---
_id: '12521'
abstract:
- lang: eng
text: Differentiated X chromosomes are expected to have higher rates of adaptive
divergence than autosomes, if new beneficial mutations are recessive (the “faster-X
effect”), largely because these mutations are immediately exposed to selection
in males. The evolution of X chromosomes after they stop recombining in males,
but before they become hemizygous, has not been well explored theoretically. We
use the diffusion approximation to infer substitution rates of beneficial and
deleterious mutations under such a scenario. Our results show that selection is
less efficient on diploid X loci than on autosomal and hemizygous X loci under
a wide range of parameters. This “slower-X” effect is stronger for genes affecting
primarily (or only) male fitness, and for sexually antagonistic genes. These unusual
dynamics suggest that some of the peculiar features of X chromosomes, such as
the differential accumulation of genes with sex-specific functions, may start
arising earlier than previously appreciated.
acknowledgement: We thank the Vicoso and Barton groups and ISTA Scientific Computing
Unit. We also thank two anonymous reviewers for their valuable comments. This work
was supported by the European Research Council under the European Union’s Horizon
2020 research and innovation program (grant agreements no. 715257 and no. 716117).
article_number: qrac004
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Andrea
full_name: Mrnjavac, Andrea
id: 353FAC84-AE61-11E9-8BFC-00D3E5697425
last_name: Mrnjavac
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: 'Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. Slower-X: Reduced efficiency
of selection in the early stages of X chromosome evolution. Evolution Letters.
2023;7(1). doi:10.1093/evlett/qrac004'
apa: 'Mrnjavac, A., Khudiakova, K., Barton, N. H., & Vicoso, B. (2023). Slower-X:
Reduced efficiency of selection in the early stages of X chromosome evolution.
Evolution Letters. Oxford University Press. https://doi.org/10.1093/evlett/qrac004'
chicago: 'Mrnjavac, Andrea, Kseniia Khudiakova, Nicholas H Barton, and Beatriz Vicoso.
“Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome
Evolution.” Evolution Letters. Oxford University Press, 2023. https://doi.org/10.1093/evlett/qrac004.'
ieee: 'A. Mrnjavac, K. Khudiakova, N. H. Barton, and B. Vicoso, “Slower-X: Reduced
efficiency of selection in the early stages of X chromosome evolution,” Evolution
Letters, vol. 7, no. 1. Oxford University Press, 2023.'
ista: 'Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. 2023. Slower-X: Reduced efficiency
of selection in the early stages of X chromosome evolution. Evolution Letters.
7(1), qrac004.'
mla: 'Mrnjavac, Andrea, et al. “Slower-X: Reduced Efficiency of Selection in the
Early Stages of X Chromosome Evolution.” Evolution Letters, vol. 7, no.
1, qrac004, Oxford University Press, 2023, doi:10.1093/evlett/qrac004.'
short: A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (2023).
corr_author: '1'
date_created: 2023-02-06T13:59:12Z
date_published: 2023-02-01T00:00:00Z
date_updated: 2026-04-22T22:30:24Z
day: '01'
ddc:
- '570'
department:
- _id: GradSch
- _id: BeVi
doi: 10.1093/evlett/qrac004
ec_funded: 1
external_id:
isi:
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pmid:
- '37065438'
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creator: dernst
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keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
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call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Evolution Letters
publication_identifier:
issn:
- 2056-3744
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
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relation: dissertation_contains
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scopus_import: '1'
status: public
title: 'Slower-X: Reduced efficiency of selection in the early stages of X chromosome
evolution'
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: 7
year: '2023'
...
---
OA_place: publisher
_id: '14622'
abstract:
- lang: eng
text: "This Ph.D. thesis presents a detailed investigation into Variational Quantum
Algorithms\r\n(VQAs), a promising class of quantum algorithms that are well suited
for near-term quantum\r\ncomputation due to their moderate hardware requirements
and resilience to noise. Our\r\nprimary focus lies on two particular types of
VQAs: the Quantum Approximate Optimization\r\nAlgorithm (QAOA), used for solving
binary optimization problems, and the Variational Quantum\r\nEigensolver (VQE),
utilized for finding ground states of quantum many-body systems.\r\nIn the first
part of the thesis, we examine the issue of effective parameter initialization
for\r\nthe QAOA. The work demonstrates that random initialization of the QAOA
often leads to\r\nconvergence in local minima with sub-optimal performance. To
mitigate this issue, we propose\r\nan initialization of QAOA parameters based
on the Trotterized Quantum Annealing (TQA).\r\nWe show that TQA initialization
leads to the same performance as the best of an exponentially\r\nscaling number
of random initializations.\r\nThe second study introduces Transition States (TS),
stationary points with a single direction\r\nof descent, as a tool for systematically
exploring the QAOA optimization landscape. This\r\nleads us to propose a novel
greedy parameter initialization strategy that guarantees for the\r\nenergy to
decrease with increasing number of circuit layers.\r\nIn the third section, we
extend the QAOA to qudit systems, which are higher-dimensional\r\ngeneralizations
of qubits. This chapter provides theoretical insights and practical strategies
for\r\nleveraging the increased computational power of qudits in the context of
quantum optimization\r\nalgorithms and suggests a quantum circuit for implementing
the algorithm on an ion trap\r\nquantum computer.\r\nFinally, we propose an algorithm
to avoid “barren plateaus”, regions in parameter space with\r\nvanishing gradients
that obstruct efficient parameter optimization. This novel approach relies\r\non
defining a notion of weak barren plateaus based on the entropies of local reduced
density\r\nmatrices and showcases how these can be efficiently quantified using
shadow tomography.\r\nTo illustrate the approach we employ the strategy in the
VQE and show that it allows to\r\nsuccessfully avoid barren plateaus in the initialization
and throughout the optimization.\r\nTaken together, this thesis greatly enhances
our understanding of parameter initialization and\r\noptimization in VQAs, expands
the scope of QAOA to higher-dimensional quantum systems,\r\nand presents a method
to address the challenge of barren plateaus using the VQE. These\r\ninsights are
instrumental in advancing the field of near-term quantum computation."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Stefan
full_name: Sack, Stefan
id: dd622248-f6e0-11ea-865d-ce382a1c81a5
last_name: Sack
orcid: 0000-0001-5400-8508
citation:
ama: 'Sack S. Improving variational quantum algorithms : Innovative initialization
techniques and extensions to qudit systems. 2023. doi:10.15479/at:ista:14622'
apa: 'Sack, S. (2023). Improving variational quantum algorithms : Innovative
initialization techniques and extensions to qudit systems. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:14622'
chicago: 'Sack, Stefan. “Improving Variational Quantum Algorithms : Innovative Initialization
Techniques and Extensions to Qudit Systems.” Institute of Science and Technology
Austria, 2023. https://doi.org/10.15479/at:ista:14622.'
ieee: 'S. Sack, “Improving variational quantum algorithms : Innovative initialization
techniques and extensions to qudit systems,” Institute of Science and Technology
Austria, 2023.'
ista: 'Sack S. 2023. Improving variational quantum algorithms : Innovative initialization
techniques and extensions to qudit systems. Institute of Science and Technology
Austria.'
mla: 'Sack, Stefan. Improving Variational Quantum Algorithms : Innovative Initialization
Techniques and Extensions to Qudit Systems. Institute of Science and Technology
Austria, 2023, doi:10.15479/at:ista:14622.'
short: 'S. Sack, Improving Variational Quantum Algorithms : Innovative Initialization
Techniques and Extensions to Qudit Systems, Institute of Science and Technology
Austria, 2023.'
corr_author: '1'
date_created: 2023-11-28T10:58:13Z
date_published: 2023-11-30T00:00:00Z
date_updated: 2026-04-07T13:53:47Z
day: '30'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MaSe
doi: 10.15479/at:ista:14622
ec_funded: 1
file:
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checksum: 068fd3570506ec42b2faa390de784bc4
content_type: application/pdf
creator: ssack
date_created: 2023-11-30T15:53:10Z
date_updated: 2024-11-30T23:30:03Z
embargo: 2024-11-30
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file_name: PhD_Thesis.pdf
file_size: 11947523
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file_id: '14636'
file_name: PhD Thesis (1).zip
file_size: 18422964
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language:
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month: '11'
oa: 1
oa_version: Published Version
page: '142'
project:
- _id: bd660c93-d553-11ed-ba76-fb0fb6f49c0d
name: IMB PhD Nomination Fellowship - Stefan Sack
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '13125'
relation: part_of_dissertation
status: public
- id: '11471'
relation: part_of_dissertation
status: public
- id: '9760'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
title: 'Improving variational quantum algorithms : Innovative initialization techniques
and extensions to qudit systems'
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: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
_id: '13125'
abstract:
- lang: eng
text: 'The quantum approximate optimization algorithm (QAOA) is a variational quantum
algorithm, where a quantum computer implements a variational ansatz consisting
of p layers of alternating unitary operators and a classical computer is used
to optimize the variational parameters. For a random initialization, the optimization
typically leads to local minima with poor performance, motivating the search for
initialization strategies of QAOA variational parameters. Although numerous heuristic
initializations exist, an analytical understanding and performance guarantees
for large p remain evasive.We introduce a greedy initialization of QAOA which
guarantees improving performance with an increasing number of layers. Our main
result is an analytic construction of 2p + 1 transition states—saddle points with
a unique negative curvature direction—for QAOA with p + 1 layers that use the
local minimum of QAOA with p layers. Transition states connect to new local minima,
which are guaranteed to lower the energy compared to the minimum found for p layers.
We use the GREEDY procedure to navigate the exponentially increasing with p number
of local minima resulting from the recursive application of our analytic construction.
The performance of the GREEDY procedure matches available initialization strategies
while providing a guarantee for the minimal energy to decrease with an increasing
number of layers p. '
acknowledgement: 'We thank V. Verteletskyi for a joint collaboration on numerical
studies of the QAOA during his internship at ISTA that inspired analytic results
on TS reported in this work. We acknowledge A. A. Mele and M. Brooks for discussions
and D. Egger, P. Love, and D. Wierichs for valuable feedback on the manuscript.
S.H.S., R.A.M., and M.S. acknowledge support by the European Research Council (ERC)
under the European Union’s Horizon 2020 research and innovation program (Grant Agreement
No. 850899). R.K. is supported by the SFB BeyondC (Grant No. F7107-N38) and the
project QuantumReady (FFG 896217). '
article_number: '062404'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Stefan
full_name: Sack, Stefan
id: dd622248-f6e0-11ea-865d-ce382a1c81a5
last_name: Sack
orcid: 0000-0001-5400-8508
- first_name: Raimel A
full_name: Medina Ramos, Raimel A
id: CE680B90-D85A-11E9-B684-C920E6697425
last_name: Medina Ramos
orcid: 0000-0002-5383-2869
- first_name: Richard
full_name: Kueng, Richard
last_name: Kueng
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Sack S, Medina Ramos RA, Kueng R, Serbyn M. Recursive greedy initialization
of the quantum approximate optimization algorithm with guaranteed improvement.
Physical Review A. 2023;107(6). doi:10.1103/physreva.107.062404
apa: Sack, S., Medina Ramos, R. A., Kueng, R., & Serbyn, M. (2023). Recursive
greedy initialization of the quantum approximate optimization algorithm with guaranteed
improvement. Physical Review A. American Physical Society. https://doi.org/10.1103/physreva.107.062404
chicago: Sack, Stefan, Raimel A Medina Ramos, Richard Kueng, and Maksym Serbyn.
“Recursive Greedy Initialization of the Quantum Approximate Optimization Algorithm
with Guaranteed Improvement.” Physical Review A. American Physical Society,
2023. https://doi.org/10.1103/physreva.107.062404.
ieee: S. Sack, R. A. Medina Ramos, R. Kueng, and M. Serbyn, “Recursive greedy initialization
of the quantum approximate optimization algorithm with guaranteed improvement,”
Physical Review A, vol. 107, no. 6. American Physical Society, 2023.
ista: Sack S, Medina Ramos RA, Kueng R, Serbyn M. 2023. Recursive greedy initialization
of the quantum approximate optimization algorithm with guaranteed improvement.
Physical Review A. 107(6), 062404.
mla: Sack, Stefan, et al. “Recursive Greedy Initialization of the Quantum Approximate
Optimization Algorithm with Guaranteed Improvement.” Physical Review A,
vol. 107, no. 6, 062404, American Physical Society, 2023, doi:10.1103/physreva.107.062404.
short: S. Sack, R.A. Medina Ramos, R. Kueng, M. Serbyn, Physical Review A 107 (2023).
corr_author: '1'
date_created: 2023-06-07T06:57:32Z
date_published: 2023-06-02T00:00:00Z
date_updated: 2026-04-22T22:30:25Z
day: '02'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1103/physreva.107.062404
ec_funded: 1
external_id:
arxiv:
- '2209.01159'
isi:
- '001016927100012'
file:
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checksum: 0d71423888eeccaa60d8f41197f26306
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creator: dernst
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date_updated: 2023-06-13T07:28:36Z
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file_name: 2023_PhysRevA_Sack.pdf
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- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review A
publication_identifier:
eissn:
- 2469-9934
issn:
- 2469-9926
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
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relation: dissertation_contains
status: public
scopus_import: '1'
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title: Recursive greedy initialization of the quantum approximate optimization algorithm
with guaranteed improvement
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: 107
year: '2023'
...
---
OA_place: publisher
_id: '14697'
abstract:
- lang: eng
text: "During my Ph.D. research, I managed a series of projects, each focused on
the\r\nmechanisms underlying cell migration. My work involved an in-depth examination
of\r\nthe complex strategies employed by neutrophils, with a specific focus on
their ability to\r\nsynchronize spatial-temporal cues and optimize their gradient
perception. However, it\r\nis essential to acknowledge that not all projects yielded
successful results, as some\r\nideas were discontinued and are archived for future
reference within this thesis.\r\nMy main project investigated how neutrophils
decode spatial cues for precise navigation. Human neutrophils showcased distinct
movement patterns based on source\r\ntype – linear or point-like. By combining
single-cell tracking in 3D environments with\r\nproxy dyes, this project linked
cell behaviors to gradient changes, revealing a stronger\r\nresponse to semi-exponential
gradients from point sources. In addition, neutrophils\r\nexhibited oscillating
migration speeds, using speed minima to adjust trajectories toward sources. Experiencing
continuous concentration changes, they accelerated over\r\ntime and employed a
\"Run and Fumble\" strategy, alternating between consistent runs\r\nand strategic
\"tumbles\" for efficient navigation.\r\nThe project extended to the possibility
of cells amplifying perceived gradients by\r\nenclosing their immediate surroundings,
pushing attractants forward for enrichment\r\nwhile depleting it at the cell rear.
Microfluidic devices were employed, and various experimental parameters configurations
were optimized. Although significant differences\r\nin migratory efficacy were
detected across pore sizes and device heights, quantifying\r\ngradient manipulation
effects proved challenging.\r\nThe \"Laser-Assisted Protein Adsorption by Photobleaching\"
(LAPAP) project was\r\npromising, as it allowed the printing of gradients. Initially
successful with dendritic cells,\r\nwe aimed to adapt it for neutrophils. Through
extensive experimentation with multiple\r\nparameters, we attempted to trigger
responses from neutrophils. Despite these efforts\r\nand collaboration, the project
failed due to practical challenges and limitations.\r\nFacing a lack of neutrophil-like
cells at IST, we initially established the SCF-HoxB8\r\nprimary murine cell line.
Despite their existence, their migratory behavior was largely\r\nunexplored due
to potential limitations. Through differentiation protocol refinements we\r\nenhanced
their migratory capabilities, though their capacity still lagged behind human\r\nneutrophils.
Despite this, the improved migration potential of these cells pointed toward\r\ntheir
utility for in vitro murine neutrophil migration studies."
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Julian A
full_name: Stopp, Julian A
id: 489E3F00-F248-11E8-B48F-1D18A9856A87
last_name: Stopp
citation:
ama: 'Stopp JA. Neutrophils on the hunt : Migratory strategies employed by neutrophils
to fulfill their effector function. 2023. doi:10.15479/at:ista:14697'
apa: 'Stopp, J. A. (2023). Neutrophils on the hunt : Migratory strategies employed
by neutrophils to fulfill their effector function. Institute of Science and
Technology Austria. https://doi.org/10.15479/at:ista:14697'
chicago: 'Stopp, Julian A. “Neutrophils on the Hunt : Migratory Strategies Employed
by Neutrophils to Fulfill Their Effector Function.” Institute of Science and Technology
Austria, 2023. https://doi.org/10.15479/at:ista:14697.'
ieee: 'J. A. Stopp, “Neutrophils on the hunt : Migratory strategies employed by
neutrophils to fulfill their effector function,” Institute of Science and Technology
Austria, 2023.'
ista: 'Stopp JA. 2023. Neutrophils on the hunt : Migratory strategies employed by
neutrophils to fulfill their effector function. Institute of Science and Technology
Austria.'
mla: 'Stopp, Julian A. Neutrophils on the Hunt : Migratory Strategies Employed
by Neutrophils to Fulfill Their Effector Function. Institute of Science and
Technology Austria, 2023, doi:10.15479/at:ista:14697.'
short: 'J.A. Stopp, Neutrophils on the Hunt : Migratory Strategies Employed by Neutrophils
to Fulfill Their Effector Function, Institute of Science and Technology Austria,
2023.'
corr_author: '1'
date_created: 2023-12-18T19:14:28Z
date_published: 2023-12-20T00:00:00Z
date_updated: 2026-04-07T13:57:40Z
day: '20'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MiSi
doi: 10.15479/at:ista:14697
ec_funded: 1
file:
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creator: jstopp
date_created: 2023-12-20T09:35:34Z
date_updated: 2024-12-20T23:30:04Z
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language:
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oa: 1
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page: '226'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
isbn:
- 978-3-99078-038-1
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '14360'
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status: public
- id: '6328'
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status: public
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relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
title: 'Neutrophils on the hunt : Migratory strategies employed by neutrophils to
fulfill their effector function'
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
_id: '14274'
abstract:
- lang: eng
text: Immune responses rely on the rapid and coordinated migration of leukocytes.
Whereas it is well established that single-cell migration is often guided by gradients
of chemokines and other chemoattractants, it remains poorly understood how these
gradients are generated, maintained, and modulated. By combining experimental
data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor
(GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor
that steers migration, CCR7 also acts as a generator and a modulator of chemotactic
gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively
internalize the receptor and ligand as part of the canonical GPCR desensitization
response. We show that CCR7 internalization also acts as an effective sink for
the chemoattractant, dynamically shaping the spatiotemporal distribution of the
chemokine. This mechanism drives complex collective migration patterns, enabling
DCs to create or sharpen chemotactic gradients. We further show that these self-generated
gradients can sustain the long-range guidance of DCs, adapt collective migration
patterns to the size and geometry of the environment, and provide a guidance cue
for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses
and consumes its ligand can thus provide a novel mode of cellular self-organization.
acknowledgement: "We thank I. de Vries and the Scientific Service Units (Life Sciences,
Bioimaging, Nanofabrication, Preclinical and Miba Machine Shop) of the Institute
of Science and Technology Austria for excellent support, as well as all the rotation
students assisting in the laboratory work (B. Zens, H. Schön, and D. Babic).\r\nThis
work was supported by grants from the European Research Council under the European
Union’s Horizon 2020 research to M.S. (grant agreement no. 724373) and to E.H. (grant
agreement no. 851288), and a grant by the Austrian Science Fund (DK Nanocell W1250-B20)
to M.S. J.A. was supported by the Jenny and Antti Wihuri Foundation and Research
Council of Finland's Flagship Programme InFLAMES (decision number: 357910). M.C.U.
was supported by the European Union’s Horizon 2020 research and innovation programme
under the Marie Skłodowska-Curie grant agreement no. 754411."
article_number: adc9584
article_processing_charge: No
article_type: original
author:
- first_name: Jonna H
full_name: Alanko, Jonna H
id: 2CC12E8C-F248-11E8-B48F-1D18A9856A87
last_name: Alanko
orcid: 0000-0002-7698-3061
- first_name: Mehmet C
full_name: Ucar, Mehmet C
id: 50B2A802-6007-11E9-A42B-EB23E6697425
last_name: Ucar
orcid: 0000-0003-0506-4217
- first_name: Nikola
full_name: Canigova, Nikola
id: 3795523E-F248-11E8-B48F-1D18A9856A87
last_name: Canigova
orcid: 0000-0002-8518-5926
- first_name: Julian A
full_name: Stopp, Julian A
id: 489E3F00-F248-11E8-B48F-1D18A9856A87
last_name: Stopp
- first_name: Jan
full_name: Schwarz, Jan
id: 346C1EC6-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Alanko JH, Ucar MC, Canigova N, et al. CCR7 acts as both a sensor and a sink
for CCL19 to coordinate collective leukocyte migration. Science Immunology.
2023;8(87). doi:10.1126/sciimmunol.adc9584
apa: Alanko, J. H., Ucar, M. C., Canigova, N., Stopp, J. A., Schwarz, J., Merrin,
J., … Sixt, M. K. (2023). CCR7 acts as both a sensor and a sink for CCL19 to coordinate
collective leukocyte migration. Science Immunology. American Association
for the Advancement of Science. https://doi.org/10.1126/sciimmunol.adc9584
chicago: Alanko, Jonna H, Mehmet C Ucar, Nikola Canigova, Julian A Stopp, Jan Schwarz,
Jack Merrin, Edouard B Hannezo, and Michael K Sixt. “CCR7 Acts as Both a Sensor
and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science
Immunology. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciimmunol.adc9584.
ieee: J. H. Alanko et al., “CCR7 acts as both a sensor and a sink for CCL19
to coordinate collective leukocyte migration,” Science Immunology, vol.
8, no. 87. American Association for the Advancement of Science, 2023.
ista: Alanko JH, Ucar MC, Canigova N, Stopp JA, Schwarz J, Merrin J, Hannezo EB,
Sixt MK. 2023. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective
leukocyte migration. Science Immunology. 8(87), adc9584.
mla: Alanko, Jonna H., et al. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to
Coordinate Collective Leukocyte Migration.” Science Immunology, vol. 8,
no. 87, adc9584, American Association for the Advancement of Science, 2023, doi:10.1126/sciimmunol.adc9584.
short: J.H. Alanko, M.C. Ucar, N. Canigova, J.A. Stopp, J. Schwarz, J. Merrin, E.B.
Hannezo, M.K. Sixt, Science Immunology 8 (2023).
corr_author: '1'
date_created: 2023-09-06T08:07:51Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2026-04-22T22:30:27Z
day: '01'
department:
- _id: MiSi
- _id: EdHa
- _id: NanoFab
doi: 10.1126/sciimmunol.adc9584
ec_funded: 1
external_id:
isi:
- '001062110600003'
pmid:
- '37656776'
intvolume: ' 8'
isi: 1
issue: '87'
keyword:
- General Medicine
- Immunology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1126/sciimmunol.adc9584
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular Navigation Along Spatial Gradients
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
- _id: 265E2996-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W01250-B20
name: Nano-Analytics of Cellular Systems
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Science Immunology
publication_identifier:
issn:
- 2470-9468
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
record:
- id: '14279'
relation: research_data
status: public
- id: '19745'
relation: dissertation_contains
status: public
- id: '14697'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte
migration
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2023'
...
---
_id: '14360'
abstract:
- lang: eng
text: To navigate through diverse tissues, migrating cells must balance persistent
self-propelled motion with adaptive behaviors to circumvent obstacles. We identify
a curvature-sensing mechanism underlying obstacle evasion in immune-like cells.
Specifically, we propose that actin polymerization at the advancing edge of migrating
cells is inhibited by the curvature-sensitive BAR domain protein Snx33 in regions
with inward plasma membrane curvature. The genetic perturbation of this machinery
reduces the cells’ capacity to evade obstructions combined with faster and more
persistent cell migration in obstacle-free environments. Our results show how
cells can read out their surface topography and utilize actin and plasma membrane
biophysics to interpret their environment, allowing them to adaptively decide
if they should move ahead or turn away. On the basis of our findings, we propose
that the natural diversity of BAR domain proteins may allow cells to tune their
curvature sensing machinery to match the shape characteristics in their environment.
acknowledgement: "We thank Jan Ellenberg, Leanne Strauss, Anusha Gopalan, and Jia
Hui Li for critical feedback on the manuscript and the Life Science Editors for
editing assistance. The plasmid with hSnx33 was a kind gift from Duanqing Pei. Cell
line with GFP-tagged IRSp53 was a kind gift from Orion Weiner. We thank Brian Graziano
for providing protocols, reagents, and key advice to generate CRISPR knockout HL-60
cells. We thank the EMBL flow cytometry core facility, the EMBL advanced light microscopy
facility, the EMBL proteomics facility, and the EMBL genomics core facility for
support and advice. We thank Anusha Gopalan and Martin Bergert for their support
during mechanical measurements by AFM. We thank Estela Sosa Osorio for technical
assistance for the co-immunoprecipitation. We thank the EMBL genome biology computational
support (and specially Charles Girardot and Jelle Scholtalbers) for critical assistance
during RNAseq analysis. We thank Hans Kristian Hannibal‐Bach for his technical assistance
during the lipidomic analysis of plasma membrane isolates. We thank Steffen Burgold
for their support with LLS7 microscope in the ZEISS Microscopy Customer Center Europe.
We acknowledge the financial support of the European Molecular Biology Laboratory
(EMBL) to A.D.-M., Y.S., A.K., and A.E., the EMBL Interdisciplinary Postdocs (EIPOD)
program under Marie Sklodowska-Curie COFUND actions MSCA-COFUND-FP to M.S.B. and
M. S. (grant agreement number: 847543), the BEST program funding by FCT (SFRH/BEST/150300/2019)
to S.D.A. and the Joachim Herz Stiftung Add-on Fellowship for Interdisciplinary
Science to E.S.\r\nOpen Access funding enabled and organized by Projekt DEAL."
article_number: '5644'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Ewa
full_name: Sitarska, Ewa
last_name: Sitarska
- first_name: Silvia Dias
full_name: Almeida, Silvia Dias
last_name: Almeida
- first_name: Marianne Sandvold
full_name: Beckwith, Marianne Sandvold
last_name: Beckwith
- first_name: Julian A
full_name: Stopp, Julian A
id: 489E3F00-F248-11E8-B48F-1D18A9856A87
last_name: Stopp
- first_name: Jakub
full_name: Czuchnowski, Jakub
last_name: Czuchnowski
- first_name: Marc
full_name: Siggel, Marc
last_name: Siggel
- first_name: Rita
full_name: Roessner, Rita
last_name: Roessner
- first_name: Aline
full_name: Tschanz, Aline
last_name: Tschanz
- first_name: Christer
full_name: Ejsing, Christer
last_name: Ejsing
- first_name: Yannick
full_name: Schwab, Yannick
last_name: Schwab
- first_name: Jan
full_name: Kosinski, Jan
last_name: Kosinski
- 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: Kreshuk, Anna
last_name: Kreshuk
- first_name: Anna
full_name: Erzberger, Anna
last_name: Erzberger
- first_name: Alba
full_name: Diz-Muñoz, Alba
last_name: Diz-Muñoz
citation:
ama: Sitarska E, Almeida SD, Beckwith MS, et al. Sensing their plasma membrane curvature
allows migrating cells to circumvent obstacles. Nature Communications.
2023;14. doi:10.1038/s41467-023-41173-1
apa: Sitarska, E., Almeida, S. D., Beckwith, M. S., Stopp, J. A., Czuchnowski, J.,
Siggel, M., … Diz-Muñoz, A. (2023). Sensing their plasma membrane curvature allows
migrating cells to circumvent obstacles. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-023-41173-1
chicago: Sitarska, Ewa, Silvia Dias Almeida, Marianne Sandvold Beckwith, Julian
A Stopp, Jakub Czuchnowski, Marc Siggel, Rita Roessner, et al. “Sensing Their
Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” Nature
Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41173-1.
ieee: E. Sitarska et al., “Sensing their plasma membrane curvature allows
migrating cells to circumvent obstacles,” Nature Communications, vol. 14.
Springer Nature, 2023.
ista: Sitarska E, Almeida SD, Beckwith MS, Stopp JA, Czuchnowski J, Siggel M, Roessner
R, Tschanz A, Ejsing C, Schwab Y, Kosinski J, Sixt MK, Kreshuk A, Erzberger A,
Diz-Muñoz A. 2023. Sensing their plasma membrane curvature allows migrating cells
to circumvent obstacles. Nature Communications. 14, 5644.
mla: Sitarska, Ewa, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating
Cells to Circumvent Obstacles.” Nature Communications, vol. 14, 5644, Springer
Nature, 2023, doi:10.1038/s41467-023-41173-1.
short: E. Sitarska, S.D. Almeida, M.S. Beckwith, J.A. Stopp, J. Czuchnowski, M.
Siggel, R. Roessner, A. Tschanz, C. Ejsing, Y. Schwab, J. Kosinski, M.K. Sixt,
A. Kreshuk, A. Erzberger, A. Diz-Muñoz, Nature Communications 14 (2023).
date_created: 2023-09-24T22:01:10Z
date_published: 2023-09-13T00:00:00Z
date_updated: 2026-04-22T22:30:27Z
day: '13'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1038/s41467-023-41173-1
external_id:
isi:
- '001087583700008'
pmid:
- '37704612'
file:
- access_level: open_access
checksum: ad670e3b3c64fc585675948370f6b149
content_type: application/pdf
creator: dernst
date_created: 2023-09-25T08:22:58Z
date_updated: 2023-09-25T08:22:58Z
file_id: '14365'
file_name: 2023_NatureComm_Sitarska.pdf
file_size: 2725421
relation: main_file
success: 1
file_date_updated: 2023-09-25T08:22:58Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '14697'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Sensing their plasma membrane curvature allows migrating cells to circumvent
obstacles
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: 14
year: '2023'
...
---
OA_place: publisher
_id: '14280'
abstract:
- lang: eng
text: "Cell division in Escherichia coli is performed by the divisome, a multi-protein
complex composed of more than 30 proteins. The divisome spans from the cytoplasm
through the inner membrane to the cell wall and the outer membrane. Divisome assembly
is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes
at the center of the E. coli cell and determines the position of the future cell
septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue
FtsZ, which forms treadmilling filaments. These filaments are recruited to the
inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts
with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic
components of the divisome. \r\nA previous model postulated that FtsA regulates
maturation of the divisome by switching from an oligomeric, inactive state to
a monomeric and active state. This model was based mostly on in vivo studies,
as a biochemical characterization of FtsA has been hampered by difficulties in
purifying the protein. Here, we studied FtsA using an in vitro reconstitution
approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic,
treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space
and (ii) How does FtsA regulate the maturation of the divisome?\r\nWe found that
the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact
directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments.
When we investigated the underlying mechanism by imaging single molecules of FtsNcyto,
we found the peptide to interact transiently with FtsA. An in depth analysis of
the single molecule trajectories helped to postulate a model where PG synthases
follow the dynamics of FtsZ by a diffusion and capture mechanism. \r\nFollowing
up on these findings we were interested in how the self-interaction of FtsA changes
when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer
switch. For this, we compared the behavior of the previously identified, hyperactive
mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and
transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly
however, we found that this was not due to a difference in the self-interaction
strength of the two variants, but a difference in their membrane residence time.
Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured
self-interaction of FtsA actually increased. \r\nWe propose that FtsNcyto induces
a rearrangement of the oligomeric architecture of FtsA. In further consequence
this change leads to more persistent FtsZ filaments which results in a defined
signalling zone, allowing formation of the mature divisome. The observed difference
between FtsA WT and R286W is due to the vastly different membrane turnover of
the proteins. R286W cycles 5-10x faster compared to WT which allows to sample
FtsZ filaments at faster frequencies. These findings can explain the observed
differences in toxicity for overexpression of FtsA WT and R286W and help to understand
how FtsA regulates divisome maturation."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Philipp
full_name: Radler, Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
citation:
ama: Radler P. Spatiotemporal signaling during assembly of the bacterial divisome.
2023. doi:10.15479/at:ista:14280
apa: Radler, P. (2023). Spatiotemporal signaling during assembly of the bacterial
divisome. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14280
chicago: Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial
Divisome.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14280.
ieee: P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,”
Institute of Science and Technology Austria, 2023.
ista: Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial
divisome. Institute of Science and Technology Austria.
mla: Radler, Philipp. Spatiotemporal Signaling during Assembly of the Bacterial
Divisome. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14280.
short: P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome,
Institute of Science and Technology Austria, 2023.
corr_author: '1'
date_created: 2023-09-06T10:58:25Z
date_published: 2023-09-25T00:00:00Z
date_updated: 2026-04-07T14:06:05Z
day: '25'
ddc:
- '572'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MaLo
doi: 10.15479/at:ista:14280
ec_funded: 1
file:
- access_level: closed
checksum: 87eef11fbc5c7df0826f12a3a629b444
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: pradler
date_created: 2023-10-04T10:11:53Z
date_updated: 2024-10-05T22:30:03Z
embargo_to: open_access
file_id: '14390'
file_name: PhD Thesis_Philipp Radler_20231004.docx
file_size: 114932847
relation: source_file
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checksum: 3253e099b7126469d941fd9419d68b4f
content_type: application/pdf
creator: pradler
date_created: 2023-10-04T10:11:21Z
date_updated: 2024-10-05T22:30:03Z
embargo: 2024-10-04
file_id: '14391'
file_name: PhD Thesis_Philipp Radler_20231004.pdf
file_size: 37838778
relation: main_file
file_date_updated: 2024-10-05T22:30:03Z
has_accepted_license: '1'
keyword:
- Cell Division
- Reconstitution
- FtsZ
- FtsA
- Divisome
- E.coli
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '156'
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
- _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d
grant_number: P34607
name: In vitro reconstitution of bacterial cell division
- _id: 2596EAB6-B435-11E9-9278-68D0E5697425
grant_number: ALTF 2015-1163
name: Synthesis of bacterial cell wall
- _id: 259B655A-B435-11E9-9278-68D0E5697425
grant_number: LT000824/2016
name: Reconstitution of bacterial cell wall synthesis
publication_identifier:
isbn:
- 978-3-99078-033-6
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10934'
relation: research_data
status: public
- id: '11373'
relation: part_of_dissertation
status: public
- id: '7387'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
title: Spatiotemporal signaling during assembly of the bacterial divisome
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: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
_id: '12349'
abstract:
- lang: eng
text: Statistics of natural scenes are not uniform - their structure varies dramatically
from ground to sky. It remains unknown whether these non-uniformities are reflected
in the large-scale organization of the early visual system and what benefits such
adaptations would confer. Here, by relying on the efficient coding hypothesis,
we predict that changes in the structure of receptive fields across visual space
increase the efficiency of sensory coding. We show experimentally that, in agreement
with our predictions, receptive fields of retinal ganglion cells change their
shape along the dorsoventral retinal axis, with a marked surround asymmetry at
the visual horizon. Our work demonstrates that, according to principles of efficient
coding, the panoramic structure of natural scenes is exploited by the retina across
space and cell-types.
acknowledged_ssus:
- _id: ScienComp
- _id: PreCl
- _id: LifeSc
- _id: Bio
acknowledgement: We thank Hiroki Asari for sharing the dataset of naturalistic images,
Anton Sumser for sharing visual stimulus code, Yoav Ben Simon for initial explorative
work with the generation of AAVs, and Tomas Vega-Zuñiga for help with immunostainings.
We also thank Gasper Tkacik and members of the Neuroethology group for their comments
on the manuscript. This research was supported by the Scientific Service Units of
IST Austria through resources provided by Scientific Computing, the Preclinical
Facility, the Lab Support Facility, and the Imaging and Optics Facility. This work
was supported by European Union Horizon 2020 Marie Skłodowska-Curie grant 665385
(DG), Austrian Science Fund (FWF) stand-alone grant P 34015 (WM), Human Frontiers
Science Program LT000256/2018-L (AS), EMBO ALTF 1098-2017 (AS) and the European
Research Council Starting Grant 756502 (MJ).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Divyansh
full_name: Gupta, Divyansh
id: 2A485EBE-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
orcid: 0000-0001-7400-6665
- first_name: Wiktor F
full_name: Mlynarski, Wiktor F
id: 358A453A-F248-11E8-B48F-1D18A9856A87
last_name: Mlynarski
- first_name: Anton L
full_name: Sumser, Anton L
id: 3320A096-F248-11E8-B48F-1D18A9856A87
last_name: Sumser
orcid: 0000-0002-4792-1881
- first_name: Olga
full_name: Symonova, Olga
id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87
last_name: Symonova
orcid: 0000-0003-2012-9947
- first_name: Jan
full_name: Svaton, Jan
id: f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2
last_name: Svaton
orcid: 0000-0002-6198-2939
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
citation:
ama: Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. Panoramic
visual statistics shape retina-wide organization of receptive fields. Nature
Neuroscience. 2023;26:606-614. doi:10.1038/s41593-023-01280-0
apa: Gupta, D., Mlynarski, W. F., Sumser, A. L., Symonova, O., Svaton, J., &
Jösch, M. A. (2023). Panoramic visual statistics shape retina-wide organization
of receptive fields. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-023-01280-0
chicago: Gupta, Divyansh, Wiktor F Mlynarski, Anton L Sumser, Olga Symonova, Jan
Svaton, and Maximilian A Jösch. “Panoramic Visual Statistics Shape Retina-Wide
Organization of Receptive Fields.” Nature Neuroscience. Springer Nature,
2023. https://doi.org/10.1038/s41593-023-01280-0.
ieee: D. Gupta, W. F. Mlynarski, A. L. Sumser, O. Symonova, J. Svaton, and M. A.
Jösch, “Panoramic visual statistics shape retina-wide organization of receptive
fields,” Nature Neuroscience, vol. 26. Springer Nature, pp. 606–614, 2023.
ista: Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. 2023. Panoramic
visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience.
26, 606–614.
mla: Gupta, Divyansh, et al. “Panoramic Visual Statistics Shape Retina-Wide Organization
of Receptive Fields.” Nature Neuroscience, vol. 26, Springer Nature, 2023,
pp. 606–14, doi:10.1038/s41593-023-01280-0.
short: D. Gupta, W.F. Mlynarski, A.L. Sumser, O. Symonova, J. Svaton, M.A. Jösch,
Nature Neuroscience 26 (2023) 606–614.
corr_author: '1'
date_created: 2023-01-23T14:14:19Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2026-04-22T22:30:29Z
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doi: 10.1038/s41593-023-01280-0
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publisher: Springer Nature
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title: Panoramic visual statistics shape retina-wide organization of receptive fields
tmp:
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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)
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year: '2023'
...
---
_id: '12370'
abstract:
- lang: eng
text: 'Statistics of natural scenes are not uniform - their structure varies dramatically
from ground to sky. It remains unknown whether these non-uniformities are reflected
in the large-scale organization of the early visual system and what benefits such
adaptations would confer. Here, by relying on the efficient coding hypothesis,
we predict that changes in the structure of receptive fields across visual space
increase the efficiency of sensory coding. We show experimentally that, in agreement
with our predictions, receptive fields of retinal ganglion cells change their
shape along the dorsoventral retinal axis, with a marked surround asymmetry at
the visual horizon. Our work demonstrates that, according to principles of efficient
coding, the panoramic structure of natural scenes is exploited by the retina across
space and cell-types. '
acknowledged_ssus:
- _id: ScienComp
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author:
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id: 2A485EBE-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
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- first_name: Anton L
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id: 3320A096-F248-11E8-B48F-1D18A9856A87
last_name: Sumser
orcid: 0000-0002-4792-1881
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
citation:
ama: 'Gupta D, Sumser AL, Jösch MA. Research Data for: Panoramic visual statistics
shape retina-wide organization of receptive fields. 2023. doi:10.15479/AT:ISTA:12370'
apa: 'Gupta, D., Sumser, A. L., & Jösch, M. A. (2023). Research Data for: Panoramic
visual statistics shape retina-wide organization of receptive fields. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12370'
chicago: 'Gupta, Divyansh, Anton L Sumser, and Maximilian A Jösch. “Research Data
for: Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12370.'
ieee: 'D. Gupta, A. L. Sumser, and M. A. Jösch, “Research Data for: Panoramic visual
statistics shape retina-wide organization of receptive fields.” Institute of Science
and Technology Austria, 2023.'
ista: 'Gupta D, Sumser AL, Jösch MA. 2023. Research Data for: Panoramic visual statistics
shape retina-wide organization of receptive fields, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:12370.'
mla: 'Gupta, Divyansh, et al. Research Data for: Panoramic Visual Statistics
Shape Retina-Wide Organization of Receptive Fields. Institute of Science and
Technology Austria, 2023, doi:10.15479/AT:ISTA:12370.'
short: D. Gupta, A.L. Sumser, M.A. Jösch, (2023).
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first_name: Jan
id: f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2
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date_updated: 2026-04-22T22:30:29Z
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title: 'Research Data for: Panoramic visual statistics shape retina-wide organization
of receptive fields'
tmp:
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...
---
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abstract:
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text: 'The evolutionary processes that brought about today’s plethora of living
species and the many billions more ancient ones all underlie biology. Evolutionary
pathways are neither directed nor deterministic, but rather an interplay between
selection, migration, mutation, genetic drift and other environmental factors.
Hybrid zones, as natural crossing experiments, offer a great opportunity to use
cline analysis to deduce different evolutionary processes - for example, selection
strength. Theoretical cline models, largely assuming uniform distribution of individuals,
often lack the capability of incorporating population structure. Since in reality
organisms mostly live in patchy distributions and their dispersal is hardly ever
Gaussian, it is necessary to unravel the effect of these different elements of
population structure on cline parameters and shape. In this thesis, I develop
a simulation inspired by the A. majus hybrid zone of a single selected locus under
frequency dependent selection. This simulation enables us to untangle the effects
of different elements of population structure as for example a low-density center
and long-range dispersal. This thesis is therefore a first step towards theoretically
untangling the effects of different elements of population structure on cline
parameters and shape. '
alternative_title:
- ISTA Master's Thesis
article_processing_charge: No
author:
- first_name: Mara
full_name: Julseth, Mara
id: 1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1
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ama: Julseth M. The effect of local population structure on genetic variation at
selected loci in the A. majus hybrid zone. 2023. doi:10.15479/at:ista:12800
apa: Julseth, M. (2023). The effect of local population structure on genetic
variation at selected loci in the A. majus hybrid zone. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:12800
chicago: Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation
at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology
Austria, 2023. https://doi.org/10.15479/at:ista:12800.
ieee: M. Julseth, “The effect of local population structure on genetic variation
at selected loci in the A. majus hybrid zone,” Institute of Science and Technology
Austria, 2023.
ista: Julseth M. 2023. The effect of local population structure on genetic variation
at selected loci in the A. majus hybrid zone. Institute of Science and Technology
Austria.
mla: Julseth, Mara. The Effect of Local Population Structure on Genetic Variation
at Selected Loci in the A. Majus Hybrid Zone. Institute of Science and Technology
Austria, 2023, doi:10.15479/at:ista:12800.
short: M. Julseth, The Effect of Local Population Structure on Genetic Variation
at Selected Loci in the A. Majus Hybrid Zone, Institute of Science and Technology
Austria, 2023.
corr_author: '1'
date_created: 2023-04-04T18:57:11Z
date_published: 2023-04-05T00:00:00Z
date_updated: 2026-04-07T14:01:51Z
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ddc:
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degree_awarded: MS
department:
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status: public
supervisor:
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full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: The effect of local population structure on genetic variation at selected loci
in the A. majus hybrid zone
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
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...
---
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_id: '12781'
abstract:
- lang: eng
text: "Most energy in humans is produced in form of ATP by the mitochondrial respiratory
chain consisting of several protein assemblies embedded into lipid membrane (complexes
I-V). Complex I is the first and the largest enzyme of the respiratory chain which
is essential for energy production. It couples the transfer of two electrons from
NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial
membrane. The coupling mechanism between electron transfer and proton translocation
is one of the biggest enigma in bioenergetics and structural biology. Even though
the enzyme has been studied for decades, only recent technological advances in
cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from
E.coli appears to be of special importance because it is a perfect model system
with a rich mutant library, however the structure of the entire complex was unknown.
In this thesis I have resolved structures of the minimal complex I version from
E. coli in different states including reduced, inhibited, under reaction turnover
and several others. Extensive structural analyses of these structures and comparison
to structures from other species allowed to derive general features of conformational
dynamics and propose a universal coupling mechanism. The mechanism is straightforward,
robust and consistent with decades of experimental data available for complex
I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I)
is a part of broad complex I superfamily and was studied as well in this thesis.
It plays an important role in cyclic electron transfer (CET), during which electrons
are cycled within PSI through ferredoxin and plastoquinone to generate proton
gradient without NADPH production. Here, I solved structure of NDH and revealed
additional state, which was not observed before. The novel “resting” state allowed
to propose the mechanism of CET regulation. Moreover, conformational dynamics
of NDH resembles one in complex I which suggest more broad universality of the
proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped
to interpret decades of experimental data for complex I and contributed to fundamental
mechanistic understanding of protein function.\r\n"
acknowledged_ssus:
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
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last_name: Kravchuk
orcid: 0000-0001-9523-9089
citation:
ama: Kravchuk V. Structural and mechanistic study of bacterial complex I and its
cyanobacterial ortholog. 2023. doi:10.15479/at:ista:12781
apa: Kravchuk, V. (2023). Structural and mechanistic study of bacterial complex
I and its cyanobacterial ortholog. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:12781
chicago: Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex
I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria,
2023. https://doi.org/10.15479/at:ista:12781.
ieee: V. Kravchuk, “Structural and mechanistic study of bacterial complex I and
its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023.
ista: Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I
and its cyanobacterial ortholog. Institute of Science and Technology Austria.
mla: Kravchuk, Vladyslav. Structural and Mechanistic Study of Bacterial Complex
I and Its Cyanobacterial Ortholog. Institute of Science and Technology Austria,
2023, doi:10.15479/at:ista:12781.
short: V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and
Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023.
corr_author: '1'
date_created: 2023-03-31T12:24:42Z
date_published: 2023-03-23T00:00:00Z
date_updated: 2026-04-07T14:10:40Z
day: '23'
ddc:
- '570'
- '572'
degree_awarded: PhD
department:
- _id: GradSch
- _id: LeSa
doi: 10.15479/at:ista:12781
ec_funded: 1
file:
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checksum: 5ebb6345cb4119f93460c81310265a6d
content_type: application/pdf
creator: vkravchu
date_created: 2023-04-19T14:33:41Z
date_updated: 2024-04-22T22:30:06Z
embargo: 2024-04-20
file_id: '12852'
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relation: source_file
file_date_updated: 2024-04-22T22:30:06Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '127'
project:
- _id: 238A0A5A-32DE-11EA-91FC-C7463DDC885E
grant_number: '25541'
name: 'Structural characterization of E. coli complex I: an important mechanistic
model'
- _id: 627abdeb-2b32-11ec-9570-ec31a97243d3
call_identifier: H2020
grant_number: '101020697'
name: Structure and mechanism of respiratory chain molecular machines
publication_identifier:
isbn:
- 978-3-99078-029-9
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12138'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
title: Structural and mechanistic study of bacterial complex I and its cyanobacterial
ortholog
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
OA_place: publisher
_id: '14510'
abstract:
- lang: eng
text: "Clathrin-mediated endocytosis (CME) is vital for the regulation of plant
growth and\r\ndevelopment by controlling plasma membrane protein composition and
cargo uptake. CME\r\nrelies on the precise recruitment control of protein regulators
for vesicle maturation and\r\nrelease. During the early stages of endocytosis,
an area of flat membrane is remodelled by\r\nproteins to create a spherical vesicle
against intracellular forces. After the Clathrin-coated\r\nvesicle (CCV) is fully
formed, scission machinery releases it from the plasma membrane,\r\nand cargo
proceeds for recycling or degradation through early endosomes / Trans Golgi\r\nnetwork.
Protein machineries that mediate membrane bending and vesicle release in plants\r\nare
unknown. However, studies show, that plant endocytosis is actin independent, thus\r\nindicating
that plants utilize a unique mechanism to mediate membrane bending against highturgor
pressure compared to other model systems. First, by using biochemical and advanced\r\nlive
microscopy approaches we investigate the TPLATE complex, a plant-specific\r\nendocytosis
protein complex. We found that TPLATE is peripherally associated with\r\nclathrin-coated
vesicles and localises at the rim of endocytosis events. Next, our study of\r\nplant
Dynamin-related protein 1C (DRP1C), which was hypothesised previously to play
a\r\nrole in vesicle release, shows the recruitment of the protein already at
the early stages of\r\nendocytosis. Moreover, DRP1C assembles into organised ring-like
structures and is able to\r\ninduce membrane deformation and tubulation, suggesting
its role also in membrane bending\r\nduring early CME. Based on the data from
mammalian and yeast systems, plant DynaminRelated Proteins 2 and SH3P2 protein
are strong candidates to be part of the plant vesicle\r\nscission machinery; however,
their precise role in plant CME has not been yet elucidated.\r\nHere, we characterised
DRP2s and SH3P2 roles in CME by combining high-resolution\r\nimaging of endocytic
events in vivo and protein characterisation. Although DRP2s and\r\nSH3P2 arrive
together during late CME and physically interact, genetic analysis using\r\n∆sh3p1,2,3
mutant and complementation with non-DRP2-interacting SH3P2 variants suggest\r\nthat
SH3P2 does not directly recruit DRP2s to the site of endocytosis. Summarising
our\r\nresearch, these observations provide new important insights into the mechanism
of plant\r\nCME and show that, despite plants posses many homologues of mammalian
and yeast CME\r\ncomponents, they do not necessarily act in the same manner. "
acknowledged_ssus:
- _id: EM-Fac
- _id: Bio
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Nataliia
full_name: Gnyliukh, Nataliia
id: 390C1120-F248-11E8-B48F-1D18A9856A87
last_name: Gnyliukh
orcid: 0000-0002-2198-0509
citation:
ama: Gnyliukh N. Mechanism of clathrin-coated vesicle formation during endocytosis
in plants. 2023. doi:10.15479/at:ista:14510
apa: Gnyliukh, N. (2023). Mechanism of clathrin-coated vesicle formation during
endocytosis in plants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14510
chicago: Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle Formation during
Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14510.
ieee: N. Gnyliukh, “Mechanism of clathrin-coated vesicle formation during endocytosis
in plants,” Institute of Science and Technology Austria, 2023.
ista: Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle formation during endocytosis
in plants. Institute of Science and Technology Austria.
mla: Gnyliukh, Nataliia. Mechanism of Clathrin-Coated Vesicle Formation during
Endocytosis in Plants. Institute of Science and Technology Austria, 2023,
doi:10.15479/at:ista:14510.
short: N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis
in Plants, Institute of Science and Technology Austria, 2023.
corr_author: '1'
date_created: 2023-11-10T09:10:06Z
date_published: 2023-11-10T00:00:00Z
date_updated: 2026-04-22T22:30:33Z
day: '10'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JiFr
- _id: MaLo
doi: 10.15479/at:ista:14510
ec_funded: 1
file:
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date_created: 2023-11-20T09:18:51Z
date_updated: 2024-11-23T23:30:38Z
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file_size: 20824903
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content_type: application/pdf
creator: ngnyliuk
date_created: 2023-11-20T09:23:11Z
date_updated: 2024-11-23T23:30:38Z
embargo: 2024-11-23
file_id: '14568'
file_name: Thesis_Gnyliukh_final_20_11_23.pdf
file_size: 24871844
relation: main_file
file_date_updated: 2024-11-23T23:30:38Z
has_accepted_license: '1'
keyword:
- Clathrin-Mediated Endocytosis
- vesicle scission
- Dynamin-Related Protein 2
- SH3P2
- TPLATE complex
- Total internal reflection fluorescence microscopy
- Arabidopsis thaliana
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '180'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
isbn:
- 978-3-99078-037-4
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '14591'
relation: part_of_dissertation
status: public
- id: '9887'
relation: part_of_dissertation
status: public
- id: '8139'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
title: Mechanism of clathrin-coated vesicle formation during endocytosis in plants
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: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
OA_place: repository
_id: '14591'
abstract:
- lang: eng
text: Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth
and development by controlling plasma membrane protein composition and cargo uptake.
CME relies on the precise recruitment of regulators for vesicle maturation and
release. Homologues of components of mammalian vesicle scission are strong candidates
to be part of the scissin machinery in plants, but the precise roles of these
proteins in this process is not fully understood. Here, we characterised the roles
of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein
2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin,
in the CME by combining high-resolution imaging of endocytic events in vivo and
characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive
similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3
triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants
suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis.
These observations imply that despite the presence of many well-conserved endocytic
components, plants have acquired a distinct mechanism for CME. One Sentence Summary
In contrast to predictions based on mammalian systems, plant Dynamin-related proteins
2 are recruited to the site of Clathrin-mediated endocytosis independently of
BAR-SH3 proteins.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: Bio
article_processing_charge: No
author:
- first_name: Nataliia
full_name: Gnyliukh, Nataliia
id: 390C1120-F248-11E8-B48F-1D18A9856A87
last_name: Gnyliukh
orcid: 0000-0002-2198-0509
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Marie-Kristin
full_name: Nagel, Marie-Kristin
last_name: Nagel
- first_name: Aline
full_name: Monzer, Aline
id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425
last_name: Monzer
- first_name: Annamaria
full_name: Hlavata, Annamaria
id: 36062FEC-F248-11E8-B48F-1D18A9856A87
last_name: Hlavata
- first_name: Erika
full_name: Isono, Erika
last_name: Isono
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Gnyliukh N, Johnson AJ, Nagel M-K, et al. Role of dynamin-related proteins
2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. doi:10.1101/2023.10.09.561523
apa: Gnyliukh, N., Johnson, A. J., Nagel, M.-K., Monzer, A., Hlavata, A., Isono,
E., … Friml, J. (n.d.). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated
endocytosis in plants. bioRxiv. https://doi.org/10.1101/2023.10.09.561523
chicago: Gnyliukh, Nataliia, Alexander J Johnson, Marie-Kristin Nagel, Aline Monzer,
Annamaria Hlavata, Erika Isono, Martin Loose, and Jiří Friml. “Role of Dynamin-Related
Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv,
n.d. https://doi.org/10.1101/2023.10.09.561523.
ieee: N. Gnyliukh et al., “Role of dynamin-related proteins 2 and SH3P2 in
clathrin-mediated endocytosis in plants,” bioRxiv. .
ista: Gnyliukh N, Johnson AJ, Nagel M-K, Monzer A, Hlavata A, Isono E, Loose M,
Friml J. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis
in plants. bioRxiv, 10.1101/2023.10.09.561523.
mla: Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in
Clathrin-Mediated Endocytosis in Plants.” BioRxiv, doi:10.1101/2023.10.09.561523.
short: N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono,
M. Loose, J. Friml, BioRxiv (n.d.).
corr_author: '1'
date_created: 2023-11-22T10:17:49Z
date_published: 2023-10-10T00:00:00Z
date_updated: 2026-04-22T22:30:32Z
day: '10'
department:
- _id: JiFr
- _id: MaLo
- _id: CaBe
doi: 10.1101/2023.10.09.561523
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2023.10.09.561523
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: bioRxiv
publication_status: draft
related_material:
record:
- id: '15330'
relation: later_version
status: public
- id: '14510'
relation: dissertation_contains
status: public
status: public
title: Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis
in plants
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
OA_place: publisher
_id: '14226'
abstract:
- lang: eng
text: "We introduce the notion of a Faustian interchange in a 1-parameter family
of smooth\r\nfunctions to generalize the medial axis to critical points of index
larger than 0.\r\nWe construct and implement a general purpose algorithm for approximating
such\r\ngeneralized medial axes."
alternative_title:
- ISTA Master's Thesis
article_processing_charge: No
author:
- first_name: Elizabeth R
full_name: Stephenson, Elizabeth R
id: 2D04F932-F248-11E8-B48F-1D18A9856A87
last_name: Stephenson
orcid: 0000-0002-6862-208X
citation:
ama: Stephenson ER. Generalizing medial axes with homology switches. 2023. doi:10.15479/at:ista:14226
apa: Stephenson, E. R. (2023). Generalizing medial axes with homology switches.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14226
chicago: Stephenson, Elizabeth R. “Generalizing Medial Axes with Homology Switches.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14226.
ieee: E. R. Stephenson, “Generalizing medial axes with homology switches,” Institute
of Science and Technology Austria, 2023.
ista: Stephenson ER. 2023. Generalizing medial axes with homology switches. Institute
of Science and Technology Austria.
mla: Stephenson, Elizabeth R. Generalizing Medial Axes with Homology Switches.
Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14226.
short: E.R. Stephenson, Generalizing Medial Axes with Homology Switches, Institute
of Science and Technology Austria, 2023.
corr_author: '1'
date_created: 2023-08-24T13:01:18Z
date_published: 2023-08-24T00:00:00Z
date_updated: 2026-04-07T14:02:30Z
day: '24'
ddc:
- '500'
degree_awarded: MS
department:
- _id: GradSch
- _id: HeEd
doi: 10.15479/at:ista:14226
file:
- access_level: closed
checksum: 453caf851d75c3478c10ed09bd242a91
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creator: cchlebak
date_created: 2023-08-24T13:02:49Z
date_updated: 2024-02-26T23:30:03Z
embargo_to: open_access
file_id: '14227'
file_name: documents-export-2023-08-24.zip
file_size: 15501411
relation: source_file
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checksum: 7349d29963d6695e555e171748648d9a
content_type: application/pdf
creator: cchlebak
date_created: 2023-08-24T13:03:42Z
date_updated: 2024-02-26T23:30:03Z
embargo: 2024-02-25
file_id: '14228'
file_name: thesis_pdf_a.pdf
file_size: 6854783
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file_date_updated: 2024-02-26T23:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '43'
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
title: Generalizing medial axes with homology switches
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
OA_place: publisher
_id: '12470'
abstract:
- lang: eng
text: "The brain is an exceptionally sophisticated organ consisting of billions
of cells and trillions of \r\nconnections that orchestrate our cognition and behavior.
To decode its complex connectivity, it is \r\npivotal to disentangle its intricate
architecture spanning from cm-sized circuits down to tens of \r\nnm-small synapses.\r\nTo
achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue
across \r\nScales, a versatile toolbox for obtaining a holistic view of nervous
tissue context with (super\x02resolution) fluorescence microscopy. CATS combines
comprehensive labeling of the extracellular\r\nspace, that is compatible with
chemical fixation, with information on molecular markers, super\x02resolved data
acquisition and machine-learning based data analysis for segmentation and synapse
\r\nidentification.\r\nI used CATS to analyze key features of nervous tissue connectivity,
ranging from whole tissue \r\narchitecture, neuronal in- and output-fields, down
to synapse morphology.\r\nFocusing on the hippocampal circuitry, I quantified
synaptic transmission properties of mossy \r\nfiber boutons and analyzed the connectivity
pattern of dentate gyrus granule cells with CA3 \r\npyramidal neurons. This shows
that CATS is a viable tool to study hallmarks of neuronal \r\nconnectivity with
light microscopy."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
- _id: EM-Fac
- _id: M-Shop
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Julia M
full_name: Michalska, Julia M
id: 443DB6DE-F248-11E8-B48F-1D18A9856A87
last_name: Michalska
orcid: 0000-0003-3862-1235
citation:
ama: Michalska JM. A versatile toolbox for the comprehensive analysis of nervous
tissue organization with light microscopy. 2023. doi:10.15479/at:ista:12470
apa: Michalska, J. M. (2023). A versatile toolbox for the comprehensive analysis
of nervous tissue organization with light microscopy. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:12470
chicago: Michalska, Julia M. “A Versatile Toolbox for the Comprehensive Analysis
of Nervous Tissue Organization with Light Microscopy.” Institute of Science and
Technology Austria, 2023. https://doi.org/10.15479/at:ista:12470.
ieee: J. M. Michalska, “A versatile toolbox for the comprehensive analysis of nervous
tissue organization with light microscopy,” Institute of Science and Technology
Austria, 2023.
ista: Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of
nervous tissue organization with light microscopy. Institute of Science and Technology
Austria.
mla: Michalska, Julia M. A Versatile Toolbox for the Comprehensive Analysis of
Nervous Tissue Organization with Light Microscopy. Institute of Science and
Technology Austria, 2023, doi:10.15479/at:ista:12470.
short: J.M. Michalska, A Versatile Toolbox for the Comprehensive Analysis of Nervous
Tissue Organization with Light Microscopy, Institute of Science and Technology
Austria, 2023.
corr_author: '1'
date_created: 2023-01-31T15:10:53Z
date_published: 2023-01-09T00:00:00Z
date_updated: 2026-04-07T14:11:10Z
day: '09'
ddc:
- '610'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoDa
doi: 10.15479/at:ista:12470
ec_funded: 1
file:
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checksum: 1a2306e5f59f52df598e7ecfadf921ac
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creator: cchlebak
date_created: 2023-01-31T15:11:42Z
date_updated: 2023-07-27T22:30:54Z
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checksum: 0bebbdee0773443959e1f6ab8caf281f
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date_created: 2023-01-31T15:11:51Z
date_updated: 2023-07-10T22:30:04Z
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file_name: 20230109_PhD_thesis_JM_final.docx
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file_date_updated: 2023-07-27T22:30:54Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: '201'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication_identifier:
isbn:
- 978-3-99078-026-8
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
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relation: part_of_dissertation
status: public
- id: '11950'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
title: A versatile toolbox for the comprehensive analysis of nervous tissue organization
with light 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: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
OA_place: publisher
_id: '12531'
abstract:
- lang: eng
text: "All visual experiences of the vertebrates begin with light being converted
into electrical signals\r\nby the eye retina. Retinal ganglion cells (RGCs) are
the neurons of the innermost layer of the\r\nmammal retina, and they transmit
visual information to the rest of the brain.\r\nIt has been shown that RGCs vary
in their morphology and genetic profiles, moreover they can\r\nbe unambiguously
grouped into subtypes that share the same morphological and/or molecular\r\nproperties.
However, in terms of RGCs function, it remains unclear how many distinct types\r\nthere
are and what response properties their typology relies on. Even given the recent
studies\r\nthat successfully classified RGCs in a patch of the retina [1] and
in scotopic conditions [2], the\r\nquestion remains whether the found subtypes
persist across the entire retina.\r\nIn this work, using a novel imaging method,
we show that, when sampled from a large portion\r\nof the retina, RGCs can not
be clearly divided into functional subtypes. We found that in\r\nphotopic conditions,
which implies more prominent natural scene statistic differences across\r\nthe
visual field, response properties can be exhibited by cells differently depending
on their\r\nlocation in the retina, which leads to formation of a gradient of
features rather than distinct\r\nclasses.\r\nThis finding suggests that RGCs follow
a global organization across the visual field of the\r\nanimal, adapting each
RGC subtype to the requirements imposed by the natural scene statistics."
alternative_title:
- ISTA Master's Thesis
article_processing_charge: No
author:
- first_name: Kseniia
full_name: Kirillova, Kseniia
id: 8e3f931e-dc85-11ea-9058-e7b957bf23f0
last_name: Kirillova
citation:
ama: Kirillova K. Panoramic functional gradients across the mouse retina. 2023.
doi:10.15479/at:ista:12531
apa: Kirillova, K. (2023). Panoramic functional gradients across the mouse retina.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12531
chicago: Kirillova, Kseniia. “Panoramic Functional Gradients across the Mouse Retina.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12531.
ieee: K. Kirillova, “Panoramic functional gradients across the mouse retina,” Institute
of Science and Technology Austria, 2023.
ista: Kirillova K. 2023. Panoramic functional gradients across the mouse retina.
Institute of Science and Technology Austria.
mla: Kirillova, Kseniia. Panoramic Functional Gradients across the Mouse Retina.
Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12531.
short: K. Kirillova, Panoramic Functional Gradients across the Mouse Retina, Institute
of Science and Technology Austria, 2023.
corr_author: '1'
date_created: 2023-02-09T07:45:05Z
date_published: 2023-02-08T00:00:00Z
date_updated: 2026-04-07T14:06:26Z
day: '08'
ddc:
- '570'
degree_awarded: MS
department:
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- _id: MaJö
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month: '02'
oa: 1
oa_version: Published Version
page: '46'
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
title: Panoramic functional gradients across the mouse retina
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short: CC BY-NC-SA (4.0)
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user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
OA_place: publisher
_id: '14323'
abstract:
- lang: eng
text: Morphogens are signaling molecules that are known for their prominent role
in pattern formation within developing tissues. In addition to patterning, morphogens
also control tissue growth. However, the underlying mechanisms are poorly understood.
We studied the role of morphogens in regulating tissue growth in the developing
vertebrate neural tube. In this system, opposing morphogen gradients of Shh and
BMP establish the dorsoventral pattern of neural progenitor domains. Perturbations
in these morphogen pathways result in alterations in tissue growth and cell cycle
progression, however, it has been unclear what cellular process is affected. To
address this, we analysed the rates of cell proliferation and cell death in mouse
mutants in which signaling is perturbed, as well as in chick neural plate explants
exposed to defined concentrations of signaling activators or inhibitors. Our results
indicated that the rate of cell proliferation was not altered in these assays.
By contrast, both the Shh and BMP signaling pathways had profound effects on neural
progenitor survival. Our results indicate that these pathways synergise to promote
cell survival within neural progenitors. Consistent with this, we found that progenitors
within the intermediate region of the neural tube, where the combined levels of
Shh and BMP are the lowest, are most prone to cell death when signaling activity
is inhibited. In addition, we found that downregulation of Shh results in increased
apoptosis within the roof plate, which is the dorsal source of BMP ligand production.
This revealed a cross-interaction between the Shh and BMP morphogen signaling
pathways that may be relevant for understanding how gradients scale in neural
tubes with different overall sizes. We further studied the mechanism acting downstream
of Shh in cell survival regulation using genetic and genomic approaches. We propose
that Shh transcriptionally regulates a non-canonical apoptotic pathway. Altogether,
our study points to a novel role of opposing morphogen gradients in tissue size
regulation and provides new insights into complex interactions between Shh and
BMP signaling gradients in the neural tube.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Katarzyna
full_name: Kuzmicz-Kowalska, Katarzyna
id: 4CED352A-F248-11E8-B48F-1D18A9856A87
last_name: Kuzmicz-Kowalska
citation:
ama: Kuzmicz-Kowalska K. Regulation of neural progenitor survival by Shh and BMP
in the developing spinal cord. 2023. doi:10.15479/at:ista:14323
apa: Kuzmicz-Kowalska, K. (2023). Regulation of neural progenitor survival by
Shh and BMP in the developing spinal cord. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:14323
chicago: Kuzmicz-Kowalska, Katarzyna. “Regulation of Neural Progenitor Survival
by Shh and BMP in the Developing Spinal Cord.” Institute of Science and Technology
Austria, 2023. https://doi.org/10.15479/at:ista:14323.
ieee: K. Kuzmicz-Kowalska, “Regulation of neural progenitor survival by Shh and
BMP in the developing spinal cord,” Institute of Science and Technology Austria,
2023.
ista: Kuzmicz-Kowalska K. 2023. Regulation of neural progenitor survival by Shh
and BMP in the developing spinal cord. Institute of Science and Technology Austria.
mla: Kuzmicz-Kowalska, Katarzyna. Regulation of Neural Progenitor Survival by
Shh and BMP in the Developing Spinal Cord. Institute of Science and Technology
Austria, 2023, doi:10.15479/at:ista:14323.
short: K. Kuzmicz-Kowalska, Regulation of Neural Progenitor Survival by Shh and
BMP in the Developing Spinal Cord, Institute of Science and Technology Austria,
2023.
corr_author: '1'
date_created: 2023-09-13T10:07:18Z
date_published: 2023-09-13T00:00:00Z
date_updated: 2026-04-14T09:50:54Z
day: '13'
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degree_awarded: PhD
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language:
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month: '09'
oa: 1
oa_version: Published Version
page: '151'
project:
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name: The role of morphogens in the regulation of neural tube growth
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7883'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
title: Regulation of neural progenitor survival by Shh and BMP in the developing spinal
cord
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
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(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
_id: '13136'
abstract:
- lang: eng
text: Despite its fundamental importance for development, the question of how organs
achieve their correct size and shape is poorly understood. This complex process
requires coordination between the generation of cell mass and the morphogenetic
mechanisms that sculpt tissues. These processes are regulated by morphogen signalling
pathways and mechanical forces. Yet, in many systems, it is unclear how biochemical
and mechanical signalling are quantitatively interpreted to determine the behaviours
of individual cells and how they contribute to growth and morphogenesis at the
tissue scale. In this review, we discuss the development of the vertebrate neural
tube and somites as an example of the state of knowledge, as well as the challenges
in understanding the mechanisms of tissue size control in vertebrate organogenesis.
We highlight how the recent advances in stem cell differentiation and organoid
approaches can be harnessed to provide new insights into this question.
acknowledgement: 'We thank J. Briscoe for comments on the manuscript. Work in the
AK lab is supported by ISTA, the European Research Council under Horizon Europe:
grant 101044579, and Austrian Science Fund (FWF): F78 (Stem Cell Modulation). SR
is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship
SC19-011.'
article_number: '100459'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Thomas
full_name: Minchington, Thomas
id: 7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f
last_name: Minchington
- first_name: Stefanie
full_name: Rus, Stefanie
id: 4D9EC9B6-F248-11E8-B48F-1D18A9856A87
last_name: Rus
orcid: 0000-0001-8703-1093
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
citation:
ama: Minchington T, Rus S, Kicheva A. Control of tissue dimensions in the developing
neural tube and somites. Current Opinion in Systems Biology. 2023;35. doi:10.1016/j.coisb.2023.100459
apa: Minchington, T., Rus, S., & Kicheva, A. (2023). Control of tissue dimensions
in the developing neural tube and somites. Current Opinion in Systems Biology.
Elsevier. https://doi.org/10.1016/j.coisb.2023.100459
chicago: Minchington, Thomas, Stefanie Rus, and Anna Kicheva. “Control of Tissue
Dimensions in the Developing Neural Tube and Somites.” Current Opinion in Systems
Biology. Elsevier, 2023. https://doi.org/10.1016/j.coisb.2023.100459.
ieee: T. Minchington, S. Rus, and A. Kicheva, “Control of tissue dimensions in the
developing neural tube and somites,” Current Opinion in Systems Biology,
vol. 35. Elsevier, 2023.
ista: Minchington T, Rus S, Kicheva A. 2023. Control of tissue dimensions in the
developing neural tube and somites. Current Opinion in Systems Biology. 35, 100459.
mla: Minchington, Thomas, et al. “Control of Tissue Dimensions in the Developing
Neural Tube and Somites.” Current Opinion in Systems Biology, vol. 35,
100459, Elsevier, 2023, doi:10.1016/j.coisb.2023.100459.
short: T. Minchington, S. Rus, A. Kicheva, Current Opinion in Systems Biology 35
(2023).
corr_author: '1'
date_created: 2023-06-18T22:00:46Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2026-04-22T22:30:58Z
day: '01'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1016/j.coisb.2023.100459
file:
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checksum: 8a75c4e29fd9b62e3c50663c2265b173
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date_updated: 2024-01-29T11:06:45Z
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success: 1
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intvolume: ' 35'
language:
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month: '09'
oa: 1
oa_version: Published Version
project:
- _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa
grant_number: '101044579'
name: Mechanisms of tissue size regulation in spinal cord development
- _id: 059DF620-7A3F-11EA-A408-12923DDC885E
grant_number: F7802
name: Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen
control of growth and pattern in the spinal cord
- _id: 9B9B39FA-BA93-11EA-9121-9846C619BF3A
grant_number: SC19-011
name: The regulatory logic of pattern formation in the vertebrate dorsal neural
tube
publication: Current Opinion in Systems Biology
publication_identifier:
eissn:
- 2452-3100
publication_status: published
publisher: Elsevier
quality_controlled: '1'
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Control of tissue dimensions in the developing neural tube and somites
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
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(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2023'
...
---
_id: '12837'
abstract:
- lang: eng
text: As developing tissues grow in size and undergo morphogenetic changes, their
material properties may be altered. Such changes result from tension dynamics
at cell contacts or cellular jamming. Yet, in many cases, the cellular mechanisms
controlling the physical state of growing tissues are unclear. We found that at
early developmental stages, the epithelium in the developing mouse spinal cord
maintains both high junctional tension and high fluidity. This is achieved via
a mechanism in which interkinetic nuclear movements generate cell area dynamics
that drive extensive cell rearrangements. Over time, the cell proliferation rate
declines, effectively solidifying the tissue. Thus, unlike well-studied jamming
transitions, the solidification uncovered here resembles a glass transition that
depends on the dynamical stresses generated by proliferation and differentiation.
Our finding that the fluidity of developing epithelia is linked to interkinetic
nuclear movements and the dynamics of growth is likely to be relevant to multiple
developing tissues.
acknowledgement: 'We thank S. Hippenmeyer for the reagents and C. P. Heisenberg, J.
Briscoe and K. Page for comments on the manuscript. This work was supported by IST
Austria; the European Research Council under Horizon 2020 research and innovation
programme grant no. 680037 and Horizon Europe grant 101044579 (A.K.); Austrian Science
Fund (FWF): F78 (Stem Cell Modulation) (A.K.); ISTFELLOW postdoctoral program (A.S.);
Narodowe Centrum Nauki, Poland SONATA, 2017/26/D/NZ2/00454 (M.Z.); and the Polish
National Agency for Academic Exchange (M.Z.).'
article_processing_charge: No
article_type: original
author:
- first_name: Laura
full_name: Bocanegra, Laura
id: 4896F754-F248-11E8-B48F-1D18A9856A87
last_name: Bocanegra
- first_name: Amrita
full_name: Singh, Amrita
id: 76250f9f-3a21-11eb-9a80-a6180a0d7958
last_name: Singh
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
citation:
ama: Bocanegra L, Singh A, Hannezo EB, Zagórski MP, Kicheva A. Cell cycle dynamics
control fluidity of the developing mouse neuroepithelium. Nature Physics.
2023;19:1050-1058. doi:10.1038/s41567-023-01977-w
apa: Bocanegra, L., Singh, A., Hannezo, E. B., Zagórski, M. P., & Kicheva, A.
(2023). Cell cycle dynamics control fluidity of the developing mouse neuroepithelium.
Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-01977-w
chicago: Bocanegra, Laura, Amrita Singh, Edouard B Hannezo, Marcin P Zagórski, and
Anna Kicheva. “Cell Cycle Dynamics Control Fluidity of the Developing Mouse Neuroepithelium.”
Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-01977-w.
ieee: L. Bocanegra, A. Singh, E. B. Hannezo, M. P. Zagórski, and A. Kicheva, “Cell
cycle dynamics control fluidity of the developing mouse neuroepithelium,” Nature
Physics, vol. 19. Springer Nature, pp. 1050–1058, 2023.
ista: Bocanegra L, Singh A, Hannezo EB, Zagórski MP, Kicheva A. 2023. Cell cycle
dynamics control fluidity of the developing mouse neuroepithelium. Nature Physics.
19, 1050–1058.
mla: Bocanegra, Laura, et al. “Cell Cycle Dynamics Control Fluidity of the Developing
Mouse Neuroepithelium.” Nature Physics, vol. 19, Springer Nature, 2023,
pp. 1050–58, doi:10.1038/s41567-023-01977-w.
short: L. Bocanegra, A. Singh, E.B. Hannezo, M.P. Zagórski, A. Kicheva, Nature Physics
19 (2023) 1050–1058.
corr_author: '1'
date_created: 2023-04-16T22:01:09Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2026-04-22T22:31:00Z
day: '01'
ddc:
- '570'
department:
- _id: EdHa
- _id: AnKi
doi: 10.1038/s41567-023-01977-w
ec_funded: 1
external_id:
isi:
- '000964029300003'
pmid:
- '37456593'
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checksum: 858225a4205b74406e5045006cdd853f
content_type: application/pdf
creator: dernst
date_created: 2023-10-04T11:13:28Z
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call_identifier: H2020
grant_number: '680037'
name: Coordination of Patterning And Growth In the Spinal Cord
- _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa
grant_number: '101044579'
name: Mechanisms of tissue size regulation in spinal cord development
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control of growth and pattern in the spinal cord
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call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Nature Physics
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eissn:
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issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
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scopus_import: '1'
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title: Cell cycle dynamics control fluidity of the developing mouse neuroepithelium
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)
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type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2023'
...
---
OA_place: publisher
_id: '13081'
abstract:
- lang: eng
text: During development, tissues undergo changes in size and shape to form functional
organs. Distinct cellular processes such as cell division and cell rearrangements
underlie tissue morphogenesis. Yet how the distinct processes are controlled and
coordinated, and how they contribute to morphogenesis is poorly understood. In
our study, we addressed these questions using the developing mouse neural tube.
This epithelial organ transforms from a flat epithelial sheet to an epithelial
tube while increasing in size and undergoing morpho-gen-mediated patterning. The
extent and mechanism of neural progenitor rearrangement within the developing
mouse neuroepithelium is unknown. To investigate this, we per-formed high resolution
lineage tracing analysis to quantify the extent of epithelial rear-rangement at
different stages of neural tube development. We quantitatively described the relationship
between apical cell size with cell cycle dependent interkinetic nuclear migra-tions
(IKNM) and performed high cellular resolution live imaging of the neuroepithelium
to study the dynamics of junctional remodeling. Furthermore, developed a vertex
model of the neuroepithelium to investigate the quantitative contribution of cell
proliferation, cell differentiation and mechanical properties to the epithelial
rearrangement dynamics and validated the model predictions through functional
experiments. Our analysis revealed that at early developmental stages, the apical
cell area kinetics driven by IKNM induce high lev-els of cell rearrangements in
a regime of high junctional tension and contractility. After E9.5, there is a
sharp decline in the extent of cell rearrangements, suggesting that the epi-thelium
transitions from a fluid-like to a solid-like state. We found that this transition
is regulated by the growth rate of the tissue, rather than by changes in cell-cell
adhesion and contractile forces. Overall, our study provides a quantitative description
of the relationship between tissue growth, cell cycle dynamics, epithelia rearrangements
and the emergent tissue material properties, and novel insights on how epithelial
cell dynamics influences tissue morphogenesis.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Laura
full_name: Bocanegra, Laura
id: 4896F754-F248-11E8-B48F-1D18A9856A87
last_name: Bocanegra
citation:
ama: Bocanegra L. Epithelial dynamics during mouse neural tube development. 2023.
doi:10.15479/at:ista:13081
apa: Bocanegra, L. (2023). Epithelial dynamics during mouse neural tube development.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13081
chicago: Bocanegra, Laura. “Epithelial Dynamics during Mouse Neural Tube Development.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13081.
ieee: L. Bocanegra, “Epithelial dynamics during mouse neural tube development,”
Institute of Science and Technology Austria, 2023.
ista: Bocanegra L. 2023. Epithelial dynamics during mouse neural tube development.
Institute of Science and Technology Austria.
mla: Bocanegra, Laura. Epithelial Dynamics during Mouse Neural Tube Development.
Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13081.
short: L. Bocanegra, Epithelial Dynamics during Mouse Neural Tube Development, Institute
of Science and Technology Austria, 2023.
corr_author: '1'
date_created: 2023-05-23T19:10:42Z
date_published: 2023-05-23T00:00:00Z
date_updated: 2026-04-14T09:50:54Z
day: '23'
ddc:
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degree_awarded: PhD
department:
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- _id: AnKi
doi: 10.15479/at:ista:13081
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supervisor:
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full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
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orcid: 0000-0003-4509-4998
title: Epithelial dynamics during mouse neural tube development
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...