---
OA_place: repository
_id: '18144'
abstract:
- lang: eng
text: "High kinetic inductance superconductors are gaining increasing interest for\r\nthe
realisation of qubits, amplifiers and detectors. Moreover, thanks to their\r\nhigh
impedance, quantum buses made of such materials enable large zero-point\r\nfluctuations
of the voltage, boosting the coupling rates to spin and charge\r\nqubits. However,
fully exploiting the potential of disordered or granular\r\nsuperconductors is
challenging, as their inductance and, therefore, impedance\r\nat high values are
difficult to control. Here we have integrated a granular\r\naluminium resonator,
having a characteristic impedance exceeding the resistance\r\nquantum, with a
germanium double quantum dot and demonstrate strong\r\ncharge-photon coupling
with a rate of $g_\\text{c}/2\\pi= (566 \\pm 2)$ MHz. This\r\nwas achieved due
to the realisation of a wireless ohmmeter, which allows\r\n\\emph{in situ} measurements
during film deposition and, therefore, control of\r\nthe kinetic inductance of
granular aluminium films. Reproducible fabrication of\r\ncircuits with impedances
(inductances) exceeding 13 k$\\Omega$ (1 nH per square)\r\nis now possible. This
broadly applicable method opens the path for novel qubits\r\nand high-fidelity,
long-distance two-qubit gates."
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: "We acknowledge Franco De Palma, Mahya Khorramshahi, Fabian Oppliger,
Thomas Reisinger, Pasquale Scarlino and Xiao Xue for helpful discussions. This research
was supported by the Scientific Service Units of ISTA through resources provided
by the MIBA Machine Shop and the Nanofabrication facility. This research and related
results were made possible with the support of the NOMIS Foundation, the HORIZON-RIA
101069515 project, the FWF Projects with DOI:10.55776/P32235, DOI:10.55776/I5060
and DOI:10.55776/P36507. IMP acknowledges funding from the Deutsche Forschungsgemeinschaft
(DFG – German Research Foundation) under project number 450396347 (GeHoldeQED).
ICN2 acknowledges funding from Generalitat de Catalunya 2021SGR00457. We acknowledge
support from CSIC Interdisciplinary Thematic Platform (PTI+) on Quantum Technologies
(PTI-QTEP+). This research work has been funded by the European Commission – NextGenerationEU
(Regulation EU 2020/2094), through CSIC’s\r\nQuantum Technologies Platform (QTEP).
ICN2 is supported by the Severo Ochoa program from Spanish MCIN/AEI (Grant No.:
CEX2021-001214-S) and is funded by the CERCA Programme/Generalitat de Catalunya.
Part of the present work has been performed in the framework of Universitat Autònoma
de Barcelona Materials Science PhD program. AGM has received funding from Grant
RYC2021-033479-I funded by MCIN/AEI/10.13039/501100011033 and by European Union
NextGenerationEU/PRTR. M.B. acknowledges support from SUR Generalitat de Catalunya
and the EU Social Fund; project ref. 2020 FI 00103. The authors\r\nacknowledge the
use of instrumentation and the technical advice provided by the Joint Electron Microscopy
Center at ALBA (JEMCA). ICN2 acknowledges funding from Grant IU16-014206 (METCAM-FIB)
funded by the European Union through the European Regional Development\r\nFund (ERDF),
with the support of the Ministry of Research and Universities, Generalitat de Catalunya.
ICN2 is a founding member of e-DREAM [60]."
article_number: '2407.03079'
article_processing_charge: No
arxiv: 1
author:
- first_name: Marian
full_name: Janik, Marian
id: 396A1950-F248-11E8-B48F-1D18A9856A87
last_name: Janik
orcid: 0009-0003-9037-8831
- first_name: Kevin Etienne Robert
full_name: Roux, Kevin Etienne Robert
id: 53f93ea2-803f-11ed-ab7e-b283135794ef
last_name: Roux
- first_name: Carla N
full_name: Borja Espinosa, Carla N
id: 18777c01-896a-11ed-bdf8-e4851dc07d16
last_name: Borja Espinosa
- first_name: Oliver
full_name: Sagi, Oliver
id: 71616374-A8E9-11E9-A7CA-09ECE5697425
last_name: Sagi
- first_name: Abdulhamid
full_name: Baghdadi, Abdulhamid
id: 160D87FA-96B5-11E9-BF77-7626E6697425
last_name: Baghdadi
- first_name: Thomas
full_name: Adletzberger, Thomas
id: 38756BB2-F248-11E8-B48F-1D18A9856A87
last_name: Adletzberger
- first_name: Stefano
full_name: Calcaterra, Stefano
last_name: Calcaterra
- first_name: Marc
full_name: Botifoll, Marc
last_name: Botifoll
- first_name: Alba Garzón
full_name: Manjón, Alba Garzón
last_name: Manjón
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Daniel
full_name: Chrastina, Daniel
last_name: Chrastina
- first_name: Giovanni
full_name: Isella, Giovanni
last_name: Isella
- first_name: Ioan M.
full_name: Pop, Ioan M.
last_name: Pop
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Janik M, Roux KER, Borja Espinosa CN, et al. Strong charge-photon coupling
in planar germanium enabled by granular aluminium superinductors. arXiv.
doi:10.48550/arXiv.2407.03079
apa: Janik, M., Roux, K. E. R., Borja Espinosa, C. N., Sagi, O., Baghdadi, A., Adletzberger,
T., … Katsaros, G. (n.d.). Strong charge-photon coupling in planar germanium enabled
by granular aluminium superinductors. arXiv. https://doi.org/10.48550/arXiv.2407.03079
chicago: Janik, Marian, Kevin Etienne Robert Roux, Carla N Borja Espinosa, Oliver
Sagi, Abdulhamid Baghdadi, Thomas Adletzberger, Stefano Calcaterra, et al. “Strong
Charge-Photon Coupling in Planar Germanium Enabled by Granular Aluminium Superinductors.”
ArXiv, n.d. https://doi.org/10.48550/arXiv.2407.03079.
ieee: M. Janik et al., “Strong charge-photon coupling in planar germanium
enabled by granular aluminium superinductors,” arXiv. .
ista: Janik M, Roux KER, Borja Espinosa CN, Sagi O, Baghdadi A, Adletzberger T,
Calcaterra S, Botifoll M, Manjón AG, Arbiol J, Chrastina D, Isella G, Pop IM,
Katsaros G. Strong charge-photon coupling in planar germanium enabled by granular
aluminium superinductors. arXiv, 2407.03079.
mla: Janik, Marian, et al. “Strong Charge-Photon Coupling in Planar Germanium Enabled
by Granular Aluminium Superinductors.” ArXiv, 2407.03079, doi:10.48550/arXiv.2407.03079.
short: M. Janik, K.E.R. Roux, C.N. Borja Espinosa, O. Sagi, A. Baghdadi, T. Adletzberger,
S. Calcaterra, M. Botifoll, A.G. Manjón, J. Arbiol, D. Chrastina, G. Isella, I.M.
Pop, G. Katsaros, ArXiv (n.d.).
corr_author: '1'
date_created: 2024-09-26T09:50:43Z
date_published: 2024-07-03T00:00:00Z
date_updated: 2026-05-27T22:30:24Z
day: '03'
department:
- _id: GeKa
- _id: GradSch
- _id: JoFi
doi: 10.48550/arXiv.2407.03079
external_id:
arxiv:
- '2407.03079'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2407.03079
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 34c0acea-11ca-11ed-8bc3-8775e10fd452
grant_number: '101069515'
name: Integrated Germanium Quantum Technology
- _id: 237B3DA4-32DE-11EA-91FC-C7463DDC885E
call_identifier: FWF
grant_number: P32235
name: Towards scalable hut wire quantum devices
- _id: bd8bd29e-d553-11ed-ba76-f0070d4b237a
grant_number: P36507
name: Merging spin and superconducting qubits in planar Ge
- _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1
grant_number: I05060
name: High impedance circuit quantum electrodynamics with hole spins
publication: arXiv
publication_status: draft
related_material:
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status: public
title: Strong charge-photon coupling in planar germanium enabled by granular aluminium
superinductors
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: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
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_id: '14843'
abstract:
- lang: eng
text: The coupling between Ca2+ channels and release sensors is a key factor defining
the signaling properties of a synapse. However, the coupling nanotopography at
many synapses remains unknown, and it is unclear how it changes during development.
To address these questions, we examined coupling at the cerebellar inhibitory
basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission
by paired recording and intracellular pipette perfusion revealed that the effects
of exogenous Ca2+ chelators decreased during development, despite constant reliance
of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica
labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic
P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked
vesicles were only clustered at later developmental stages. Modeling suggested
a developmental transformation from a more random to a more clustered coupling
nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point
configuration, optimizing speed, reliability, and energy efficiency of synaptic
transmission.
acknowledged_ssus:
- _id: EM-Fac
- _id: PreCl
- _id: M-Shop
acknowledgement: We thank Drs. David DiGregorio and Erwin Neher for critically reading
an earlier version of the manuscript, Ralf Schneggenburger for helpful discussions,
Benjamin Suter and Katharina Lichter for support with image analysis, Chris Wojtan
for advice on numerical solution of partial differential equations, Maria Reva for
help with Ripley analysis, Alois Schlögl for programming, and Akari Hagiwara and
Toshihisa Ohtsuka for anti-ELKS antibody. We are grateful to Florian Marr, Christina
Altmutter, and Vanessa Zheden for excellent technical assistance and to Eleftheria
Kralli-Beller for manuscript editing. This research was supported by the Scientific
Services Units (SSUs) of ISTA (Electron Microscopy Facility, Preclinical Facility,
and Machine Shop). The project received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation program (grant
agreement no. 692692), the Fonds zur Förderung der Wissenschaftlichen Forschung
(Z 312-B27, Wittgenstein award; P 36232-B), all to P.J., and a DOC fellowship of
the Austrian Academy of Sciences to J.-J.C.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: JingJing
full_name: Chen, JingJing
id: 2C4E65C8-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Chong
full_name: Chen, Chong
id: 3DFD581A-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Itaru
full_name: Arai, Itaru
id: 32A73F6C-F248-11E8-B48F-1D18A9856A87
last_name: Arai
- first_name: Olena
full_name: Kim, Olena
id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87
last_name: Kim
orcid: 0000-0003-2344-1039
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Chen J, Kaufmann W, Chen C, et al. Developmental transformation of Ca2+ channel-vesicle
nanotopography at a central GABAergic synapse. Neuron. 2024;112(5):755-771.e9.
doi:10.1016/j.neuron.2023.12.002
apa: Chen, J., Kaufmann, W., Chen, C., Arai, itaru, Kim, O., Shigemoto, R., &
Jonas, P. M. (2024). Developmental transformation of Ca2+ channel-vesicle nanotopography
at a central GABAergic synapse. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.12.002
chicago: Chen, JingJing, Walter Kaufmann, Chong Chen, itaru Arai, Olena Kim, Ryuichi
Shigemoto, and Peter M Jonas. “Developmental Transformation of Ca2+ Channel-Vesicle
Nanotopography at a Central GABAergic Synapse.” Neuron. Elsevier, 2024.
https://doi.org/10.1016/j.neuron.2023.12.002.
ieee: J. Chen et al., “Developmental transformation of Ca2+ channel-vesicle
nanotopography at a central GABAergic synapse,” Neuron, vol. 112, no. 5.
Elsevier, p. 755–771.e9, 2024.
ista: Chen J, Kaufmann W, Chen C, Arai itaru, Kim O, Shigemoto R, Jonas PM. 2024.
Developmental transformation of Ca2+ channel-vesicle nanotopography at a central
GABAergic synapse. Neuron. 112(5), 755–771.e9.
mla: Chen, JingJing, et al. “Developmental Transformation of Ca2+ Channel-Vesicle
Nanotopography at a Central GABAergic Synapse.” Neuron, vol. 112, no. 5,
Elsevier, 2024, p. 755–771.e9, doi:10.1016/j.neuron.2023.12.002.
short: J. Chen, W. Kaufmann, C. Chen, itaru Arai, O. Kim, R. Shigemoto, P.M. Jonas,
Neuron 112 (2024) 755–771.e9.
corr_author: '1'
date_created: 2024-01-21T23:00:56Z
date_published: 2024-03-06T00:00:00Z
date_updated: 2026-05-27T22:30:26Z
day: '06'
ddc:
- '570'
department:
- _id: PeJo
- _id: EM-Fac
- _id: RySh
doi: 10.1016/j.neuron.2023.12.002
ec_funded: 1
external_id:
isi:
- '001202925700001'
pmid:
- '38215739'
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oa_version: Published Version
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call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
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grant_number: P36232
name: Mechanisms of GABA release in hippocampal circuits
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grant_number: '25383'
name: Development of nanodomain coupling between Ca2+ channels and release sensors
at a central inhibitory synapse
publication: Neuron
publication_identifier:
eissn:
- 1097-4199
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/synapses-brought-to-the-point/
record:
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scopus_import: '1'
status: public
title: Developmental transformation of Ca2+ channel-vesicle nanotopography at a central
GABAergic synapse
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: 112
year: '2024'
...
---
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abstract:
- lang: eng
text: "The coupling between presynaptic Ca2+ channels and release sensors is a key
factor that\r\ndetermines speed and efficacy of synapse transmission. At some
excitatory synapses,\r\nchannel–sensor coupling becomes tighter during development,
and tightening is often\r\nassociated with a switch in the reliance on different
Ca2+ channel subtypes. However, the\r\ncoupling topography at many synapses remains
unknown, and it is unclear how it changes\r\nduring development. To address this
question, we analyzed the coupling configuration at the\r\ncerebellar basket cell
(BC) to Purkinje cell (PC) synapse at different developmental stages,\r\ncombining
biophysical analysis, structural analysis, and modeling.\r\nQuantal analysis of
BC–PC indicated that release probability decreased, while the\r\nnumber of functional
sites increased during development. Although transmitter release\r\npersistently
relied on P/Q-type Ca2+ channels in the time period postnatal day 7–23, effects\r\nof
the Ca2+ chelator EGTA and BAPTA applied by intracellular pipette perfusion decreased\r\nduring
development, indicative of tightening of source-sensor coupling. Furthermore,\r\npresynaptic
action potentials became shorter during development, suggesting reduced\r\nefficacy
of Ca2+ channel activation.\r\nStructural analysis by freeze-fracture replica
labeling (FRL) and transmission electron\r\nmicroscopy (EM) indicated that presynaptic
P/Q-type Ca2+ channels formed nanoclusters\r\nthroughout development, whereas
docked vesicles were only clustered at later\r\ndevelopmental stages. The number
of functional release sites correlated better with the AZ\r\nnumber early in development,
but match better with the Ca2+ channel cluster number at later\r\nstages.\r\nModeling
suggested a developmental transformation from a more random to a more\r\nclustered
coupling nanotopography. Thus, presynaptic signaling developmentally approaches\r\na
point-to-point configuration, optimizing speed, reliability, and energy efficiency
of synaptic\r\ntransmission."
acknowledged_ssus:
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: JingJing
full_name: Chen, JingJing
id: 2C4E65C8-F248-11E8-B48F-1D18A9856A87
last_name: Chen
citation:
ama: Chen J. Developmental transformation of nanodomain coupling between Ca2+ channels
and release sensors at a central GABAergic synapse. 2024. doi:10.15479/at:ista:15101
apa: Chen, J. (2024). Developmental transformation of nanodomain coupling between
Ca2+ channels and release sensors at a central GABAergic synapse. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:15101
chicago: Chen, JingJing. “Developmental Transformation of Nanodomain Coupling between
Ca2+ Channels and Release Sensors at a Central GABAergic Synapse.” Institute of
Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15101.
ieee: J. Chen, “Developmental transformation of nanodomain coupling between Ca2+
channels and release sensors at a central GABAergic synapse,” Institute of Science
and Technology Austria, 2024.
ista: Chen J. 2024. Developmental transformation of nanodomain coupling between
Ca2+ channels and release sensors at a central GABAergic synapse. Institute of
Science and Technology Austria.
mla: Chen, JingJing. Developmental Transformation of Nanodomain Coupling between
Ca2+ Channels and Release Sensors at a Central GABAergic Synapse. Institute
of Science and Technology Austria, 2024, doi:10.15479/at:ista:15101.
short: J. Chen, Developmental Transformation of Nanodomain Coupling between Ca2+
Channels and Release Sensors at a Central GABAergic Synapse, Institute of Science
and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-03-11T10:09:54Z
date_published: 2024-03-11T00:00:00Z
date_updated: 2026-04-07T13:24:22Z
day: '11'
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page: '84'
project:
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call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
- _id: bd88be38-d553-11ed-ba76-81d5a70a6ef5
grant_number: P36232
name: Mechanisms of GABA release in hippocampal circuits
- _id: 26B66A3E-B435-11E9-9278-68D0E5697425
grant_number: '25383'
name: Development of nanodomain coupling between Ca2+ channels and release sensors
at a central inhibitory synapse
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
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status: public
supervisor:
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
title: Developmental transformation of nanodomain coupling between Ca2+ channels and
release sensors at a central GABAergic synapse
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: '2024'
...
---
OA_place: publisher
_id: '17881'
abstract:
- lang: eng
text: "This work can be broadly classified into the study of critical phenomena
in a one dimensional\r\narray of Josephson junctions. While we study quantum criticality
when the array is in thermal\r\nequilibrium at zero bias, the non-equilibrium
study involves understanding the bistability of the\r\narray at a critical non-zero
bias. This work furthers our knowledge in understanding quantum\r\ncritical behaviour
at finite temperatures in a one dimensional Josephson array, while also\r\nestablishing
relaxation behaviour dual to that observed in a single Josephson junction.\r\nChapter
1 briefly introduces the model to understand superconductor-insulator phase transition\r\nin
a one dimensional Josephson array and points out the state of the field from where
we\r\nstarted our zero-bias experiments. In this context it discusses the phase-charge
duality observed\r\nin a Josephson array and its dual hysteretic behaviour to
that of a single junction, setting the\r\nground for our non-equilibrium study
of the array.\r\nChapter 2 shows the experimental setup and the chip layout of
the device we measured.\r\nIn chapter 3 we show that, unlike the typical quantum-critical
broadening scenario, in one dimensional Josephson arrays temperature dramatically
shifts the critical region. This shift leads\r\nto a regime of superconductivity
at high temperature, arising from the melted zero-temperature\r\ninsulator. Our
results quantitatively explain the low-temperature onset of superconductivity
in\r\nnominally insulating regimes, and the transition to the strongly insulating
phase. We further\r\npresent, to our knowledge, the first understanding of the
onset of anomalous-metallic resistance\r\nsaturation [30]. This work demonstrates
a non-trivial interplay between thermal effects and\r\nquantum criticality. A
practical consequence is that, counterintuitively, the coherence of\r\nhigh-impedance
quantum circuits is expected to be stabilized by thermal fluctuations.\r\nIn chapter
4, we show relaxation oscillations in a current-biased one dimensional array of\r\nJosephson
junctions. These oscillations are well described by a circuit model, dual to the\r\nordinary
Josephson relaxation oscillations [72]. Injection locking these oscillations results
in\r\ncurrent plateaux. The relaxation step is found to obey a characteristic
self-consistent relation,\r\nsuggesting that it is governed by overheating effects.\r\nChapter
5 describes the various checks and analysis we performed to support our conclusions\r\nmade
in chapters 3 and 4.\r\nFinally, chapter 6 describes the nanofabrication steps
and the finite element electromagnetic\r\nsimulations we performed to fabricate
our devices."
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Soham
full_name: Mukhopadhyay, Soham
id: FDE60288-A89D-11E9-947F-1AF6E5697425
last_name: Mukhopadhyay
orcid: 0000-0001-5263-5559
citation:
ama: Mukhopadhyay S. Thermal effects in one dimensional Josephson chains. 2024.
doi:10.15479/at:ista:17881
apa: Mukhopadhyay, S. (2024). Thermal effects in one dimensional Josephson chains.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17881
chicago: Mukhopadhyay, Soham. “Thermal Effects in One Dimensional Josephson Chains.”
Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17881.
ieee: S. Mukhopadhyay, “Thermal effects in one dimensional Josephson chains,” Institute
of Science and Technology Austria, 2024.
ista: Mukhopadhyay S. 2024. Thermal effects in one dimensional Josephson chains.
Institute of Science and Technology Austria.
mla: Mukhopadhyay, Soham. Thermal Effects in One Dimensional Josephson Chains.
Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17881.
short: S. Mukhopadhyay, Thermal Effects in One Dimensional Josephson Chains, Institute
of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-09-08T10:23:25Z
date_published: 2024-09-10T00:00:00Z
date_updated: 2026-04-07T13:04:06Z
day: '10'
ddc:
- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: AnHi
doi: 10.15479/at:ista:17881
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month: '09'
oa: 1
oa_version: Published Version
page: '82'
project:
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grant_number: P33692
name: Cavity electromechanics across a quantum phase transition
publication_identifier:
isbn:
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issn:
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publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '14032'
relation: part_of_dissertation
status: public
- id: '18057'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
title: Thermal effects in one dimensional Josephson chains
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
OA_place: repository
_id: '18057'
abstract:
- lang: eng
text: "We report relaxation oscillations in a one-dimensional array of Josephson\r\njunctions.
The oscillations are circuit-dual to those ordinarily observed in\r\nsingle junctions.
The dual circuit quantitatively accounts for temporal\r\ndynamics of the array,
including the dependence on biasing conditions.\r\nInjection locking the oscillations
results in well-developed current plateaux.\r\nA thermal model explains the relaxation
step of the oscillations."
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
acknowledgement: "We gratefully acknowledge support from the MIBA machine shop and
Nanofabrication Facility at IST Austria. Work was supported by Austrian FWF grant
P33692-N (S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and
Innovation program under the Marie Sk lodowska-Curie Grant Agreement No. 754411
(J.S.), and a NOMIS foundation research grant (A.P.H.).\r\n"
article_number: '2408.07829'
article_processing_charge: No
arxiv: 1
author:
- first_name: Soham
full_name: Mukhopadhyay, Soham
id: FDE60288-A89D-11E9-947F-1AF6E5697425
last_name: Mukhopadhyay
orcid: 0000-0001-5263-5559
- first_name: Diego A
full_name: Lancheros Naranjo, Diego A
id: 6c55e976-15b2-11ec-abd3-d790e8937fde
last_name: Lancheros Naranjo
- first_name: Jorden L
full_name: Senior, Jorden L
id: 5479D234-2D30-11EA-89CC-40953DDC885E
last_name: Senior
orcid: 0000-0002-0672-9295
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
citation:
ama: Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation
oscillations in a Josephson junction array. arXiv. doi:10.48550/arXiv.2408.07829
apa: Mukhopadhyay, S., Lancheros Naranjo, D. A., Senior, J. L., & Higginbotham,
A. P. (n.d.). Dual relaxation oscillations in a Josephson junction array. arXiv.
https://doi.org/10.48550/arXiv.2408.07829
chicago: Mukhopadhyay, Soham, Diego A Lancheros Naranjo, Jorden L Senior, and Andrew
P Higginbotham. “Dual Relaxation Oscillations in a Josephson Junction Array.”
ArXiv, n.d. https://doi.org/10.48550/arXiv.2408.07829.
ieee: S. Mukhopadhyay, D. A. Lancheros Naranjo, J. L. Senior, and A. P. Higginbotham,
“Dual relaxation oscillations in a Josephson junction array,” arXiv. .
ista: Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation
oscillations in a Josephson junction array. arXiv, 2408.07829.
mla: Mukhopadhyay, Soham, et al. “Dual Relaxation Oscillations in a Josephson Junction
Array.” ArXiv, 2408.07829, doi:10.48550/arXiv.2408.07829.
short: S. Mukhopadhyay, D.A. Lancheros Naranjo, J.L. Senior, A.P. Higginbotham,
ArXiv (n.d.).
corr_author: '1'
date_created: 2024-09-11T09:25:22Z
date_published: 2024-08-14T00:00:00Z
date_updated: 2026-05-27T22:30:27Z
day: '14'
department:
- _id: AnHi
- _id: GradSch
doi: 10.48550/arXiv.2408.07829
ec_funded: 1
external_id:
arxiv:
- '2408.07829'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2408.07829
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 0aa3608a-070f-11eb-9043-e9cd8a2bd931
grant_number: P33692
name: Cavity electromechanics across a quantum phase transition
- _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2
name: Protected states of quantum matter
publication: arXiv
publication_status: draft
related_material:
record:
- id: '20324'
relation: later_version
status: public
- id: '17881'
relation: dissertation_contains
status: public
status: public
title: Dual relaxation oscillations in a Josephson junction array
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
APC_amount: 5887,8 EUR
OA_place: publisher
OA_type: hybrid
_id: '15084'
abstract:
- lang: eng
text: "GABAB receptor (GBR) activation inhibits neurotransmitter release in axon
terminals in the brain, except in medial habenula (MHb) terminals, which show
robust potentiation. However, mechanisms underlying this enigmatic potentiation
remain elusive. Here, we report that GBR activation on MHb terminals induces an
activity-dependent transition from a facilitating, tonic to a depressing, phasic
neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase
in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked
synaptic vesicles (SVs) at the presynaptic active zone (AZ). Strikingly, the depressing
phasic release exhibits looser coupling distance than the tonic release. Furthermore,
the tonic and phasic release are selectively affected by deletion of synaptoporin
(SPO) and Ca\r\n 2+\r\n -dependent
activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation,
the short-term plasticity associated with tonic release, and CAPS2 retains the
increased RRP for initial responses in phasic response trains. The cytosolic protein
CAPS2 showed a SV-associated distribution similar to the vesicular transmembrane
protein SPO, and they were colocalized in the same terminals. We developed the
“Flash and Freeze-fracture” method, and revealed the release of SPO-associated
vesicles in both tonic and phasic modes and activity-dependent recruitment of
CAPS2 to the AZ during phasic release, which lasted several minutes. Overall,
these results indicate that GBR activation translocates CAPS2 to the AZ along
with the fusion of CAPS2-associated SVs, contributing to persistency of the RRP
increase. Thus, we identified structural and molecular mechanisms underlying tonic
and phasic neurotransmitter release and their transition by GBR activation in
MHb terminals."
acknowledged_ssus:
- _id: M-Shop
- _id: PreCl
- _id: EM-Fac
acknowledgement: We thank Erwin Neher and Ipe Ninan for critical comments on the manuscript.
This project has received funding from the European Research Council (ERC) and European
Commission, under the European Union’s Horizon 2020 research and innovation program
(ERC grant agreement no. 694539 to R.S. and the Marie Skłodowska-Curie grant agreement
no. 665385 to C.Ö.). This study was supported by the Cooperative Study Program of
Center for Animal Resources and Collaborative Study of NINS. We thank Kohgaku Eguchi
for statistical analysis, Yu Kasugai for additional EM imaging, Robert Beattie for
the design of the slice recovery chamber for Flash and Freeze experiments, Todor
Asenov from the ISTA machine shop for custom part preparations for high-pressure
freezing, the ISTA preclinical facility for animal caretaking, and the ISTA EM facilities
for technical support.
article_number: e2301449121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Peter
full_name: Koppensteiner, Peter
id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87
last_name: Koppensteiner
orcid: 0000-0002-3509-1948
- first_name: Pradeep
full_name: Bhandari, Pradeep
id: 45EDD1BC-F248-11E8-B48F-1D18A9856A87
last_name: Bhandari
orcid: 0000-0003-0863-4481
- first_name: Hüseyin C
full_name: Önal, Hüseyin C
id: 4659D740-F248-11E8-B48F-1D18A9856A87
last_name: Önal
orcid: 0000-0002-2771-2011
- first_name: Carolina
full_name: Borges Merjane, Carolina
id: 4305C450-F248-11E8-B48F-1D18A9856A87
last_name: Borges Merjane
orcid: 0000-0003-0005-401X
- first_name: Elodie
full_name: Le Monnier, Elodie
id: 3B59276A-F248-11E8-B48F-1D18A9856A87
last_name: Le Monnier
- first_name: Utsa
full_name: Roy, Utsa
id: 4d26cf11-5355-11ee-ae5a-eb05e255b9b2
last_name: Roy
- first_name: Yukihiro
full_name: Nakamura, Yukihiro
last_name: Nakamura
- first_name: Tetsushi
full_name: Sadakata, Tetsushi
last_name: Sadakata
- first_name: Makoto
full_name: Sanbo, Makoto
last_name: Sanbo
- first_name: Masumi
full_name: Hirabayashi, Masumi
last_name: Hirabayashi
- first_name: JeongSeop
full_name: Rhee, JeongSeop
last_name: Rhee
- first_name: Nils
full_name: Brose, Nils
last_name: Brose
- 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: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Koppensteiner P, Bhandari P, Önal C, et al. GABAB receptors induce phasic release
from medial habenula terminals through activity-dependent recruitment of release-ready
vesicles. Proceedings of the National Academy of Sciences of the United States
of America. 2024;121(8). doi:10.1073/pnas.2301449121
apa: Koppensteiner, P., Bhandari, P., Önal, C., Borges Merjane, C., Le Monnier,
E., Roy, U., … Shigemoto, R. (2024). GABAB receptors induce phasic release from
medial habenula terminals through activity-dependent recruitment of release-ready
vesicles. Proceedings of the National Academy of Sciences of the United States
of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2301449121
chicago: Koppensteiner, Peter, Pradeep Bhandari, Cihan Önal, Carolina Borges Merjane,
Elodie Le Monnier, Utsa Roy, Yukihiro Nakamura, et al. “GABAB Receptors Induce
Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment
of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences
of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2301449121.
ieee: P. Koppensteiner et al., “GABAB receptors induce phasic release from
medial habenula terminals through activity-dependent recruitment of release-ready
vesicles,” Proceedings of the National Academy of Sciences of the United States
of America, vol. 121, no. 8. National Academy of Sciences, 2024.
ista: Koppensteiner P, Bhandari P, Önal C, Borges Merjane C, Le Monnier E, Roy U,
Nakamura Y, Sadakata T, Sanbo M, Hirabayashi M, Rhee J, Brose N, Jonas PM, Shigemoto
R. 2024. GABAB receptors induce phasic release from medial habenula terminals
through activity-dependent recruitment of release-ready vesicles. Proceedings
of the National Academy of Sciences of the United States of America. 121(8), e2301449121.
mla: Koppensteiner, Peter, et al. “GABAB Receptors Induce Phasic Release from Medial
Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 121, no. 8, e2301449121, National Academy of Sciences, 2024, doi:10.1073/pnas.2301449121.
short: P. Koppensteiner, P. Bhandari, C. Önal, C. Borges Merjane, E. Le Monnier,
U. Roy, Y. Nakamura, T. Sadakata, M. Sanbo, M. Hirabayashi, J. Rhee, N. Brose,
P.M. Jonas, R. Shigemoto, Proceedings of the National Academy of Sciences of the
United States of America 121 (2024).
corr_author: '1'
date_created: 2024-03-05T09:23:55Z
date_published: 2024-02-20T00:00:00Z
date_updated: 2026-05-27T22:30:28Z
day: '20'
ddc:
- '570'
department:
- _id: RySh
- _id: PeJo
doi: 10.1073/pnas.2301449121
ec_funded: 1
external_id:
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month: '02'
oa: 1
oa_version: Published Version
pmid: 1
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: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/neuronal-insights-flash-and-freeze-fracture/
record:
- id: '13173'
relation: research_data
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title: GABAB receptors induce phasic release from medial habenula terminals through
activity-dependent recruitment of release-ready vesicles
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
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year: '2024'
...
---
OA_embargo: '6'
OA_place: publisher
_id: '18531'
abstract:
- lang: eng
text: "Sex chromosomes and autosomes exhibit very different evolutionary dynamics.\r\nThe
Y chromosome usually degenerates, leaving many X-linked loci hemizygous in\r\nmales.
Since recessive X-linked mutations are always exposed to selection in males,\r\nselection
is more efficient on the X chromosome than on autosomes on recessive\r\nmutations,
leading to faster adaptation on the X chromosome than other genomic\r\nregions,
if beneficial mutations are on average recessive (known as the Faster-X\r\neffect).
In the presence of the functional, but non-recombining gametolog on the Y (as\r\nis
often the case in young non-recombining regions), recessive mutations are\r\nsheltered
from selection on the X chromosome. We model this scenario and show that\r\nthe
efficiency of selection is reduced on diploid X loci due to sheltering by the
Y\r\nchromosome. Reduced efficiency of selection leads to slower adaptation and\r\nincreased
accumulation of deleterious mutations (Slower-X effect). We extended this\r\nmodel
to explore the effect of sex-specific selection on degeneration of sex\r\nchromosomes,
showing theoretically that male-limited genes degenerate on the X\r\nchromosome
and female-biased genes degenerate on the Y chromosome. This\r\nprediction depends
on the effective population size and the mutation rate, explaining\r\nthe variety
of sex chromosome degeneration patterns observed in nature.\r\nTo test for direct
evidence of a Slower-X (or Slower-Z) effect, we analyzed the\r\nZW sex chromosomes
of the flatworm Schistosoma japonicum, which have a very\r\nyoung non-recombining
region with non-degenerated W. Diploid Z-linked genes have\r\nhigher ratios of
non-synonymous to synonymous polymorphisms than autosomal\r\ngenes, supporting
reduced efficiency of selection on the diploid Z region. These results\r\nprovide
evidence of sheltering by the W chromosome, a mechanism that could\r\ncontribute
to Z (X) chromosome degeneration, and illustrate contrasting evolutionary\r\npatterns
in old and young sex chromosome regions. In addition, genes with sexspecific patterns
of expression show opposite patterns of selection in the young\r\n(diploid) and
old (hemizygous) Z, showing the complex manner in which sex-specific selection
shapes the evolutionary patterns of sex chromosomes. "
acknowledged_ssus:
- _id: ScienComp
- _id: CampIT
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Andrea
full_name: Mrnjavac, Andrea
id: 353FAC84-AE61-11E9-8BFC-00D3E5697425
last_name: Mrnjavac
citation:
ama: Mrnjavac A. Early stages of sex chromosome evolution. 2024. doi:10.15479/at:ista:18531
apa: Mrnjavac, A. (2024). Early stages of sex chromosome evolution. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:18531
chicago: Mrnjavac, Andrea. “Early Stages of Sex Chromosome Evolution.” Institute
of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18531.
ieee: A. Mrnjavac, “Early stages of sex chromosome evolution,” Institute of Science
and Technology Austria, 2024.
ista: Mrnjavac A. 2024. Early stages of sex chromosome evolution. Institute of Science
and Technology Austria.
mla: Mrnjavac, Andrea. Early Stages of Sex Chromosome Evolution. Institute
of Science and Technology Austria, 2024, doi:10.15479/at:ista:18531.
short: A. Mrnjavac, Early Stages of Sex Chromosome Evolution, Institute of Science
and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-11-11T08:40:45Z
date_published: 2024-11-11T00:00:00Z
date_updated: 2026-04-07T13:22:45Z
day: '11'
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degree_awarded: PhD
department:
- _id: GradSch
- _id: BeVi
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date_created: 2024-11-13T12:15:54Z
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embargo: 2025-05-11
file_id: '18552'
file_name: AMrnjavac_thesis_library.pdf
file_size: 4228766
relation: main_file
title: Early stages of sex chromosome evolution
file_date_updated: 2025-05-11T22:30:04Z
has_accepted_license: '1'
keyword:
- Sex chromosomes
- evolution
- selection
- sheltering
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '181'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
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relation: part_of_dissertation
status: public
- id: '18549'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
title: Early stages of sex chromosome evolution
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: publisher
_id: '18661'
abstract:
- lang: eng
text: "Across the tree of life, distinct designs of cellular membranes have evolved
that are both stable\r\nand flexible. In bacteria and eukaryotes this trade-off
is accomplished by single-headed lipids\r\nthat self-assemble into flexible bilayer
membranes. By contrast, archaea in many cases possess\r\nboth bilayer and double-headed,
monolayer spanning bolalipids. This composition is believed\r\nto enable extremophile
archaea to survive harsh environments. Here, through the creation of a\r\nminimal
computational model for bolalipid membranes, we discover trade-offs when forming\r\nmembranes
using lipids of a single type. Similar to living archaea, we can tune the stiffness
of\r\nbolalipid molecules. We find that membranes made out of flexible bolalipid
molecules resemble\r\nbilayer membranes as they can adopt U-shaped conformations
to enable higher curvatures.\r\nConversely, rigid bolalipid molecules, like those
found in archaea at higher temperatures,\r\npreferentially take on a straight
conformation to self-assemble into liquid membranes that are\r\nstable, stiff,
prone to pore formation, and which tear during membrane reshaping. Strikingly,\r\nhowever,
our analysis reveals that it is possible to achieve the best of both worlds –
membranes\r\nthat are fluid, stable at high temperatures and flexible enough to
be reshaped without leaking –\r\nthrough the inclusion of a small fraction of
bilayer lipids into a bolalipid membrane. Additionally,\r\nthe curvature-dependent
softening of bolalipid membranes made of lipids with tension-sensitive\r\nconformation
can also enable high rigidity at low curvatures while softening at high curvatures,\r\nmaking
the membrane effectively a plastic material. Taken together, our study compares
the\r\ndifferent membrane designs across the tree of life and indicates how combining
lipids can be\r\nused to resolve trade-offs when generating membranes for (bio)technological
applications.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Miguel
full_name: Santana de Freitas Amaral, Miguel
id: 4f2d02dd-47a9-11ec-ad10-82820ed3f501
last_name: Santana de Freitas Amaral
citation:
ama: 'Santana de Freitas Amaral M. Archaeal membranes : In silico modelling and
design. 2024. doi:10.15479/at:ista:18661'
apa: 'Santana de Freitas Amaral, M. (2024). Archaeal membranes : In silico modelling
and design. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18661'
chicago: 'Santana de Freitas Amaral, Miguel. “Archaeal Membranes : In Silico Modelling
and Design.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18661.'
ieee: 'M. Santana de Freitas Amaral, “Archaeal membranes : In silico modelling and
design,” Institute of Science and Technology Austria, 2024.'
ista: 'Santana de Freitas Amaral M. 2024. Archaeal membranes : In silico modelling
and design. Institute of Science and Technology Austria.'
mla: 'Santana de Freitas Amaral, Miguel. Archaeal Membranes : In Silico Modelling
and Design. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18661.'
short: 'M. Santana de Freitas Amaral, Archaeal Membranes : In Silico Modelling and
Design, Institute of Science and Technology Austria, 2024.'
corr_author: '1'
date_created: 2024-12-16T10:53:39Z
date_published: 2024-12-17T00:00:00Z
date_updated: 2026-04-07T13:22:29Z
day: '17'
ddc:
- '572'
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: AnSa
doi: 10.15479/at:ista:18661
file:
- access_level: closed
checksum: eca06497a29078558395455c890a32d9
content_type: application/zip
creator: mamaral
date_created: 2024-12-18T12:27:01Z
date_updated: 2025-06-18T22:30:03Z
embargo_to: open_access
file_id: '18671'
file_name: 2024_msfa_thesis.zip
file_size: 19161387
relation: source_file
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checksum: 2dc30ea46c5daf48d07e4cccb3c3de00
content_type: application/pdf
creator: mamaral
date_created: 2024-12-18T12:26:30Z
date_updated: 2025-06-18T22:30:03Z
embargo: 2025-06-18
file_id: '18672'
file_name: 2024_msfa_thesis.pdf
file_size: 16530084
relation: main_file
file_date_updated: 2025-06-18T22:30:03Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-sa/4.0/
month: '12'
oa: 1
oa_version: Published Version
page: '57'
publication_identifier:
isbn:
- 978-3-99078-046-6
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '18670'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
title: 'Archaeal membranes : In silico modelling and design'
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: repository
_id: '18670'
abstract:
- lang: eng
text: Across the tree of life, distinct designs of cellular membranes have evolved.
In bacteria and eukaryotes single-headed lipids self-assemble into flexible bilayer
membranes. By contrast, archaea often possess double-headed, monolayer spanning
bolalipids, mixed with bilayer lipids, enabling them to survive in harsh environments.
Here, using a minimal computational model for bolalipid membranes, we discover
trade-offs when forming membranes. We find that membranes made out of flexible
bolalipids resemble bilayer membranes as bolalipids exhibit conformational switch
into U-shaped conformations to enable higher curvatures. Conversely, stiffer bolalipids,
resembling those in extremophile archaea, take on straight conformations and form
liquid membranes that are stiff, and prone to pore formation during membrane reshaping.
Strikingly, we show how to achieve fluid bolalipid membranes that are both stable
and flexible – by including small amounts of bilayer lipids, as archaea do. Our
study explains how different organisms resolve trade-offs when generating membranes
of desired material properties.
acknowledgement: "MA, BB, and AŠ acknowledge funding by the\r\nVolkswagen Foundation
Grant Az 96727. FF\r\nacknowledges fnancial support by the NOMIS\r\nfoundation.
AŠ acknowledges funding by ERC\r\nStarting Grant “NEPA” 802960. We thank\r\nClaudia
Flandoli for help with illustrations."
article_processing_charge: No
author:
- first_name: Miguel
full_name: Santana de Freitas Amaral, Miguel
id: 4f2d02dd-47a9-11ec-ad10-82820ed3f501
last_name: Santana de Freitas Amaral
- first_name: Felix F
full_name: Frey, Felix F
id: a0270b37-8f1a-11ec-95c7-8e710c59a4f3
last_name: Frey
orcid: 0000-0001-8501-6017
- first_name: Xiuyun
full_name: Jiang, Xiuyun
last_name: Jiang
- first_name: Buzz
full_name: Baum, Buzz
last_name: Baum
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: 'Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability
vs flexibility: Reshaping archaeal membranes in silico. bioRxiv. doi:10.1101/2024.10.18.619072'
apa: 'Santana de Freitas Amaral, M., Frey, F. F., Jiang, X., Baum, B., & Šarić,
A. (n.d.). Stability vs flexibility: Reshaping archaeal membranes in silico. bioRxiv.
https://doi.org/10.1101/2024.10.18.619072'
chicago: 'Santana de Freitas Amaral, Miguel, Felix F Frey, Xiuyun Jiang, Buzz Baum,
and Anđela Šarić. “Stability vs Flexibility: Reshaping Archaeal Membranes in Silico.”
BioRxiv, n.d. https://doi.org/10.1101/2024.10.18.619072.'
ieee: 'M. Santana de Freitas Amaral, F. F. Frey, X. Jiang, B. Baum, and A. Šarić,
“Stability vs flexibility: Reshaping archaeal membranes in silico,” bioRxiv.
.'
ista: 'Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability
vs flexibility: Reshaping archaeal membranes in silico. bioRxiv, 10.1101/2024.10.18.619072.'
mla: 'Santana de Freitas Amaral, Miguel, et al. “Stability vs Flexibility: Reshaping
Archaeal Membranes in Silico.” BioRxiv, doi:10.1101/2024.10.18.619072.'
short: M. Santana de Freitas Amaral, F.F. Frey, X. Jiang, B. Baum, A. Šarić, BioRxiv
(n.d.).
corr_author: '1'
date_created: 2024-12-18T10:07:45Z
date_published: 2024-11-27T00:00:00Z
date_updated: 2026-05-27T22:30:30Z
day: '27'
department:
- _id: AnSa
doi: 10.1101/2024.10.18.619072
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2024.10.18.619072
month: '11'
oa: 1
oa_version: Preprint
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
publication: bioRxiv
publication_status: draft
related_material:
record:
- id: '18661'
relation: dissertation_contains
status: public
status: public
title: 'Stability vs flexibility: Reshaping archaeal membranes in silico'
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: '18549'
abstract:
- lang: eng
text: "Sex-linked and autosomal loci experience different selective pressures and\r\nevolutionary
dynamics. X (or Z) chromosomes are often hemizygous, as Y (or W)\r\nchromosomes
often degenerate. Such hemizygous regions can be under greater\r\nefficacy of
selection, as recessive mutations are immediately exposed to selection in\r\nthe
heterogametic sex (the so-called Faster-X or Faster-Z effect). However, in young\r\nnon-recombining
regions, Y/W chromosomes often have many functional genes, and\r\nmany X/Z-linked
loci are therefore diploid. The sheltering of recessive mutations on\r\nthe X/Z
by the Y/W homolog is expected to drive a Slower-X (Slower-Z) effect for\r\ndiploid
X/Z loci, i.e. a reduction in the efficacy of selection. While the Faster-X effect\r\nhas
been studied extensively, much less is known empirically about the evolutionary\r\ndynamics
of diploid X or Z chromosomes. Here, we took advantage of published\r\npopulation
genomic data in the female-heterogametic human parasite Schistosoma\r\njaponicum
to characterize the gene content and diversity levels of the diploid and\r\nhemizygous
regions of the Z chromosome. We used different metrics of selective\r\npressures
acting on genes to test for differences in the efficacy of selection in\r\nhemizygous
and diploid Z regions, relative to autosomes. We found consistent\r\npatterns
suggesting reduced Ne, and reduced efficacy of purifying selection, on both\r\nhemizygous
and diploid Z regions. Moreover, relaxed selection was particularly\r\npronounced
for female-biased genes on the diploid Z, as predicted by Slower-Z\r\ntheory.\r\n"
article_processing_charge: No
author:
- first_name: Andrea
full_name: Mrnjavac, Andrea
id: 353FAC84-AE61-11E9-8BFC-00D3E5697425
last_name: Mrnjavac
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Mrnjavac A, Vicoso B. Evidence of a Slower-Z effect in Schistosoma japonicum.
bioRxiv. doi:10.1101/2024.07.02.601697
apa: Mrnjavac, A., & Vicoso, B. (n.d.). Evidence of a Slower-Z effect in Schistosoma
japonicum. bioRxiv. https://doi.org/10.1101/2024.07.02.601697
chicago: Mrnjavac, Andrea, and Beatriz Vicoso. “Evidence of a Slower-Z Effect in
Schistosoma Japonicum.” BioRxiv, n.d. https://doi.org/10.1101/2024.07.02.601697.
ieee: A. Mrnjavac and B. Vicoso, “Evidence of a Slower-Z effect in Schistosoma japonicum,”
bioRxiv. .
ista: Mrnjavac A, Vicoso B. Evidence of a Slower-Z effect in Schistosoma japonicum.
bioRxiv, 10.1101/2024.07.02.601697.
mla: Mrnjavac, Andrea, and Beatriz Vicoso. “Evidence of a Slower-Z Effect in Schistosoma
Japonicum.” BioRxiv, doi:10.1101/2024.07.02.601697.
short: A. Mrnjavac, B. Vicoso, BioRxiv (n.d.).
corr_author: '1'
date_created: 2024-11-13T09:12:08Z
date_published: 2024-07-04T00:00:00Z
date_updated: 2026-05-27T22:30:29Z
day: '04'
department:
- _id: BeVi
doi: 10.1101/2024.07.02.601697
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2024.07.02.601697
month: '07'
oa: 1
oa_version: Preprint
publication: bioRxiv
publication_status: draft
related_material:
record:
- id: '19370'
relation: later_version
status: public
- id: '18531'
relation: dissertation_contains
status: public
status: public
title: Evidence of a Slower-Z effect in Schistosoma japonicum
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: publisher
_id: '18104'
abstract:
- lang: eng
text: "We introduce a new all-electric platform, that strong couples light to mechanical
motion\r\nby ensuring that the external environmental coupling dominates over
internal mechanical\r\ndissipation. The system only has three everyday components:
AC, DC, and a fip-chip, in which\r\na metallized silicon nitride membrane is fipped
on top of the device under test. This everyday\r\nelectromechanical device can
be operated at low or room temperature and has 10000× lower\r\ninsertion loss
than a comparable commercial quartz crystal, achieves a position imprecision\r\nmatching
state-of-the-art optical interferometer, and enables remote cooling of mechanical\r\nmotion.
The spatial properties of higher order mechanical modes are a promising feature
for\r\nreconstructing unknown charge distributions.\r\n"
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Denise
full_name: Puglia, Denise
id: 4D495994-AE37-11E9-AC72-31CAE5697425
last_name: Puglia
orcid: 0000-0003-1144-2763
citation:
ama: 'Puglia D. Everyday electromechanics: Capacitive strong coupling to mechanical
motion. 2024. doi:10.15479/at:ista:18104'
apa: 'Puglia, D. (2024). Everyday electromechanics: Capacitive strong coupling
to mechanical motion. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18104'
chicago: 'Puglia, Denise. “Everyday Electromechanics: Capacitive Strong Coupling
to Mechanical Motion.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18104.'
ieee: 'D. Puglia, “Everyday electromechanics: Capacitive strong coupling to mechanical
motion,” Institute of Science and Technology Austria, 2024.'
ista: 'Puglia D. 2024. Everyday electromechanics: Capacitive strong coupling to
mechanical motion. Institute of Science and Technology Austria.'
mla: 'Puglia, Denise. Everyday Electromechanics: Capacitive Strong Coupling to
Mechanical Motion. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18104.'
short: 'D. Puglia, Everyday Electromechanics: Capacitive Strong Coupling to Mechanical
Motion, Institute of Science and Technology Austria, 2024.'
corr_author: '1'
date_created: 2024-09-20T12:13:30Z
date_published: 2024-09-20T00:00:00Z
date_updated: 2026-04-07T13:22:10Z
day: '20'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: AnHi
doi: 10.15479/at:ista:18104
file:
- access_level: open_access
checksum: 7969263451b2356bfa0924725aa9de10
content_type: application/pdf
creator: cchlebak
date_created: 2024-09-20T12:07:48Z
date_updated: 2025-05-20T22:30:05Z
embargo: 2025-05-20
file_id: '18105'
file_name: PhD_DPuglia_Final.pdf
file_size: 10778238
relation: main_file
- access_level: closed
checksum: 98dfe7675775e30efffa03f7ff7c091b
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2024-09-20T12:13:09Z
date_updated: 2025-05-20T22:30:05Z
embargo_to: open_access
file_id: '18106'
file_name: PhD_DPuglia_Thesis.zip
file_size: 385419748
relation: source_file
file_date_updated: 2025-05-20T22:30:05Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '09'
oa: 1
oa_version: Published Version
page: '63'
project:
- _id: 0aa3608a-070f-11eb-9043-e9cd8a2bd931
grant_number: P33692
name: Cavity electromechanics across a quantum phase transition
- _id: 62843413-2b32-11ec-9570-c4ec6eabfae7
grant_number: '26088'
name: Surface Charge and Tunneling Multi-Mode Imaging
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '18143'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
title: 'Everyday electromechanics: Capacitive strong coupling to mechanical motion'
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: '2024'
...
---
OA_place: repository
_id: '18143'
abstract:
- lang: eng
text: "Strong optomechanical coupling -- a regime where mechanical motion is damped\r\nby
environmental radiation -- has traditionally required demanding experimental\r\ningredients
such as superconducting resonators, high-quality optical cavities,\r\nor large
magnetic fields. Here we demonstrate a room temperature, cavity-free,\r\nall-electric
device reaching this regime at radio frequencies, enabled by a\r\nmechanically
compliant parallel-plate capacitor with a nanoscale plate\r\nseparation and an
aspect ratio exceeding 1,000. The device has four orders of\r\nmagnitude lower
insertion loss than a comparable commercial quartz crystal, and\r\nachieves a
position imprecision rivaling an optical interferometer. With the\r\nhelp of a
back-action isolation scheme, we observe radiative cooling of\r\nmechanical motion
by a remote cryogenic load. This work provides a\r\ntechnologically accessible
route to high-precision sensing, transduction, and\r\nsignal processing."
article_number: '2407.15314'
article_processing_charge: No
arxiv: 1
author:
- first_name: Denise
full_name: Puglia, Denise
id: 4D495994-AE37-11E9-AC72-31CAE5697425
last_name: Puglia
orcid: 0000-0003-1144-2763
- first_name: Rachel H
full_name: Odessey, Rachel H
id: 9a7a5123-8972-11ed-ae7b-dd1f2af457bd
last_name: Odessey
- first_name: Peter S.
full_name: Burns, Peter S.
last_name: Burns
- first_name: Niklas
full_name: Luhmann, Niklas
last_name: Luhmann
- first_name: Silvan
full_name: Schmid, Silvan
last_name: Schmid
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
citation:
ama: Puglia D, Odessey RH, Burns PS, Luhmann N, Schmid S, Higginbotham AP. Room
temperature, cavity-free capacitive strong coupling to mechanical motion. arXiv.
doi:10.48550/arXiv.2407.15314
apa: Puglia, D., Odessey, R. H., Burns, P. S., Luhmann, N., Schmid, S., & Higginbotham,
A. P. (n.d.). Room temperature, cavity-free capacitive strong coupling to mechanical
motion. arXiv. https://doi.org/10.48550/arXiv.2407.15314
chicago: Puglia, Denise, Rachel H Odessey, Peter S. Burns, Niklas Luhmann, Silvan
Schmid, and Andrew P Higginbotham. “Room Temperature, Cavity-Free Capacitive Strong
Coupling to Mechanical Motion.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2407.15314.
ieee: D. Puglia, R. H. Odessey, P. S. Burns, N. Luhmann, S. Schmid, and A. P. Higginbotham,
“Room temperature, cavity-free capacitive strong coupling to mechanical motion,”
arXiv. .
ista: Puglia D, Odessey RH, Burns PS, Luhmann N, Schmid S, Higginbotham AP. Room
temperature, cavity-free capacitive strong coupling to mechanical motion. arXiv,
2407.15314.
mla: Puglia, Denise, et al. “Room Temperature, Cavity-Free Capacitive Strong Coupling
to Mechanical Motion.” ArXiv, 2407.15314, doi:10.48550/arXiv.2407.15314.
short: D. Puglia, R.H. Odessey, P.S. Burns, N. Luhmann, S. Schmid, A.P. Higginbotham,
ArXiv (n.d.).
corr_author: '1'
date_created: 2024-09-26T06:58:27Z
date_published: 2024-08-24T00:00:00Z
date_updated: 2026-05-27T22:30:31Z
day: '24'
department:
- _id: AnHi
doi: 10.48550/arXiv.2407.15314
external_id:
arxiv:
- '2407.15314'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2407.15314
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 62843413-2b32-11ec-9570-c4ec6eabfae7
grant_number: '26088'
name: Surface Charge and Tunneling Multi-Mode Imaging
- _id: 0aa3608a-070f-11eb-9043-e9cd8a2bd931
grant_number: P33692
name: Cavity electromechanics across a quantum phase transition
publication: arXiv
publication_status: draft
related_material:
record:
- id: '19026'
relation: later_version
status: public
- id: '18104'
relation: dissertation_contains
status: public
status: public
title: Room temperature, cavity-free capacitive strong coupling to mechanical motion
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: publisher
_id: '18642'
abstract:
- lang: eng
text: "This thesis consists of two pieces of work in the broader feld of computational
biology,\r\nboth of which are methods for the analysis of large scale biological
data, implemented in\r\nefcient software.\r\nChapter 2 introduces a statistical
software for causal discovery and inference from observed\r\ngenetic marker and
phenotypic trait data. We explore in simulation how well the method\r\ncan fne-map
genetic efects, fnd the correct causal structure among tens of traits and\r\nmillions
of genetic markers, and infer the causal efect size for the discovered causal\r\nrelations.
We then apply the method to 8 million markers and 17 traits from the UK\r\nBiobank
and show that many relationships found with other methods are likely due to\r\nthe
efects of hidden confounders.\r\nChapter 3 describes how this method can be applied
to longitudinal data. I show how one\r\ncan incorporate the background knowledge
present in the known order of measurements to\r\nimprove the accuracy of the causal
discovery process, and explore the method’s ability to\r\nidentify age specifc
genetic efects, and how the error rates of this recovery are infuenced\r\nby missing
data due to diferent censoring mechanisms.\r\nChapter 4 introduces a statistical
software for the comparison of chromatin contact maps\r\nbased on the structural
similarity index. We explore the robustness of the method to\r\nnoise and size
diferences of the compared maps, show how it can measure evolutionary\r\nconservation
of topological features by providing a similarity ranking of syntenic regions,\r\nand
fnally how it can detect alterations in 3D genome structure due to genetic mutations\r\nin
samples of medical relevance.\r\n"
acknowledgement: "I would like to thank the Swiss National Science Foundation for
funding parts of this work\r\nthrough the Eccellenza Grant \"Improving estimation
and prediction of common complex\r\ndisease risk\" with grant number PCEGP3_181181."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Nick N
full_name: Machnik, Nick N
id: 3591A0AA-F248-11E8-B48F-1D18A9856A87
last_name: Machnik
orcid: 0000-0001-6617-9742
citation:
ama: Machnik NN. Algorithms for causal learning and comparative analysis for genomic
data. 2024. doi:10.15479/at:ista:18642
apa: Machnik, N. N. (2024). Algorithms for causal learning and comparative analysis
for genomic data. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18642
chicago: Machnik, Nick N. “Algorithms for Causal Learning and Comparative Analysis
for Genomic Data.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18642.
ieee: N. N. Machnik, “Algorithms for causal learning and comparative analysis for
genomic data,” Institute of Science and Technology Austria, 2024.
ista: Machnik NN. 2024. Algorithms for causal learning and comparative analysis
for genomic data. Institute of Science and Technology Austria.
mla: Machnik, Nick N. Algorithms for Causal Learning and Comparative Analysis
for Genomic Data. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18642.
short: N.N. Machnik, Algorithms for Causal Learning and Comparative Analysis for
Genomic Data, Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-12-10T13:49:15Z
date_published: 2024-12-11T00:00:00Z
date_updated: 2026-04-07T13:23:06Z
day: '11'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MaRo
doi: 10.15479/at:ista:18642
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date_updated: 2025-06-12T22:30:02Z
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date_updated: 2025-06-12T22:30:02Z
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file_size: 14189810
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language:
- iso: eng
month: '12'
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oa_version: Published Version
page: '138'
project:
- _id: 9B8D11D6-BA93-11EA-9121-9846C619BF3A
grant_number: PCEGP3_181181
name: Improving estimation and prediction of common complex disease risk
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '18648'
relation: part_of_dissertation
status: public
- id: '8707'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
title: Algorithms for causal learning and comparative analysis for genomic data
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
OA_place: repository
OA_type: free access
_id: '18648'
abstract:
- lang: eng
text: "Statistical causal learning in genomics relies on the instrumental variable
method of\r\nMendelian Randomization (MR). Currently, an overwhelming number of
MR studies\r\npurport to show causal relationships among a wide range of risk
factors and outcomes.\r\nHere, we show that selecting instrument variables from
genome-wide association study\r\nestimates leads to high false discovery rates
for many MR approaches, which can be\r\ngreatly reduced by employing a graphical
inference approach which: (i) explicitly tests\r\ninstrumental variable assumptions;
(ii) distinguishes direct from indirect factors in very\r\nhigh-dimensional data;
(iii) discriminates pleiotropic from trait-specific markers, controlling for LD
genome-wide; (iv) accommodates rare variants and binary outcomes in a\r\nprincipled
way; and (v) identifies potential unobserved latent confounding. For 17 traits\r\nand
8.4M variants recorded for 458,747 individuals in the UK Biobank, we show that\r\nstandard
MR analysis gives an abundance of findings that disappear under stringent\r\nassumption
checks, with many relationships reflecting potential unmeasured confounding. This
implies that mixtures of temporal precedence and potential for reverse-causality\r\nprohibit
understanding the underlying nature of phenotypic and genetic correlations in\r\nbiobank
data. We propose that well-curated longitudinal records are likely needed and\r\nthat
our approach provides a first-step toward robust principled screening for potential\r\ncausal
links.\r\n"
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We thank Zoltan Kutalik and members of the Robinson group \r\nat
ISTA for their comments, which improved this manuscript. This work was funded \r\nby
a research collaboration agreement between Boehringer Ingelheim and the research
\r\ngroup of MRR at the Institute of Science and Technology Austria. Additional
funding \r\nwas also provided by an SNSF Eccellenza Grant to MRR (PCEGP3-181181),
and by \r\ncore funding from the Institute of Science and Technology Austria. We
would like \r\nto acknowledge the participants and investigators of the UK Biobank
study. High- \r\nperformance computing was supported by the Scientific Service Units
(SSU) of IST \r\nAustria through resources provided by Scientific Computing (SciComp). "
article_processing_charge: No
author:
- first_name: Nick N
full_name: Machnik, Nick N
id: 3591A0AA-F248-11E8-B48F-1D18A9856A87
last_name: Machnik
orcid: 0000-0001-6617-9742
- first_name: Seyed Mahdi
full_name: Mahmoudi, Seyed Mahdi
id: b9f6d5ef-7774-11eb-a47f-df2c75c02ee7
last_name: Mahmoudi
- first_name: Malgorzata
full_name: Borczyk, Malgorzata
last_name: Borczyk
- first_name: Ilse
full_name: Krätschmer, Ilse
id: 30d4014e-7753-11eb-b44b-db6d61112e73
last_name: Krätschmer
orcid: 0000-0002-5636-9259
- first_name: Markus J.
full_name: Bauer, Markus J.
last_name: Bauer
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
citation:
ama: Machnik NN, Mahmoudi SM, Borczyk M, Krätschmer I, Bauer MJ, Robinson MR. Causal
inference for multiple risk factors and diseases from genomics data. bioRxiv.
2024. doi:10.1101/2023.12.06.570392
apa: Machnik, N. N., Mahmoudi, S. M., Borczyk, M., Krätschmer, I., Bauer, M. J.,
& Robinson, M. R. (2024). Causal inference for multiple risk factors and diseases
from genomics data. bioRxiv. https://doi.org/10.1101/2023.12.06.570392
chicago: Machnik, Nick N, Seyed Mahdi Mahmoudi, Malgorzata Borczyk, Ilse Krätschmer,
Markus J. Bauer, and Matthew Richard Robinson. “Causal Inference for Multiple
Risk Factors and Diseases from Genomics Data.” BioRxiv, 2024. https://doi.org/10.1101/2023.12.06.570392.
ieee: N. N. Machnik, S. M. Mahmoudi, M. Borczyk, I. Krätschmer, M. J. Bauer, and
M. R. Robinson, “Causal inference for multiple risk factors and diseases from
genomics data,” bioRxiv. 2024.
ista: Machnik NN, Mahmoudi SM, Borczyk M, Krätschmer I, Bauer MJ, Robinson MR. 2024.
Causal inference for multiple risk factors and diseases from genomics data. bioRxiv,
10.1101/2023.12.06.570392.
mla: Machnik, Nick N., et al. “Causal Inference for Multiple Risk Factors and Diseases
from Genomics Data.” BioRxiv, 2024, doi:10.1101/2023.12.06.570392.
short: N.N. Machnik, S.M. Mahmoudi, M. Borczyk, I. Krätschmer, M.J. Bauer, M.R.
Robinson, BioRxiv (2024).
corr_author: '1'
date_created: 2024-12-11T10:42:59Z
date_published: 2024-08-10T00:00:00Z
date_updated: 2026-05-27T22:30:33Z
day: '10'
department:
- _id: MaRo
doi: 10.1101/2023.12.06.570392
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2023.12.06.570392
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 9B8D11D6-BA93-11EA-9121-9846C619BF3A
grant_number: PCEGP3_181181
name: Improving estimation and prediction of common complex disease risk
- _id: bd936e6f-d553-11ed-ba76-a82299f63e8c
grant_number: '590359'
name: Advanced statistical modelling to facilitate more accurate characterisation
of disease phenotypes, improved genetic mapping, and effective therapeutic hypothesis
generation
publication: bioRxiv
publication_status: published
related_material:
record:
- id: '18642'
relation: dissertation_contains
status: public
status: public
title: Causal inference for multiple risk factors and diseases from genomics data
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2024'
...
---
OA_embargo: '12'
OA_place: publisher
_id: '18574'
abstract:
- lang: eng
text: "Biological vision is unlike a camera; rather than transmitting light information
faithfully, early\r\nvisual circuits process the visual scene to convey only the
relevant information in an efficient\r\nmanner. Consequentially, the nature of
this visual processing then depends on what is the\r\nrelevant information in
a scene and on the notion of efficiency. In this work, I study how visual\r\nprocessing
is modulated by two different variations in the visual scene. First, I discovered
that\r\nin the mouse (Mus musculus) retina, Retinal Ganglion Cells in the upper
and lower visual\r\nfield have differences in the center surround structure of
their receptive fields. Comparison\r\nwith models of efficient coding show that
this adaptation likely evolved to cope with the\r\nbrightness gradient from the
sky to the ground that is pervasive in natural scenes. In the\r\nsecond project,
I study how the downstream neurons in the Superior Colliculus dynamically\r\nchange
their temporal selectivity depending on the ambient luminance and behavioral state.\r\nAs
the scene gets darker or when the animal is is less aroused, the neuronal responses
get\r\nlaggier, while still maintaining their relative timing with respect to
the population. Overall, this\r\nwork emphasises the need to understand visual
processing in the context of specific demands\r\nof the animal in its the environment.
The adaptive changes in the visual system, from the\r\nretinal ganglion cells
to the superior colliculus, highlight the intricate ways in which biological\r\nvision
optimizes the processing of visual information.\r\n"
acknowledged_ssus:
- _id: Bio
- _id: ScienComp
- _id: PreCl
- _id: LifeSc
- _id: M-Shop
- _id: E-Lib
acknowledgement: "This work would have been impossible without the Scientific Service
Units of IST Austria. The resources and expertise provided by Scientific Computing
(especially Alois Schlögl), the MIBA Machine Shop (especially Todor Asenov), the
Preclinical Facility (especially Freyja Langer), the Library, the Lab Support Facility
and the Imaging and Optics Facility were the essential bedrock I could build upon.
I would also like to thank IT support at ISTA for powering through remote work and
a cyberattack.\r\nI am grateful for having been funded initially by the European
Union Horizon 2020 Marie Skłodowska-Curie grant 665385 and later by Prof. Maximilian
Joesch's the European Research Council Starting (756502) and Consolidator (101086580)
Grants."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Divyansh
full_name: Gupta, Divyansh
id: 2A485EBE-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
orcid: 0000-0001-7400-6665
citation:
ama: Gupta D. Visual adaptations to natural statistics. 2024. doi:10.15479/at:ista:18574
apa: Gupta, D. (2024). Visual adaptations to natural statistics. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:18574
chicago: Gupta, Divyansh. “Visual Adaptations to Natural Statistics.” Institute
of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18574.
ieee: D. Gupta, “Visual adaptations to natural statistics,” Institute of Science
and Technology Austria, 2024.
ista: Gupta D. 2024. Visual adaptations to natural statistics. Institute of Science
and Technology Austria.
mla: Gupta, Divyansh. Visual Adaptations to Natural Statistics. Institute
of Science and Technology Austria, 2024, doi:10.15479/at:ista:18574.
short: D. Gupta, Visual Adaptations to Natural Statistics, Institute of Science
and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-11-20T21:30:44Z
date_published: 2024-11-22T00:00:00Z
date_updated: 2026-04-07T13:24:48Z
day: '22'
ddc:
- '573'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MaJö
doi: 10.15479/at:ista:18574
ec_funded: 1
file:
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checksum: ebb000d361c36b22ed6e639a931c6b7c
content_type: application/zip
creator: dgupta
date_created: 2024-11-25T14:44:03Z
date_updated: 2025-11-11T23:30:02Z
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file_name: PhD Thesis - Divyansh Gupta.zip
file_size: 75512262
relation: source_file
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checksum: 1282401eb71598bc311058b0fcefc6a1
content_type: application/pdf
creator: dgupta
date_created: 2024-11-26T11:43:19Z
date_updated: 2025-11-11T23:30:02Z
embargo: 2025-11-11
file_id: '18591'
file_name: PDFA_PhD_Thesis___Divyansh_Gupta-26_11_24.pdf
file_size: 6412619
relation: main_file
file_date_updated: 2025-11-11T23:30:02Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '11'
oa: 1
oa_version: Published Version
page: '86'
project:
- _id: bdaf81a8-d553-11ed-ba76-c95961984540
grant_number: '101086580'
name: 'Action Selection in the Midbrain: Neuromodulation of Visuomotor Senses'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 2634E9D2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '756502'
name: Circuits of Visual Attention
publication_identifier:
isbn:
- 978-3-99078-050-3
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12349'
relation: part_of_dissertation
status: public
- id: '12370'
relation: research_data
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: Visual adaptations to natural statistics
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: '18471'
abstract:
- lang: eng
text: "Spatial omics technologies are enriching our understanding of complex biological
samples, by\r\nallowing us to study their molecular composition while preserving
the spatial relationships\r\nbetween molecules in their native context. As the
field continues to advance, there are\r\ntechnical challenges that need to be
addressed in order to take full advantage of the spatial\r\ncapabilities of these
methods. In this work, I present two technical developments that I\r\nestablished
for multiplexed error robust FISH (MERFISH) throughout my PhD: (1) pushing the\r\nspatial
resolution limits to the nanoscale, and (2) adding rich tissue context to the
mouse brain\r\ntranscriptome. To achieve nanoscale resolution with MERFISH in
cultured cells, I combined it\r\nwith stimulated emission depletion (STED) and
expansion microscopy (ExM) to achieve a\r\nspatial resolution as low as ~20 nm,
and explored the compatibility of MERFISH with singlemolecule localization microscopy
(SMLM) techniques. To visualize targeted mRNAs in mouse\r\nbrain tissue, I applied
the comprehensive analysis of tissues across scales (CATS) toolbox, which\r\nprovides
an unbiased morphological readout by labeling the extracellular domain. I\r\nsuccessfully
established this method, which we call CATS-MERFISH-ExM, to work with thick\r\nmouse
brain slices, being able to extract transcriptomics information with 3D tissue
context.\r\nCATS-MERFISH-ExM enabled us to identify cell types and further visualize
the subcellular\r\ndistribution of transcripts in mouse brain tissue, shedding
light on the neuropil-specific\r\ntranscriptome. This method provides integrated
information on cellular structure and\r\ntranscriptomes in situ, and could potentially
be applied with other modalities, opening new\r\navenues for scientific discovery. "
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
- _id: M-Shop
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Nathalie
full_name: Agudelo Duenas, Nathalie
id: 40E7F008-F248-11E8-B48F-1D18A9856A87
last_name: Agudelo Duenas
citation:
ama: Agudelo Duenas N. Visualizing the neuronal transcriptional landscape with tissue
context. 2024. doi:10.15479/at:ista:18471
apa: Agudelo Duenas, N. (2024). Visualizing the neuronal transcriptional landscape
with tissue context. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18471
chicago: Agudelo Duenas, Nathalie. “Visualizing the Neuronal Transcriptional Landscape
with Tissue Context.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18471.
ieee: N. Agudelo Duenas, “Visualizing the neuronal transcriptional landscape with
tissue context,” Institute of Science and Technology Austria, 2024.
ista: Agudelo Duenas N. 2024. Visualizing the neuronal transcriptional landscape
with tissue context. Institute of Science and Technology Austria.
mla: Agudelo Duenas, Nathalie. Visualizing the Neuronal Transcriptional Landscape
with Tissue Context. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18471.
short: N. Agudelo Duenas, Visualizing the Neuronal Transcriptional Landscape with
Tissue Context, Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-10-26T20:02:42Z
date_published: 2024-10-28T00:00:00Z
date_updated: 2026-04-14T08:34:37Z
day: '28'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoDa
doi: 10.15479/at:ista:18471
ec_funded: 1
file:
- access_level: closed
checksum: 6d7c7725d040d8debc070dcb35ac965d
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: nagudelo
date_created: 2024-10-26T22:29:06Z
date_updated: 2025-05-05T22:30:04Z
embargo_to: open_access
file_id: '18475'
file_name: PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.docx
file_size: 183077763
relation: source_file
- access_level: open_access
checksum: 52f9c0bf2bdafa3baf827b73814a53ff
content_type: application/pdf
creator: nagudelo
date_created: 2024-10-26T23:13:33Z
date_updated: 2025-05-05T22:30:04Z
embargo: 2025-05-05
file_id: '18476'
file_name: PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.pdf
file_size: 47027710
relation: main_file
file_date_updated: 2025-05-05T22:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '97'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232
name: Molecular Drug Targets
publication_identifier:
isbn:
- 978-3-99078-044-2
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
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: Visualizing the neuronal transcriptional landscape with tissue context
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: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '17148'
abstract:
- lang: eng
text: During neural tube (NT) development, the notochord induces an organizer, the
floorplate, which secretes Sonic Hedgehog (SHH) to pattern neural progenitors.
Conversely, NT organoids (NTOs) from embryonic stem cells (ESCs) spontaneously
form floorplates without the notochord, demonstrating that stem cells can self-organize
without embryonic inducers. Here, we investigated floorplate self-organization
in clonal mouse NTOs. Expression of the floorplate marker FOXA2 was initially
spatially scattered before resolving into multiple clusters, which underwent competition
and sorting, resulting in a stable “winning” floorplate. We identified that BMP
signaling governed long-range cluster competition. FOXA2+ clusters expressed BMP4,
suppressing FOXA2 in receiving cells while simultaneously expressing the BMP-inhibitor
NOGGIN, promoting cluster persistence. Noggin mutation perturbed floorplate formation
in NTOs and in the NT in vivo at mid/hindbrain regions, demonstrating how the
floorplate can form autonomously without the notochord. Identifying the pathways
governing organizer self-organization is critical for harnessing the developmental
plasticity of stem cells in tissue engineering.
acknowledgement: We thank P. Pasierbek, A.C. Moreno, T. Lendl, and K. Aumayr for microscopy
support; G. Schmauss for FACS support; M. Novatchkova for assistance with Bioinformatic
analyses; J. Ahel, A. Polikarpova, S. Horer, E. Cesare, and E. Norouzi for technical
assistance; A. Meinhardt for supervision; DRESDEN-concept Genome Center, A. Vogt,
A. Sommer, and the Vienna BioCenter NGS facility for RNA sequencing. We are grateful
to M. Placzek and E. Martí for discussions about the floorplate; to S. Shvartsman
for valuable input; to A. Aszodi, W. Masselink, and S. Raiders for advice on statistical
analyses; to J. Cornwall Scoones, G. Martello, and Tanaka lab members for critical
reading of the manuscript; E. Bassat and E. Chatzidaki for contributing schematics;
and to K. Lust for support. This project has received funding from the European
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
programme (grant agreement ERC AdG 742046) to E.M.T. This research was funded in
whole or in part by the Austrian Science Fund (FWF) (10.55776/F7803-B) (Stem Cell
Modulation) to E.M.T. and A.K., Sir Henry Wellcome postdoctoral fellowship to H.T.S.,
ELBE fellowship to K.I., and National Science Foundation (US) Phy 2013131 to E.S.
The A.K. lab is also supported by ISTA and the European Research Council under Horizon
Europe grant 101044579, and S.L. is supported by Gesellschaft für Forschungsförderung
Niederösterreich m.b.H. fellowship SC19-011. This work was supported in part by
the Francis Crick Institute, which receives its core funding from Cancer Research
UK (CC001051), the UK Medical Research Council (CC001051), and the Wellcome Trust
(CC001051). For the purpose of open access, the authors have applied a CC BY public
copyright license to any author accepted manuscript (AAM) version arising from this
submission.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Teresa
full_name: Krammer, Teresa
last_name: Krammer
- first_name: Hannah T.
full_name: Stuart, Hannah T.
last_name: Stuart
- first_name: Elena
full_name: Gromberg, Elena
last_name: Gromberg
- first_name: Keisuke
full_name: Ishihara, Keisuke
last_name: Ishihara
- first_name: Dillon
full_name: Cislo, Dillon
last_name: Cislo
- first_name: Manuela
full_name: Melchionda, Manuela
last_name: Melchionda
- first_name: Fernando
full_name: Becerril Perez, Fernando
last_name: Becerril Perez
- first_name: Jingkui
full_name: Wang, Jingkui
last_name: Wang
- first_name: Elena
full_name: Costantini, Elena
last_name: Costantini
- first_name: Stefanie
full_name: Rus, Stefanie
id: 4D9EC9B6-F248-11E8-B48F-1D18A9856A87
last_name: Rus
orcid: 0000-0001-8703-1093
- first_name: Laura
full_name: Arbanas, Laura
last_name: Arbanas
- first_name: Alexandra
full_name: Hörmann, Alexandra
last_name: Hörmann
- first_name: Ralph A.
full_name: Neumüller, Ralph A.
last_name: Neumüller
- first_name: Nicola
full_name: Elvassore, Nicola
last_name: Elvassore
- first_name: Eric
full_name: Siggia, Eric
last_name: Siggia
- first_name: James
full_name: Briscoe, James
last_name: Briscoe
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Elly M.
full_name: Tanaka, Elly M.
last_name: Tanaka
citation:
ama: Krammer T, Stuart HT, Gromberg E, et al. Mouse neural tube organoids self-organize
floorplate through BMP-mediated cluster competition. Developmental Cell.
2024;59(15):1940-1953.e10. doi:10.1016/j.devcel.2024.04.021
apa: Krammer, T., Stuart, H. T., Gromberg, E., Ishihara, K., Cislo, D., Melchionda,
M., … Tanaka, E. M. (2024). Mouse neural tube organoids self-organize floorplate
through BMP-mediated cluster competition. Developmental Cell. Elsevier.
https://doi.org/10.1016/j.devcel.2024.04.021
chicago: Krammer, Teresa, Hannah T. Stuart, Elena Gromberg, Keisuke Ishihara, Dillon
Cislo, Manuela Melchionda, Fernando Becerril Perez, et al. “Mouse Neural Tube
Organoids Self-Organize Floorplate through BMP-Mediated Cluster Competition.”
Developmental Cell. Elsevier, 2024. https://doi.org/10.1016/j.devcel.2024.04.021.
ieee: T. Krammer et al., “Mouse neural tube organoids self-organize floorplate
through BMP-mediated cluster competition,” Developmental Cell, vol. 59,
no. 15. Elsevier, p. 1940–1953.e10, 2024.
ista: Krammer T, Stuart HT, Gromberg E, Ishihara K, Cislo D, Melchionda M, Becerril
Perez F, Wang J, Costantini E, Rus S, Arbanas L, Hörmann A, Neumüller RA, Elvassore
N, Siggia E, Briscoe J, Kicheva A, Tanaka EM. 2024. Mouse neural tube organoids
self-organize floorplate through BMP-mediated cluster competition. Developmental
Cell. 59(15), 1940–1953.e10.
mla: Krammer, Teresa, et al. “Mouse Neural Tube Organoids Self-Organize Floorplate
through BMP-Mediated Cluster Competition.” Developmental Cell, vol. 59,
no. 15, Elsevier, 2024, p. 1940–1953.e10, doi:10.1016/j.devcel.2024.04.021.
short: T. Krammer, H.T. Stuart, E. Gromberg, K. Ishihara, D. Cislo, M. Melchionda,
F. Becerril Perez, J. Wang, E. Costantini, S. Rus, L. Arbanas, A. Hörmann, R.A.
Neumüller, N. Elvassore, E. Siggia, J. Briscoe, A. Kicheva, E.M. Tanaka, Developmental
Cell 59 (2024) 1940–1953.e10.
date_created: 2024-06-16T22:01:07Z
date_published: 2024-08-01T00:00:00Z
date_updated: 2026-05-27T22:31:10Z
day: '01'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1016/j.devcel.2024.04.021
external_id:
isi:
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pmid:
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file:
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creator: dernst
date_created: 2025-01-13T10:59:12Z
date_updated: 2025-01-13T10:59:12Z
file_id: '18841'
file_name: 2024_DevelopmentalCell_Krammer.pdf
file_size: 6249076
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file_date_updated: 2025-01-13T10:59:12Z
has_accepted_license: '1'
intvolume: ' 59'
isi: 1
issue: '15'
language:
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month: '08'
oa: 1
oa_version: Published Version
page: 1940-1953.e10
pmid: 1
project:
- _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa
grant_number: '101044579'
name: Mechanisms of tissue size regulation in spinal cord development
- _id: 9B9B39FA-BA93-11EA-9121-9846C619BF3A
grant_number: SC19-011
name: The regulatory logic of pattern formation in the vertebrate dorsal neural
tube
publication: Developmental Cell
publication_identifier:
eissn:
- 1878-1551
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster
competition
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 59
year: '2024'
...
---
APC_amount: 804 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18601'
abstract:
- lang: eng
text: "Geometrically controlled stem cell differentiation promotes reproducible
pattern formation. Here, we present a protocol to fabricate elastomeric stencils
for patterned stem cell differentiation. We describe procedures for using photolithography
to produce molds, followed by molding polydimethylsiloxane (PDMS) to obtain stencils
with through holes. We then provide instructions for culturing cells on stencils
and, finally, removing stencils to allow colony growth and cell migration. This
approach yields reproducible two-dimensional organoids tailored for quantitative
studies of growth and pattern formation.\r\nFor complete details on the use and
execution of this protocol, please refer to Lehr et al.1"
acknowledged_ssus:
- _id: NanoFab
acknowledgement: We thank the nanofabrication facility at ISTA for technical assistance.
Work in the A.K. lab is supported by ISTA, the European Research Council under Horizon
Europe (grant 101044579), and the Austrian Science Fund (FWF) (grant https://doi.org/10.55776/F78).
S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H.
fellowship SC19-011.
article_number: '103187'
article_processing_charge: Yes
article_type: original
author:
- first_name: Stefanie
full_name: Rus, Stefanie
id: 4D9EC9B6-F248-11E8-B48F-1D18A9856A87
last_name: Rus
orcid: 0000-0001-8703-1093
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Monika Aleksandra
full_name: Kulig, Monika Aleksandra
id: 3331f5ae-e896-11ec-af79-eeb79769bcb7
last_name: Kulig
- first_name: Thomas
full_name: Minchington, Thomas
id: 7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f
last_name: Minchington
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
citation:
ama: Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. Protocol for fabricating
elastomeric stencils for patterned stem cell differentiation. STAR Protocols.
2024;5(4). doi:10.1016/j.xpro.2024.103187
apa: Rus, S., Merrin, J., Kulig, M. A., Minchington, T., & Kicheva, A. (2024).
Protocol for fabricating elastomeric stencils for patterned stem cell differentiation.
STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2024.103187
chicago: Rus, Stefanie, Jack Merrin, Monika Aleksandra Kulig, Thomas Minchington,
and Anna Kicheva. “Protocol for Fabricating Elastomeric Stencils for Patterned
Stem Cell Differentiation.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2024.103187.
ieee: S. Rus, J. Merrin, M. A. Kulig, T. Minchington, and A. Kicheva, “Protocol
for fabricating elastomeric stencils for patterned stem cell differentiation,”
STAR Protocols, vol. 5, no. 4. Elsevier, 2024.
ista: Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. 2024. Protocol for fabricating
elastomeric stencils for patterned stem cell differentiation. STAR Protocols.
5(4), 103187.
mla: Rus, Stefanie, et al. “Protocol for Fabricating Elastomeric Stencils for Patterned
Stem Cell Differentiation.” STAR Protocols, vol. 5, no. 4, 103187, Elsevier,
2024, doi:10.1016/j.xpro.2024.103187.
short: S. Rus, J. Merrin, M.A. Kulig, T. Minchington, A. Kicheva, STAR Protocols
5 (2024).
corr_author: '1'
date_created: 2024-12-01T23:01:53Z
date_published: 2024-12-20T00:00:00Z
date_updated: 2026-05-27T22:31:09Z
day: '20'
ddc:
- '570'
department:
- _id: AnKi
- _id: NanoFab
doi: 10.1016/j.xpro.2024.103187
external_id:
pmid:
- '39602310'
file:
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checksum: 0c61a6f9978608a103865905e06f4581
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creator: dernst
date_created: 2024-12-03T10:53:23Z
date_updated: 2024-12-03T10:53:23Z
file_id: '18610'
file_name: 2024_STARProtoc_Lehr.pdf
file_size: 4989169
relation: main_file
success: 1
file_date_updated: 2024-12-03T10:53:23Z
has_accepted_license: '1'
intvolume: ' 5'
issue: '4'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa
grant_number: '101044579'
name: Mechanisms of tissue size regulation in spinal cord development
- _id: 9B9B39FA-BA93-11EA-9121-9846C619BF3A
grant_number: SC19-011
name: The regulatory logic of pattern formation in the vertebrate dorsal neural
tube
publication: STAR Protocols
publication_identifier:
eissn:
- 2666-1667
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '19763'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Protocol for fabricating elastomeric stencils for patterned stem cell differentiation
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: '2024'
...
---
APC_amount: 3145,39 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '17890'
abstract:
- lang: eng
text: Our understanding of the molecular pathways that regulate oogenesis and define
cellular identity in the Arthropod female reproductive system and the extent of
their conservation is currently very limited. This is due to the focus on model
systems, including Drosophila and Daphnia, which do not reflect the observed diversity
of morphologies, reproductive modes, and sex chromosome systems. We use single-nucleus
RNA and ATAC sequencing to produce a comprehensive single nucleus atlas of the
adult Artemia franciscana female reproductive system. We map our data to the Fly
Cell Atlas single-nucleus dataset of the Drosophila melanogaster ovary, shedding
light on the conserved regulatory programs between the two distantly related Arthropod
species. We identify the major cell types known to be present in the Artemia ovary,
including germ cells, follicle cells, and ovarian muscle cells. Additionally,
we use the germ cells to explore gene regulation and expression of the Z chromosome
during meiosis, highlighting its unique regulatory dynamics and allowing us to
explore the presence of meiotic sex chromosome silencing in this group.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We thank the Vicoso group for their valuable comments on the earlier
draft of the manuscript. We would also like to thank the Vienna BioCenter Next Generation
Sequencing (NGS) facility staff, and in particular, Thomas Grentzinger for his support
with the handling and sequencing of the samples, the scientific computing unit at
ISTA for the computational resources, Brittney Wick for the help with hosting our
data on the UCSC Cell Browser, and Lora B. Sweeney for her valuable input at the
different stages of the project.\r\nThis research was funded by the Austrian science
fund (FWF), as part of the SFB Meiosis consortium https://sfbmeiosis.org/, grant
ID FWF SFB F88-10) to BV. "
article_number: e1011376
article_processing_charge: Yes
article_type: original
author:
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Elkrewi MN, Vicoso B. Single-nucleus atlas of the Artemia female reproductive
system suggests germline repression of the Z chromosome. PLoS Genetics.
2024;20(8). doi:10.1371/journal.pgen.1011376
apa: Elkrewi, M. N., & Vicoso, B. (2024). Single-nucleus atlas of the Artemia
female reproductive system suggests germline repression of the Z chromosome. PLoS
Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1011376
chicago: Elkrewi, Marwan N, and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia
Female Reproductive System Suggests Germline Repression of the Z Chromosome.”
PLoS Genetics. Public Library of Science, 2024. https://doi.org/10.1371/journal.pgen.1011376.
ieee: M. N. Elkrewi and B. Vicoso, “Single-nucleus atlas of the Artemia female reproductive
system suggests germline repression of the Z chromosome,” PLoS Genetics,
vol. 20, no. 8. Public Library of Science, 2024.
ista: Elkrewi MN, Vicoso B. 2024. Single-nucleus atlas of the Artemia female reproductive
system suggests germline repression of the Z chromosome. PLoS Genetics. 20(8),
e1011376.
mla: Elkrewi, Marwan N., and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia
Female Reproductive System Suggests Germline Repression of the Z Chromosome.”
PLoS Genetics, vol. 20, no. 8, e1011376, Public Library of Science, 2024,
doi:10.1371/journal.pgen.1011376.
short: M.N. Elkrewi, B. Vicoso, PLoS Genetics 20 (2024).
corr_author: '1'
date_created: 2024-09-08T22:01:11Z
date_published: 2024-08-30T00:00:00Z
date_updated: 2026-05-27T22:31:20Z
day: '30'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1371/journal.pgen.1011376
external_id:
isi:
- '001304090200001'
pmid:
- '39213449'
file:
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checksum: f5d96b9af57126fc1063e951440477d6
content_type: application/pdf
creator: dernst
date_created: 2024-09-11T07:54:12Z
date_updated: 2024-09-11T07:54:12Z
file_id: '18056'
file_name: 2024_PloSGenetics_Elkrewi.pdf
file_size: 8962687
relation: main_file
success: 1
file_date_updated: 2024-09-11T07:54:12Z
has_accepted_license: '1'
intvolume: ' 20'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1
call_identifier: FWF
name: FWF Open Access Fund
- _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396
grant_number: F8810
name: The highjacking of meiosis for asexual reproduction
publication: PLoS Genetics
publication_identifier:
eissn:
- 1553-7404
issn:
- 1553-7390
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/Melkrewi/Artemia-snRNAseq-Project
record:
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relation: research_data
status: public
- id: '19386'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Single-nucleus atlas of the Artemia female reproductive system suggests germline
repression of the Z chromosome
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: 20
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '15009'
abstract:
- lang: eng
text: Since the commercialization of brine shrimp (genus Artemia) in the 1950s,
this lineage, and in particular the model species Artemia franciscana, has been
the subject of extensive research. However, our understanding of the genetic mechanisms
underlying various aspects of their reproductive biology, including sex determination,
is still lacking. This is partly due to the scarcity of genomic resources for
Artemia species and crustaceans in general. Here, we present a chromosome-level
genome assembly of A. franciscana (Kellogg 1906), from the Great Salt Lake, United
States. The genome is 1 GB, and the majority of the genome (81%) is scaffolded
into 21 linkage groups using a previously published high-density linkage map.
We performed coverage and FST analyses using male and female genomic and transcriptomic
reads to quantify the extent of differentiation between the Z and W chromosomes.
Additionally, we quantified the expression levels in male and female heads and
gonads and found further evidence for dosage compensation in this species.
article_number: evae006
article_processing_charge: Yes
article_type: original
author:
- first_name: Vincent K
full_name: Bett, Vincent K
id: 57854184-AAE0-11E9-8D04-98D6E5697425
last_name: Bett
- first_name: Ariana
full_name: Macon, Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
citation:
ama: Bett VK, Macon A, Vicoso B, Elkrewi MN. Chromosome-level assembly of Artemia
franciscana sheds light on sex chromosome differentiation. Genome Biology and
Evolution. 2024;16(1). doi:10.1093/gbe/evae006
apa: Bett, V. K., Macon, A., Vicoso, B., & Elkrewi, M. N. (2024). Chromosome-level
assembly of Artemia franciscana sheds light on sex chromosome differentiation.
Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evae006
chicago: Bett, Vincent K, Ariana Macon, Beatriz Vicoso, and Marwan N Elkrewi. “Chromosome-Level
Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.”
Genome Biology and Evolution. Oxford University Press, 2024. https://doi.org/10.1093/gbe/evae006.
ieee: V. K. Bett, A. Macon, B. Vicoso, and M. N. Elkrewi, “Chromosome-level assembly
of Artemia franciscana sheds light on sex chromosome differentiation,” Genome
Biology and Evolution, vol. 16, no. 1. Oxford University Press, 2024.
ista: Bett VK, Macon A, Vicoso B, Elkrewi MN. 2024. Chromosome-level assembly of
Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology
and Evolution. 16(1), evae006.
mla: Bett, Vincent K., et al. “Chromosome-Level Assembly of Artemia Franciscana
Sheds Light on Sex Chromosome Differentiation.” Genome Biology and Evolution,
vol. 16, no. 1, evae006, Oxford University Press, 2024, doi:10.1093/gbe/evae006.
short: V.K. Bett, A. Macon, B. Vicoso, M.N. Elkrewi, Genome Biology and Evolution
16 (2024).
corr_author: '1'
date_created: 2024-02-18T23:01:02Z
date_published: 2024-01-20T00:00:00Z
date_updated: 2026-05-27T22:31:20Z
day: '20'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/gbe/evae006
external_id:
isi:
- '001153952800001'
pmid:
- '38245839'
file:
- access_level: open_access
checksum: 106a40f10443b2e7ba66749844ebbdf1
content_type: application/pdf
creator: dernst
date_created: 2024-02-26T09:54:59Z
date_updated: 2024-02-26T09:54:59Z
file_id: '15029'
file_name: 2024_GBE_Bett.pdf
file_size: 5213306
relation: main_file
success: 1
file_date_updated: 2024-02-26T09:54:59Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology and Evolution
publication_identifier:
eissn:
- 1759-6653
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '14705'
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relation: dissertation_contains
status: public
scopus_import: '1'
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title: Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome
differentiation
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: 16
year: '2024'
...