---
OA_type: free access
_id: '3943'
abstract:
- lang: eng
text: Neutrophil granulocytes form the body's first line of antibacterial defense,
but they also contribute to tissue injury and noninfectious, chronic inflammation.
Proteinase 3 (PR3) and neutrophil elastase (NE) are 2 abundant neutrophil serine
proteases implicated in antimicrobial defense with overlapping and potentially
redundant substrate specificity. Here, we unraveled a cooperative role for PR3
and NE in neutrophil activation and noninfectious inflammation in vivo, which
we believe to be novel. Mice lacking both PR3 and NE demonstrated strongly diminished
immune complex-mediated (IC-mediated) neutrophil infiltration in vivo as well
as reduced activation of isolated neutrophils by ICs in vitro. In contrast, in
mice lacking just NE, neutrophil recruitment to ICs was only marginally impaired.
The defects in mice lacking both PR3 and NE were directly linked to the accumulation
of antiinflammatory progranulin (PGRN). Both PR3 and NE cleaved PGRN in vitro
and during neutrophil activation and inflammation in vivo. Local administration
of recombinant PGRN potently inhibited neutrophilic inflammation in vivo, demonstrating
that PGRN represents a crucial inflammation-suppressing mediator. We conclude
that PR3 and NE enhance neutrophil-dependent inflammation by eliminating the local
antiinflammatory activity of PGRN. Our results support the use of serine protease
inhibitors as antiinflammatory agents.
article_processing_charge: No
article_type: original
author:
- first_name: Kai
full_name: Kessenbrock, Kai
last_name: Kessenbrock
- first_name: Leopold
full_name: Fröhlich, Leopold
last_name: Fröhlich
- 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: Tim
full_name: Lämmermann, Tim
last_name: Lämmermann
- first_name: Heiko
full_name: Pfister, Heiko
last_name: Pfister
- first_name: Andrew
full_name: Bateman, Andrew
last_name: Bateman
- first_name: Azzaq
full_name: Belaaouaj, Azzaq
last_name: Belaaouaj
- first_name: Johannes
full_name: Ring, Johannes
last_name: Ring
- first_name: Markus
full_name: Ollert, Markus
last_name: Ollert
- first_name: Reinhard
full_name: Fässler, Reinhard
last_name: Fässler
- first_name: Dieter
full_name: Jenne, Dieter
last_name: Jenne
citation:
ama: Kessenbrock K, Fröhlich L, Sixt MK, et al. Proteinase 3 and neutrophil elastase
enhance inflammation in mice by inactivating antiinflammatory progranulin. The
Journal of Clinical Investigation. 2008;118(7):2438-2447. doi:10.1172/JCI34694
apa: Kessenbrock, K., Fröhlich, L., Sixt, M. K., Lämmermann, T., Pfister, H., Bateman,
A., … Jenne, D. (2008). Proteinase 3 and neutrophil elastase enhance inflammation
in mice by inactivating antiinflammatory progranulin. The Journal of Clinical
Investigation. American Society for Clinical Investigation. https://doi.org/10.1172/JCI34694
chicago: Kessenbrock, Kai, Leopold Fröhlich, Michael K Sixt, Tim Lämmermann, Heiko
Pfister, Andrew Bateman, Azzaq Belaaouaj, et al. “Proteinase 3 and Neutrophil
Elastase Enhance Inflammation in Mice by Inactivating Antiinflammatory Progranulin.”
The Journal of Clinical Investigation. American Society for Clinical Investigation,
2008. https://doi.org/10.1172/JCI34694.
ieee: K. Kessenbrock et al., “Proteinase 3 and neutrophil elastase enhance
inflammation in mice by inactivating antiinflammatory progranulin,” The Journal
of Clinical Investigation, vol. 118, no. 7. American Society for Clinical
Investigation, pp. 2438–2447, 2008.
ista: Kessenbrock K, Fröhlich L, Sixt MK, Lämmermann T, Pfister H, Bateman A, Belaaouaj
A, Ring J, Ollert M, Fässler R, Jenne D. 2008. Proteinase 3 and neutrophil elastase
enhance inflammation in mice by inactivating antiinflammatory progranulin. The
Journal of Clinical Investigation. 118(7), 2438–2447.
mla: Kessenbrock, Kai, et al. “Proteinase 3 and Neutrophil Elastase Enhance Inflammation
in Mice by Inactivating Antiinflammatory Progranulin.” The Journal of Clinical
Investigation, vol. 118, no. 7, American Society for Clinical Investigation,
2008, pp. 2438–47, doi:10.1172/JCI34694.
short: K. Kessenbrock, L. Fröhlich, M.K. Sixt, T. Lämmermann, H. Pfister, A. Bateman,
A. Belaaouaj, J. Ring, M. Ollert, R. Fässler, D. Jenne, The Journal of Clinical
Investigation 118 (2008) 2438–2447.
date_created: 2018-12-11T12:06:01Z
date_published: 2008-06-20T00:00:00Z
date_updated: 2026-05-29T09:19:48Z
day: '20'
doi: 10.1172/JCI34694
extern: '1'
external_id:
pmid:
- '18568075'
intvolume: ' 118'
issue: '7'
language:
- iso: eng
month: '06'
oa_version: None
page: 2438 - 2447
pmid: 1
publication: The Journal of Clinical Investigation
publication_identifier:
eissn:
- 1558-8238
issn:
- 0021-9738
publication_status: published
publisher: American Society for Clinical Investigation
publist_id: '2183'
status: public
title: Proteinase 3 and neutrophil elastase enhance inflammation in mice by inactivating
antiinflammatory progranulin
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 118
year: '2008'
...
---
OA_type: closed access
_id: '3944'
abstract:
- lang: eng
text: Live imaging of the actin cytoskeleton is crucial for the study of many fundamental
biological processes, but current approaches to visualize actin have several limitations.
Here we describe Lifeact, a 17-amino-acid peptide, which stained filamentous actin
(F-actin) structures in eukaryotic cells and tissues. Lifeact did not interfere
with actin dynamics in vitro and in vivo and in its chemically modified peptide
form allowed visualization of actin dynamics in nontransfectable cells.
article_processing_charge: No
article_type: original
author:
- first_name: Julia
full_name: Riedl, Julia
last_name: Riedl
- first_name: Alvaro
full_name: Crevenna, Alvaro
last_name: Crevenna
- first_name: Kai
full_name: Kessenbrock, Kai
last_name: Kessenbrock
- first_name: Jerry
full_name: Yu, Jerry
last_name: Yu
- first_name: Dorothee
full_name: Neukirchen, Dorothee
last_name: Neukirchen
- first_name: Michal
full_name: Bista, Michal
last_name: Bista
- first_name: Frank
full_name: Bradke, Frank
last_name: Bradke
- first_name: Dieter
full_name: Jenne, Dieter
last_name: Jenne
- first_name: Tad
full_name: Holak, Tad
last_name: Holak
- first_name: Zena
full_name: Werb, Zena
last_name: Werb
- 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: Roland
full_name: Wedlich Soldner, Roland
last_name: Wedlich Soldner
citation:
ama: 'Riedl J, Crevenna A, Kessenbrock K, et al. Lifeact: a versatile marker to
visualize F-actin. Nature Methods. 2008;5(7):605-607. doi:10.1038/nmeth.1220'
apa: 'Riedl, J., Crevenna, A., Kessenbrock, K., Yu, J., Neukirchen, D., Bista, M.,
… Wedlich Soldner, R. (2008). Lifeact: a versatile marker to visualize F-actin.
Nature Methods. Nature Publishing Group. https://doi.org/10.1038/nmeth.1220'
chicago: 'Riedl, Julia, Alvaro Crevenna, Kai Kessenbrock, Jerry Yu, Dorothee Neukirchen,
Michal Bista, Frank Bradke, et al. “Lifeact: A Versatile Marker to Visualize F-Actin.”
Nature Methods. Nature Publishing Group, 2008. https://doi.org/10.1038/nmeth.1220.'
ieee: 'J. Riedl et al., “Lifeact: a versatile marker to visualize F-actin,”
Nature Methods, vol. 5, no. 7. Nature Publishing Group, pp. 605–607, 2008.'
ista: 'Riedl J, Crevenna A, Kessenbrock K, Yu J, Neukirchen D, Bista M, Bradke F,
Jenne D, Holak T, Werb Z, Sixt MK, Wedlich Soldner R. 2008. Lifeact: a versatile
marker to visualize F-actin. Nature Methods. 5(7), 605–607.'
mla: 'Riedl, Julia, et al. “Lifeact: A Versatile Marker to Visualize F-Actin.” Nature
Methods, vol. 5, no. 7, Nature Publishing Group, 2008, pp. 605–07, doi:10.1038/nmeth.1220.'
short: J. Riedl, A. Crevenna, K. Kessenbrock, J. Yu, D. Neukirchen, M. Bista, F.
Bradke, D. Jenne, T. Holak, Z. Werb, M.K. Sixt, R. Wedlich Soldner, Nature Methods
5 (2008) 605–607.
date_created: 2018-12-11T12:06:02Z
date_published: 2008-06-08T00:00:00Z
date_updated: 2026-05-29T09:21:50Z
day: '08'
doi: 10.1038/nmeth.1220
extern: '1'
external_id:
pmid:
- '18536722'
intvolume: ' 5'
issue: '7'
language:
- iso: eng
month: '06'
oa_version: None
page: 605 - 607
pmid: 1
publication: Nature Methods
publication_identifier:
eissn:
- 1548-7105
issn:
- 1548-7091
publication_status: published
publisher: Nature Publishing Group
publist_id: '2184'
status: public
title: 'Lifeact: a versatile marker to visualize F-actin'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 5
year: '2008'
...
---
OA_type: closed access
_id: '3945'
abstract:
- lang: eng
text: Langerhans cells and dermal dendritic cells migrate to the draining lymph
nodes through dermal lymphatic vessels. They do so in the steady-state and under
inflammatory conditions. Peripheral T cell tolerance or T cell priming, respectively,
are the consequences of migration. The nature of dendritic cell-containing vessels
was mostly defined by electron microscopy or by their lack of blood endothelial
markers. Selective markers for murine lymph endothelium were hitherto rare or
not available. Here, we utilised recently developed antibodies against the murine
hyaluronan receptor, LYVE-1, to study the lymph vessel network in mouse skin in
more detail. In hairless skin from the ears, lymph vessels were spread out in
a horizontal plane. They formed anastomoses, and they possessed frequent blind
endings that were occasionally open. Lymph vessels were wider than blood vessels,
which were identified by their strong CD31 expression. In body wall skin LYVE-1
reactive vessels did not extend laterally but they dived straight down into the
deeper dermis. There, they are connected to each other and formed a network similar
to ear skin. The number and width of lymph vessels did not grossly change upon
inflammatory stimuli such as skin explant culture or tape stripping. There were
also no marked changes in caliber in response to the TLR 7/8 ligand Imiquimod.
Double-labelling experiments of cultured skin showed that most of the strongly
cell surface MHC II-expressing (i.e. activated) dendritic cells were confined
to the lymph vessels. Langerin/CD207(+) cells within this population appeared
later than dermal dendritic cells, i.e. langerin-negative cells. Comparable results
were obtained after stimulating the skin in vivo with the TLR 7/8 ligand Imiquimod
or by tape stripping. In untreated skin (i.e. steady state) a few MHC II(+) and
Langerin/CD207(+) cells, presumably migrating skin dendritic cells including epidermal
Langerhans cells, were consistently observed within the lymph vessels. The novel
antibody reagents may serve as important tools to further study the dendritic
cell traffic in the skin under physiological conditions as well as in conditions
of adoptive dendritic cell transfer in immunotherapy.
article_processing_charge: No
article_type: original
author:
- first_name: Christoph
full_name: Tripp, Christoph
last_name: Tripp
- first_name: Bernhard
full_name: Haid, Bernhard
last_name: Haid
- first_name: Vincent
full_name: Flacher, Vincent
last_name: Flacher
- 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: Hannes
full_name: Peter, Hannes
last_name: Peter
- first_name: Julia
full_name: Farkas, Julia
last_name: Farkas
- first_name: Robert
full_name: Gschwentner, Robert
last_name: Gschwentner
- first_name: Lydia
full_name: Sorokin, Lydia
last_name: Sorokin
- first_name: Nikolaus
full_name: Romani, Nikolaus
last_name: Romani
- first_name: Patrizia
full_name: Stoitzner, Patrizia
last_name: Stoitzner
citation:
ama: Tripp C, Haid B, Flacher V, et al. The lymph vessel network in mouse skin visualised
with antibodies against the hyaluronan receptor LYVE-1. Immunobiology.
2008;213(9-10):715-728. doi:10.1016/j.imbio.2008.07.025
apa: Tripp, C., Haid, B., Flacher, V., Sixt, M. K., Peter, H., Farkas, J., … Stoitzner,
P. (2008). The lymph vessel network in mouse skin visualised with antibodies against
the hyaluronan receptor LYVE-1. Immunobiology. Elsevier. https://doi.org/10.1016/j.imbio.2008.07.025
chicago: Tripp, Christoph, Bernhard Haid, Vincent Flacher, Michael K Sixt, Hannes
Peter, Julia Farkas, Robert Gschwentner, Lydia Sorokin, Nikolaus Romani, and Patrizia
Stoitzner. “The Lymph Vessel Network in Mouse Skin Visualised with Antibodies
against the Hyaluronan Receptor LYVE-1.” Immunobiology. Elsevier, 2008.
https://doi.org/10.1016/j.imbio.2008.07.025.
ieee: C. Tripp et al., “The lymph vessel network in mouse skin visualised
with antibodies against the hyaluronan receptor LYVE-1,” Immunobiology,
vol. 213, no. 9–10. Elsevier, pp. 715–728, 2008.
ista: Tripp C, Haid B, Flacher V, Sixt MK, Peter H, Farkas J, Gschwentner R, Sorokin
L, Romani N, Stoitzner P. 2008. The lymph vessel network in mouse skin visualised
with antibodies against the hyaluronan receptor LYVE-1. Immunobiology. 213(9–10),
715–728.
mla: Tripp, Christoph, et al. “The Lymph Vessel Network in Mouse Skin Visualised
with Antibodies against the Hyaluronan Receptor LYVE-1.” Immunobiology,
vol. 213, no. 9–10, Elsevier, 2008, pp. 715–28, doi:10.1016/j.imbio.2008.07.025.
short: C. Tripp, B. Haid, V. Flacher, M.K. Sixt, H. Peter, J. Farkas, R. Gschwentner,
L. Sorokin, N. Romani, P. Stoitzner, Immunobiology 213 (2008) 715–728.
date_created: 2018-12-11T12:06:02Z
date_published: 2008-08-30T00:00:00Z
date_updated: 2026-05-29T09:17:45Z
day: '30'
doi: 10.1016/j.imbio.2008.07.025
extern: '1'
external_id:
pmid:
- '18926287'
intvolume: ' 213'
issue: 9-10
language:
- iso: eng
month: '08'
oa_version: None
page: 715 - 728
pmid: 1
publication: Immunobiology
publication_identifier:
eissn:
- 1878-3279
issn:
- 0171-2985
publication_status: published
publisher: Elsevier
publist_id: '2182'
status: public
title: The lymph vessel network in mouse skin visualised with antibodies against the
hyaluronan receptor LYVE-1
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 213
year: '2008'
...
---
_id: '3969'
abstract:
- lang: eng
text: Persistent homology is an algebraic tool for measuring topological features
of shapes and functions. It casts the multi-scale organization we frequently observe
in nature into a mathematical formalism. Here we give a record of the short history
of persistent homology and present its basic concepts. Besides the mathematics
we focus on algorithms and mention the various connections to applications, including
to biomolecules, biological networks, data analysis, and geometric modeling.
acknowledgement: Supported in part by DARPA under grants HR0011-05-1-0007 and HR0011-05-0057
and by the NSF under grant DBI-06-06873.
alternative_title:
- Contemporary Mathematics
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
- first_name: John
full_name: Harer, John
last_name: Harer
citation:
ama: 'Edelsbrunner H, Harer J. Persistent homology - a survey. In: Surveys on
Discrete and Computational Geometry: Twenty Years Later. American Mathematical
Society; 2008:257-282.'
apa: 'Edelsbrunner, H., & Harer, J. (2008). Persistent homology - a survey.
In Surveys on Discrete and Computational Geometry: Twenty Years Later (pp.
257–282). American Mathematical Society.'
chicago: 'Edelsbrunner, Herbert, and John Harer. “Persistent Homology - a Survey.”
In Surveys on Discrete and Computational Geometry: Twenty Years Later,
257–82. American Mathematical Society, 2008.'
ieee: 'H. Edelsbrunner and J. Harer, “Persistent homology - a survey,” in Surveys
on Discrete and Computational Geometry: Twenty Years Later, American Mathematical
Society, 2008, pp. 257–282.'
ista: 'Edelsbrunner H, Harer J. 2008.Persistent homology - a survey. In: Surveys
on Discrete and Computational Geometry: Twenty Years Later. Contemporary Mathematics,
, 257–282.'
mla: 'Edelsbrunner, Herbert, and John Harer. “Persistent Homology - a Survey.” Surveys
on Discrete and Computational Geometry: Twenty Years Later, American Mathematical
Society, 2008, pp. 257–82.'
short: 'H. Edelsbrunner, J. Harer, in:, Surveys on Discrete and Computational Geometry:
Twenty Years Later, American Mathematical Society, 2008, pp. 257–282.'
date_created: 2018-12-11T12:06:11Z
date_published: 2008-03-28T00:00:00Z
date_updated: 2026-05-21T11:47:36Z
day: '28'
extern: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: 257 - 282
publication: 'Surveys on Discrete and Computational Geometry: Twenty Years Later'
publication_status: published
publisher: American Mathematical Society
publist_id: '2156'
status: public
title: Persistent homology - a survey
type: book_chapter
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2008'
...
---
OA_place: publisher
OA_type: gold
_id: '3970'
abstract:
- lang: eng
text: 'While genome-wide gene expression data are generated at an increasing rate,
the repertoire of approaches for pattern discovery in these data is still limited.
Identifying subtle patterns of interest in large amounts of data (tens of thousands
of profiles) associated with a certain level of noise remains a challenge. A microarray
time series was recently generated to study the transcriptional program of the
mouse segmentation clock, a biological oscillator associated with the periodic
formation of the segments of the body axis. A method related to Fourier analysis,
the Lomb-Scargle periodogram, was used to detect periodic profiles in the dataset,
leading to the identification of a novel set of cyclic genes associated with the
segmentation clock. Here, we applied to the same microarray time series dataset
four distinct mathematical methods to identify significant patterns in gene expression
profiles. These methods are called: Phase consistency, Address reduction, Cyclohedron
test and Stable persistence, and are based on different conceptual frameworks
that are either hypothesis- or data-driven. Some of the methods, unlike Fourier
transforms, are not dependent on the assumption of periodicity of the pattern
of interest. Remarkably, these methods identified blindly the expression profiles
of known cyclic genes as the most significant patterns in the dataset. Many candidate
genes predicted by more than one approach appeared to be true positive cyclic
genes and will be of particular interest for future research. In addition, these
methods predicted novel candidate cyclic genes that were consistent with previous
biological knowledge and experimental validation in mouse embryos. Our results
demonstrate the utility of these novel pattern detection strategies, notably for
detection of periodic profiles, and suggest that combining several distinct mathematical
approaches to analyze microarray datasets is a valuable strategy for identifying
genes that exhibit novel, interesting transcriptional patterns.'
acknowledgement: This research was partially supported by DARPA grant HR 0011-05-1-0057.
HE and YM mathematical work was supported by DARPA grant HR0011-05-1-0007. AS research
was supported by a Lucent Technologies Bell Labs Graduate Research. Fellowship;
AK and MR research was supported by NIH grant GM U54 GM74942; and SA research was
supported by Association pour la Recherche sur le Cancer (ARC), France. OP, AM,
MLD, EG and GH research was supported by the Stowers Institute for Medical Research.
OP is a Howard Hughes Medical Institute Investigator.
article_processing_charge: No
article_type: original
author:
- first_name: Mary
full_name: Dequéant, Mary
last_name: Dequéant
- first_name: Sebastian
full_name: Ahnert, Sebastian
last_name: Ahnert
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Thomas
full_name: Fink, Thomas
last_name: Fink
- first_name: Earl
full_name: Glynn, Earl
last_name: Glynn
- first_name: Gaye
full_name: Hattem, Gaye
last_name: Hattem
- first_name: Andrzej
full_name: Kudlicki, Andrzej
last_name: Kudlicki
- first_name: Yuriy
full_name: Mileyko, Yuriy
last_name: Mileyko
- first_name: Jason
full_name: Morton, Jason
last_name: Morton
- first_name: Arcady
full_name: Mushegian, Arcady
last_name: Mushegian
- first_name: Lior
full_name: Pachter, Lior
last_name: Pachter
- first_name: Maga
full_name: Rowicka, Maga
last_name: Rowicka
- first_name: Anne
full_name: Shiu, Anne
last_name: Shiu
- first_name: Bernd
full_name: Sturmfels, Bernd
last_name: Sturmfels
- first_name: Olivier
full_name: Pourquie, Olivier
last_name: Pourquie
citation:
ama: Dequéant M, Ahnert S, Edelsbrunner H, et al. Comparison of pattern detection
methods in microarray time series of the segmentation clock. PLoS One.
2008;3(8). doi:10.1371/journal.pone.0002856
apa: Dequéant, M., Ahnert, S., Edelsbrunner, H., Fink, T., Glynn, E., Hattem, G.,
… Pourquie, O. (2008). Comparison of pattern detection methods in microarray time
series of the segmentation clock. PLoS One. Public Library of Science.
https://doi.org/10.1371/journal.pone.0002856
chicago: Dequéant, Mary, Sebastian Ahnert, Herbert Edelsbrunner, Thomas Fink, Earl
Glynn, Gaye Hattem, Andrzej Kudlicki, et al. “Comparison of Pattern Detection
Methods in Microarray Time Series of the Segmentation Clock.” PLoS One.
Public Library of Science, 2008. https://doi.org/10.1371/journal.pone.0002856.
ieee: M. Dequéant et al., “Comparison of pattern detection methods in microarray
time series of the segmentation clock,” PLoS One, vol. 3, no. 8. Public
Library of Science, 2008.
ista: Dequéant M, Ahnert S, Edelsbrunner H, Fink T, Glynn E, Hattem G, Kudlicki
A, Mileyko Y, Morton J, Mushegian A, Pachter L, Rowicka M, Shiu A, Sturmfels B,
Pourquie O. 2008. Comparison of pattern detection methods in microarray time series
of the segmentation clock. PLoS One. 3(8).
mla: Dequéant, Mary, et al. “Comparison of Pattern Detection Methods in Microarray
Time Series of the Segmentation Clock.” PLoS One, vol. 3, no. 8, Public
Library of Science, 2008, doi:10.1371/journal.pone.0002856.
short: M. Dequéant, S. Ahnert, H. Edelsbrunner, T. Fink, E. Glynn, G. Hattem, A.
Kudlicki, Y. Mileyko, J. Morton, A. Mushegian, L. Pachter, M. Rowicka, A. Shiu,
B. Sturmfels, O. Pourquie, PLoS One 3 (2008).
date_created: 2018-12-11T12:06:11Z
date_published: 2008-08-06T00:00:00Z
date_updated: 2026-05-29T09:10:12Z
day: '06'
doi: 10.1371/journal.pone.0002856
extern: '1'
external_id:
pmid:
- '18682743'
intvolume: ' 3'
issue: '8'
language:
- iso: eng
month: '08'
oa_version: None
pmid: 1
publication: PLoS One
publication_identifier:
eissn:
- 1932-6203
publication_status: published
publisher: Public Library of Science
publist_id: '2157'
status: public
title: Comparison of pattern detection methods in microarray time series of the segmentation
clock
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 3
year: '2008'
...
---
OA_type: free access
_id: '3971'
abstract:
- lang: eng
text: The Reeb graph is a useful tool in visualizing real-valued data obtained from
computational simulations of physical processes. We characterize the evolution
of the Reeb graph of a time-varying continuous function defined in three-dimensional
space. We show how to maintain the Reeb graph over time and compress the entire
sequence of Reeb graphs into a single, partially persistent data structure, and
augment this data structure with Betti numbers to describe the topology of level
sets and with path seeds to assist in the fast extraction of level sets for visualization.
article_processing_charge: No
article_type: original
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: John
full_name: Harer, John
last_name: Harer
- first_name: Ajith
full_name: Mascarenhas, Ajith
last_name: Mascarenhas
- first_name: Valerio
full_name: Pascucci, Valerio
last_name: Pascucci
- first_name: Jack
full_name: Snoeyink, Jack
last_name: Snoeyink
citation:
ama: 'Edelsbrunner H, Harer J, Mascarenhas A, Pascucci V, Snoeyink J. Time-varying
Reeb graphs for continuous space-time data. Computational Geometry: Theory
and Applications. 2008;41(3):149-166. doi:10.1016/j.comgeo.2007.11.001'
apa: 'Edelsbrunner, H., Harer, J., Mascarenhas, A., Pascucci, V., & Snoeyink,
J. (2008). Time-varying Reeb graphs for continuous space-time data. Computational
Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2007.11.001'
chicago: 'Edelsbrunner, Herbert, John Harer, Ajith Mascarenhas, Valerio Pascucci,
and Jack Snoeyink. “Time-Varying Reeb Graphs for Continuous Space-Time Data.”
Computational Geometry: Theory and Applications. Elsevier, 2008. https://doi.org/10.1016/j.comgeo.2007.11.001.'
ieee: 'H. Edelsbrunner, J. Harer, A. Mascarenhas, V. Pascucci, and J. Snoeyink,
“Time-varying Reeb graphs for continuous space-time data,” Computational Geometry:
Theory and Applications, vol. 41, no. 3. Elsevier, pp. 149–166, 2008.'
ista: 'Edelsbrunner H, Harer J, Mascarenhas A, Pascucci V, Snoeyink J. 2008. Time-varying
Reeb graphs for continuous space-time data. Computational Geometry: Theory and
Applications. 41(3), 149–166.'
mla: 'Edelsbrunner, Herbert, et al. “Time-Varying Reeb Graphs for Continuous Space-Time
Data.” Computational Geometry: Theory and Applications, vol. 41, no. 3,
Elsevier, 2008, pp. 149–66, doi:10.1016/j.comgeo.2007.11.001.'
short: 'H. Edelsbrunner, J. Harer, A. Mascarenhas, V. Pascucci, J. Snoeyink, Computational
Geometry: Theory and Applications 41 (2008) 149–166.'
date_created: 2018-12-11T12:06:12Z
date_published: 2008-11-01T00:00:00Z
date_updated: 2026-05-29T09:15:13Z
day: '01'
doi: 10.1016/j.comgeo.2007.11.001
extern: '1'
intvolume: ' 41'
issue: '3'
language:
- iso: eng
month: '11'
oa_version: None
page: 149 - 166
publication: 'Computational Geometry: Theory and Applications'
publication_identifier:
eissn:
- 1879-081X
issn:
- 0925-7721
publication_status: published
publisher: Elsevier
publist_id: '2158'
status: public
title: Time-varying Reeb graphs for continuous space-time data
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 41
year: '2008'
...
---
_id: '3974'
abstract:
- lang: eng
text: Generalizing the concept of a Reeb graph, the Reeb space of a multivariate
continuous mapping identifies points of the domain that belong to a common component
of the preimage of a point in the range. We study the local and global structure
of this space for generic, piecewise linear mappings on a combinatorial manifold.
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
- first_name: John
full_name: Harer, John
last_name: Harer
- first_name: Amit
full_name: Patel, Amit
id: 34A254A0-F248-11E8-B48F-1D18A9856A87
last_name: Patel
citation:
ama: 'Edelsbrunner H, Harer J, Patel A. Reeb spaces of piecewise linear mappings.
In: Proceedings of the Twenty-Fourth Annual Symposium on Computational Geometry.
Association for Computing Machinery; 2008:242-250. doi:10.1145/1377676.1377720'
apa: 'Edelsbrunner, H., Harer, J., & Patel, A. (2008). Reeb spaces of piecewise
linear mappings. In Proceedings of the twenty-fourth annual symposium on Computational
geometry (pp. 242–250). College Park, MD, United States: Association for Computing
Machinery. https://doi.org/10.1145/1377676.1377720'
chicago: Edelsbrunner, Herbert, John Harer, and Amit Patel. “Reeb Spaces of Piecewise
Linear Mappings.” In Proceedings of the Twenty-Fourth Annual Symposium on Computational
Geometry, 242–50. Association for Computing Machinery, 2008. https://doi.org/10.1145/1377676.1377720.
ieee: H. Edelsbrunner, J. Harer, and A. Patel, “Reeb spaces of piecewise linear
mappings,” in Proceedings of the twenty-fourth annual symposium on Computational
geometry, College Park, MD, United States, 2008, pp. 242–250.
ista: 'Edelsbrunner H, Harer J, Patel A. 2008. Reeb spaces of piecewise linear mappings.
Proceedings of the twenty-fourth annual symposium on Computational geometry. SCG:
Symposium on Computational Geometry, 242–250.'
mla: Edelsbrunner, Herbert, et al. “Reeb Spaces of Piecewise Linear Mappings.” Proceedings
of the Twenty-Fourth Annual Symposium on Computational Geometry, Association
for Computing Machinery, 2008, pp. 242–50, doi:10.1145/1377676.1377720.
short: H. Edelsbrunner, J. Harer, A. Patel, in:, Proceedings of the Twenty-Fourth
Annual Symposium on Computational Geometry, Association for Computing Machinery,
2008, pp. 242–250.
conference:
end_date: 2008-06-11
location: College Park, MD, United States
name: 'SCG: Symposium on Computational Geometry'
start_date: 2008-06-09
date_created: 2018-12-11T12:06:13Z
date_published: 2008-06-09T00:00:00Z
date_updated: 2026-05-29T09:01:13Z
day: '09'
doi: 10.1145/1377676.1377720
extern: '1'
language:
- iso: eng
month: '06'
oa_version: None
page: 242 - 250
publication: Proceedings of the twenty-fourth annual symposium on Computational geometry
publication_identifier:
isbn:
- '9781605580715'
publication_status: published
publisher: Association for Computing Machinery
publist_id: '2155'
status: public
title: Reeb spaces of piecewise linear mappings
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2008'
...
---
_id: '4135'
abstract:
- lang: eng
text: There have been several attempts to build a unified framework for macroecological
patterns. However, these have mostly been based either on questionable assumptions
or have had to be parameterized to obtain realistic predictions. Here, we propose
a new model explicitly considering patterns of aggregated species distributions
on multiple spatial scales, the property which lies behind all spatial macroecological
patterns, using the idea we term ‘generalized fractals’. Species’ spatial distributions
were modelled by a random hierarchical process in which the original ‘habitat’
patches were randomly replaced by sets of smaller patches nested within them,
and the statistical properties of modelled species assemblages were compared with
macroecological patterns in observed bird data. Without parameterization based
on observed patterns, this simple model predicts realistic patterns of species
abundance, distribution and diversity, including fractal-like spatial distributions,
the frequency distribution of species occupancies/abundances and the species–area
relationship. Although observed macroecological patterns may differ in some quantitative
properties, our concept of random hierarchical aggregation can be considered as
an appropriate null model of fundamental macroecological patterns which can potentially
be modified to accommodate ecologically important variables.
article_processing_charge: No
author:
- first_name: D.
full_name: Storch, D.
last_name: Storch
- first_name: A.
full_name: Šizling, A.
last_name: Šizling
- first_name: J.
full_name: Reif, J.
last_name: Reif
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
- first_name: E.
full_name: Šizlingová, E.
last_name: Šizlingová
- first_name: K.
full_name: Gaston, K.
last_name: Gaston
citation:
ama: 'Storch D, Šizling A, Reif J, Polechova J, Šizlingová E, Gaston K. The quest
for a null model for macroecological patterns: Geometry of species distributions
at multiple spatial scales. Ecology Letters. 2008;11(8):771-784. doi:10.1111/j.1461-0248.2008.01206.x'
apa: 'Storch, D., Šizling, A., Reif, J., Polechova, J., Šizlingová, E., & Gaston,
K. (2008). The quest for a null model for macroecological patterns: Geometry of
species distributions at multiple spatial scales. Ecology Letters. Wiley.
https://doi.org/10.1111/j.1461-0248.2008.01206.x'
chicago: 'Storch, D., A. Šizling, J. Reif, Jitka Polechova, E. Šizlingová, and K.
Gaston. “The Quest for a Null Model for Macroecological Patterns: Geometry of
Species Distributions at Multiple Spatial Scales.” Ecology Letters. Wiley,
2008. https://doi.org/10.1111/j.1461-0248.2008.01206.x.'
ieee: 'D. Storch, A. Šizling, J. Reif, J. Polechova, E. Šizlingová, and K. Gaston,
“The quest for a null model for macroecological patterns: Geometry of species
distributions at multiple spatial scales,” Ecology Letters, vol. 11, no.
8. Wiley, pp. 771–784, 2008.'
ista: 'Storch D, Šizling A, Reif J, Polechova J, Šizlingová E, Gaston K. 2008. The
quest for a null model for macroecological patterns: Geometry of species distributions
at multiple spatial scales. Ecology Letters. 11(8), 771–784.'
mla: 'Storch, D., et al. “The Quest for a Null Model for Macroecological Patterns:
Geometry of Species Distributions at Multiple Spatial Scales.” Ecology Letters,
vol. 11, no. 8, Wiley, 2008, pp. 771–84, doi:10.1111/j.1461-0248.2008.01206.x.'
short: D. Storch, A. Šizling, J. Reif, J. Polechova, E. Šizlingová, K. Gaston, Ecology
Letters 11 (2008) 771–784.
date_created: 2018-12-11T12:07:09Z
date_published: 2008-08-01T00:00:00Z
date_updated: 2025-07-02T05:52:43Z
day: '01'
doi: 10.1111/j.1461-0248.2008.01206.x
extern: '1'
intvolume: ' 11'
issue: '8'
language:
- iso: eng
month: '08'
oa_version: None
page: 771 - 784
publication: Ecology Letters
publication_status: published
publisher: Wiley
publist_id: '1985'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The quest for a null model for macroecological patterns: Geometry of species
distributions at multiple spatial scales'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2008'
...
---
OA_type: free access
_id: '4141'
abstract:
- lang: eng
text: The zyxin-related LPP protein is localized at focal adhesions and cell-cell
contacts and is involved in the regulation of smooth muscle cell migration. A
known interaction partner of LPP in human is the tumor suppressor protein SCRIB.
Knocking down scrib expression c uring zebrafish embryonic development results
in defects of convergence and extension (C&E) movements, which occur during
gastrulation and mediate elongation of the anterior-posterior body axis. Mediolateral
cell polarization underlying C&E is regulated by a noncanonical Writ signaling
pathway constituting the vertebrate planar cell polarity (PCP) pathway. Here,
we investigated the role of Lpp during early zebrafish development. We show that
morpholino knockdown of Ipp results in defects of C&E, phenocopying noncanonical
Wnt signaling mutants. Time-lapse analysis associates the defective dorsal convergence
movements with a reduced ability to migrate along straight paths. In addition,
expression of Lpp is significantly reduced in Wnt11 morphants and in embryos overexpressing
Wnt11 or a dominant-negative form of Rho kinase 2, which is a downstream effector
of Wnt11, Suggesting that Lpp expression is dependent on noncanonical Wnt signaling.
Finally, we demonstrate that Lpp interacts with the PCP protein Scrib in zebrafish,
and that Lpp and Scrib cooperate for the mediation of C&E. (C) 2008 Elsevier
Inc. All rights reserved.
article_processing_charge: No
article_type: original
author:
- first_name: Hilke
full_name: Vervenne, Hilke
last_name: Vervenne
- first_name: Koen
full_name: Crombez, Koen
last_name: Crombez
- first_name: Kathleen
full_name: Lambaerts, Kathleen
last_name: Lambaerts
- first_name: Lara
full_name: Carvalho, Lara
last_name: Carvalho
- first_name: Mathias
full_name: Köppen, Mathias
last_name: Köppen
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Wim
full_name: Van De Ven, Wim
last_name: Van De Ven
- first_name: Marleen
full_name: Petit, Marleen
last_name: Petit
citation:
ama: Vervenne H, Crombez K, Lambaerts K, et al. Lpp is involved in Wnt/PCP signaling
and acts together with Scrib to mediate convergence and extension movements during
zebrafish gastrulation. Developmental Biology. 2008;320(1):267-277. doi:10.1016/j.ydbio.2008.05.529
apa: Vervenne, H., Crombez, K., Lambaerts, K., Carvalho, L., Köppen, M., Heisenberg,
C.-P. J., … Petit, M. (2008). Lpp is involved in Wnt/PCP signaling and acts together
with Scrib to mediate convergence and extension movements during zebrafish gastrulation.
Developmental Biology. Elsevier. https://doi.org/10.1016/j.ydbio.2008.05.529
chicago: Vervenne, Hilke, Koen Crombez, Kathleen Lambaerts, Lara Carvalho, Mathias
Köppen, Carl-Philipp J Heisenberg, Wim Van De Ven, and Marleen Petit. “Lpp Is
Involved in Wnt/PCP Signaling and Acts Together with Scrib to Mediate Convergence
and Extension Movements during Zebrafish Gastrulation.” Developmental Biology.
Elsevier, 2008. https://doi.org/10.1016/j.ydbio.2008.05.529.
ieee: H. Vervenne et al., “Lpp is involved in Wnt/PCP signaling and acts
together with Scrib to mediate convergence and extension movements during zebrafish
gastrulation,” Developmental Biology, vol. 320, no. 1. Elsevier, pp. 267–277,
2008.
ista: Vervenne H, Crombez K, Lambaerts K, Carvalho L, Köppen M, Heisenberg C-PJ,
Van De Ven W, Petit M. 2008. Lpp is involved in Wnt/PCP signaling and acts together
with Scrib to mediate convergence and extension movements during zebrafish gastrulation.
Developmental Biology. 320(1), 267–277.
mla: Vervenne, Hilke, et al. “Lpp Is Involved in Wnt/PCP Signaling and Acts Together
with Scrib to Mediate Convergence and Extension Movements during Zebrafish Gastrulation.”
Developmental Biology, vol. 320, no. 1, Elsevier, 2008, pp. 267–77, doi:10.1016/j.ydbio.2008.05.529.
short: H. Vervenne, K. Crombez, K. Lambaerts, L. Carvalho, M. Köppen, C.-P.J. Heisenberg,
W. Van De Ven, M. Petit, Developmental Biology 320 (2008) 267–277.
date_created: 2018-12-11T12:07:11Z
date_published: 2008-08-01T00:00:00Z
date_updated: 2026-05-29T08:31:06Z
day: '01'
doi: 10.1016/j.ydbio.2008.05.529
extern: '1'
external_id:
pmid:
- '18582857'
intvolume: ' 320'
issue: '1'
language:
- iso: eng
month: '08'
oa_version: None
page: 267 - 277
pmid: 1
publication: Developmental Biology
publication_identifier:
issn:
- 0012-1606
publication_status: published
publisher: Elsevier
publist_id: '1978'
status: public
title: Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate
convergence and extension movements during zebrafish gastrulation
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 320
year: '2008'
...
---
OA_place: publisher
OA_type: free access
_id: '4150'
abstract:
- lang: eng
text: This study provides direct functional evidence that differential adhesion,
measurable as quantitative differences in tissue surface tension, influences spatial
positioning between zebrafish germ layer tissues. We show that embryonic ectodermal
and mesendodermal tissues generated by mRNA-overexpression behave on long-time
scales like immiscible fluids. When mixed in hanging drop culture, their cells
segregate into discrete phases with ectoderm adopting an internal position relative
to the mesendoderm. The position adopted directly correlates with differences
in tissue surface tension. We also show that germ layer tissues from untreated
embryos, when extirpated and placed in culture, adopt a configuration similar
to those of their mRNA-overexpressing counterparts. Down-regulating E-cadherin
expression in the ectoderm leads to reduced surface tension and results in phase
reversal with E-cadherin-depleted ectoderm cells now adopting an external position
relative to the mesendoderm. These results show that in vitro cell sorting of
zebrafish mesendoderm and ectoderm tissues is specified by tissue interfacial
tensions. We perform a mathematical analysis indicating that tissue interfacial
tension between actively motile cells contributes to the spatial organization
and dynamics of these zebrafish germ layers in vivo.
article_processing_charge: No
article_type: original
author:
- first_name: Eva
full_name: Schötz, Eva
last_name: Schötz
- first_name: Rebecca
full_name: Burdine, Rebecca
last_name: Burdine
- first_name: Frank
full_name: Julicher, Frank
last_name: Julicher
- first_name: Malcolm
full_name: Steinberg, Malcolm
last_name: Steinberg
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Ramsey
full_name: Foty, Ramsey
last_name: Foty
citation:
ama: Schötz E, Burdine R, Julicher F, Steinberg M, Heisenberg C-PJ, Foty R. Quantitative
differences in tissue surface tension influence zebrafish germ layer positioning.
HFSP Journal. 2008;2(1):42-56. doi:10.2976/1.2834817
apa: Schötz, E., Burdine, R., Julicher, F., Steinberg, M., Heisenberg, C.-P. J.,
& Foty, R. (2008). Quantitative differences in tissue surface tension influence
zebrafish germ layer positioning. HFSP Journal. HFSP Publishing. https://doi.org/10.2976/1.2834817
chicago: Schötz, Eva, Rebecca Burdine, Frank Julicher, Malcolm Steinberg, Carl-Philipp
J Heisenberg, and Ramsey Foty. “Quantitative Differences in Tissue Surface Tension
Influence Zebrafish Germ Layer Positioning.” HFSP Journal. HFSP Publishing,
2008. https://doi.org/10.2976/1.2834817.
ieee: E. Schötz, R. Burdine, F. Julicher, M. Steinberg, C.-P. J. Heisenberg, and
R. Foty, “Quantitative differences in tissue surface tension influence zebrafish
germ layer positioning,” HFSP Journal, vol. 2, no. 1. HFSP Publishing,
pp. 42–56, 2008.
ista: Schötz E, Burdine R, Julicher F, Steinberg M, Heisenberg C-PJ, Foty R. 2008.
Quantitative differences in tissue surface tension influence zebrafish germ layer
positioning. HFSP Journal. 2(1), 42–56.
mla: Schötz, Eva, et al. “Quantitative Differences in Tissue Surface Tension Influence
Zebrafish Germ Layer Positioning.” HFSP Journal, vol. 2, no. 1, HFSP Publishing,
2008, pp. 42–56, doi:10.2976/1.2834817.
short: E. Schötz, R. Burdine, F. Julicher, M. Steinberg, C.-P.J. Heisenberg, R.
Foty, HFSP Journal 2 (2008) 42–56.
date_created: 2018-12-11T12:07:14Z
date_published: 2008-02-01T00:00:00Z
date_updated: 2026-06-02T09:01:41Z
day: '01'
doi: 10.2976/1.2834817
extern: '1'
external_id:
pmid:
- '19404452'
intvolume: ' 2'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.2976/1.2834817
month: '02'
oa: 1
oa_version: Published Version
page: 42 - 56
pmid: 1
publication: HFSP Journal
publication_status: published
publisher: HFSP Publishing
publist_id: '1969'
status: public
title: Quantitative differences in tissue surface tension influence zebrafish germ
layer positioning
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2008'
...
---
OA_type: closed access
_id: '4161'
abstract:
- lang: eng
text: Handedness of the vertebrate body plan critically depends on transient embryonic
structures/ organs that generate cilia-dependent leftward fluid flow within constrained
extracellular environments. Although the function of ciliated organs in laterality
determination has been extensively studied, how they are formed during embryogenesis
is still poorly understood. Here we show that Kupffer's vesicle (KV), the zebrafish
organ of laterality, arises from a surface epithelium previously thought to adopt
exclusively extra-embryonic fates. Live multi-photon confocal imaging reveals
that surface epithelial cells undergo Nodal/TGF beta signalling-dependent ingression
at the dorsal germ ring margin prior to gastrulation, to give rise to dorsal forerunner
cells (DFCs), the precursors of KV. DFCs then migrate attached to the overlying
surface epithelium and rearrange into rosette-like epithelial structures at the
end of gastrulation. During early somitogenesis, these epithelial rosettes coalesce
into a single rosette that differentiates into the KV with a ciliated lumen at
its apical centre. Our results provide novel insights into the morphogenetic transformations
that shape the laterality organ in zebrafish and suggest a conserved progenitor
role of the surface epithelium during laterality organ formation in vertebrates.
article_processing_charge: No
article_type: original
author:
- first_name: Pablo
full_name: Oteíza, Pablo
last_name: Oteíza
- first_name: Mathias
full_name: Köppen, Mathias
last_name: Köppen
- first_name: Miguel
full_name: Concha, Miguel
last_name: Concha
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Oteíza P, Köppen M, Concha M, Heisenberg C-PJ. Origin and shaping of the laterality
organ in zebrafish. Development. 2008;135(16):2807-2813. doi:10.1242/dev.022228
apa: Oteíza, P., Köppen, M., Concha, M., & Heisenberg, C.-P. J. (2008). Origin
and shaping of the laterality organ in zebrafish. Development. Company
of Biologists. https://doi.org/10.1242/dev.022228
chicago: Oteíza, Pablo, Mathias Köppen, Miguel Concha, and Carl-Philipp J Heisenberg.
“Origin and Shaping of the Laterality Organ in Zebrafish.” Development.
Company of Biologists, 2008. https://doi.org/10.1242/dev.022228.
ieee: P. Oteíza, M. Köppen, M. Concha, and C.-P. J. Heisenberg, “Origin and shaping
of the laterality organ in zebrafish,” Development, vol. 135, no. 16. Company
of Biologists, pp. 2807–2813, 2008.
ista: Oteíza P, Köppen M, Concha M, Heisenberg C-PJ. 2008. Origin and shaping of
the laterality organ in zebrafish. Development. 135(16), 2807–2813.
mla: Oteíza, Pablo, et al. “Origin and Shaping of the Laterality Organ in Zebrafish.”
Development, vol. 135, no. 16, Company of Biologists, 2008, pp. 2807–13,
doi:10.1242/dev.022228.
short: P. Oteíza, M. Köppen, M. Concha, C.-P.J. Heisenberg, Development 135 (2008)
2807–2813.
date_created: 2018-12-11T12:07:19Z
date_published: 2008-08-15T00:00:00Z
date_updated: 2026-05-29T07:25:53Z
day: '15'
doi: 10.1242/dev.022228
extern: '1'
external_id:
pmid:
- '18635607'
intvolume: ' 135'
issue: '16'
language:
- iso: eng
month: '08'
oa_version: None
page: 2807 - 2813
pmid: 1
publication: Development
publication_identifier:
eissn:
- 1477-9129
issn:
- 0950-1991
publication_status: published
publisher: Company of Biologists
publist_id: '1956'
status: public
title: Origin and shaping of the laterality organ in zebrafish
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 135
year: '2008'
...
---
OA_type: closed access
_id: '4180'
abstract:
- lang: eng
text: '(Figure Presented) The name''s Bond: Separated cells form membranous nanotubes
whose tips are tethered by adhesive bonds (see picture). The lifetime of receptor-ligand
interactions can be measured by using membrane nanotubes of living cells as constant
force actuators. Because the nanotubes are extruded from living cells at conditions
approaching the physiological, cellular processes can be both studied and utilized. '
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Krieg, Michael
last_name: Krieg
- first_name: Jonne
full_name: Helenius, Jonne
last_name: Helenius
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Daniel
full_name: Mueller, Daniel
last_name: Mueller
citation:
ama: 'Krieg M, Helenius J, Heisenberg C-PJ, Mueller D. A Bond for a Lifetime: Employing
Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics. Angewandte
Chemie - International Edition. 2008;47(50):9775-9777. doi:10.1002/anie.200803552'
apa: 'Krieg, M., Helenius, J., Heisenberg, C.-P. J., & Mueller, D. (2008). A
Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine
Receptor-Ligand Kinetics. Angewandte Chemie - International Edition. Wiley-Blackwell.
https://doi.org/10.1002/anie.200803552'
chicago: 'Krieg, Michael, Jonne Helenius, Carl-Philipp J Heisenberg, and Daniel
Mueller. “A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells
to Determine Receptor-Ligand Kinetics.” Angewandte Chemie - International Edition.
Wiley-Blackwell, 2008. https://doi.org/10.1002/anie.200803552.'
ieee: 'M. Krieg, J. Helenius, C.-P. J. Heisenberg, and D. Mueller, “A Bond for a
Lifetime: Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand
Kinetics,” Angewandte Chemie - International Edition, vol. 47, no. 50.
Wiley-Blackwell, pp. 9775–9777, 2008.'
ista: 'Krieg M, Helenius J, Heisenberg C-PJ, Mueller D. 2008. A Bond for a Lifetime:
Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics.
Angewandte Chemie - International Edition. 47(50), 9775–9777.'
mla: 'Krieg, Michael, et al. “A Bond for a Lifetime: Employing Membrane Nanotubes
from Living Cells to Determine Receptor-Ligand Kinetics.” Angewandte Chemie
- International Edition, vol. 47, no. 50, Wiley-Blackwell, 2008, pp. 9775–77,
doi:10.1002/anie.200803552.'
short: M. Krieg, J. Helenius, C.-P.J. Heisenberg, D. Mueller, Angewandte Chemie
- International Edition 47 (2008) 9775–9777.
date_created: 2018-12-11T12:07:26Z
date_published: 2008-11-26T00:00:00Z
date_updated: 2026-05-29T07:20:40Z
day: '26'
doi: 10.1002/anie.200803552
extern: '1'
external_id:
pmid:
- '19035533'
intvolume: ' 47'
issue: '50'
language:
- iso: eng
month: '11'
oa_version: None
page: 9775 - 9777
pmid: 1
publication: Angewandte Chemie - International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: published
publisher: Wiley-Blackwell
publist_id: '1939'
status: public
title: 'A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine
Receptor-Ligand Kinetics'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 47
year: '2008'
...
---
OA_type: closed access
_id: '4181'
abstract:
- lang: eng
text: Understanding the factors that direct tissue organization during development
is one of the most fundamental goals in developmental biology. Various hypotheses
explain cell sorting and tissue organization on the basis of the adhesive and
mechanical properties of the constituent cells(1). However, validating these hypotheses
has been difficult due to the lack of appropriate tools to measure these parameters.
Here we use atomic force microscopy ( AFM) to quantify the adhesive and mechanical
properties of individual ectoderm, mesoderm and endoderm progenitor cells from
gastrulating zebrafish embryos. Combining these data with tissue self-assembly
in vitro and the sorting behaviour of progenitors in vivo, we have shown that
differential actomyosin-dependent cell-cortex tension, regulated by Nodal/ TGF
beta-signalling ( transforming growth factor beta), constitutes a key factor that
directs progenitor-cell sorting. These results demonstrate a previously unrecognized
role for Nodal-controlled cell-cortex tension in germ-layer organization during
gastrulation.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Michael
full_name: Krieg, Michael
last_name: Krieg
- first_name: Yohanna
full_name: Arboleda Estudillo, Yohanna
last_name: Arboleda Estudillo
- first_name: Pierre
full_name: Puech, Pierre
last_name: Puech
- first_name: Jos
full_name: Käfer, Jos
last_name: Käfer
- first_name: François
full_name: Graner, François
last_name: Graner
- first_name: Daniel
full_name: Mueller, Daniel
last_name: Mueller
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Krieg M, Arboleda Estudillo Y, Puech P, et al. Tensile forces govern germ-layer
organization in zebrafish. Nature Cell Biology. 2008;10(4):429-436. doi:10.1038/ncb1705
apa: Krieg, M., Arboleda Estudillo, Y., Puech, P., Käfer, J., Graner, F., Mueller,
D., & Heisenberg, C.-P. J. (2008). Tensile forces govern germ-layer organization
in zebrafish. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb1705
chicago: Krieg, Michael, Yohanna Arboleda Estudillo, Pierre Puech, Jos Käfer, François
Graner, Daniel Mueller, and Carl-Philipp J Heisenberg. “Tensile Forces Govern
Germ-Layer Organization in Zebrafish.” Nature Cell Biology. Nature Publishing
Group, 2008. https://doi.org/10.1038/ncb1705.
ieee: M. Krieg et al., “Tensile forces govern germ-layer organization in
zebrafish,” Nature Cell Biology, vol. 10, no. 4. Nature Publishing Group,
pp. 429–436, 2008.
ista: Krieg M, Arboleda Estudillo Y, Puech P, Käfer J, Graner F, Mueller D, Heisenberg
C-PJ. 2008. Tensile forces govern germ-layer organization in zebrafish. Nature
Cell Biology. 10(4), 429–436.
mla: Krieg, Michael, et al. “Tensile Forces Govern Germ-Layer Organization in Zebrafish.”
Nature Cell Biology, vol. 10, no. 4, Nature Publishing Group, 2008, pp.
429–36, doi:10.1038/ncb1705.
short: M. Krieg, Y. Arboleda Estudillo, P. Puech, J. Käfer, F. Graner, D. Mueller,
C.-P.J. Heisenberg, Nature Cell Biology 10 (2008) 429–436.
date_created: 2018-12-11T12:07:26Z
date_published: 2008-03-23T00:00:00Z
date_updated: 2026-05-29T07:13:59Z
day: '23'
doi: 10.1038/ncb1705
extern: '1'
external_id:
pmid:
- '18364700 '
intvolume: ' 10'
issue: '4'
language:
- iso: eng
month: '03'
oa_version: None
page: 429 - 436
pmid: 1
publication: Nature Cell Biology
publication_identifier:
eissn:
- 1476-4679
issn:
- 1465-7392
publication_status: published
publisher: Nature Publishing Group
publist_id: '1938'
status: public
title: Tensile forces govern germ-layer organization in zebrafish
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 10
year: '2008'
...
---
OA_place: repository
OA_type: green
_id: '4190'
abstract:
- lang: eng
text: During vertebrate gastrulation, cells forming the prechordal plate undergo
directed migration as a cohesive cluster. Recent studies revealed that E-cadherin-mediated
coherence between these cells plays an important role in effective anterior migration,
and that platelet-derived growth factor (Pdgf) appears to act as a guidance cue
in this process. However, the mechanisms underlying this process at the individual
cell level remain poorly understood. We have identified miles apart (mil) as a
suppressor of defective anterior migration of the prospective prechordal plate
in silberblick (slb)/wnt11 mutant embryos, in which E-cadherin-mediated coherence
of cell movement is reduced. mil encodes Edg5, a sphingosine-1-phosphate (S1P)
receptor belonging to a family of five G-protein-coupled receptors (S1PRs). S1P
is a lipid signalling molecule that has been implicated in regulating cytoskeletal
rearrangements, cell motility and cell adhesion in a variety of cell types. We
examined the roles of Mil in anterior migration of prechordal plate progenitor
cells and found that, in slb embryos injected with mil-MO, cells migrate with
increased motility but decreased directionality, without restoring the coherence
of cell migration. This indicates that prechordal plate progenitor cells can migrate
effectively as individuals, as well as in a coherent cluster of cells. Moreover,
we demonstrate that Mil regulates cell motility and polarisation through Pdgf
and its intracellular effecter PI3K, but modulates cell coherence independently
of the Pdgf/PI3K pathway, thus co-ordinating cell motility and coherence. These
results suggest that the net migration of prechordal plate progenitors is determined
by different parameters, including motility, persistence and coherence.
article_processing_charge: No
article_type: original
author:
- first_name: Masatake
full_name: Kai, Masatake
last_name: Kai
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Masazumi
full_name: Tada, Masazumi
last_name: Tada
citation:
ama: Kai M, Heisenberg C-PJ, Tada M. Sphingosine-1-phosphate receptors regulate
individual cell behaviours underlying the directed migration of prechordal plate
progenitor cells during zebrafish gastrulation. Development. 2008;135(18):3043-3051.
doi:10.1242/dev.020396
apa: Kai, M., Heisenberg, C.-P. J., & Tada, M. (2008). Sphingosine-1-phosphate
receptors regulate individual cell behaviours underlying the directed migration
of prechordal plate progenitor cells during zebrafish gastrulation. Development.
Company of Biologists. https://doi.org/10.1242/dev.020396
chicago: Kai, Masatake, Carl-Philipp J Heisenberg, and Masazumi Tada. “Sphingosine-1-Phosphate
Receptors Regulate Individual Cell Behaviours Underlying the Directed Migration
of Prechordal Plate Progenitor Cells during Zebrafish Gastrulation.” Development.
Company of Biologists, 2008. https://doi.org/10.1242/dev.020396.
ieee: M. Kai, C.-P. J. Heisenberg, and M. Tada, “Sphingosine-1-phosphate receptors
regulate individual cell behaviours underlying the directed migration of prechordal
plate progenitor cells during zebrafish gastrulation,” Development, vol.
135, no. 18. Company of Biologists, pp. 3043–3051, 2008.
ista: Kai M, Heisenberg C-PJ, Tada M. 2008. Sphingosine-1-phosphate receptors regulate
individual cell behaviours underlying the directed migration of prechordal plate
progenitor cells during zebrafish gastrulation. Development. 135(18), 3043–3051.
mla: Kai, Masatake, et al. “Sphingosine-1-Phosphate Receptors Regulate Individual
Cell Behaviours Underlying the Directed Migration of Prechordal Plate Progenitor
Cells during Zebrafish Gastrulation.” Development, vol. 135, no. 18, Company
of Biologists, 2008, pp. 3043–51, doi:10.1242/dev.020396.
short: M. Kai, C.-P.J. Heisenberg, M. Tada, Development 135 (2008) 3043–3051.
date_created: 2018-12-11T12:07:29Z
date_published: 2008-09-15T00:00:00Z
date_updated: 2026-05-21T08:53:00Z
day: '15'
doi: 10.1242/dev.020396
extern: '1'
external_id:
pmid:
- '18701549'
intvolume: ' 135'
issue: '18'
language:
- iso: eng
month: '09'
oa_version: None
page: 3043 - 3051
pmid: 1
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '1928'
status: public
title: Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying
the directed migration of prechordal plate progenitor cells during zebrafish gastrulation
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 135
year: '2008'
...
---
OA_place: repository
OA_type: green
_id: '4193'
abstract:
- lang: eng
text: The controlled adhesion of cells to each other and to the extracellular matrix
is crucial for tissue development and maintenance. Numerous assays have been developed
to quantify cell adhesion. Among these, the use of atomic force microscopy (AFM)
for single-cell force spectroscopy (SCFS) has recently been established. This
assay permits the adhesion of living cells to be studied in near-physiological
conditions. This implementation of AFM allows unrivaled spatial and temporal control
of cells, as well as highly quantitative force actuation and force measurement
that is sufficiently sensitive to characterize the interaction of single molecules.
Therefore, not only overall cell adhesion but also the properties of single adhesion-receptor-ligand
interactions can be studied. Here we describe current implementations and applications
of SCFS, as well as potential pitfalls, and outline how developments will provide
insight into the forces, energetics and kinetics of cell-adhesion processes.
article_processing_charge: No
article_type: comment
author:
- first_name: Jonne
full_name: Helenius, Jonne
last_name: Helenius
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Hermann
full_name: Gaub, Hermann
last_name: Gaub
- first_name: Daniel
full_name: Mueller, Daniel
last_name: Mueller
citation:
ama: Helenius J, Heisenberg C-PJ, Gaub H, Mueller D. Single-cell force spectroscopy.
Journal of Cell Science. 2008;121(11):1785-1791. doi:10.1242/jcs.030999
apa: Helenius, J., Heisenberg, C.-P. J., Gaub, H., & Mueller, D. (2008). Single-cell
force spectroscopy. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.030999
chicago: Helenius, Jonne, Carl-Philipp J Heisenberg, Hermann Gaub, and Daniel Mueller.
“Single-Cell Force Spectroscopy.” Journal of Cell Science. Company of Biologists,
2008. https://doi.org/10.1242/jcs.030999.
ieee: J. Helenius, C.-P. J. Heisenberg, H. Gaub, and D. Mueller, “Single-cell force
spectroscopy,” Journal of Cell Science, vol. 121, no. 11. Company of Biologists,
pp. 1785–1791, 2008.
ista: Helenius J, Heisenberg C-PJ, Gaub H, Mueller D. 2008. Single-cell force spectroscopy.
Journal of Cell Science. 121(11), 1785–1791.
mla: Helenius, Jonne, et al. “Single-Cell Force Spectroscopy.” Journal of Cell
Science, vol. 121, no. 11, Company of Biologists, 2008, pp. 1785–91, doi:10.1242/jcs.030999.
short: J. Helenius, C.-P.J. Heisenberg, H. Gaub, D. Mueller, Journal of Cell Science
121 (2008) 1785–1791.
date_created: 2018-12-11T12:07:30Z
date_published: 2008-06-01T00:00:00Z
date_updated: 2026-05-28T14:11:54Z
day: '01'
doi: 10.1242/jcs.030999
extern: '1'
external_id:
pmid:
- '18492792'
intvolume: ' 121'
issue: '11'
language:
- iso: eng
month: '06'
oa_version: None
page: 1785 - 1791
pmid: 1
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- 0021-9533
publication_status: published
publisher: Company of Biologists
publist_id: '1924'
status: public
title: Single-cell force spectroscopy
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 121
year: '2008'
...
---
OA_type: closed access
_id: '4198'
abstract:
- lang: eng
text: Animal body plan arises during gastrulation and organogenesis by the coordination
of inductive events and cell movements. Several signaling pathways, such as BMP,
FGF, Hedgehog, Nodal, and Wnt have well-recognized instructive roles in cell fate
specification during vertebrate embryogenesis. Growing evidence indicates that
BMP, Nodal, and FGF signaling also regulate cell movements, and that they do so
through mechanisms distinct from those that specify cell fates. Moreover, pathways
controlling cell movements can also indirectly influence cell fate specification
by regulating dimensions and relative positions of interacting tissues. The current
challenge is to delineate the molecular mechanisms via which the major signaling
pathways regulate cell fate specification and movements, and how these two processes
are coordinated to ensure normal development.
article_processing_charge: No
article_type: review
author:
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Lilianna
full_name: Solnica Krezel, Lilianna
last_name: Solnica Krezel
citation:
ama: Heisenberg C-PJ, Solnica Krezel L. Back and forth between cell fate specification
and movement during vertebrate gastrulation. Current Opinion in Genetics &
Development. 2008;18(4):311-316. doi:10.1016/j.gde.2008.07.011
apa: Heisenberg, C.-P. J., & Solnica Krezel, L. (2008). Back and forth between
cell fate specification and movement during vertebrate gastrulation. Current
Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2008.07.011
chicago: Heisenberg, Carl-Philipp J, and Lilianna Solnica Krezel. “Back and Forth
between Cell Fate Specification and Movement during Vertebrate Gastrulation.”
Current Opinion in Genetics & Development. Elsevier, 2008. https://doi.org/10.1016/j.gde.2008.07.011.
ieee: C.-P. J. Heisenberg and L. Solnica Krezel, “Back and forth between cell fate
specification and movement during vertebrate gastrulation,” Current Opinion
in Genetics & Development, vol. 18, no. 4. Elsevier, pp. 311–316, 2008.
ista: Heisenberg C-PJ, Solnica Krezel L. 2008. Back and forth between cell fate
specification and movement during vertebrate gastrulation. Current Opinion in
Genetics & Development. 18(4), 311–316.
mla: Heisenberg, Carl-Philipp J., and Lilianna Solnica Krezel. “Back and Forth between
Cell Fate Specification and Movement during Vertebrate Gastrulation.” Current
Opinion in Genetics & Development, vol. 18, no. 4, Elsevier, 2008, pp.
311–16, doi:10.1016/j.gde.2008.07.011.
short: C.-P.J. Heisenberg, L. Solnica Krezel, Current Opinion in Genetics &
Development 18 (2008) 311–316.
date_created: 2018-12-11T12:07:32Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2026-05-28T14:03:47Z
day: '01'
doi: 10.1016/j.gde.2008.07.011
extern: '1'
external_id:
pmid:
- '18721878'
intvolume: ' 18'
issue: '4'
language:
- iso: eng
month: '01'
oa_version: None
page: 311 - 316
pmid: 1
publication: Current Opinion in Genetics & Development
publication_identifier:
eissn:
- 1879-0380
issn:
- 0959-437X
publication_status: published
publisher: Elsevier
publist_id: '1918'
status: public
title: Back and forth between cell fate specification and movement during vertebrate
gastrulation
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 18
year: '2008'
...
---
OA_type: closed access
_id: '4227'
abstract:
- lang: eng
text: 'Morphogen concentration gradients provide positional information by activating
target genes in a concentration-dependent manner. Recent reports show that the
gradient of the syncytial morphogen Bicoid seems to provide precise positional
information to determine target gene domains. For secreted morphogenetic ligands,
the precision of the gradients, the signal transduction and the reliability of
target gene expression domains have not been studied. Here we investigate these
issues for the TGF-beta-type morphogen Dpp. We first studied theoretically how
cell-to-cell variability in the source, the target tissue, or both, contribute
to the variations of the gradient. Fluctuations in the source and target generate
a local maximum of precision at a finite distance to the source. We then determined
experimentally in the wing epithelium: (1) the precision of the Dpp concentration
gradient; (2) the precision of the Dpp signaling activity profile; and (3) the
precision of activation of the Dpp target gene spalt. As captured by our theoretical
description, the Dpp gradient provides positional information with a maximal precision
a few cells away from the source. This maximal precision corresponds to a positional
uncertainly of about a single cell diameter. The precision of the Dpp gradient
accounts for the precision of the spalt expression range, implying that Dpp can
act as a morphogen to coarsely determine the expression pattern of target genes.'
article_processing_charge: No
article_type: original
author:
- first_name: Tobias
full_name: Bollenbach, Tobias
last_name: Bollenbach
- first_name: Periklis
full_name: Pantazis, Periklis
last_name: Pantazis
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Christian
full_name: Bokel, Christian
last_name: Bokel
- first_name: Marcos
full_name: González Gaitán, Marcos
last_name: González Gaitán
- first_name: Frank
full_name: Julicher, Frank
last_name: Julicher
citation:
ama: Bollenbach T, Pantazis P, Kicheva A, Bokel C, González Gaitán M, Julicher F.
Precision of the Dpp gradient. Development. 2008;135(6):1137-1146. doi:10.1242/dev.012062
apa: Bollenbach, T., Pantazis, P., Kicheva, A., Bokel, C., González Gaitán, M.,
& Julicher, F. (2008). Precision of the Dpp gradient. Development.
Company of Biologists. https://doi.org/10.1242/dev.012062
chicago: Bollenbach, Tobias, Periklis Pantazis, Anna Kicheva, Christian Bokel, Marcos
González Gaitán, and Frank Julicher. “Precision of the Dpp Gradient.” Development.
Company of Biologists, 2008. https://doi.org/10.1242/dev.012062.
ieee: T. Bollenbach, P. Pantazis, A. Kicheva, C. Bokel, M. González Gaitán, and
F. Julicher, “Precision of the Dpp gradient,” Development, vol. 135, no.
6. Company of Biologists, pp. 1137–1146, 2008.
ista: Bollenbach T, Pantazis P, Kicheva A, Bokel C, González Gaitán M, Julicher
F. 2008. Precision of the Dpp gradient. Development. 135(6), 1137–1146.
mla: Bollenbach, Tobias, et al. “Precision of the Dpp Gradient.” Development,
vol. 135, no. 6, Company of Biologists, 2008, pp. 1137–46, doi:10.1242/dev.012062.
short: T. Bollenbach, P. Pantazis, A. Kicheva, C. Bokel, M. González Gaitán, F.
Julicher, Development 135 (2008) 1137–1146.
date_created: 2018-12-11T12:07:42Z
date_published: 2008-03-15T00:00:00Z
date_updated: 2026-05-28T13:59:30Z
day: '15'
doi: 10.1242/dev.012062
extern: '1'
external_id:
pmid:
- '18296653'
intvolume: ' 135'
issue: '6'
language:
- iso: eng
month: '03'
oa_version: None
page: 1137 - 1146
pmid: 1
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '1889'
status: public
title: Precision of the Dpp gradient
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 135
year: '2008'
...
---
OA_type: closed access
_id: '4244'
abstract:
- lang: eng
text: This paper presents a new approach to optimization of an energy-constrained
modulation scheme for wireless sensor networks by taking advantage of a novel
bio-inspired optimization algorithm. The algorithm is inspired by Wrightpsilas
shifting balance theory (SBT) of evolution in population genetics. The total energy
consumption of an energy-constrained modulation scheme is minimized by using the
new SBT-based optimization algorithm. The results obtained by this new algorithm
are compared with other popular optimization algorithms. Numerical experiments
are performed to demonstrate that the SBT-based algorithm could be used as an
efficient optimizer for solving the optimization problems arising from currently
emerging energy-efficient wireless sensor networks.
article_processing_charge: No
author:
- first_name: Erfu
full_name: Yang, Erfu
last_name: Yang
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Tughrul
full_name: Arslan, Tughrul
last_name: Arslan
- first_name: Ahmet
full_name: Erdogan, Ahmet
last_name: Erdogan
citation:
ama: 'Yang E, Barton NH, Arslan T, Erdogan A. A novel shifting balance theory-based
approach to optimization of an energy-constrained modulation scheme for wireless
sensor networks. In: IEEE; 2008:2749-2756. doi:10.1109/CEC.2008.4631167'
apa: 'Yang, E., Barton, N. H., Arslan, T., & Erdogan, A. (2008). A novel shifting
balance theory-based approach to optimization of an energy-constrained modulation
scheme for wireless sensor networks (pp. 2749–2756). Presented at the WCCI: IEEE
World Congress on Computational Intelligence, Hong Kong: IEEE. https://doi.org/10.1109/CEC.2008.4631167'
chicago: Yang, Erfu, Nicholas H Barton, Tughrul Arslan, and Ahmet Erdogan. “A Novel
Shifting Balance Theory-Based Approach to Optimization of an Energy-Constrained
Modulation Scheme for Wireless Sensor Networks,” 2749–56. IEEE, 2008. https://doi.org/10.1109/CEC.2008.4631167.
ieee: 'E. Yang, N. H. Barton, T. Arslan, and A. Erdogan, “A novel shifting balance
theory-based approach to optimization of an energy-constrained modulation scheme
for wireless sensor networks,” presented at the WCCI: IEEE World Congress on Computational
Intelligence, Hong Kong, 2008, pp. 2749–2756.'
ista: 'Yang E, Barton NH, Arslan T, Erdogan A. 2008. A novel shifting balance theory-based
approach to optimization of an energy-constrained modulation scheme for wireless
sensor networks. WCCI: IEEE World Congress on Computational Intelligence, 2749–2756.'
mla: Yang, Erfu, et al. A Novel Shifting Balance Theory-Based Approach to Optimization
of an Energy-Constrained Modulation Scheme for Wireless Sensor Networks. IEEE,
2008, pp. 2749–56, doi:10.1109/CEC.2008.4631167.
short: E. Yang, N.H. Barton, T. Arslan, A. Erdogan, in:, IEEE, 2008, pp. 2749–2756.
conference:
end_date: 2008-06-06
location: Hong Kong
name: 'WCCI: IEEE World Congress on Computational Intelligence'
start_date: 2008-06-01
date_created: 2018-12-11T12:07:49Z
date_published: 2008-09-23T00:00:00Z
date_updated: 2026-05-28T13:57:07Z
day: '23'
doi: 10.1109/CEC.2008.4631167
extern: '1'
language:
- iso: eng
month: '09'
oa_version: None
page: 2749 - 2756
publication_identifier:
isbn:
- '9781424418237'
publication_status: published
publisher: IEEE
publist_id: '1861'
status: public
title: A novel shifting balance theory-based approach to optimization of an energy-constrained
modulation scheme for wireless sensor networks
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2008'
...
---
OA_type: closed access
_id: '4245'
abstract:
- lang: eng
text: Sex allocation theory has proved extremely successful at predicting when individuals
should adjust the sex of their offspring in response to environmental conditions.
However, we know rather little about the underlying genetics of sex ratio or how
genetic architecture might constrain adaptive sex-ratio behavior. We examined
how mutation influenced genetic variation in the sex ratios produced by the parasitoid
wasp Nasonia vitripennis. In a mutation accumulation experiment, we determined
the mutability of sex ratio, and compared this with the amount of genetic variation
observed in natural populations. We found that the mutability (h2m) ranges from
0.001 to 0.002, similar to estimates for life-history traits in other organisms.
These estimates suggest one mutation every 5–60 generations, which shift the sex
ratio by approximately 0.01 (proportion males). In this and other studies, the
genetic variation in N. vitripennis sex ratio ranged from 0.02 to 0.17 (broad-sense
heritability, H2). If sex ratio is maintained by mutation–selection balance, a
higher genetic variance would be expected given our mutational parameters. Instead,
the observed genetic variance perhaps suggests additional selection against sex-ratio
mutations with deleterious effects on other fitness traits as well as sex ratio
(i.e., pleiotropy), as has been argued to be the case more generally.
article_processing_charge: No
article_type: original
author:
- first_name: Bart
full_name: Pannebakker, Bart
last_name: Pannebakker
- first_name: Daniel
full_name: Halligan, Daniel
last_name: Halligan
- first_name: K Tracy
full_name: Reynolds, K Tracy
last_name: Reynolds
- first_name: Gavin
full_name: Ballantyne, Gavin
last_name: Ballantyne
- first_name: David
full_name: Shuker, David
last_name: Shuker
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Stuart
full_name: West, Stuart
last_name: West
citation:
ama: Pannebakker B, Halligan D, Reynolds KT, et al. Effects of spontaneous mutation
accumulation on sex ratio traits. Evolution; International Journal of Organic
Evolution. 2008;62(8):1921-1935. doi:10.1111/j.1558-5646.2008.00434.x
apa: Pannebakker, B., Halligan, D., Reynolds, K. T., Ballantyne, G., Shuker, D.,
Barton, N. H., & West, S. (2008). Effects of spontaneous mutation accumulation
on sex ratio traits. Evolution; International Journal of Organic Evolution.
Oxford Academic. https://doi.org/10.1111/j.1558-5646.2008.00434.x
chicago: Pannebakker, Bart, Daniel Halligan, K Tracy Reynolds, Gavin Ballantyne,
David Shuker, Nicholas H Barton, and Stuart West. “Effects of Spontaneous Mutation
Accumulation on Sex Ratio Traits.” Evolution; International Journal of Organic
Evolution. Oxford Academic, 2008. https://doi.org/10.1111/j.1558-5646.2008.00434.x.
ieee: B. Pannebakker et al., “Effects of spontaneous mutation accumulation
on sex ratio traits,” Evolution; International Journal of Organic Evolution,
vol. 62, no. 8. Oxford Academic, pp. 1921–1935, 2008.
ista: Pannebakker B, Halligan D, Reynolds KT, Ballantyne G, Shuker D, Barton NH,
West S. 2008. Effects of spontaneous mutation accumulation on sex ratio traits.
Evolution; International Journal of Organic Evolution. 62(8), 1921–1935.
mla: Pannebakker, Bart, et al. “Effects of Spontaneous Mutation Accumulation on
Sex Ratio Traits.” Evolution; International Journal of Organic Evolution,
vol. 62, no. 8, Oxford Academic, 2008, pp. 1921–35, doi:10.1111/j.1558-5646.2008.00434.x.
short: B. Pannebakker, D. Halligan, K.T. Reynolds, G. Ballantyne, D. Shuker, N.H.
Barton, S. West, Evolution; International Journal of Organic Evolution 62 (2008)
1921–1935.
date_created: 2018-12-11T12:07:49Z
date_published: 2008-08-01T00:00:00Z
date_updated: 2026-05-28T13:46:48Z
day: '01'
doi: 10.1111/j.1558-5646.2008.00434.x
extern: '1'
external_id:
pmid:
- '18522711'
intvolume: ' 62'
issue: '8'
language:
- iso: eng
month: '08'
oa_version: None
page: 1921 - 1935
pmid: 1
publication: Evolution; International Journal of Organic Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Oxford Academic
publist_id: '1860'
status: public
title: Effects of spontaneous mutation accumulation on sex ratio traits
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 62
year: '2008'
...
---
_id: '1749'
abstract:
- lang: eng
text: Scanning probe microscopy; Semiconductor quantum dots; Composition gradients;
Composition profiles; Nanotomography; Single quantum dots; Strained sige/si; Three-dimensional
(3D); Wet-chemical etchings; X-ray scattering measurements; quantum dot; methodology;
nanotechnology; optical tomography; scanning probe microscopy; three dimensional
imaging; Imaging, Three-Dimensional; Materials Testing; Microscopy, Scanning Probe;
Nanotechnology; Quantum Dots; Tomography,
acknowledgement: This work was supported by the BMBF (No. 03N8711) and the EU project
D-DotFET (No. 012150)
author:
- first_name: Armando
full_name: Rastelli, Armando
last_name: Rastelli
- first_name: Mathieu
full_name: Stoffel, Mathieu
last_name: Stoffel
- first_name: Ângelo
full_name: Malachias, Ângelo S
last_name: Malachias
- first_name: Tsvetelina
full_name: Merdzhanova, Tsvetelina
last_name: Merdzhanova
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Klaus
full_name: Kern, Klaus
last_name: Kern
- first_name: Till
full_name: Metzger, Till H
last_name: Metzger
- first_name: Oliver
full_name: Schmidt, Oliver G
last_name: Schmidt
citation:
ama: Rastelli A, Stoffel M, Malachias Â, et al. Three-dimensional composition profiles
of single quantum dots determined by scanning-probe-microscopy-based nanotomography.
Nano Letters. 2008;8(5):1404-1409. doi:10.1021/nl080290y
apa: Rastelli, A., Stoffel, M., Malachias, Â., Merdzhanova, T., Katsaros, G., Kern,
K., … Schmidt, O. (2008). Three-dimensional composition profiles of single quantum
dots determined by scanning-probe-microscopy-based nanotomography. Nano Letters.
American Chemical Society. https://doi.org/10.1021/nl080290y
chicago: Rastelli, Armando, Mathieu Stoffel, Ângelo Malachias, Tsvetelina Merdzhanova,
Georgios Katsaros, Klaus Kern, Till Metzger, and Oliver Schmidt. “Three-Dimensional
Composition Profiles of Single Quantum Dots Determined by Scanning-Probe-Microscopy-Based
Nanotomography.” Nano Letters. American Chemical Society, 2008. https://doi.org/10.1021/nl080290y.
ieee: A. Rastelli et al., “Three-dimensional composition profiles of single
quantum dots determined by scanning-probe-microscopy-based nanotomography,” Nano
Letters, vol. 8, no. 5. American Chemical Society, pp. 1404–1409, 2008.
ista: Rastelli A, Stoffel M, Malachias Â, Merdzhanova T, Katsaros G, Kern K, Metzger
T, Schmidt O. 2008. Three-dimensional composition profiles of single quantum dots
determined by scanning-probe-microscopy-based nanotomography. Nano Letters. 8(5),
1404–1409.
mla: Rastelli, Armando, et al. “Three-Dimensional Composition Profiles of Single
Quantum Dots Determined by Scanning-Probe-Microscopy-Based Nanotomography.” Nano
Letters, vol. 8, no. 5, American Chemical Society, 2008, pp. 1404–09, doi:10.1021/nl080290y.
short: A. Rastelli, M. Stoffel, Â. Malachias, T. Merdzhanova, G. Katsaros, K. Kern,
T. Metzger, O. Schmidt, Nano Letters 8 (2008) 1404–1409.
date_created: 2018-12-11T11:53:48Z
date_published: 2008-05-01T00:00:00Z
date_updated: 2021-01-12T06:52:57Z
day: '01'
doi: 10.1021/nl080290y
extern: 1
intvolume: ' 8'
issue: '5'
month: '05'
page: 1404 - 1409
publication: Nano Letters
publication_status: published
publisher: American Chemical Society
publist_id: '5374'
quality_controlled: 0
status: public
title: Three-dimensional composition profiles of single quantum dots determined by
scanning-probe-microscopy-based nanotomography
type: journal_article
volume: 8
year: '2008'
...