---
_id: '12428'
abstract:
- lang: eng
text: The mammary gland consists of a bilayered epithelial structure with an extensively
branched morphology. The majority of this epithelial tree is laid down during
puberty, during which actively proliferating terminal end buds repeatedly elongate
and bifurcate to form the basic structure of the ductal tree. Mammary ducts consist
of a basal and luminal cell layer with a multitude of identified sub-lineages
within both layers. The understanding of how these different cell lineages are
cooperatively driving branching morphogenesis is a problem of crossing multiple
scales, as this requires information on the macroscopic branched structure of
the gland, as well as data on single-cell dynamics driving the morphogenic program.
Here we describe a method to combine genetic lineage tracing with whole-gland
branching analysis. Quantitative data on the global organ structure can be used
to derive a model for mammary gland branching morphogenesis and provide a backbone
on which the dynamics of individual cell lineages can be simulated and compared
to lineage-tracing approaches. Eventually, these quantitative models and experiments
allow to understand the couplings between the macroscopic shape of the mammary
gland and the underlying single-cell dynamics driving branching morphogenesis.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Colinda L.G.J.
full_name: Scheele, Colinda L.G.J.
last_name: Scheele
citation:
ama: 'Hannezo EB, Scheele CLGJ. A Guide Toward Multi-scale and Quantitative Branching
Analysis in the Mammary Gland. In: Margadant C, ed. Cell Migration in Three
Dimensions. Vol 2608. MIMB. Springer Nature; 2023:183-205. doi:10.1007/978-1-0716-2887-4_12'
apa: Hannezo, E. B., & Scheele, C. L. G. J. (2023). A Guide Toward Multi-scale
and Quantitative Branching Analysis in the Mammary Gland. In C. Margadant (Ed.),
Cell Migration in Three Dimensions (Vol. 2608, pp. 183–205). Springer Nature.
https://doi.org/10.1007/978-1-0716-2887-4_12
chicago: Hannezo, Edouard B, and Colinda L.G.J. Scheele. “A Guide Toward Multi-Scale
and Quantitative Branching Analysis in the Mammary Gland.” In Cell Migration
in Three Dimensions, edited by Coert Margadant, 2608:183–205. MIMB. Springer
Nature, 2023. https://doi.org/10.1007/978-1-0716-2887-4_12.
ieee: E. B. Hannezo and C. L. G. J. Scheele, “A Guide Toward Multi-scale and Quantitative
Branching Analysis in the Mammary Gland,” in Cell Migration in Three Dimensions,
vol. 2608, C. Margadant, Ed. Springer Nature, 2023, pp. 183–205.
ista: 'Hannezo EB, Scheele CLGJ. 2023.A Guide Toward Multi-scale and Quantitative
Branching Analysis in the Mammary Gland. In: Cell Migration in Three Dimensions.
Methods in Molecular Biology, vol. 2608, 183–205.'
mla: Hannezo, Edouard B., and Colinda L. G. J. Scheele. “A Guide Toward Multi-Scale
and Quantitative Branching Analysis in the Mammary Gland.” Cell Migration in
Three Dimensions, edited by Coert Margadant, vol. 2608, Springer Nature, 2023,
pp. 183–205, doi:10.1007/978-1-0716-2887-4_12.
short: E.B. Hannezo, C.L.G.J. Scheele, in:, C. Margadant (Ed.), Cell Migration in
Three Dimensions, Springer Nature, 2023, pp. 183–205.
date_created: 2023-01-29T23:00:58Z
date_published: 2023-01-19T00:00:00Z
date_updated: 2023-02-03T10:58:56Z
day: '19'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1007/978-1-0716-2887-4_12
editor:
- first_name: Coert
full_name: Margadant, Coert
last_name: Margadant
external_id:
pmid:
- '36653709'
file:
- access_level: open_access
checksum: aec1b8d3ba938ddf9d8fcb777f3c38ee
content_type: application/pdf
creator: dernst
date_created: 2023-02-03T10:56:39Z
date_updated: 2023-02-03T10:56:39Z
file_id: '12500'
file_name: 2023_MIMB_Hannezo.pdf
file_size: 826598
relation: main_file
success: 1
file_date_updated: 2023-02-03T10:56:39Z
has_accepted_license: '1'
intvolume: ' 2608'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 183-205
pmid: 1
publication: Cell Migration in Three Dimensions
publication_identifier:
eisbn:
- '9781071628874'
eissn:
- 1940-6029
isbn:
- '9781071628867'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: MIMB
status: public
title: A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary
Gland
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: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2608
year: '2023'
...
---
_id: '12720'
abstract:
- lang: eng
text: Here we describe the in vivo DNA assembly approach, where molecular cloning
procedures are performed using an E. coli recA-independent recombination pathway,
which assembles linear fragments of DNA with short homologous termini. This pathway
is present in all standard laboratory E. coli strains and, by bypassing the need
for in vitro DNA assembly, allows simplified molecular cloning to be performed
without the plasmid instability issues associated with specialized recombination-cloning
bacterial strains. The methodology requires specific primer design and can perform
all standard plasmid modifications (insertions, deletions, mutagenesis, and sub-cloning)
in a rapid, simple, and cost-efficient manner, as it does not require commercial
kits or specialized bacterial strains. Additionally, this approach can be used
to perform complex procedures such as multiple modifications to a plasmid, as
up to 6 linear fragments can be assembled in vivo by this recombination pathway.
Procedures generally require less than 3 h, involving PCR amplification, DpnI
digestion of template DNA, and transformation, upon which circular plasmids are
assembled. In this chapter we describe the requirements, procedure, and potential
pitfalls when using this technique, as well as protocol variations to overcome
the most common issues.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Sandra
full_name: Arroyo-Urea, Sandra
last_name: Arroyo-Urea
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Javier
full_name: García-Nafría, Javier
last_name: García-Nafría
citation:
ama: 'Arroyo-Urea S, Watson J, García-Nafría J. Molecular Cloning Using In Vivo
DNA Assembly. In: Scarlett G, ed. DNA Manipulation and Analysis. Vol 2633.
MIMB. New York, NY, United States: Springer Nature; 2023:33-44. doi:10.1007/978-1-0716-3004-4_3'
apa: 'Arroyo-Urea, S., Watson, J., & García-Nafría, J. (2023). Molecular Cloning
Using In Vivo DNA Assembly. In G. Scarlett (Ed.), DNA Manipulation and Analysis
(Vol. 2633, pp. 33–44). New York, NY, United States: Springer Nature. https://doi.org/10.1007/978-1-0716-3004-4_3'
chicago: 'Arroyo-Urea, Sandra, Jake Watson, and Javier García-Nafría. “Molecular
Cloning Using In Vivo DNA Assembly.” In DNA Manipulation and Analysis,
edited by Garry Scarlett, 2633:33–44. MIMB. New York, NY, United States: Springer
Nature, 2023. https://doi.org/10.1007/978-1-0716-3004-4_3.'
ieee: 'S. Arroyo-Urea, J. Watson, and J. García-Nafría, “Molecular Cloning Using
In Vivo DNA Assembly,” in DNA Manipulation and Analysis, vol. 2633, G.
Scarlett, Ed. New York, NY, United States: Springer Nature, 2023, pp. 33–44.'
ista: 'Arroyo-Urea S, Watson J, García-Nafría J. 2023.Molecular Cloning Using In
Vivo DNA Assembly. In: DNA Manipulation and Analysis. Methods in Molecular Biology,
vol. 2633, 33–44.'
mla: Arroyo-Urea, Sandra, et al. “Molecular Cloning Using In Vivo DNA Assembly.”
DNA Manipulation and Analysis, edited by Garry Scarlett, vol. 2633, Springer
Nature, 2023, pp. 33–44, doi:10.1007/978-1-0716-3004-4_3.
short: S. Arroyo-Urea, J. Watson, J. García-Nafría, in:, G. Scarlett (Ed.), DNA
Manipulation and Analysis, Springer Nature, New York, NY, United States, 2023,
pp. 33–44.
date_created: 2023-03-12T23:01:02Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-03-16T08:34:24Z
day: '01'
department:
- _id: PeJo
doi: 10.1007/978-1-0716-3004-4_3
editor:
- first_name: Garry
full_name: Scarlett, Garry
last_name: Scarlett
external_id:
pmid:
- '36853454'
intvolume: ' 2633'
language:
- iso: eng
month: '03'
oa_version: None
page: 33-44
place: New York, NY, United States
pmid: 1
publication: DNA Manipulation and Analysis
publication_identifier:
eisbn:
- 978-1-0716-3004-4
eissn:
- 1940-6029
isbn:
- 978-1-0716-3003-7
issn:
- 1064-3745
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: MIMB
status: public
title: Molecular Cloning Using In Vivo DNA Assembly
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2633
year: '2023'
...
---
_id: '13052'
abstract:
- lang: eng
text: Imaging of the immunological synapse (IS) between dendritic cells (DCs) and
T cells in suspension is hampered by suboptimal alignment of cell-cell contacts
along the vertical imaging plane. This requires optical sectioning that often
results in unsatisfactory resolution in time and space. Here, we present a workflow
where DCs and T cells are confined between a layer of glass and polydimethylsiloxane
(PDMS) that orients the cells along one, horizontal imaging plane, allowing for
fast en-face-imaging of the DC-T cell IS.
acknowledged_ssus:
- _id: Bio
- _id: NanoFab
- _id: M-Shop
acknowledgement: 'A.L. was funded by an Erwin Schrödinger postdoctoral fellowship
of the Austrian Science Fund (FWF, project number: J4542-B) and is an EMBO non-stipendiary
postdoctoral fellow. This work was supported by a European Research Council grant
ERC-CoG-72437 to M.S. We thank the Imaging & Optics facility, the Nanofabrication
facility, and the Miba Machine Shop of ISTA for their excellent support.'
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Alexander F
full_name: Leithner, Alexander F
id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87
last_name: Leithner
orcid: 0000-0002-1073-744X
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- 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: 'Leithner AF, Merrin J, Sixt MK. En-Face Imaging of T Cell-Dendritic Cell Immunological
Synapses. In: Baldari C, Dustin M, eds. The Immune Synapse. Vol 2654. MIMB.
New York, NY: Springer Nature; 2023:137-147. doi:10.1007/978-1-0716-3135-5_9'
apa: 'Leithner, A. F., Merrin, J., & Sixt, M. K. (2023). En-Face Imaging of
T Cell-Dendritic Cell Immunological Synapses. In C. Baldari & M. Dustin (Eds.),
The Immune Synapse (Vol. 2654, pp. 137–147). New York, NY: Springer Nature.
https://doi.org/10.1007/978-1-0716-3135-5_9'
chicago: 'Leithner, Alexander F, Jack Merrin, and Michael K Sixt. “En-Face Imaging
of T Cell-Dendritic Cell Immunological Synapses.” In The Immune Synapse,
edited by Cosima Baldari and Michael Dustin, 2654:137–47. MIMB. New York, NY:
Springer Nature, 2023. https://doi.org/10.1007/978-1-0716-3135-5_9.'
ieee: 'A. F. Leithner, J. Merrin, and M. K. Sixt, “En-Face Imaging of T Cell-Dendritic
Cell Immunological Synapses,” in The Immune Synapse, vol. 2654, C. Baldari
and M. Dustin, Eds. New York, NY: Springer Nature, 2023, pp. 137–147.'
ista: 'Leithner AF, Merrin J, Sixt MK. 2023.En-Face Imaging of T Cell-Dendritic
Cell Immunological Synapses. In: The Immune Synapse. Methods in Molecular Biology,
vol. 2654, 137–147.'
mla: Leithner, Alexander F., et al. “En-Face Imaging of T Cell-Dendritic Cell Immunological
Synapses.” The Immune Synapse, edited by Cosima Baldari and Michael Dustin,
vol. 2654, Springer Nature, 2023, pp. 137–47, doi:10.1007/978-1-0716-3135-5_9.
short: A.F. Leithner, J. Merrin, M.K. Sixt, in:, C. Baldari, M. Dustin (Eds.), The
Immune Synapse, Springer Nature, New York, NY, 2023, pp. 137–147.
date_created: 2023-05-22T08:41:48Z
date_published: 2023-04-28T00:00:00Z
date_updated: 2023-10-17T08:44:53Z
day: '28'
department:
- _id: MiSi
- _id: NanoFab
doi: 10.1007/978-1-0716-3135-5_9
ec_funded: 1
editor:
- first_name: Cosima
full_name: Baldari, Cosima
last_name: Baldari
- first_name: Michael
full_name: Dustin, Michael
last_name: Dustin
external_id:
pmid:
- '37106180'
intvolume: ' 2654'
language:
- iso: eng
month: '04'
oa_version: None
page: 137-147
place: New York, NY
pmid: 1
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular navigation along spatial gradients
publication: The Immune Synapse
publication_identifier:
eisbn:
- '9781071631355'
eissn:
- 1940-6029
isbn:
- '9781071631348'
issn:
- 1064-3745
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: MIMB
status: public
title: En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2654
year: '2023'
...
---
_id: '9245'
abstract:
- lang: eng
text: Tissue morphogenesis is driven by mechanical forces triggering cell movements
and shape changes. Quantitatively measuring tension within tissues is of great
importance for understanding the role of mechanical signals acting on the cell
and tissue level during morphogenesis. Here we introduce laser ablation as a useful
tool to probe tissue tension within the granulosa layer, an epithelial monolayer
of somatic cells that surround the zebrafish female gamete during folliculogenesis.
We describe in detail how to isolate follicles, mount samples, perform laser surgery,
and analyze the data.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: We thank Prof. Masazumi Tada and Roland Dosch for providing transgenic
zebrafish lines, the Heisenberg lab for technical assistance and feedback on the
manuscript, and the Bioimaging and Fish facilities of IST Austria for continuous
support. This work was funded by an ERC advanced grant (MECSPEC to C.-P.H.).
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Peng
full_name: Xia, Peng
id: 4AB6C7D0-F248-11E8-B48F-1D18A9856A87
last_name: Xia
orcid: 0000-0002-5419-7756
- 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: 'Xia P, Heisenberg C-PJ. Quantifying tissue tension in the granulosa layer
after laser surgery. In: Dosch R, ed. Germline Development in the Zebrafish.
Vol 2218. Humana; 2021:117-128. doi:10.1007/978-1-0716-0970-5_10'
apa: Xia, P., & Heisenberg, C.-P. J. (2021). Quantifying tissue tension in the
granulosa layer after laser surgery. In R. Dosch (Ed.), Germline Development
in the Zebrafish (Vol. 2218, pp. 117–128). Humana. https://doi.org/10.1007/978-1-0716-0970-5_10
chicago: Xia, Peng, and Carl-Philipp J Heisenberg. “Quantifying Tissue Tension in
the Granulosa Layer after Laser Surgery.” In Germline Development in the Zebrafish,
edited by Roland Dosch, 2218:117–28. Humana, 2021. https://doi.org/10.1007/978-1-0716-0970-5_10.
ieee: P. Xia and C.-P. J. Heisenberg, “Quantifying tissue tension in the granulosa
layer after laser surgery,” in Germline Development in the Zebrafish, vol.
2218, R. Dosch, Ed. Humana, 2021, pp. 117–128.
ista: 'Xia P, Heisenberg C-PJ. 2021.Quantifying tissue tension in the granulosa
layer after laser surgery. In: Germline Development in the Zebrafish. Methods
in Molecular Biology, vol. 2218, 117–128.'
mla: Xia, Peng, and Carl-Philipp J. Heisenberg. “Quantifying Tissue Tension in the
Granulosa Layer after Laser Surgery.” Germline Development in the Zebrafish,
edited by Roland Dosch, vol. 2218, Humana, 2021, pp. 117–28, doi:10.1007/978-1-0716-0970-5_10.
short: P. Xia, C.-P.J. Heisenberg, in:, R. Dosch (Ed.), Germline Development in
the Zebrafish, Humana, 2021, pp. 117–128.
date_created: 2021-03-14T23:01:34Z
date_published: 2021-02-20T00:00:00Z
date_updated: 2022-06-03T10:57:55Z
day: '20'
department:
- _id: CaHe
doi: 10.1007/978-1-0716-0970-5_10
ec_funded: 1
editor:
- first_name: Roland
full_name: Dosch, Roland
last_name: Dosch
external_id:
pmid:
- '33606227'
intvolume: ' 2218'
keyword:
- Tissue tension
- Morphogenesis
- Laser ablation
- Zebrafish folliculogenesis
- Granulosa cells
language:
- iso: eng
month: '02'
oa_version: None
page: 117-128
pmid: 1
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
publication: Germline Development in the Zebrafish
publication_identifier:
eisbn:
- 978-1-0716-0970-5
eissn:
- 1940-6029
isbn:
- 978-1-0716-0969-9
issn:
- 1064-3745
publication_status: published
publisher: Humana
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantifying tissue tension in the granulosa layer after laser surgery
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2218
year: '2021'
...
---
_id: '10268'
abstract:
- lang: eng
text: The analysis of dynamic cellular processes such as plant cytokinesis stands
and falls with live-cell time-lapse confocal imaging. Conventional approaches
to time-lapse imaging of cell division in Arabidopsis root tips are tedious and
have low throughput. Here, we describe a protocol for long-term time-lapse simultaneous
imaging of multiple root tips on a vertical-stage confocal microscope with automated
root tracking. We also provide modifications of the basic protocol to implement
this imaging method in the analysis of genetic, pharmacological or laser ablation
wounding-mediated experimental manipulations. Our method dramatically improves
the efficiency of cell division time-lapse imaging by increasing the throughput,
while reducing the person-hour requirements of such experiments.
acknowledged_ssus:
- _id: Bio
acknowledgement: We thank B. De Rybel for allowing M.G. to work on this manuscript
during a postdoc in his laboratory, and EMBO for supporting M.G. with a Long-Term
fellowship (ALTF 1005-2019) during this time. We acknowledge the service and support
by the Bioimaging Facility at IST Austria, and finally, we thank A. Mally for proofreading
and correcting the manuscript.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Matous
full_name: Glanc, Matous
id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2
last_name: Glanc
orcid: 0000-0003-0619-7783
citation:
ama: 'Hörmayer L, Friml J, Glanc M. Automated time-lapse imaging and manipulation
of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy.
In: Plant Cell Division. Vol 2382. MIMB. Humana Press; 2021:105-114. doi:10.1007/978-1-0716-1744-1_6'
apa: Hörmayer, L., Friml, J., & Glanc, M. (2021). Automated time-lapse imaging
and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal
microscopy. In Plant Cell Division (Vol. 2382, pp. 105–114). Humana Press.
https://doi.org/10.1007/978-1-0716-1744-1_6
chicago: Hörmayer, Lukas, Jiří Friml, and Matous Glanc. “Automated Time-Lapse Imaging
and Manipulation of Cell Divisions in Arabidopsis Roots by Vertical-Stage Confocal
Microscopy.” In Plant Cell Division, 2382:105–14. MIMB. Humana Press, 2021.
https://doi.org/10.1007/978-1-0716-1744-1_6.
ieee: L. Hörmayer, J. Friml, and M. Glanc, “Automated time-lapse imaging and manipulation
of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy,”
in Plant Cell Division, vol. 2382, Humana Press, 2021, pp. 105–114.
ista: 'Hörmayer L, Friml J, Glanc M. 2021.Automated time-lapse imaging and manipulation
of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy.
In: Plant Cell Division. Methods in Molecular Biology, vol. 2382, 105–114.'
mla: Hörmayer, Lukas, et al. “Automated Time-Lapse Imaging and Manipulation of Cell
Divisions in Arabidopsis Roots by Vertical-Stage Confocal Microscopy.” Plant
Cell Division, vol. 2382, Humana Press, 2021, pp. 105–14, doi:10.1007/978-1-0716-1744-1_6.
short: L. Hörmayer, J. Friml, M. Glanc, in:, Plant Cell Division, Humana Press,
2021, pp. 105–114.
date_created: 2021-11-11T10:03:30Z
date_published: 2021-10-28T00:00:00Z
date_updated: 2022-06-03T06:47:06Z
day: '28'
department:
- _id: JiFr
doi: 10.1007/978-1-0716-1744-1_6
external_id:
pmid:
- '34705235'
intvolume: ' 2382'
language:
- iso: eng
month: '10'
oa_version: None
page: 105-114
pmid: 1
publication: Plant Cell Division
publication_identifier:
eisbn:
- 978-1-0716-1744-1
eissn:
- 1940-6029
isbn:
- 978-1-0716-1743-4
issn:
- 1064-3745
publication_status: published
publisher: Humana Press
quality_controlled: '1'
scopus_import: '1'
series_title: MIMB
status: public
title: Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis
roots by vertical-stage confocal microscopy
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2382
year: '2021'
...
---
_id: '11847'
abstract:
- lang: eng
text: This paper serves as a user guide to the Vienna graph clustering framework.
We review our general memetic algorithm, VieClus, to tackle the graph clustering
problem. A key component of our contribution are natural recombine operators that
employ ensemble clusterings as well as multi-level techniques. Lastly, we combine
these techniques with a scalable communication protocol, producing a system that
is able to compute high-quality solutions in a short amount of time. After giving
a description of the algorithms employed, we establish the connection of the graph
clustering problem to protein–protein interaction networks and moreover give a
description on how the software can be used, what file formats are expected, and
how this can be used to find functional groups in protein–protein interaction
networks.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Sonja
full_name: Biedermann, Sonja
last_name: Biedermann
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Christian
full_name: Schulz, Christian
last_name: Schulz
- first_name: Bernhard
full_name: Schuster, Bernhard
last_name: Schuster
citation:
ama: 'Biedermann S, Henzinger MH, Schulz C, Schuster B. Vienna Graph Clustering.
In: Canzar S, Rojas Ringeling F, eds. Protein-Protein Interaction Networks.
Vol 2074. MIMB. Springer Nature; 2019:215–231. doi:10.1007/978-1-4939-9873-9_16'
apa: Biedermann, S., Henzinger, M. H., Schulz, C., & Schuster, B. (2019). Vienna
Graph Clustering. In S. Canzar & F. Rojas Ringeling (Eds.), Protein-Protein
Interaction Networks (Vol. 2074, pp. 215–231). Springer Nature. https://doi.org/10.1007/978-1-4939-9873-9_16
chicago: Biedermann, Sonja, Monika H Henzinger, Christian Schulz, and Bernhard Schuster.
“Vienna Graph Clustering.” In Protein-Protein Interaction Networks, edited
by Stefan Canzar and Francisca Rojas Ringeling, 2074:215–231. MIMB. Springer Nature,
2019. https://doi.org/10.1007/978-1-4939-9873-9_16.
ieee: S. Biedermann, M. H. Henzinger, C. Schulz, and B. Schuster, “Vienna Graph
Clustering,” in Protein-Protein Interaction Networks, vol. 2074, S. Canzar
and F. Rojas Ringeling, Eds. Springer Nature, 2019, pp. 215–231.
ista: 'Biedermann S, Henzinger MH, Schulz C, Schuster B. 2019.Vienna Graph Clustering.
In: Protein-Protein Interaction Networks. Methods in Molecular Biology, vol. 2074,
215–231.'
mla: Biedermann, Sonja, et al. “Vienna Graph Clustering.” Protein-Protein Interaction
Networks, edited by Stefan Canzar and Francisca Rojas Ringeling, vol. 2074,
Springer Nature, 2019, pp. 215–231, doi:10.1007/978-1-4939-9873-9_16.
short: S. Biedermann, M.H. Henzinger, C. Schulz, B. Schuster, in:, S. Canzar, F.
Rojas Ringeling (Eds.), Protein-Protein Interaction Networks, Springer Nature,
2019, pp. 215–231.
date_created: 2022-08-16T06:54:48Z
date_published: 2019-10-04T00:00:00Z
date_updated: 2023-02-17T09:34:26Z
day: '04'
doi: 10.1007/978-1-4939-9873-9_16
editor:
- first_name: Stefan
full_name: Canzar, Stefan
last_name: Canzar
- first_name: Francisca
full_name: Rojas Ringeling, Francisca
last_name: Rojas Ringeling
extern: '1'
external_id:
pmid:
- '31583641'
intvolume: ' 2074'
language:
- iso: eng
month: '10'
oa_version: None
page: 215–231
pmid: 1
publication: Protein-Protein Interaction Networks
publication_identifier:
eisbn:
- '9781493998739'
eissn:
- 1940-6029
isbn:
- '9781493998722'
issn:
- 1064-3745
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: MIMB
status: public
title: Vienna Graph Clustering
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2074
year: '2019'
...
---
_id: '6178'
abstract:
- lang: eng
text: Mechanically coupled cells can generate forces driving cell and tissue morphogenesis
during development. Visualization and measuring of these forces is of major importance
to better understand the complexity of the biomechanic processes that shape cells
and tissues. Here, we describe how UV laser ablation can be utilized to quantitatively
assess mechanical tension in different tissues of the developing zebrafish and
in cultures of primary germ layer progenitor cells ex vivo.
article_processing_charge: No
author:
- first_name: Michael
full_name: Smutny, Michael
id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87
last_name: Smutny
orcid: 0000-0002-5920-9090
- first_name: Martin
full_name: Behrndt, Martin
id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87
last_name: Behrndt
- first_name: Pedro
full_name: Campinho, Pedro
id: 3AFBBC42-F248-11E8-B48F-1D18A9856A87
last_name: Campinho
orcid: 0000-0002-8526-5416
- first_name: Verena
full_name: Ruprecht, Verena
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- 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: 'Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. UV laser ablation
to measure cell and tissue-generated forces in the zebrafish embryo in vivo and
ex vivo. In: Nelson C, ed. Tissue Morphogenesis. Vol 1189. Methods in Molecular
Biology. New York, NY: Springer; 2014:219-235. doi:10.1007/978-1-4939-1164-6_15'
apa: 'Smutny, M., Behrndt, M., Campinho, P., Ruprecht, V., & Heisenberg, C.-P.
J. (2014). UV laser ablation to measure cell and tissue-generated forces in the
zebrafish embryo in vivo and ex vivo. In C. Nelson (Ed.), Tissue Morphogenesis
(Vol. 1189, pp. 219–235). New York, NY: Springer. https://doi.org/10.1007/978-1-4939-1164-6_15'
chicago: 'Smutny, Michael, Martin Behrndt, Pedro Campinho, Verena Ruprecht, and
Carl-Philipp J Heisenberg. “UV Laser Ablation to Measure Cell and Tissue-Generated
Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” In Tissue Morphogenesis,
edited by Celeste Nelson, 1189:219–35. Methods in Molecular Biology. New York,
NY: Springer, 2014. https://doi.org/10.1007/978-1-4939-1164-6_15.'
ieee: 'M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, and C.-P. J. Heisenberg,
“UV laser ablation to measure cell and tissue-generated forces in the zebrafish
embryo in vivo and ex vivo,” in Tissue Morphogenesis, vol. 1189, C. Nelson,
Ed. New York, NY: Springer, 2014, pp. 219–235.'
ista: 'Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. 2014.UV laser
ablation to measure cell and tissue-generated forces in the zebrafish embryo in
vivo and ex vivo. In: Tissue Morphogenesis. vol. 1189, 219–235.'
mla: Smutny, Michael, et al. “UV Laser Ablation to Measure Cell and Tissue-Generated
Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” Tissue Morphogenesis,
edited by Celeste Nelson, vol. 1189, Springer, 2014, pp. 219–35, doi:10.1007/978-1-4939-1164-6_15.
short: M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, C.-P.J. Heisenberg, in:,
C. Nelson (Ed.), Tissue Morphogenesis, Springer, New York, NY, 2014, pp. 219–235.
date_created: 2019-03-26T08:55:59Z
date_published: 2014-08-22T00:00:00Z
date_updated: 2023-09-05T14:12:00Z
day: '22'
department:
- _id: CaHe
doi: 10.1007/978-1-4939-1164-6_15
editor:
- first_name: Celeste
full_name: Nelson, Celeste
last_name: Nelson
external_id:
pmid:
- '25245697'
intvolume: ' 1189'
language:
- iso: eng
month: '08'
oa_version: None
page: 219-235
place: New York, NY
pmid: 1
publication: Tissue Morphogenesis
publication_identifier:
eissn:
- 1940-6029
isbn:
- '9781493911639'
- '9781493911646'
issn:
- 1064-3745
publication_status: published
publisher: Springer
quality_controlled: '1'
series_title: Methods in Molecular Biology
status: public
title: UV laser ablation to measure cell and tissue-generated forces in the zebrafish
embryo in vivo and ex vivo
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 1189
year: '2014'
...
---
_id: '10900'
abstract:
- lang: eng
text: Leukocyte migration through the interstitial space is crucial for the maintenance
of tolerance and immunity. The main cues for leukocyte trafficking are chemokines
thought to directionally guide these cells towards their targets. However, model
systems that facilitate quantification of chemokine-guided leukocyte migration
in vivo are uncommon. Here we describe an ex vivo crawl-in assay using explanted
mouse ears that allows the visualization of chemokine-dependent dendritic cell
(DC) motility in the dermal interstitium in real time. We present methods for
the preparation of mouse ear sheets and their use in multidimensional confocal
imaging experiments to monitor and analyze the directional migration of fluorescently
labelled DCs through the dermis and into afferent lymphatic vessels. The assay
provides a more physiological approach to study leukocyte migration than in vitro
three-dimensional (3D) or 2-dimensional (2D) migration assays such as collagen
gels and transwell assays.
acknowledgement: We would like to thank Alexander Eichner and Ingrid de Vries for
discussion and critical reading of the manuscript, and Mary Frank for assistance
with the recording of videos and images in Fig. 1. M.S. is supported through funding
from the German Research Foundation (DFG). M.W. acknowledges the Alexander von Humboldt
Foundation for funding.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Michele
full_name: Weber, Michele
id: 3A3FC708-F248-11E8-B48F-1D18A9856A87
last_name: Weber
- 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: 'Weber M, Sixt MK. Live Cell Imaging of Chemotactic Dendritic Cell Migration
in Explanted Mouse Ear Preparations. In: Cardona A, Ubogu E, eds. Chemokines.
Vol 1013. MIMB. Totowa, NJ: Humana Press; 2013:215-226. doi:10.1007/978-1-62703-426-5_14'
apa: 'Weber, M., & Sixt, M. K. (2013). Live Cell Imaging of Chemotactic Dendritic
Cell Migration in Explanted Mouse Ear Preparations. In A. Cardona & E. Ubogu
(Eds.), Chemokines (Vol. 1013, pp. 215–226). Totowa, NJ: Humana Press.
https://doi.org/10.1007/978-1-62703-426-5_14'
chicago: 'Weber, Michele, and Michael K Sixt. “Live Cell Imaging of Chemotactic
Dendritic Cell Migration in Explanted Mouse Ear Preparations.” In Chemokines,
edited by Astrid Cardona and Eroboghene Ubogu, 1013:215–26. MIMB. Totowa, NJ:
Humana Press, 2013. https://doi.org/10.1007/978-1-62703-426-5_14.'
ieee: 'M. Weber and M. K. Sixt, “Live Cell Imaging of Chemotactic Dendritic Cell
Migration in Explanted Mouse Ear Preparations,” in Chemokines, vol. 1013,
A. Cardona and E. Ubogu, Eds. Totowa, NJ: Humana Press, 2013, pp. 215–226.'
ista: 'Weber M, Sixt MK. 2013.Live Cell Imaging of Chemotactic Dendritic Cell Migration
in Explanted Mouse Ear Preparations. In: Chemokines. Methods in Molecular Biology,
vol. 1013, 215–226.'
mla: Weber, Michele, and Michael K. Sixt. “Live Cell Imaging of Chemotactic Dendritic
Cell Migration in Explanted Mouse Ear Preparations.” Chemokines, edited
by Astrid Cardona and Eroboghene Ubogu, vol. 1013, Humana Press, 2013, pp. 215–26,
doi:10.1007/978-1-62703-426-5_14.
short: M. Weber, M.K. Sixt, in:, A. Cardona, E. Ubogu (Eds.), Chemokines, Humana
Press, Totowa, NJ, 2013, pp. 215–226.
date_created: 2022-03-21T07:47:41Z
date_published: 2013-04-03T00:00:00Z
date_updated: 2023-09-05T13:15:33Z
day: '03'
department:
- _id: MiSi
doi: 10.1007/978-1-62703-426-5_14
editor:
- first_name: Astrid
full_name: Cardona, Astrid
last_name: Cardona
- first_name: Eroboghene
full_name: Ubogu, Eroboghene
last_name: Ubogu
external_id:
pmid:
- '23625502'
intvolume: ' 1013'
language:
- iso: eng
month: '04'
oa_version: None
page: 215-226
place: Totowa, NJ
pmid: 1
publication: Chemokines
publication_identifier:
eisbn:
- '9781627034265'
eissn:
- 1940-6029
isbn:
- '9781627034258'
issn:
- 1064-3745
publication_status: published
publisher: Humana Press
quality_controlled: '1'
scopus_import: '1'
series_title: MIMB
status: public
title: Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse
Ear Preparations
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 1013
year: '2013'
...