---
_id: '7651'
abstract:
- lang: eng
text: The growth of snail shells can be described by simple mathematical rules.
Variation in a few parameters can explain much of the diversity of shell shapes
seen in nature. However, empirical studies of gastropod shell shape variation
typically use geometric morphometric approaches, which do not capture this growth
pattern. We have developed a way to infer a set of developmentally descriptive
shape parameters based on three-dimensional logarithmic helicospiral growth and
using landmarks from two-dimensional shell images as input. We demonstrate the
utility of this approach, and compare it to the geometric morphometric approach,
using a large set of Littorina saxatilis shells in which locally adapted populations
differ in shape. Our method can be modified easily to make it applicable to a
wide range of shell forms, which would allow for investigations of the similarities
and differences between and within many different species of gastropods.
article_number: '20190721'
article_processing_charge: No
article_type: original
author:
- first_name: J.
full_name: Larsson, J.
last_name: Larsson
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: S.
full_name: Bengmark, S.
last_name: Bengmark
- first_name: T.
full_name: Lundh, T.
last_name: Lundh
- first_name: R. K.
full_name: Butlin, R. K.
last_name: Butlin
citation:
ama: Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. A developmentally descriptive
method for quantifying shape in gastropod shells. Journal of the Royal Society
Interface. 2020;17(163). doi:10.1098/rsif.2019.0721
apa: Larsson, J., Westram, A. M., Bengmark, S., Lundh, T., & Butlin, R. K. (2020).
A developmentally descriptive method for quantifying shape in gastropod shells.
Journal of the Royal Society Interface. Royal Society. https://doi.org/10.1098/rsif.2019.0721
chicago: Larsson, J., Anja M Westram, S. Bengmark, T. Lundh, and R. K. Butlin. “A
Developmentally Descriptive Method for Quantifying Shape in Gastropod Shells.”
Journal of the Royal Society Interface. Royal Society, 2020. https://doi.org/10.1098/rsif.2019.0721.
ieee: J. Larsson, A. M. Westram, S. Bengmark, T. Lundh, and R. K. Butlin, “A developmentally
descriptive method for quantifying shape in gastropod shells,” Journal of the
Royal Society Interface, vol. 17, no. 163. Royal Society, 2020.
ista: Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. 2020. A developmentally
descriptive method for quantifying shape in gastropod shells. Journal of the Royal
Society Interface. 17(163), 20190721.
mla: Larsson, J., et al. “A Developmentally Descriptive Method for Quantifying Shape
in Gastropod Shells.” Journal of the Royal Society Interface, vol. 17,
no. 163, 20190721, Royal Society, 2020, doi:10.1098/rsif.2019.0721.
short: J. Larsson, A.M. Westram, S. Bengmark, T. Lundh, R.K. Butlin, Journal of
the Royal Society Interface 17 (2020).
date_created: 2020-04-08T15:19:17Z
date_published: 2020-02-01T00:00:00Z
date_updated: 2026-08-12T14:06:19Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1098/rsif.2019.0721
file:
- access_level: open_access
checksum: 4eb102304402f5c56432516b84df86d6
content_type: application/pdf
creator: dernst
date_created: 2020-04-14T12:31:16Z
date_updated: 2020-07-14T12:48:01Z
file_id: '7660'
file_name: 2020_JournRoyalSociety_Larsson.pdf
file_size: 1556190
relation: main_file
file_date_updated: 2020-07-14T12:48:01Z
fulldoi: https://doi.org/10.1098/rsif.2019.0721
has_accepted_license: '1'
intvolume: ' 17'
issue: '163'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '02'
oa: 1
oa_version: Published Version
publication: Journal of the Royal Society Interface
publication_identifier:
eissn:
- 1742-5662
issn:
- 1742-5689
publication_status: published
publisher: Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: A developmentally descriptive method for quantifying shape in gastropod shells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2020'
...
---
_id: '7431'
abstract:
- lang: eng
text: 'In many real-world systems, information can be transmitted in two qualitatively
different ways: by copying or by transformation. Copying occurs when messages
are transmitted without modification, e.g. when an offspring receives an unaltered
copy of a gene from its parent. Transformation occurs when messages are modified
systematically during transmission, e.g. when mutational biases occur during genetic
replication. Standard information-theoretic measures do not distinguish these
two modes of information transfer, although they may reflect different mechanisms
and have different functional consequences. Starting from a few simple axioms,
we derive a decomposition of mutual information into the information transmitted
by copying versus the information transmitted by transformation. We begin with
a decomposition that applies when the source and destination of the channel have
the same set of messages and a notion of message identity exists. We then generalize
our decomposition to other kinds of channels, which can involve different source
and destination sets and broader notions of similarity. In addition, we show that
copy information can be interpreted as the minimal work needed by a physical copying
process, which is relevant for understanding the physics of replication. We use
the proposed decomposition to explore a model of amino acid substitution rates.
Our results apply to any system in which the fidelity of copying, rather than
simple predictability, is of critical relevance.'
acknowledgement: "AK was supported by Grant No. FQXi-RFP-1622 from the FQXi foundation,
and Grant No. CHE-1648973 from the U.S.\r\nNational Science Foundation. AK would
like to thank the Santa Fe Institute for supporting this research. The authors\r\nthank
Jordi Fortuny, Rudolf Hanel, Joshua Garland, and Blai Vidiella for helpful discussions,
as well as the anonymous\r\nreviewers for their insightful suggestions. "
article_number: '0623'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Artemy
full_name: Kolchinsky, Artemy
last_name: Kolchinsky
- first_name: Bernat
full_name: Corominas-Murtra, Bernat
id: 43BE2298-F248-11E8-B48F-1D18A9856A87
last_name: Corominas-Murtra
orcid: 0000-0001-9806-5643
citation:
ama: Kolchinsky A, Corominas-Murtra B. Decomposing information into copying versus
transformation. Journal of the Royal Society Interface. 2020;17(162). doi:10.1098/rsif.2019.0623
apa: Kolchinsky, A., & Corominas-Murtra, B. (2020). Decomposing information
into copying versus transformation. Journal of the Royal Society Interface.
Royal Society. https://doi.org/10.1098/rsif.2019.0623
chicago: Kolchinsky, Artemy, and Bernat Corominas-Murtra. “Decomposing Information
into Copying versus Transformation.” Journal of the Royal Society Interface.
Royal Society, 2020. https://doi.org/10.1098/rsif.2019.0623.
ieee: A. Kolchinsky and B. Corominas-Murtra, “Decomposing information into copying
versus transformation,” Journal of the Royal Society Interface, vol. 17,
no. 162. Royal Society, 2020.
ista: Kolchinsky A, Corominas-Murtra B. 2020. Decomposing information into copying
versus transformation. Journal of the Royal Society Interface. 17(162), 0623.
mla: Kolchinsky, Artemy, and Bernat Corominas-Murtra. “Decomposing Information into
Copying versus Transformation.” Journal of the Royal Society Interface,
vol. 17, no. 162, 0623, Royal Society, 2020, doi:10.1098/rsif.2019.0623.
short: A. Kolchinsky, B. Corominas-Murtra, Journal of the Royal Society Interface
17 (2020).
date_created: 2020-02-02T23:01:03Z
date_published: 2020-01-29T00:00:00Z
date_updated: 2026-08-12T14:08:47Z
day: '29'
department:
- _id: EdHa
doi: 10.1098/rsif.2019.0623
external_id:
arxiv:
- '1903.10693'
isi:
- '000538369800002'
pmid:
- '31964273'
fulldoi: https://doi.org/10.1098/rsif.2019.0623
intvolume: ' 17'
isi: 1
issue: '162'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1903.10693
month: '01'
oa: 1
oa_version: Preprint
pmid: 1
publication: Journal of the Royal Society Interface
publication_identifier:
eissn:
- 1742-5662
publication_status: published
publisher: Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Decomposing information into copying versus transformation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2020'
...
---
OA_place: publisher
OA_type: hybrid
_id: '9814'
abstract:
- lang: eng
text: Data and mathematica notebooks for plotting figures from Language learning
with communication between learners
article_processing_charge: No
author:
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. Data and mathematica notebooks
for plotting figures from language learning with communication between learners
from language acquisition with communication between learners. 2020. doi:10.6084/m9.figshare.5973013.v1
apa: Ibsen-Jensen, R., Tkadlec, J., Chatterjee, K., & Nowak, M. (2020). Data
and mathematica notebooks for plotting figures from language learning with communication
between learners from language acquisition with communication between learners.
Royal Society. https://doi.org/10.6084/m9.figshare.5973013.v1
chicago: Ibsen-Jensen, Rasmus, Josef Tkadlec, Krishnendu Chatterjee, and Martin
Nowak. “Data and Mathematica Notebooks for Plotting Figures from Language Learning
with Communication between Learners from Language Acquisition with Communication
between Learners.” Royal Society, 2020. https://doi.org/10.6084/m9.figshare.5973013.v1.
ieee: R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, and M. Nowak, “Data and mathematica
notebooks for plotting figures from language learning with communication between
learners from language acquisition with communication between learners.” Royal
Society, 2020.
ista: Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. 2020. Data and mathematica
notebooks for plotting figures from language learning with communication between
learners from language acquisition with communication between learners, Royal
Society, 10.6084/m9.figshare.5973013.v1.
mla: Ibsen-Jensen, Rasmus, et al. Data and Mathematica Notebooks for Plotting
Figures from Language Learning with Communication between Learners from Language
Acquisition with Communication between Learners. Royal Society, 2020, doi:10.6084/m9.figshare.5973013.v1.
short: R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, M. Nowak, (2020).
date_created: 2021-08-06T13:09:57Z
date_published: 2020-10-15T00:00:00Z
date_updated: 2026-08-12T14:08:28Z
day: '15'
department:
- _id: KrCh
doi: 10.6084/m9.figshare.5973013.v1
fulldoi: https://doi.org/10.6084/m9.figshare.5973013.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.5973013.v1
month: '10'
oa: 1
oa_version: Published Version
publisher: Royal Society
related_material:
record:
- id: '198'
relation: used_in_publication
status: public
status: public
title: Data and mathematica notebooks for plotting figures from language learning
with communication between learners from language acquisition with communication
between learners
type: research_data_reference
user_id: 0043cee0-e5fc-11ee-9736-f83bc23afbf0
year: '2020'
...
---
_id: '7563'
abstract:
- lang: eng
text: "We introduce “state space persistence analysis” for deducing the symbolic
dynamics of time series data obtained from high-dimensional chaotic attractors.
To this end, we adapt a topological data analysis technique known as persistent
homology for the characterization of state space projections of chaotic trajectories
and periodic orbits. By comparing the shapes along a chaotic trajectory to those
of the periodic orbits, state space persistence analysis quantifies the shape
similarity of chaotic trajectory segments and periodic orbits. We demonstrate
the method by applying it to the three-dimensional Rössler system and a 30-dimensional
discretization of the Kuramoto–Sivashinsky partial differential equation in (1+1)
dimensions.\r\nOne way of studying chaotic attractors systematically is through
their symbolic dynamics, in which one partitions the state space into qualitatively
different regions and assigns a symbol to each such region.1–3 This yields a “coarse-grained”
state space of the system, which can then be reduced to a Markov chain encoding
all possible transitions between the states of the system. While it is possible
to obtain the symbolic dynamics of low-dimensional chaotic systems with standard
tools such as Poincaré maps, when applied to high-dimensional systems such as
turbulent flows, these tools alone are not sufficient to determine symbolic dynamics.4,5
In this paper, we develop “state space persistence analysis” and demonstrate that
it can be utilized to infer the symbolic dynamics in very high-dimensional settings."
article_number: '033109'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Gökhan
full_name: Yalniz, Gökhan
id: 66E74FA2-D8BF-11E9-8249-8DE2E5697425
last_name: Yalniz
orcid: 0000-0002-8490-9312
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
citation:
ama: Yalniz G, Budanur NB. Inferring symbolic dynamics of chaotic flows from persistence.
Chaos. 2020;30(3). doi:10.1063/1.5122969
apa: Yalniz, G., & Budanur, N. B. (2020). Inferring symbolic dynamics of chaotic
flows from persistence. Chaos. AIP Publishing. https://doi.org/10.1063/1.5122969
chicago: Yalniz, Gökhan, and Nazmi B Budanur. “Inferring Symbolic Dynamics of Chaotic
Flows from Persistence.” Chaos. AIP Publishing, 2020. https://doi.org/10.1063/1.5122969.
ieee: G. Yalniz and N. B. Budanur, “Inferring symbolic dynamics of chaotic flows
from persistence,” Chaos, vol. 30, no. 3. AIP Publishing, 2020.
ista: Yalniz G, Budanur NB. 2020. Inferring symbolic dynamics of chaotic flows from
persistence. Chaos. 30(3), 033109.
mla: Yalniz, Gökhan, and Nazmi B. Budanur. “Inferring Symbolic Dynamics of Chaotic
Flows from Persistence.” Chaos, vol. 30, no. 3, 033109, AIP Publishing,
2020, doi:10.1063/1.5122969.
short: G. Yalniz, N.B. Budanur, Chaos 30 (2020).
corr_author: '1'
date_created: 2020-03-04T08:06:25Z
date_published: 2020-03-03T00:00:00Z
date_updated: 2026-09-02T08:16:31Z
day: '03'
ddc:
- '530'
department:
- _id: BjHo
doi: 10.1063/1.5122969
external_id:
arxiv:
- '1910.04584'
isi:
- '000519254800002'
fulldoi: https://doi.org/10.1063/1.5122969
intvolume: ' 30'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1063/1.5122969
month: '03'
oa: 1
oa_version: Published Version
publication: Chaos
publication_identifier:
eissn:
- 1089-7682
issn:
- 1054-1500
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
record:
- id: '19684'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Inferring symbolic dynamics of chaotic flows from persistence
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2020'
...
---
_id: '8755'
abstract:
- lang: eng
text: 'The superconducting circuit community has recently discovered the promising
potential of superinductors. These circuit elements have a characteristic impedance
exceeding the resistance quantum RQ ≈ 6.45 kΩ which leads to a suppression of
ground state charge fluctuations. Applications include the realization of hardware
protected qubits for fault tolerant quantum computing, improved coupling to small
dipole moment objects and defining a new quantum metrology standard for the ampere.
In this work we refute the widespread notion that superinductors can only be implemented
based on kinetic inductance, i.e. using disordered superconductors or Josephson
junction arrays. We present modeling, fabrication and characterization of 104
planar aluminum coil resonators with a characteristic impedance up to 30.9 kΩ
at 5.6 GHz and a capacitance down to ≤ 1 fF, with lowloss and a power handling
reaching 108 intra-cavity photons. Geometric superinductors are free of uncontrolled
tunneling events and offer high reproducibility, linearity and the ability to
couple magnetically - properties that significantly broaden the scope of future
quantum circuits. '
acknowledged_ssus:
- _id: NanoFab
acknowledgement: "The authors acknowledge the support from I. Prieto and the IST Nanofabrication
Facility. This work was supported by IST Austria and a NOMIS foundation research
grant and the Austrian Science Fund (FWF) through BeyondC (F71). MP is the recipient
of a P¨ottinger scholarship at IST Austria. JMF acknowledges support from the European
Union’s Horizon 2020 research and innovation programs under grant agreement No 732894
(FET Proactive HOT), 862644 (FET Open QUARTET), and the European Research Council
under grant agreement\r\nnumber 758053 (ERC StG QUNNECT). "
article_number: '044055'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Matilda
full_name: Peruzzo, Matilda
id: 3F920B30-F248-11E8-B48F-1D18A9856A87
last_name: Peruzzo
orcid: 0000-0002-3415-4628
- first_name: Andrea
full_name: Trioni, Andrea
id: 42F71B44-F248-11E8-B48F-1D18A9856A87
last_name: Trioni
- first_name: Farid
full_name: Hassani, Farid
id: 2AED110C-F248-11E8-B48F-1D18A9856A87
last_name: Hassani
orcid: 0000-0001-6937-5773
- first_name: Martin
full_name: Zemlicka, Martin
id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87
last_name: Zemlicka
orcid: 0009-0005-0878-3032
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. Surpassing the resistance
quantum with a geometric superinductor. Physical Review Applied. 2020;14(4).
doi:10.1103/PhysRevApplied.14.044055
apa: Peruzzo, M., Trioni, A., Hassani, F., Zemlicka, M., & Fink, J. M. (2020).
Surpassing the resistance quantum with a geometric superinductor. Physical
Review Applied. American Physical Society. https://doi.org/10.1103/PhysRevApplied.14.044055
chicago: Peruzzo, Matilda, Andrea Trioni, Farid Hassani, Martin Zemlicka, and Johannes
M Fink. “Surpassing the Resistance Quantum with a Geometric Superinductor.” Physical
Review Applied. American Physical Society, 2020. https://doi.org/10.1103/PhysRevApplied.14.044055.
ieee: M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, and J. M. Fink, “Surpassing
the resistance quantum with a geometric superinductor,” Physical Review Applied,
vol. 14, no. 4. American Physical Society, 2020.
ista: Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. 2020. Surpassing the
resistance quantum with a geometric superinductor. Physical Review Applied. 14(4),
044055.
mla: Peruzzo, Matilda, et al. “Surpassing the Resistance Quantum with a Geometric
Superinductor.” Physical Review Applied, vol. 14, no. 4, 044055, American
Physical Society, 2020, doi:10.1103/PhysRevApplied.14.044055.
short: M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, J.M. Fink, Physical Review
Applied 14 (2020).
date_created: 2020-11-15T23:01:17Z
date_published: 2020-10-29T00:00:00Z
date_updated: 2026-10-02T11:28:16Z
day: '29'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.1103/PhysRevApplied.14.044055
ec_funded: 1
external_id:
arxiv:
- '2007.01644'
isi:
- '000582797300003'
file:
- access_level: open_access
checksum: 2a634abe75251ae7628cd54c8a4ce2e8
content_type: application/pdf
creator: dernst
date_created: 2021-03-29T11:43:20Z
date_updated: 2021-03-29T11:43:20Z
file_id: '9300'
file_name: 2020_PhysReviewApplied_Peruzzo.pdf
file_size: 2607823
relation: main_file
success: 1
file_date_updated: 2021-03-29T11:43:20Z
fulldoi: https://doi.org/10.1103/PhysRevApplied.14.044055
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 257EB838-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '732894'
name: Hybrid Optomechanical Technologies
- _id: 237CBA6C-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '862644'
name: Quantum readout techniques and technologies
- _id: 26336814-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '758053'
name: A Fiber Optic Transceiver for Superconducting Qubits
- _id: bdb108fd-d553-11ed-ba76-83dc74a9864f
grant_number: F07105
name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration
of Superconducting Quantum Circuits
publication: Physical Review Applied
publication_identifier:
eissn:
- 2331-7019
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '13070'
relation: research_data
status: public
- id: '9920'
relation: dissertation_contains
status: public
- id: '20371'
relation: dissertation_contains
status: public
- id: '17133'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Surpassing the resistance quantum with a geometric superinductor
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2020'
...
---
_id: '8272'
abstract:
- lang: eng
text: We study turn-based stochastic zero-sum games with lexicographic preferences
over reachability and safety objectives. Stochastic games are standard models
in control, verification, and synthesis of stochastic reactive systems that exhibit
both randomness as well as angelic and demonic non-determinism. Lexicographic
order allows to consider multiple objectives with a strict preference order over
the satisfaction of the objectives. To the best of our knowledge, stochastic games
with lexicographic objectives have not been studied before. We establish determinacy
of such games and present strategy and computational complexity results. For strategy
complexity, we show that lexicographically optimal strategies exist that are deterministic
and memory is only required to remember the already satisfied and violated objectives.
For a constant number of objectives, we show that the relevant decision problem
is in NP∩coNP , matching the current known bound for single objectives; and
in general the decision problem is PSPACE -hard and can be solved in NEXPTIME∩coNEXPTIME
. We present an algorithm that computes the lexicographically optimal strategies
via a reduction to computation of optimal strategies in a sequence of single-objectives
games. We have implemented our algorithm and report experimental results on various
case studies.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Joost P
full_name: Katoen, Joost P
id: 4524F760-F248-11E8-B48F-1D18A9856A87
last_name: Katoen
orcid: 0000-0002-6143-1926
- first_name: Maximilian
full_name: Weininger, Maximilian
last_name: Weininger
- first_name: Tobias
full_name: Winkler, Tobias
last_name: Winkler
citation:
ama: 'Chatterjee K, Katoen JP, Weininger M, Winkler T. Stochastic games with lexicographic
reachability-safety objectives. In: International Conference on Computer Aided
Verification. Vol 12225. Springer Nature; 2020:398-420. doi:10.1007/978-3-030-53291-8_21'
apa: Chatterjee, K., Katoen, J. P., Weininger, M., & Winkler, T. (2020). Stochastic
games with lexicographic reachability-safety objectives. In International Conference
on Computer Aided Verification (Vol. 12225, pp. 398–420). Springer Nature.
https://doi.org/10.1007/978-3-030-53291-8_21
chicago: Chatterjee, Krishnendu, Joost P Katoen, Maximilian Weininger, and Tobias
Winkler. “Stochastic Games with Lexicographic Reachability-Safety Objectives.”
In International Conference on Computer Aided Verification, 12225:398–420.
Springer Nature, 2020. https://doi.org/10.1007/978-3-030-53291-8_21.
ieee: K. Chatterjee, J. P. Katoen, M. Weininger, and T. Winkler, “Stochastic games
with lexicographic reachability-safety objectives,” in International Conference
on Computer Aided Verification, 2020, vol. 12225, pp. 398–420.
ista: 'Chatterjee K, Katoen JP, Weininger M, Winkler T. 2020. Stochastic games with
lexicographic reachability-safety objectives. International Conference on Computer
Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 12225, 398–420.'
mla: Chatterjee, Krishnendu, et al. “Stochastic Games with Lexicographic Reachability-Safety
Objectives.” International Conference on Computer Aided Verification, vol.
12225, Springer Nature, 2020, pp. 398–420, doi:10.1007/978-3-030-53291-8_21.
short: K. Chatterjee, J.P. Katoen, M. Weininger, T. Winkler, in:, International
Conference on Computer Aided Verification, Springer Nature, 2020, pp. 398–420.
conference:
name: 'CAV: Computer Aided Verification'
date_created: 2020-08-16T22:00:58Z
date_published: 2020-07-14T00:00:00Z
date_updated: 2026-10-16T08:04:15Z
day: '14'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-030-53291-8_21
ec_funded: 1
external_id:
arxiv:
- '2005.04018'
isi:
- '000695272500021'
file:
- access_level: open_access
checksum: 093d4788d7d5b2ce0ffe64fbe7820043
content_type: application/pdf
creator: dernst
date_created: 2020-08-17T11:32:44Z
date_updated: 2020-08-17T11:32:44Z
file_id: '8276'
file_name: 2020_LNCS_CAV_Chatterjee.pdf
file_size: 625056
relation: main_file
success: 1
file_date_updated: 2020-08-17T11:32:44Z
fulldoi: https://doi.org/10.1007/978-3-030-53291-8_21
has_accepted_license: '1'
intvolume: ' 12225'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 398-420
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication: International Conference on Computer Aided Verification
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030532901'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '12738'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Stochastic games with lexicographic reachability-safety objectives
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: conference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 12225
year: '2020'
...
---
_id: '8586'
abstract:
- lang: eng
text: Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights
into biological processes and structures within a native context. However, a major
challenge still lies in the efficient and reproducible preparation of adherent
cells for subsequent cryo-EM analysis. This is due to the sensitivity of many
cellular specimens to the varying seeding and culturing conditions required for
EM experiments, the often limited amount of cellular material and also the fragility
of EM grids and their substrate. Here, we present low-cost and reusable 3D printed
grid holders, designed to improve specimen preparation when culturing challenging
cellular samples directly on grids. The described grid holders increase cell culture
reproducibility and throughput, and reduce the resources required for cell culturing.
We show that grid holders can be integrated into various cryo-EM workflows, including
micro-patterning approaches to control cell seeding on grids, and for generating
samples for cryo-focused ion beam milling and cryo-electron tomography experiments.
Their adaptable design allows for the generation of specialized grid holders customized
to a large variety of applications.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: Bio
- _id: EM-Fac
acknowledgement: This work was supported by the Austrian Science Fund (FWF, P33367)
to FKMS. BZ acknowledges support by the Niederösterreich Fond. This research was
also supported by the Scientific Service Units (SSU) of IST Austria through resources
provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the
BioImaging Facility (BIF) and the Electron Microscopy Facility (EMF). We thank Georgi
Dimchev (IST Austria) and Sonja Jacob (Vienna Biocenter Core Facilities) for testing
our grid holders in different experimental setups and Daniel Gütl and the Kondrashov
group (IST Austria) for granting us repeated access to their 3D printers. We also
thank Jonna Alanko and the Sixt lab (IST Austria) for providing us HeLa cells, primary
BL6 mouse tail fibroblasts, NIH 3T3 fibroblasts and human telomerase immortalised
foreskin fibroblasts for our experiments. We are thankful to Ori Avinoam and William
Wan for helpful comments on the manuscript and also thank Dorotea Fracchiolla (Art&Science)
for illustrating the graphical abstract.
article_number: '107633'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Bettina
full_name: Zens, Bettina
id: 45FD126C-F248-11E8-B48F-1D18A9856A87
last_name: Zens
orcid: 0000-0002-9561-1239
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Fäßler F, Zens B, Hauschild R, Schur FK. 3D printed cell culture grid holders
for improved cellular specimen preparation in cryo-electron microscopy. Journal
of Structural Biology. 2020;212(3). doi:10.1016/j.jsb.2020.107633
apa: Fäßler, F., Zens, B., Hauschild, R., & Schur, F. K. (2020). 3D printed
cell culture grid holders for improved cellular specimen preparation in cryo-electron
microscopy. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2020.107633
chicago: Fäßler, Florian, Bettina Zens, Robert Hauschild, and Florian KM Schur.
“3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation
in Cryo-Electron Microscopy.” Journal of Structural Biology. Elsevier,
2020. https://doi.org/10.1016/j.jsb.2020.107633.
ieee: F. Fäßler, B. Zens, R. Hauschild, and F. K. Schur, “3D printed cell culture
grid holders for improved cellular specimen preparation in cryo-electron microscopy,”
Journal of Structural Biology, vol. 212, no. 3. Elsevier, 2020.
ista: Fäßler F, Zens B, Hauschild R, Schur FK. 2020. 3D printed cell culture grid
holders for improved cellular specimen preparation in cryo-electron microscopy.
Journal of Structural Biology. 212(3), 107633.
mla: Fäßler, Florian, et al. “3D Printed Cell Culture Grid Holders for Improved
Cellular Specimen Preparation in Cryo-Electron Microscopy.” Journal of Structural
Biology, vol. 212, no. 3, 107633, Elsevier, 2020, doi:10.1016/j.jsb.2020.107633.
short: F. Fäßler, B. Zens, R. Hauschild, F.K. Schur, Journal of Structural Biology
212 (2020).
corr_author: '1'
date_created: 2020-09-29T13:24:06Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2026-10-25T23:30:02Z
day: '01'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1016/j.jsb.2020.107633
external_id:
isi:
- '000600997800008'
pmid:
- '32987119'
file:
- access_level: open_access
checksum: c48cbf594e84fc2f91966ffaafc0918c
content_type: application/pdf
creator: dernst
date_created: 2020-12-10T14:01:10Z
date_updated: 2020-12-10T14:01:10Z
file_id: '8937'
file_name: 2020_JourStrucBiology_Faessler.pdf
file_size: 7076870
relation: main_file
success: 1
file_date_updated: 2020-12-10T14:01:10Z
fulldoi: https://doi.org/10.1016/j.jsb.2020.107633
has_accepted_license: '1'
intvolume: ' 212'
isi: 1
issue: '3'
keyword:
- electron microscopy
- cryo-EM
- EM sample preparation
- 3D printing
- cell culture
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
- _id: 059B463C-7A3F-11EA-A408-12923DDC885E
name: NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria
publication: Journal of Structural Biology
publication_identifier:
issn:
- 1047-8477
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '14592'
relation: used_in_publication
status: public
- id: '12491'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 3D printed cell culture grid holders for improved cellular specimen preparation
in cryo-electron microscopy
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 212
year: '2020'
...
---
_id: '7473'
abstract:
- lang: eng
text: How structural and functional properties of synapses relate to each other
is a fundamental question in neuroscience. Electrophysiology has elucidated mechanisms
of synaptic transmission, and electron microscopy (EM) has provided insight into
morphological properties of synapses. Here we describe an enhanced method for
functional EM (“flash and freeze”), combining optogenetic stimulation with high-pressure
freezing. We demonstrate that the improved method can be applied to intact networks
in acute brain slices and organotypic slice cultures from mice. As a proof of
concept, we probed vesicle pool changes during synaptic transmission at the hippocampal
mossy fiber-CA3 pyramidal neuron synapse. Our findings show overlap of the docked
vesicle pool and the functionally defined readily releasable pool and provide
evidence of fast endocytosis at this synapse. Functional EM with acute slices
and slice cultures has the potential to reveal the structural and functional mechanisms
of transmission in intact, genetically perturbed, and disease-affected synapses.
acknowledgement: This project has received funding from the European Research Council
(ERC) and European Commission (EC), under the European Union’s Horizon 2020 research
and innovation programme (ERC grant agreement No. 692692 and Marie Sklodowska-Curie
708497) and from Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27
Wittgenstein award and DK W1205-B09). We thank Johann Danzl and Ryuichi Shigemoto
for critically reading the manuscript; Walter Kaufmann, Daniel Gutl, and Vanessa
Zheden for extensive EM training, advice, and experimental assistance; Benjamin
Suter for substantial help with light stimulation, ImageJ plugins for analysis,
and manuscript editing; Florian Marr and Christina Altmutter for technical support;
Eleftheria Kralli-Beller for manuscript editing; Julia König and Paul Wurzinger
(Leica Microsystems) for helpful technical discussions; and Taija Makinen for providing
the Prox1-CreERT2 mouse line.
article_processing_charge: No
article_type: original
author:
- first_name: Carolina
full_name: Borges Merjane, Carolina
id: 4305C450-F248-11E8-B48F-1D18A9856A87
last_name: Borges Merjane
orcid: 0000-0003-0005-401X
- first_name: Olena
full_name: Kim, Olena
id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87
last_name: Kim
orcid: 0000-0003-2344-1039
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Borges Merjane C, Kim O, Jonas PM. Functional electron microscopy (“Flash and
Freeze”) of identified cortical synapses in acute brain slices. Neuron.
2020;105:992-1006. doi:10.1016/j.neuron.2019.12.022
apa: Borges Merjane, C., Kim, O., & Jonas, P. M. (2020). Functional electron
microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain
slices. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.12.022
chicago: Borges Merjane, Carolina, Olena Kim, and Peter M Jonas. “Functional Electron
Microscopy (‘Flash and Freeze’) of Identified Cortical Synapses in Acute Brain
Slices.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2019.12.022.
ieee: C. Borges Merjane, O. Kim, and P. M. Jonas, “Functional electron microscopy
(‘Flash and Freeze’) of identified cortical synapses in acute brain slices,” Neuron,
vol. 105. Elsevier, pp. 992–1006, 2020.
ista: Borges Merjane C, Kim O, Jonas PM. 2020. Functional electron microscopy (“Flash
and Freeze”) of identified cortical synapses in acute brain slices. Neuron. 105,
992–1006.
mla: Borges Merjane, Carolina, et al. “Functional Electron Microscopy (‘Flash and
Freeze’) of Identified Cortical Synapses in Acute Brain Slices.” Neuron,
vol. 105, Elsevier, 2020, pp. 992–1006, doi:10.1016/j.neuron.2019.12.022.
short: C. Borges Merjane, O. Kim, P.M. Jonas, Neuron 105 (2020) 992–1006.
corr_author: '1'
date_created: 2020-02-10T15:59:45Z
date_published: 2020-03-18T00:00:00Z
date_updated: 2026-10-25T23:30:04Z
day: '18'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1016/j.neuron.2019.12.022
ec_funded: 1
external_id:
isi:
- '000520854700008'
pmid:
- '31928842'
file:
- access_level: open_access
checksum: 3582664addf26859e86ac5bec3e01416
content_type: application/pdf
creator: dernst
date_created: 2020-11-20T08:58:53Z
date_updated: 2020-11-20T08:58:53Z
file_id: '8778'
file_name: 2020_Neuron_BorgesMerjane.pdf
file_size: 9712957
relation: main_file
success: 1
file_date_updated: 2020-11-20T08:58:53Z
fulldoi: https://doi.org/10.1016/j.neuron.2019.12.022
has_accepted_license: '1'
intvolume: ' 105'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '03'
oa: 1
oa_version: Published Version
page: 992-1006
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 25BAF7B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '708497'
name: Presynaptic calcium channels distribution and impact on coupling at the hippocampal
mossy fiber synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
- _id: 25C3DBB6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W01205
name: Zellkommunikation in Gesundheit und Krankheit
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/flash-and-freeze-reveals-dynamics-of-nerve-connections/
record:
- id: '11196'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Functional electron microscopy (“Flash and Freeze”) of identified cortical
synapses in acute brain slices
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 105
year: '2020'
...
---
_id: '7387'
abstract:
- lang: eng
text: Most bacteria accomplish cell division with the help of a dynamic protein
complex called the divisome, which spans the cell envelope in the plane of division.
Assembly and activation of this machinery are coordinated by the tubulin-related
GTPase FtsZ, which was found to form treadmilling filaments on supported bilayers
in vitro1, as well as in live cells, in which filaments circle around the cell
division site2,3. Treadmilling of FtsZ is thought to actively move proteins around
the division septum, thereby distributing peptidoglycan synthesis and coordinating
the inward growth of the septum to form the new poles of the daughter cells4.
However, the molecular mechanisms underlying this function are largely unknown.
Here, to study how FtsZ polymerization dynamics are coupled to downstream proteins,
we reconstituted part of the bacterial cell division machinery using its purified
components FtsZ, FtsA and truncated transmembrane proteins essential for cell
division. We found that the membrane-bound cytosolic peptides of FtsN and FtsQ
co-migrated with treadmilling FtsZ–FtsA filaments, but despite their directed
collective behaviour, individual peptides showed random motion and transient confinement.
Our work suggests that divisome proteins follow treadmilling FtsZ filaments by
a diffusion-and-capture mechanism, which can give rise to a moving zone of signalling
activity at the division site.
acknowledgement: We acknowledge members of the Loose laboratory at IST Austria for
helpful discussions—in particular, P. Caldas for help with the treadmilling analysis,
M. Jimenez, A. Raso and N. Ropero for providing Alexa Fluor 488- and Alexa Fluor
647-labelled FtsA for the MST and analytical ultracentrifugation experiments. We
thank C. You for providing the DODA-tris-NTA phospholipids, as well as J. Piehler
and C. Richter (Department of Biology, University of Osnabruck, Germany) for the
SLIMfast single-molecule tracking software and help with the confinement analysis.
We thank J. Errington and H. Murray (both at Newcastle University, UK) for critical
reading of the manuscript, and J. Brugués (MPI-CBG and MPI-PKS, Dresden, Germany)
for help with the MATLAB programming and reading of the manuscript. This work was
supported by the European Research Council through grant ERC-2015-StG-679239 to
M.L. and grants HFSP LT 000824/2016-L4 and EMBO ALTF 1163-2015 to N.B., a grant
from the Ministry of Economy and Competitiveness of the Spanish Government (BFU2016-75471-C2-1-P)
to C.A. and G.R., and a Wellcome Trust Senior Investigator award (101824/Z/13/Z)
and a grant from the BBSRC (BB/R017409/1) to W.V.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Natalia S.
full_name: Baranova, Natalia S.
id: 38661662-F248-11E8-B48F-1D18A9856A87
last_name: Baranova
orcid: 0000-0002-3086-9124
- first_name: Philipp
full_name: Radler, Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
- first_name: Víctor M.
full_name: Hernández-Rocamora, Víctor M.
last_name: Hernández-Rocamora
- first_name: Carlos
full_name: Alfonso, Carlos
last_name: Alfonso
- first_name: Maria D
full_name: Lopez Pelegrin, Maria D
id: 319AA9CE-F248-11E8-B48F-1D18A9856A87
last_name: Lopez Pelegrin
- first_name: Germán
full_name: Rivas, Germán
last_name: Rivas
- first_name: Waldemar
full_name: Vollmer, Waldemar
last_name: Vollmer
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: Baranova NS, Radler P, Hernández-Rocamora VM, et al. Diffusion and capture
permits dynamic coupling between treadmilling FtsZ filaments and cell division
proteins. Nature Microbiology. 2020;5:407-417. doi:10.1038/s41564-019-0657-5
apa: Baranova, N. S., Radler, P., Hernández-Rocamora, V. M., Alfonso, C., Lopez
Pelegrin, M. D., Rivas, G., … Loose, M. (2020). Diffusion and capture permits
dynamic coupling between treadmilling FtsZ filaments and cell division proteins.
Nature Microbiology. Springer Nature. https://doi.org/10.1038/s41564-019-0657-5
chicago: Baranova, Natalia S., Philipp Radler, Víctor M. Hernández-Rocamora, Carlos
Alfonso, Maria D Lopez Pelegrin, Germán Rivas, Waldemar Vollmer, and Martin Loose.
“Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments
and Cell Division Proteins.” Nature Microbiology. Springer Nature, 2020.
https://doi.org/10.1038/s41564-019-0657-5.
ieee: N. S. Baranova et al., “Diffusion and capture permits dynamic coupling
between treadmilling FtsZ filaments and cell division proteins,” Nature Microbiology,
vol. 5. Springer Nature, pp. 407–417, 2020.
ista: Baranova NS, Radler P, Hernández-Rocamora VM, Alfonso C, Lopez Pelegrin MD,
Rivas G, Vollmer W, Loose M. 2020. Diffusion and capture permits dynamic coupling
between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology.
5, 407–417.
mla: Baranova, Natalia S., et al. “Diffusion and Capture Permits Dynamic Coupling
between Treadmilling FtsZ Filaments and Cell Division Proteins.” Nature Microbiology,
vol. 5, Springer Nature, 2020, pp. 407–17, doi:10.1038/s41564-019-0657-5.
short: N.S. Baranova, P. Radler, V.M. Hernández-Rocamora, C. Alfonso, M.D. Lopez
Pelegrin, G. Rivas, W. Vollmer, M. Loose, Nature Microbiology 5 (2020) 407–417.
corr_author: '1'
date_created: 2020-01-28T16:14:41Z
date_published: 2020-01-20T00:00:00Z
date_updated: 2026-10-25T23:30:08Z
day: '20'
department:
- _id: MaLo
doi: 10.1038/s41564-019-0657-5
ec_funded: 1
external_id:
isi:
- '000508584700007'
pmid:
- '31959972'
fulldoi: https://doi.org/10.1038/s41564-019-0657-5
intvolume: ' 5'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://europepmc.org/article/PMC/7048620
month: '01'
oa: 1
oa_version: Submitted Version
page: 407-417
pmid: 1
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
- _id: 259B655A-B435-11E9-9278-68D0E5697425
grant_number: LT000824/2016
name: Reconstitution of bacterial cell wall synthesis
- _id: 2596EAB6-B435-11E9-9278-68D0E5697425
grant_number: ALTF 2015-1163
name: Synthesis of bacterial cell wall
publication: Nature Microbiology
publication_identifier:
issn:
- 2058-5276
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/little-cell-big-cover-story/
record:
- id: '14280'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments
and cell division proteins
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 5
year: '2020'
...
---
_id: '7888'
abstract:
- lang: eng
text: Embryonic stem cell cultures are thought to self-organize into embryoid bodies,
able to undergo symmetry-breaking, germ layer specification and even morphogenesis.
Yet, it is unclear how to reconcile this remarkable self-organization capacity
with classical experiments demonstrating key roles for extrinsic biases by maternal
factors and/or extraembryonic tissues in embryogenesis. Here, we show that zebrafish
embryonic tissue explants, prepared prior to germ layer induction and lacking
extraembryonic tissues, can specify all germ layers and form a seemingly complete
mesendoderm anlage. Importantly, explant organization requires polarized inheritance
of maternal factors from dorsal-marginal regions of the blastoderm. Moreover,
induction of endoderm and head-mesoderm, which require peak Nodal-signaling levels,
is highly variable in explants, reminiscent of embryos with reduced Nodal signals
from the extraembryonic tissues. Together, these data suggest that zebrafish explants
do not undergo bona fide self-organization, but rather display features of genetically
encoded self-assembly, where intrinsic genetic programs control the emergence
of order.
article_number: e55190
article_processing_charge: No
article_type: original
author:
- first_name: Alexandra
full_name: Schauer, Alexandra
id: 30A536BA-F248-11E8-B48F-1D18A9856A87
last_name: Schauer
orcid: 0000-0001-7659-9142
- first_name: Diana C
full_name: Nunes Pinheiro, Diana C
id: 2E839F16-F248-11E8-B48F-1D18A9856A87
last_name: Nunes Pinheiro
orcid: 0000-0003-4333-7503
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- 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: Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. Zebrafish embryonic
explants undergo genetically encoded self-assembly. eLife. 2020;9. doi:10.7554/elife.55190
apa: Schauer, A., Nunes Pinheiro, D. C., Hauschild, R., & Heisenberg, C.-P.
J. (2020). Zebrafish embryonic explants undergo genetically encoded self-assembly.
ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.55190
chicago: Schauer, Alexandra, Diana C Nunes Pinheiro, Robert Hauschild, and Carl-Philipp
J Heisenberg. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.”
ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.55190.
ieee: A. Schauer, D. C. Nunes Pinheiro, R. Hauschild, and C.-P. J. Heisenberg, “Zebrafish
embryonic explants undergo genetically encoded self-assembly,” eLife, vol.
9. eLife Sciences Publications, 2020.
ista: Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. 2020. Zebrafish
embryonic explants undergo genetically encoded self-assembly. eLife. 9, e55190.
mla: Schauer, Alexandra, et al. “Zebrafish Embryonic Explants Undergo Genetically
Encoded Self-Assembly.” ELife, vol. 9, e55190, eLife Sciences Publications,
2020, doi:10.7554/elife.55190.
short: A. Schauer, D.C. Nunes Pinheiro, R. Hauschild, C.-P.J. Heisenberg, ELife
9 (2020).
corr_author: '1'
date_created: 2020-05-25T15:01:40Z
date_published: 2020-04-06T00:00:00Z
date_updated: 2026-10-25T23:30:12Z
day: '06'
ddc:
- '570'
department:
- _id: CaHe
- _id: Bio
doi: 10.7554/elife.55190
ec_funded: 1
external_id:
isi:
- '000531544400001'
pmid:
- '32250246'
file:
- access_level: open_access
checksum: f6aad884cf706846ae9357fcd728f8b5
content_type: application/pdf
creator: dernst
date_created: 2020-05-25T15:15:43Z
date_updated: 2020-07-14T12:48:04Z
file_id: '7890'
file_name: 2020_eLife_Schauer.pdf
file_size: 7744848
relation: main_file
file_date_updated: 2020-07-14T12:48:04Z
fulldoi: https://doi.org/10.7554/elife.55190
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
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
- _id: 26B1E39C-B435-11E9-9278-68D0E5697425
grant_number: '25239'
name: 'Mesendoderm specification in zebrafish: The role of extraembryonic tissues'
- _id: 26520D1E-B435-11E9-9278-68D0E5697425
grant_number: ALTF 850-2017
name: Coordination of mesendoderm cell fate specification and internalization during
zebrafish gastrulation
- _id: 266BC5CE-B435-11E9-9278-68D0E5697425
grant_number: LT000429
name: Coordination of mesendoderm fate specification and internalization during
zebrafish gastrulation
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
record:
- id: '12891'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Zebrafish embryonic explants undergo genetically encoded self-assembly
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2020'
...
---
OA_place: repository
OA_type: green
_id: '7885'
abstract:
- lang: eng
text: Eukaryotic cells migrate by coupling the intracellular force of the actin
cytoskeleton to the environment. While force coupling is usually mediated by transmembrane
adhesion receptors, especially those of the integrin family, amoeboid cells such
as leukocytes can migrate extremely fast despite very low adhesive forces1. Here
we show that leukocytes cannot only migrate under low adhesion but can also transmit
forces in the complete absence of transmembrane force coupling. When confined
within three-dimensional environments, they use the topographical features of
the substrate to propel themselves. Here the retrograde flow of the actin cytoskeleton
follows the texture of the substrate, creating retrograde shear forces that are
sufficient to drive the cell body forwards. Notably, adhesion-dependent and adhesion-independent
migration are not mutually exclusive, but rather are variants of the same principle
of coupling retrograde actin flow to the environment and thus can potentially
operate interchangeably and simultaneously. As adhesion-free migration is independent
of the chemical composition of the environment, it renders cells completely autonomous
in their locomotive behaviour.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: M-Shop
acknowledgement: We thank A. Leithner and J. Renkawitz for discussion and critical
reading of the manuscript; J. Schwarz and M. Mehling for establishing the microfluidic
setups; the Bioimaging Facility of IST Austria for excellent support, as well as
the Life Science Facility and the Miba Machine Shop of IST Austria; and F. N. Arslan,
L. E. Burnett and L. Li for their work during their rotation in the IST PhD programme.
This work was supported by the European Research Council (ERC StG 281556 and CoG
724373) to M.S. and grants from the Austrian Science Fund (FWF P29911) and the WWTF
to M.S. M.H. was supported by the European Regional Development Fund Project (CZ.02.1.01/0.0/0.0/15_003/0000476).
F.G. received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie grant agreement no. 747687.
article_processing_charge: No
article_type: original
author:
- first_name: Anne
full_name: Reversat, Anne
id: 35B76592-F248-11E8-B48F-1D18A9856A87
last_name: Reversat
orcid: 0000-0003-0666-8928
- first_name: Florian R
full_name: Gärtner, Florian R
id: 397A88EE-F248-11E8-B48F-1D18A9856A87
last_name: Gärtner
orcid: 0000-0001-6120-3723
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Julian A
full_name: Stopp, Julian A
id: 489E3F00-F248-11E8-B48F-1D18A9856A87
last_name: Stopp
- first_name: Saren
full_name: Tasciyan, Saren
id: 4323B49C-F248-11E8-B48F-1D18A9856A87
last_name: Tasciyan
orcid: 0000-0003-1671-393X
- first_name: Juan L
full_name: Aguilera Servin, Juan L
id: 2A67C376-F248-11E8-B48F-1D18A9856A87
last_name: Aguilera Servin
orcid: 0000-0002-2862-8372
- first_name: Ingrid
full_name: De Vries, Ingrid
id: 4C7D837E-F248-11E8-B48F-1D18A9856A87
last_name: De Vries
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Miroslav
full_name: Hons, Miroslav
id: 4167FE56-F248-11E8-B48F-1D18A9856A87
last_name: Hons
orcid: 0000-0002-6625-3348
- first_name: Matthieu
full_name: Piel, Matthieu
last_name: Piel
- first_name: Andrew
full_name: Callan-Jones, Andrew
last_name: Callan-Jones
- first_name: Raphael
full_name: Voituriez, Raphael
last_name: Voituriez
- 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: Reversat A, Gärtner FR, Merrin J, et al. Cellular locomotion using environmental
topography. Nature. 2020;582:582–585. doi:10.1038/s41586-020-2283-z
apa: Reversat, A., Gärtner, F. R., Merrin, J., Stopp, J. A., Tasciyan, S., Aguilera
Servin, J. L., … Sixt, M. K. (2020). Cellular locomotion using environmental topography.
Nature. Springer Nature. https://doi.org/10.1038/s41586-020-2283-z
chicago: Reversat, Anne, Florian R Gärtner, Jack Merrin, Julian A Stopp, Saren Tasciyan,
Juan L Aguilera Servin, Ingrid de Vries, et al. “Cellular Locomotion Using Environmental
Topography.” Nature. Springer Nature, 2020. https://doi.org/10.1038/s41586-020-2283-z.
ieee: A. Reversat et al., “Cellular locomotion using environmental topography,”
Nature, vol. 582. Springer Nature, pp. 582–585, 2020.
ista: Reversat A, Gärtner FR, Merrin J, Stopp JA, Tasciyan S, Aguilera Servin JL,
de Vries I, Hauschild R, Hons M, Piel M, Callan-Jones A, Voituriez R, Sixt MK.
2020. Cellular locomotion using environmental topography. Nature. 582, 582–585.
mla: Reversat, Anne, et al. “Cellular Locomotion Using Environmental Topography.”
Nature, vol. 582, Springer Nature, 2020, pp. 582–585, doi:10.1038/s41586-020-2283-z.
short: A. Reversat, F.R. Gärtner, J. Merrin, J.A. Stopp, S. Tasciyan, J.L. Aguilera
Servin, I. de Vries, R. Hauschild, M. Hons, M. Piel, A. Callan-Jones, R. Voituriez,
M.K. Sixt, Nature 582 (2020) 582–585.
date_created: 2020-05-24T22:01:01Z
date_published: 2020-06-25T00:00:00Z
date_updated: 2026-10-25T23:30:16Z
day: '25'
department:
- _id: NanoFab
- _id: Bio
- _id: MiSi
doi: 10.1038/s41586-020-2283-z
ec_funded: 1
external_id:
isi:
- '000532688300008'
pmid:
- '32581372'
fulldoi: https://doi.org/10.1038/s41586-020-2283-z
intvolume: ' 582'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/793919
month: '06'
oa: 1
oa_version: Preprint
page: 582–585
pmid: 1
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular Navigation Along Spatial Gradients
- _id: 26018E70-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29911
name: Mechanical adaptation of lamellipodial actin
- _id: 260AA4E2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '747687'
name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/off-road-mode-enables-mobile-cells-to-move-freely/
record:
- id: '12401'
relation: dissertation_contains
status: public
- id: '14697'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Cellular locomotion using environmental topography
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 582
year: '2020'
...
---
_id: '7815'
abstract:
- lang: eng
text: Beginning from a limited pool of progenitors, the mammalian cerebral cortex
forms highly organized functional neural circuits. However, the underlying cellular
and molecular mechanisms regulating lineage transitions of neural stem cells (NSCs)
and eventual production of neurons and glia in the developing neuroepithelium
remains unclear. Methods to trace NSC division patterns and map the lineage of
clonally related cells have advanced dramatically. However, many contemporary
lineage tracing techniques suffer from the lack of cellular resolution of progeny
cell fate, which is essential for deciphering progenitor cell division patterns.
Presented is a protocol using mosaic analysis with double markers (MADM) to perform
in vivo clonal analysis. MADM concomitantly manipulates individual progenitor
cells and visualizes precise division patterns and lineage progression at unprecedented
single cell resolution. MADM-based interchromosomal recombination events during
the G2-X phase of mitosis, together with temporally inducible CreERT2, provide
exact information on the birth dates of clones and their division patterns. Thus,
MADM lineage tracing provides unprecedented qualitative and quantitative optical
readouts of the proliferation mode of stem cell progenitors at the single cell
level. MADM also allows for examination of the mechanisms and functional requirements
of candidate genes in NSC lineage progression. This method is unique in that comparative
analysis of control and mutant subclones can be performed in the same tissue environment
in vivo. Here, the protocol is described in detail, and experimental paradigms
to employ MADM for clonal analysis and lineage tracing in the developing cerebral
cortex are demonstrated. Importantly, this protocol can be adapted to perform
MADM clonal analysis in any murine stem cell niche, as long as the CreERT2 driver
is present.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
article_number: e61147
article_processing_charge: No
article_type: original
author:
- first_name: Robert J
full_name: Beattie, Robert J
id: 2E26DF60-F248-11E8-B48F-1D18A9856A87
last_name: Beattie
orcid: 0000-0002-8483-8753
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Giselle T
full_name: Cheung, Giselle T
id: 471195F6-F248-11E8-B48F-1D18A9856A87
last_name: Cheung
orcid: 0000-0001-8457-2572
- first_name: Ximena
full_name: Contreras, Ximena
id: 475990FE-F248-11E8-B48F-1D18A9856A87
last_name: Contreras
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Beattie RJ, Streicher C, Amberg N, et al. Lineage tracing and clonal analysis
in developing cerebral cortex using mosaic analysis with double markers (MADM).
Journal of Visual Experiments. 2020;(159). doi:10.3791/61147
apa: Beattie, R. J., Streicher, C., Amberg, N., Cheung, G. T., Contreras, X., Hansen,
A. H., & Hippenmeyer, S. (2020). Lineage tracing and clonal analysis in developing
cerebral cortex using mosaic analysis with double markers (MADM). Journal of
Visual Experiments. MyJove Corporation. https://doi.org/10.3791/61147
chicago: Beattie, Robert J, Carmen Streicher, Nicole Amberg, Giselle T Cheung, Ximena
Contreras, Andi H Hansen, and Simon Hippenmeyer. “Lineage Tracing and Clonal Analysis
in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).”
Journal of Visual Experiments. MyJove Corporation, 2020. https://doi.org/10.3791/61147.
ieee: R. J. Beattie et al., “Lineage tracing and clonal analysis in developing
cerebral cortex using mosaic analysis with double markers (MADM),” Journal
of Visual Experiments, no. 159. MyJove Corporation, 2020.
ista: Beattie RJ, Streicher C, Amberg N, Cheung GT, Contreras X, Hansen AH, Hippenmeyer
S. 2020. Lineage tracing and clonal analysis in developing cerebral cortex using
mosaic analysis with double markers (MADM). Journal of Visual Experiments. (159),
e61147.
mla: Beattie, Robert J., et al. “Lineage Tracing and Clonal Analysis in Developing
Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).” Journal
of Visual Experiments, no. 159, e61147, MyJove Corporation, 2020, doi:10.3791/61147.
short: R.J. Beattie, C. Streicher, N. Amberg, G.T. Cheung, X. Contreras, A.H. Hansen,
S. Hippenmeyer, Journal of Visual Experiments (2020).
corr_author: '1'
date_created: 2020-05-11T08:31:20Z
date_published: 2020-05-08T00:00:00Z
date_updated: 2026-10-25T23:30:20Z
day: '08'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.3791/61147
ec_funded: 1
external_id:
isi:
- '000546406600043'
pmid:
- '32449730'
file:
- access_level: open_access
checksum: 3154ea7f90b9fb45e084cd1c2770597d
content_type: application/pdf
creator: rbeattie
date_created: 2020-05-11T08:28:38Z
date_updated: 2020-07-14T12:48:03Z
file_id: '7816'
file_name: jove-protocol-61147-lineage-tracing-clonal-analysis-developing-cerebral-cortex-using.pdf
file_size: 1352186
relation: main_file
file_date_updated: 2020-07-14T12:48:03Z
fulldoi: https://doi.org/10.3791/61147
has_accepted_license: '1'
isi: 1
issue: '159'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 264E56E2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02416
name: Molecular Mechanisms Regulating Gliogenesis in the Neocortex
- _id: 268F8446-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: T01031
name: Role of Eed in neural stem cell lineage progression
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 2625A13E-B435-11E9-9278-68D0E5697425
grant_number: '24812'
name: Molecular mechanisms of radial neuronal migration
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: Journal of Visual Experiments
publication_identifier:
issn:
- 1940-087X
publication_status: published
publisher: MyJove Corporation
quality_controlled: '1'
related_material:
record:
- id: '7902'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Lineage tracing and clonal analysis in developing cerebral cortex using mosaic
analysis with double markers (MADM)
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
OA_place: publisher
_id: '7902'
abstract:
- lang: eng
text: "Mosaic genetic analysis has been widely used in different model organisms
such as the fruit fly to study gene-function in a cell-autonomous or tissue-specific
fashion. More recently, and less easily conducted, mosaic genetic analysis in
mice has also been enabled with the ambition to shed light on human gene function
and disease. These genetic tools are of particular interest, but not restricted
to, the study of the brain. Notably, the MADM technology offers a genetic approach
in mice to visualize and concomitantly manipulate small subsets of genetically
defined cells at a clonal level and single cell resolution. MADM-based analysis
has already advanced the study of genetic mechanisms regulating brain development
and is expected that further MADM-based analysis of genetic alterations will continue
to reveal important insights on the fundamental principles of development and
disease to potentially assist in the development of new therapies or treatments.\r\nIn
summary, this work completed and characterized the necessary genome-wide genetic
tools to perform MADM-based analysis at single cell level of the vast majority
of mouse genes in virtually any cell type and provided a protocol to perform lineage
tracing using the novel MADM resource. Importantly, this work also explored and
revealed novel aspects of biologically relevant events in an in vivo context,
such as the chromosome-specific bias of chromatid sister segregation pattern,
the generation of cell-type diversity in the cerebral cortex and in the cerebellum
and finally, the relevance of the interplay between the cell-autonomous gene function
and cell-non-autonomous (community) effects in radial glial progenitor lineage
progression.\r\nThis work provides a foundation and opens the door to further
elucidating the molecular mechanisms underlying neuronal diversity and astrocyte
generation."
acknowledged_ssus:
- _id: PreCl
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Ximena
full_name: Contreras, Ximena
id: 475990FE-F248-11E8-B48F-1D18A9856A87
last_name: Contreras
citation:
ama: Contreras X. Genetic dissection of neural development in health and disease
at single cell resolution. 2020. doi:10.15479/AT:ISTA:7902
apa: Contreras, X. (2020). Genetic dissection of neural development in health
and disease at single cell resolution. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:7902
chicago: Contreras, Ximena. “Genetic Dissection of Neural Development in Health
and Disease at Single Cell Resolution.” Institute of Science and Technology Austria,
2020. https://doi.org/10.15479/AT:ISTA:7902.
ieee: X. Contreras, “Genetic dissection of neural development in health and disease
at single cell resolution,” Institute of Science and Technology Austria, 2020.
ista: Contreras X. 2020. Genetic dissection of neural development in health and
disease at single cell resolution. Institute of Science and Technology Austria.
mla: Contreras, Ximena. Genetic Dissection of Neural Development in Health and
Disease at Single Cell Resolution. Institute of Science and Technology Austria,
2020, doi:10.15479/AT:ISTA:7902.
short: X. Contreras, Genetic Dissection of Neural Development in Health and Disease
at Single Cell Resolution, Institute of Science and Technology Austria, 2020.
corr_author: '1'
date_created: 2020-05-29T08:27:32Z
date_published: 2020-06-05T00:00:00Z
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project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
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relation: dissertation_contains
status: public
- id: '7815'
relation: dissertation_contains
status: public
- id: '6830'
relation: dissertation_contains
status: public
status: public
supervisor:
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
title: Genetic dissection of neural development in health and disease at single cell
resolution
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2020'
...
---
_id: '8190'
article_number: e202007029
article_processing_charge: No
article_type: letter_note
author:
- 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: Anna
full_name: Huttenlocher, Anna
last_name: Huttenlocher
citation:
ama: 'Sixt MK, Huttenlocher A. Zena Werb (1945-2020): Cell biology in context. The
Journal of Cell Biology. 2020;219(8). doi:10.1083/jcb.202007029'
apa: 'Sixt, M. K., & Huttenlocher, A. (2020). Zena Werb (1945-2020): Cell biology
in context. The Journal of Cell Biology. Rockefeller University Press.
https://doi.org/10.1083/jcb.202007029'
chicago: 'Sixt, Michael K, and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology
in Context.” The Journal of Cell Biology. Rockefeller University Press,
2020. https://doi.org/10.1083/jcb.202007029.'
ieee: 'M. K. Sixt and A. Huttenlocher, “Zena Werb (1945-2020): Cell biology in context,”
The Journal of Cell Biology, vol. 219, no. 8. Rockefeller University Press,
2020.'
ista: 'Sixt MK, Huttenlocher A. 2020. Zena Werb (1945-2020): Cell biology in context.
The Journal of Cell Biology. 219(8), e202007029.'
mla: 'Sixt, Michael K., and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology
in Context.” The Journal of Cell Biology, vol. 219, no. 8, e202007029,
Rockefeller University Press, 2020, doi:10.1083/jcb.202007029.'
short: M.K. Sixt, A. Huttenlocher, The Journal of Cell Biology 219 (2020).
date_created: 2020-08-02T22:00:57Z
date_published: 2020-07-22T00:00:00Z
date_updated: 2025-06-12T07:34:40Z
day: '22'
ddc:
- '570'
department:
- _id: MiSi
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- '32699885'
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issue: '8'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: The Journal of Cell Biology
publication_identifier:
eissn:
- 1540-8140
publication_status: published
publisher: Rockefeller University Press
scopus_import: '1'
status: public
title: 'Zena Werb (1945-2020): Cell biology in context'
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 219
year: '2020'
...
---
_id: '8350'
abstract:
- lang: eng
text: "Cytoplasm is a gel-like crowded environment composed of tens of thousands
of macromolecules, organelles, cytoskeletal networks and cytosol. The structure
of the cytoplasm is thought to be highly organized and heterogeneous due to the
crowding of its constituents and their effective compartmentalization. In such
an environment, the diffusive dynamics of the molecules is very restricted, an
effect that is further amplified by clustering and anchoring of molecules. Despite
the jammed nature of the cytoplasm at the microscopic scale, large-scale reorganization
of cytoplasm is essential for important cellular functions, such as nuclear positioning
and cell division. How such mesoscale reorganization of the cytoplasm is achieved,
especially for very large cells such as oocytes or syncytial tissues that can
span hundreds of micrometers in size, has only begun to be understood.\r\nIn this
thesis, I focus on the recent advances in elucidating the molecular, cellular
and biophysical principles underlying cytoplasmic organization across different
scales, structures and species. First, I outline which of these principles have
been identified by reductionist approaches, such as in vitro reconstitution assays,
where boundary conditions and components can be modulated at ease. I then describe
how the theoretical and experimental framework established in these reduced systems
have been applied to their more complex in vivo counterparts, in particular oocytes
and embryonic syncytial structures, and discuss how such complex biological systems
can initiate symmetry breaking and establish patterning.\r\nSpecifically, I examine
an example of large-scale reorganizations taking place in zebrafish embryos, where
extensive cytoplasmic streaming leads to the segregation of cytoplasm from yolk
granules along the animal-vegetal axis of the embryo. Using biophysical experimentation
and theory, I investigate the forces underlying this process, to show that this
process does not rely on cortical actin reorganization, as previously thought,
but instead on a cell-cycle-dependent bulk actin polymerization wave traveling
from the animal to the vegetal pole of the embryo. This wave functions in segregation
by both pulling cytoplasm animally and pushing yolk granules vegetally. Cytoplasm
pulling is mediated by bulk actin network flows exerting friction forces on the
cytoplasm, while yolk granule pushing is achieved by a mechanism closely resembling
actin comet formation on yolk granules. This study defines a novel role of bulk
actin polymerization waves in embryo polarization via cytoplasmic segregation.
Lastly, I describe the cytoplasmic reorganizations taking place during zebrafish
oocyte maturation, where the initial segregation of the cytoplasm and yolk granules
occurs. Here, I demonstrate a previously uncharacterized wave of microtubule aster
formation, traveling the oocyte along the animal-vegetal axis. Further research
is required to determine the role of such microtubule structures in cytoplasmic
reorganizations therein.\r\nCollectively, these studies provide further evidence
for the coupling between cell cytoskeleton and cell cycle machinery, which can
underlie a core self-organizing mechanism for orchestrating large-scale reorganizations
in a cell-cycle-tunable manner, where the modulations of the force-generating
machinery and cytoplasmic mechanics can be harbored to fulfill cellular functions."
acknowledged_ssus:
- _id: PreCl
- _id: Bio
- _id: EM-Fac
acknowledgement: "I would have had no fish and hence no results without our wonderful
fish facility crew, Verena Mayer, Eva Schlegl, Andreas Mlak and Matthias Nowak.
Special thanks to Verena for being always happy to help and dealing with our chaotic
schedules in the lab. Danke auch, Verena, für deine Geduld, mit mir auf Deutsch
zu sprechen. Das hat mir sehr geholfen.\r\nSpecial thanks to the Bioimaging and
EM facilities at IST Austria for supporting us every day. Very special thanks would
go to Robert Hauschild for his continuous support on data analysis and also to Jack
Merrin for designing and building microfabricated chambers for the project and for
the various discussions on making zebrafish extracts."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Shayan
full_name: Shamipour, Shayan
id: 40B34FE2-F248-11E8-B48F-1D18A9856A87
last_name: Shamipour
citation:
ama: Shamipour S. Bulk actin dynamics drive phase segregation in zebrafish oocytes
. 2020. doi:10.15479/AT:ISTA:8350
apa: Shamipour, S. (2020). Bulk actin dynamics drive phase segregation in zebrafish
oocytes . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8350
chicago: Shamipour, Shayan. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish
Oocytes .” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8350.
ieee: S. Shamipour, “Bulk actin dynamics drive phase segregation in zebrafish oocytes
,” Institute of Science and Technology Austria, 2020.
ista: Shamipour S. 2020. Bulk actin dynamics drive phase segregation in zebrafish
oocytes . Institute of Science and Technology Austria.
mla: Shamipour, Shayan. Bulk Actin Dynamics Drive Phase Segregation in Zebrafish
Oocytes . Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8350.
short: S. Shamipour, Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes
, Institute of Science and Technology Austria, 2020.
corr_author: '1'
date_created: 2020-09-09T11:12:10Z
date_published: 2020-09-09T00:00:00Z
date_updated: 2025-09-11T07:08:52Z
day: '09'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: BjHo
- _id: CaHe
doi: 10.15479/AT:ISTA:8350
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month: '09'
oa: 1
oa_version: None
page: '107'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7001'
relation: part_of_dissertation
status: public
- id: '6508'
relation: part_of_dissertation
status: public
- id: '735'
relation: part_of_dissertation
status: public
- id: '661'
relation: part_of_dissertation
status: public
status: public
supervisor:
- 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: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
title: 'Bulk actin dynamics drive phase segregation in zebrafish oocytes '
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8434'
abstract:
- lang: eng
text: 'Efficient migration on adhesive surfaces involves the protrusion of lamellipodial
actin networks and their subsequent stabilization by nascent adhesions. The actin-binding
protein lamellipodin (Lpd) is thought to play a critical role in lamellipodium
protrusion, by delivering Ena/VASP proteins onto the growing plus ends of actin
filaments and by interacting with the WAVE regulatory complex, an activator of
the Arp2/3 complex, at the leading edge. Using B16-F1 melanoma cell lines, we
demonstrate that genetic ablation of Lpd compromises protrusion efficiency and
coincident cell migration without altering essential parameters of lamellipodia,
including their maximal rate of forward advancement and actin polymerization.
We also confirmed lamellipodia and migration phenotypes with CRISPR/Cas9-mediated
Lpd knockout Rat2 fibroblasts, excluding cell type-specific effects. Moreover,
computer-aided analysis of cell-edge morphodynamics on B16-F1 cell lamellipodia
revealed that loss of Lpd correlates with reduced temporal protrusion maintenance
as a prerequisite of nascent adhesion formation. We conclude that Lpd optimizes
protrusion and nascent adhesion formation by counteracting frequent, chaotic retraction
and membrane ruffling.This article has an associated First Person interview with
the first author of the paper. '
acknowledgement: This work was supported in part by Deutsche Forschungsgemeinschaft
(DFG)[GRK2223/1, RO2414/5-1 (to K.R.), FA350/11-1 (to M.F.) and FA330/11-1 (to J.F.)],as
well as by intramural funding from the Helmholtz Association (to T.E.B.S. andK.R.).
G.D. was additionally funded by the Austrian Science Fund (FWF) LiseMeitner Program
[M-2495]. A.C.H. and M.W. are supported by the Francis CrickInstitute, which receives
its core funding from Cancer Research UK [FC001209], theMedical Research Council
[FC001209] and the Wellcome Trust [FC001209]. M.K. issupported by the Biotechnology
and Biological Sciences Research Council [BB/F011431/1, BB/J000590/1, BB/N000226/1].
Deposited in PMC for release after 6months.
article_number: jcs239020
article_processing_charge: No
article_type: original
author:
- first_name: Georgi A
full_name: Dimchev, Georgi A
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
orcid: 0000-0001-8370-6161
- first_name: Behnam
full_name: Amiri, Behnam
last_name: Amiri
- first_name: Ashley C.
full_name: Humphries, Ashley C.
last_name: Humphries
- first_name: Matthias
full_name: Schaks, Matthias
last_name: Schaks
- first_name: Vanessa
full_name: Dimchev, Vanessa
last_name: Dimchev
- first_name: Theresia E. B.
full_name: Stradal, Theresia E. B.
last_name: Stradal
- first_name: Jan
full_name: Faix, Jan
last_name: Faix
- first_name: Matthias
full_name: Krause, Matthias
last_name: Krause
- first_name: Michael
full_name: Way, Michael
last_name: Way
- first_name: Martin
full_name: Falcke, Martin
last_name: Falcke
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
citation:
ama: Dimchev GA, Amiri B, Humphries AC, et al. Lamellipodin tunes cell migration
by stabilizing protrusions and promoting adhesion formation. Journal of Cell
Science. 2020;133(7). doi:10.1242/jcs.239020
apa: Dimchev, G. A., Amiri, B., Humphries, A. C., Schaks, M., Dimchev, V., Stradal,
T. E. B., … Rottner, K. (2020). Lamellipodin tunes cell migration by stabilizing
protrusions and promoting adhesion formation. Journal of Cell Science.
The Company of Biologists. https://doi.org/10.1242/jcs.239020
chicago: Dimchev, Georgi A, Behnam Amiri, Ashley C. Humphries, Matthias Schaks,
Vanessa Dimchev, Theresia E. B. Stradal, Jan Faix, et al. “Lamellipodin Tunes
Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” Journal
of Cell Science. The Company of Biologists, 2020. https://doi.org/10.1242/jcs.239020.
ieee: G. A. Dimchev et al., “Lamellipodin tunes cell migration by stabilizing
protrusions and promoting adhesion formation,” Journal of Cell Science,
vol. 133, no. 7. The Company of Biologists, 2020.
ista: Dimchev GA, Amiri B, Humphries AC, Schaks M, Dimchev V, Stradal TEB, Faix
J, Krause M, Way M, Falcke M, Rottner K. 2020. Lamellipodin tunes cell migration
by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science.
133(7), jcs239020.
mla: Dimchev, Georgi A., et al. “Lamellipodin Tunes Cell Migration by Stabilizing
Protrusions and Promoting Adhesion Formation.” Journal of Cell Science,
vol. 133, no. 7, jcs239020, The Company of Biologists, 2020, doi:10.1242/jcs.239020.
short: G.A. Dimchev, B. Amiri, A.C. Humphries, M. Schaks, V. Dimchev, T.E.B. Stradal,
J. Faix, M. Krause, M. Way, M. Falcke, K. Rottner, Journal of Cell Science 133
(2020).
date_created: 2020-09-17T14:00:33Z
date_published: 2020-04-09T00:00:00Z
date_updated: 2025-04-15T07:52:13Z
day: '09'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1242/jcs.239020
external_id:
isi:
- '000534387800005'
pmid:
- ' 32094266'
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- Cell Biology
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project:
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call_identifier: FWF
grant_number: M02495
name: Protein structure and function in filopodia across scales
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- 0021-9533
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lamellipodin tunes cell migration by stabilizing protrusions and promoting
adhesion formation
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 133
year: '2020'
...
---
OA_place: publisher
_id: '8983'
abstract:
- lang: eng
text: Metabolic adaptation is a critical feature of migrating cells. It tunes the
metabolic programs of migrating cells to allow them to efficiently exert their
crucial roles in development, inflammatory responses and tumor metastasis. Cell
migration through physically challenging contexts requires energy. However, how
the metabolic reprogramming that underlies in vivo cell invasion is controlled
is still unanswered. In my PhD project, I identify a novel conserved metabolic
shift in Drosophila melanogaster immune cells that by modulating their bioenergetic
potential controls developmentally programmed tissue invasion. We show that this
regulation requires a novel conserved nuclear protein, named Atossa. Atossa enhances
the transcription of a set of proteins, including an RNA helicase Porthos and
two metabolic enzymes, each of which increases the tissue invasion of leading
Drosophila macrophages and can rescue the atossa mutant phenotype. Porthos selectively
regulates the translational efficiency of a subset of mRNAs containing a 5’-UTR
cis-regulatory TOP-like sequence. These 5’TOPL mRNA targets encode mitochondrial-related
proteins, including subunits of mitochondrial oxidative phosphorylation (OXPHOS)
components III and V and other metabolic-related proteins. Porthos powers up mitochondrial
OXPHOS to engender a sufficient ATP supply, which is required for tissue invasion
of leading macrophages. Atossa’s two vertebrate orthologs rescue the invasion
defect. In my PhD project, I elucidate that Atossa displays a conserved developmental
metabolic control to modulate metabolic capacities and the cellular energy state,
through altered transcription and translation, to aid the tissue infiltration
of leading cells into energy demanding barriers.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: E-Lib
- _id: CampIT
acknowledgement: Also, I would like to express my appreciation and thanks to the Bioimaging
facility, LSF, GSO, library, and IT people at IST Austria.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Shamsi
full_name: Emtenani, Shamsi
id: 49D32318-F248-11E8-B48F-1D18A9856A87
last_name: Emtenani
orcid: 0000-0001-6981-6938
citation:
ama: Emtenani S. Metabolic regulation of Drosophila macrophage tissue invasion.
2020. doi:10.15479/AT:ISTA:8983
apa: Emtenani, S. (2020). Metabolic regulation of Drosophila macrophage tissue
invasion. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8983
chicago: Emtenani, Shamsi. “Metabolic Regulation of Drosophila Macrophage Tissue
Invasion.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8983.
ieee: S. Emtenani, “Metabolic regulation of Drosophila macrophage tissue invasion,”
Institute of Science and Technology Austria, 2020.
ista: Emtenani S. 2020. Metabolic regulation of Drosophila macrophage tissue invasion.
Institute of Science and Technology Austria.
mla: Emtenani, Shamsi. Metabolic Regulation of Drosophila Macrophage Tissue Invasion.
Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8983.
short: S. Emtenani, Metabolic Regulation of Drosophila Macrophage Tissue Invasion,
Institute of Science and Technology Austria, 2020.
corr_author: '1'
date_created: 2020-12-30T15:41:26Z
date_published: 2020-12-30T00:00:00Z
date_updated: 2026-04-08T07:28:54Z
day: '30'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: DaSi
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status: public
supervisor:
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full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
title: Metabolic regulation of Drosophila macrophage tissue invasion
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2020'
...
---
_id: '8557'
abstract:
- lang: eng
text: The infiltration of immune cells into tissues underlies the establishment
of tissue resident macrophages, and responses to infections and tumors. Yet the
mechanisms immune cells utilize to negotiate tissue barriers in living organisms
are not well understood, and a role for cortical actin has not been examined.
Here we find that the tissue invasion of Drosophila macrophages, also known as
plasmatocytes or hemocytes, utilizes enhanced cortical F-actin levels stimulated
by the Drosophila member of the fos proto oncogene transcription factor family
(Dfos, Kayak). RNA sequencing analysis and live imaging show that Dfos enhances
F-actin levels around the entire macrophage surface by increasing mRNA levels
of the membrane spanning molecular scaffold tetraspanin TM4SF, and the actin cross-linking
filamin Cheerio which are themselves required for invasion. Cortical F-actin levels
are critical as expressing a dominant active form of Diaphanous, a actin polymerizing
Formin, can rescue the Dfos Dominant Negative macrophage invasion defect. In vivo
imaging shows that Dfos is required to enhance the efficiency of the initial phases
of macrophage tissue entry. Genetic evidence argues that this Dfos-induced program
in macrophages counteracts the constraint produced by the tension of surrounding
tissues and buffers the mechanical properties of the macrophage nucleus from affecting
tissue entry. We thus identify tuning the cortical actin cytoskeleton through
Dfos as a key process allowing efficient forward movement of an immune cell into
surrounding tissues.
acknowledged_ssus:
- _id: LifeSc
acknowledgement: 'We thank the following for their contributions: The Drosophila Genomics
Resource Center supported by NIH grant 2P40OD010949-10A1 for plasmids, K. Brueckner.
B. Stramer, M. Uhlirova, O. Schuldiner, the Bloomington Drosophila Stock Center
supported by NIH grant P40OD018537 and the Vienna Drosophila Resource Center for
fly stocks, FlyBase (Thurmond et al., 2019) for essential genomic information, and
the BDGP in situ database for data (Tomancak et al., 2002, 2007). For antibodies,
we thank the Developmental Studies Hybridoma Bank, which was created by the Eunice
Kennedy Shriver National Institute of Child Health and Human Development of the
NIH, and is maintained at the University of Iowa, as well as J. Zeitlinger for her
generous gift of Dfos antibody. We thank the Vienna BioCenter Core Facilities for
RNA sequencing and analysis and the Life Scientific Service Units at IST Austria
for technical support and assistance with microscopy and FACS analysis. We thank
C.P. Heisenberg, P. Martin, M. Sixt and Siekhaus group members for discussions and
T.Hurd, A. Ratheesh and P. Rangan for comments on the manuscript. A.G. was supported
by the Austrian Science Fund (FWF) grant DASI_FWF01_P29638S, D.E.S. by Marie Curie
CIG 334077/IRTIM. M.S. is supported by the FWF, PhD program W1212 915 and the European
Research Council (ERC) Advanced grant (ERC-2015-AdG TNT-Tumors 694883). S.W. is
supported by an OEAW, DOC fellowship.'
article_processing_charge: No
author:
- first_name: Vera
full_name: Belyaeva, Vera
id: 47F080FE-F248-11E8-B48F-1D18A9856A87
last_name: Belyaeva
- first_name: Stephanie
full_name: Wachner, Stephanie
id: 2A95E7B0-F248-11E8-B48F-1D18A9856A87
last_name: Wachner
- first_name: Igor
full_name: Gridchyn, Igor
id: 4B60654C-F248-11E8-B48F-1D18A9856A87
last_name: Gridchyn
orcid: 0000-0002-1807-1929
- first_name: Markus
full_name: Linder, Markus
last_name: Linder
- first_name: Shamsi
full_name: Emtenani, Shamsi
id: 49D32318-F248-11E8-B48F-1D18A9856A87
last_name: Emtenani
orcid: 0000-0001-6981-6938
- first_name: Attila
full_name: György, Attila
id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87
last_name: György
orcid: 0000-0002-1819-198X
- first_name: Maria
full_name: Sibilia, Maria
last_name: Sibilia
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
citation:
ama: Belyaeva V, Wachner S, Gridchyn I, et al. Cortical actin properties controlled
by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance.
bioRxiv. doi:10.1101/2020.09.18.301481
apa: Belyaeva, V., Wachner, S., Gridchyn, I., Linder, M., Emtenani, S., György,
A., … Siekhaus, D. E. (n.d.). Cortical actin properties controlled by Drosophila
Fos aid macrophage infiltration against surrounding tissue resistance. bioRxiv.
https://doi.org/10.1101/2020.09.18.301481
chicago: Belyaeva, Vera, Stephanie Wachner, Igor Gridchyn, Markus Linder, Shamsi
Emtenani, Attila György, Maria Sibilia, and Daria E Siekhaus. “Cortical Actin
Properties Controlled by Drosophila Fos Aid Macrophage Infiltration against Surrounding
Tissue Resistance.” BioRxiv, n.d. https://doi.org/10.1101/2020.09.18.301481.
ieee: V. Belyaeva et al., “Cortical actin properties controlled by Drosophila
Fos aid macrophage infiltration against surrounding tissue resistance,” bioRxiv.
.
ista: Belyaeva V, Wachner S, Gridchyn I, Linder M, Emtenani S, György A, Sibilia
M, Siekhaus DE. Cortical actin properties controlled by Drosophila Fos aid macrophage
infiltration against surrounding tissue resistance. bioRxiv, 10.1101/2020.09.18.301481.
mla: Belyaeva, Vera, et al. “Cortical Actin Properties Controlled by Drosophila
Fos Aid Macrophage Infiltration against Surrounding Tissue Resistance.” BioRxiv,
doi:10.1101/2020.09.18.301481.
short: V. Belyaeva, S. Wachner, I. Gridchyn, M. Linder, S. Emtenani, A. György,
M. Sibilia, D.E. Siekhaus, BioRxiv (n.d.).
corr_author: '1'
date_created: 2020-09-23T09:36:47Z
date_published: 2020-09-18T00:00:00Z
date_updated: 2026-10-25T23:30:25Z
day: '18'
department:
- _id: DaSi
- _id: JoCs
doi: 10.1101/2020.09.18.301481
ec_funded: 1
fulldoi: https://doi.org/10.1101/2020.09.18.301481
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2020.09.18.301481
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 253B6E48-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29638
name: The role of Drosophila TNF alpha in immune cell invasion
- _id: 2536F660-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '334077'
name: Investigating the role of transporters in invasive migration through junctions
- _id: 26199CA4-B435-11E9-9278-68D0E5697425
grant_number: '24800'
name: Implications of a TGFβ/Dpp-activated subpopulation for Drosophila macrophage
migration
publication: bioRxiv
publication_status: draft
related_material:
record:
- id: '10614'
relation: later_version
status: public
- id: '8983'
relation: dissertation_contains
status: public
status: public
title: Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration
against surrounding tissue resistance
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
OA_place: publisher
OA_type: hybrid
_id: '8002'
abstract:
- lang: eng
text: Wound healing in plant tissues, consisting of rigid cell wall-encapsulated
cells, represents a considerable challenge and occurs through largely unknown
mechanisms distinct from those in animals. Owing to their inability to migrate,
plant cells rely on targeted cell division and expansion to regenerate wounds.
Strict coordination of these wound-induced responses is essential to ensure efficient,
spatially restricted wound healing. Single-cell tracking by live imaging allowed
us to gain mechanistic insight into the wound perception and coordination of wound
responses after laser-based wounding in Arabidopsis root. We revealed a crucial
contribution of the collapse of damaged cells in wound perception and detected
an auxin increase specific to cells immediately adjacent to the wound. This localized
auxin increase balances wound-induced cell expansion and restorative division
rates in a dose-dependent manner, leading to tumorous overproliferation when the
canonical TIR1 auxin signaling is disrupted. Auxin and wound-induced turgor pressure
changes together also spatially define the activation of key components of regeneration,
such as the transcription regulator ERF115. Our observations suggest that the
wound signaling involves the sensing of collapse of damaged cells and a local
auxin signaling activation to coordinate the downstream transcriptional responses
in the immediate wound vicinity.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
article_number: '202003346'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
orcid: 0000-0001-8295-2926
- first_name: Juan C
full_name: Montesinos López, Juan C
id: 310A8E3E-F248-11E8-B48F-1D18A9856A87
last_name: Montesinos López
orcid: 0000-0001-9179-6099
- first_name: Petra
full_name: Marhavá, Petra
id: 44E59624-F248-11E8-B48F-1D18A9856A87
last_name: Marhavá
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Saiko
full_name: Yoshida, Saiko
id: 2E46069C-F248-11E8-B48F-1D18A9856A87
last_name: Yoshida
orcid: 0000-0001-6111-9353
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Hörmayer L, Montesinos López JC, Marhavá P, Benková E, Yoshida S, Friml J.
Wounding-induced changes in cellular pressure and localized auxin signalling spatially
coordinate restorative divisions in roots. Proceedings of the National Academy
of Sciences of the United States of America. 2020;117(26). doi:10.1073/pnas.2003346117
apa: Hörmayer, L., Montesinos López, J. C., Marhavá, P., Benková, E., Yoshida, S.,
& Friml, J. (2020). Wounding-induced changes in cellular pressure and localized
auxin signalling spatially coordinate restorative divisions in roots. Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences. https://doi.org/10.1073/pnas.2003346117
chicago: Hörmayer, Lukas, Juan C Montesinos López, Petra Marhavá, Eva Benková, Saiko
Yoshida, and Jiří Friml. “Wounding-Induced Changes in Cellular Pressure and Localized
Auxin Signalling Spatially Coordinate Restorative Divisions in Roots.” Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2003346117.
ieee: L. Hörmayer, J. C. Montesinos López, P. Marhavá, E. Benková, S. Yoshida, and
J. Friml, “Wounding-induced changes in cellular pressure and localized auxin signalling
spatially coordinate restorative divisions in roots,” Proceedings of the National
Academy of Sciences of the United States of America, vol. 117, no. 26. National
Academy of Sciences, 2020.
ista: Hörmayer L, Montesinos López JC, Marhavá P, Benková E, Yoshida S, Friml J.
2020. Wounding-induced changes in cellular pressure and localized auxin signalling
spatially coordinate restorative divisions in roots. Proceedings of the National
Academy of Sciences of the United States of America. 117(26), 202003346.
mla: Hörmayer, Lukas, et al. “Wounding-Induced Changes in Cellular Pressure and
Localized Auxin Signalling Spatially Coordinate Restorative Divisions in Roots.”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 117, no. 26, 202003346, National Academy of Sciences, 2020, doi:10.1073/pnas.2003346117.
short: L. Hörmayer, J.C. Montesinos López, P. Marhavá, E. Benková, S. Yoshida, J.
Friml, Proceedings of the National Academy of Sciences of the United States of
America 117 (2020).
corr_author: '1'
date_created: 2020-06-22T13:33:52Z
date_published: 2020-06-30T00:00:00Z
date_updated: 2026-10-25T23:30:26Z
day: '30'
ddc:
- '580'
department:
- _id: JiFr
- _id: EvBe
doi: 10.1073/pnas.2003346117
ec_funded: 1
external_id:
isi:
- '000565729700033'
pmid:
- '32541049'
file:
- access_level: open_access
checksum: 908b09437680181de9990915f2113aca
content_type: application/pdf
creator: dernst
date_created: 2020-06-23T11:30:53Z
date_updated: 2020-07-14T12:48:07Z
file_id: '8009'
file_name: 2020_PNAS_Hoermayer.pdf
file_size: 2407102
relation: main_file
file_date_updated: 2020-07-14T12:48:07Z
fulldoi: https://doi.org/10.1073/pnas.2003346117
has_accepted_license: '1'
intvolume: ' 117'
isi: 1
issue: '26'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 262EF96E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29988
name: RNA-directed DNA methylation in plant development
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/how-wounded-plants-coordinate-their-healing/
record:
- id: '9992'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Wounding-induced changes in cellular pressure and localized auxin signalling
spatially coordinate restorative divisions in roots
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 117
year: '2020'
...
---
_id: '9633'
abstract:
- lang: eng
text: The search for biologically faithful synaptic plasticity rules has resulted
in a large body of models. They are usually inspired by – and fitted to – experimental
data, but they rarely produce neural dynamics that serve complex functions. These
failures suggest that current plasticity models are still under-constrained by
existing data. Here, we present an alternative approach that uses meta-learning
to discover plausible synaptic plasticity rules. Instead of experimental data,
the rules are constrained by the functions they implement and the structure they
are meant to produce. Briefly, we parameterize synaptic plasticity rules by a
Volterra expansion and then use supervised learning methods (gradient descent
or evolutionary strategies) to minimize a problem-dependent loss function that
quantifies how effectively a candidate plasticity rule transforms an initially
random network into one with the desired function. We first validate our approach
by re-discovering previously described plasticity rules, starting at the single-neuron
level and “Oja’s rule”, a simple Hebbian plasticity rule that captures the direction
of most variability of inputs to a neuron (i.e., the first principal component).
We expand the problem to the network level and ask the framework to find Oja’s
rule together with an anti-Hebbian rule such that an initially random two-layer
firing-rate network will recover several principal components of the input space
after learning. Next, we move to networks of integrate-and-fire neurons with plastic
inhibitory afferents. We train for rules that achieve a target firing rate by
countering tuned excitation. Our algorithm discovers a specific subset of the
manifold of rules that can solve this task. Our work is a proof of principle of
an automated and unbiased approach to unveil synaptic plasticity rules that obey
biological constraints and can solve complex functions.
acknowledgement: We would like to thank Chaitanya Chintaluri, Georgia Christodoulou,
Bill Podlaski and Merima Šabanovic for useful discussions and comments. This work
was supported by a Wellcome Trust ´ Senior Research Fellowship (214316/Z/18/Z),
a BBSRC grant (BB/N019512/1), an ERC consolidator Grant (SYNAPSEEK), a Leverhulme
Trust Project Grant (RPG-2016-446), and funding from École Polytechnique, Paris.
alternative_title:
- Advances in Neural Information Processing Systems
article_processing_charge: No
author:
- first_name: Basile J
full_name: Confavreux, Basile J
id: C7610134-B532-11EA-BD9F-F5753DDC885E
last_name: Confavreux
- first_name: Friedemann
full_name: Zenke, Friedemann
last_name: Zenke
- first_name: Everton J.
full_name: Agnes, Everton J.
last_name: Agnes
- first_name: Timothy
full_name: Lillicrap, Timothy
last_name: Lillicrap
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: 'Confavreux BJ, Zenke F, Agnes EJ, Lillicrap T, Vogels TP. A meta-learning
approach to (re)discover plasticity rules that carve a desired function into a
neural network. In: 34th Conference on Neural Information Processing Systems.
Vol 33. Neural Information Processing Systems Foundation; 2020:16398-16408.'
apa: 'Confavreux, B. J., Zenke, F., Agnes, E. J., Lillicrap, T., & Vogels, T.
P. (2020). A meta-learning approach to (re)discover plasticity rules that carve
a desired function into a neural network. In 34th Conference on Neural Information
Processing Systems (Vol. 33, pp. 16398–16408). Vancouver, Canada: Neural Information
Processing Systems Foundation.'
chicago: Confavreux, Basile J, Friedemann Zenke, Everton J. Agnes, Timothy Lillicrap,
and Tim P Vogels. “A Meta-Learning Approach to (Re)Discover Plasticity Rules That
Carve a Desired Function into a Neural Network.” In 34th Conference on Neural
Information Processing Systems, 33:16398–408. Neural Information Processing
Systems Foundation, 2020.
ieee: B. J. Confavreux, F. Zenke, E. J. Agnes, T. Lillicrap, and T. P. Vogels, “A
meta-learning approach to (re)discover plasticity rules that carve a desired function
into a neural network,” in 34th Conference on Neural Information Processing
Systems, Vancouver, Canada, 2020, vol. 33, pp. 16398–16408.
ista: 'Confavreux BJ, Zenke F, Agnes EJ, Lillicrap T, Vogels TP. 2020. A meta-learning
approach to (re)discover plasticity rules that carve a desired function into a
neural network. 34th Conference on Neural Information Processing Systems. NeurIPS:
Conference on Neural Information Processing Systems, Advances in Neural Information
Processing Systems, vol. 33, 16398–16408.'
mla: Confavreux, Basile J., et al. “A Meta-Learning Approach to (Re)Discover Plasticity
Rules That Carve a Desired Function into a Neural Network.” 34th Conference
on Neural Information Processing Systems, vol. 33, Neural Information Processing
Systems Foundation, 2020, pp. 16398–408.
short: B.J. Confavreux, F. Zenke, E.J. Agnes, T. Lillicrap, T.P. Vogels, in:, 34th
Conference on Neural Information Processing Systems, Neural Information Processing
Systems Foundation, 2020, pp. 16398–16408.
conference:
end_date: 2020-12-12
location: Vancouver, Canada
name: 'NeurIPS: Conference on Neural Information Processing Systems'
start_date: 2020-12-06
das_tickbox: '1'
date_created: 2021-07-04T22:01:27Z
date_published: 2020-12-06T00:00:00Z
date_updated: 2026-10-25T23:30:28Z
day: '06'
ddc:
- '570'
department:
- _id: TiVo
ec_funded: 1
intvolume: ' 33'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://proceedings.neurips.cc/paper/2020/hash/bdbd5ebfde4934142c8a88e7a3796cd5-Abstract.html
month: '12'
oa: 1
oa_version: Published Version
page: 16398-16408
project:
- _id: 0aacfa84-070f-11eb-9043-d7eb2c709234
call_identifier: H2020
grant_number: '819603'
name: Learning the shape of synaptic plasticity rules for neuronal architectures
and function through machine learning.
- _id: c084a126-5a5b-11eb-8a69-d75314a70a87
grant_number: 214316/Z/18/Z
name: What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent
neuronal networks.
publication: 34th Conference on Neural Information Processing Systems
publication_identifier:
issn:
- 1049-5258
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
related_material:
link:
- relation: is_continued_by
url: https://doi.org/10.1101/2020.10.24.353409
record:
- id: '14422'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: A meta-learning approach to (re)discover plasticity rules that carve a desired
function into a neural network
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2020'
...