---
OA_place: repository
_id: '21137'
acknowledged_ssus:
- _id: Bio
- _id: EM-Fac
- _id: ScienComp
- _id: LifeSc
acknowledgement: We thank all members of the Heisenberg, Henkes, and Hannezo groups
for their support. We are also grateful to the Imaging and Optics, Scientific Computing,
Life Science Support, and Cryo-Electron Microscopy facilities at ISTA for their
technical assistance and support. Numerical simulations were performed using the
computational resources from Lorentz Institute and the Academic Leiden Interdisciplinary
Cluster Environment (ALICE) provided by Leiden University, and from PMMH provided
by Sorbonne Université. S.N has received funding from European Union’s Horizon 2020
research and innovation programme (grant agreement No. 665385). This work was supported
by the Austrian Science Fund (FWF) under projects PAT5044023 and W1250 awarded to
C.-P.H.
article_processing_charge: No
author:
- first_name: Suyash
full_name: Naik, Suyash
id: 2C0B105C-F248-11E8-B48F-1D18A9856A87
last_name: Naik
orcid: 0000-0001-8421-5508
citation:
ama: Naik S. Data associated with Keratins coordinate tissue spreading . 2026. doi:10.15479/AT-ISTA-21137
apa: Naik, S. (2026). Data associated with Keratins coordinate tissue spreading
. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21137
chicago: Naik, Suyash. “Data Associated with Keratins Coordinate Tissue Spreading
.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21137.
ieee: S. Naik, “Data associated with Keratins coordinate tissue spreading .” Institute
of Science and Technology Austria, 2026.
ista: Naik S. 2026. Data associated with Keratins coordinate tissue spreading ,
Institute of Science and Technology Austria, 10.15479/AT-ISTA-21137.
mla: Naik, Suyash. Data Associated with Keratins Coordinate Tissue Spreading
. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21137.
short: S. Naik, (2026).
contributor:
- contributor_type: researcher
first_name: Yann-Edwin
last_name: Keta
- contributor_type: supervisor
first_name: 'Silke '
last_name: Henkes
- contributor_type: supervisor
first_name: Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- contributor_type: supervisor
first_name: Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
corr_author: '1'
date_created: 2026-02-04T16:38:02Z
date_published: 2026-03-24T00:00:00Z
date_updated: 2026-06-10T09:44:10Z
day: '24'
department:
- _id: GradSch
- _id: CaHe
- _id: EdHa
doi: 10.15479/AT-ISTA-21137
ec_funded: 1
file:
- access_level: open_access
checksum: 5d1fda7e410f24c311fcf6bcf725698f
content_type: application/zip
creator: snaik
date_created: 2026-03-16T11:51:10Z
date_updated: 2026-03-16T11:51:10Z
description: 'Python3 library written in C++20 to integrate vertex models. Please
read the readme at https://github.com/yketa/cells/blob/main/README.md for detailed
instructions for installation and usage of the code in this repository. '
file_id: '21461'
file_name: cells-main.zip
file_size: 725916
relation: main_file
title: Cell git repository
- access_level: open_access
checksum: ee350c8eaed99f3ca348c47c8b190d3c
content_type: application/x-zip-compressed
creator: snaik
date_created: 2026-03-18T14:52:02Z
date_updated: 2026-03-18T14:52:02Z
file_id: '21464'
file_name: DevBranchDataRepo.zip
file_size: 282168895
relation: main_file
success: 1
- access_level: open_access
checksum: 1ecaf2c1a2ce8ff9c75a128cc02d0b8f
content_type: text/markdown
creator: snaik
date_created: 2026-03-18T15:01:32Z
date_updated: 2026-03-18T15:01:32Z
file_id: '21466'
file_name: ReadMe.md
file_size: 2231
relation: main_file
success: 1
- access_level: open_access
checksum: da9a4687e5144b61a64ca341f922046a
content_type: image/svg+xml
creator: snaik
date_created: 2026-03-18T15:12:57Z
date_updated: 2026-03-18T15:12:57Z
file_id: '21467'
file_name: PaperSchematics.svg
file_size: 1951210
relation: main_file
success: 1
- access_level: open_access
checksum: 9ac1054b16c212c6f34d402dce2c80e0
content_type: application/octet-stream
creator: snaik
date_created: 2026-03-21T03:37:43Z
date_updated: 2026-03-21T03:37:43Z
file_id: '21468'
file_name: maxwell_sketch.tex
file_size: 1897
relation: main_file
success: 1
- access_level: open_access
checksum: 7c9ecf78e2593b3830d96fa94baa08df
content_type: application/x-zip-compressed
creator: snaik
date_created: 2026-03-24T07:21:43Z
date_updated: 2026-03-24T07:21:43Z
file_id: '21495'
file_name: DataRepo.zip
file_size: 749368723
relation: main_file
success: 1
file_date_updated: 2026-03-24T07:21:43Z
has_accepted_license: '1'
license: https://creativecommons.org/licenses/by-sa/4.0/
month: '3'
oa: 1
oa_version: Published Version
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 8f060199-16d5-11f0-9cad-f3253b266c46
grant_number: PAT 5044023
name: Keratins in epithelial tissue spreading
- _id: 252C3B08-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1250-B20
name: Nano-Analytics of Cellular Systems
publisher: Institute of Science and Technology Austria
status: public
title: 'Data associated with Keratins coordinate tissue spreading '
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: research_data
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19003'
abstract:
- lang: eng
text: 'Super-resolution methods provide far better spatial resolution than the optical
diffraction limit of about half the wavelength of light (∼200-300 nm). Nevertheless,
they have yet to attain widespread use in plants, largely due to plants’ challenging
optical properties. Expansion microscopy improves effective resolution by isotropically
increasing the physical distances between sample structures while preserving relative
spatial arrangements and clearing the sample. However, its application to plants
has been hindered by the rigid, mechanically cohesive structure of plant tissues.
Here, we report on whole-mount expansion microscopy of thale cress (Arabidopsis
thaliana) root tissues (PlantEx), achieving a four-fold resolution increase over
conventional microscopy. Our results highlight the microtubule cytoskeleton organization
and interaction between molecularly defined cellular constituents. Combining PlantEx
with stimulated emission depletion (STED) microscopy, we increase nanoscale resolution
and visualize the complex organization of subcellular organelles from intact tissues
by example of the densely packed COPI-coated vesicles associated with the Golgi
apparatus and put these into a cellular structural context. Our results show that
expansion microscopy can be applied to increase effective imaging resolution in
Arabidopsis root specimens. '
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: E-Lib
- _id: M-Shop
acknowledgement: "We gratefully acknowledge support by the Scientific Service Units
at ISTA, including the Imaging and Optics and Lab Support facilities and the mechanical
workshop and Library. We thank Philipp Velicky for STED microscope alignment.\r\nThis
project has received funding from the European Research Council under the Horizon
2020 Framework Programme (grant agreement No 742985, J.F.). It has also received
funding from the Horizon 2020 Framework Programme under the Marie Skłodowska-Curie
Grant Agreement No. 665385 (M.G.). S.T. has received funding as an ISTplus Fellow
from the Horizon 2020 Framework Programme under Marie Skłodowska-Curie grant agreement
no. 754411 and from EMBO via a Long-Term Fellowship (grant number ALTF 679-2018).
M.R.T. received funding from the Austrian Academy of Sciences with DOC fellowship
no. 26137. The project has further received funding from the Austrian Science Fund,
via grant DK W1232 (M.R.T., N.A.D., and J.G.D). W.J. received a postdoctoral fellowship
from the Human Frontier Science Program (LT000557/2018). The funders had no role
in study design, data collection and analysis, decision to publish or preparation
of the manuscript."
article_number: koaf006
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- first_name: Sven M
full_name: Truckenbrodt, Sven M
id: 45812BD4-F248-11E8-B48F-1D18A9856A87
last_name: Truckenbrodt
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Syamala
full_name: Inumella, Syamala
id: F8660870-D756-11E9-98C5-34DFE5697425
last_name: Inumella
orcid: 0009-0002-5890-120X
- first_name: Vitali
full_name: Vistunou, Vitali
id: 7e146587-8972-11ed-ae7b-d7a32ea86a81
last_name: Vistunou
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- first_name: Nathalie
full_name: Agudelo Duenas, Nathalie
id: 40E7F008-F248-11E8-B48F-1D18A9856A87
last_name: Agudelo Duenas
- first_name: Jakob
full_name: Vorlaufer, Jakob
id: 937696FA-C996-11E9-8C7C-CF13E6697425
last_name: Vorlaufer
orcid: 0009-0000-7590-3501
- first_name: Wiebke
full_name: Jahr, Wiebke
id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
last_name: Jahr
orcid: 0000-0003-0201-2315
- first_name: Marek
full_name: Randuch, Marek
id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
last_name: Randuch
- 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: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Gallei MC, Truckenbrodt SM, Kreuzinger C, et al. Super-resolution expansion
microscopy in plant roots. The Plant Cell. 2025;37(4). doi:10.1093/plcell/koaf006
apa: Gallei, M. C., Truckenbrodt, S. M., Kreuzinger, C., Inumella, S., Vistunou,
V., Sommer, C. M., … Danzl, J. G. (2025). Super-resolution expansion microscopy
in plant roots. The Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koaf006
chicago: Gallei, Michelle C, Sven M Truckenbrodt, Caroline Kreuzinger, Syamala Inumella,
Vitali Vistunou, Christoph M Sommer, Mojtaba Tavakoli, et al. “Super-Resolution
Expansion Microscopy in Plant Roots.” The Plant Cell. Oxford University
Press, 2025. https://doi.org/10.1093/plcell/koaf006.
ieee: M. C. Gallei et al., “Super-resolution expansion microscopy in plant
roots,” The Plant Cell, vol. 37, no. 4. Oxford University Press, 2025.
ista: Gallei MC, Truckenbrodt SM, Kreuzinger C, Inumella S, Vistunou V, Sommer CM,
Tavakoli M, Agudelo Duenas N, Vorlaufer J, Jahr W, Randuch M, Johnson AJ, Benková
E, Friml J, Danzl JG. 2025. Super-resolution expansion microscopy in plant roots.
The Plant Cell. 37(4), koaf006.
mla: Gallei, Michelle C., et al. “Super-Resolution Expansion Microscopy in Plant
Roots.” The Plant Cell, vol. 37, no. 4, koaf006, Oxford University Press,
2025, doi:10.1093/plcell/koaf006.
short: M.C. Gallei, S.M. Truckenbrodt, C. Kreuzinger, S. Inumella, V. Vistunou,
C.M. Sommer, M. Tavakoli, N. Agudelo Duenas, J. Vorlaufer, W. Jahr, M. Randuch,
A.J. Johnson, E. Benková, J. Friml, J.G. Danzl, The Plant Cell 37 (2025).
corr_author: '1'
date_created: 2025-02-05T06:52:06Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2026-06-10T08:30:19Z
day: '01'
ddc:
- '580'
department:
- _id: EvBe
- _id: JoDa
- _id: JiFr
doi: 10.1093/plcell/koaf006
ec_funded: 1
external_id:
isi:
- '001462763100001'
pmid:
- '39792900'
file:
- access_level: open_access
checksum: 9d3f8218ff37a29f29c48a7bbe831bd3
content_type: application/pdf
creator: dernst
date_created: 2025-07-31T07:03:43Z
date_updated: 2025-07-31T07:03:43Z
file_id: '20092'
file_name: 2025_PlantCell_Gallei.pdf
file_size: 53904111
relation: main_file
success: 1
file_date_updated: 2025-07-31T07:03:43Z
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 269B5B22-B435-11E9-9278-68D0E5697425
grant_number: ALTF 679-2018
name: UltraX - achieving sub-nanometer resolution in light microscopy using iterative
X10 microscopy in combination with nanobodies and STED
- _id: 6285a163-2b32-11ec-9570-8e204ca2dba5
grant_number: '26137'
name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
Microscopy
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: The Plant Cell
publication_identifier:
eissn:
- 1532-298X
issn:
- 1040-4651
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '18689'
relation: earlier_version
status: public
- id: '18837'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Super-resolution expansion microscopy in plant roots
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: 37
year: '2025'
...
---
APC_amount: 3317,75 EUR
OA_place: publisher
OA_type: hybrid
_id: '19453'
abstract:
- lang: eng
text: A key feature of biological and artificial neural networks is the progressive
refinement of their neural representations with experience. In neuroscience, this
fact has inspired several recent studies in sensory and motor systems. However,
less is known about how higher associational cortical areas, such as the hippocampus,
modify representations throughout the learning of complex tasks. Here, we focus
on associative learning, a process that requires forming a connection between
the representations of different variables for appropriate behavioral response.
We trained rats in a space-context associative task and monitored hippocampal
neural activity throughout the entire learning period, over several days. This
allowed us to assess changes in the representations of context, movement direction,
and position, as well as their relationship to behavior. We identified a hierarchical
representational structure in the encoding of these three task variables that
was preserved throughout learning. Nevertheless, we also observed changes at the
lower levels of the hierarchy where context was encoded. These changes were local
in neural activity space and restricted to physical positions where context identification
was necessary for correct decision-making, supporting better context decoding
and contextual code compression. Our results demonstrate that the hippocampal
code not only accommodates hierarchical relationships between different variables
but also enables efficient learning through minimal changes in neural activity
space. Beyond the hippocampus, our work reveals a representation learning mechanism
that might be implemented in other biological and artificial networks performing
similar tasks.
acknowledgement: We would like to thank Rebecca Morse for performing the recordings
in one of the animals under the supervision of H.S.C.C., Jago Wallenschus for the
technical support, especially with maze design, Wiktor Mlynarski for the advice
and discussions and Andrea Cumpelik for suggestions during the writing. M.N. was
supported by the Howard Hughes Medical Institute. H.S.C.C. received funding from
the European Union’s Horizon 2020 research and innovation programme under the Marie
Skłodowska-Curie grant agreement No 665385.
article_number: e2417025122
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Heloisa
full_name: Chiossi, Heloisa
id: 2BBA502C-F248-11E8-B48F-1D18A9856A87
last_name: Chiossi
orcid: 0009-0004-2973-278X
- first_name: Michele
full_name: Nardin, Michele
id: 30BD0376-F248-11E8-B48F-1D18A9856A87
last_name: Nardin
orcid: 0000-0001-8849-6570
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Chiossi HSC, Nardin M, Tkačik G, Csicsvari JL. Learning reshapes the hippocampal
representation hierarchy. Proceedings of the National Academy of Sciences.
2025;122(11). doi:10.1073/pnas.2417025122
apa: Chiossi, H. S. C., Nardin, M., Tkačik, G., & Csicsvari, J. L. (2025). Learning
reshapes the hippocampal representation hierarchy. Proceedings of the National
Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2417025122
chicago: Chiossi, Heloisa S. C., Michele Nardin, Gašper Tkačik, and Jozsef L Csicsvari.
“Learning Reshapes the Hippocampal Representation Hierarchy.” Proceedings of
the National Academy of Sciences. National Academy of Sciences, 2025. https://doi.org/10.1073/pnas.2417025122.
ieee: H. S. C. Chiossi, M. Nardin, G. Tkačik, and J. L. Csicsvari, “Learning reshapes
the hippocampal representation hierarchy,” Proceedings of the National Academy
of Sciences, vol. 122, no. 11. National Academy of Sciences, 2025.
ista: Chiossi HSC, Nardin M, Tkačik G, Csicsvari JL. 2025. Learning reshapes the
hippocampal representation hierarchy. Proceedings of the National Academy of Sciences.
122(11), e2417025122.
mla: Chiossi, Heloisa S. C., et al. “Learning Reshapes the Hippocampal Representation
Hierarchy.” Proceedings of the National Academy of Sciences, vol. 122,
no. 11, e2417025122, National Academy of Sciences, 2025, doi:10.1073/pnas.2417025122.
short: H.S.C. Chiossi, M. Nardin, G. Tkačik, J.L. Csicsvari, Proceedings of the
National Academy of Sciences 122 (2025).
corr_author: '1'
date_created: 2025-03-25T07:38:35Z
date_published: 2025-03-10T00:00:00Z
date_updated: 2026-05-06T13:12:01Z
day: '10'
ddc:
- '570'
department:
- _id: GaTk
- _id: JoCs
doi: 10.1073/pnas.2417025122
ec_funded: 1
external_id:
isi:
- '001459499500001'
pmid:
- '40063792'
file:
- access_level: open_access
checksum: 1217207c254553154faa065964990988
content_type: application/pdf
creator: dernst
date_created: 2025-03-25T07:49:04Z
date_updated: 2025-03-25T07:49:04Z
file_id: '19454'
file_name: 2025_PNAS_Chiossi.pdf
file_size: 1553502
relation: main_file
success: 1
file_date_updated: 2025-03-25T07:49:04Z
has_accepted_license: '1'
intvolume: ' 122'
isi: 1
issue: '11'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/hchiossi/hpc-hierarchy
record:
- id: '18991'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Learning reshapes the hippocampal representation hierarchy
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 122
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19704'
abstract:
- lang: eng
text: The information-processing capability of the brain’s cellular network depends
on the physical wiring pattern between neurons and their molecular and functional
characteristics. Mapping neurons and resolving their individual synaptic connections
can be achieved by volumetric imaging at nanoscale resolution1,2 with dense cellular
labelling. Light microscopy is uniquely positioned to visualize specific molecules,
but dense, synapse-level circuit reconstruction by light microscopy has been out
of reach, owing to limitations in resolution, contrast and volumetric imaging
capability. Here we describe light-microscopy-based connectomics (LICONN). We
integrated specifically engineered hydrogel embedding and expansion with comprehensive
deep-learning-based segmentation and analysis of connectivity, thereby directly
incorporating molecular information into synapse-level reconstructions of brain
tissue. LICONN will allow synapse-level phenotyping of brain tissue in biological
experiments in a readily adoptable manner.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: ScienComp
- _id: PreCl
- _id: M-Shop
- _id: E-Lib
acknowledgement: 'We thank S. Dorkenwald and P. Li for critical reading of the manuscript,
S. Loomba for discussions and E. Miguel for support with data handling. We acknowledge
support from ISTA’s scientific service units: Imaging and Optics, Lab Support, Scientific
Computing, the preclinical facility, the Miba Machine Shop and the library. We acknowledge
funding from the following sources: Austrian Science Fund (FWF) grant DK W1232 (J.G.D.
and M.R.T.); Austrian Academy of Sciences DOC fellowship 26137 (M.R.T.); Gesellschaft
für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); the European Union’s
Horizon 2020 research and innovation programme and Marie Skłodowska-Curie Actions
Fellowship 665385 (J.L.); and the European Union’s Horizon 2020 research and innovation
programme and European Research Council (ERC) grant 101044865 ‘SecretAutism’ (G.N.).Open
access funding provided by Institute of Science and Technology (IST Austria).'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- first_name: Michał
full_name: Januszewski, Michał
last_name: Januszewski
- first_name: Vitali
full_name: Vistunou, Vitali
id: 7e146587-8972-11ed-ae7b-d7a32ea86a81
last_name: Vistunou
- first_name: Nathalie
full_name: Agudelo Duenas, Nathalie
id: 40E7F008-F248-11E8-B48F-1D18A9856A87
last_name: Agudelo Duenas
- first_name: Jakob
full_name: Vorlaufer, Jakob
id: 937696FA-C996-11E9-8C7C-CF13E6697425
last_name: Vorlaufer
orcid: 0009-0000-7590-3501
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Bárbara
full_name: Oliveira, Bárbara
id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87
last_name: Oliveira
- first_name: Alban
full_name: Cenameri, Alban
id: 9ac8f577-2357-11eb-997a-e566c5550886
last_name: Cenameri
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Viren
full_name: Jain, Viren
last_name: Jain
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Tavakoli M, Lyudchik J, Januszewski M, et al. Light-microscopy-based connectomic
reconstruction of mammalian brain tissue. Nature. 2025;642:398-410. doi:10.1038/s41586-025-08985-1
apa: Tavakoli, M., Lyudchik, J., Januszewski, M., Vistunou, V., Agudelo Duenas,
N., Vorlaufer, J., … Danzl, J. G. (2025). Light-microscopy-based connectomic reconstruction
of mammalian brain tissue. Nature. Springer Nature. https://doi.org/10.1038/s41586-025-08985-1
chicago: Tavakoli, Mojtaba, Julia Lyudchik, Michał Januszewski, Vitali Vistunou,
Nathalie Agudelo Duenas, Jakob Vorlaufer, Christoph M Sommer, et al. “Light-Microscopy-Based
Connectomic Reconstruction of Mammalian Brain Tissue.” Nature. Springer
Nature, 2025. https://doi.org/10.1038/s41586-025-08985-1.
ieee: M. Tavakoli et al., “Light-microscopy-based connectomic reconstruction
of mammalian brain tissue,” Nature, vol. 642. Springer Nature, pp. 398–410,
2025.
ista: Tavakoli M, Lyudchik J, Januszewski M, Vistunou V, Agudelo Duenas N, Vorlaufer
J, Sommer CM, Kreuzinger C, Oliveira B, Cenameri A, Novarino G, Jain V, Danzl
JG. 2025. Light-microscopy-based connectomic reconstruction of mammalian brain
tissue. Nature. 642, 398–410.
mla: Tavakoli, Mojtaba, et al. “Light-Microscopy-Based Connectomic Reconstruction
of Mammalian Brain Tissue.” Nature, vol. 642, Springer Nature, 2025, pp.
398–410, doi:10.1038/s41586-025-08985-1.
short: M. Tavakoli, J. Lyudchik, M. Januszewski, V. Vistunou, N. Agudelo Duenas,
J. Vorlaufer, C.M. Sommer, C. Kreuzinger, B. Oliveira, A. Cenameri, G. Novarino,
V. Jain, J.G. Danzl, Nature 642 (2025) 398–410.
corr_author: '1'
date_created: 2025-05-18T22:02:51Z
date_published: 2025-06-12T00:00:00Z
date_updated: 2026-04-28T13:33:34Z
day: '12'
ddc:
- '570'
department:
- _id: JoDa
- _id: GradSch
- _id: Bio
- _id: GaNo
doi: 10.1038/s41586-025-08985-1
ec_funded: 1
external_id:
isi:
- '001483477000001'
pmid:
- '40335689'
file:
- access_level: open_access
checksum: ebc99d7108e728f46db0a009292675ef
content_type: application/pdf
creator: dernst
date_created: 2025-07-03T06:55:20Z
date_updated: 2025-07-03T06:55:20Z
file_id: '19959'
file_name: 2025_Nature_Tavakoli.pdf
file_size: 133201290
relation: main_file
success: 1
file_date_updated: 2025-07-03T06:55:20Z
has_accepted_license: '1'
intvolume: ' 642'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 398-410
pmid: 1
project:
- _id: 6285a163-2b32-11ec-9570-8e204ca2dba5
grant_number: '26137'
name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
Microscopy
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 34ba8964-11ca-11ed-8bc3-e15864e7e9a6
grant_number: '101044865'
name: Toward an understanding of the brain interstitial system and the extracellular
proteome in health and autism spectrum disorders
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/piecing-together-the-brain-puzzle/
record:
- id: '18677'
relation: earlier_version
status: public
- id: '18697'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Light-microscopy-based connectomic reconstruction of mammalian brain tissue
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 642
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19795'
abstract:
- lang: eng
text: Super-resolution microscopy often entails long acquisition times of minutes
to hours. Since drifts during the acquisition adversely affect data quality, active
sample stabilization is commonly used for some of these techniques to reach their
full potential. Although drifts in the lateral plane can often be corrected after
acquisition, this is not always possible or may come with drawbacks. Therefore,
it is appealing to stabilize sample position in three dimensions (3D) during acquisition.
Various schemes for active sample stabilization have been demonstrated previously,
with some reaching sub-nanometer stability in 3D. Here, we present a scheme for
active drift correction that delivers the nanometer-scale 3D stability demanded
by state-of-the-art super-resolution techniques and is straightforward to implement
compared to previous schemes capable of reaching this level of stabilization precision.
Using a refined algorithm that can handle various types of reference structure,
without sparse signal peaks being mandatory, we stabilized sample position to
∼1 nm in 3D using objective lenses both with high and low numerical aperture.
Our implementation requires only the addition of a simple widefield imaging path
and we provide an open-source control software with graphical user interface to
facilitate easy adoption of the module. Finally, we demonstrate how this has the
potential to enhance data collection for diffraction-limited and super-resolution
imaging techniques using single-molecule localization microscopy and cryo-confocal
imaging as showcases.
acknowledged_ssus:
- _id: M-Shop
- _id: EM-Fac
- _id: LifeSc
acknowledgement: 'We acknowledge expert support by ISTA’s scientific service units,
including the Miba Machine Shop, the Electron Microscopy Facility, and the Lab Support
Facility. This work has been made possible in part by CZI grant DAF2021-234754 and
grant DOI: https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative
DAF, an advised fund of Silicon Valley Community Foundation (funder DOI: https://doi.org/10.13039/100014989)
(F.K.M.S. and J.G.D.). We further gratefully acknowledge funding by the following
sources: Austrian Science Fund (FWF) grant DK W1232 (M.R.T. and J.G.D.); Austrian
Academy of Sciences DOC fellowship 26137 (M.R.T.); Marie Skłodowska-Curie Actions
Fellowship GA no. 665385 under the EU Horizon 2020 program (J.L.); ISTA postdoctoral
fellowship IST fellow (A.W.); and Human Frontier Science Program postdoctoral fellowship
LT000557/2018 (W.J.).'
article_number: '100211'
article_processing_charge: Yes
article_type: original
author:
- first_name: Jakob
full_name: Vorlaufer, Jakob
id: 937696FA-C996-11E9-8C7C-CF13E6697425
last_name: Vorlaufer
orcid: 0009-0000-7590-3501
- first_name: Nikolai
full_name: Semenov, Nikolai
id: e64d39c7-72ef-11ef-b75a-ee3046860d1b
last_name: Semenov
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Manjunath
full_name: Javoor, Manjunath
id: 305ab18b-dc7d-11ea-9b2f-b58195228ea2
last_name: Javoor
orcid: 0000-0003-2311-2112
- first_name: Bettina
full_name: Zens, Bettina
id: 45FD126C-F248-11E8-B48F-1D18A9856A87
last_name: Zens
orcid: 0000-0002-9561-1239
- first_name: Nathalie
full_name: Agudelo Duenas, Nathalie
id: 40E7F008-F248-11E8-B48F-1D18A9856A87
last_name: Agudelo Duenas
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- first_name: Marek
full_name: Suplata, Marek
id: EE8452B8-C26A-11E9-B157-E80CE6697425
last_name: Suplata
- first_name: Wiebke
full_name: Jahr, Wiebke
id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
last_name: Jahr
orcid: 0000-0003-0201-2315
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- first_name: Andreas
full_name: Wartak, Andreas
id: 60aaa06c-3de5-11eb-9e53-baa88e955dcb
last_name: Wartak
- first_name: Florian Km
full_name: Schur, Florian Km
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Vorlaufer J, Semenov N, Kreuzinger C, et al. Image-based 3D active sample stabilization
on the nanometer scale for optical microscopy. Biophysical Reports. 2025;5(2).
doi:10.1016/j.bpr.2025.100211
apa: Vorlaufer, J., Semenov, N., Kreuzinger, C., Javoor, M., Zens, B., Agudelo Duenas,
N., … Danzl, J. G. (2025). Image-based 3D active sample stabilization on the nanometer
scale for optical microscopy. Biophysical Reports. Elsevier. https://doi.org/10.1016/j.bpr.2025.100211
chicago: Vorlaufer, Jakob, Nikolai Semenov, Caroline Kreuzinger, Manjunath Javoor,
Bettina Zens, Nathalie Agudelo Duenas, Mojtaba Tavakoli, et al. “Image-Based 3D
Active Sample Stabilization on the Nanometer Scale for Optical Microscopy.” Biophysical
Reports. Elsevier, 2025. https://doi.org/10.1016/j.bpr.2025.100211.
ieee: J. Vorlaufer et al., “Image-based 3D active sample stabilization on
the nanometer scale for optical microscopy,” Biophysical Reports, vol.
5, no. 2. Elsevier, 2025.
ista: Vorlaufer J, Semenov N, Kreuzinger C, Javoor M, Zens B, Agudelo Duenas N,
Tavakoli M, Suplata M, Jahr W, Lyudchik J, Wartak A, Schur FK, Danzl JG. 2025.
Image-based 3D active sample stabilization on the nanometer scale for optical
microscopy. Biophysical Reports. 5(2), 100211.
mla: Vorlaufer, Jakob, et al. “Image-Based 3D Active Sample Stabilization on the
Nanometer Scale for Optical Microscopy.” Biophysical Reports, vol. 5, no.
2, 100211, Elsevier, 2025, doi:10.1016/j.bpr.2025.100211.
short: J. Vorlaufer, N. Semenov, C. Kreuzinger, M. Javoor, B. Zens, N. Agudelo Duenas,
M. Tavakoli, M. Suplata, W. Jahr, J. Lyudchik, A. Wartak, F.K. Schur, J.G. Danzl,
Biophysical Reports 5 (2025).
corr_author: '1'
date_created: 2025-06-08T22:01:22Z
date_published: 2025-06-11T00:00:00Z
date_updated: 2026-04-07T11:48:07Z
day: '11'
ddc:
- '570'
department:
- _id: JoDa
- _id: GradSch
- _id: FlSc
- _id: EM-Fac
doi: 10.1016/j.bpr.2025.100211
ec_funded: 1
file:
- access_level: open_access
checksum: 4018c833f25a3ad3b57e3577fed70334
content_type: application/pdf
creator: dernst
date_created: 2025-06-10T07:24:46Z
date_updated: 2025-06-10T07:24:46Z
file_id: '19802'
file_name: 2025_BiophysicalReports_Vorlaufer.pdf
file_size: 7238179
relation: main_file
success: 1
file_date_updated: 2025-06-10T07:24:46Z
has_accepted_license: '1'
intvolume: ' 5'
issue: '2'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 62909c6f-2b32-11ec-9570-e1476aab5308
grant_number: CZI01
name: CryoMinflux-guided in-situ molecular census and structure determination
- _id: 6285a163-2b32-11ec-9570-8e204ca2dba5
grant_number: '26137'
name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
Microscopy
- _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
- _id: 2668BFA0-B435-11E9-9278-68D0E5697425
grant_number: LT00057
name: High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration
publication: Biophysical Reports
publication_identifier:
eissn:
- 2667-0747
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '20206'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Image-based 3D active sample stabilization on the nanometer scale for optical
microscopy
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20330'
abstract:
- lang: eng
text: The evolution of sexual dimorphism (the difference in average trait values
between females and males, SD), is often thought to be constrained by shared genetic
architecture between the sexes. Indeed, it is commonly expected that SD should
negatively correlate with the intersex correlation (the genetic correlation between
effects of segregating variants in females and males, r fm), either because (1)
traits with ancestrally low r fm are less constrained in their ability to respond
to sex-specific selection and thus evolve to be more dimorphic, or because (2)
sex-specific selection, driving sexual dimorphism evolution, also acts to reduce
r fm. Despite the intuitive appeal and prominence of these ideas, their generality
and the conditions in which they hold remain unclear. Here, we develop models
incorporating sex-specific stabilizing selection, mutation and genetic drift to
examine the relationship between r fm and SD. We show that the two commonly-discussed
mechanisms with the potential to generate a negative correlation between SD and
r fm could just as easily generate a positive association, since the standard
line of reasoning hinges on a hidden assumption that sex-specific adaptation more
frequently favors increased dimorphism than reduced dimorphism. Our results provide,
to our knowledge, the first mechanistic framework for understanding the conditions
under which a correlation between r fm and SD may arise and offer a compelling
explanation for inconsistent empirical evidence. We also make the intriguing observation
that—even when selection between the two sexes is identical—drift generates nonzero
SD. We quantify this effect and discuss its significance.
acknowledgement: We thank Tim Connallon for useful discussions and correspondence,
Himani Sachdeva and Nick Barton for comments on the manuscript and the Scientific
Computing unit at ISTA for technical support. GP is the recipient of a DOC Fellowship
of the Austrian Academy of Sciences at the Institute of Science and Technology Austria
(DOC 25817) and received funding from the European Union’s Horizon 2020 research
and innovation program under the Marie Skłodowska-Curie Grant (agreement no. 665385).
LH received funding from the European Research Council, under the HaplotypeStructure
Grant (grant no. 101055327) to Nick Barton.
article_number: iyaf175
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Gemma
full_name: Puixeu Sala, Gemma
id: 33AB266C-F248-11E8-B48F-1D18A9856A87
last_name: Puixeu Sala
orcid: 0000-0001-8330-1754
- first_name: Laura
full_name: Hayward, Laura
id: fc885ee5-24bf-11eb-ad7b-bcc5104c0c1b
last_name: Hayward
citation:
ama: 'Puixeu Sala G, Hayward L. The relationship between sexual dimorphism and intersex
correlation: Do models support intuition? Genetics. 2025;231(3). doi:10.1093/genetics/iyaf175'
apa: 'Puixeu Sala, G., & Hayward, L. (2025). The relationship between sexual
dimorphism and intersex correlation: Do models support intuition? Genetics.
Oxford University Press. https://doi.org/10.1093/genetics/iyaf175'
chicago: 'Puixeu Sala, Gemma, and Laura Hayward. “The Relationship between Sexual
Dimorphism and Intersex Correlation: Do Models Support Intuition?” Genetics.
Oxford University Press, 2025. https://doi.org/10.1093/genetics/iyaf175.'
ieee: 'G. Puixeu Sala and L. Hayward, “The relationship between sexual dimorphism
and intersex correlation: Do models support intuition?,” Genetics, vol.
231, no. 3. Oxford University Press, 2025.'
ista: 'Puixeu Sala G, Hayward L. 2025. The relationship between sexual dimorphism
and intersex correlation: Do models support intuition? Genetics. 231(3), iyaf175.'
mla: 'Puixeu Sala, Gemma, and Laura Hayward. “The Relationship between Sexual Dimorphism
and Intersex Correlation: Do Models Support Intuition?” Genetics, vol.
231, no. 3, iyaf175, Oxford University Press, 2025, doi:10.1093/genetics/iyaf175.'
short: G. Puixeu Sala, L. Hayward, Genetics 231 (2025).
corr_author: '1'
date_created: 2025-09-10T05:48:04Z
date_published: 2025-11-01T00:00:00Z
date_updated: 2026-01-05T13:04:07Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1093/genetics/iyaf175
ec_funded: 1
external_id:
isi:
- '001598595000001'
file:
- access_level: open_access
checksum: bbb73bbf8617812d4d8db4af92be9538
content_type: application/pdf
creator: dernst
date_created: 2026-01-05T13:03:18Z
date_updated: 2026-01-05T13:03:18Z
file_id: '20946'
file_name: 2025_Genetics_Puixeu.pdf
file_size: 1550562
relation: main_file
success: 1
file_date_updated: 2026-01-05T13:03:18Z
has_accepted_license: '1'
intvolume: ' 231'
isi: 1
issue: '3'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 9B9DFC9E-BA93-11EA-9121-9846C619BF3A
grant_number: '25817'
name: 'Sexual conflict: resolution, constraints and biomedical implications'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication: Genetics
publication_identifier:
issn:
- 1943-2631
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The relationship between sexual dimorphism and intersex correlation: Do models
support intuition?'
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: 231
year: '2025'
...
---
OA_place: publisher
_id: '20371'
abstract:
- lang: eng
text: "Quantum mechanics reveals a world that defies classical determinism, where
uncertainty, superposition, and fluctuations are fundamental aspects. Engineering
devices that harness these quantum features requires not only precision, but also
a deep understanding of how they interact with their surrounding environment.
Superconducting circuits, which exploit\r\nmacroscopic quantum coherence in low-loss
superconducting materials, provide a scalable platform for implementing such systems.
Among the critical elements in these circuits, superinductors—high-impedance,
dissipation-free inductive components—play a central role by suppressing charge
fluctuations. They allow quantum states to be delocalized in phase space, protect
qubits from environmental noise, and facilitate access to phenomena such as dual
Josephson physics and ultra-strong coupling regimes. \r\nThis thesis explores
two complementary implementations of high-impedance circuits: geometric superinductors,
demonstrating that high impedance can be achieved beyond kinetic inductance,\r\nand
Josephson junction chains, used to investigate both microwave mode properties
and DC transport across the superconductor-to-insulator transition. \r\nPart I
addresses geometric superinductors. Contrary to the common belief that high-impedance
superconducting circuits require kinetic inductance, we demonstrate that purely
geometric designs can achieve characteristic impedance exceeding the resistance
quantum. By exploiting mutual coupling between adjacent turns, coil-based inductors
achieve enhanced self-inductance, creating a reliable platform for qubits and
resonators. Modeling, simulation, fabrication, and\r\ncharacterization confirm
that these elements behave as superinductor. With low loss, high linearity, and
minimal stray capacitance, these elements are reproducible, free of uncontrolled
tunneling events, and capable of strong magnetic coupling. This establishes geometric
superinductors as robust, single-wave-function superconducting devices suitable
for hardware protected qubits and hybrid systems.\r\nPart II presents classical
numerical simulations of a Quantum Phase Slip circuit to study dual Shapiro steps.
The circuit consists of an ideal Quantum Phase Slip element embedded in a resistive-inductive
environment with a parasitic capacitance.\r\nPart III extends the investigation
of high characteristic-impedance circuit elements to one-dimensional Josephson
junction chains, which act as a quantum simulator for many-body physics and the
superconductor–insulator transition. Different devices are realized on both sides
of the DC phase transition, showing either a supercurrent branch or Coulomb blockade
at zero bias. The effect of the crossover on microwave modes, however, remains
insufficiently investigated. Studying these modes provides insight into the interplay
between disorder and phase-slip events. Small differences in circuit component
sizes determine which side of the transition a device falls on, making these results
relevant not only for fundamental understanding but also for the design of quantum
devices, emphasizing the crucial role of the\r\nelectromagnetic environment in
stabilizing and controlling fragile quantum states. \r\nTogether, these results
illustrate how carefully engineered high characteristic-impedance elements provide
a link between macroscopic circuits and the inherently uncertain quantum world,
enabling experiments that probe, control, and ultimately exploit quantum fluctuations
for applications in quantum information, metrology, solid state physics and beyond.\r\n\r\n"
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
acknowledgement: "I also gratefully acknowledge the generous support of the NOMIS
Foundation Project \"Protected\r\nStates of Quantum Matter\" and the grant from
the Beyond-C consortium. Their funding\r\nmade this research possible and gave me
the freedom to ask ambitious questions, and try to\r\nanswer them.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Andrea
full_name: Trioni, Andrea
id: 42F71B44-F248-11E8-B48F-1D18A9856A87
last_name: Trioni
citation:
ama: 'Trioni A. High-impedance quantum circuits for mesoscopic physics : Geometric
superinductors and insulating Josephson Chains. 2025. doi:10.15479/AT-ISTA-20371'
apa: 'Trioni, A. (2025). High-impedance quantum circuits for mesoscopic physics :
Geometric superinductors and insulating Josephson Chains. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT-ISTA-20371'
chicago: 'Trioni, Andrea. “High-Impedance Quantum Circuits for Mesoscopic Physics :
Geometric Superinductors and Insulating Josephson Chains.” Institute of Science
and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20371.'
ieee: 'A. Trioni, “High-impedance quantum circuits for mesoscopic physics : Geometric
superinductors and insulating Josephson Chains,” Institute of Science and Technology
Austria, 2025.'
ista: 'Trioni A. 2025. High-impedance quantum circuits for mesoscopic physics :
Geometric superinductors and insulating Josephson Chains. Institute of Science
and Technology Austria.'
mla: 'Trioni, Andrea. High-Impedance Quantum Circuits for Mesoscopic Physics :
Geometric Superinductors and Insulating Josephson Chains. Institute of Science
and Technology Austria, 2025, doi:10.15479/AT-ISTA-20371.'
short: 'A. Trioni, High-Impedance Quantum Circuits for Mesoscopic Physics : Geometric
Superinductors and Insulating Josephson Chains, Institute of Science and Technology
Austria, 2025.'
corr_author: '1'
date_created: 2025-09-23T09:57:57Z
date_published: 2025-09-23T00:00:00Z
date_updated: 2026-04-15T06:43:02Z
day: '23'
ddc:
- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoFi
doi: 10.15479/AT-ISTA-20371
ec_funded: 1
file:
- access_level: open_access
checksum: 6fb925648dfa5f4384814c552ee2f099
content_type: application/pdf
creator: atrioni
date_created: 2025-09-25T07:15:05Z
date_updated: 2025-09-25T14:25:31Z
file_id: '20392'
file_name: 2025_Trioni_Andrea_Thesis.pdf
file_size: 22351676
relation: main_file
- access_level: closed
checksum: 619dc614bdfbf3999b76ac8890b2cebd
content_type: application/x-zip-compressed
creator: atrioni
date_created: 2025-09-25T14:45:43Z
date_updated: 2025-09-26T07:20:48Z
file_id: '20396'
file_name: 2025_Trioni_Andrea_Thesis.zip
file_size: 60079009
relation: source_file
file_date_updated: 2025-09-26T07:20:48Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '202'
project:
- _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2
name: Protected states of quantum matter
- _id: bdb108fd-d553-11ed-ba76-83dc74a9864f
grant_number: F07105
name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration
of Superconducting Quantum Circuits
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
isbn:
- 978-3-99078-067-1
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8755'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
title: 'High-impedance quantum circuits for mesoscopic physics : Geometric superinductors
and insulating Josephson Chains'
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_place: publisher
_id: '20485'
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
acknowledgement: "I would also like to acknowledge the funding that I received from
the European Union’s\r\nHorizon 2020 research and Innovation programme under the
Marie Sklodowska-Curie\r\nGrant Agreement No. 665385. This work would not have been
possible without the contribution and support of people\r\nbehind the scientific
service units at ISTA: the Life Science Facility (LSF), Imaging and\r\nOptics Facility
(IOF), the Bioinformatics Unit, Protein Services Unit and\r\nElectrophysiology Unit.
I would also like to recognize the work of people at the Vienna\r\nBiocenter (VBC)
Mass Spectrometry Facility, particularly Markus Hartl and WeiQiang\r\nChen. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michaela
full_name: Misova, Michaela
id: 495A3C32-F248-11E8-B48F-1D18A9856A87
last_name: Misova
orcid: 0000-0003-2427-6856
citation:
ama: Misova M. Dissecting gap junction biology using the C. elegans nervous system.
2025. doi:10.15479/AT-ISTA-20485
apa: Misova, M. (2025). Dissecting gap junction biology using the C. elegans
nervous system. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20485
chicago: Misova, Michaela. “Dissecting Gap Junction Biology Using the C. Elegans
Nervous System.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20485.
ieee: M. Misova, “Dissecting gap junction biology using the C. elegans nervous system,”
Institute of Science and Technology Austria, 2025.
ista: Misova M. 2025. Dissecting gap junction biology using the C. elegans nervous
system. Institute of Science and Technology Austria.
mla: Misova, Michaela. Dissecting Gap Junction Biology Using the C. Elegans Nervous
System. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20485.
short: M. Misova, Dissecting Gap Junction Biology Using the C. Elegans Nervous System,
Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-10-17T16:15:09Z
date_published: 2025-10-23T00:00:00Z
date_updated: 2026-04-07T11:54:00Z
day: '23'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MaDe
doi: 10.15479/AT-ISTA-20485
ec_funded: 1
file:
- access_level: closed
checksum: e042ea314e7e13fce76c6c95e126779a
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: mmisova
date_created: 2025-10-23T08:22:35Z
date_updated: 2025-11-06T11:08:06Z
file_id: '20518'
file_name: 2025-Misova-Michaela-Thesis.docx
file_size: 75070995
relation: source_file
- access_level: closed
checksum: fcd8973d6a025256eb0eb1a82c02172c
content_type: application/pdf
creator: mmisova
date_created: 2025-10-23T08:21:21Z
date_updated: 2025-10-23T08:21:21Z
embargo: 2026-10-23
embargo_to: open_access
file_id: '20519'
file_name: 2025-Misova-Michaela-Thesis.pdf
file_size: 10974630
relation: main_file
file_date_updated: 2025-11-06T11:08:06Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa_version: Published Version
page: '155'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
isbn:
- 978-3-99078-068-8
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
title: Dissecting gap junction biology using the C. elegans nervous system
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: '2025'
...
---
OA_place: publisher
OA_type: diamond
_id: '20668'
abstract:
- lang: eng
text: "The Message Layer Security (MLS) protocol has recently been standardized
by the IETF. MLS is a scalable secure group messaging protocol expected to run
more efficiently compared to the Signal protocol at scale, while offering a similar
level of strong security. Even though MLS has undergone extensive examination
by researchers, the majority of the works have focused on confidentiality.\r\n\r\nIn
this work, we focus on the authenticity of the application messages exchanged
in MLS. Currently, MLS authenticates every application message with an EdDSA signature
and while manageable, the overhead is greatly amplified in the post-quantum setting
as the NIST-recommended Dilithium signature results in a 40x increase in size.
We view this as an invitation to explore new authentication modes that can be
used instead. We start by taking a systematic view on how application messages
are authenticated in MLS and categorize authenticity into four different security
notions. We then propose several authentication modes, offering a range of different
efficiency and security profiles. For instance, in one of our modes, COSMOS++,
we replace signatures with one-time tokens and a MAC tag, offering roughly a 75x
savings in the post-quantum communication overhead. While this comes at the cost
of weakening security compared to the authentication mode used by MLS, the lower
communication overhead seems to make it a worthwhile trade-off with security."
acknowledgement: This research was partially supported by JST CREST JPMJCR22M1, Japan
and funded by the European Union’s Horizon 2020 research and innovation programme
under the Marie Skłodowska-Curie Grant Agreement No.665385.
article_processing_charge: No
author:
- first_name: Keitaro
full_name: Hashimoto, Keitaro
last_name: Hashimoto
- first_name: Shuichi
full_name: Katsumata, Shuichi
last_name: Katsumata
- first_name: Guillermo
full_name: Pascual Perez, Guillermo
id: 2D7ABD02-F248-11E8-B48F-1D18A9856A87
last_name: Pascual Perez
orcid: 0000-0001-8630-415X
citation:
ama: 'Hashimoto K, Katsumata S, Pascual Perez G. Exploring how to authenticate application
messages in MLS: More efficient, post-quantum, and anonymous blocklistable. In:
34th Usenix Security Symposium. Usenix Association; 2025:6699-6716.'
apa: 'Hashimoto, K., Katsumata, S., & Pascual Perez, G. (2025). Exploring how
to authenticate application messages in MLS: More efficient, post-quantum, and
anonymous blocklistable. In 34th Usenix Security Symposium (pp. 6699–6716).
Seattle, WA, USA: Usenix Association.'
chicago: 'Hashimoto, Keitaro, Shuichi Katsumata, and Guillermo Pascual Perez. “Exploring
How to Authenticate Application Messages in MLS: More Efficient, Post-Quantum,
and Anonymous Blocklistable.” In 34th Usenix Security Symposium, 6699–6716.
Usenix Association, 2025.'
ieee: 'K. Hashimoto, S. Katsumata, and G. Pascual Perez, “Exploring how to authenticate
application messages in MLS: More efficient, post-quantum, and anonymous blocklistable,”
in 34th Usenix Security Symposium, Seattle, WA, USA, 2025, pp. 6699–6716.'
ista: 'Hashimoto K, Katsumata S, Pascual Perez G. 2025. Exploring how to authenticate
application messages in MLS: More efficient, post-quantum, and anonymous blocklistable.
34th Usenix Security Symposium. USENIX: Security Symposium, 6699–6716.'
mla: 'Hashimoto, Keitaro, et al. “Exploring How to Authenticate Application Messages
in MLS: More Efficient, Post-Quantum, and Anonymous Blocklistable.” 34th Usenix
Security Symposium, Usenix Association, 2025, pp. 6699–716.'
short: K. Hashimoto, S. Katsumata, G. Pascual Perez, in:, 34th Usenix Security Symposium,
Usenix Association, 2025, pp. 6699–6716.
conference:
end_date: 2025-08-15
location: Seattle, WA, USA
name: 'USENIX: Security Symposium'
start_date: 2025-08-13
corr_author: '1'
cryptoeprintid: 1
das_tickbox: '1'
date_created: 2025-11-23T23:01:40Z
date_published: 2025-01-01T00:00:00Z
date_updated: 2026-07-07T06:02:03Z
day: '01'
ddc:
- '000'
ec_funded: 1
external_id:
cryptoeprintid:
- 2025/426
file:
- access_level: open_access
checksum: fcfe8851aeb751af98c0b1335a0ef149
content_type: application/pdf
creator: dernst
date_created: 2025-11-24T07:44:08Z
date_updated: 2025-11-24T07:44:08Z
file_id: '20671'
file_name: 2025_Usenix_Hashimoto.pdf
file_size: 710733
relation: main_file
success: 1
file_date_updated: 2025-11-24T07:44:08Z
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2025/426
month: '01'
oa: 1
oa_version: Published Version
page: 6699-6716
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: 34th Usenix Security Symposium
publication_identifier:
isbn:
- '9781939133526'
publication_status: published
publisher: Usenix Association
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Exploring how to authenticate application messages in MLS: More efficient,
post-quantum, and anonymous blocklistable'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_embargo: '6'
OA_place: publisher
_id: '19745'
abstract:
- lang: eng
text: "Cell migration is a crucial process in animal development and maintenance.
It is incredibly\r\nheterogeneous, with different cell types utilizing fundamentally
distinct migration strategies.\r\nThe strategies also depend on the cellular microenvironment,
where cells can switch between\r\nmigration modes as they encounter new environmental
cues. In this thesis, we investigated\r\nhow dendritic cells adapt their migration
strategy when encountering geometrically,\r\nmechanically and chemically distinct
environments.\r\nWhen dendritic cells are embedded in a homogeneous fibrous network,
they migrate in a fast\r\nand directional amoeboid manner. In this migration strategy,
extracellular proteolysis and\r\nintegrin-mediated adhesions are dispensable.
Instead, the cells use topography of the\r\nenvironment to propel their cell body
forward. To migrate efficiently in the maze of different\r\npore sizes, they position
the nucleus ahead of the microtubule organizing center (MTOC) and\r\nuse it to
gauge the pores to identify the path of least resistance. Our aim was to identify\r\nwhether
dendritic cells adapt their migration strategy when encountering asymmetrical\r\ntransitions
into much denser environments with limited choice of large pores. In such invasive\r\ntransitions
it is unclear if the cells can cross tight pores without the use of adhesions
and\r\nextracellular proteolysis and whether they maintain the nucleus in the
cell front.\r\nUsing various cell migration assays such as fibrous 3D collagen
gels, geometrically defined\r\nmicrochannels with constrictions and simplistic
under agarose migration assay, we provide\r\na comprehensive characterization
of invasive migration of dendritic cells. We show that\r\nduring invasion the
cells stall and stretch, reflecting the difficulty to translocate the bulky cell\r\nbody
into the dense environment. In collagen gels, we show that dendritic cells can
invade\r\nwithout proteolysis and adhesions. Instead, they utilize contractility,
which can lead to largescale collagen compressions. During invasion, the nucleus
stalls at tight constrictions, leading\r\nto a transient organelle reorientation.
To resolve the stalling, upregulated rear contractility is\r\nrequired. This contractile
force is simultaneously necessary for reverting the nucleus back to\r\nthe cell
front after invasion and maintaining this positioning during permissive migration.\r\nA
functional role of the reorientation was uncovered in the first collaboration
project.\r\nA prominent central actin pool was identified around the MTOC, especially
pronounced in\r\ndense and compressive environments. The actin pool was shown
to generate pushing forces\r\nto dilate the space for cell translocation. These
forces are only necessary in non-permissive\r\nenvironments, where the nucleus
reorients to the cell rear, allowing the actin pool to\r\ngenerate space. In permissive
environments where space generation is dispensable, the\r\nMTOC is located behind
the nucleus and the actin cloud has reduced intensity, allowing more\r\nactin
to be incorporated into the lamellipodium, speeding up migration.\r\nIn the second
collaboration project, we investigated the effects of distinct chemical\r\nenvironments
on dendritic cell migration. The strikingly persistent migration of these cells\r\nwas
explained by their ability to modulate and even self-generate chemokine gradients.
This\r\nallows the cells to migrate faster and more persistent in uniform chemokine
fields compared\r\nto imposed chemokine gradients. The chemokine receptor CCR7
was identified as a crucial\r\nplayer in this process, both sensing the signal
and internalizing the chemokine to create a sink."
acknowledgement: "This project has received funding from the Austrian Science Fund
(FWF) via the doctorate\r\ncollege DK NanoCell and from the European Union’s Horizon
2020 research and innovation\r\nprogramme under the Marie Skłodowska-Curie Grant
Agreement No. 665385.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Nikola
full_name: Canigova, Nikola
id: 3795523E-F248-11E8-B48F-1D18A9856A87
last_name: Canigova
orcid: 0000-0002-8518-5926
citation:
ama: Canigova N. Adaptive strategies of dendritic cell migration in response to
environmental cues. 2025. doi:10.15479/AT-ISTA-19745
apa: Canigova, N. (2025). Adaptive strategies of dendritic cell migration in
response to environmental cues. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT-ISTA-19745
chicago: Canigova, Nikola. “Adaptive Strategies of Dendritic Cell Migration in Response
to Environmental Cues.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19745.
ieee: N. Canigova, “Adaptive strategies of dendritic cell migration in response
to environmental cues,” Institute of Science and Technology Austria, 2025.
ista: Canigova N. 2025. Adaptive strategies of dendritic cell migration in response
to environmental cues. Institute of Science and Technology Austria.
mla: Canigova, Nikola. Adaptive Strategies of Dendritic Cell Migration in Response
to Environmental Cues. Institute of Science and Technology Austria, 2025,
doi:10.15479/AT-ISTA-19745.
short: N. Canigova, Adaptive Strategies of Dendritic Cell Migration in Response
to Environmental Cues, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-05-26T08:49:00Z
date_published: 2025-05-27T00:00:00Z
date_updated: 2026-06-18T17:34:48Z
day: '27'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: MiSi
- _id: GradSch
doi: 10.15479/AT-ISTA-19745
ec_funded: 1
file:
- access_level: closed
checksum: 1a2d1525d19347fbb879ef57c02951bf
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: cchlebak
date_created: 2025-05-28T07:38:17Z
date_updated: 2025-11-27T23:30:02Z
embargo_to: open_access
file_id: '19748'
file_name: NikolaCanigova_Thesis_final.docx
file_size: 103879193
relation: source_file
- access_level: open_access
checksum: c1d8f9a40a8e19fcf895373f4b773a46
content_type: application/pdf
creator: cchlebak
date_created: 2025-05-28T07:39:53Z
date_updated: 2025-11-27T23:30:02Z
embargo: 2025-11-27
file_id: '19749'
file_name: NikolaCanigova_Thesis_final_PDFA2a_fixed.pdf
file_size: 194530600
relation: main_file
file_date_updated: 2025-11-27T23:30:02Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '133'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 265E2996-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W01250-B20
name: Nano-Analytics of Cellular Systems
publication_identifier:
isbn:
- 978-3-99078-058-9
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '14274'
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: Adaptive strategies of dendritic cell migration in response to environmental
cues
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_place: publisher
_id: '19271'
abstract:
- lang: eng
text: "The medial habenula (MHb) is implicated in regulating emotional responses\r\nto
aversive events. Studies in zebrafish have identified a remarkable morphological\r\nleft-right
asymmetry in the dorsal habenula (zebrafish equivalent of mammalian\r\nMHb)-to-interpeduncular
nucleus (IPN) pathway and its left-side specific role in\r\nmodulating fear responses.
However, there is little evidence for structural or\r\nfunctional lateralization
in the mammalian MHb-IPN pathway.\r\nHere, I investigated the synaptic properties
of the left and right MHb\r\nafferents to the IPN in mice and addressed whether
these synaptic connections\r\nselectively influence the expression of conditioned
fear in mice. My findings reveal\r\nthat each individual IPN neuron receives inputs
from both left and right MHb.\r\nElectrophysiological recordings from the same
postsynaptic IPN neurons\r\ndemonstrate that the left MHb-originating synapses
exhibit lower release\r\nprobability and higher \U0001D6FE-aminobutyric acid type
B receptor (GABABR)-mediated\r\npotentiation compared to the right MHb-originating
synapses. Interestingly,\r\nchemogenetic inhibition of cholinergic neurons in
the left but not the right MHb\r\nsignificantly attenuated cue-dependent fear
recall. Furthermore, conditional\r\ndeletion of GABABR in the left MHb interfered
with the recall of cued fear memory,\r\nwhereas that in the right MHb neurons
spared fear memory expression.\r\nCollectively, I demonstrate a functional asymmetry
of the MHb in mice,\r\nrevealing a predominant role for GABABR-mediated signaling
in the left MHb-IPN\r\npathway in the modulation of fear memories. These findings
suggest that\r\nlateralized pathways could represent a fundamental principle in
the neural\r\nregulation of emotion across species."
acknowledged_ssus:
- _id: PreCl
- _id: M-Shop
acknowledgement: "I would like to thank the European Research Council and European
Commission, under the European Union’s Horizon 2020 research and innovation program
(ERC grant agreement no. 694539 to Ryuichi Shigemoto and the Marie Skłodowska-Curie
grant agreement no. 665385 to Cihan Önal), and the Austrian Neuroscience Association
for providing financial support and opportunities, which were important in allowing
me to present my work. I also wish to thank the\r\nPreclinical Facility, especially
Michael Schunn, for always welcoming me from my earliest days as an intern. My gratitude
goes as well to the Miba Machine Shop, in particular Todor Asenov, Astrit Arslani,
and Thomas Menner, whose technical expertise often saved the day."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Hüseyin C
full_name: Önal, Hüseyin C
id: 4659D740-F248-11E8-B48F-1D18A9856A87
last_name: Önal
orcid: 0000-0002-2771-2011
citation:
ama: Önal C. Asymmetrical modulation of fear expression via GABAB receptors in the
mouse medial habenula. 2025. doi:10.15479/AT-ISTA-19271
apa: Önal, C. (2025). Asymmetrical modulation of fear expression via GABAB receptors
in the mouse medial habenula. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT-ISTA-19271
chicago: Önal, Cihan. “Asymmetrical Modulation of Fear Expression via GABAB Receptors
in the Mouse Medial Habenula.” Institute of Science and Technology Austria, 2025.
https://doi.org/10.15479/AT-ISTA-19271.
ieee: C. Önal, “Asymmetrical modulation of fear expression via GABAB receptors in
the mouse medial habenula,” Institute of Science and Technology Austria, 2025.
ista: Önal C. 2025. Asymmetrical modulation of fear expression via GABAB receptors
in the mouse medial habenula. Institute of Science and Technology Austria.
mla: Önal, Cihan. Asymmetrical Modulation of Fear Expression via GABAB Receptors
in the Mouse Medial Habenula. Institute of Science and Technology Austria,
2025, doi:10.15479/AT-ISTA-19271.
short: C. Önal, Asymmetrical Modulation of Fear Expression via GABAB Receptors in
the Mouse Medial Habenula, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-02-28T14:15:53Z
date_published: 2025-03-04T00:00:00Z
date_updated: 2026-04-07T12:40:42Z
day: '04'
ddc:
- '570'
- '571'
- '573'
- '599'
degree_awarded: PhD
department:
- _id: GradSch
- _id: RySh
doi: 10.15479/AT-ISTA-19271
ec_funded: 1
file:
- access_level: closed
checksum: c1a4d75a7471de9f954697b06cd18d28
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: hoenal
date_created: 2025-02-28T13:57:01Z
date_updated: 2026-02-01T23:30:02Z
embargo_to: open_access
file_id: '19272'
file_name: Cihan_Onal_Thesis_Final.docx
file_size: 25869143
relation: source_file
- access_level: open_access
checksum: de4e62147ab9f04098dc8cd898c630da
content_type: application/pdf
creator: hoenal
date_created: 2025-02-28T13:57:04Z
date_updated: 2026-02-01T23:30:02Z
embargo: 2026-02-01
file_id: '19273'
file_name: Cihan_Onal_Thesis_Final_pdfa.pdf
file_size: 12077596
relation: main_file
file_date_updated: 2026-02-01T23:30:02Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
eissn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9437'
relation: part_of_dissertation
status: public
- id: '15084'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
title: Asymmetrical modulation of fear expression via GABAB receptors in the mouse
medial habenula
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_place: publisher
_id: '19906'
abstract:
- lang: eng
text: "Flows of ordinary fluids such as water or air transition from laminar to
turbulent\r\nmotion as the velocity increases. This simple dependence of the flow
state\r\nsolely on inertia, does not apply to more complex substances such as
polymericand biofluids which commonly have elastic as well as viscous properties.
Here\r\nvarious different instabilities and turbulent states can arise at low
and even\r\nvanishing inertia, while high inertia turbulence counterintuitively
is suppressed\r\nand its drag strongly reduced. We here show in experiments of
a viscoelastic\r\nmodel fluid that the phenomena observed at low and high inertia
have a\r\ncommon origin and that the same dynamical state, elasto-inertial turbulence,\r\npersists
across four orders of magnitude in Reynolds number, ranging from\r\nvery low inertia,
all the way to high inertia Maximum drag reduction (MDR)\r\nasymptote. We also
explore the transitions from Newtonian turbulence to\r\nMDR, and specific cases
of flow at high polymer concentrations, exploring the\r\nrelationship between
flow at these wide range of control parameters.\r\n"
acknowledged_ssus:
- _id: M-Shop
acknowledgement: "This work was partially funded by the European Union’s Horizon 2020
research\r\nand innovation programme under the Marie Skłodowska-Curie grant agreement\r\nNo.
665385."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Sarath S
full_name: Suresh, Sarath S
id: 3D126CC4-F248-11E8-B48F-1D18A9856A87
last_name: Suresh
citation:
ama: 'Suresh SS. Turbulence in polymeric flows : A characterisation of elasto-inertial
turbulence and the maximum drag reduction asymptote. 2025. doi:10.15479/AT-ISTA-19906'
apa: 'Suresh, S. S. (2025). Turbulence in polymeric flows : A characterisation
of elasto-inertial turbulence and the maximum drag reduction asymptote. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19906'
chicago: 'Suresh, Sarath S. “Turbulence in Polymeric Flows : A Characterisation
of Elasto-Inertial Turbulence and the Maximum Drag Reduction Asymptote.” Institute
of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19906.'
ieee: 'S. S. Suresh, “Turbulence in polymeric flows : A characterisation of elasto-inertial
turbulence and the maximum drag reduction asymptote,” Institute of Science and
Technology Austria, 2025.'
ista: 'Suresh SS. 2025. Turbulence in polymeric flows : A characterisation of elasto-inertial
turbulence and the maximum drag reduction asymptote. Institute of Science and
Technology Austria.'
mla: 'Suresh, Sarath S. Turbulence in Polymeric Flows : A Characterisation of
Elasto-Inertial Turbulence and the Maximum Drag Reduction Asymptote. Institute
of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19906.'
short: 'S.S. Suresh, Turbulence in Polymeric Flows : A Characterisation of Elasto-Inertial
Turbulence and the Maximum Drag Reduction Asymptote, Institute of Science and
Technology Austria, 2025.'
corr_author: '1'
date_created: 2025-06-26T08:39:08Z
date_published: 2025-06-26T00:00:00Z
date_updated: 2026-04-07T12:39:19Z
day: '26'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: BjHo
doi: 10.15479/AT-ISTA-19906
ec_funded: 1
file:
- access_level: open_access
checksum: 302a07605a9e64ac247c2036d5f5b1cd
content_type: application/pdf
creator: cchlebak
date_created: 2025-06-26T08:40:53Z
date_updated: 2025-12-27T23:30:02Z
embargo: 2025-12-27
file_id: '19907'
file_name: Thesis_v9_PDFA2b.pdf
file_size: 6504571
relation: main_file
- access_level: closed
checksum: 5d69d10bdacc24c27f02924379405bd9
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2025-06-26T08:41:24Z
date_updated: 2025-12-27T23:30:02Z
embargo_to: open_access
file_id: '19908'
file_name: Thesis Template - ISTA [istaustriathesis].zip
file_size: 59092991
relation: source_file
file_date_updated: 2025-12-27T23:30:02Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '06'
oa: 1
oa_version: Published Version
page: '82'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10299'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
title: 'Turbulence in polymeric flows : A characterisation of elasto-inertial turbulence
and the maximum drag reduction asymptote'
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: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '14257'
abstract:
- lang: eng
text: Mapping the complex and dense arrangement of cells and their connectivity
in brain tissue demands nanoscale spatial resolution imaging. Super-resolution
optical microscopy excels at visualizing specific molecules and individual cells
but fails to provide tissue context. Here we developed Comprehensive Analysis
of Tissues across Scales (CATS), a technology to densely map brain tissue architecture
from millimeter regional to nanometer synaptic scales in diverse chemically fixed
brain preparations, including rodent and human. CATS uses fixation-compatible
extracellular labeling and optical imaging, including stimulated emission depletion
or expansion microscopy, to comprehensively delineate cellular structures. It
enables three-dimensional reconstruction of single synapses and mapping of synaptic
connectivity by identification and analysis of putative synaptic cleft regions.
Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed
and quantified the synaptic input and output structure of identified neurons.
We furthermore demonstrate applicability to clinically derived human tissue samples,
including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing
the cellular architecture of brain tissue in health and disease.
acknowledged_ssus:
- _id: ScienComp
- _id: Bio
- _id: PreCl
- _id: LifeSc
- _id: M-Shop
- _id: E-Lib
acknowledgement: 'We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak
for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I.
Erber for technical assistance; and M. Tomschik for support with obtaining human
samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata
for computational support and hardware control. We are grateful to R. Shigemoto
and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University)
for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly
provided by S. Grant (University of Edinburgh). We acknowledge expert support by
Institute of Science and Technology Austria’s scientific computing, imaging and
optics, preclinical and lab support facilities and by the Miba machine shop and
library. We gratefully acknowledge funding by the following sources: Austrian Science
Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232
(J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award
(P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27
(R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.);
European Union’s Horizon 2020 research and innovation programme, European Research
Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020
research and innovation programme, European Research Council (ERC) grant 692692
– GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under
the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions
Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Julia M
full_name: Michalska, Julia M
id: 443DB6DE-F248-11E8-B48F-1D18A9856A87
last_name: Michalska
orcid: 0000-0003-3862-1235
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- first_name: Philipp
full_name: Velicky, Philipp
id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
last_name: Velicky
orcid: 0000-0002-2340-7431
- first_name: Hana
full_name: Korinkova, Hana
id: ee3cb6ca-ec98-11ea-ae11-ff703e2254ed
last_name: Korinkova
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Alban
full_name: Cenameri, Alban
id: 9ac8f577-2357-11eb-997a-e566c5550886
last_name: Cenameri
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Alessandro
full_name: Venturino, Alessandro
id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
last_name: Venturino
orcid: 0000-0003-2356-9403
- first_name: Karl
full_name: Roessler, Karl
last_name: Roessler
- first_name: Thomas
full_name: Czech, Thomas
last_name: Czech
- first_name: Romana
full_name: Höftberger, Romana
last_name: Höftberger
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture
across millimeter to nanometer scales. Nature Biotechnology. 2024;42:1051-1064.
doi:10.1038/s41587-023-01911-8
apa: Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri,
A., … Danzl, J. G. (2024). Imaging brain tissue architecture across millimeter
to nanometer scales. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-023-01911-8
chicago: Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake
Watson, Alban Cenameri, Christoph M Sommer, et al. “Imaging Brain Tissue Architecture
across Millimeter to Nanometer Scales.” Nature Biotechnology. Springer
Nature, 2024. https://doi.org/10.1038/s41587-023-01911-8.
ieee: J. M. Michalska et al., “Imaging brain tissue architecture across millimeter
to nanometer scales,” Nature Biotechnology, vol. 42. Springer Nature, pp.
1051–1064, 2024.
ista: Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer
CM, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino
G, Jonas PM, Danzl JG. 2024. Imaging brain tissue architecture across millimeter
to nanometer scales. Nature Biotechnology. 42, 1051–1064.
mla: Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter
to Nanometer Scales.” Nature Biotechnology, vol. 42, Springer Nature, 2024,
pp. 1051–64, doi:10.1038/s41587-023-01911-8.
short: J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri,
C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S.
Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology 42 (2024) 1051–1064.
corr_author: '1'
date_created: 2023-09-03T22:01:15Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2026-04-14T08:34:35Z
day: '01'
ddc:
- '570'
department:
- _id: SaSi
- _id: GaNo
- _id: PeJo
- _id: JoDa
- _id: Bio
- _id: RySh
doi: 10.1038/s41587-023-01911-8
ec_funded: 1
external_id:
isi:
- '001065254200001'
pmid:
- '37653226'
file:
- access_level: open_access
checksum: 57d5fafb16f02dcb9f7dddb1bd7e2a71
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T07:48:01Z
date_updated: 2025-01-09T07:48:01Z
file_id: '18784'
file_name: 2024_NatureBiotech_Michalska.pdf
file_size: 26065165
relation: main_file
success: 1
file_date_updated: 2025-01-09T07:48:01Z
has_accepted_license: '1'
intvolume: ' 42'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1051-1064
pmid: 1
project:
- _id: 265CB4D0-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03600
name: Optical control of synaptic function via adhesion molecules
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232
name: Molecular Drug Targets
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
- _id: 23889792-32DE-11EA-91FC-C7463DDC885E
grant_number: LS18-022
name: High content imaging to decode human immune cell interactions in health and
allergic disease
- _id: 25444568-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715508'
name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo
and in vitro Models
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9
call_identifier: H2020
grant_number: '101026635'
name: Synaptic computations of the hippocampal CA3 circuitry
publication: Nature Biotechnology
publication_identifier:
eissn:
- 1546-1696
issn:
- 1087-0156
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/danzllab/CATS
record:
- id: '18660'
relation: dissertation_contains
status: deleted
- id: '13126'
relation: research_data
status: public
- id: '18674'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Imaging brain tissue architecture across millimeter to nanometer scales
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: 42
year: '2024'
...
---
OA_place: publisher
_id: '14711'
abstract:
- lang: eng
text: "In nature, different species find their niche in a range of environments,
each with its unique characteristics. While some thrive in uniform (homogeneous)
landscapes where environmental conditions stay relatively consistent across space,
others traverse the complexities of spatially heterogeneous terrains. Comprehending
how species are distributed and how they interact within these landscapes holds
the key to gaining insights into their evolutionary dynamics while also informing
conservation and management strategies.\r\n\r\nFor species inhabiting heterogeneous
landscapes, when the rate of dispersal is low compared to spatial fluctuations
in selection pressure, localized adaptations may emerge. Such adaptation in response
to varying selection strengths plays an important role in the persistence of populations
in our rapidly changing world. Hence, species in nature are continuously in a
struggle to adapt to local environmental conditions, to ensure their continued
survival. Natural populations can often adapt in time scales short enough for
evolutionary changes to influence ecological dynamics and vice versa, thereby
creating a feedback between evolution and demography. The analysis of this feedback
and the relative contributions of gene flow, demography, drift, and natural selection
to genetic variation and differentiation has remained a recurring theme in evolutionary
biology. Nevertheless, the effective role of these forces in maintaining variation
and shaping patterns of diversity is not fully understood. Even in homogeneous
environments devoid of local adaptations, such understanding remains elusive.
Understanding this feedback is crucial, for example in determining the conditions
under which extinction risk can be mitigated in peripheral populations subject
to deleterious mutation accumulation at the edges of species’ ranges\r\nas well
as in highly fragmented populations.\r\n\r\nIn this thesis we explore both uniform
and spatially heterogeneous metapopulations, investigating and providing theoretical
insights into the dynamics of local adaptation in the latter and examining the
dynamics of load and extinction as well as the impact of joint ecological and
evolutionary (eco-evolutionary) dynamics in the former. The thesis is divided
into 5 chapters.\r\n\r\nChapter 1 provides a general introduction into the subject
matter, clarifying concepts and ideas used throughout the thesis. In chapter 2,
we explore how fast a species distributed across a heterogeneous landscape adapts
to changing conditions marked by alterations in carrying capacity, selection pressure,
and migration rate.\r\n\r\nIn chapter 3, we investigate how migration selection
and drift influences adaptation and the maintenance of variation in a metapopulation
with three habitats, an extension of previous models of adaptation in two habitats.
We further develop analytical approximations for the critical threshold required
for polymorphism to persist.\r\n\r\nThe focus of chapter 4 of the thesis is on
understanding the interplay between ecology and evolution as coupled processes.
We investigate how eco-evolutionary feedback between migration, selection, drift,
and demography influences eco-evolutionary outcomes in marginal populations subject
to deleterious mutation accumulation. Using simulations as well as theoretical
approximations of the coupled dynamics of population size and allele frequency,
we analyze how gene flow from a large mainland source influences genetic load
and population size on an island (i.e., in a marginal population) under genetically
realistic assumptions. Analyses of this sort are important because small isolated
populations, are repeatedly affected by complex interactions between ecological
and evolutionary processes, which can lead to their death. Understanding these
interactions can therefore provide an insight into the conditions under which
extinction risk can be mitigated in peripheral populations thus, contributing
to conservation and restoration efforts.\r\n\r\nChapter 5 extends the analysis
in chapter 4 to consider the dynamics of load (due to deleterious mutation accumulation)
and extinction risk in a metapopulation. We explore the role of gene flow, selection,
and dominance on load and extinction risk and further pinpoint critical thresholds
required for metapopulation persistence.\r\n\r\nOverall this research contributes
to our understanding of ecological and evolutionary mechanisms that shape species’
persistence in fragmented landscapes, a crucial foundation for successful conservation
efforts and biodiversity management."
acknowledged_ssus:
- _id: SSU
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Oluwafunmilola O
full_name: Olusanya, Oluwafunmilola O
id: 41AD96DC-F248-11E8-B48F-1D18A9856A87
last_name: Olusanya
orcid: 0000-0003-1971-8314
citation:
ama: Olusanya OO. Local adaptation, genetic load and extinction in metapopulations.
2024. doi:10.15479/at:ista:14711
apa: Olusanya, O. O. (2024). Local adaptation, genetic load and extinction in
metapopulations. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14711
chicago: Olusanya, Oluwafunmilola O. “Local Adaptation, Genetic Load and Extinction
in Metapopulations.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:14711.
ieee: O. O. Olusanya, “Local adaptation, genetic load and extinction in metapopulations,”
Institute of Science and Technology Austria, 2024.
ista: Olusanya OO. 2024. Local adaptation, genetic load and extinction in metapopulations.
Institute of Science and Technology Austria.
mla: Olusanya, Oluwafunmilola O. Local Adaptation, Genetic Load and Extinction
in Metapopulations. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:14711.
short: O.O. Olusanya, Local Adaptation, Genetic Load and Extinction in Metapopulations,
Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2023-12-26T22:49:53Z
date_published: 2024-01-19T00:00:00Z
date_updated: 2026-04-07T12:54:29Z
day: '19'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
- _id: GradSch
doi: 10.15479/at:ista:14711
ec_funded: 1
file:
- access_level: closed
checksum: de179b1c6758f182ff0c70d8b38c1501
content_type: application/zip
creator: oolusany
date_created: 2024-01-03T18:30:13Z
date_updated: 2024-01-03T18:30:13Z
file_id: '14730'
file_name: FinalSubmission_Thesis_OLUSANYA.zip
file_size: 16986244
relation: source_file
- access_level: open_access
checksum: 0e331585e3cd4823320aab4e69e64ccf
content_type: application/pdf
creator: oolusany
date_created: 2024-01-03T18:31:34Z
date_updated: 2024-01-03T18:31:34Z
file_id: '14731'
file_name: FinalSubmission2_Thesis_OLUSANYA.pdf
file_size: 6460403
relation: main_file
success: 1
file_date_updated: 2024-01-03T18:31:34Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: '183'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: c08d3278-5a5b-11eb-8a69-fdb09b55f4b8
grant_number: P32896
name: Causes and consequences of population fragmentation
- _id: 34c872fe-11ca-11ed-8bc3-8534b82131e6
grant_number: '26380'
name: Polygenic Adaptation in a Metapopulation
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10787'
relation: part_of_dissertation
status: public
- id: '10658'
relation: part_of_dissertation
status: public
- id: '14732'
relation: part_of_dissertation
status: public
status: public
supervisor:
- 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: Jitka
full_name: Polechova, Jitka
last_name: Polechova
- first_name: Himani
full_name: Sachdeva, Himani
last_name: Sachdeva
title: Local adaptation, genetic load and extinction in metapopulations
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: '2024'
...
---
OA_place: publisher
_id: '15020'
abstract:
- lang: eng
text: "This thesis consists of four distinct pieces of work within theoretical biology,
with two themes in common: the concept of optimization in biological systems,
and the use of information-theoretic tools to quantify biological stochasticity
and statistical uncertainty.\r\nChapter 2 develops a statistical framework for
studying biological systems which we believe to be optimized for a particular
utility function, such as retinal neurons conveying information about visual stimuli.
We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the
expected utility. We explore how such priors aid inference of system parameters
with limited data and enable optimality hypothesis testing: is the utility higher
than by chance?\r\nChapter 3 examines the ultimate biological optimization process:
evolution by natural selection. As some individuals survive and reproduce more
successfully than others, populations evolve towards fitter genotypes and phenotypes.
We formalize this as accumulation of genetic information, and use population genetics
theory to study how much such information can be accumulated per generation and
maintained in the face of random mutation and genetic drift. We identify the population
size and fitness variance as the key quantities that control information accumulation
and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter
3, but from a different perspective: we ask how much genetic information organisms
actually need, in particular in the context of gene regulation. For example, how
much information is needed to bind transcription factors at correct locations
within the genome? Population genetics provides us with a refined answer: with
an increasing population size, populations achieve higher fitness by maintaining
more genetic information. Moreover, regulatory parameters experience selection
pressure to optimize the fitness-information trade-off, i.e. minimize the information
needed for a given fitness. This provides an evolutionary derivation of the optimization
priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information
between a signal and a communication channel output (such as neural activity).
Mutual information is an important utility measure for biological systems, but
its practical use can be difficult due to the large dimensionality of many biological
channels. Sometimes, a lower bound on mutual information is computed by replacing
the high-dimensional channel outputs with decodes (signal estimates). Our result
provides a corresponding upper bound, provided that the decodes are the maximum
posterior estimates of the signal."
acknowledged_ssus:
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michal
full_name: Hledik, Michal
id: 4171253A-F248-11E8-B48F-1D18A9856A87
last_name: Hledik
citation:
ama: Hledik M. Genetic information and biological optimization. 2024. doi:10.15479/at:ista:15020
apa: Hledik, M. (2024). Genetic information and biological optimization.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15020
chicago: Hledik, Michal. “Genetic Information and Biological Optimization.” Institute
of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15020.
ieee: M. Hledik, “Genetic information and biological optimization,” Institute of
Science and Technology Austria, 2024.
ista: Hledik M. 2024. Genetic information and biological optimization. Institute
of Science and Technology Austria.
mla: Hledik, Michal. Genetic Information and Biological Optimization. Institute
of Science and Technology Austria, 2024, doi:10.15479/at:ista:15020.
short: M. Hledik, Genetic Information and Biological Optimization, Institute of
Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-02-23T14:02:04Z
date_published: 2024-02-23T00:00:00Z
date_updated: 2026-04-07T12:59:25Z
day: '23'
ddc:
- '576'
- '519'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
- _id: GaTk
doi: 10.15479/at:ista:15020
ec_funded: 1
file:
- access_level: open_access
checksum: b2d3da47c98d481577a4baf68944fe41
content_type: application/pdf
creator: mhledik
date_created: 2024-02-23T13:50:53Z
date_updated: 2024-02-23T13:50:53Z
file_id: '15021'
file_name: hledik thesis pdfa 2b.pdf
file_size: 7102089
relation: main_file
success: 1
- access_level: closed
checksum: eda9b9430da2610fee7ce1c1419a479a
content_type: application/zip
creator: mhledik
date_created: 2024-02-23T13:50:54Z
date_updated: 2024-02-23T14:20:16Z
file_id: '15022'
file_name: hledik thesis source.zip
file_size: 14014790
relation: source_file
file_date_updated: 2024-02-23T14:20:16Z
has_accepted_license: '1'
keyword:
- Theoretical biology
- Optimality
- Evolution
- Information
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '158'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 2665AAFE-B435-11E9-9278-68D0E5697425
grant_number: RGP0034/2018
name: Can evolution minimize spurious signaling crosstalk to reach optimal performance?
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7606'
relation: part_of_dissertation
status: public
- id: '12081'
relation: part_of_dissertation
status: public
- id: '7553'
relation: part_of_dissertation
status: public
status: public
supervisor:
- 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: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
title: Genetic information and biological optimization
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15330'
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 scission machinery in plants, but the precise roles of these
proteins in this process are 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 sh3p123
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.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: Bio
acknowledgement: "Nataliia Gnyliukh was partially funded by the European Union’s Horizon
2020 research and\r\ninnovation program (2018-2020) under the Marie Sklodowska-Curie
Grant (agreement no.\r\n665385). Taif University Researchers Supporting Project:
TURSP-HC2022/02. and Austrian\r\nScience Fund (FWF): I 6123-B.We thank Prof. Eileen
Lafer and Liping Wang for their suggestions regarding the optimisation of protein
expression and purification. We thank Prof. Sebastian Y. Bednarek for the useful
comments and constructive criticism of the project. We thank Maciek Adamowski for
providing genetic material. This research was supported by the Scientific Service
Units (SSU) of IST-Austria through resources provided by the Electron microscopy
(EMF), Lab Support Facility (LSF) (particularly Dorota Jaworska) and the Bioimaging
Facility (BIF)."
article_number: jcs.261720
article_processing_charge: Yes (via OA deal)
article_type: original
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: MK
full_name: Nagel, MK
last_name: Nagel
- first_name: Aline
full_name: Monzer, Aline
id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425
last_name: Monzer
- first_name: David
full_name: Babic, David
id: db566d23-f6e0-11ea-865d-e6f270e968e7
last_name: Babic
- first_name: Annamaria
full_name: Hlavata, Annamaria
id: 36062FEC-F248-11E8-B48F-1D18A9856A87
last_name: Hlavata
- first_name: SS
full_name: Alotaibi, SS
last_name: Alotaibi
- first_name: E
full_name: Isono, E
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, et al. Role of dynamin-related proteins 2
and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana. Journal
of Cell Science. 2024;137(8). doi:10.1242/jcs.261720
apa: Gnyliukh, N., Johnson, A. J., Nagel, M., Monzer, A., Babic, D., Hlavata, A.,
… Friml, J. (2024). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated
endocytosis in Arabidopsis thaliana. Journal of Cell Science. The Company
of Biologists. https://doi.org/10.1242/jcs.261720
chicago: Gnyliukh, Nataliia, Alexander J Johnson, MK Nagel, Aline Monzer, David
Babic, Annamaria Hlavata, SS Alotaibi, E Isono, Martin Loose, and Jiří Friml.
“Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis
in Arabidopsis Thaliana.” Journal of Cell Science. The Company of Biologists,
2024. https://doi.org/10.1242/jcs.261720.
ieee: N. Gnyliukh et al., “Role of dynamin-related proteins 2 and SH3P2 in
clathrin-mediated endocytosis in Arabidopsis thaliana,” Journal of Cell Science,
vol. 137, no. 8. The Company of Biologists, 2024.
ista: Gnyliukh N, Johnson AJ, Nagel M, Monzer A, Babic D, Hlavata A, Alotaibi S,
Isono E, Loose M, Friml J. 2024. Role of dynamin-related proteins 2 and SH3P2
in clathrin-mediated endocytosis in Arabidopsis thaliana. Journal of Cell Science.
137(8), jcs. 261720.
mla: Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in
Clathrin-Mediated Endocytosis in Arabidopsis Thaliana.” Journal of Cell Science,
vol. 137, no. 8, jcs. 261720, The Company of Biologists, 2024, doi:10.1242/jcs.261720.
short: N. Gnyliukh, A.J. Johnson, M. Nagel, A. Monzer, D. Babic, A. Hlavata, S.
Alotaibi, E. Isono, M. Loose, J. Friml, Journal of Cell Science 137 (2024).
corr_author: '1'
date_created: 2024-04-19T09:54:59Z
date_published: 2024-04-01T00:00:00Z
date_updated: 2025-09-04T13:49:45Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
- _id: JiFr
- _id: CaBe
doi: 10.1242/jcs.261720
ec_funded: 1
external_id:
isi:
- '001266917100005'
pmid:
- '38506228'
file:
- access_level: open_access
checksum: 6dc023f0cc7052ad3cf0a42589d2e30f
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T08:41:16Z
date_updated: 2025-01-09T08:41:16Z
file_id: '18792'
file_name: 2024_JourCellScience_Gnyliukh.pdf
file_size: 25845948
relation: main_file
success: 1
file_date_updated: 2025-01-09T08:41:16Z
has_accepted_license: '1'
intvolume: ' 137'
isi: 1
issue: '8'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: bd76d395-d553-11ed-ba76-f678c14f9033
grant_number: I06123
name: Peptide receptors for auxin canalization in Arabidopsis
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- 0021-9533
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
related_material:
record:
- id: '14591'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis
in Arabidopsis thaliana
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 137
year: '2024'
...
---
OA_place: publisher
_id: '18568'
abstract:
- lang: eng
text: "Locomotion is ubiquitous in the animal kingdom because an animal's survival
depends on its ability to navigate its environment to find food, avoid predators
and locate potential mates. These behaviours require control mechanisms that can
extract information from the environment, particularly visual cues. Selective
evolutionary pressures have thus refined such visuomotor transformations in a
species-specific manner to meet the specific ecological and ethological challenges
of each organism. However, a common challenge across organisms as visual information
processing\r\nbecomes increasingly detailed is the mechanisms required to synthesise
disparate pieces of information into a coherent percept or unified picture of
the world. In this thesis, I investigate how disparate visual information is combined
in the brain of Drosophila melanogaster to effectively guide locomotion.\r\nFor
this, I first designed and built a behavioural setup to record locomotion and
present visual stimuli to freely-walking fruit flies in a closed-loop manner.
This setup allowed the investigation of innate visually-guided behaviours, including
the optomotor reflex and courtship.\r\nSecond, taking advantage of my system I
investigated the optomotor response, a reflexive visual stabilisation behaviour
in which flies turn in the direction of global motion to minimise retinal slip.
This behaviour is thought to be mediated by Lobula plate tangential cells (LPTCs);
a complex network of optic-flow-sensitive neurons essential for self-motion estimation.
Using a novel genetic mutant, I demonstrate that electrical coupling between two
LPTC subtypes, contralateral HS and H2 neurons, regulates the balance between
smooth optomotor turning and saccadic anti-optomotor responses. These findings
underscore the critical role of binocular motion cue integration in guiding course
control. Finally, I developed a novel behavioural paradigm in which a sexually
aroused male fruit fly is presented with an optomotor distractor. This setup creates
competition between two visual behaviours, courtship tracking and the optomotor
response, enabling me to explore how the visual system resolves this conflict.
In this setting, males\r\nengaged in courtship selectively suppress their optomotor
response based on the female's location. Furthermore, when this experiment is
replicated with an “artificial female”, optogenetically aroused males alternate
between tracking and optomotor responses. The probability and dynamics of this
switching are determined by the relative strengths of the two competing stimuli.
In summary, the results presented in this thesis explore two mechanisms – integration
and competition - through which visual information is combined in the brain of
the fruit fly to drive locomotion."
acknowledged_ssus:
- _id: M-Shop
acknowledgement: I am incredibly thankful for the outstanding support provided by
ISTA, especially the Machine Shop team, who made conducting research much easier
and more efficient. I am also grateful for the funding provided by European Union’s
Horizon 2020 research and innovation program under the Marie Skłodowska-Curie programme
(665385) and The German Research Foundation grant DFG (SPP2205) “Evolutionary optimization
of neuronal processing”.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Roshan K
full_name: Satapathy, Roshan K
id: 46046B7A-F248-11E8-B48F-1D18A9856A87
last_name: Satapathy
orcid: 0009-0006-2974-5075
citation:
ama: Satapathy RK. Mechanisms of visual integration and competition in innate behaviours
in Drosophila melanogaster. 2024. doi:10.15479/at:ista:18568
apa: Satapathy, R. K. (2024). Mechanisms of visual integration and competition
in innate behaviours in Drosophila melanogaster. Institute of Science and
Technology Austria. https://doi.org/10.15479/at:ista:18568
chicago: Satapathy, Roshan K. “Mechanisms of Visual Integration and Competition
in Innate Behaviours in Drosophila Melanogaster.” Institute of Science and Technology
Austria, 2024. https://doi.org/10.15479/at:ista:18568.
ieee: R. K. Satapathy, “Mechanisms of visual integration and competition in innate
behaviours in Drosophila melanogaster,” Institute of Science and Technology Austria,
2024.
ista: Satapathy RK. 2024. Mechanisms of visual integration and competition in innate
behaviours in Drosophila melanogaster. Institute of Science and Technology Austria.
mla: Satapathy, Roshan K. Mechanisms of Visual Integration and Competition in
Innate Behaviours in Drosophila Melanogaster. Institute of Science and Technology
Austria, 2024, doi:10.15479/at:ista:18568.
short: R.K. Satapathy, Mechanisms of Visual Integration and Competition in Innate
Behaviours in Drosophila Melanogaster, Institute of Science and Technology Austria,
2024.
corr_author: '1'
date_created: 2024-11-19T12:34:30Z
date_published: 2024-11-20T00:00:00Z
date_updated: 2026-04-07T13:00:36Z
day: '20'
ddc:
- '573'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MaJö
doi: 10.15479/at:ista:18568
ec_funded: 1
file:
- access_level: open_access
checksum: 340f2bfe882c8a85e11ec0687ca15f5e
content_type: application/pdf
creator: rsatapat
date_created: 2024-11-19T12:39:55Z
date_updated: 2024-11-19T12:39:55Z
file_id: '18570'
file_name: Roshan PhD thesis-Final.pdf
file_size: 10960975
relation: main_file
success: 1
- access_level: closed
checksum: 0f846fce60d6ea511e07f77eff59a6a1
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: rsatapat
date_created: 2024-11-19T12:46:47Z
date_updated: 2024-12-13T10:27:25Z
file_id: '18571'
file_name: Roshan PhD thesis-Final.docx
file_size: 36695917
relation: source_file
file_date_updated: 2024-12-13T10:27:25Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '114'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
isbn:
- 978-3-99078-047-3
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '18444'
relation: part_of_dissertation
status: public
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: Mechanisms of visual integration and competition in innate behaviours in Drosophila
melanogaster
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
OA_place: publisher
_id: '18674'
abstract:
- lang: eng
text: Mapping the complex and dense arrangement of cells and their connectivity
in brain tissue requires volumetric imaging at nanoscale spatial resolution. While
light microscopy excels at visualizing specific molecules and individual cells,
achieving dense, synapse-level circuit reconstruction has not been possible with
any light microscopy technique. Thus, the goal of my work was to develop image
and data analysis pipelines for brain tissue visualization and reconstruction
with light microscopy. To achieve dense circuit reconstruction with single-synapse
resolution, I developed both conventional and deep-learning-based synapse detection
algorithms, as well as connectivity analysis pipelines that integrate synapse
detection with volumetric segmentation of brain tissue.
acknowledged_ssus:
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
citation:
ama: Lyudchik J. Image analysis for brain tissue reconstruction with super-resolution
light microscopy. 2024. doi:10.15479/at:ista:18674
apa: Lyudchik, J. (2024). Image analysis for brain tissue reconstruction with
super-resolution light microscopy. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:18674
chicago: Lyudchik, Julia. “Image Analysis for Brain Tissue Reconstruction with Super-Resolution
Light Microscopy.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18674.
ieee: J. Lyudchik, “Image analysis for brain tissue reconstruction with super-resolution
light microscopy,” Institute of Science and Technology Austria, 2024.
ista: Lyudchik J. 2024. Image analysis for brain tissue reconstruction with super-resolution
light microscopy. Institute of Science and Technology Austria.
mla: Lyudchik, Julia. Image Analysis for Brain Tissue Reconstruction with Super-Resolution
Light Microscopy. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18674.
short: J. Lyudchik, Image Analysis for Brain Tissue Reconstruction with Super-Resolution
Light Microscopy, Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-12-18T14:24:43Z
date_published: 2024-12-18T00:00:00Z
date_updated: 2026-04-14T08:34:35Z
day: '18'
ddc:
- '004'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoDa
doi: 10.15479/at:ista:18674
ec_funded: 1
file:
- access_level: open_access
checksum: 1b42b8073e2bc09fc504da52372248c1
content_type: application/pdf
creator: jlyudchi
date_created: 2024-12-18T14:17:34Z
date_updated: 2024-12-18T14:17:34Z
file_id: '18675'
file_name: 18122024_PhDthesis_corrected_final_pdfa.pdf
file_size: 160536833
relation: main_file
success: 1
- access_level: closed
checksum: b4da84624060745519723698f7ddf54b
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: jlyudchi
date_created: 2024-12-18T14:21:06Z
date_updated: 2024-12-18T14:41:53Z
file_id: '18676'
file_name: 18122024_PhDthesis_corrected_final_JL_markup.docx
file_size: 99172203
relation: source_file
file_date_updated: 2024-12-18T14:41:53Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '217'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
isbn:
- ' 978-3-99078-051-0'
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11160'
relation: part_of_dissertation
status: public
- id: '18677'
relation: part_of_dissertation
status: public
- id: '13267'
relation: part_of_dissertation
status: public
- id: '14257'
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: Image analysis for brain tissue reconstruction with super-resolution light
microscopy
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
OA_place: repository
_id: '18677'
abstract:
- lang: eng
text: The information-processing capability of the brain’s cellular network depends
on the physical wiring pattern between neurons and their molecular and functional
characteristics. Mapping neurons and resolving their individual synaptic connections
can be achieved by volumetric imaging at nanoscale resolution with dense cellular
labeling. Light microscopy is uniquely positioned to visualize specific molecules
but dense, synapse-level circuit reconstruction by light microscopy has been out
of reach due to limitations in resolution, contrast, and volumetric imaging capability.
Here we developed light-microscopy based connectomics (LICONN). We integrated
specifically engineered hydrogel embedding and expansion with comprehensive deep-learning
based segmentation and analysis of connectivity, thus directly incorporating molecular
information in synapse-level brain tissue reconstructions. LICONN will allow synapse-level
brain tissue phenotyping in biological experiments in a readily adoptable manner.
acknowledged_ssus:
- _id: E-Lib
- _id: M-Shop
- _id: LifeSc
- _id: Bio
- _id: ScienComp
acknowledgement: "We thank Sven Dorkenwald and Peter Li for critical reading of the\r\nmanuscript.
We acknowledge expert support by ISTA’s scientific service units: Imaging and\r\nOptics,
Lab Support, Scientific Computing, Preclinical Facility, Miba Machine Shop, and
Library.\r\nWe gratefully acknowledge funding by the following sources:\r\nAustrian
Science Fund (FWF) grant DK W1232 (JGD, MRT)\r\nAustrian Academy of Sciences DOC
fellowship 26137 (MRT)\r\nEU Horizon 2020 program, Marie Skłodowska-Curie Actions
Fellowship 665385 (JL)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022
(JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European
Research\r\nCouncil (ERC) grant 101044865 “SecretAutism.”\r\n"
article_processing_charge: No
author:
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- first_name: Michał
full_name: Januszewski, Michał
last_name: Januszewski
- first_name: Vitali
full_name: Vistunou, Vitali
id: 7e146587-8972-11ed-ae7b-d7a32ea86a81
last_name: Vistunou
- first_name: Nathalie
full_name: Agudelo Duenas, Nathalie
id: 40E7F008-F248-11E8-B48F-1D18A9856A87
last_name: Agudelo Duenas
- first_name: Jakob
full_name: Vorlaufer, Jakob
id: 937696FA-C996-11E9-8C7C-CF13E6697425
last_name: Vorlaufer
orcid: 0009-0000-7590-3501
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Bárbara
full_name: Oliveira, Bárbara
id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87
last_name: Oliveira
- first_name: Alban
full_name: Cenameri, Alban
id: 9ac8f577-2357-11eb-997a-e566c5550886
last_name: Cenameri
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Viren
full_name: Jain, Viren
last_name: Jain
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Tavakoli M, Lyudchik J, Januszewski M, et al. Light-microscopy based dense
connectomic reconstruction of mammalian brain tissue. bioRxiv. doi:10.1101/2024.03.01.582884
apa: Tavakoli, M., Lyudchik, J., Januszewski, M., Vistunou, V., Agudelo Duenas,
N., Vorlaufer, J., … Danzl, J. G. (n.d.). Light-microscopy based dense connectomic
reconstruction of mammalian brain tissue. bioRxiv. https://doi.org/10.1101/2024.03.01.582884
chicago: Tavakoli, Mojtaba, Julia Lyudchik, Michał Januszewski, Vitali Vistunou,
Nathalie Agudelo Duenas, Jakob Vorlaufer, Christoph M Sommer, et al. “Light-Microscopy
Based Dense Connectomic Reconstruction of Mammalian Brain Tissue.” BioRxiv,
n.d. https://doi.org/10.1101/2024.03.01.582884.
ieee: M. Tavakoli et al., “Light-microscopy based dense connectomic reconstruction
of mammalian brain tissue,” bioRxiv. .
ista: Tavakoli M, Lyudchik J, Januszewski M, Vistunou V, Agudelo Duenas N, Vorlaufer
J, Sommer CM, Kreuzinger C, Oliveira B, Cenameri A, Novarino G, Jain V, Danzl
JG. Light-microscopy based dense connectomic reconstruction of mammalian brain
tissue. bioRxiv, 10.1101/2024.03.01.582884.
mla: Tavakoli, Mojtaba, et al. “Light-Microscopy Based Dense Connectomic Reconstruction
of Mammalian Brain Tissue.” BioRxiv, doi:10.1101/2024.03.01.582884.
short: M. Tavakoli, J. Lyudchik, M. Januszewski, V. Vistunou, N. Agudelo Duenas,
J. Vorlaufer, C.M. Sommer, C. Kreuzinger, B. Oliveira, A. Cenameri, G. Novarino,
V. Jain, J.G. Danzl, BioRxiv (n.d.).
corr_author: '1'
date_created: 2024-12-18T14:48:24Z
date_published: 2024-07-08T00:00:00Z
date_updated: 2026-04-28T13:33:34Z
day: '08'
department:
- _id: GaNo
- _id: JoDa
doi: 10.1101/2024.03.01.582884
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2024.03.01.582884
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 6285a163-2b32-11ec-9570-8e204ca2dba5
grant_number: '26137'
name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
Microscopy
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 34ba8964-11ca-11ed-8bc3-e15864e7e9a6
grant_number: '101044865'
name: Toward an understanding of the brain interstitial system and the extracellular
proteome in health and autism spectrum disorders
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: bioRxiv
publication_status: draft
related_material:
record:
- id: '18681'
relation: dissertation_contains
status: public
- id: '18674'
relation: dissertation_contains
status: public
- id: '19704'
relation: later_version
status: public
status: public
title: Light-microscopy based dense connectomic reconstruction of mammalian brain
tissue
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: repository
_id: '18689'
abstract:
- lang: eng
text: Multiplexed fluorescence microscopy imaging is widely used in biomedical applications.
However, simultaneous imaging of multiple fluorophores can result in spectral
leaks and overlapping, which greatly degrades image quality and subsequent analysis.
Existing popular spectral unmixing methods are mainly based on computational intensive
linear models and the performance is heavily dependent on the reference spectra,
which may greatly preclude its further applications. In this paper, we propose
a deep learning-based blindly spectral unmixing method, termed AutoUnmix, to imitate
the physical spectral mixing process. A tranfer learning framework is further
devised to allow our AutoUnmix adapting to a variety of imaging systems without
retraining the network. Our proposed method has demonstrated real-time unmixing
capabilities, surpassing existing methods by up to 100-fold in terms of unmixing
speed. We further validate the reconstruction performance on both synthetic datasets
and biological samples. The unmixing results of AutoUnmix achieve a highest SSIM
of 0.99 in both three- and four-color imaging, with nearly up to 20% higher than
other popular unmixing methods. Due to the desirable property of data independency
and superior blind unmixing performance, we believe AutoUnmix is a powerful tool
to study the interaction process of different organelles labeled by multiple fluorophores.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: M-Shop
- _id: E-Lib
acknowledgement: "We gratefully acknowledge support by the Scientific Service Units
at ISTA, including the Imaging and Optics and Lab Support facilities and the mechanical
workshop and Library. We thank Philipp Velicky for STED microscope alignment.\r\n\r\nThis
project has received funding from the Austrian Science Fund (FWF): I 3630-B25 (J.G.D)
and the European Research Council (ERC) under the European Union’s Horizon 2020
research and innovation programme (grant agreement No 742985, J.F.). It has also
received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. S.T. has
received funding as an ISTplus Fellow from the European Union’s Horizon 2020 Research
and Innovation Programme under Marie Skłodowska-Curie grant agreement no. 754411
and from an EMBO Long-Term Fellowship (grant number ALTF 679-2018). It has further
received funding from the Austrian Science Fund (FWF) grant DK W1232 (M.T, N.A-D.,
J.G.D). W.J. received funding via a Human Frontier Science Program postdoctoral
fellowship LT000557/2018.\r\n\r\nThe funders had no role in study design, data collection
and analysis, decision to publish or preparation of the manuscript."
article_processing_charge: No
author:
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- first_name: Sven M
full_name: Truckenbrodt, Sven M
id: 45812BD4-F248-11E8-B48F-1D18A9856A87
last_name: Truckenbrodt
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Syamala
full_name: Inumella, Syamala
id: F8660870-D756-11E9-98C5-34DFE5697425
last_name: Inumella
orcid: 0009-0002-5890-120X
- first_name: Vitali
full_name: Vistunou, Vitali
id: 7e146587-8972-11ed-ae7b-d7a32ea86a81
last_name: Vistunou
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- first_name: Nathalie
full_name: Agudelo Duenas, Nathalie
id: 40E7F008-F248-11E8-B48F-1D18A9856A87
last_name: Agudelo Duenas
- first_name: Jakob
full_name: Vorlaufer, Jakob
id: 937696FA-C996-11E9-8C7C-CF13E6697425
last_name: Vorlaufer
orcid: 0009-0000-7590-3501
- first_name: Wiebke
full_name: Jahr, Wiebke
id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
last_name: Jahr
orcid: 0000-0003-0201-2315
- first_name: Marek
full_name: Randuch, Marek
id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
last_name: Randuch
- 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: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Gallei MC, Truckenbrodt SM, Kreuzinger C, et al. Super-resolution expansion
microscopy in plant roots. bioRxiv. doi:10.1101/2024.02.21.581330
apa: Gallei, M. C., Truckenbrodt, S. M., Kreuzinger, C., Inumella, S., Vistunou,
V., Sommer, C. M., … Danzl, J. G. (n.d.). Super-resolution expansion microscopy
in plant roots. bioRxiv. https://doi.org/10.1101/2024.02.21.581330
chicago: Gallei, Michelle C, Sven M Truckenbrodt, Caroline Kreuzinger, Syamala Inumella,
Vitali Vistunou, Christoph M Sommer, Mojtaba Tavakoli, et al. “Super-Resolution
Expansion Microscopy in Plant Roots.” BioRxiv, n.d. https://doi.org/10.1101/2024.02.21.581330.
ieee: M. C. Gallei et al., “Super-resolution expansion microscopy in plant
roots,” bioRxiv. .
ista: Gallei MC, Truckenbrodt SM, Kreuzinger C, Inumella S, Vistunou V, Sommer CM,
Tavakoli M, Agudelo Duenas N, Vorlaufer J, Jahr W, Randuch M, Johnson AJ, Benková
E, Friml J, Danzl JG. Super-resolution expansion microscopy in plant roots. bioRxiv,
10.1101/2024.02.21.581330.
mla: Gallei, Michelle C., et al. “Super-Resolution Expansion Microscopy in Plant
Roots.” BioRxiv, doi:10.1101/2024.02.21.581330.
short: M.C. Gallei, S.M. Truckenbrodt, C. Kreuzinger, S. Inumella, V. Vistunou,
C.M. Sommer, M. Tavakoli, N. Agudelo Duenas, J. Vorlaufer, W. Jahr, M. Randuch,
A.J. Johnson, E. Benková, J. Friml, J.G. Danzl, BioRxiv (n.d.).
corr_author: '1'
date_created: 2024-12-19T12:28:00Z
date_published: 2024-02-21T00:00:00Z
date_updated: 2026-04-07T12:56:36Z
day: '21'
department:
- _id: EvBe
- _id: JoDa
- _id: JiFr
doi: 10.1101/2024.02.21.581330
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2024.02.21.581330
month: '02'
oa: 1
oa_version: Preprint
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
- _id: 269B5B22-B435-11E9-9278-68D0E5697425
grant_number: ALTF 679-2018
name: UltraX - achieving sub-nanometer resolution in light microscopy using iterative
X10 microscopy in combination with nanobodies and STED
publication: bioRxiv
publication_status: draft
related_material:
record:
- id: '19003'
relation: later_version
status: public
- id: '18681'
relation: dissertation_contains
status: public
status: public
title: Super-resolution expansion microscopy in plant roots
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...