---
OA_place: repository
OA_type: green
_id: '21691'
abstract:
- lang: eng
text: Light-matter interaction with squeezed vacuum has received much interest for
the ability to enhance the native interaction strength between an atom and a photon
with a reservoir assumed to have an infinite bandwidth. Here, we study a model
of parametrically driven cavity quantum electrodynamics (cavity QED) for enhancing
light-matter interaction while subjected to a finite-bandwidth squeezed vacuum
drive. Our method is capable of unveiling the effect of relative bandwidth as
well as squeezing required to observe the anticipated anti-crossing spectrum and
enhanced cooperativity without the ideal squeezed bath assumption. Furthermore,
we analyze the practicality of said models when including intrinsic photon loss
due to resonators imperfection. With these results, we outline the requirements
for experimentally implementing an effectively squeezed bath in solid-state platforms
such as InAs quantum dot cavity QED such that \textit{in situ} control and enhancement
of light-matter interaction could be realized.
article_number: '2412.15068'
article_processing_charge: No
arxiv: 1
author:
- first_name: Trung Kiên
full_name: Lê, Trung Kiên
last_name: Lê
- first_name: Daniil M.
full_name: Lukin, Daniil M.
last_name: Lukin
- first_name: Charles
full_name: Roques-Carmes, Charles
id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82
last_name: Roques-Carmes
- first_name: Aviv
full_name: Karnieli, Aviv
last_name: Karnieli
- first_name: Eran
full_name: Lustig, Eran
last_name: Lustig
- first_name: Melissa A.
full_name: Guidry, Melissa A.
last_name: Guidry
- first_name: Shanhui
full_name: Fan, Shanhui
last_name: Fan
- first_name: Jelena
full_name: Vučković, Jelena
last_name: Vučković
citation:
ama: Lê TK, Lukin DM, Roques-Carmes C, et al. Cavity quantum electrodynamics in
finite-bandwidth squeezed reservoir. arXiv. doi:10.48550/arXiv.2412.15068
apa: Lê, T. K., Lukin, D. M., Roques-Carmes, C., Karnieli, A., Lustig, E., Guidry,
M. A., … Vučković, J. (n.d.). Cavity quantum electrodynamics in finite-bandwidth
squeezed reservoir. arXiv. https://doi.org/10.48550/arXiv.2412.15068
chicago: Lê, Trung Kiên, Daniil M. Lukin, Charles Roques-Carmes, Aviv Karnieli,
Eran Lustig, Melissa A. Guidry, Shanhui Fan, and Jelena Vučković. “Cavity Quantum
Electrodynamics in Finite-Bandwidth Squeezed Reservoir.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2412.15068.
ieee: T. K. Lê et al., “Cavity quantum electrodynamics in finite-bandwidth
squeezed reservoir,” arXiv. .
ista: Lê TK, Lukin DM, Roques-Carmes C, Karnieli A, Lustig E, Guidry MA, Fan S,
Vučković J. Cavity quantum electrodynamics in finite-bandwidth squeezed reservoir.
arXiv, 2412.15068.
mla: Lê, Trung Kiên, et al. “Cavity Quantum Electrodynamics in Finite-Bandwidth
Squeezed Reservoir.” ArXiv, 2412.15068, doi:10.48550/arXiv.2412.15068.
short: T.K. Lê, D.M. Lukin, C. Roques-Carmes, A. Karnieli, E. Lustig, M.A. Guidry,
S. Fan, J. Vučković, ArXiv (n.d.).
date_created: 2026-04-09T09:10:41Z
date_published: 2024-12-19T00:00:00Z
date_updated: 2026-04-13T09:50:09Z
day: '19'
doi: 10.48550/arXiv.2412.15068
extern: '1'
external_id:
arxiv:
- '2412.15068'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2412.15068
month: '12'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
scopus_import: '1'
status: public
title: Cavity quantum electrodynamics in finite-bandwidth squeezed reservoir
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '21684'
abstract:
- lang: eng
text: This study focuses on advancing metascintillators to break the 100 ps barrier
and approach the 10 ps target. We exploit nanophotonic features, specifically
the Purcell effect, to shape and enhance the scintillation properties of the first-generation
metascintillator. We demonstrate that a faster emission is achievable along with
a more efficient conversion efficiency. This results in a coincidence time resolution
improved by a factor of 1.6, crucial for TOF-PET applications.
article_number: '2406.15058'
article_processing_charge: No
arxiv: 1
author:
- first_name: Avner
full_name: Shultzman, Avner
last_name: Shultzman
- first_name: Roman
full_name: Schütz, Roman
last_name: Schütz
- first_name: Yaniv
full_name: Kurman, Yaniv
last_name: Kurman
- first_name: Neta
full_name: Lahav, Neta
last_name: Lahav
- first_name: George
full_name: Dosovitskiy, George
last_name: Dosovitskiy
- first_name: Charles
full_name: Roques-Carmes, Charles
id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82
last_name: Roques-Carmes
- first_name: Yehonadav
full_name: Bekenstein, Yehonadav
last_name: Bekenstein
- first_name: Georgios
full_name: Konstantinou, Georgios
last_name: Konstantinou
- first_name: Riccardo
full_name: Latella, Riccardo
last_name: Latella
- first_name: Lei
full_name: Zhang, Lei
last_name: Zhang
- first_name: Francis Loignon-Houle
full_name: Francis Loignon-Houle, Francis Loignon-Houle
last_name: Francis Loignon-Houle
- first_name: Antonio J.
full_name: Gonzalez, Antonio J.
last_name: Gonzalez
- first_name: José María
full_name: Benlloch, José María
last_name: Benlloch
- first_name: Ido
full_name: Kaminer, Ido
last_name: Kaminer
- first_name: Paul
full_name: Lecoq, Paul
last_name: Lecoq
citation:
ama: Shultzman A, Schütz R, Kurman Y, et al. Towards a second generation of metascintillators
using the Purcell effect. arXiv. doi:10.48550/arXiv.2406.15058
apa: Shultzman, A., Schütz, R., Kurman, Y., Lahav, N., Dosovitskiy, G., Roques-Carmes,
C., … Lecoq, P. (n.d.). Towards a second generation of metascintillators using
the Purcell effect. arXiv. https://doi.org/10.48550/arXiv.2406.15058
chicago: Shultzman, Avner, Roman Schütz, Yaniv Kurman, Neta Lahav, George Dosovitskiy,
Charles Roques-Carmes, Yehonadav Bekenstein, et al. “Towards a Second Generation
of Metascintillators Using the Purcell Effect.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2406.15058.
ieee: A. Shultzman et al., “Towards a second generation of metascintillators
using the Purcell effect,” arXiv. .
ista: Shultzman A, Schütz R, Kurman Y, Lahav N, Dosovitskiy G, Roques-Carmes C,
Bekenstein Y, Konstantinou G, Latella R, Zhang L, Francis Loignon-Houle FL-H,
Gonzalez AJ, Benlloch JM, Kaminer I, Lecoq P. Towards a second generation of metascintillators
using the Purcell effect. arXiv, 2406.15058.
mla: Shultzman, Avner, et al. “Towards a Second Generation of Metascintillators
Using the Purcell Effect.” ArXiv, 2406.15058, doi:10.48550/arXiv.2406.15058.
short: A. Shultzman, R. Schütz, Y. Kurman, N. Lahav, G. Dosovitskiy, C. Roques-Carmes,
Y. Bekenstein, G. Konstantinou, R. Latella, L. Zhang, F.L.-H. Francis Loignon-Houle,
A.J. Gonzalez, J.M. Benlloch, I. Kaminer, P. Lecoq, ArXiv (n.d.).
date_created: 2026-04-09T09:10:41Z
date_published: 2024-06-21T00:00:00Z
date_updated: 2026-04-13T10:50:23Z
day: '21'
doi: 10.48550/arXiv.2406.15058
extern: '1'
external_id:
arxiv:
- '2406.15058'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2406.15058
month: '06'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
scopus_import: '1'
status: public
title: Towards a second generation of metascintillators using the Purcell effect
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '21680'
abstract:
- lang: eng
text: Multimode squeezed light is enticing for several applications, from squeezed
frequency combs for spectroscopy to signal multiplexing in optical computing.
To generate squeezing in multiple frequency modes, optical parametric oscillators
have been vital in realizing multimode squeezed vacuum states through second-order
nonlinear processes. However, most work has focused on generating multimode squeezed
vacua and squeezing in mode superpositions (supermodes). Bright squeezing in multiple
discrete frequency modes, if realized, could unlock novel applications in quantum-enhanced
spectroscopy and optical quantum computing. Here, we show how $Q$ factor engineering
of a multimode nonlinear cavity with cascaded three wave mixing processes creates
strong, spectrally tunable single mode output amplitude noise squeezing over 10
dB below the shot noise limit. In addition, we demonstrate squeezing for multiple
discrete frequency modes above threshold. This bright squeezing arises from enhancement
of the (noiseless) nonlinear rate relative to decay rates in the system due to
the cascaded generation of photons in a single idler "bath" mode. A natural consequence
of the strong nonlinear coupling in our system is the creation of an effective
cavity in the synthetic frequency dimension that sustains Bloch oscillations in
the modal energy distribution. Bloch mode engineering could provide an opportunity
to better control nonlinear energy flow in the synthetic frequency dimension,
with exciting applications in quantum random walks and topological photonics.
Lastly, we show evidence of long-range correlations in amplitude noise between
discrete frequency modes, pointing towards the potential of long-range entanglement
in a synthetic frequency dimension.
article_number: '2405.05201'
article_processing_charge: No
arxiv: 1
author:
- first_name: Sahil
full_name: Pontula, Sahil
last_name: Pontula
- first_name: Yannick
full_name: Salamin, Yannick
last_name: Salamin
- first_name: Charles
full_name: Roques-Carmes, Charles
id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82
last_name: Roques-Carmes
- first_name: Marin
full_name: Soljacic, Marin
last_name: Soljacic
citation:
ama: Pontula S, Salamin Y, Roques-Carmes C, Soljacic M. Multimode amplitude squeezing
through cascaded nonlinear optical processes. arXiv. doi:10.48550/arXiv.2405.05201
apa: Pontula, S., Salamin, Y., Roques-Carmes, C., & Soljacic, M. (n.d.). Multimode
amplitude squeezing through cascaded nonlinear optical processes. arXiv.
https://doi.org/10.48550/arXiv.2405.05201
chicago: Pontula, Sahil, Yannick Salamin, Charles Roques-Carmes, and Marin Soljacic.
“Multimode Amplitude Squeezing through Cascaded Nonlinear Optical Processes.”
ArXiv, n.d. https://doi.org/10.48550/arXiv.2405.05201.
ieee: S. Pontula, Y. Salamin, C. Roques-Carmes, and M. Soljacic, “Multimode amplitude
squeezing through cascaded nonlinear optical processes,” arXiv. .
ista: Pontula S, Salamin Y, Roques-Carmes C, Soljacic M. Multimode amplitude squeezing
through cascaded nonlinear optical processes. arXiv, 2405.05201.
mla: Pontula, Sahil, et al. “Multimode Amplitude Squeezing through Cascaded Nonlinear
Optical Processes.” ArXiv, 2405.05201, doi:10.48550/arXiv.2405.05201.
short: S. Pontula, Y. Salamin, C. Roques-Carmes, M. Soljacic, ArXiv (n.d.).
date_created: 2026-04-09T09:10:41Z
date_published: 2024-05-08T00:00:00Z
date_updated: 2026-04-13T10:51:17Z
day: '08'
doi: 10.48550/arXiv.2405.05201
extern: '1'
external_id:
arxiv:
- '2405.05201'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2405.05201
month: '05'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
scopus_import: '1'
status: public
title: Multimode amplitude squeezing through cascaded nonlinear optical processes
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '21679'
abstract:
- lang: eng
text: 'The observation that free electrons can interact coherently with quantized
electromagnetic fields and matter systems has led to a plethora of proposals leveraging
the unique quantum properties of free electrons. At the heart of these proposals
lies the assumption of a strong quantum interaction between a flying free electron
and a photonic mode. However, existing schemes are intrinsically limited by electron
diffraction, which puts an upper bound on the interaction length and therefore
the quantum coupling strength. Here, we propose the use of "free-electron fibers'''':
effectively one-dimensional photonic systems where free electrons co-propagate
with two guided modes. The first mode applies a ponderomotive trap to the free
electron, effectively lifting the limitations due to electron diffraction. The
second mode strongly couples to the guided free electron, with an enhanced coupling
that is orders of magnitude larger than previous designs. Moreover, the extended
interaction lengths enabled by our scheme allows for strong single-photon nonlinearities
mediated by free electrons. We predict a few interesting observable quantum effects
in our system, such as deterministic single-photon emission and complex, nonlinear
multimode dynamics. Our proposal paves the way towards the realization of many
anticipated effects in free-electron quantum optics, such as non-Gaussian light
generation, deterministic single photon emission, and quantum gates controlled
by free-electron--photon interactions.'
article_number: '2403.13071'
article_processing_charge: No
arxiv: 1
author:
- first_name: Aviv
full_name: Karnieli, Aviv
last_name: Karnieli
- first_name: Charles
full_name: Roques-Carmes, Charles
id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82
last_name: Roques-Carmes
- first_name: Nicholas
full_name: Rivera, Nicholas
last_name: Rivera
- first_name: Shanhui
full_name: Fan, Shanhui
last_name: Fan
citation:
ama: Karnieli A, Roques-Carmes C, Rivera N, Fan S. Strong coupling and single-photon
nonlinearity in free-electron quantum optics. arXiv. doi:10.48550/arXiv.2403.13071
apa: Karnieli, A., Roques-Carmes, C., Rivera, N., & Fan, S. (n.d.). Strong coupling
and single-photon nonlinearity in free-electron quantum optics. arXiv.
https://doi.org/10.48550/arXiv.2403.13071
chicago: Karnieli, Aviv, Charles Roques-Carmes, Nicholas Rivera, and Shanhui Fan.
“Strong Coupling and Single-Photon Nonlinearity in Free-Electron Quantum Optics.”
ArXiv, n.d. https://doi.org/10.48550/arXiv.2403.13071.
ieee: A. Karnieli, C. Roques-Carmes, N. Rivera, and S. Fan, “Strong coupling and
single-photon nonlinearity in free-electron quantum optics,” arXiv. .
ista: Karnieli A, Roques-Carmes C, Rivera N, Fan S. Strong coupling and single-photon
nonlinearity in free-electron quantum optics. arXiv, 2403.13071.
mla: Karnieli, Aviv, et al. “Strong Coupling and Single-Photon Nonlinearity in Free-Electron
Quantum Optics.” ArXiv, 2403.13071, doi:10.48550/arXiv.2403.13071.
short: A. Karnieli, C. Roques-Carmes, N. Rivera, S. Fan, ArXiv (n.d.).
date_created: 2026-04-09T09:10:41Z
date_published: 2024-03-19T00:00:00Z
date_updated: 2026-04-13T10:57:33Z
day: '19'
doi: 10.48550/arXiv.2403.13071
extern: '1'
external_id:
arxiv:
- '2403.13071'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2403.13071
month: '03'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
scopus_import: '1'
status: public
title: Strong coupling and single-photon nonlinearity in free-electron quantum optics
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '21681'
abstract:
- lang: eng
text: Enhancing interactions in many-body quantum systems, while protecting them
from environmental decoherence, is at the heart of many quantum technologies.
Waveguide quantum electrodynamics is a promising platform for achieving this,
as it hosts infinite-range interactions and decoherence-free subspaces of quantum
emitters. However, as coherent interactions between emitters are typically washed
out in the wavelength-spacing regime hosting decoherence-free states, coherent
control over the latter becomes limited, and many-body Hamiltonians in this important
regime remain out of reach. Here we show that by incorporating emitter arrays
with nonlinear waveguides hosting parametric gain, we obtain a unique class of
many-body interaction Hamiltonians with coupling strengths that increase with
emitter spacing, and persist even for wavelength-spaced arrays. We then propose
to use these Hamiltonians to coherently generate decoherence-free states directly
from the ground state, using only global squeezing drives, without the need for
local addressing of individual emitters. Interestingly, we find that the dynamics
approaches a unitary evolution in the limit of weak intra-waveguide squeezing,
and discuss potential experimental realizations of this effect. Our results pave
the way towards coherent control protocols in waveguide quantum electrodynamics,
with applications including quantum computing, simulation, memory and nonclassical
light generation.
article_number: '2405.20241'
article_processing_charge: No
arxiv: 1
author:
- first_name: Aviv
full_name: Karnieli, Aviv
last_name: Karnieli
- first_name: Offek
full_name: Tziperman, Offek
last_name: Tziperman
- first_name: Charles
full_name: Roques-Carmes, Charles
id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82
last_name: Roques-Carmes
- first_name: Shanhui
full_name: Fan, Shanhui
last_name: Fan
citation:
ama: Karnieli A, Tziperman O, Roques-Carmes C, Fan S. Decoherence-free many-body
Hamiltonians in nonlinear waveguide quantum electrodynamics. arXiv. doi:10.48550/arXiv.2405.20241
apa: Karnieli, A., Tziperman, O., Roques-Carmes, C., & Fan, S. (n.d.). Decoherence-free
many-body Hamiltonians in nonlinear waveguide quantum electrodynamics. arXiv.
https://doi.org/10.48550/arXiv.2405.20241
chicago: Karnieli, Aviv, Offek Tziperman, Charles Roques-Carmes, and Shanhui Fan.
“Decoherence-Free Many-Body Hamiltonians in Nonlinear Waveguide Quantum Electrodynamics.”
ArXiv, n.d. https://doi.org/10.48550/arXiv.2405.20241.
ieee: A. Karnieli, O. Tziperman, C. Roques-Carmes, and S. Fan, “Decoherence-free
many-body Hamiltonians in nonlinear waveguide quantum electrodynamics,” arXiv.
.
ista: Karnieli A, Tziperman O, Roques-Carmes C, Fan S. Decoherence-free many-body
Hamiltonians in nonlinear waveguide quantum electrodynamics. arXiv, 2405.20241.
mla: Karnieli, Aviv, et al. “Decoherence-Free Many-Body Hamiltonians in Nonlinear
Waveguide Quantum Electrodynamics.” ArXiv, 2405.20241, doi:10.48550/arXiv.2405.20241.
short: A. Karnieli, O. Tziperman, C. Roques-Carmes, S. Fan, ArXiv (n.d.).
date_created: 2026-04-09T09:10:41Z
date_published: 2024-05-30T00:00:00Z
date_updated: 2026-04-13T10:53:32Z
day: '30'
doi: 10.48550/arXiv.2405.20241
extern: '1'
external_id:
arxiv:
- '2405.20241'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2405.20241
month: '05'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
scopus_import: '1'
status: public
title: Decoherence-free many-body Hamiltonians in nonlinear waveguide quantum electrodynamics
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '21683'
abstract:
- lang: eng
text: Optical computing often employs tailor-made hardware to implement specific
algorithms, trading generality for improved performance in key aspects like speed
and power efficiency. An important computing approach that is still missing its
corresponding optical hardware is probabilistic computing, used e.g. for solving
difficult combinatorial optimization problems. In this study, we propose an experimentally
viable photonic approach to solve arbitrary probabilistic computing problems.
Our method relies on the insight that coherent Ising machines composed of coupled
and biased optical parametric oscillators can emulate stochastic logic. We demonstrate
the feasibility of our approach by using numerical simulations equivalent to the
full density matrix formulation of coupled optical parametric oscillators.
article_number: '2406.04000'
article_processing_charge: No
arxiv: 1
author:
- first_name: Michael
full_name: Horodynski, Michael
last_name: Horodynski
- first_name: Charles
full_name: Roques-Carmes, Charles
id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82
last_name: Roques-Carmes
- first_name: Yannick
full_name: Salamin, Yannick
last_name: Salamin
- first_name: Seou
full_name: Choi, Seou
last_name: Choi
- first_name: Jamison
full_name: Sloan, Jamison
last_name: Sloan
- first_name: Di
full_name: Luo, Di
last_name: Luo
- first_name: Marin
full_name: Soljačić, Marin
last_name: Soljačić
citation:
ama: Horodynski M, Roques-Carmes C, Salamin Y, et al. Stochastic logic in biased
coupled photonic probabilistic bits. arXiv. doi:10.48550/arXiv.2406.04000
apa: Horodynski, M., Roques-Carmes, C., Salamin, Y., Choi, S., Sloan, J., Luo, D.,
& Soljačić, M. (n.d.). Stochastic logic in biased coupled photonic probabilistic
bits. arXiv. https://doi.org/10.48550/arXiv.2406.04000
chicago: Horodynski, Michael, Charles Roques-Carmes, Yannick Salamin, Seou Choi,
Jamison Sloan, Di Luo, and Marin Soljačić. “Stochastic Logic in Biased Coupled
Photonic Probabilistic Bits.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2406.04000.
ieee: M. Horodynski et al., “Stochastic logic in biased coupled photonic
probabilistic bits,” arXiv. .
ista: Horodynski M, Roques-Carmes C, Salamin Y, Choi S, Sloan J, Luo D, Soljačić
M. Stochastic logic in biased coupled photonic probabilistic bits. arXiv, 2406.04000.
mla: Horodynski, Michael, et al. “Stochastic Logic in Biased Coupled Photonic Probabilistic
Bits.” ArXiv, 2406.04000, doi:10.48550/arXiv.2406.04000.
short: M. Horodynski, C. Roques-Carmes, Y. Salamin, S. Choi, J. Sloan, D. Luo, M.
Soljačić, ArXiv (n.d.).
date_created: 2026-04-09T09:10:41Z
date_published: 2024-06-06T00:00:00Z
date_updated: 2026-04-13T10:52:25Z
day: '06'
doi: 10.48550/arXiv.2406.04000
extern: '1'
external_id:
arxiv:
- '2406.04000'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2406.04000
month: '06'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
scopus_import: '1'
status: public
title: Stochastic logic in biased coupled photonic probabilistic bits
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_id: '12875'
abstract:
- lang: eng
text: The superior colliculus (SC) in the mammalian midbrain is essential for multisensory
integration and is composed of a rich diversity of excitatory and inhibitory neurons
and glia. However, the developmental principles directing the generation of SC
cell-type diversity are not understood. Here, we pursued systematic cell lineage
tracing in silico and in vivo, preserving full spatial information, using genetic
mosaic analysis with double markers (MADM)-based clonal analysis with single-cell
sequencing (MADM-CloneSeq). The analysis of clonally related cell lineages revealed
that radial glial progenitors (RGPs) in SC are exceptionally multipotent. Individual
resident RGPs have the capacity to produce all excitatory and inhibitory SC neuron
types, even at the stage of terminal division. While individual clonal units show
no pre-defined cellular composition, the establishment of appropriate relative
proportions of distinct neuronal types occurs in a PTEN-dependent manner. Collectively,
our findings provide an inaugural framework at the single-RGP/-cell level of the
mammalian SC ontogeny.
acknowledged_ssus:
- _id: Bio
- _id: M-Shop
- _id: LifeSc
- _id: PreCl
acknowledgement: "We thank Liqun Luo for his continued support, for providing essential
resources for generating Fzd10-CreER mice which were generated in his laboratory,
and for comments on the manuscript; W. Zhong for providing Nestin-Cre transgenic
mouse line for this study; A. Heger for mouse colony management; R. Beattie and
T. Asenov for designing and producing components of acute slice recovery chamber
for MADM-CloneSeq experiments; and K. Leopold, J. Rodarte and N. Amberg for initial
experiments, technical support and/or assistance. This study was supported by the
Scientific Service Units (SSU) of IST Austria through resources provided by the
Imaging & Optics Facility (IOF), Laboratory Support Facility (LSF), Miba Machine
Shop, and Pre-clinical Facility (PCF). G.C. received funding from European Commission
(IST plus postdoctoral fellowship). This work was supported by ISTA institutional\r\nfunds;
the Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation)
to S.H. "
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Giselle T
full_name: Cheung, Giselle T
id: 471195F6-F248-11E8-B48F-1D18A9856A87
last_name: Cheung
orcid: 0000-0001-8457-2572
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Peter
full_name: Koppensteiner, Peter
id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87
last_name: Koppensteiner
orcid: 0000-0002-3509-1948
- first_name: Thomas
full_name: Krausgruber, Thomas
last_name: Krausgruber
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Martin
full_name: Schrammel, Martin
id: f13e7cae-e8bd-11ed-841a-96dedf69f46d
last_name: Schrammel
- first_name: Natalie Y
full_name: Özgen, Natalie Y
id: e68ece33-f6e0-11ea-865d-ae1031dcc090
last_name: Özgen
- first_name: Alexis
full_name: Ivec, Alexis
id: 1d144691-e8be-11ed-9b33-bdd3077fad4c
last_name: Ivec
- first_name: Christoph
full_name: Bock, Christoph
last_name: Bock
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Cheung GT, Pauler F, Koppensteiner P, et al. Multipotent progenitors instruct
ontogeny of the superior colliculus. Neuron. 2024;112(2):230-246.e11. doi:10.1016/j.neuron.2023.11.009
apa: Cheung, G. T., Pauler, F., Koppensteiner, P., Krausgruber, T., Streicher, C.,
Schrammel, M., … Hippenmeyer, S. (2024). Multipotent progenitors instruct ontogeny
of the superior colliculus. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.11.009
chicago: Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, Thomas Krausgruber,
Carmen Streicher, Martin Schrammel, Natalie Y Özgen, et al. “Multipotent Progenitors
Instruct Ontogeny of the Superior Colliculus.” Neuron. Elsevier, 2024.
https://doi.org/10.1016/j.neuron.2023.11.009.
ieee: G. T. Cheung et al., “Multipotent progenitors instruct ontogeny of
the superior colliculus,” Neuron, vol. 112, no. 2. Elsevier, p. 230–246.e11,
2024.
ista: Cheung GT, Pauler F, Koppensteiner P, Krausgruber T, Streicher C, Schrammel
M, Özgen NY, Ivec A, Bock C, Shigemoto R, Hippenmeyer S. 2024. Multipotent progenitors
instruct ontogeny of the superior colliculus. Neuron. 112(2), 230–246.e11.
mla: Cheung, Giselle T., et al. “Multipotent Progenitors Instruct Ontogeny of the
Superior Colliculus.” Neuron, vol. 112, no. 2, Elsevier, 2024, p. 230–246.e11,
doi:10.1016/j.neuron.2023.11.009.
short: G.T. Cheung, F. Pauler, P. Koppensteiner, T. Krausgruber, C. Streicher, M.
Schrammel, N.Y. Özgen, A. Ivec, C. Bock, R. Shigemoto, S. Hippenmeyer, Neuron
112 (2024) 230–246.e11.
corr_author: '1'
date_created: 2023-04-27T09:41:48Z
date_published: 2024-01-17T00:00:00Z
date_updated: 2025-12-30T10:54:12Z
day: '17'
ddc:
- '570'
department:
- _id: SiHi
- _id: RySh
doi: 10.1016/j.neuron.2023.11.009
external_id:
isi:
- '001163937900001'
pmid:
- '38096816'
file:
- access_level: open_access
checksum: 32b3788f7085cf44a84108d8faaff3ce
content_type: application/pdf
creator: dernst
date_created: 2024-02-06T13:56:15Z
date_updated: 2024-02-06T13:56:15Z
file_id: '14944'
file_name: 2024_Neuron_Cheung.pdf
file_size: 5942467
relation: main_file
success: 1
file_date_updated: 2024-02-06T13:56:15Z
has_accepted_license: '1'
intvolume: ' 112'
isi: 1
issue: '2'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '01'
oa: 1
oa_version: Published Version
page: 230-246.e11
pmid: 1
project:
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
grant_number: F7805
name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular
Mechanisms of Neural Stem Cell Lineage Progression
publication: Neuron
publication_identifier:
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/the-pedigree-of-brain-cells/
scopus_import: '1'
status: public
title: Multipotent progenitors instruct ontogeny of the superior colliculus
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'
...
---
_id: '14683'
abstract:
- lang: eng
text: "Mosaic analysis with double markers (MADM) technology enables the generation
of genetic mosaic tissue in mice and high-resolution phenotyping at the individual
cell level. Here, we present a protocol for isolating MADM-labeled cells with
high yield for downstream molecular analyses using fluorescence-activated cell
sorting (FACS). We describe steps for generating MADM-labeled mice, perfusion,
single-cell suspension, and debris removal. We then detail procedures for cell
sorting by FACS and downstream analysis. This protocol is suitable for embryonic
to adult mice.\r\nFor complete details on the use and execution of this protocol,
please refer to Contreras et al. (2021).1"
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: This research was supported by the Scientific Service Units (SSU)
at IST Austria through resources provided by the Imaging & Optics Facility (IOF)
and Preclinical Facilities (PCF). N.A. received support from FWF Firnberg-Programme
(T 1031). G.C. received support from the European Union’s Horizon 2020 research
and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411
as an ISTplus postdoctoral fellow. This work was also supported by IST Austria institutional
funds, FWF SFB F78 to S.H., and the European Research Council (ERC) under the European
Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780
LinPro) to S.H.
article_number: '102771'
article_processing_charge: Yes (in subscription journal)
article_type: review
author:
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Giselle T
full_name: Cheung, Giselle T
id: 471195F6-F248-11E8-B48F-1D18A9856A87
last_name: Cheung
orcid: 0000-0001-8457-2572
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Amberg N, Cheung GT, Hippenmeyer S. Protocol for sorting cells from mouse brains
labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols.
2024;5(1). doi:10.1016/j.xpro.2023.102771
apa: Amberg, N., Cheung, G. T., & Hippenmeyer, S. (2024). Protocol for sorting
cells from mouse brains labeled with mosaic analysis with double markers by flow
cytometry. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2023.102771
chicago: Amberg, Nicole, Giselle T Cheung, and Simon Hippenmeyer. “Protocol for
Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers
by Flow Cytometry.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2023.102771.
ieee: N. Amberg, G. T. Cheung, and S. Hippenmeyer, “Protocol for sorting cells from
mouse brains labeled with mosaic analysis with double markers by flow cytometry,”
STAR Protocols, vol. 5, no. 1. Elsevier, 2024.
ista: Amberg N, Cheung GT, Hippenmeyer S. 2024. Protocol for sorting cells from
mouse brains labeled with mosaic analysis with double markers by flow cytometry.
STAR Protocols. 5(1), 102771.
mla: Amberg, Nicole, et al. “Protocol for Sorting Cells from Mouse Brains Labeled
with Mosaic Analysis with Double Markers by Flow Cytometry.” STAR Protocols,
vol. 5, no. 1, 102771, Elsevier, 2024, doi:10.1016/j.xpro.2023.102771.
short: N. Amberg, G.T. Cheung, S. Hippenmeyer, STAR Protocols 5 (2024).
corr_author: '1'
date_created: 2023-12-13T11:48:05Z
date_published: 2024-03-15T00:00:00Z
date_updated: 2025-04-15T08:23:06Z
day: '15'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.xpro.2023.102771
ec_funded: 1
external_id:
pmid:
- '38070137'
file:
- access_level: open_access
checksum: 3f0ee62e04bf5a44b45b035662826e95
content_type: application/pdf
creator: dernst
date_created: 2024-07-16T11:50:03Z
date_updated: 2024-07-16T11:50:03Z
file_id: '17260'
file_name: 2024_STARProtoc_Amberg.pdf
file_size: 8871807
relation: main_file
success: 1
file_date_updated: 2024-07-16T11:50:03Z
has_accepted_license: '1'
intvolume: ' 5'
issue: '1'
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Neuroscience
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 268F8446-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: T01031
name: Role of Eed in neural stem cell lineage progression
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
grant_number: F7805
name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular
Mechanisms of Neural Stem Cell Lineage Progression
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: STAR Protocols
publication_identifier:
issn:
- 2666-1667
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Protocol for sorting cells from mouse brains labeled with mosaic analysis with
double markers by flow cytometry
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: 804 EUR
OA_place: publisher
OA_type: gold
_id: '17187'
abstract:
- lang: eng
text: "The generation of diverse cell types during development is fundamental to
brain\r\nfunctions. We outline a protocol to quantitatively assess the clonal
output of individual neural progenitors using mosaic analysis with double markers
(MADM) in\r\nmice. We first describe steps to acquire and reconstruct adult MADM
clones in\r\nthe superior colliculus. Then we detail analysis pipelines to determine
clonal\r\ncomposition and architecture. This protocol enables the buildup of quantitative\r\nframeworks
of lineage progression with precise spatial resolution in the brain.\r\nFor complete
details on the use and execution of this protocol, please refer to\r\nCheung et
al.1"
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: We thank A. Heger for mouse breeding support. This work was supported
by the Scientific Service Units of IST Austria through resources provided by the
Imaging & Optics and Preclinical facilities. G.C. received funding from the European
Commission (IST plus postdoctoral fellowship); S.H. was funded by ISTA institutional
funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro
Stem Modulation).
article_number: '103157'
article_processing_charge: Yes
article_type: original
author:
- first_name: Giselle T
full_name: Cheung, Giselle T
id: 471195F6-F248-11E8-B48F-1D18A9856A87
last_name: Cheung
orcid: 0000-0001-8457-2572
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Cheung GT, Streicher C, Hippenmeyer S. Protocol for quantitative reconstruction
of cell lineage using mosaic analysis with double markers in mice. STAR Protocols.
2024;5(3). doi:10.1016/j.xpro.2024.103157
apa: Cheung, G. T., Streicher, C., & Hippenmeyer, S. (2024). Protocol for quantitative
reconstruction of cell lineage using mosaic analysis with double markers in mice.
STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2024.103157
chicago: Cheung, Giselle T, Carmen Streicher, and Simon Hippenmeyer. “Protocol for
Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double
Markers in Mice.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2024.103157.
ieee: G. T. Cheung, C. Streicher, and S. Hippenmeyer, “Protocol for quantitative
reconstruction of cell lineage using mosaic analysis with double markers in mice,”
STAR Protocols, vol. 5, no. 3. Elsevier, 2024.
ista: Cheung GT, Streicher C, Hippenmeyer S. 2024. Protocol for quantitative reconstruction
of cell lineage using mosaic analysis with double markers in mice. STAR Protocols.
5(3), 103157.
mla: Cheung, Giselle T., et al. “Protocol for Quantitative Reconstruction of Cell
Lineage Using Mosaic Analysis with Double Markers in Mice.” STAR Protocols,
vol. 5, no. 3, 103157, Elsevier, 2024, doi:10.1016/j.xpro.2024.103157.
short: G.T. Cheung, C. Streicher, S. Hippenmeyer, STAR Protocols 5 (2024).
corr_author: '1'
date_created: 2024-06-30T22:01:04Z
date_published: 2024-09-20T00:00:00Z
date_updated: 2025-12-30T10:54:11Z
day: '20'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.xpro.2024.103157
ec_funded: 1
external_id:
pmid:
- '38935508'
file:
- access_level: open_access
checksum: d8a8cdba82a394e731aa699ace1ae433
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T12:12:40Z
date_updated: 2025-01-09T12:12:40Z
file_id: '18809'
file_name: 2024_STARProtoc_Cheung.pdf
file_size: 5186071
relation: main_file
success: 1
file_date_updated: 2025-01-09T12:12:40Z
has_accepted_license: '1'
intvolume: ' 5'
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
grant_number: F7805
name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular
Mechanisms of Neural Stem Cell Lineage Progression
publication: STAR Protocols
publication_identifier:
eissn:
- 2666-1667
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Protocol for quantitative reconstruction of cell lineage using mosaic analysis
with double markers in mice
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2024'
...
---
APC_amount: 804 EUR
OA_place: publisher
OA_type: gold
_id: '17232'
abstract:
- lang: eng
text: "The lineage relationship of clonally-related cells offers important insights
into the ontogeny and cytoarchitecture of the brain in health and disease. Here,
we provide a protocol to concurrently assess cell lineage relationship and cell-type
identity among clonally-related cells in situ. We first describe the preparation
and screening of acute brain slices containing clonally-related cells labeled
using mosaic analysis with double markers (MADM). We then outline steps to collect
RNA from individual cells for downstream applications and cell-type identification
using RNA sequencing.\r\nFor complete details on the use and execution of this
protocol, please refer to Cheung et al.\r\n1"
acknowledged_ssus:
- _id: Bio
- _id: M-Shop
- _id: PreCl
acknowledgement: We thank R. Beattie and T. Asenov for designing and producing components
of the multi-well slice recover chamber. We thank R. Shigemoto for providing equipment
access. We thank C. Streicher and A. Heger for mouse breeding support. This work
was supported by the Scientific Service Units of IST Austria through resources provided
by the Imaging & Optics, Miba Machine Shop, and Preclinical facilities. G.C. received
funding from the European Commission (IST plus postdoctoral fellowship) and S.H.
was funded by ISTA institutional funds and the Austrian Science Fund Special Research
Programmes (FWF SFB-F78 Neuro Stem Modulation).
article_number: '103168'
article_processing_charge: Yes
article_type: original
author:
- first_name: Giselle T
full_name: Cheung, Giselle T
id: 471195F6-F248-11E8-B48F-1D18A9856A87
last_name: Cheung
orcid: 0000-0001-8457-2572
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Peter
full_name: Koppensteiner, Peter
id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87
last_name: Koppensteiner
orcid: 0000-0002-3509-1948
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. Protocol for mapping cell
lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq.
STAR Protocols. 2024;5(3). doi:10.1016/j.xpro.2024.103168
apa: Cheung, G. T., Pauler, F., Koppensteiner, P., & Hippenmeyer, S. (2024).
Protocol for mapping cell lineage and cell-type identity of clonally-related cells
in situ using MADM-CloneSeq. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2024.103168
chicago: Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, and Simon Hippenmeyer.
“Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related
Cells in Situ Using MADM-CloneSeq.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2024.103168.
ieee: G. T. Cheung, F. Pauler, P. Koppensteiner, and S. Hippenmeyer, “Protocol for
mapping cell lineage and cell-type identity of clonally-related cells in situ
using MADM-CloneSeq,” STAR Protocols, vol. 5, no. 3. Elsevier, 2024.
ista: Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. 2024. Protocol for mapping
cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq.
STAR Protocols. 5(3), 103168.
mla: Cheung, Giselle T., et al. “Protocol for Mapping Cell Lineage and Cell-Type
Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” STAR Protocols,
vol. 5, no. 3, 103168, Elsevier, 2024, doi:10.1016/j.xpro.2024.103168.
short: G.T. Cheung, F. Pauler, P. Koppensteiner, S. Hippenmeyer, STAR Protocols
5 (2024).
corr_author: '1'
date_created: 2024-07-14T22:01:10Z
date_published: 2024-09-20T00:00:00Z
date_updated: 2025-12-30T10:54:12Z
day: '20'
ddc:
- '570'
department:
- _id: SiHi
- _id: PreCl
doi: 10.1016/j.xpro.2024.103168
external_id:
pmid:
- '38968076'
file:
- access_level: open_access
checksum: 464f52ecc6ec92f509552823bb82bf79
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T12:16:53Z
date_updated: 2025-01-09T12:16:53Z
file_id: '18810'
file_name: 2024_STARProtoc_Cheung2.pdf
file_size: 6445556
relation: main_file
success: 1
file_date_updated: 2025-01-09T12:16:53Z
has_accepted_license: '1'
intvolume: ' 5'
issue: '3'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
grant_number: F7805
name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular
Mechanisms of Neural Stem Cell Lineage Progression
publication: STAR Protocols
publication_identifier:
eissn:
- 2666-1667
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Protocol for mapping cell lineage and cell-type identity of clonally-related
cells in situ using MADM-CloneSeq
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2024'
...
---
_id: '17425'
abstract:
- lang: eng
text: Mosaic Analysis with Double Markers (MADM) is a powerful genetic method typically
used for lineage tracing and to disentangle cell autonomous and tissue-wide roles
of candidate genes with single cell resolution. Given the relatively sparse labeling,
depending on which of the 19 MADM chromosomes one chooses, the MADM approach represents
the perfect opportunity for cell morphology analysis. Various MADM studies include
reports of morphological anomalies and phenotypes in the central nervous system
(CNS). MADM for any candidate gene can easily incorporate morphological analysis
within the experimental workflow. Here, we describe the methods of morphological
cell analysis which we developed in the course of diverse recent MADM studies.
This chapter will specifically focus on methods to quantify aspects of the morphology
of neurons and astrocytes within the CNS, but these methods can broadly be applied
to any MADM-labeled cells throughout the entire organism. We will cover two analyses—soma
volume and dendrite characterization—of physical characteristics of pyramidal
neurons in the somatosensory cortex, and two analyses—volume and Sholl analysis—of
astrocyte morphology.
acknowledged_ssus:
- _id: Bio
acknowledgement: We thank all Hippenmeyer lab members for support and discussions.
This work was supported by the Scientific Service Units (SSU) at ISTA through resources
provided by the Imaging & Optics Facility (IOF). O.A.M was a recipient of a DOC
Fellowship (26253) of the Austrian Academy of Sciences. This work was supported
by ISTA institutional funds, and The Austrian Science Fund Special Research Programmes
(FWF SFB F78 Neuro Stem Modulation) to S.H.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Osvaldo
full_name: Miranda, Osvaldo
id: 862A3C56-A8BF-11E9-B4FA-D9E3E5697425
last_name: Miranda
orcid: 0000-0001-6618-6889
- first_name: Giselle T
full_name: Cheung, Giselle T
id: 471195F6-F248-11E8-B48F-1D18A9856A87
last_name: Cheung
orcid: 0000-0001-8457-2572
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: 'Miranda O, Cheung GT, Hippenmeyer S. Morphological Analysis of Neurons and
Glia Using Mosaic Analysis with Double Markers. In: Toyooka K, ed. Neuronal
Morphogenesis. Vol 2831. 1st ed. MIMB. New York, NY: Springer Nature; 2024:283-299.
doi:10.1007/978-1-0716-3969-6_19'
apa: 'Miranda, O., Cheung, G. T., & Hippenmeyer, S. (2024). Morphological Analysis
of Neurons and Glia Using Mosaic Analysis with Double Markers. In K. Toyooka (Ed.),
Neuronal Morphogenesis (1st ed., Vol. 2831, pp. 283–299). New York, NY:
Springer Nature. https://doi.org/10.1007/978-1-0716-3969-6_19'
chicago: 'Miranda, Osvaldo, Giselle T Cheung, and Simon Hippenmeyer. “Morphological
Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” In Neuronal
Morphogenesis, edited by Kazuhito Toyooka, 1st ed., 2831:283–99. MIMB. New
York, NY: Springer Nature, 2024. https://doi.org/10.1007/978-1-0716-3969-6_19.'
ieee: 'O. Miranda, G. T. Cheung, and S. Hippenmeyer, “Morphological Analysis of
Neurons and Glia Using Mosaic Analysis with Double Markers,” in Neuronal Morphogenesis,
1st ed., vol. 2831, K. Toyooka, Ed. New York, NY: Springer Nature, 2024, pp. 283–299.'
ista: 'Miranda O, Cheung GT, Hippenmeyer S. 2024.Morphological Analysis of Neurons
and Glia Using Mosaic Analysis with Double Markers. In: Neuronal Morphogenesis.
Methods in Molecular Biology, vol. 2831, 283–299.'
mla: Miranda, Osvaldo, et al. “Morphological Analysis of Neurons and Glia Using
Mosaic Analysis with Double Markers.” Neuronal Morphogenesis, edited by
Kazuhito Toyooka, 1st ed., vol. 2831, Springer Nature, 2024, pp. 283–99, doi:10.1007/978-1-0716-3969-6_19.
short: O. Miranda, G.T. Cheung, S. Hippenmeyer, in:, K. Toyooka (Ed.), Neuronal
Morphogenesis, 1st ed., Springer Nature, New York, NY, 2024, pp. 283–299.
corr_author: '1'
date_created: 2024-08-13T12:16:41Z
date_published: 2024-08-13T00:00:00Z
date_updated: 2026-04-07T12:32:35Z
day: '13'
department:
- _id: GradSch
- _id: SiHi
doi: 10.1007/978-1-0716-3969-6_19
edition: '1'
editor:
- first_name: Kazuhito
full_name: Toyooka, Kazuhito
last_name: Toyooka
external_id:
pmid:
- '39134857'
intvolume: ' 2831'
language:
- iso: eng
month: '08'
oa_version: None
page: 283-299
place: New York, NY
pmid: 1
project:
- _id: 34c9fbcb-11ca-11ed-8bc3-98fa5658610d
grant_number: '26253'
name: Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression
and Astrocyte Development
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
grant_number: F7805
name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular
Mechanisms of Neural Stem Cell Lineage Progression
publication: Neuronal Morphogenesis
publication_identifier:
eisbn:
- '9781071639696'
eissn:
- 1940-6029
isbn:
- '9781071639689'
issn:
- 1064-3745
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '20212'
relation: dissertation_contains
status: public
scopus_import: '1'
series_title: MIMB
status: public
title: Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double
Markers
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2831
year: '2024'
...
---
OA_place: repository
_id: '18688'
abstract:
- lang: eng
text: The human brain has remarkable computational power. It generates sophisticated
behavioral sequences, stores engrams over an individual’s lifetime, and produces
higher cognitive functions up to the level of consciousness. However, so little
of our neuroscience knowledge covers the human brain, and it remains unknown whether
this organ is truly unique, or is a scaled version of the extensively studied
rodent brain. To address this fundamental question, we determined the cellular,
synaptic, and connectivity rules of the hippocampal CA3 recurrent circuit using
multicellular patch clamp-recording. This circuit is the largest autoassociative
network in the brain, and plays a key role in memory and higher-order computations
such as pattern separation and pattern completion. We demonstrate that human hippocampal
CA3 employs sparse connectivity, in stark contrast to neocortical recurrent networks.
Connectivity sparsifies from rodents to humans, providing a circuit architecture
that maximizes associational power. Unitary synaptic events at human CA3–CA3 synapses
showed both distinct species-specific and circuit-dependent properties, with high
reliability, unique amplitude precision, and long integration times. We also identify
differential scaling rules between hippocampal pathways from rodents to humans,
with a moderate increase in the convergence of CA3 inputs per cell, but a marked
increase in human mossy fiber innervation. Anatomically guided full-scale modeling
suggests that the human brain’s sparse connectivity, expanded neuronal number,
and reliable synaptic signaling combine to enhance the associative memory storage
capacity of CA3. Together, our results reveal unique rules of connectivity and
synaptic signaling in the human hippocampus, demonstrating the absolute necessity
of human brain research and beginning to unravel the remarkable performance of
our autoassociative memory circuits.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: M-Shop
- _id: PreCl
- _id: ScienComp
acknowledgement: We thank Florian Marr for excellent technical assistance, Christina
Altmutter and Julia Flor for technical support, Alois Schlögl for programming, Todor
Asenov for development of the transportation box for human brain tissue, Tim Vogels
for guidance on simulations, Marcus Huber for mathematical advice, and Eleftheria
Kralli-Beller for manuscript editing. This research was supported by the Scientific
Services Units (SSUs) of ISTA, and we are particularly grateful for assistance from
Christoph Sommer and the Imaging and Optics Facility, Preclinical Facility, Life
Science Facility, Miba Machine Shop, and Scientific Computing. We also acknowledge
the excellent support of the Medical University of Vienna Department of Neurosurgery
staff, Romana Hoeftberger and the Division of Neuropathology and Neurochemistry,
and Gregor Kasprian and the Division of Neuroradiology and Musculoskeletal Radiology.
The project received funding from the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation programme (Marie Skłodowska-Curie
Actions Individual Fellowship no. 101026635 to J.F.W.), the Austrian Science Fund
(FWF; grant PAT 4178023 to P.J.; grant DK W1232 to M.R.T. and J.G.D.) and the Austrian
Academy of Sciences (DOC fellowship 26137 to M.R.T.).
article_processing_charge: No
author:
- first_name: Jake F.
full_name: Watson, Jake F.
last_name: Watson
- first_name: Victor
full_name: Vargas-Barroso, Victor
last_name: Vargas-Barroso
- first_name: Rebecca J.
full_name: Morse-Mora, Rebecca J.
last_name: Morse-Mora
- first_name: Andrea
full_name: Navas-Olive, Andrea
last_name: Navas-Olive
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Matthias
full_name: Tomschik, Matthias
last_name: Tomschik
- first_name: Karl
full_name: Rössler, Karl
last_name: Rössler
- 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: Watson JF, Vargas-Barroso V, Morse-Mora RJ, et al. Human hippocampal CA3 uses
specific functional connectivity rules for efficient associative memory. bioRxiv.
doi:10.1101/2024.05.02.592169
apa: Watson, J. F., Vargas-Barroso, V., Morse-Mora, R. J., Navas-Olive, A., Tavakoli,
M., Danzl, J. G., … Jonas, P. M. (n.d.). Human hippocampal CA3 uses specific functional
connectivity rules for efficient associative memory. bioRxiv. https://doi.org/10.1101/2024.05.02.592169
chicago: Watson, Jake F., Victor Vargas-Barroso, Rebecca J. Morse-Mora, Andrea Navas-Olive,
Mojtaba Tavakoli, Johann G Danzl, Matthias Tomschik, Karl Rössler, and Peter M
Jonas. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for
Efficient Associative Memory.” BioRxiv, n.d. https://doi.org/10.1101/2024.05.02.592169.
ieee: J. F. Watson et al., “Human hippocampal CA3 uses specific functional
connectivity rules for efficient associative memory,” bioRxiv. .
ista: Watson JF, Vargas-Barroso V, Morse-Mora RJ, Navas-Olive A, Tavakoli M, Danzl
JG, Tomschik M, Rössler K, Jonas PM. Human hippocampal CA3 uses specific functional
connectivity rules for efficient associative memory. bioRxiv, 10.1101/2024.05.02.592169.
mla: Watson, Jake F., et al. “Human Hippocampal CA3 Uses Specific Functional Connectivity
Rules for Efficient Associative Memory.” BioRxiv, doi:10.1101/2024.05.02.592169.
short: J.F. Watson, V. Vargas-Barroso, R.J. Morse-Mora, A. Navas-Olive, M. Tavakoli,
J.G. Danzl, M. Tomschik, K. Rössler, P.M. Jonas, BioRxiv (n.d.).
corr_author: '1'
date_created: 2024-12-19T11:35:08Z
date_published: 2024-05-02T00:00:00Z
date_updated: 2026-04-14T08:34:32Z
day: '02'
department:
- _id: JoDa
- _id: PeJo
doi: 10.1101/2024.05.02.592169
ec_funded: 1
language:
- iso: eng
main_file_link:
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url: https://doi.org/10.1101/2024.05.02.592169
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9
call_identifier: H2020
grant_number: '101026635'
name: Synaptic computations of the hippocampal CA3 circuitry
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
- _id: 6285a163-2b32-11ec-9570-8e204ca2dba5
grant_number: '26137'
name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
Microscopy
publication: bioRxiv
publication_status: draft
related_material:
record:
- id: '18681'
relation: dissertation_contains
status: public
- id: '18879'
relation: later_version
status: public
status: public
title: Human hippocampal CA3 uses specific functional connectivity rules for efficient
associative memory
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '14257'
abstract:
- lang: eng
text: Mapping the complex and dense arrangement of cells and their connectivity
in brain tissue demands nanoscale spatial resolution imaging. Super-resolution
optical microscopy excels at visualizing specific molecules and individual cells
but fails to provide tissue context. Here we developed Comprehensive Analysis
of Tissues across Scales (CATS), a technology to densely map brain tissue architecture
from millimeter regional to nanometer synaptic scales in diverse chemically fixed
brain preparations, including rodent and human. CATS uses fixation-compatible
extracellular labeling and optical imaging, including stimulated emission depletion
or expansion microscopy, to comprehensively delineate cellular structures. It
enables three-dimensional reconstruction of single synapses and mapping of synaptic
connectivity by identification and analysis of putative synaptic cleft regions.
Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed
and quantified the synaptic input and output structure of identified neurons.
We furthermore demonstrate applicability to clinically derived human tissue samples,
including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing
the cellular architecture of brain tissue in health and disease.
acknowledged_ssus:
- _id: ScienComp
- _id: Bio
- _id: PreCl
- _id: LifeSc
- _id: M-Shop
- _id: E-Lib
acknowledgement: 'We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak
for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I.
Erber for technical assistance; and M. Tomschik for support with obtaining human
samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata
for computational support and hardware control. We are grateful to R. Shigemoto
and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University)
for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly
provided by S. Grant (University of Edinburgh). We acknowledge expert support by
Institute of Science and Technology Austria’s scientific computing, imaging and
optics, preclinical and lab support facilities and by the Miba machine shop and
library. We gratefully acknowledge funding by the following sources: Austrian Science
Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232
(J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award
(P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27
(R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.);
European Union’s Horizon 2020 research and innovation programme, European Research
Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020
research and innovation programme, European Research Council (ERC) grant 692692
– GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under
the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions
Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Julia M
full_name: Michalska, Julia M
id: 443DB6DE-F248-11E8-B48F-1D18A9856A87
last_name: Michalska
orcid: 0000-0003-3862-1235
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- first_name: Philipp
full_name: Velicky, Philipp
id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
last_name: Velicky
orcid: 0000-0002-2340-7431
- first_name: Hana
full_name: Korinkova, Hana
id: ee3cb6ca-ec98-11ea-ae11-ff703e2254ed
last_name: Korinkova
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Alban
full_name: Cenameri, Alban
id: 9ac8f577-2357-11eb-997a-e566c5550886
last_name: Cenameri
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Alessandro
full_name: Venturino, Alessandro
id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
last_name: Venturino
orcid: 0000-0003-2356-9403
- first_name: Karl
full_name: Roessler, Karl
last_name: Roessler
- first_name: Thomas
full_name: Czech, Thomas
last_name: Czech
- first_name: Romana
full_name: Höftberger, Romana
last_name: Höftberger
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture
across millimeter to nanometer scales. Nature Biotechnology. 2024;42:1051-1064.
doi:10.1038/s41587-023-01911-8
apa: Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri,
A., … Danzl, J. G. (2024). Imaging brain tissue architecture across millimeter
to nanometer scales. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-023-01911-8
chicago: Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake
Watson, Alban Cenameri, Christoph M Sommer, et al. “Imaging Brain Tissue Architecture
across Millimeter to Nanometer Scales.” Nature Biotechnology. Springer
Nature, 2024. https://doi.org/10.1038/s41587-023-01911-8.
ieee: J. M. Michalska et al., “Imaging brain tissue architecture across millimeter
to nanometer scales,” Nature Biotechnology, vol. 42. Springer Nature, pp.
1051–1064, 2024.
ista: Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer
CM, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino
G, Jonas PM, Danzl JG. 2024. Imaging brain tissue architecture across millimeter
to nanometer scales. Nature Biotechnology. 42, 1051–1064.
mla: Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter
to Nanometer Scales.” Nature Biotechnology, vol. 42, Springer Nature, 2024,
pp. 1051–64, doi:10.1038/s41587-023-01911-8.
short: J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri,
C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S.
Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology 42 (2024) 1051–1064.
corr_author: '1'
date_created: 2023-09-03T22:01:15Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2026-04-14T08:34:35Z
day: '01'
ddc:
- '570'
department:
- _id: SaSi
- _id: GaNo
- _id: PeJo
- _id: JoDa
- _id: Bio
- _id: RySh
doi: 10.1038/s41587-023-01911-8
ec_funded: 1
external_id:
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- '001065254200001'
pmid:
- '37653226'
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oa_version: Published Version
page: 1051-1064
pmid: 1
project:
- _id: 265CB4D0-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03600
name: Optical control of synaptic function via adhesion molecules
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232
name: Molecular Drug Targets
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
- _id: 23889792-32DE-11EA-91FC-C7463DDC885E
grant_number: LS18-022
name: High content imaging to decode human immune cell interactions in health and
allergic disease
- _id: 25444568-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715508'
name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo
and in vitro Models
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9
call_identifier: H2020
grant_number: '101026635'
name: Synaptic computations of the hippocampal CA3 circuitry
publication: Nature Biotechnology
publication_identifier:
eissn:
- 1546-1696
issn:
- 1087-0156
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
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scopus_import: '1'
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title: Imaging brain tissue architecture across millimeter to nanometer scales
tmp:
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legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
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type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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year: '2024'
...
---
OA_place: publisher
_id: '18674'
abstract:
- lang: eng
text: Mapping the complex and dense arrangement of cells and their connectivity
in brain tissue requires volumetric imaging at nanoscale spatial resolution. While
light microscopy excels at visualizing specific molecules and individual cells,
achieving dense, synapse-level circuit reconstruction has not been possible with
any light microscopy technique. Thus, the goal of my work was to develop image
and data analysis pipelines for brain tissue visualization and reconstruction
with light microscopy. To achieve dense circuit reconstruction with single-synapse
resolution, I developed both conventional and deep-learning-based synapse detection
algorithms, as well as connectivity analysis pipelines that integrate synapse
detection with volumetric segmentation of brain tissue.
acknowledged_ssus:
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
citation:
ama: Lyudchik J. Image analysis for brain tissue reconstruction with super-resolution
light microscopy. 2024. doi:10.15479/at:ista:18674
apa: Lyudchik, J. (2024). Image analysis for brain tissue reconstruction with
super-resolution light microscopy. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:18674
chicago: Lyudchik, Julia. “Image Analysis for Brain Tissue Reconstruction with Super-Resolution
Light Microscopy.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18674.
ieee: J. Lyudchik, “Image analysis for brain tissue reconstruction with super-resolution
light microscopy,” Institute of Science and Technology Austria, 2024.
ista: Lyudchik J. 2024. Image analysis for brain tissue reconstruction with super-resolution
light microscopy. Institute of Science and Technology Austria.
mla: Lyudchik, Julia. Image Analysis for Brain Tissue Reconstruction with Super-Resolution
Light Microscopy. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18674.
short: J. Lyudchik, Image Analysis for Brain Tissue Reconstruction with Super-Resolution
Light Microscopy, Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-12-18T14:24:43Z
date_published: 2024-12-18T00:00:00Z
date_updated: 2026-04-14T08:34:35Z
day: '18'
ddc:
- '004'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoDa
doi: 10.15479/at:ista:18674
ec_funded: 1
file:
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date_created: 2024-12-18T14:17:34Z
date_updated: 2024-12-18T14:17:34Z
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date_created: 2024-12-18T14:21:06Z
date_updated: 2024-12-18T14:41:53Z
file_id: '18676'
file_name: 18122024_PhDthesis_corrected_final_JL_markup.docx
file_size: 99172203
relation: source_file
file_date_updated: 2024-12-18T14:41:53Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '217'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
isbn:
- ' 978-3-99078-051-0'
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
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relation: part_of_dissertation
status: public
- id: '18677'
relation: part_of_dissertation
status: public
- id: '13267'
relation: part_of_dissertation
status: public
- id: '14257'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
title: Image analysis for brain tissue reconstruction with super-resolution light
microscopy
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
APC_amount: 3197,23 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18481'
abstract:
- lang: eng
text: A tight regulation of morphogen production is key for morphogen gradient formation
and thereby for reproducible and organised organ development. Although many genetic
interactions involved in the establishment of morphogen production domains are
known, the biophysical mechanisms of morphogen source formation are poorly understood.
Here we addressed this by focusing on the morphogen Sonic hedgehog (Shh) in the
vertebrate neural tube. Shh is produced by the adjacently located notochord and
by the floor plate of the neural tube. Using a data-constrained computational
screen, we identified different possible mechanisms by which floor plate formation
can occur, only one of which is consistent with experimental data. In this mechanism,
the floor plate is established rapidly in response to Shh from the notochord and
the dynamics of regulatory interactions within the neural tube. In this process,
uniform activators and Shh-dependent repressors are key for establishing the floor
plate size. Subsequently, the floor plate becomes insensitive to Shh and increases
in size due to tissue growth, leading to scaling of the floor plate with neural
tube size. In turn, this results in scaling of the Shh amplitude with tissue growth.
Thus, this mechanism ensures a separation of time scales in floor plate formation,
so that the floor plate domain becomes growth-dependent after an initial rapid
establishment phase. Our study raises the possibility that the time scale separation
between specification and growth might be a common strategy for scaling the morphogen
gradient amplitude in growing organs. The model that we developed provides a new
opportunity for quantitative studies of morphogen source formation in growing
tissues.
acknowledgement: "We thank Martina Greunz-Schindler for technical support, and Thomas
Minchington and James Briscoe for comments on the manuscript.\r\nRDJGH, MM and MZ
were supported by a grant from the Priority Research Area DigiWorld\r\nunder the
Strategic Programme Excellence Initiative at Jagiellonian University. The research\r\nwas
supported by the Polish National Agency for Academic Exchange, PN/PPO/2018/1/00011/U/00001
which paid the salary of MM and MZ up to Feb 2023. The research received support
from National Science Center, Poland, 2021/42/E/NZ2/00188 which paid salary of MZ.
Work in the AK labis supported by ISTA to KK and AK, the European\r\nResearch Council
under Horizon Europe: grant 101044579 to AK, and Austrian Science Fund\r\n(FWF):
Grant DOI 10.55776/F78 to AK. The salaries of AK and KK were paid by ISTA. The funders
had no role in study design, data collection and analysis, decision to publish,
or preparation of the manuscript."
article_number: e1012508
article_processing_charge: No
article_type: original
author:
- first_name: Richard D.J.G.
full_name: Ho, Richard D.J.G.
last_name: Ho
- first_name: Kasumi
full_name: Kishi, Kasumi
id: 3065DFC4-F248-11E8-B48F-1D18A9856A87
last_name: Kishi
orcid: 0000-0001-6060-4795
- first_name: Maciej
full_name: Majka, Maciej
last_name: Majka
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
citation:
ama: Ho RDJG, Kishi K, Majka M, Kicheva A, Zagórski MP. Dynamics of morphogen source
formation in a growing tissue. PLoS Computational Biology. 2024;20. doi:10.1371/journal.pcbi.1012508
apa: Ho, R. D. J. G., Kishi, K., Majka, M., Kicheva, A., & Zagórski, M. P. (2024).
Dynamics of morphogen source formation in a growing tissue. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1012508
chicago: Ho, Richard D.J.G., Kasumi Kishi, Maciej Majka, Anna Kicheva, and Marcin
P Zagórski. “Dynamics of Morphogen Source Formation in a Growing Tissue.” PLoS
Computational Biology. Public Library of Science, 2024. https://doi.org/10.1371/journal.pcbi.1012508.
ieee: R. D. J. G. Ho, K. Kishi, M. Majka, A. Kicheva, and M. P. Zagórski, “Dynamics
of morphogen source formation in a growing tissue,” PLoS Computational Biology,
vol. 20. Public Library of Science, 2024.
ista: Ho RDJG, Kishi K, Majka M, Kicheva A, Zagórski MP. 2024. Dynamics of morphogen
source formation in a growing tissue. PLoS Computational Biology. 20, e1012508.
mla: Ho, Richard D. J. G., et al. “Dynamics of Morphogen Source Formation in a Growing
Tissue.” PLoS Computational Biology, vol. 20, e1012508, Public Library
of Science, 2024, doi:10.1371/journal.pcbi.1012508.
short: R.D.J.G. Ho, K. Kishi, M. Majka, A. Kicheva, M.P. Zagórski, PLoS Computational
Biology 20 (2024).
corr_author: '1'
date_created: 2024-10-27T23:01:45Z
date_published: 2024-10-14T00:00:00Z
date_updated: 2026-04-07T12:31:58Z
day: '14'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1371/journal.pcbi.1012508
external_id:
isi:
- '001331700300003'
pmid:
- '39401260'
file:
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checksum: 42fa714459943cb3961b40fab8fd82c8
content_type: application/pdf
creator: dernst
date_created: 2024-10-29T11:59:09Z
date_updated: 2024-10-29T11:59:09Z
file_id: '18487'
file_name: 2024_PloSComBio_Ho.pdf
file_size: 3732443
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file_date_updated: 2024-10-29T11:59:09Z
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intvolume: ' 20'
isi: 1
language:
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month: '10'
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: 059DF620-7A3F-11EA-A408-12923DDC885E
grant_number: F7802
name: Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen
control of growth and pattern in the spinal cord
publication: PLoS Computational Biology
publication_identifier:
eissn:
- 1553-7358
issn:
- 1553-734X
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
record:
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Dynamics of morphogen source formation in a growing tissue
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 20
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18902'
acknowledgement: 'MZ is supported by National Science Center, Poland, 2021/42/E/NZ2/00188,
the Polish National Agency for Academic Exchange, and by a grant from the Priority
Research Area DigiWorld under the Strategic Programme Excellence Initiative at Jagiellonian
University. Work in JB’s lab is supported by the Francis Crick Institute, which
receives its core funding from Cancer Research UK, the UK Medical Research Council
and Wellcome Trust (all under CC001051). Work in the AK lab is supported by ISTA,
the European Research Council under Horizon Europe: grant 101044579, and Austrian
Science Fund (FWF): F78 (Neural Stem Cell Modulation).'
article_number: '929'
article_processing_charge: Yes
article_type: letter_note
author:
- first_name: Marcin
full_name: Zagorski, Marcin
last_name: Zagorski
- first_name: Nathalie
full_name: Brandenberg, Nathalie
last_name: Brandenberg
- first_name: Matthias
full_name: Lutolf, Matthias
last_name: Lutolf
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
- 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
citation:
ama: Zagorski M, Brandenberg N, Lutolf M, et al. Assessing the precision of morphogen
gradients in neural tube development. Nature Communications. 2024;15. doi:10.1038/s41467-024-45148-8
apa: Zagorski, M., Brandenberg, N., Lutolf, M., Tkačik, G., Bollenbach, M. T., Briscoe,
J., & Kicheva, A. (2024). Assessing the precision of morphogen gradients in
neural tube development. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-45148-8
chicago: Zagorski, Marcin, Nathalie Brandenberg, Matthias Lutolf, Gašper Tkačik,
Mark Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Assessing the Precision
of Morphogen Gradients in Neural Tube Development.” Nature Communications.
Springer Nature, 2024. https://doi.org/10.1038/s41467-024-45148-8.
ieee: M. Zagorski et al., “Assessing the precision of morphogen gradients
in neural tube development,” Nature Communications, vol. 15. Springer Nature,
2024.
ista: Zagorski M, Brandenberg N, Lutolf M, Tkačik G, Bollenbach MT, Briscoe J, Kicheva
A. 2024. Assessing the precision of morphogen gradients in neural tube development.
Nature Communications. 15, 929.
mla: Zagorski, Marcin, et al. “Assessing the Precision of Morphogen Gradients in
Neural Tube Development.” Nature Communications, vol. 15, 929, Springer
Nature, 2024, doi:10.1038/s41467-024-45148-8.
short: M. Zagorski, N. Brandenberg, M. Lutolf, G. Tkačik, M.T. Bollenbach, J. Briscoe,
A. Kicheva, Nature Communications 15 (2024).
corr_author: '1'
date_created: 2025-01-27T13:01:01Z
date_published: 2024-02-01T00:00:00Z
date_updated: 2025-12-30T10:57:08Z
day: '01'
ddc:
- '570'
department:
- _id: GaTk
- _id: AnKi
doi: 10.1038/s41467-024-45148-8
external_id:
isi:
- '001156218500022'
pmid:
- '38302459'
file:
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date_updated: 2025-01-27T13:04:03Z
file_id: '18903'
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intvolume: ' 15'
isi: 1
language:
- iso: eng
month: '02'
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: 059DF620-7A3F-11EA-A408-12923DDC885E
grant_number: F7802
name: Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen
control of growth and pattern in the spinal cord
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Assessing the precision of morphogen gradients in neural tube development
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: 15
year: '2024'
...
---
OA_place: publisher
_id: '17133'
abstract:
- lang: eng
text: "An ideal quantum computer relies on qubits capable of performing fast gate
operations and\r\nmaintaining strong interconnections while preserving their quantum
coherence. Since the\r\ninception of experimental eforts toward building a quantum
computer, the community has\r\nfaced challenges in engineering such a system.
Among the various methods of implementing a\r\nquantum computer, superconducting
qubits have shown fast gates close to tens of nanoseconds,\r\nwith the state-of-the-art
reaching a coherence of a few milliseconds. However, achieving\r\nsimultaneously
long lifetimes with fast qubit operations poses an inherent paradox. Qubits\r\nwith
high coherence require isolation from the environment, while fast operation necessitates\r\nstrong
coupling of the qubit. This thesis approaches this issue by proposing the idea
of\r\nengineering superconducting qubits capable of transitioning between operating
in a protected\r\nregime, where the qubit is completely isolated from the environment,
and coupling to the\r\ncommunication channels as needed. In this direction, we
use the geometric superinductor to\r\nscan the parameter space of rf-SQUID devices,
searching for a regime where we can take the\r\nqubit protection to its extreme.\r\n\r\nThis
leads us to the inductively shunted transmon (IST) regime, characterized by EJ
/EC ≫ 1\r\nand EJ /EL ≫ 1, where the circuit potential exhibits a double well
with a large barrier\r\nseparating the local ground states of each quantum well.
In this regime, although it is\r\nanticipated that the two quantum wells would
be isolated from each other, we observe single\r\nfuxon tunneling between them.
The interplay of the cavity photons and the fuxon transition\r\nforms a rich physical
system, containing resonance conditions that allow the preparation of the\r\nfuxon
ground or excited states. This enables us to study the relaxation rate of such
transition\r\nand show that it can be as large as 3.6 hours. Dynamically controlling
the barrier height\r\nbetween the two quantum wells allows for controllable coupling,
which scales exponentially,\r\nfor a qubit encoded in two fuxon states.\r\nThe
0-π qubit is one of the very few known superconducting circuit types that ofers
exponential\r\nprotection from both relaxation and dephasing simultaneously. However,
this qubit is not\r\nexempt from the fact that such protection comes at the expense
of complex readout and\r\ncontrol. In this thesis, we propose a way to controllably
break the circuit symmetry, the\r\nkey reason for the protection, to momentarily
restore the ability to control and manipulate\r\nthe qubit. An asymmetry in capacitances
and inductances in the 0-π circuit is detrimental\r\nsince they lead to coupling
of the protected state to the thermally occupied parasitic mode\r\nof the circuit.
However, here we try to exploit a controlled asymmetry in Josephson energies\r\nand
show that this can be used as a tunable coupler between the protected states.
In the\r\nfuture, this should allow to perform gate operations by dynamically
controlling the asymmetry\r\ninstead of driving the protected transition with
microwave pulses. Therefore, we believe that\r\nthe proposed method can make the
use of protected qubits more practical in experimental\r\nrealizations of quantum
computing."
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Farid
full_name: Hassani, Farid
id: 2AED110C-F248-11E8-B48F-1D18A9856A87
last_name: Hassani
orcid: 0000-0001-6937-5773
citation:
ama: Hassani F. Superconducting qubits capable of dynamic switching between protected
and high-speed control regimes. 2024. doi:10.15479/at:ista:17133
apa: Hassani, F. (2024). Superconducting qubits capable of dynamic switching
between protected and high-speed control regimes. Institute of Science and
Technology Austria. https://doi.org/10.15479/at:ista:17133
chicago: Hassani, Farid. “Superconducting Qubits Capable of Dynamic Switching between
Protected and High-Speed Control Regimes.” Institute of Science and Technology
Austria, 2024. https://doi.org/10.15479/at:ista:17133.
ieee: F. Hassani, “Superconducting qubits capable of dynamic switching between protected
and high-speed control regimes,” Institute of Science and Technology Austria,
2024.
ista: Hassani F. 2024. Superconducting qubits capable of dynamic switching between
protected and high-speed control regimes. Institute of Science and Technology
Austria.
mla: Hassani, Farid. Superconducting Qubits Capable of Dynamic Switching between
Protected and High-Speed Control Regimes. Institute of Science and Technology
Austria, 2024, doi:10.15479/at:ista:17133.
short: F. Hassani, Superconducting Qubits Capable of Dynamic Switching between Protected
and High-Speed Control Regimes, Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-06-11T18:20:05Z
date_published: 2024-06-11T00:00:00Z
date_updated: 2026-04-15T06:43:02Z
day: '11'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoFi
doi: 10.15479/at:ista:17133
file:
- access_level: open_access
checksum: 258c353d47fa37ea63ea43b1e10a34a0
content_type: application/pdf
creator: fhassani
date_created: 2024-06-12T07:53:19Z
date_updated: 2024-06-20T11:52:22Z
file_id: '17137'
file_name: Thesis_main_final.pdf
file_size: 28370759
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checksum: deffa5d0db88093f74812fa71520d5e1
content_type: text/x-tex
creator: fhassani
date_created: 2024-06-12T07:54:27Z
date_updated: 2024-06-12T07:54:27Z
file_id: '17138'
file_name: Thesis_main.tex
file_size: 445735
relation: source_file
file_date_updated: 2024-06-20T11:52:22Z
has_accepted_license: '1'
keyword:
- Quantum information
- Qubits
- Superconducting devices
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '06'
oa: 1
oa_version: Published Version
page: '161'
project:
- _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A
name: NOMIS Fellowship Program
- _id: bdb108fd-d553-11ed-ba76-83dc74a9864f
grant_number: F07105
name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration
of Superconducting Quantum Circuits
publication_identifier:
isbn:
- 978-3-99078-040-4
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '13227'
relation: part_of_dissertation
status: public
- id: '9928'
relation: part_of_dissertation
status: public
- id: '8755'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
title: Superconducting qubits capable of dynamic switching between protected and high-speed
control regimes
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
OA_type: hybrid
_id: '15362'
abstract:
- lang: eng
text: Constitutional heterozygous pathogenic variants in the exonuclease domain
of POLE and POLD1, which affect the proofreading activity of the corresponding
polymerases, cause a cancer predisposition syndrome characterized by increased
risk of gastrointestinal polyposis, colorectal cancer, endometrial cancer and
other tumor types. The generally accepted explanation for the connection between
the disruption of the proofreading activity of polymerases epsilon and delta and
cancer development is through an increase in the somatic mutation rate. Here we
studied an extended family with multiple members heterozygous for the pathogenic
POLD1 variant c.1421T>C p.(Leu474Pro), which segregates with the polyposis and
cancer phenotypes. Through the analysis of mutational patterns of patient-derived
fibroblasts colonies and de novo mutations obtained by parent-offspring comparisons,
we concluded that heterozygous POLD1 L474P just subtly increases the somatic and
germline mutation burden. In contrast, tumors developed in individuals with a
heterozygous mutation in the exonuclease domain of POLD1, including L474P, have
an extremely high mutation rate (>100 mut/Mb) associated with signature SBS10d.
We solved this contradiction through the observation that tumorigenesis involves
somatic inactivation of the wildtype POLD1 allele. These results imply that exonuclease
deficiency of polymerase delta has a recessive effect on mutation rate.
acknowledgement: 'This study was funded by the Spanish Ministry of Science and Innovation
(Agencia Estatal de Investigación), co-funded by FEDER funds a way to build Europe
[PID2020-112595RB-I00 (LV)], Instituto de Salud Carlos III [CIBERONC CB16/12/00234
(LV); ISCIII-AES-2017 PI17/01082 (JLS), PMP22/00064], Government of Catalonia [AGAUR
2021SGR01112, CERCA Program for institutional support (LV)], Scientific Foundation
Asociación Española Contra el Cáncer [AECC Investigador (MT)], Austrian Science
Fund FWF [Grant Agreement # I5127-B (FK)], German Research Foundation DFG [Grant
Agreement # 429960716 (FK)], and ERC Consolidator [Grant Agreement # 771209 ChrFL
(FK)].'
article_processing_charge: No
article_type: original
author:
- first_name: Maria A.
full_name: Andrianova, Maria A.
last_name: Andrianova
- first_name: Vladimir B.
full_name: Seplyarskiy, Vladimir B.
last_name: Seplyarskiy
- first_name: Mariona
full_name: Terradas, Mariona
last_name: Terradas
- first_name: Ana Beatriz
full_name: Sánchez-Heras, Ana Beatriz
last_name: Sánchez-Heras
- first_name: Pilar
full_name: Mur, Pilar
last_name: Mur
- first_name: José Luis
full_name: Soto, José Luis
last_name: Soto
- first_name: Gemma
full_name: Aiza, Gemma
last_name: Aiza
- first_name: Emma
full_name: Borràs, Emma
last_name: Borràs
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Alexey S.
full_name: Kondrashov, Alexey S.
last_name: Kondrashov
- first_name: Georgii A.
full_name: Bazykin, Georgii A.
last_name: Bazykin
- first_name: Laura
full_name: Valle, Laura
last_name: Valle
citation:
ama: Andrianova MA, Seplyarskiy VB, Terradas M, et al. Discovery of recessive effect
of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated
normal and cancer cells. European Journal of Human Genetics. 2024;32:837-845.
doi:10.1038/s41431-024-01598-8
apa: Andrianova, M. A., Seplyarskiy, V. B., Terradas, M., Sánchez-Heras, A. B.,
Mur, P., Soto, J. L., … Valle, L. (2024). Discovery of recessive effect of human
polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated
normal and cancer cells. European Journal of Human Genetics. Springer Nature.
https://doi.org/10.1038/s41431-024-01598-8
chicago: Andrianova, Maria A., Vladimir B. Seplyarskiy, Mariona Terradas, Ana Beatriz
Sánchez-Heras, Pilar Mur, José Luis Soto, Gemma Aiza, et al. “Discovery of Recessive
Effect of Human Polymerase δ Proofreading Deficiency through Mutational Analysis
of POLD1-Mutated Normal and Cancer Cells.” European Journal of Human Genetics.
Springer Nature, 2024. https://doi.org/10.1038/s41431-024-01598-8.
ieee: M. A. Andrianova et al., “Discovery of recessive effect of human polymerase
δ proofreading deficiency through mutational analysis of POLD1-mutated normal
and cancer cells,” European Journal of Human Genetics, vol. 32. Springer
Nature, pp. 837–845, 2024.
ista: Andrianova MA, Seplyarskiy VB, Terradas M, Sánchez-Heras AB, Mur P, Soto JL,
Aiza G, Borràs E, Kondrashov F, Kondrashov AS, Bazykin GA, Valle L. 2024. Discovery
of recessive effect of human polymerase δ proofreading deficiency through mutational
analysis of POLD1-mutated normal and cancer cells. European Journal of Human Genetics.
32, 837–845.
mla: Andrianova, Maria A., et al. “Discovery of Recessive Effect of Human Polymerase
δ Proofreading Deficiency through Mutational Analysis of POLD1-Mutated Normal
and Cancer Cells.” European Journal of Human Genetics, vol. 32, Springer
Nature, 2024, pp. 837–45, doi:10.1038/s41431-024-01598-8.
short: M.A. Andrianova, V.B. Seplyarskiy, M. Terradas, A.B. Sánchez-Heras, P. Mur,
J.L. Soto, G. Aiza, E. Borràs, F. Kondrashov, A.S. Kondrashov, G.A. Bazykin, L.
Valle, European Journal of Human Genetics 32 (2024) 837–845.
date_created: 2024-05-05T22:01:04Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2026-04-15T08:51:09Z
day: '01'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1038/s41431-024-01598-8
ec_funded: 1
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call_identifier: H2020
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publication: European Journal of Human Genetics
publication_identifier:
eissn:
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issn:
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publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Discovery of recessive effect of human polymerase δ proofreading deficiency
through mutational analysis of POLD1-mutated normal and cancer cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
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type: journal_article
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---
OA_place: publisher
_id: '18135'
abstract:
- lang: eng
text: "This thesis consists of two separate parts. In the first part we consider
a dilute Fermi gas interacting through a repulsive interaction in dimensions $d=1,2,3$.
Our focus is mostly on the physically most relevant dimension $d=3$ \r\nand the
setting of a spin-polarized (equivalently spinless) gas, where the Pauli exclusion
principle plays a key role. We show that, at zero temperature, the ground state
energy density of the interacting spin-polarized gas differs (to leading order)
from that of the free (i.e. non-interacting) gas by a term of order $a_p^d\\rho^{2+2/d}$
\ with $a_p$ the $p$-wave scattering length of the repulsive interaction and $\\rho$
the density. Further, we extend this to positive temperature and show that the
pressure of an interacting spin-polarized gas differs from that of the free gas
by a now temperature dependent term, again of order $a_p^d\\rho^{2+2/d}$. Lastly,
we consider the setting of a spin-$\\frac{1}{2}$ Fermi gas in $d=3$ dimensions
and show that here, as an upper bound, the ground state energy density differs
from that of the free system by a term of order $a_s \\rho^2$ with an error smaller
than $a_s \\rho^2 (a_s\\rho^{1/3})^{1-\\eps}$ for any $\\eps > 0$, where $a_s$
is the $s$-wave scattering length of the repulsive interaction. \r\n\r\nThese
asymptotic formulas complement the similar formulas in the literature for the
dilute Bose and spin-$\\frac{1}{2}$ Fermi gas, where the ground state energies
or pressures differ from that of the corresponding free systems by a term of order
$a_s \\rho^2$ in dimension $d=3$. In the spin-polarized setting, the corrections,
of order $a_p^3\\rho^{8/3}$ in dimension $d=3$, are thus much smaller and requires
a more delicate analysis.\r\n\r\nIn the second part of the thesis we consider
the Bardeen--Cooper--Schrieffer (BCS) theory of superconductivity and in particular
its associated critical temperature and energy gap. We prove that the ratio of
the zero-temperature energy gap and critical temperature $\\Xi(T=0)/T_c$ approaches
a universal constant $\\pi e^{-\\gamma}\\approx 1.76$ in both the limit of high
density in dimension $d=3$ and in the limit of weak coupling in dimensions $d=1,2$.
This complements the proofs in the literature of this universal behaviour in the
limit of weak coupling or low density in dimension $d=3$. Secondly, we prove that
the ratio of the energy gap at positive temperature and critical temperature $\\Xi(T)/T_c$
approaches a universal function of the relative temperature $T/T_c$ in the limit
of weak coupling in dimensions $d=1,2,3$."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Asbjørn Bækgaard
full_name: Lauritsen, Asbjørn Bækgaard
id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1
last_name: Lauritsen
orcid: 0000-0003-4476-2288
citation:
ama: Lauritsen AB. Energies of dilute Fermi gases and universalities in BCS theory.
2024. doi:10.15479/at:ista:18135
apa: Lauritsen, A. B. (2024). Energies of dilute Fermi gases and universalities
in BCS theory. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18135
chicago: Lauritsen, Asbjørn Bækgaard. “Energies of Dilute Fermi Gases and Universalities
in BCS Theory.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18135.
ieee: A. B. Lauritsen, “Energies of dilute Fermi gases and universalities in BCS
theory,” Institute of Science and Technology Austria, 2024.
ista: Lauritsen AB. 2024. Energies of dilute Fermi gases and universalities in BCS
theory. Institute of Science and Technology Austria.
mla: Lauritsen, Asbjørn Bækgaard. Energies of Dilute Fermi Gases and Universalities
in BCS Theory. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18135.
short: A.B. Lauritsen, Energies of Dilute Fermi Gases and Universalities in BCS
Theory, Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-09-24T10:56:25Z
date_published: 2024-09-23T00:00:00Z
date_updated: 2026-04-16T08:17:55Z
day: '23'
ddc:
- '515'
- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: RoSe
doi: 10.15479/at:ista:18135
ec_funded: 1
file:
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language:
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month: '09'
oa: 1
oa_version: Published Version
page: '353'
project:
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grant_number: I06427
name: Mathematical Challenges in BCS Theory of Superconductivity
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication_identifier:
isbn:
- 978-3-99078-042-8
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
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relation: part_of_dissertation
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relation: part_of_dissertation
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relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
title: Energies of dilute Fermi gases and universalities in BCS theory
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'
...
---
_id: '14931'
abstract:
- lang: eng
text: We prove an upper bound on the ground state energy of the dilute spin-polarized
Fermi gas capturing the leading correction to the kinetic energy resulting from
repulsive interactions. One of the main ingredients in the proof is a rigorous
implementation of the fermionic cluster expansion of Gaudin et al. (1971) [15].
acknowledgement: A.B.L. would like to thank Johannes Agerskov and Jan Philip Solovej
for valuable discussions. We thank Alessandro Giuliani for helpful discussions and
for pointing out the reference [18]. Funding from the European Union's Horizon 2020
research and innovation programme under the ERC grant agreement No 694227 is acknowledged.
Financial support by the Austrian Science Fund (FWF) through project number I 6427-N
(as part of the SFB/TRR 352) is gratefully acknowledged.
article_number: '110320'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Asbjørn Bækgaard
full_name: Lauritsen, Asbjørn Bækgaard
id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1
last_name: Lauritsen
orcid: 0000-0003-4476-2288
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Lauritsen AB, Seiringer R. Ground state energy of the dilute spin-polarized
Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis.
2024;286(7). doi:10.1016/j.jfa.2024.110320'
apa: 'Lauritsen, A. B., & Seiringer, R. (2024). Ground state energy of the dilute
spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional
Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2024.110320'
chicago: 'Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy
of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” Journal
of Functional Analysis. Elsevier, 2024. https://doi.org/10.1016/j.jfa.2024.110320.'
ieee: 'A. B. Lauritsen and R. Seiringer, “Ground state energy of the dilute spin-polarized
Fermi gas: Upper bound via cluster expansion,” Journal of Functional Analysis,
vol. 286, no. 7. Elsevier, 2024.'
ista: 'Lauritsen AB, Seiringer R. 2024. Ground state energy of the dilute spin-polarized
Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis.
286(7), 110320.'
mla: 'Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of
the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” Journal
of Functional Analysis, vol. 286, no. 7, 110320, Elsevier, 2024, doi:10.1016/j.jfa.2024.110320.'
short: A.B. Lauritsen, R. Seiringer, Journal of Functional Analysis 286 (2024).
corr_author: '1'
date_created: 2024-02-04T23:00:53Z
date_published: 2024-04-01T00:00:00Z
date_updated: 2026-04-16T08:17:56Z
day: '01'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1016/j.jfa.2024.110320
ec_funded: 1
external_id:
arxiv:
- '2301.04894'
isi:
- '001170294000001'
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month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: bda63fe5-d553-11ed-ba76-a16e3d2f256b
grant_number: I06427
name: Mathematical Challenges in BCS Theory of Superconductivity
publication: Journal of Functional Analysis
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eissn:
- 1096-0783
issn:
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publisher: Elsevier
quality_controlled: '1'
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scopus_import: '1'
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title: 'Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via
cluster expansion'
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image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
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...