_id: '1565'
abstract:
- lang: eng
text: Leptin is an adipokine produced by the adipose tissue regulating body weight
through its appetite-suppressing effect. Besides being expressed in the hypothalamus
and hippocampus, leptin receptors (ObRs) are also present in chromaffin cells
of the adrenal medulla. In the present study, we report the effect of leptin on
mouse chromaffin cell (MCC) functionality, focusing on cell excitability and catecholamine
secretion. Acute application of leptin (1 nm) on spontaneously firing MCCs caused
a slowly developing membrane hyperpolarization followed by complete blockade of
action potential (AP) firing. This inhibitory effect at rest was abolished by
the BK channel blocker paxilline (1 μm), suggesting the involvement of BK potassium
channels. Single-channel recordings in 'perforated microvesicles' confirmed that
leptin increased BK channel open probability without altering its unitary conductance.
BK channel up-regulation was associated with the phosphoinositide 3-kinase (PI3K)
signalling cascade because the PI3K specific inhibitor wortmannin (100 nm) fully
prevented BK current increase. We also tested the effect of leptin on evoked AP
firing and Ca2+-driven exocytosis. Although leptin preserves well-adapted AP trains
of lower frequency, APs are broader and depolarization-evoked exocytosis is increased
as a result of the larger size of the ready-releasable pool and higher frequency
of vesicle release. The kinetics and quantal size of single secretory events remained
unaltered. Leptin had no effect on firing and secretion in db-/db- mice lacking
the ObR gene, confirming its specificity. In conclusion, leptin exhibits a dual
action on MCC activity. It dampens AP firing at rest but preserves AP firing and
increases catecholamine secretion during sustained stimulation, highlighting the
importance of the adipo-adrenal axis in the leptin-mediated increase of sympathetic
tone and catecholamine release.
acknowledgement: "This work was supported by the Compagnia di San Paolo Foundation
‘Neuroscience Program’ to VC and ‘Progetto di Ateneo 2011-13’ to EC.\r\nWe thank
Dr Claudio Franchino for cell preparation and for providing excellent technical
support."
author:
- first_name: Daniela
full_name: Gavello, Daniela
last_name: Gavello
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Sara
full_name: Gosso, Sara
last_name: Gosso
- first_name: Emilio
full_name: Carbone, Emilio
last_name: Carbone
- first_name: Valentina
full_name: Carabelli, Valentina
last_name: Carabelli
citation:
ama: Gavello D, Vandael DH, Gosso S, Carbone E, Carabelli V. Dual action of leptin
on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven
BK channel up-regulation in mouse chromaffin cells. Journal of Physiology.
2015;593(22):4835-4853. doi:10.1113/JP271078
apa: Gavello, D., Vandael, D. H., Gosso, S., Carbone, E., & Carabelli, V. (2015).
Dual action of leptin on rest-firing and stimulated catecholamine release via
phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells.
Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/JP271078
chicago: Gavello, Daniela, David H Vandael, Sara Gosso, Emilio Carbone, and Valentina
Carabelli. “Dual Action of Leptin on Rest-Firing and Stimulated Catecholamine
Release via Phosphoinositide 3-Kinase-Riven BK Channel up-Regulation in Mouse
Chromaffin Cells.” Journal of Physiology. Wiley-Blackwell, 2015. https://doi.org/10.1113/JP271078.
ieee: D. Gavello, D. H. Vandael, S. Gosso, E. Carbone, and V. Carabelli, “Dual action
of leptin on rest-firing and stimulated catecholamine release via phosphoinositide
3-kinase-riven BK channel up-regulation in mouse chromaffin cells,” Journal
of Physiology, vol. 593, no. 22. Wiley-Blackwell, pp. 4835–4853, 2015.
ista: Gavello D, Vandael DH, Gosso S, Carbone E, Carabelli V. 2015. Dual action
of leptin on rest-firing and stimulated catecholamine release via phosphoinositide
3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of
Physiology. 593(22), 4835–4853.
mla: Gavello, Daniela, et al. “Dual Action of Leptin on Rest-Firing and Stimulated
Catecholamine Release via Phosphoinositide 3-Kinase-Riven BK Channel up-Regulation
in Mouse Chromaffin Cells.” Journal of Physiology, vol. 593, no. 22, Wiley-Blackwell,
2015, pp. 4835–53, doi:10.1113/JP271078.
short: D. Gavello, D.H. Vandael, S. Gosso, E. Carbone, V. Carabelli, Journal of
Physiology 593 (2015) 4835–4853.
date_created: 2018-12-11T11:52:45Z
date_published: 2015-11-15T00:00:00Z
date_updated: 2021-01-12T06:51:38Z
day: '15'
department:
- _id: PeJo
doi: 10.1113/JP271078
external_id:
pmid:
- '26282459'
intvolume: ' 593'
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650409/
month: '11'
oa: 1
oa_version: Submitted Version
page: 4835 - 4853
pmid: 1
publication: Journal of Physiology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5606'
quality_controlled: '1'
scopus_import: 1
status: public
title: Dual action of leptin on rest-firing and stimulated catecholamine release via
phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 593
year: '2015'
...
---
_id: '1566'
abstract:
- lang: eng
text: Deposits of misfolded proteins in the human brain are associated with the
development of many neurodegenerative diseases. Recent studies show that these
proteins have common traits even at the monomer level. Among them, a polyglutamine
region that is present in huntingtin is known to exhibit a correlation between
the length of the chain and the severity as well as the earliness of the onset
of Huntington disease. Here, we apply bias exchange molecular dynamics to generate
structures of polyglutamine expansions of several lengths and characterize the
resulting independent conformations. We compare the properties of these conformations
to those of the standard proteins, as well as to other homopolymeric tracts. We
find that, similar to the previously studied polyvaline chains, the set of possible
transient folds is much broader than the set of known-to-date folds, although
the conformations have different structures. We show that the mechanical stability
is not related to any simple geometrical characteristics of the structures. We
demonstrate that long polyglutamine expansions result in higher mechanical stability
than the shorter ones. They also have a longer life span and are substantially
more prone to form knotted structures. The knotted region has an average length
of 35 residues, similar to the typical threshold for most polyglutamine-related
diseases. Similarly, changes in shape and mechanical stability appear once the
total length of the peptide exceeds this threshold of 35 glutamine residues. We
suggest that knotted conformers may also harm the cellular machinery and thus
lead to disease.
acknowledgement: 'We acknowledge the support by the EU Joint Programme in Neurodegenerative
Diseases (JPND AC14/00037) project. The project is supported through the following
funding organisations under the aegis of JPND—www.jpnd.eu: Ireland, HRB; Poland,
National Science Centre; and Spain, ISCIII. '
article_number: e1004541
author:
- first_name: Àngel
full_name: Gómez Sicilia, Àngel
last_name: Gómez Sicilia
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Marek
full_name: Cieplak, Marek
last_name: Cieplak
- first_name: Mariano
full_name: Carrión Vázquez, Mariano
last_name: Carrión Vázquez
citation:
ama: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of
the universe of polyglutamine structures. PLoS Computational Biology. 2015;11(10).
doi:10.1371/journal.pcbi.1004541
apa: Gómez Sicilia, À., Sikora, M. K., Cieplak, M., & Carrión Vázquez, M. (2015).
An exploration of the universe of polyglutamine structures. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004541
chicago: Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión
Vázquez. “An Exploration of the Universe of Polyglutamine Structures.” PLoS
Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004541.
ieee: À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration
of the universe of polyglutamine structures,” PLoS Computational Biology,
vol. 11, no. 10. Public Library of Science, 2015.
ista: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration
of the universe of polyglutamine structures. PLoS Computational Biology. 11(10),
e1004541.
mla: Gómez Sicilia, Àngel, et al. “An Exploration of the Universe of Polyglutamine
Structures.” PLoS Computational Biology, vol. 11, no. 10, e1004541, Public
Library of Science, 2015, doi:10.1371/journal.pcbi.1004541.
short: À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, PLoS Computational
Biology 11 (2015).
date_created: 2018-12-11T11:52:45Z
date_published: 2015-10-23T00:00:00Z
date_updated: 2023-02-23T14:05:55Z
day: '23'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1371/journal.pcbi.1004541
file:
- access_level: open_access
checksum: 8b67d729be663bfc9af04bfd94459655
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:21Z
date_updated: 2020-07-14T12:45:02Z
file_id: '5207'
file_name: IST-2016-478-v1+1_journal.pcbi.1004541.pdf
file_size: 1412511
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5605'
pubrep_id: '478'
quality_controlled: '1'
related_material:
record:
- id: '9714'
relation: research_data
status: public
scopus_import: 1
status: public
title: An exploration of the universe of polyglutamine structures
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2015'
...
---
_id: '1567'
abstract:
- lang: eng
text: My personal journey to the fascinating world of geometric forms started more
than 30 years ago with the invention of alpha shapes in the plane. It took about
10 years before we generalized the concept to higher dimensions, we produced working
software with a graphics interface for the three-dimensional case. At the same
time, we added homology to the computations. Needless to say that this foreshadowed
the inception of persistent homology, because it suggested the study of filtrations
to capture the scale of a shape or data set. Importantly, this method has fast
algorithms. The arguably most useful result on persistent homology is the stability
of its diagrams under perturbations.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Edelsbrunner H. Shape, homology, persistence, and stability. In: 23rd International
Symposium. Vol 9411. Springer Nature; 2015.'
apa: 'Edelsbrunner, H. (2015). Shape, homology, persistence, and stability. In 23rd
International Symposium (Vol. 9411). Los Angeles, CA, United States: Springer
Nature.'
chicago: Edelsbrunner, Herbert. “Shape, Homology, Persistence, and Stability.” In
23rd International Symposium, Vol. 9411. Springer Nature, 2015.
ieee: H. Edelsbrunner, “Shape, homology, persistence, and stability,” in 23rd
International Symposium, Los Angeles, CA, United States, 2015, vol. 9411.
ista: 'Edelsbrunner H. 2015. Shape, homology, persistence, and stability. 23rd International
Symposium. GD: Graph Drawing and Network Visualization, LNCS, vol. 9411.'
mla: Edelsbrunner, Herbert. “Shape, Homology, Persistence, and Stability.” 23rd
International Symposium, vol. 9411, Springer Nature, 2015.
short: H. Edelsbrunner, in:, 23rd International Symposium, Springer Nature, 2015.
conference:
end_date: 2015-09-26
location: Los Angeles, CA, United States
name: 'GD: Graph Drawing and Network Visualization'
start_date: 2015-09-24
date_created: 2018-12-11T11:52:46Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2022-01-28T08:25:00Z
day: '01'
department:
- _id: HeEd
intvolume: ' 9411'
language:
- iso: eng
month: '01'
oa_version: None
publication: 23rd International Symposium
publication_status: published
publisher: Springer Nature
publist_id: '5604'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Shape, homology, persistence, and stability
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9411
year: '2015'
...
---
_id: '1568'
abstract:
- lang: eng
text: Aiming at the automatic diagnosis of tumors from narrow band imaging (NBI)
magnifying endoscopy (ME) images of the stomach, we combine methods from image
processing, computational topology, and machine learning to classify patterns
into normal, tubular, vessel. Training the algorithm on a small number of images
of each type, we achieve a high rate of correct classifications. The analysis
of the learning algorithm reveals that a handful of geometric and topological
features are responsible for the overwhelming majority of decisions.
acknowledgement: This research is supported by the project No. 477 of P.G. Demidov
Yaroslavl State University within State Assignment for Research.
author:
- first_name: Olga
full_name: Dunaeva, Olga
last_name: Dunaeva
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Anton
full_name: Lukyanov, Anton
last_name: Lukyanov
- first_name: Michael
full_name: Machin, Michael
last_name: Machin
- first_name: Daria
full_name: Malkova, Daria
last_name: Malkova
citation:
ama: 'Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D. The classification
of endoscopy images with persistent homology. In: Proceedings - 16th International
Symposium on Symbolic and Numeric Algorithms for Scientific Computing. IEEE;
2015:7034731. doi:10.1109/SYNASC.2014.81'
apa: 'Dunaeva, O., Edelsbrunner, H., Lukyanov, A., Machin, M., & Malkova, D.
(2015). The classification of endoscopy images with persistent homology. In Proceedings
- 16th International Symposium on Symbolic and Numeric Algorithms for Scientific
Computing (p. 7034731). Timisoara, Romania: IEEE. https://doi.org/10.1109/SYNASC.2014.81'
chicago: Dunaeva, Olga, Herbert Edelsbrunner, Anton Lukyanov, Michael Machin, and
Daria Malkova. “The Classification of Endoscopy Images with Persistent Homology.”
In Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms
for Scientific Computing, 7034731. IEEE, 2015. https://doi.org/10.1109/SYNASC.2014.81.
ieee: O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, and D. Malkova, “The
classification of endoscopy images with persistent homology,” in Proceedings
- 16th International Symposium on Symbolic and Numeric Algorithms for Scientific
Computing, Timisoara, Romania, 2015, p. 7034731.
ista: 'Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D. 2015. The classification
of endoscopy images with persistent homology. Proceedings - 16th International
Symposium on Symbolic and Numeric Algorithms for Scientific Computing. SYNASC:
Symbolic and Numeric Algorithms for Scientific Computing, 7034731.'
mla: Dunaeva, Olga, et al. “The Classification of Endoscopy Images with Persistent
Homology.” Proceedings - 16th International Symposium on Symbolic and Numeric
Algorithms for Scientific Computing, IEEE, 2015, p. 7034731, doi:10.1109/SYNASC.2014.81.
short: O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, D. Malkova, in:, Proceedings
- 16th International Symposium on Symbolic and Numeric Algorithms for Scientific
Computing, IEEE, 2015, p. 7034731.
conference:
end_date: 2014-09-25
location: Timisoara, Romania
name: 'SYNASC: Symbolic and Numeric Algorithms for Scientific Computing'
start_date: 2014-09-22
date_created: 2018-12-11T11:52:46Z
date_published: 2015-02-05T00:00:00Z
date_updated: 2023-02-21T16:57:29Z
day: '05'
department:
- _id: HeEd
doi: 10.1109/SYNASC.2014.81
language:
- iso: eng
month: '02'
oa_version: None
page: '7034731'
publication: Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms
for Scientific Computing
publication_status: published
publisher: IEEE
publist_id: '5603'
quality_controlled: '1'
related_material:
record:
- id: '1289'
relation: later_version
status: public
scopus_import: 1
status: public
title: The classification of endoscopy images with persistent homology
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1569'
abstract:
- lang: eng
text: Spatial regulation of the plant hormone indole-3-acetic acid (IAA, or auxin)
is essential for plant development. Auxin gradient establishment is mediated by
polarly localized auxin transporters, including PIN-FORMED (PIN) proteins. Their
localization and abundance at the plasma membrane are tightly regulated by endomembrane
machinery, especially the endocytic and recycling pathways mediated by the ADP
ribosylation factor guanine nucleotide exchange factor (ARF-GEF) GNOM. We assessed
the role of the early secretory pathway in establishing PIN1 polarity in Arabidopsis
thaliana by pharmacological and genetic approaches. We identified the compound
endosidin 8 (ES8), which selectively interferes with PIN1 basal polarity without
altering the polarity of apical proteins. ES8 alters the auxin distribution pattern
in the root and induces a strong developmental phenotype, including reduced root
length. The ARF-GEF- defective mutants gnom-like 1 ( gnl1-1) and gnom ( van7)
are significantly resistant to ES8. The compound does not affect recycling or
vacuolar trafficking of PIN1 but leads to its intracellular accumulation, resulting
in loss of PIN1 basal polarity at the plasma membrane. Our data confirm a role
for GNOM in endoplasmic reticulum (ER) - Golgi trafficking and reveal that a GNL1/GNOM-mediated
early secretory pathway selectively regulates PIN1 basal polarity establishment
in a manner essential for normal plant development.
acknowledgement: 'This work was supported by Vetenskapsrådet and Vinnova (Verket för
Innovationssystemet) (S.M.D., T.V., M.Ł., and S.R.), Knut och Alice Wallenbergs
Stiftelse (S.M.D., A.R., and C.V.), Kempestiftelserna (A.H. and Q.M.), Carl Tryggers
Stiftelse för Vetenskaplig Forskning (Q.M.), European Research Council Grant ERC-2011-StG-20101109-PSDP
(to J.F.), US Department of Energy Grant DE-FG02-02ER15295 (to N.V.R.), and National
Science Foundation Grant MCB-0817916 (to N.V.R. and G.R.H.). '
author:
- first_name: Siamsa
full_name: Doyle, Siamsa
last_name: Doyle
- first_name: Ash
full_name: Haegera, Ash
last_name: Haegera
- first_name: Thomas
full_name: Vain, Thomas
last_name: Vain
- first_name: Adeline
full_name: Rigala, Adeline
last_name: Rigala
- first_name: Corrado
full_name: Viotti, Corrado
last_name: Viotti
- first_name: Małgorzata
full_name: Łangowskaa, Małgorzata
last_name: Łangowskaa
- first_name: Qian
full_name: Maa, Qian
last_name: Maa
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Natasha
full_name: Raikhel, Natasha
last_name: Raikhel
- first_name: Glenn
full_name: Hickse, Glenn
last_name: Hickse
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
citation:
ama: Doyle S, Haegera A, Vain T, et al. An early secretory pathway mediated by gnom-like
1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana.
PNAS. 2015;112(7):E806-E815. doi:10.1073/pnas.1424856112
apa: Doyle, S., Haegera, A., Vain, T., Rigala, A., Viotti, C., Łangowskaa, M., …
Robert, S. (2015). An early secretory pathway mediated by gnom-like 1 and gnom
is essential for basal polarity establishment in Arabidopsis thaliana. PNAS.
National Academy of Sciences. https://doi.org/10.1073/pnas.1424856112
chicago: Doyle, Siamsa, Ash Haegera, Thomas Vain, Adeline Rigala, Corrado Viotti,
Małgorzata Łangowskaa, Qian Maa, et al. “An Early Secretory Pathway Mediated by
Gnom-like 1 and Gnom Is Essential for Basal Polarity Establishment in Arabidopsis
Thaliana.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1424856112.
ieee: S. Doyle et al., “An early secretory pathway mediated by gnom-like
1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana,”
PNAS, vol. 112, no. 7. National Academy of Sciences, pp. E806–E815, 2015.
ista: Doyle S, Haegera A, Vain T, Rigala A, Viotti C, Łangowskaa M, Maa Q, Friml
J, Raikhel N, Hickse G, Robert S. 2015. An early secretory pathway mediated by
gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis
thaliana. PNAS. 112(7), E806–E815.
mla: Doyle, Siamsa, et al. “An Early Secretory Pathway Mediated by Gnom-like 1 and
Gnom Is Essential for Basal Polarity Establishment in Arabidopsis Thaliana.” PNAS,
vol. 112, no. 7, National Academy of Sciences, 2015, pp. E806–15, doi:10.1073/pnas.1424856112.
short: S. Doyle, A. Haegera, T. Vain, A. Rigala, C. Viotti, M. Łangowskaa, Q. Maa,
J. Friml, N. Raikhel, G. Hickse, S. Robert, PNAS 112 (2015) E806–E815.
date_created: 2018-12-11T11:52:46Z
date_published: 2015-02-17T00:00:00Z
date_updated: 2021-01-12T06:51:39Z
day: '17'
department:
- _id: JiFr
doi: 10.1073/pnas.1424856112
ec_funded: 1
intvolume: ' 112'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4343110/
month: '02'
oa: 1
oa_version: Published Version
page: E806 - E815
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5602'
quality_controlled: '1'
scopus_import: 1
status: public
title: An early secretory pathway mediated by gnom-like 1 and gnom is essential for
basal polarity establishment in Arabidopsis thaliana
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '1570'
abstract:
- lang: eng
text: Grounding autonomous behavior in the nervous system is a fundamental challenge
for neuroscience. In particular, self-organized behavioral development provides
more questions than answers. Are there special functional units for curiosity,
motivation, and creativity? This paper argues that these features can be grounded
in synaptic plasticity itself, without requiring any higher-level constructs.
We propose differential extrinsic plasticity (DEP) as a new synaptic rule for
self-learning systems and apply it to a number of complex robotic systems as a
test case. Without specifying any purpose or goal, seemingly purposeful and adaptive
rhythmic behavior is developed, displaying a certain level of sensorimotor intelligence.
These surprising results require no systemspecific modifications of the DEP rule.
They rather arise from the underlying mechanism of spontaneous symmetry breaking,which
is due to the tight brain body environment coupling. The new synaptic rule is
biologically plausible and would be an interesting target for neurobiological
investigation. We also argue that this neuronal mechanism may have been a catalyst
in natural evolution.
author:
- first_name: Ralf
full_name: Der, Ralf
last_name: Der
- first_name: Georg S
full_name: Martius, Georg S
id: 3A276B68-F248-11E8-B48F-1D18A9856A87
last_name: Martius
citation:
ama: Der R, Martius GS. Novel plasticity rule can explain the development of sensorimotor
intelligence. PNAS. 2015;112(45):E6224-E6232. doi:10.1073/pnas.1508400112
apa: Der, R., & Martius, G. S. (2015). Novel plasticity rule can explain the
development of sensorimotor intelligence. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.1508400112
chicago: Der, Ralf, and Georg S Martius. “Novel Plasticity Rule Can Explain the
Development of Sensorimotor Intelligence.” PNAS. National Academy of Sciences,
2015. https://doi.org/10.1073/pnas.1508400112.
ieee: R. Der and G. S. Martius, “Novel plasticity rule can explain the development
of sensorimotor intelligence,” PNAS, vol. 112, no. 45. National Academy
of Sciences, pp. E6224–E6232, 2015.
ista: Der R, Martius GS. 2015. Novel plasticity rule can explain the development
of sensorimotor intelligence. PNAS. 112(45), E6224–E6232.
mla: Der, Ralf, and Georg S. Martius. “Novel Plasticity Rule Can Explain the Development
of Sensorimotor Intelligence.” PNAS, vol. 112, no. 45, National Academy
of Sciences, 2015, pp. E6224–32, doi:10.1073/pnas.1508400112.
short: R. Der, G.S. Martius, PNAS 112 (2015) E6224–E6232.
date_created: 2018-12-11T11:52:47Z
date_published: 2015-11-10T00:00:00Z
date_updated: 2021-01-12T06:51:40Z
day: '10'
department:
- _id: ChLa
- _id: GaTk
doi: 10.1073/pnas.1508400112
ec_funded: 1
external_id:
pmid:
- '26504200'
intvolume: ' 112'
issue: '45'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4653169/
month: '11'
oa: 1
oa_version: Submitted Version
page: E6224 - E6232
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5601'
quality_controlled: '1'
scopus_import: 1
status: public
title: Novel plasticity rule can explain the development of sensorimotor intelligence
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '1571'
abstract:
- lang: eng
text: Epistatic interactions can frustrate and shape evolutionary change. Indeed,
phenotypes may fail to evolve when essential mutations are only accessible through
positive selection if they are fixed simultaneously. How environmental variability
affects such constraints is poorly understood. Here, we studied genetic constraints
in fixed and fluctuating environments using the Escherichia coli lac operon as
a model system for genotype-environment interactions. We found that, in different
fixed environments, all trajectories that were reconstructed by applying point
mutations within the transcription factor-operator interface became trapped at
suboptima, where no additional improvements were possible. Paradoxically, repeated
switching between these same environments allows unconstrained adaptation by continuous
improvements. This evolutionary mode is explained by pervasive cross-environmental
tradeoffs that reposition the peaks in such a way that trapped genotypes can repeatedly
climb ascending slopes and hence, escape adaptive stasis. Using a Markov approach,
we developed a mathematical framework to quantify the landscape-crossing rates
and show that this ratchet-like adaptive mechanism is robust in a wide spectrum
of fluctuating environments. Overall, this study shows that genetic constraints
can be overcome by environmental change and that crossenvironmental tradeoffs
do not necessarily impede but also, can facilitate adaptive evolution. Because
tradeoffs and environmental variability are ubiquitous in nature, we speculate
this evolutionary mode to be of general relevance.
acknowledgement: This work is part of the research program of the Foundation for Fundamental
Research on Matter, which is part of the Netherlands Organization for Scientific
Research (NWO). M.G.J.d.V. was (partially) funded by NWO Earth and Life Sciences
(ALW), project 863.14.015. We thank D. M. Weinreich, J. A. G. M. de Visser, T. Paixão,
J. Polechová, T. Friedlander, and A. E. Mayo for reading and commenting on earlier
versions of the manuscript and B. Houchmandzadeh, O. Rivoire, and M. Hemery for
discussions and suggestions on the Markov computation. Furthermore, we thank F.
J. Poelwijk for sharing plasmid pCascade5 and pRD007 and Y. Yokobayashi for sharing
plasmid pINV-110. We also thank the anonymous reviewers for remarks on the initial
version of the manuscript.
author:
- first_name: Marjon
full_name: De Vos, Marjon
id: 3111FFAC-F248-11E8-B48F-1D18A9856A87
last_name: De Vos
- first_name: Alexandre
full_name: Dawid, Alexandre
last_name: Dawid
- first_name: Vanda
full_name: Šunderlíková, Vanda
last_name: Šunderlíková
- first_name: Sander
full_name: Tans, Sander
last_name: Tans
citation:
ama: de Vos M, Dawid A, Šunderlíková V, Tans S. Breaking evolutionary constraint
with a tradeoff ratchet. PNAS. 2015;112(48):14906-14911. doi:10.1073/pnas.1510282112
apa: de Vos, M., Dawid, A., Šunderlíková, V., & Tans, S. (2015). Breaking evolutionary
constraint with a tradeoff ratchet. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.1510282112
chicago: Vos, Marjon de, Alexandre Dawid, Vanda Šunderlíková, and Sander Tans. “Breaking
Evolutionary Constraint with a Tradeoff Ratchet.” PNAS. National Academy
of Sciences, 2015. https://doi.org/10.1073/pnas.1510282112.
ieee: M. de Vos, A. Dawid, V. Šunderlíková, and S. Tans, “Breaking evolutionary
constraint with a tradeoff ratchet,” PNAS, vol. 112, no. 48. National Academy
of Sciences, pp. 14906–14911, 2015.
ista: de Vos M, Dawid A, Šunderlíková V, Tans S. 2015. Breaking evolutionary constraint
with a tradeoff ratchet. PNAS. 112(48), 14906–14911.
mla: de Vos, Marjon, et al. “Breaking Evolutionary Constraint with a Tradeoff Ratchet.”
PNAS, vol. 112, no. 48, National Academy of Sciences, 2015, pp. 14906–11,
doi:10.1073/pnas.1510282112.
short: M. de Vos, A. Dawid, V. Šunderlíková, S. Tans, PNAS 112 (2015) 14906–14911.
date_created: 2018-12-11T11:52:47Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2021-01-12T06:51:40Z
day: '01'
department:
- _id: ToBo
doi: 10.1073/pnas.1510282112
intvolume: ' 112'
issue: '48'
language:
- iso: eng
month: '12'
oa_version: None
page: 14906 - 14911
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5600'
quality_controlled: '1'
scopus_import: 1
status: public
title: Breaking evolutionary constraint with a tradeoff ratchet
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '1572'
abstract:
- lang: eng
text: "We consider the quantum ferromagnetic Heisenberg model in three dimensions,
for all spins S ≥ 1/2. We rigorously prove the validity of the spin-wave approximation
for the excitation spectrum, at the level of the first non-trivial contribution
to the free energy at low temperatures. Our proof comes with explicit, constructive
upper and lower bounds on the error term. It uses in an essential way the bosonic
formulation of the model in terms of the Holstein-Primakoff representation. In
this language, the model describes interacting bosons with a hard-core on-site
repulsion and a nearest-neighbor attraction. This attractive interaction makes
the lower bound on the free energy particularly tricky: the key idea there is
to prove a differential inequality for the two-particle density, which is thereby
shown to be smaller than the probability density of a suitably weighted two-particle
random process on the lattice.\r\n"
author:
- first_name: Michele
full_name: Correggi, Michele
last_name: Correggi
- first_name: Alessandro
full_name: Giuliani, Alessandro
last_name: Giuliani
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Correggi M, Giuliani A, Seiringer R. Validity of the spin-wave approximation
for the free energy of the Heisenberg ferromagnet. Communications in Mathematical
Physics. 2015;339(1):279-307. doi:10.1007/s00220-015-2402-0
apa: Correggi, M., Giuliani, A., & Seiringer, R. (2015). Validity of the spin-wave
approximation for the free energy of the Heisenberg ferromagnet. Communications
in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-015-2402-0
chicago: Correggi, Michele, Alessandro Giuliani, and Robert Seiringer. “Validity
of the Spin-Wave Approximation for the Free Energy of the Heisenberg Ferromagnet.”
Communications in Mathematical Physics. Springer, 2015. https://doi.org/10.1007/s00220-015-2402-0.
ieee: M. Correggi, A. Giuliani, and R. Seiringer, “Validity of the spin-wave approximation
for the free energy of the Heisenberg ferromagnet,” Communications in Mathematical
Physics, vol. 339, no. 1. Springer, pp. 279–307, 2015.
ista: Correggi M, Giuliani A, Seiringer R. 2015. Validity of the spin-wave approximation
for the free energy of the Heisenberg ferromagnet. Communications in Mathematical
Physics. 339(1), 279–307.
mla: Correggi, Michele, et al. “Validity of the Spin-Wave Approximation for the
Free Energy of the Heisenberg Ferromagnet.” Communications in Mathematical
Physics, vol. 339, no. 1, Springer, 2015, pp. 279–307, doi:10.1007/s00220-015-2402-0.
short: M. Correggi, A. Giuliani, R. Seiringer, Communications in Mathematical Physics
339 (2015) 279–307.
date_created: 2018-12-11T11:52:47Z
date_published: 2015-06-23T00:00:00Z
date_updated: 2021-01-12T06:51:41Z
day: '23'
department:
- _id: RoSe
doi: 10.1007/s00220-015-2402-0
intvolume: ' 339'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1312.7873
month: '06'
oa: 1
oa_version: Preprint
page: 279 - 307
publication: Communications in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '5599'
quality_controlled: '1'
scopus_import: 1
status: public
title: Validity of the spin-wave approximation for the free energy of the Heisenberg
ferromagnet
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 339
year: '2015'
...
---
_id: '1573'
abstract:
- lang: eng
text: We present a new, simpler proof of the unconditional uniqueness of solutions
to the cubic Gross-Pitaevskii hierarchy in ℝ3. One of the main tools in our analysis
is the quantum de Finetti theorem. Our uniqueness result is equivalent to the
one established in the celebrated works of Erdos, Schlein, and Yau.
author:
- first_name: Thomas
full_name: Chen, Thomas
last_name: Chen
- first_name: Christian
full_name: Hainzl, Christian
last_name: Hainzl
- first_name: Nataša
full_name: Pavlović, Nataša
last_name: Pavlović
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Chen T, Hainzl C, Pavlović N, Seiringer R. Unconditional uniqueness for the
cubic gross pitaevskii hierarchy via quantum de finetti. Communications on
Pure and Applied Mathematics. 2015;68(10):1845-1884. doi:10.1002/cpa.21552
apa: Chen, T., Hainzl, C., Pavlović, N., & Seiringer, R. (2015). Unconditional
uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications
on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.21552
chicago: Chen, Thomas, Christian Hainzl, Nataša Pavlović, and Robert Seiringer.
“Unconditional Uniqueness for the Cubic Gross Pitaevskii Hierarchy via Quantum
de Finetti.” Communications on Pure and Applied Mathematics. Wiley, 2015.
https://doi.org/10.1002/cpa.21552.
ieee: T. Chen, C. Hainzl, N. Pavlović, and R. Seiringer, “Unconditional uniqueness
for the cubic gross pitaevskii hierarchy via quantum de finetti,” Communications
on Pure and Applied Mathematics, vol. 68, no. 10. Wiley, pp. 1845–1884, 2015.
ista: Chen T, Hainzl C, Pavlović N, Seiringer R. 2015. Unconditional uniqueness
for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications
on Pure and Applied Mathematics. 68(10), 1845–1884.
mla: Chen, Thomas, et al. “Unconditional Uniqueness for the Cubic Gross Pitaevskii
Hierarchy via Quantum de Finetti.” Communications on Pure and Applied Mathematics,
vol. 68, no. 10, Wiley, 2015, pp. 1845–84, doi:10.1002/cpa.21552.
short: T. Chen, C. Hainzl, N. Pavlović, R. Seiringer, Communications on Pure and
Applied Mathematics 68 (2015) 1845–1884.
date_created: 2018-12-11T11:52:48Z
date_published: 2015-10-01T00:00:00Z
date_updated: 2021-01-12T06:51:41Z
day: '01'
department:
- _id: RoSe
doi: 10.1002/cpa.21552
intvolume: ' 68'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1307.3168
month: '10'
oa: 1
oa_version: Preprint
page: 1845 - 1884
project:
- _id: 26450934-B435-11E9-9278-68D0E5697425
name: NSERC Postdoctoral fellowship
publication: Communications on Pure and Applied Mathematics
publication_status: published
publisher: Wiley
publist_id: '5598'
quality_controlled: '1'
scopus_import: 1
status: public
title: Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum
de finetti
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 68
year: '2015'
...
---
_id: '1574'
abstract:
- lang: eng
text: Multiple plant developmental processes, such as lateral root development,
depend on auxin distribution patterns that are in part generated by the PIN-formed
family of auxin-efflux transporters. Here we propose that AUXIN RESPONSE FACTOR7
(ARF7) and the ARF7-regulated FOUR LIPS/MYB124 (FLP) transcription factors jointly
form a coherent feed-forward motif that mediates the auxin-responsive PIN3 transcription
in planta to steer the early steps of lateral root formation. This regulatory
mechanism might endow the PIN3 circuitry with a temporal 'memory' of auxin stimuli,
potentially maintaining and enhancing the robustness of the auxin flux directionality
during lateral root development. The cooperative action between canonical auxin
signalling and other transcription factors might constitute a general mechanism
by which transcriptional auxin-sensitivity can be regulated at a tissue-specific
level.
acknowledgement: 'of the European Research Council (project ERC-2011-StG-20101109-PSDP)
(to J.F.), a FEBS long-term fellowship (to P.M.) '
article_number: '8821'
author:
- first_name: Qian
full_name: Chen, Qian
last_name: Chen
- first_name: Yang
full_name: Liu, Yang
last_name: Liu
- first_name: Steven
full_name: Maere, Steven
last_name: Maere
- first_name: Eunkyoung
full_name: Lee, Eunkyoung
last_name: Lee
- first_name: Gert
full_name: Van Isterdael, Gert
last_name: Van Isterdael
- first_name: Zidian
full_name: Xie, Zidian
last_name: Xie
- first_name: Wei
full_name: Xuan, Wei
last_name: Xuan
- first_name: Jessica
full_name: Lucas, Jessica
last_name: Lucas
- first_name: Valya
full_name: Vassileva, Valya
last_name: Vassileva
- first_name: Saeko
full_name: Kitakura, Saeko
last_name: Kitakura
- first_name: Peter
full_name: Marhavy, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Krzysztof T
full_name: Wabnik, Krzysztof T
id: 4DE369A4-F248-11E8-B48F-1D18A9856A87
last_name: Wabnik
orcid: 0000-0001-7263-0560
- first_name: Niko
full_name: Geldner, Niko
last_name: Geldner
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jie
full_name: Le, Jie
last_name: Le
- first_name: Hidehiro
full_name: Fukaki, Hidehiro
last_name: Fukaki
- first_name: Erich
full_name: Grotewold, Erich
last_name: Grotewold
- first_name: Chuanyou
full_name: Li, Chuanyou
last_name: Li
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Fred
full_name: Sack, Fred
last_name: Sack
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
citation:
ama: Chen Q, Liu Y, Maere S, et al. A coherent transcriptional feed-forward motif
model for mediating auxin-sensitive PIN3 expression during lateral root development.
Nature Communications. 2015;6. doi:10.1038/ncomms9821
apa: Chen, Q., Liu, Y., Maere, S., Lee, E., Van Isterdael, G., Xie, Z., … Vanneste,
S. (2015). A coherent transcriptional feed-forward motif model for mediating auxin-sensitive
PIN3 expression during lateral root development. Nature Communications.
Nature Publishing Group. https://doi.org/10.1038/ncomms9821
chicago: Chen, Qian, Yang Liu, Steven Maere, Eunkyoung Lee, Gert Van Isterdael,
Zidian Xie, Wei Xuan, et al. “A Coherent Transcriptional Feed-Forward Motif Model
for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.”
Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9821.
ieee: Q. Chen et al., “A coherent transcriptional feed-forward motif model
for mediating auxin-sensitive PIN3 expression during lateral root development,”
Nature Communications, vol. 6. Nature Publishing Group, 2015.
ista: Chen Q, Liu Y, Maere S, Lee E, Van Isterdael G, Xie Z, Xuan W, Lucas J, Vassileva
V, Kitakura S, Marhavý P, Wabnik KT, Geldner N, Benková E, Le J, Fukaki H, Grotewold
E, Li C, Friml J, Sack F, Beeckman T, Vanneste S. 2015. A coherent transcriptional
feed-forward motif model for mediating auxin-sensitive PIN3 expression during
lateral root development. Nature Communications. 6, 8821.
mla: Chen, Qian, et al. “A Coherent Transcriptional Feed-Forward Motif Model for
Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” Nature
Communications, vol. 6, 8821, Nature Publishing Group, 2015, doi:10.1038/ncomms9821.
short: Q. Chen, Y. Liu, S. Maere, E. Lee, G. Van Isterdael, Z. Xie, W. Xuan, J.
Lucas, V. Vassileva, S. Kitakura, P. Marhavý, K.T. Wabnik, N. Geldner, E. Benková,
J. Le, H. Fukaki, E. Grotewold, C. Li, J. Friml, F. Sack, T. Beeckman, S. Vanneste,
Nature Communications 6 (2015).
date_created: 2018-12-11T11:52:48Z
date_published: 2015-11-18T00:00:00Z
date_updated: 2021-01-12T06:51:42Z
day: '18'
ddc:
- '580'
department:
- _id: EvBe
- _id: JiFr
doi: 10.1038/ncomms9821
file:
- access_level: open_access
checksum: 8ff5c108899b548806e1cb7a302fe76d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:32Z
date_updated: 2020-07-14T12:45:02Z
file_id: '5085'
file_name: IST-2016-477-v1+1_ncomms9821.pdf
file_size: 1701815
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5597'
pubrep_id: '477'
quality_controlled: '1'
scopus_import: 1
status: public
title: A coherent transcriptional feed-forward motif model for mediating auxin-sensitive
PIN3 expression during lateral root 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2015'
...
---
_id: '1575'
abstract:
- lang: eng
text: The immune response relies on the migration of leukocytes and on their ability
to stop in precise anatomical locations to fulfil their task. How leukocyte migration
and function are coordinated is unknown. Here we show that in immature dendritic
cells, which patrol their environment by engulfing extracellular material, cell
migration and antigen capture are antagonistic. This antagonism results from transient
enrichment of myosin IIA at the cell front, which disrupts the back-to-front gradient
of the motor protein, slowing down locomotion but promoting antigen capture. We
further highlight that myosin IIA enrichment at the cell front requires the MHC
class II-associated invariant chain (Ii). Thus, by controlling myosin IIA localization,
Ii imposes on dendritic cells an intermittent antigen capture behaviour that might
facilitate environment patrolling. We propose that the requirement for myosin
II in both cell migration and specific cell functions may provide a general mechanism
for their coordination in time and space.
acknowledgement: M.C. and M.L.H. were supported by fellowships from the Fondation
pour la Recherche Médicale and the Association pour la Recherche contre le Cancer,
respectively. This work was funded by grants from the City of Paris and the European
Research Council to A.-M.L.-D. (Strapacemi 243103), the Association Nationale pour
la Recherche (ANR-09-PIRI-0027-PCVI) and the InnaBiosanté foundation (Micemico)
to A.-M.L.-D., M.P. and R.V., and the DCBIOL Labex from the French Government (ANR-10-IDEX-0001-02-PSL*
and ANR-11-LABX-0043). The super-resolution SIM microscope was funded through an
ERC Advanced Investigator Grant (250367) to Edith Heard (CNRS UMR3215/Inserm U934,
Institut Curie).
article_number: '7526'
author:
- first_name: Mélanie
full_name: Chabaud, Mélanie
last_name: Chabaud
- first_name: Mélina
full_name: Heuzé, Mélina
last_name: Heuzé
- first_name: Marine
full_name: Bretou, Marine
last_name: Bretou
- first_name: Pablo
full_name: Vargas, Pablo
last_name: Vargas
- first_name: Paolo
full_name: Maiuri, Paolo
last_name: Maiuri
- first_name: Paola
full_name: Solanes, Paola
last_name: Solanes
- first_name: Mathieu
full_name: Maurin, Mathieu
last_name: Maurin
- first_name: Emmanuel
full_name: Terriac, Emmanuel
last_name: Terriac
- first_name: Maël
full_name: Le Berre, Maël
last_name: Le Berre
- first_name: Danielle
full_name: Lankar, Danielle
last_name: Lankar
- first_name: Tristan
full_name: Piolot, Tristan
last_name: Piolot
- first_name: Robert
full_name: Adelstein, Robert
last_name: Adelstein
- first_name: Yingfan
full_name: Zhang, Yingfan
last_name: Zhang
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Jordan
full_name: Jacobelli, Jordan
last_name: Jacobelli
- first_name: Olivier
full_name: Bénichou, Olivier
last_name: Bénichou
- first_name: Raphaël
full_name: Voituriez, Raphaël
last_name: Voituriez
- first_name: Matthieu
full_name: Piel, Matthieu
last_name: Piel
- first_name: Ana
full_name: Lennon Duménil, Ana
last_name: Lennon Duménil
citation:
ama: Chabaud M, Heuzé M, Bretou M, et al. Cell migration and antigen capture are
antagonistic processes coupled by myosin II in dendritic cells. Nature Communications.
2015;6. doi:10.1038/ncomms8526
apa: Chabaud, M., Heuzé, M., Bretou, M., Vargas, P., Maiuri, P., Solanes, P., …
Lennon Duménil, A. (2015). Cell migration and antigen capture are antagonistic
processes coupled by myosin II in dendritic cells. Nature Communications.
Nature Publishing Group. https://doi.org/10.1038/ncomms8526
chicago: Chabaud, Mélanie, Mélina Heuzé, Marine Bretou, Pablo Vargas, Paolo Maiuri,
Paola Solanes, Mathieu Maurin, et al. “Cell Migration and Antigen Capture Are
Antagonistic Processes Coupled by Myosin II in Dendritic Cells.” Nature Communications.
Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms8526.
ieee: M. Chabaud et al., “Cell migration and antigen capture are antagonistic
processes coupled by myosin II in dendritic cells,” Nature Communications,
vol. 6. Nature Publishing Group, 2015.
ista: Chabaud M, Heuzé M, Bretou M, Vargas P, Maiuri P, Solanes P, Maurin M, Terriac
E, Le Berre M, Lankar D, Piolot T, Adelstein R, Zhang Y, Sixt MK, Jacobelli J,
Bénichou O, Voituriez R, Piel M, Lennon Duménil A. 2015. Cell migration and antigen
capture are antagonistic processes coupled by myosin II in dendritic cells. Nature
Communications. 6, 7526.
mla: Chabaud, Mélanie, et al. “Cell Migration and Antigen Capture Are Antagonistic
Processes Coupled by Myosin II in Dendritic Cells.” Nature Communications,
vol. 6, 7526, Nature Publishing Group, 2015, doi:10.1038/ncomms8526.
short: M. Chabaud, M. Heuzé, M. Bretou, P. Vargas, P. Maiuri, P. Solanes, M. Maurin,
E. Terriac, M. Le Berre, D. Lankar, T. Piolot, R. Adelstein, Y. Zhang, M.K. Sixt,
J. Jacobelli, O. Bénichou, R. Voituriez, M. Piel, A. Lennon Duménil, Nature Communications
6 (2015).
date_created: 2018-12-11T11:52:48Z
date_published: 2015-06-25T00:00:00Z
date_updated: 2021-01-12T06:51:42Z
day: '25'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1038/ncomms8526
file:
- access_level: open_access
checksum: bae12e86be2adb28253f890b8bba8315
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:58Z
date_updated: 2020-07-14T12:45:02Z
file_id: '4915'
file_name: IST-2016-476-v1+1_ncomms8526.pdf
file_size: 4530215
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5596'
pubrep_id: '476'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cell migration and antigen capture are antagonistic processes coupled by myosin
II in dendritic 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2015'
...
---
_id: '1576'
abstract:
- lang: eng
text: 'Gene expression is controlled primarily by interactions between transcription
factor proteins (TFs) and the regulatory DNA sequence, a process that can be captured
well by thermodynamic models of regulation. These models, however, neglect regulatory
crosstalk: the possibility that noncognate TFs could initiate transcription, with
potentially disastrous effects for the cell. Here, we estimate the importance
of crosstalk, suggest that its avoidance strongly constrains equilibrium models
of TF binding, and propose an alternative nonequilibrium scheme that implements
kinetic proofreading to suppress erroneous initiation. This proposal is consistent
with the observed covalent modifications of the transcriptional apparatus and
predicts increased noise in gene expression as a trade-off for improved specificity.
Using information theory, we quantify this trade-off to find when optimal proofreading
architectures are favored over their equilibrium counterparts. Such architectures
exhibit significant super-Poisson noise at low expression in steady state.'
article_number: '248101'
author:
- first_name: Sarah A
full_name: Cepeda Humerez, Sarah A
id: 3DEE19A4-F248-11E8-B48F-1D18A9856A87
last_name: Cepeda Humerez
- first_name: Georg
full_name: Rieckh, Georg
id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87
last_name: Rieckh
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Cepeda Humerez SA, Rieckh G, Tkačik G. Stochastic proofreading mechanism alleviates
crosstalk in transcriptional regulation. Physical Review Letters. 2015;115(24).
doi:10.1103/PhysRevLett.115.248101
apa: Cepeda Humerez, S. A., Rieckh, G., & Tkačik, G. (2015). Stochastic proofreading
mechanism alleviates crosstalk in transcriptional regulation. Physical Review
Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.115.248101
chicago: Cepeda Humerez, Sarah A, Georg Rieckh, and Gašper Tkačik. “Stochastic Proofreading
Mechanism Alleviates Crosstalk in Transcriptional Regulation.” Physical Review
Letters. American Physical Society, 2015. https://doi.org/10.1103/PhysRevLett.115.248101.
ieee: S. A. Cepeda Humerez, G. Rieckh, and G. Tkačik, “Stochastic proofreading mechanism
alleviates crosstalk in transcriptional regulation,” Physical Review Letters,
vol. 115, no. 24. American Physical Society, 2015.
ista: Cepeda Humerez SA, Rieckh G, Tkačik G. 2015. Stochastic proofreading mechanism
alleviates crosstalk in transcriptional regulation. Physical Review Letters. 115(24),
248101.
mla: Cepeda Humerez, Sarah A., et al. “Stochastic Proofreading Mechanism Alleviates
Crosstalk in Transcriptional Regulation.” Physical Review Letters, vol.
115, no. 24, 248101, American Physical Society, 2015, doi:10.1103/PhysRevLett.115.248101.
short: S.A. Cepeda Humerez, G. Rieckh, G. Tkačik, Physical Review Letters 115 (2015).
date_created: 2018-12-11T11:52:49Z
date_published: 2015-12-08T00:00:00Z
date_updated: 2023-09-07T12:55:21Z
day: '08'
department:
- _id: GaTk
doi: 10.1103/PhysRevLett.115.248101
ec_funded: 1
intvolume: ' 115'
issue: '24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1504.05716
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5595'
quality_controlled: '1'
related_material:
record:
- id: '6473'
relation: part_of_dissertation
status: public
scopus_import: 1
status: public
title: Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 115
year: '2015'
...
---
_id: '1577'
abstract:
- lang: eng
text: Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked
genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be
unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y
transposition must be the main source of Drosophila Y-linked genes. Here we show
how these genes were acquired. We found a previously unidentified gene (flagrante
delicto Y, FDY) that originated from a recent duplication of the autosomal gene
vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were
duplicated along with vig2, but they became pseudogenes through the accumulation
of deletions and transposable element insertions, whereas FDY remained functional,
acquired testis-specific expression, and now accounts for ∼20% of the vig2-like
mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and
DNA sequence divergence indicates that the duplication to the Y chromosome occurred
∼2 million years ago. Thus, FDY provides a snapshot of the early stages of the
establishment of a Y-linked gene and demonstrates how the Drosophila Y has been
accumulating autosomal genes.
acknowledgement: "This work was supported by grants from Conselho Nacional de Desenvolvimento
Científico e Tecnológico (CNPq), FAPERJ, and CAPES (to A.B.C.), and National Institutes
of Health Grant R01 GM64590 (to A.G.C. and A.B.C.).\r\nWe thank M. Vibranovski,
C. Bergman, and the Berkeley Drosophila Genome Project for access to unpublished
data; M. Vibranovski, R. Hoskins, S. Celniker, C. Kennedy, J. Carlson, S. Galasinski,
B. Wakimoto, J. Yasuhara, G. Sutton, M. Kuhner, J. Felsenstein, and C. Santos for
help in various steps of the work; and B. Bitner-Mathe, R. Ventura, the members
of the A.B.C. and A.G.C. laboratories, and two reviewers for many valuable comments
on the manuscript."
article_processing_charge: No
article_type: original
author:
- first_name: Antonio
full_name: Carvalho, Antonio
last_name: Carvalho
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Claudia
full_name: Russo, Claudia
last_name: Russo
- first_name: Bonnielin
full_name: Swenor, Bonnielin
last_name: Swenor
- first_name: Andrew
full_name: Clark, Andrew
last_name: Clark
citation:
ama: Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. Birth of a new gene on the
Y chromosome of Drosophila melanogaster. PNAS. 2015;112(40):12450-12455.
doi:10.1073/pnas.1516543112
apa: Carvalho, A., Vicoso, B., Russo, C., Swenor, B., & Clark, A. (2015). Birth
of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. National
Academy of Sciences. https://doi.org/10.1073/pnas.1516543112
chicago: Carvalho, Antonio, Beatriz Vicoso, Claudia Russo, Bonnielin Swenor, and
Andrew Clark. “Birth of a New Gene on the Y Chromosome of Drosophila Melanogaster.”
PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1516543112.
ieee: A. Carvalho, B. Vicoso, C. Russo, B. Swenor, and A. Clark, “Birth of a new
gene on the Y chromosome of Drosophila melanogaster,” PNAS, vol. 112, no.
40. National Academy of Sciences, pp. 12450–12455, 2015.
ista: Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. 2015. Birth of a new gene
on the Y chromosome of Drosophila melanogaster. PNAS. 112(40), 12450–12455.
mla: Carvalho, Antonio, et al. “Birth of a New Gene on the Y Chromosome of Drosophila
Melanogaster.” PNAS, vol. 112, no. 40, National Academy of Sciences, 2015,
pp. 12450–55, doi:10.1073/pnas.1516543112.
short: A. Carvalho, B. Vicoso, C. Russo, B. Swenor, A. Clark, PNAS 112 (2015) 12450–12455.
date_created: 2018-12-11T11:52:49Z
date_published: 2015-10-06T00:00:00Z
date_updated: 2021-01-12T06:51:43Z
day: '06'
department:
- _id: BeVi
doi: 10.1073/pnas.1516543112
external_id:
pmid:
- '26385968'
intvolume: ' 112'
issue: '40'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4603513/
month: '10'
oa: 1
oa_version: Published Version
page: 12450 - 12455
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5594'
quality_controlled: '1'
scopus_import: 1
status: public
title: Birth of a new gene on the Y chromosome of Drosophila melanogaster
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '1578'
abstract:
- lang: eng
text: We prove that the dual of the digital Voronoi diagram constructed by flooding
the plane from the data points gives a geometrically and topologically correct
dual triangulation. This provides the proof of correctness for recently developed
GPU algorithms that outperform traditional CPU algorithms for constructing two-dimensional
Delaunay triangulations.
acknowledgement: "The research of the second author is partially supported by NSF
under grant DBI-0820624 and by DARPA under grants HR011-05-1-0057 and HR0011-09-006\r\n"
author:
- first_name: Thanhtung
full_name: Cao, Thanhtung
last_name: Cao
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Tiowseng
full_name: Tan, Tiowseng
last_name: Tan
citation:
ama: Cao T, Edelsbrunner H, Tan T. Triangulations from topologically correct digital
Voronoi diagrams. Computational Geometry. 2015;48(7):507-519. doi:10.1016/j.comgeo.2015.04.001
apa: Cao, T., Edelsbrunner, H., & Tan, T. (2015). Triangulations from topologically
correct digital Voronoi diagrams. Computational Geometry. Elsevier. https://doi.org/10.1016/j.comgeo.2015.04.001
chicago: Cao, Thanhtung, Herbert Edelsbrunner, and Tiowseng Tan. “Triangulations
from Topologically Correct Digital Voronoi Diagrams.” Computational Geometry.
Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2015.04.001.
ieee: T. Cao, H. Edelsbrunner, and T. Tan, “Triangulations from topologically correct
digital Voronoi diagrams,” Computational Geometry, vol. 48, no. 7. Elsevier,
pp. 507–519, 2015.
ista: Cao T, Edelsbrunner H, Tan T. 2015. Triangulations from topologically correct
digital Voronoi diagrams. Computational Geometry. 48(7), 507–519.
mla: Cao, Thanhtung, et al. “Triangulations from Topologically Correct Digital Voronoi
Diagrams.” Computational Geometry, vol. 48, no. 7, Elsevier, 2015, pp.
507–19, doi:10.1016/j.comgeo.2015.04.001.
short: T. Cao, H. Edelsbrunner, T. Tan, Computational Geometry 48 (2015) 507–519.
date_created: 2018-12-11T11:52:49Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2021-01-12T06:51:43Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.comgeo.2015.04.001
intvolume: ' 48'
issue: '7'
language:
- iso: eng
month: '08'
oa_version: None
page: 507 - 519
publication: Computational Geometry
publication_status: published
publisher: Elsevier
publist_id: '5593'
quality_controlled: '1'
scopus_import: 1
status: public
title: Triangulations from topologically correct digital Voronoi diagrams
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 48
year: '2015'
...
---
_id: '1579'
abstract:
- lang: eng
text: We show that the Galois group of any Schubert problem involving lines in projective
space contains the alternating group. This constitutes the largest family of enumerative
problems whose Galois groups have been largely determined. Using a criterion of
Vakil and a special position argument due to Schubert, our result follows from
a particular inequality among Kostka numbers of two-rowed tableaux. In most cases,
a combinatorial injection proves the inequality. For the remaining cases, we use
the Weyl integral formulas to obtain an integral formula for these Kostka numbers.
This rewrites the inequality as an integral, which we estimate to establish the
inequality.
acknowledgement: "This research was supported in part by NSF grant DMS-915211 and
the Institut Mittag-Leffler.\r\n"
article_processing_charge: No
author:
- first_name: Christopher
full_name: Brooks, Christopher
last_name: Brooks
- first_name: Abraham
full_name: Martin Del Campo Sanchez, Abraham
id: 4CF47F6A-F248-11E8-B48F-1D18A9856A87
last_name: Martin Del Campo Sanchez
- first_name: Frank
full_name: Sottile, Frank
last_name: Sottile
citation:
ama: Brooks C, Martin del Campo Sanchez A, Sottile F. Galois groups of Schubert
problems of lines are at least alternating. Transactions of the American Mathematical
Society. 2015;367(6):4183-4206. doi:10.1090/S0002-9947-2014-06192-8
apa: Brooks, C., Martin del Campo Sanchez, A., & Sottile, F. (2015). Galois
groups of Schubert problems of lines are at least alternating. Transactions
of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/S0002-9947-2014-06192-8
chicago: Brooks, Christopher, Abraham Martin del Campo Sanchez, and Frank Sottile.
“Galois Groups of Schubert Problems of Lines Are at Least Alternating.” Transactions
of the American Mathematical Society. American Mathematical Society, 2015.
https://doi.org/10.1090/S0002-9947-2014-06192-8.
ieee: C. Brooks, A. Martin del Campo Sanchez, and F. Sottile, “Galois groups of
Schubert problems of lines are at least alternating,” Transactions of the American
Mathematical Society, vol. 367, no. 6. American Mathematical Society, pp.
4183–4206, 2015.
ista: Brooks C, Martin del Campo Sanchez A, Sottile F. 2015. Galois groups of Schubert
problems of lines are at least alternating. Transactions of the American Mathematical
Society. 367(6), 4183–4206.
mla: Brooks, Christopher, et al. “Galois Groups of Schubert Problems of Lines Are
at Least Alternating.” Transactions of the American Mathematical Society,
vol. 367, no. 6, American Mathematical Society, 2015, pp. 4183–206, doi:10.1090/S0002-9947-2014-06192-8.
short: C. Brooks, A. Martin del Campo Sanchez, F. Sottile, Transactions of the American
Mathematical Society 367 (2015) 4183–4206.
date_created: 2018-12-11T11:52:50Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2021-01-12T06:51:43Z
day: '01'
department:
- _id: CaUh
doi: 10.1090/S0002-9947-2014-06192-8
intvolume: ' 367'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1207.4280
month: '06'
oa: 1
oa_version: Preprint
page: 4183 - 4206
publication: Transactions of the American Mathematical Society
publication_status: published
publisher: American Mathematical Society
publist_id: '5592'
quality_controlled: '1'
scopus_import: 1
status: public
title: Galois groups of Schubert problems of lines are at least alternating
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 367
year: '2015'
...