---
_id: '15033'
abstract:
- lang: eng
text: The GNOM (GN) Guanine nucleotide Exchange Factor for ARF small GTPases (ARF-GEF)
is among the best studied trafficking regulators in plants, playing crucial and
unique developmental roles in patterning and polarity. The current models place
GN at the Golgi apparatus (GA), where it mediates secretion/recycling, and at
the plasma membrane (PM) presumably contributing to clathrin-mediated endocytosis
(CME). The mechanistic basis of the developmental function of GN, distinct from
the other ARF-GEFs including its closest homologue GNOM-LIKE1 (GNL1), remains
elusive. Insights from this study largely extend the current notions of GN function.
We show that GN, but not GNL1, localizes to the cell periphery at long-lived structures
distinct from clathrin-coated pits, while CME and secretion proceed normally in
gn knockouts. The functional GN mutant variant GNfewerroots,
absent from the GA, suggests that the cell periphery is the major site of GN action
responsible for its developmental function. Following inhibition by Brefeldin
A, GN, but not GNL1, relocates to the PM likely on exocytic vesicles, suggesting
selective molecular associations en route to the cell periphery. A study of GN-GNL1
chimeric ARF-GEFs indicates that all GN domains contribute to the specific GN
function in a partially redundant manner. Together, this study offers significant
steps toward the elucidation of the mechanism underlying unique cellular and development
functions of GNOM.
acknowledgement: "The authors would like to gratefully acknowledge Dr Xixi Zhang for
cloning the GNL1/pDONR221 construct and for useful discussions.H2020 European Research\r\nCouncil
Advanced Grant ETAP742985 to Jiří Friml, Austrian Science Fund I 3630-B25 to Jiří
Friml"
article_processing_charge: Yes
article_type: original
author:
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Ivana
full_name: Matijevic, Ivana
id: 83c17ce3-15b2-11ec-abd3-f486545870bd
last_name: Matijevic
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Adamowski M, Matijevic I, Friml J. Developmental patterning function of GNOM
ARF-GEF mediated from the cell periphery. eLife. 2024;13. doi:10.7554/elife.68993
apa: Adamowski, M., Matijevic, I., & Friml, J. (2024). Developmental patterning
function of GNOM ARF-GEF mediated from the cell periphery. ELife. eLife
Sciences Publications. https://doi.org/10.7554/elife.68993
chicago: Adamowski, Maciek, Ivana Matijevic, and Jiří Friml. “Developmental Patterning
Function of GNOM ARF-GEF Mediated from the Cell Periphery.” ELife. eLife
Sciences Publications, 2024. https://doi.org/10.7554/elife.68993.
ieee: M. Adamowski, I. Matijevic, and J. Friml, “Developmental patterning function
of GNOM ARF-GEF mediated from the cell periphery,” eLife, vol. 13. eLife
Sciences Publications, 2024.
ista: Adamowski M, Matijevic I, Friml J. 2024. Developmental patterning function
of GNOM ARF-GEF mediated from the cell periphery. eLife. 13.
mla: Adamowski, Maciek, et al. “Developmental Patterning Function of GNOM ARF-GEF
Mediated from the Cell Periphery.” ELife, vol. 13, eLife Sciences Publications,
2024, doi:10.7554/elife.68993.
short: M. Adamowski, I. Matijevic, J. Friml, ELife 13 (2024).
date_created: 2024-02-27T07:10:11Z
date_published: 2024-02-21T00:00:00Z
date_updated: 2024-02-28T12:29:43Z
day: '21'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.7554/elife.68993
ec_funded: 1
has_accepted_license: '1'
intvolume: ' 13'
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.7554/eLife.68993
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: epub_ahead
publisher: eLife Sciences Publications
quality_controlled: '1'
status: public
title: Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery
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: 13
year: '2024'
...
---
_id: '14479'
abstract:
- lang: eng
text: 'In animals, parasitic infections impose significant fitness costs.1,2,3,4,5,6
Infected animals can alter their feeding behavior to resist infection,7,8,9,10,11,12
but parasites can manipulate animal foraging behavior to their own benefits.13,14,15,16
How nutrition influences host-parasite interactions is not well understood, as
studies have mainly focused on the host and less on the parasite.9,12,17,18,19,20,21,22,23
We used the nutritional geometry framework24 to investigate the role of amino
acids (AA) and carbohydrates (C) in a host-parasite system: the Argentine ant,
Linepithema humile, and the entomopathogenic fungus, Metarhizium brunneum. First,
using 18 diets varying in AA:C composition, we established that the fungus performed
best on the high-amino-acid diet 1:4. Second, we found that the fungus reached
this optimal diet when given various diet pairings, revealing its ability to cope
with nutritional challenges. Third, we showed that the optimal fungal diet reduced
the lifespan of healthy ants when compared with a high-carbohydrate diet but had
no effect on infected ants. Fourth, we revealed that infected ant colonies, given
a choice between the optimal fungal diet and a high-carbohydrate diet, chose the
optimal fungal diet, whereas healthy colonies avoided it. Lastly, by disentangling
fungal infection from host immune response, we demonstrated that infected ants
foraged on the optimal fungal diet in response to immune activation and not as
a result of parasite manipulation. Therefore, we revealed that infected ant colonies
chose a diet that is costly for survival in the long term but beneficial in the
short term—a form of collective self-medication.'
acknowledgement: We are sincerely grateful to the referees for their valuable comments
and suggestions, which helped us to improve the paper. We are thankful to Jorgen
Eilenberg and Nicolai V. Meyling for the fungal strain, to Simon Tragust, Abel Bernadou,
and Brian Lazarro for insightful discussions, to Iago Sanmartín-Villar, Léa Briard,
Céline Maitrel, and Nolwenn Rissen for their help with the experiments. Furthermore,
we thank Anna V. Grasse for help with the immune gene expression analyses. We thank
Sergio Ibarra for creating the graphical abstract. E.C. was supported by a Fyssen
Foundation grant and the Alexander von Humboldt Foundation. A.D. was supported by
the CNRS.
article_processing_charge: No
article_type: original
author:
- first_name: Eniko
full_name: Csata, Eniko
last_name: Csata
- first_name: Alfonso
full_name: Perez-Escudero, Alfonso
last_name: Perez-Escudero
- first_name: Emmanuel
full_name: Laury, Emmanuel
last_name: Laury
- first_name: Hanna
full_name: Leitner, Hanna
id: 8fc5c6f6-5903-11ec-abad-c83f046253e7
last_name: Leitner
- first_name: Gerard
full_name: Latil, Gerard
last_name: Latil
- first_name: Juerge
full_name: Heinze, Juerge
last_name: Heinze
- first_name: Stephen
full_name: Simpson, Stephen
last_name: Simpson
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Audrey
full_name: Dussutour, Audrey
last_name: Dussutour
citation:
ama: Csata E, Perez-Escudero A, Laury E, et al. Fungal infection alters collective
nutritional intake of ant colonies. Current Biology. 2024;34(4):902-909.e6.
doi:10.1016/j.cub.2024.01.017
apa: Csata, E., Perez-Escudero, A., Laury, E., Leitner, H., Latil, G., Heinze, J.,
… Dussutour, A. (2024). Fungal infection alters collective nutritional intake
of ant colonies. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2024.01.017
chicago: Csata, Eniko, Alfonso Perez-Escudero, Emmanuel Laury, Hanna Leitner, Gerard
Latil, Juerge Heinze, Stephen Simpson, Sylvia Cremer, and Audrey Dussutour. “Fungal
Infection Alters Collective Nutritional Intake of Ant Colonies.” Current Biology.
Elsevier, 2024. https://doi.org/10.1016/j.cub.2024.01.017.
ieee: E. Csata et al., “Fungal infection alters collective nutritional intake
of ant colonies,” Current Biology, vol. 34, no. 4. Elsevier, p. 902–909.e6,
2024.
ista: Csata E, Perez-Escudero A, Laury E, Leitner H, Latil G, Heinze J, Simpson
S, Cremer S, Dussutour A. 2024. Fungal infection alters collective nutritional
intake of ant colonies. Current Biology. 34(4), 902–909.e6.
mla: Csata, Eniko, et al. “Fungal Infection Alters Collective Nutritional Intake
of Ant Colonies.” Current Biology, vol. 34, no. 4, Elsevier, 2024, p. 902–909.e6,
doi:10.1016/j.cub.2024.01.017.
short: E. Csata, A. Perez-Escudero, E. Laury, H. Leitner, G. Latil, J. Heinze, S.
Simpson, S. Cremer, A. Dussutour, Current Biology 34 (2024) 902–909.e6.
date_created: 2023-10-31T13:30:20Z
date_published: 2024-02-26T00:00:00Z
date_updated: 2024-03-04T07:14:41Z
day: '26'
department:
- _id: SyCr
doi: 10.1016/j.cub.2024.01.017
external_id:
pmid:
- '38307022'
intvolume: ' 34'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2023.10.26.564092
month: '02'
oa: 1
oa_version: Preprint
page: 902-909.e6
pmid: 1
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fungal infection alters collective nutritional intake of ant colonies
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2024'
...
---
_id: '15045'
abstract:
- lang: eng
text: Coupling of orbital motion to a spin degree of freedom gives rise to various
transport phenomena in quantum systems that are beyond the standard paradigms
of classical physics. Here, we discuss features of spin-orbit dynamics that can
be visualized using a classical model with two coupled angular degrees of freedom.
Specifically, we demonstrate classical ‘spin’ filtering through our model and
show that the interplay between angular degrees of freedom and dissipation can
lead to asymmetric ‘spin’ transport.
acknowledgement: "We thank Mikhail Lemeshko and members of his group for many inspiring
discussions; Alberto Cappellaro for comments on the manuscript.\r\nOpen access funding
provided by Institute of Science and Technology (IST Austria)."
article_number: '12'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Atul
full_name: Varshney, Atul
id: 2A2006B2-F248-11E8-B48F-1D18A9856A87
last_name: Varshney
orcid: 0000-0002-3072-5999
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Varshney A, Ghazaryan A, Volosniev A. Classical ‘spin’ filtering with two degrees
of freedom and dissipation. Few-Body Systems. 2024;65. doi:10.1007/s00601-024-01880-x
apa: Varshney, A., Ghazaryan, A., & Volosniev, A. (2024). Classical ‘spin’ filtering
with two degrees of freedom and dissipation. Few-Body Systems. Springer
Nature. https://doi.org/10.1007/s00601-024-01880-x
chicago: Varshney, Atul, Areg Ghazaryan, and Artem Volosniev. “Classical ‘Spin’
Filtering with Two Degrees of Freedom and Dissipation.” Few-Body Systems.
Springer Nature, 2024. https://doi.org/10.1007/s00601-024-01880-x.
ieee: A. Varshney, A. Ghazaryan, and A. Volosniev, “Classical ‘spin’ filtering with
two degrees of freedom and dissipation,” Few-Body Systems, vol. 65. Springer
Nature, 2024.
ista: Varshney A, Ghazaryan A, Volosniev A. 2024. Classical ‘spin’ filtering with
two degrees of freedom and dissipation. Few-Body Systems. 65, 12.
mla: Varshney, Atul, et al. “Classical ‘Spin’ Filtering with Two Degrees of Freedom
and Dissipation.” Few-Body Systems, vol. 65, 12, Springer Nature, 2024,
doi:10.1007/s00601-024-01880-x.
short: A. Varshney, A. Ghazaryan, A. Volosniev, Few-Body Systems 65 (2024).
date_created: 2024-03-01T11:39:33Z
date_published: 2024-02-17T00:00:00Z
date_updated: 2024-03-04T07:08:16Z
day: '17'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1007/s00601-024-01880-x
external_id:
arxiv:
- '2401.08454'
file:
- access_level: open_access
checksum: c4e08cc7bc756da69b1b36fda7bb92fb
content_type: application/pdf
creator: dernst
date_created: 2024-03-04T07:07:10Z
date_updated: 2024-03-04T07:07:10Z
file_id: '15049'
file_name: 2024_FewBodySys_Varshney.pdf
file_size: 436712
relation: main_file
success: 1
file_date_updated: 2024-03-04T07:07:10Z
has_accepted_license: '1'
intvolume: ' 65'
keyword:
- Atomic and Molecular Physics
- and Optics
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Few-Body Systems
publication_identifier:
issn:
- 1432-5411
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Classical ‘spin’ filtering with two degrees of freedom and dissipation
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: 65
year: '2024'
...
---
_id: '15053'
abstract:
- lang: eng
text: Atom-based quantum simulators have had many successes in tackling challenging
quantum many-body problems, owing to the precise and dynamical control that they
provide over the systems' parameters. They are, however, often optimized to address
a specific type of problem. Here, we present the design and implementation of
a 6Li-based quantum gas platform that provides wide-ranging capabilities and is
able to address a variety of quantum many-body problems. Our two-chamber architecture
relies on a robust combination of gray molasses and optical transport from a laser-cooling
chamber to a glass cell with excellent optical access. There, we first create
unitary Fermi superfluids in a three-dimensional axially symmetric harmonic trap
and characterize them using in situ thermometry, reaching temperatures below 20
nK. This allows us to enter the deep superfluid regime with samples of extreme
diluteness, where the interparticle spacing is sufficiently large for direct single-atom
imaging. Second, we generate optical lattice potentials with triangular and honeycomb
geometry in which we study diffraction of molecular Bose-Einstein condensates,
and show how going beyond the Kapitza-Dirac regime allows us to unambiguously
distinguish between the two geometries. With the ability to probe quantum many-body
physics in both discrete and continuous space, and its suitability for bulk and
single-atom imaging, our setup represents an important step towards achieving
a wide-scope quantum simulator.
acknowledgement: We thank Clara Bachorz, Darby Bates, Markus Bohlen, Valentin Crépel,
Yann Kiefer, Joanna Lis, Mihail Rabinovic, and Julian Struck for experimental assistance
in the early stages of this project, and Sebastian Will for a critical reading of
the manuscript. This work has been supported by Agence Nationale de la Recherche
(Grant No. ANR-21-CE30-0021), the European Research Council (Grant No. ERC-2016-ADG-743159),
CNRS (Tremplin@INP 2020), and Région Ile-de-France in the framework of DIM SIRTEQ
(Super2D and SISCo) and DIM QuanTiP.
article_number: '013158'
article_processing_charge: Yes
article_type: original
author:
- first_name: Shuwei
full_name: Jin, Shuwei
last_name: Jin
- first_name: Kunlun
full_name: Dai, Kunlun
last_name: Dai
- first_name: Joris
full_name: Verstraten, Joris
last_name: Verstraten
- first_name: Maxime
full_name: Dixmerias, Maxime
last_name: Dixmerias
- first_name: Ragheed
full_name: Al Hyder, Ragheed
id: d1c405be-ae15-11ed-8510-ccf53278162e
last_name: Al Hyder
- first_name: Christophe
full_name: Salomon, Christophe
last_name: Salomon
- first_name: Bruno
full_name: Peaudecerf, Bruno
last_name: Peaudecerf
- first_name: Tim
full_name: de Jongh, Tim
last_name: de Jongh
- first_name: Tarik
full_name: Yefsah, Tarik
last_name: Yefsah
citation:
ama: Jin S, Dai K, Verstraten J, et al. Multipurpose platform for analog quantum
simulation. Physical Review Research. 2024;6(1). doi:10.1103/physrevresearch.6.013158
apa: Jin, S., Dai, K., Verstraten, J., Dixmerias, M., Al Hyder, R., Salomon, C.,
… Yefsah, T. (2024). Multipurpose platform for analog quantum simulation. Physical
Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.6.013158
chicago: Jin, Shuwei, Kunlun Dai, Joris Verstraten, Maxime Dixmerias, Ragheed Al
Hyder, Christophe Salomon, Bruno Peaudecerf, Tim de Jongh, and Tarik Yefsah. “Multipurpose
Platform for Analog Quantum Simulation.” Physical Review Research. American
Physical Society, 2024. https://doi.org/10.1103/physrevresearch.6.013158.
ieee: S. Jin et al., “Multipurpose platform for analog quantum simulation,”
Physical Review Research, vol. 6, no. 1. American Physical Society, 2024.
ista: Jin S, Dai K, Verstraten J, Dixmerias M, Al Hyder R, Salomon C, Peaudecerf
B, de Jongh T, Yefsah T. 2024. Multipurpose platform for analog quantum simulation.
Physical Review Research. 6(1), 013158.
mla: Jin, Shuwei, et al. “Multipurpose Platform for Analog Quantum Simulation.”
Physical Review Research, vol. 6, no. 1, 013158, American Physical Society,
2024, doi:10.1103/physrevresearch.6.013158.
short: S. Jin, K. Dai, J. Verstraten, M. Dixmerias, R. Al Hyder, C. Salomon, B.
Peaudecerf, T. de Jongh, T. Yefsah, Physical Review Research 6 (2024).
date_created: 2024-03-04T07:42:52Z
date_published: 2024-02-13T00:00:00Z
date_updated: 2024-03-04T07:55:29Z
day: '13'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1103/physrevresearch.6.013158
external_id:
arxiv:
- '2304.08433'
file:
- access_level: open_access
checksum: ba2ae3e3a011f8897d3803c9366a67e2
content_type: application/pdf
creator: dernst
date_created: 2024-03-04T07:53:08Z
date_updated: 2024-03-04T07:53:08Z
file_id: '15054'
file_name: 2024_PhysicalReviewResearch_Jin.pdf
file_size: 4025988
relation: main_file
success: 1
file_date_updated: 2024-03-04T07:53:08Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '1'
keyword:
- General Physics and Astronomy
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Physical Review Research
publication_identifier:
issn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Multipurpose platform for analog quantum simulation
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: 6
year: '2024'
...
---
_id: '15048'
abstract:
- lang: eng
text: Embryogenesis results from the coordinated activities of different signaling
pathways controlling cell fate specification and morphogenesis. In vertebrate
gastrulation, both Nodal and BMP signaling play key roles in germ layer specification
and morphogenesis, yet their interplay to coordinate embryo patterning with morphogenesis
is still insufficiently understood. Here, we took a reductionist approach using
zebrafish embryonic explants to study the coordination of Nodal and BMP signaling
for embryo patterning and morphogenesis. We show that Nodal signaling triggers
explant elongation by inducing mesendodermal progenitors but also suppressing
BMP signaling activity at the site of mesendoderm induction. Consistent with this,
ectopic BMP signaling in the mesendoderm blocks cell alignment and oriented mesendoderm
intercalations, key processes during explant elongation. Translating these ex
vivo observations to the intact embryo showed that, similar to explants, Nodal
signaling suppresses the effect of BMP signaling on cell intercalations in the
dorsal domain, thus allowing robust embryonic axis elongation. These findings
suggest a dual function of Nodal signaling in embryonic axis elongation by both
inducing mesendoderm and suppressing BMP effects in the dorsal portion of the
mesendoderm.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: "We thank Patrick Müller for sharing the chordintt250 mutant zebrafish
line as well as the plasmid for chrd-GFP, Katherine Rogers for sharing the bmp2b
plasmid and Andrea Pauli for sharing the draculin plasmid. Diana Pinheiro generated
the MZlefty1,2;Tg(sebox::EGFP) line. We are grateful to Patrick Müller, Diana Pinheiro
and Katherine Rogers and members of the Heisenberg lab for discussions, technical
advice and feedback on the manuscript. We also thank Anna Kicheva and Edouard Hannezo
for discussions. We thank the Imaging and Optics Facility as well as the Life Science
facility at IST Austria for support with microscopy and fish maintenance.\r\nThis
work was supported by a European Research Council Advanced Grant\r\n(MECSPEC 742573
to C.-P.H.). A.S. is a recipient of a DOC Fellowship of the Austrian\r\nAcademy
of Sciences at IST Austria. Open Access funding provided by Institute of\r\nScience
and Technology Austria. "
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Alexandra
full_name: Schauer, Alexandra
id: 30A536BA-F248-11E8-B48F-1D18A9856A87
last_name: Schauer
orcid: 0000-0001-7659-9142
- first_name: Kornelija
full_name: Pranjic-Ferscha, Kornelija
id: 4362B3C2-F248-11E8-B48F-1D18A9856A87
last_name: Pranjic-Ferscha
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. Robust axis elongation
by Nodal-dependent restriction of BMP signaling. Development. 2024;151(4):1-18.
doi:10.1242/dev.202316
apa: Schauer, A., Pranjic-Ferscha, K., Hauschild, R., & Heisenberg, C.-P. J.
(2024). Robust axis elongation by Nodal-dependent restriction of BMP signaling.
Development. The Company of Biologists. https://doi.org/10.1242/dev.202316
chicago: Schauer, Alexandra, Kornelija Pranjic-Ferscha, Robert Hauschild, and Carl-Philipp
J Heisenberg. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.”
Development. The Company of Biologists, 2024. https://doi.org/10.1242/dev.202316.
ieee: A. Schauer, K. Pranjic-Ferscha, R. Hauschild, and C.-P. J. Heisenberg, “Robust
axis elongation by Nodal-dependent restriction of BMP signaling,” Development,
vol. 151, no. 4. The Company of Biologists, pp. 1–18, 2024.
ista: Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. 2024. Robust axis
elongation by Nodal-dependent restriction of BMP signaling. Development. 151(4),
1–18.
mla: Schauer, Alexandra, et al. “Robust Axis Elongation by Nodal-Dependent Restriction
of BMP Signaling.” Development, vol. 151, no. 4, The Company of Biologists,
2024, pp. 1–18, doi:10.1242/dev.202316.
short: A. Schauer, K. Pranjic-Ferscha, R. Hauschild, C.-P.J. Heisenberg, Development
151 (2024) 1–18.
date_created: 2024-03-03T23:00:50Z
date_published: 2024-02-01T00:00:00Z
date_updated: 2024-03-04T07:28:25Z
day: '01'
ddc:
- '570'
department:
- _id: CaHe
- _id: Bio
doi: 10.1242/dev.202316
ec_funded: 1
file:
- access_level: open_access
checksum: 6961ea10012bf0d266681f9628bb8f13
content_type: application/pdf
creator: dernst
date_created: 2024-03-04T07:24:43Z
date_updated: 2024-03-04T07:24:43Z
file_id: '15050'
file_name: 2024_Development_Schauer.pdf
file_size: 14839986
relation: main_file
success: 1
file_date_updated: 2024-03-04T07:24:43Z
has_accepted_license: '1'
intvolume: ' 151'
issue: '4'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 1-18
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
- _id: 26B1E39C-B435-11E9-9278-68D0E5697425
grant_number: '25239'
name: 'Mesendoderm specification in zebrafish: The role of extraembryonic tissues'
publication: Development
publication_identifier:
eissn:
- 1477-9129
issn:
- 0950-1991
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
related_material:
record:
- id: '14926'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Robust axis elongation by Nodal-dependent restriction of BMP signaling
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: 151
year: '2024'
...
---
_id: '15052'
abstract:
- lang: eng
text: "Substrate induces mechanical strain on perovskite devices, which can result
in alterations to its lattice dynamics and thermal transport. Herein, we have
performed a theoretical investigation on the anharmonic lattice dynamics and thermal
property of perovskite Rb2SnBr6 and Cs2SnBr6 under strains using perturbation
theory up to the fourth-order terms and the unified thermal transport theory.
We demonstrate a pronounced hardening of low-frequency optical phonons as temperature
increases, indicating strong lattice anharmonicity and the necessity of adopting
temperature-dependent interatomic force constants in the lattice thermal conductivity
(\r\nκL) calculations. It is found that the low-lying optical phonon modes of
Rb2SnBr6 are extremely soft and their phonon energies are almost strain independent,
which ultimately lead to a lower \r\nκL and a weaker strain dependence than Cs2SnBr6.
We further reveal that the strain dependence of these phonon modes in the A2XB6-type
perovskites weakens as their ibrational frequency decreases. This study deepens
the understanding of lattice thermal transport in perovskites A2XB6 and provides
a perspective on the selection of materials that meet the expected thermal behaviors
in practical applications."
acknowledgement: "This work is supported by the Research Grants Council of Hong Kong
(C7002-22Y and 17318122). The authors are grateful for the research computing facilities
offered by\r\nITS, HKU. Z.Z. acknowledges the European Union’s Horizon 2020 research
and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413."
article_number: '054305'
article_processing_charge: No
article_type: original
author:
- first_name: Ruihuan
full_name: Cheng, Ruihuan
last_name: Cheng
- first_name: Zezhu
full_name: Zeng, Zezhu
id: 54a2c730-803f-11ed-ab7e-95b29d2680e7
last_name: Zeng
- first_name: Chen
full_name: Wang, Chen
last_name: Wang
- first_name: Niuchang
full_name: Ouyang, Niuchang
last_name: Ouyang
- first_name: Yue
full_name: Chen, Yue
last_name: Chen
citation:
ama: Cheng R, Zeng Z, Wang C, Ouyang N, Chen Y. Impact of strain-insensitive low-frequency
phonon modes on lattice thermal transport in AxXB6-type perovskites. Physical
Review B. 2024;109(5). doi:10.1103/physrevb.109.054305
apa: Cheng, R., Zeng, Z., Wang, C., Ouyang, N., & Chen, Y. (2024). Impact of
strain-insensitive low-frequency phonon modes on lattice thermal transport in
AxXB6-type perovskites. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.109.054305
chicago: Cheng, Ruihuan, Zezhu Zeng, Chen Wang, Niuchang Ouyang, and Yue Chen. “Impact
of Strain-Insensitive Low-Frequency Phonon Modes on Lattice Thermal Transport
in AxXB6-Type Perovskites.” Physical Review B. American Physical Society,
2024. https://doi.org/10.1103/physrevb.109.054305.
ieee: R. Cheng, Z. Zeng, C. Wang, N. Ouyang, and Y. Chen, “Impact of strain-insensitive
low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites,”
Physical Review B, vol. 109, no. 5. American Physical Society, 2024.
ista: Cheng R, Zeng Z, Wang C, Ouyang N, Chen Y. 2024. Impact of strain-insensitive
low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites.
Physical Review B. 109(5), 054305.
mla: Cheng, Ruihuan, et al. “Impact of Strain-Insensitive Low-Frequency Phonon Modes
on Lattice Thermal Transport in AxXB6-Type Perovskites.” Physical Review B,
vol. 109, no. 5, 054305, American Physical Society, 2024, doi:10.1103/physrevb.109.054305.
short: R. Cheng, Z. Zeng, C. Wang, N. Ouyang, Y. Chen, Physical Review B 109 (2024).
date_created: 2024-03-04T07:41:23Z
date_published: 2024-02-14T00:00:00Z
date_updated: 2024-03-04T07:48:55Z
day: '14'
department:
- _id: BiCh
doi: 10.1103/physrevb.109.054305
ec_funded: 1
intvolume: ' 109'
issue: '5'
language:
- iso: eng
month: '02'
oa_version: None
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Impact of strain-insensitive low-frequency phonon modes on lattice thermal
transport in AxXB6-type perovskites
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 109
year: '2024'
...
---
_id: '14926'
author:
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
citation:
ama: Hauschild R. Matlab script for analysis of clone dispersal. 2024. doi:10.15479/AT:ISTA:14926
apa: Hauschild, R. (2024). Matlab script for analysis of clone dispersal. ISTA.
https://doi.org/10.15479/AT:ISTA:14926
chicago: Hauschild, Robert. “Matlab Script for Analysis of Clone Dispersal.” ISTA,
2024. https://doi.org/10.15479/AT:ISTA:14926.
ieee: R. Hauschild, “Matlab script for analysis of clone dispersal.” ISTA, 2024.
ista: Hauschild R. 2024. Matlab script for analysis of clone dispersal, ISTA, 10.15479/AT:ISTA:14926.
mla: Hauschild, Robert. Matlab Script for Analysis of Clone Dispersal. ISTA,
2024, doi:10.15479/AT:ISTA:14926.
short: R. Hauschild, (2024).
date_created: 2024-02-02T14:42:26Z
date_published: 2024-02-02T00:00:00Z
date_updated: 2024-03-04T07:28:25Z
day: '02'
ddc:
- '570'
department:
- _id: Bio
doi: 10.15479/AT:ISTA:14926
file:
- access_level: open_access
checksum: df7f358ae19a176cf710c0a802ce31b1
content_type: application/octet-stream
creator: rhauschild
date_created: 2024-02-02T14:40:31Z
date_updated: 2024-02-02T14:40:31Z
file_id: '14927'
file_name: README.md
file_size: 736
relation: main_file
success: 1
- access_level: open_access
checksum: 10194cc11619eccd8f4b24472e465b7f
content_type: application/x-zip-compressed
creator: rhauschild
date_created: 2024-02-02T14:40:31Z
date_updated: 2024-02-02T14:40:31Z
file_id: '14928'
file_name: Supplementary_file_1.zip
file_size: 3543
relation: main_file
success: 1
file_date_updated: 2024-02-02T14:40:31Z
has_accepted_license: '1'
license: https://opensource.org/licenses/MIT
month: '02'
oa: 1
publisher: ISTA
related_material:
record:
- id: '15048'
relation: used_in_publication
status: public
status: public
title: Matlab script for analysis of clone dispersal
tmp:
legal_code_url: https://opensource.org/licenses/MIT
name: The MIT License
short: MIT
type: software
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_id: '15047'
abstract:
- lang: eng
text: Tropical precipitation extremes and their changes with surface warming are
investigated using global storm resolving simulations and high-resolution observations.
The simulations demonstrate that the mesoscale organization of convection, a process
that cannot be physically represented by conventional global climate models, is
important for the variations of tropical daily accumulated precipitation extremes.
In both the simulations and observations, daily precipitation extremes increase
in a more organized state, in association with larger, but less frequent, storms.
Repeating the simulations for a warmer climate results in a robust increase in
monthly-mean daily precipitation extremes. Higher precipitation percentiles have
a greater sensitivity to convective organization, which is predicted to increase
with warming. Without changes in organization, the strongest daily precipitation
extremes over the tropical oceans increase at a rate close to Clausius-Clapeyron
(CC) scaling. Thus, in a future warmer state with increased organization, the
strongest daily precipitation extremes over oceans increase at a faster rate than
CC scaling.
acknowledgement: This work is supported by the Max-Planck-Gesellschaft (MPG). We greatly
appreciate computational resources from Deutsches Klimarechenzentrum (DKRZ) and
the Jülich Supercomputing Centre (JSC). ICONA/O simulations are funded through the
NextGEMS project by the EU’s Horizon 2020 programme (grant agreement no. 101003470).
ICONA simulations are funded through the MONSOON-2.0 project (grant agreement no.
01LP1927A) which is supported from German Federal Ministry of Education and Research
(BMBF). J.B. acknowledges funding from the European Union’s Horizon 2020 research
and innovation programme under the Marie Skłodowska-Curie grant (grant agreement
no. 101034413). B.S. acknowledges funding from the EU’s Horizon 2020 programme (grant
agreement no. 101003470). C.M. gratefully acknowledges funding from the European
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
program (Project CLUSTER, grant agreement no. 805041).
article_number: eadj6801
article_processing_charge: Yes
article_type: original
author:
- first_name: Jiawei
full_name: Bao, Jiawei
id: bb9a7399-fefd-11ed-be3c-ae648fd1d160
last_name: Bao
- first_name: Bjorn
full_name: Stevens, Bjorn
last_name: Stevens
- first_name: Lukas
full_name: Kluft, Lukas
last_name: Kluft
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
citation:
ama: Bao J, Stevens B, Kluft L, Muller CJ. Intensification of daily tropical precipitation
extremes from more organized convection. Science Advances. 2024;10(8).
doi:10.1126/sciadv.adj6801
apa: Bao, J., Stevens, B., Kluft, L., & Muller, C. J. (2024). Intensification
of daily tropical precipitation extremes from more organized convection. Science
Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adj6801
chicago: Bao, Jiawei, Bjorn Stevens, Lukas Kluft, and Caroline J Muller. “Intensification
of Daily Tropical Precipitation Extremes from More Organized Convection.” Science
Advances. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adj6801.
ieee: J. Bao, B. Stevens, L. Kluft, and C. J. Muller, “Intensification of daily
tropical precipitation extremes from more organized convection,” Science Advances,
vol. 10, no. 8. American Association for the Advancement of Science, 2024.
ista: Bao J, Stevens B, Kluft L, Muller CJ. 2024. Intensification of daily tropical
precipitation extremes from more organized convection. Science Advances. 10(8),
eadj6801.
mla: Bao, Jiawei, et al. “Intensification of Daily Tropical Precipitation Extremes
from More Organized Convection.” Science Advances, vol. 10, no. 8, eadj6801,
American Association for the Advancement of Science, 2024, doi:10.1126/sciadv.adj6801.
short: J. Bao, B. Stevens, L. Kluft, C.J. Muller, Science Advances 10 (2024).
date_created: 2024-03-03T23:00:50Z
date_published: 2024-02-23T00:00:00Z
date_updated: 2024-03-05T09:26:47Z
day: '23'
ddc:
- '550'
department:
- _id: CaMu
doi: 10.1126/sciadv.adj6801
ec_funded: 1
external_id:
pmid:
- '38394192'
file:
- access_level: open_access
checksum: d4ec4f05a6d14745057e14d1b8bf45ae
content_type: application/pdf
creator: dernst
date_created: 2024-03-04T07:34:00Z
date_updated: 2024-03-04T07:34:00Z
file_id: '15051'
file_name: 2024_ScienceAdv_Bao.pdf
file_size: 800926
relation: main_file
success: 1
file_date_updated: 2024-03-04T07:34:00Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '8'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
- _id: 629205d8-2b32-11ec-9570-e1356ff73576
call_identifier: H2020
grant_number: '805041'
name: organization of CLoUdS, and implications of Tropical cyclones and for the
Energetics of the tropics, in current and waRming climate
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/cloud-clustering-causes-more-extreme-rain/
scopus_import: '1'
status: public
title: Intensification of daily tropical precipitation extremes from more organized
convection
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: 10
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.
date_created: 2023-04-27T09:41:48Z
date_published: 2024-01-17T00:00:00Z
date_updated: 2024-03-05T09:43:02Z
day: '17'
ddc:
- '570'
department:
- _id: SiHi
- _id: RySh
doi: 10.1016/j.neuron.2023.11.009
external_id:
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'
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 230-246.e11
pmid: 1
project:
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
grant_number: F07805
name: 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: '14979'
abstract:
- lang: eng
text: Poxviruses are among the largest double-stranded DNA viruses, with members
such as variola virus, monkeypox virus and the vaccination strain vaccinia virus
(VACV). Knowledge about the structural proteins that form the viral core has remained
sparse. While major core proteins have been annotated via indirect experimental
evidence, their structures have remained elusive and they could not be assigned
to individual core features. Hence, which proteins constitute which layers of
the core, such as the palisade layer and the inner core wall, has remained enigmatic.
Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach
in combination with AlphaFold molecular modeling, that trimers formed by the cleavage
product of VACV protein A10 are the key component of the palisade layer. This
allows us to place previously obtained descriptions of protein interactions within
the core wall into perspective and to provide a detailed model of poxvirus core
architecture. Importantly, we show that interactions within A10 trimers are likely
generalizable over members of orthopox- and parapoxviruses.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: EM-Fac
acknowledgement: "We thank A. Bergthaler (Research Center for Molecular Medicine of
the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and
his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific
Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel
and other members of the Schur group for support and helpful discussions. We also
thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help
optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map
with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S.
also received support from the Austrian Science Fund (FWF) grant P31445. This publication
has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg
from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community
Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis
research was also supported by the Scientific Service Units (SSUs) of ISTA through
resources provided by Scientific Computing (SciComp), the Life Science Facility
(LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of
COSMIC45 and Colabfold46."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Julia
full_name: Datler, Julia
id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87
last_name: Datler
orcid: 0000-0002-3616-8580
- first_name: Jesse
full_name: Hansen, Jesse
id: 1063c618-6f9b-11ec-9123-f912fccded63
last_name: Hansen
- first_name: Andreas
full_name: Thader, Andreas
id: 3A18A7B8-F248-11E8-B48F-1D18A9856A87
last_name: Thader
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Lukas W
full_name: Bauer, Lukas W
id: 0c894dcf-897b-11ed-a09c-8186353224b0
last_name: Bauer
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of
protein A10 to form the palisade layer in poxvirus cores. Nature Structural
& Molecular Biology. 2024. doi:10.1038/s41594-023-01201-6
apa: Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V.,
& Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10
to form the palisade layer in poxvirus cores. Nature Structural & Molecular
Biology. Springer Nature. https://doi.org/10.1038/s41594-023-01201-6
chicago: Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer,
Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers
of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural
& Molecular Biology. Springer Nature, 2024. https://doi.org/10.1038/s41594-023-01201-6.
ieee: J. Datler et al., “Multi-modal cryo-EM reveals trimers of protein A10
to form the palisade layer in poxvirus cores,” Nature Structural & Molecular
Biology. Springer Nature, 2024.
ista: Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK.
2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade
layer in poxvirus cores. Nature Structural & Molecular Biology.
mla: Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to
Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular
Biology, Springer Nature, 2024, doi:10.1038/s41594-023-01201-6.
short: J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau,
F.K. Schur, Nature Structural & Molecular Biology (2024).
date_created: 2024-02-12T09:59:45Z
date_published: 2024-02-05T00:00:00Z
date_updated: 2024-03-05T09:27:47Z
day: '05'
ddc:
- '570'
department:
- _id: FlSc
- _id: ScienComp
- _id: EM-Fac
doi: 10.1038/s41594-023-01201-6
external_id:
pmid:
- '38316877'
has_accepted_license: '1'
keyword:
- Molecular Biology
- Structural Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41594-023-01201-6
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26736D6A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31445
name: Structural conservation and diversity in retroviral capsid
publication: Nature Structural & Molecular Biology
publication_identifier:
eissn:
- 1545-9985
issn:
- 1545-9993
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/
status: public
title: Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer
in poxvirus cores
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_id: '14846'
abstract:
- lang: eng
text: Contraction and flow of the actin cell cortex have emerged as a common principle
by which cells reorganize their cytoplasm and take shape. However, how these cortical
flows interact with adjacent cytoplasmic components, changing their form and localization,
and how this affects cytoplasmic organization and cell shape remains unclear.
Here we show that in ascidian oocytes, the cooperative activities of cortical
actomyosin flows and deformation of the adjacent mitochondria-rich myoplasm drive
oocyte cytoplasmic reorganization and shape changes following fertilization. We
show that vegetal-directed cortical actomyosin flows, established upon oocyte
fertilization, lead to both the accumulation of cortical actin at the vegetal
pole of the zygote and compression and local buckling of the adjacent elastic
solid-like myoplasm layer due to friction forces generated at their interface.
Once cortical flows have ceased, the multiple myoplasm buckles resolve into one
larger buckle, which again drives the formation of the contraction pole—a protuberance
of the zygote’s vegetal pole where maternal mRNAs accumulate. Thus, our findings
reveal a mechanism where cortical actomyosin network flows determine cytoplasmic
reorganization and cell shape by deforming adjacent cytoplasmic components through
friction forces.
acknowledged_ssus:
- _id: EM-Fac
- _id: Bio
- _id: NanoFab
acknowledgement: We would like to thank A. McDougall, E. Hannezo and the Heisenberg
lab for fruitful discussions and reagents. We also thank E. Munro for the iMyo-YFP
and Bra>iMyo-mScarlet constructs. This research was supported by the Scientific
Service Units of the Institute of Science and Technology Austria through resources
provided by the Electron Microscopy Facility, Imaging and Optics Facility and the
Nanofabrication Facility. This work was supported by a Joint Project Grant from
the FWF (I 3601-B27).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Silvia
full_name: Caballero Mancebo, Silvia
id: 2F1E1758-F248-11E8-B48F-1D18A9856A87
last_name: Caballero Mancebo
orcid: 0000-0002-5223-3346
- first_name: Rushikesh
full_name: Shinde, Rushikesh
last_name: Shinde
- first_name: Madison
full_name: Bolger-Munro, Madison
id: 516F03FA-93A3-11EA-A7C5-D6BE3DDC885E
last_name: Bolger-Munro
orcid: 0000-0002-8176-4824
- first_name: Matilda
full_name: Peruzzo, Matilda
id: 3F920B30-F248-11E8-B48F-1D18A9856A87
last_name: Peruzzo
orcid: 0000-0002-3415-4628
- first_name: Gregory
full_name: Szep, Gregory
id: 4BFB7762-F248-11E8-B48F-1D18A9856A87
last_name: Szep
- first_name: Irene
full_name: Steccari, Irene
id: 2705C766-9FE2-11EA-B224-C6773DDC885E
last_name: Steccari
- first_name: David
full_name: Labrousse Arias, David
id: CD573DF4-9ED3-11E9-9D77-3223E6697425
last_name: Labrousse Arias
- first_name: Vanessa
full_name: Zheden, Vanessa
id: 39C5A68A-F248-11E8-B48F-1D18A9856A87
last_name: Zheden
orcid: 0000-0002-9438-4783
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Andrew
full_name: Callan-Jones, Andrew
last_name: Callan-Jones
- first_name: Raphaël
full_name: Voituriez, Raphaël
last_name: Voituriez
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Caballero Mancebo S, Shinde R, Bolger-Munro M, et al. Friction forces determine
cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization.
Nature Physics. 2024. doi:10.1038/s41567-023-02302-1
apa: Caballero Mancebo, S., Shinde, R., Bolger-Munro, M., Peruzzo, M., Szep, G.,
Steccari, I., … Heisenberg, C.-P. J. (2024). Friction forces determine cytoplasmic
reorganization and shape changes of ascidian oocytes upon fertilization. Nature
Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02302-1
chicago: Caballero Mancebo, Silvia, Rushikesh Shinde, Madison Bolger-Munro, Matilda
Peruzzo, Gregory Szep, Irene Steccari, David Labrousse Arias, et al. “Friction
Forces Determine Cytoplasmic Reorganization and Shape Changes of Ascidian Oocytes
upon Fertilization.” Nature Physics. Springer Nature, 2024. https://doi.org/10.1038/s41567-023-02302-1.
ieee: S. Caballero Mancebo et al., “Friction forces determine cytoplasmic
reorganization and shape changes of ascidian oocytes upon fertilization,” Nature
Physics. Springer Nature, 2024.
ista: Caballero Mancebo S, Shinde R, Bolger-Munro M, Peruzzo M, Szep G, Steccari
I, Labrousse Arias D, Zheden V, Merrin J, Callan-Jones A, Voituriez R, Heisenberg
C-PJ. 2024. Friction forces determine cytoplasmic reorganization and shape changes
of ascidian oocytes upon fertilization. Nature Physics.
mla: Caballero Mancebo, Silvia, et al. “Friction Forces Determine Cytoplasmic Reorganization
and Shape Changes of Ascidian Oocytes upon Fertilization.” Nature Physics,
Springer Nature, 2024, doi:10.1038/s41567-023-02302-1.
short: S. Caballero Mancebo, R. Shinde, M. Bolger-Munro, M. Peruzzo, G. Szep, I.
Steccari, D. Labrousse Arias, V. Zheden, J. Merrin, A. Callan-Jones, R. Voituriez,
C.-P.J. Heisenberg, Nature Physics (2024).
date_created: 2024-01-21T23:00:57Z
date_published: 2024-01-09T00:00:00Z
date_updated: 2024-03-05T09:33:38Z
day: '09'
department:
- _id: CaHe
- _id: JoFi
- _id: MiSi
- _id: EM-Fac
- _id: NanoFab
doi: 10.1038/s41567-023-02302-1
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41567-023-02302-1
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 2646861A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03601
name: Control of embryonic cleavage pattern
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/stranger-than-friction-a-force-initiating-life/
scopus_import: '1'
status: public
title: Friction forces determine cytoplasmic reorganization and shape changes of ascidian
oocytes upon fertilization
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_id: '14796'
abstract:
- lang: eng
text: Key innovations are fundamental to biological diversification, but their genetic
basis is poorly understood. A recent transition from egg-laying to live-bearing
in marine snails (Littorina spp.) provides the opportunity to study the genetic
architecture of an innovation that has evolved repeatedly across animals. Individuals
do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical
analysis revealed numerous small genomic regions where all live-bearers carry
the same core haplotype. Candidate regions show evidence for live-bearer–specific
positive selection and are enriched for genes that are differentially expressed
between egg-laying and live-bearing reproductive systems. Ages of selective sweeps
suggest that live-bearer–specific alleles accumulated over more than 200,000 generations.
Our results suggest that new functions evolve through the recruitment of many
alleles rather than in a single evolutionary step.
acknowledgement: "We thank J. Galindo, M. Montaño-Rendón, N. Mikhailova, A. Blakeslee,
E. Arnason, and P. Kemppainen for providing samples; R. Turney, G. Sotelo, J. Larsson,
T. Broquet, and S. Loisel for help collecting samples; Science Animated for providing
the snail cartoons shown in Fig. 1; M. Dunning for help in developing bioinformatic
pipelines; R. Faria, H. Morales, and V. Sousa for advice; and M. Hahn, J. Slate,
M. Ravinet, J. Raeymaekers, A. Comeault, and N. Barton for feedback on a draft manuscript.\r\nThis
work was supported by the Natural Environment Research Council (grant NE/P001610/1
to R.K.B.), the European Research Council (grant ERC-2015-AdG693030-BARRIERS to
R.K.B.), the Norwegian Research Council (RCN Project 315287 to A.M.W.), and the
Swedish Research Council (grant 2020-05385 to E.L.)."
article_processing_charge: No
article_type: original
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Zuzanna B.
full_name: Zagrodzka, Zuzanna B.
last_name: Zagrodzka
- first_name: Martin D.
full_name: Garlovsky, Martin D.
last_name: Garlovsky
- first_name: Arka
full_name: Pal, Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
orcid: 0000-0002-4530-8469
- first_name: Daria
full_name: Shipilina, Daria
id: 428A94B0-F248-11E8-B48F-1D18A9856A87
last_name: Shipilina
orcid: 0000-0002-1145-9226
- first_name: Diego Fernando
full_name: Garcia Castillo, Diego Fernando
id: ae681a14-dc74-11ea-a0a7-c6ef18161701
last_name: Garcia Castillo
- first_name: Hila
full_name: Lifchitz, Hila
id: d6ab5470-2fb3-11ed-8633-986a9b84edac
last_name: Lifchitz
- first_name: Alan
full_name: Le Moan, Alan
last_name: Le Moan
- first_name: Erica
full_name: Leder, Erica
last_name: Leder
- first_name: James
full_name: Reeve, James
last_name: Reeve
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: Stankowski S, Zagrodzka ZB, Garlovsky MD, et al. The genetic basis of a recent
transition to live-bearing in marine snails. Science. 2024;383(6678):114-119.
doi:10.1126/science.adi2982
apa: Stankowski, S., Zagrodzka, Z. B., Garlovsky, M. D., Pal, A., Shipilina, D.,
Garcia Castillo, D. F., … Butlin, R. K. (2024). The genetic basis of a recent
transition to live-bearing in marine snails. Science. American Association
for the Advancement of Science. https://doi.org/10.1126/science.adi2982
chicago: Stankowski, Sean, Zuzanna B. Zagrodzka, Martin D. Garlovsky, Arka Pal,
Daria Shipilina, Diego Fernando Garcia Castillo, Hila Lifchitz, et al. “The Genetic
Basis of a Recent Transition to Live-Bearing in Marine Snails.” Science.
American Association for the Advancement of Science, 2024. https://doi.org/10.1126/science.adi2982.
ieee: S. Stankowski et al., “The genetic basis of a recent transition to
live-bearing in marine snails,” Science, vol. 383, no. 6678. American Association
for the Advancement of Science, pp. 114–119, 2024.
ista: Stankowski S, Zagrodzka ZB, Garlovsky MD, Pal A, Shipilina D, Garcia Castillo
DF, Lifchitz H, Le Moan A, Leder E, Reeve J, Johannesson K, Westram AM, Butlin
RK. 2024. The genetic basis of a recent transition to live-bearing in marine snails.
Science. 383(6678), 114–119.
mla: Stankowski, Sean, et al. “The Genetic Basis of a Recent Transition to Live-Bearing
in Marine Snails.” Science, vol. 383, no. 6678, American Association for
the Advancement of Science, 2024, pp. 114–19, doi:10.1126/science.adi2982.
short: S. Stankowski, Z.B. Zagrodzka, M.D. Garlovsky, A. Pal, D. Shipilina, D.F.
Garcia Castillo, H. Lifchitz, A. Le Moan, E. Leder, J. Reeve, K. Johannesson,
A.M. Westram, R.K. Butlin, Science 383 (2024) 114–119.
date_created: 2024-01-14T23:00:56Z
date_published: 2024-01-05T00:00:00Z
date_updated: 2024-03-05T09:35:25Z
day: '05'
department:
- _id: NiBa
- _id: GradSch
doi: 10.1126/science.adi2982
external_id:
pmid:
- '38175895'
intvolume: ' 383'
issue: '6678'
language:
- iso: eng
month: '01'
oa_version: None
page: 114-119
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/the-snail-or-the-egg/
record:
- id: '14812'
relation: research_data
status: public
scopus_import: '1'
status: public
title: The genetic basis of a recent transition to live-bearing in marine snails
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 383
year: '2024'
...
---
_id: '15020'
abstract:
- lang: eng
text: "This thesis consists of four distinct pieces of work within theoretical biology,
with two themes in common: the concept of optimization in biological systems,
and the use of information-theoretic tools to quantify biological stochasticity
and statistical uncertainty.\r\nChapter 2 develops a statistical framework for
studying biological systems which we believe to be optimized for a particular
utility function, such as retinal neurons conveying information about visual stimuli.
We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the
expected utility. We explore how such priors aid inference of system parameters
with limited data and enable optimality hypothesis testing: is the utility higher
than by chance?\r\nChapter 3 examines the ultimate biological optimization process:
evolution by natural selection. As some individuals survive and reproduce more
successfully than others, populations evolve towards fitter genotypes and phenotypes.
We formalize this as accumulation of genetic information, and use population genetics
theory to study how much such information can be accumulated per generation and
maintained in the face of random mutation and genetic drift. We identify the population
size and fitness variance as the key quantities that control information accumulation
and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter
3, but from a different perspective: we ask how much genetic information organisms
actually need, in particular in the context of gene regulation. For example, how
much information is needed to bind transcription factors at correct locations
within the genome? Population genetics provides us with a refined answer: with
an increasing population size, populations achieve higher fitness by maintaining
more genetic information. Moreover, regulatory parameters experience selection
pressure to optimize the fitness-information trade-off, i.e. minimize the information
needed for a given fitness. This provides an evolutionary derivation of the optimization
priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information
between a signal and a communication channel output (such as neural activity).
Mutual information is an important utility measure for biological systems, but
its practical use can be difficult due to the large dimensionality of many biological
channels. Sometimes, a lower bound on mutual information is computed by replacing
the high-dimensional channel outputs with decodes (signal estimates). Our result
provides a corresponding upper bound, provided that the decodes are the maximum
posterior estimates of the signal."
acknowledged_ssus:
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michal
full_name: Hledik, Michal
id: 4171253A-F248-11E8-B48F-1D18A9856A87
last_name: Hledik
citation:
ama: Hledik M. Genetic information and biological optimization. 2024. doi:10.15479/at:ista:15020
apa: Hledik, M. (2024). Genetic information and biological optimization.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15020
chicago: Hledik, Michal. “Genetic Information and Biological Optimization.” Institute
of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15020.
ieee: M. Hledik, “Genetic information and biological optimization,” Institute of
Science and Technology Austria, 2024.
ista: Hledik M. 2024. Genetic information and biological optimization. Institute
of Science and Technology Austria.
mla: Hledik, Michal. Genetic Information and Biological Optimization. Institute
of Science and Technology Austria, 2024, doi:10.15479/at:ista:15020.
short: M. Hledik, Genetic Information and Biological Optimization, Institute of
Science and Technology Austria, 2024.
date_created: 2024-02-23T14:02:04Z
date_published: 2024-02-23T00:00:00Z
date_updated: 2024-03-06T14:22:52Z
day: '23'
ddc:
- '576'
- '519'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
- _id: GaTk
doi: 10.15479/at:ista:15020
ec_funded: 1
file:
- access_level: open_access
checksum: b2d3da47c98d481577a4baf68944fe41
content_type: application/pdf
creator: mhledik
date_created: 2024-02-23T13:50:53Z
date_updated: 2024-02-23T13:50:53Z
file_id: '15021'
file_name: hledik thesis pdfa 2b.pdf
file_size: 7102089
relation: main_file
success: 1
- access_level: closed
checksum: eda9b9430da2610fee7ce1c1419a479a
content_type: application/zip
creator: mhledik
date_created: 2024-02-23T13:50:54Z
date_updated: 2024-02-23T14:20:16Z
file_id: '15022'
file_name: hledik thesis source.zip
file_size: 14014790
relation: source_file
file_date_updated: 2024-02-23T14:20:16Z
has_accepted_license: '1'
keyword:
- Theoretical biology
- Optimality
- Evolution
- Information
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '158'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 2665AAFE-B435-11E9-9278-68D0E5697425
grant_number: RGP0034/2018
name: Can evolution minimize spurious signaling crosstalk to reach optimal performance?
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7553'
relation: part_of_dissertation
status: public
- id: '12081'
relation: part_of_dissertation
status: public
- id: '7606'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
title: Genetic information and biological optimization
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2024'
...
---
_id: '14842'
abstract:
- lang: eng
text: Eva Benkova received a PhD in Biophysics at the Institute of Biophysics of
the Czech Academy of Sciences in 1998. After working as a postdoc at the Max Planck
Institute in Cologne and the Center for Plant Molecular Biology (ZMBP) in Tübingen,
she became a group leader at the Plant Systems Biology Department of the Vlaams
Instituut voor Biotechnologie (VIB) in Gent. In 2012, she transitioned to an Assistant
Professor position at the Institute of Science and Technology Austria (ISTA) where
she was later promoted to Professor. Since 2021, she has served as the Dean of
the ISTA Graduate School. As a plant developmental biologist, she focuses on unraveling
the molecular mechanisms and principles that underlie hormonal interactions in
plants. In her current work, she explores the intricate connections between hormones
and regulatory pathways that mediate the perception of environmental stimuli,
including abiotic stress and nitrate availability.
article_processing_charge: No
author:
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Benková E. Eva Benkova. Vol 34. Elsevier; 2024:R3-R5. doi:10.1016/j.cub.2023.11.039
apa: Benková, E. (2024). Eva Benkova. Current Biology (Vol. 34, pp.
R3–R5). Elsevier. https://doi.org/10.1016/j.cub.2023.11.039
chicago: Benková, Eva. Eva Benkova. Current Biology. Vol. 34. Elsevier,
2024. https://doi.org/10.1016/j.cub.2023.11.039.
ieee: E. Benková, Eva Benkova, vol. 34, no. 1. Elsevier, 2024, pp. R3–R5.
ista: Benková E. 2024. Eva Benkova, Elsevier,p.
mla: Benková, Eva. “Eva Benkova.” Current Biology, vol. 34, no. 1, Elsevier,
2024, pp. R3–5, doi:10.1016/j.cub.2023.11.039.
short: E. Benková, Eva Benkova, Elsevier, 2024.
date_created: 2024-01-21T23:00:56Z
date_published: 2024-01-08T00:00:00Z
date_updated: 2024-03-12T12:19:12Z
day: '08'
department:
- _id: EvBe
doi: 10.1016/j.cub.2023.11.039
intvolume: ' 34'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2023.11.039
month: '01'
oa: 1
oa_version: Published Version
page: R3-R5
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Eva Benkova
type: other_academic_publication
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2024'
...
---
_id: '15084'
abstract:
- lang: eng
text: "GABAB receptor (GBR) activation inhibits neurotransmitter release in axon
terminals in the brain, except in medial habenula (MHb) terminals, which show
robust potentiation. However, mechanisms underlying this enigmatic potentiation
remain elusive. Here, we report that GBR activation on MHb terminals induces an
activity-dependent transition from a facilitating, tonic to a depressing, phasic
neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase
in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked
synaptic vesicles (SVs) at the presynaptic active zone (AZ). Strikingly, the depressing
phasic release exhibits looser coupling distance than the tonic release. Furthermore,
the tonic and phasic release are selectively affected by deletion of synaptoporin
(SPO) and Ca\r\n 2+\r\n -dependent
activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation,
the short-term plasticity associated with tonic release, and CAPS2 retains the
increased RRP for initial responses in phasic response trains. The cytosolic protein
CAPS2 showed a SV-associated distribution similar to the vesicular transmembrane
protein SPO, and they were colocalized in the same terminals. We developed the
“Flash and Freeze-fracture” method, and revealed the release of SPO-associated
vesicles in both tonic and phasic modes and activity-dependent recruitment of
CAPS2 to the AZ during phasic release, which lasted several minutes. Overall,
these results indicate that GBR activation translocates CAPS2 to the AZ along
with the fusion of CAPS2-associated SVs, contributing to persistency of the RRP
increase. Thus, we identified structural and molecular mechanisms underlying tonic
and phasic neurotransmitter release and their transition by GBR activation in
MHb terminals."
acknowledged_ssus:
- _id: M-Shop
- _id: PreCl
- _id: EM-Fac
acknowledgement: We thank Erwin Neher and Ipe Ninan for critical comments on the manuscript.
This project has received funding from the European Research Council (ERC) and European
Commission, under the European Union’s Horizon 2020 research and innovation program
(ERC grant agreement no. 694539 to R.S. and the Marie Skłodowska-Curie grant agreement
no. 665385 to C.Ö.). This study was supported by the Cooperative Study Program of
Center for Animal Resources and Collaborative Study of NINS. We thank Kohgaku Eguchi
for statistical analysis, Yu Kasugai for additional EM imaging, Robert Beattie for
the design of the slice recovery chamber for Flash and Freeze experiments, Todor
Asenov from the ISTA machine shop for custom part preparations for high-pressure
freezing, the ISTA preclinical facility for animal caretaking, and the ISTA EM facilities
for technical support.
article_number: e2301449121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Peter
full_name: Koppensteiner, Peter
id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87
last_name: Koppensteiner
orcid: 0000-0002-3509-1948
- first_name: Pradeep
full_name: Bhandari, Pradeep
id: 45EDD1BC-F248-11E8-B48F-1D18A9856A87
last_name: Bhandari
orcid: 0000-0003-0863-4481
- first_name: Hüseyin C
full_name: Önal, Hüseyin C
id: 4659D740-F248-11E8-B48F-1D18A9856A87
last_name: Önal
orcid: 0000-0002-2771-2011
- first_name: Carolina
full_name: Borges Merjane, Carolina
id: 4305C450-F248-11E8-B48F-1D18A9856A87
last_name: Borges Merjane
orcid: 0000-0003-0005-401X
- first_name: Elodie
full_name: Le Monnier, Elodie
id: 3B59276A-F248-11E8-B48F-1D18A9856A87
last_name: Le Monnier
- first_name: Utsa
full_name: Roy, Utsa
id: 4d26cf11-5355-11ee-ae5a-eb05e255b9b2
last_name: Roy
- first_name: Yukihiro
full_name: Nakamura, Yukihiro
last_name: Nakamura
- first_name: Tetsushi
full_name: Sadakata, Tetsushi
last_name: Sadakata
- first_name: Makoto
full_name: Sanbo, Makoto
last_name: Sanbo
- first_name: Masumi
full_name: Hirabayashi, Masumi
last_name: Hirabayashi
- first_name: JeongSeop
full_name: Rhee, JeongSeop
last_name: Rhee
- first_name: Nils
full_name: Brose, Nils
last_name: Brose
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Koppensteiner P, Bhandari P, Önal C, et al. GABAB receptors induce phasic release
from medial habenula terminals through activity-dependent recruitment of release-ready
vesicles. Proceedings of the National Academy of Sciences. 2024;121(8).
doi:10.1073/pnas.2301449121
apa: Koppensteiner, P., Bhandari, P., Önal, C., Borges Merjane, C., Le Monnier,
E., Roy, U., … Shigemoto, R. (2024). GABAB receptors induce phasic release from
medial habenula terminals through activity-dependent recruitment of release-ready
vesicles. Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences. https://doi.org/10.1073/pnas.2301449121
chicago: Koppensteiner, Peter, Pradeep Bhandari, Cihan Önal, Carolina Borges Merjane,
Elodie Le Monnier, Utsa Roy, Yukihiro Nakamura, et al. “GABAB Receptors Induce
Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment
of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2301449121.
ieee: P. Koppensteiner et al., “GABAB receptors induce phasic release from
medial habenula terminals through activity-dependent recruitment of release-ready
vesicles,” Proceedings of the National Academy of Sciences, vol. 121, no.
8. Proceedings of the National Academy of Sciences, 2024.
ista: Koppensteiner P, Bhandari P, Önal C, Borges Merjane C, Le Monnier E, Roy U,
Nakamura Y, Sadakata T, Sanbo M, Hirabayashi M, Rhee J, Brose N, Jonas PM, Shigemoto
R. 2024. GABAB receptors induce phasic release from medial habenula terminals
through activity-dependent recruitment of release-ready vesicles. Proceedings
of the National Academy of Sciences. 121(8), e2301449121.
mla: Koppensteiner, Peter, et al. “GABAB Receptors Induce Phasic Release from Medial
Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.”
Proceedings of the National Academy of Sciences, vol. 121, no. 8, e2301449121,
Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2301449121.
short: P. Koppensteiner, P. Bhandari, C. Önal, C. Borges Merjane, E. Le Monnier,
U. Roy, Y. Nakamura, T. Sadakata, M. Sanbo, M. Hirabayashi, J. Rhee, N. Brose,
P.M. Jonas, R. Shigemoto, Proceedings of the National Academy of Sciences 121
(2024).
date_created: 2024-03-05T09:23:55Z
date_published: 2024-02-20T00:00:00Z
date_updated: 2024-03-12T13:44:18Z
day: '20'
ddc:
- '570'
department:
- _id: RySh
- _id: PeJo
doi: 10.1073/pnas.2301449121
ec_funded: 1
external_id:
pmid:
- '38346189'
file:
- access_level: open_access
checksum: b25b2a057c266ff317a48b0d54d6fc8a
content_type: application/pdf
creator: dernst
date_created: 2024-03-12T13:42:42Z
date_updated: 2024-03-12T13:42:42Z
file_id: '15110'
file_name: 2024_PNAS_Koppensteiner.pdf
file_size: 13648221
relation: main_file
success: 1
file_date_updated: 2024-03-12T13:42:42Z
has_accepted_license: '1'
intvolume: ' 121'
issue: '8'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/neuronal-insights-flash-and-freeze-fracture/
record:
- id: '13173'
relation: research_data
status: public
status: public
title: GABAB receptors induce phasic release from medial habenula terminals through
activity-dependent recruitment of release-ready vesicles
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
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: 121
year: '2024'
...
---
_id: '15083'
abstract:
- lang: eng
text: 'Direct reciprocity is a powerful mechanism for cooperation in social
dilemmas. The very logic of reciprocity, however, seems to require that individuals
are symmetric, and that everyone has the same means to influence each others’
payoffs. Yet in many applications, individuals are asymmetric. Herein, we study
the effect of asymmetry in linear public good games. Individuals may differ in
their endowments (their ability to contribute to a public good) and in their productivities
(how effective their contributions are). Given the individuals’ productivities,
we ask which allocation of endowments is optimal for cooperation. To this end,
we consider two notions of optimality. The first notion focuses on the resilience
of cooperation. The respective endowment distribution ensures that full cooperation
is feasible even under the most adverse conditions. The second notion focuses
on efficiency. The corresponding endowment distribution maximizes group welfare.
Using analytical methods, we fully characterize these two endowment distributions.
This analysis reveals that both optimality notions favor some endowment inequality:
More productive players ought to get higher endowments. Yet the two notions disagree
on how unequal endowments are supposed to be. A focus on resilience results in
less inequality. With additional simulations, we show that the optimal endowment
allocation needs to account for both the resilience and the efficiency of cooperation.'
acknowledgement: 'This work was supported by the European Research Council CoG 863818
(ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529:
E-DIRECT (to C.H.), the European Union’s Horizon 2020 research and innovation program
under the Marie Skłodowska-Curie Grant Agreement #754411 and the French Agence Nationale
de la Recherche (under the Investissement d’Avenir Programme, ANR-17-EURE-0010)
(to M.K.).'
article_number: e2315558121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Valentin
full_name: Hübner, Valentin
id: 2c8aa207-dc7d-11ea-9b2f-f22972ecd910
last_name: Hübner
- first_name: Manuel
full_name: Staab, Manuel
last_name: Staab
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Maria
full_name: Kleshnina, Maria
last_name: Kleshnina
citation:
ama: Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. Efficiency and resilience
of cooperation in asymmetric social dilemmas. Proceedings of the National Academy
of Sciences. 2024;121(10). doi:10.1073/pnas.2315558121
apa: Hübner, V., Staab, M., Hilbe, C., Chatterjee, K., & Kleshnina, M. (2024).
Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings
of the National Academy of Sciences. Proceedings of the National Academy of
Sciences. https://doi.org/10.1073/pnas.2315558121
chicago: Hübner, Valentin, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee,
and Maria Kleshnina. “Efficiency and Resilience of Cooperation in Asymmetric Social
Dilemmas.” Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2315558121.
ieee: V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, and M. Kleshnina, “Efficiency
and resilience of cooperation in asymmetric social dilemmas,” Proceedings of
the National Academy of Sciences, vol. 121, no. 10. Proceedings of the National
Academy of Sciences, 2024.
ista: Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. 2024. Efficiency and
resilience of cooperation in asymmetric social dilemmas. Proceedings of the National
Academy of Sciences. 121(10), e2315558121.
mla: Hübner, Valentin, et al. “Efficiency and Resilience of Cooperation in Asymmetric
Social Dilemmas.” Proceedings of the National Academy of Sciences, vol.
121, no. 10, e2315558121, Proceedings of the National Academy of Sciences, 2024,
doi:10.1073/pnas.2315558121.
short: V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, M. Kleshnina, Proceedings of
the National Academy of Sciences 121 (2024).
date_created: 2024-03-05T09:18:49Z
date_published: 2024-03-05T00:00:00Z
date_updated: 2024-03-12T13:29:25Z
day: '05'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1073/pnas.2315558121
ec_funded: 1
external_id:
pmid:
- '38408249'
file:
- access_level: open_access
checksum: 068520e3efd4d008bb9177e8aedb7d22
content_type: application/pdf
creator: dernst
date_created: 2024-03-12T13:12:22Z
date_updated: 2024-03-12T13:12:22Z
file_id: '15109'
file_name: 2024_PNAS_Huebner.pdf
file_size: 2203220
relation: main_file
success: 1
file_date_updated: 2024-03-12T13:12:22Z
has_accepted_license: '1'
intvolume: ' 121'
issue: '10'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/what-math-tells-us-about-social-dilemmas/
record:
- id: '15108'
relation: research_data
status: public
status: public
title: Efficiency and resilience of cooperation in asymmetric social dilemmas
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: 121
year: '2024'
...
---
_id: '15108'
abstract:
- lang: eng
text: "in the research article \"Efficiency and resilience of cooperation in asymmetric
social dilemmas\" (by Valentin Hübner, Manuel Staab, Christian Hilbe, Krishnendu
Chatterjee, and Maria Kleshnina).\r\n\r\nWe used different implementations for
the case of two and three players, both described below."
article_processing_charge: No
author:
- first_name: Valentin
full_name: Hübner, Valentin
id: 2c8aa207-dc7d-11ea-9b2f-f22972ecd910
last_name: Hübner
- first_name: Maria
full_name: Kleshnina, Maria
last_name: Kleshnina
citation:
ama: Hübner V, Kleshnina M. Computer code for “Efficiency and resilience of cooperation
in asymmetric social dilemmas.” 2024. doi:10.5281/ZENODO.10639167
apa: Hübner, V., & Kleshnina, M. (2024). Computer code for “Efficiency and resilience
of cooperation in asymmetric social dilemmas.” Zenodo. https://doi.org/10.5281/ZENODO.10639167
chicago: Hübner, Valentin, and Maria Kleshnina. “Computer Code for ‘Efficiency and
Resilience of Cooperation in Asymmetric Social Dilemmas.’” Zenodo, 2024. https://doi.org/10.5281/ZENODO.10639167.
ieee: V. Hübner and M. Kleshnina, “Computer code for ‘Efficiency and resilience
of cooperation in asymmetric social dilemmas.’” Zenodo, 2024.
ista: Hübner V, Kleshnina M. 2024. Computer code for ‘Efficiency and resilience
of cooperation in asymmetric social dilemmas’, Zenodo, 10.5281/ZENODO.10639167.
mla: Hübner, Valentin, and Maria Kleshnina. Computer Code for “Efficiency and
Resilience of Cooperation in Asymmetric Social Dilemmas.” Zenodo, 2024, doi:10.5281/ZENODO.10639167.
short: V. Hübner, M. Kleshnina, (2024).
date_created: 2024-03-12T13:02:58Z
date_published: 2024-02-09T00:00:00Z
date_updated: 2024-03-12T13:29:26Z
day: '09'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.5281/ZENODO.10639167
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://10.5281/zenodo.10639167
month: '02'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '15083'
relation: used_in_publication
status: public
status: public
title: Computer code for "Efficiency and resilience of cooperation in asymmetric social
dilemmas"
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: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_id: '15097'
abstract:
- lang: eng
text: Global storm-resolving models (GSRMs) use strongly refined horizontal grids
compared with the climate models typically used in the Coupled Model Intercomparison
Project (CMIP) but employ comparable vertical grid spacings. Here, we study how
changes in the vertical grid spacing and adjustments to the integration time step
affect the basic climate quantities simulated by the ICON-Sapphire atmospheric
GSRM. Simulations are performed over a 45 d period for five different vertical
grids with between 55 and 540 vertical layers and maximum tropospheric vertical
grid spacings of between 800 and 50 m, respectively. The effects of changes in
the vertical grid spacing are compared with the effects of reducing the horizontal
grid spacing from 5 to 2.5 km. For most of the quantities considered, halving
the vertical grid spacing has a smaller effect than halving the horizontal grid
spacing, but it is not negligible. Each halving of the vertical grid spacing,
along with the necessary reductions in time step length, increases cloud liquid
water by about 7 %, compared with an approximate 16 % decrease for halving the
horizontal grid spacing. The effect is due to both the vertical grid refinement
and the time step reduction. There is no tendency toward convergence in the range
of grid spacings tested here. The cloud ice amount also increases with a refinement
in the vertical grid, but it is hardly affected by the time step length and does
show a tendency to converge. While the effect on shortwave radiation is globally
dominated by the altered reflection due to the change in the cloud liquid water
content, the effect on longwave radiation is more difficult to interpret because
changes in the cloud ice concentration and cloud fraction are anticorrelated in
some regions. The simulations show that using a maximum tropospheric vertical
grid spacing larger than 400 m would increase the truncation error strongly. Computing
time investments in a further vertical grid refinement can affect the truncation
errors of GSRMs similarly to comparable investments in horizontal refinement,
because halving the vertical grid spacing is generally cheaper than halving the
horizontal grid spacing. However, convergence of boundary layer cloud properties
cannot be expected, even for the smallest maximum tropospheric grid spacing of
50 m used in this study.
acknowledgement: "The authors wish to thank Ann Kristin Naumann and three anonymous
reviewers for very helpful comments on an earlier version of this paper. We are
grateful to René Redler and Karl-Hermann Wieners for useful recommendations regarding
running the simulations. We thank Luis Kornblueh for providing an external vertical
grid generator and resolving the memory requirements for the very fine vertical
grids. We acknowledge Hauke Schulz for providing the radiosonde data. The simulations
were run at the German Climate Computing Center (DKRZ), and we thank the DKRZ staff
for their support.\r\nHauke Schmidt and Diego Jimenez-de la Cuesta received financial
support from the SOCTOC project within the framework of the ROMIC program, funded
by the German Ministry of Education and Research (BMBF) (grant no. 01LG1903A).\r\nThe
article processing charges for this open-access publication were covered by the
Max Planck Society."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Hauke
full_name: Schmidt, Hauke
last_name: Schmidt
- first_name: Sebastian
full_name: Rast, Sebastian
last_name: Rast
- first_name: Jiawei
full_name: Bao, Jiawei
id: bb9a7399-fefd-11ed-be3c-ae648fd1d160
last_name: Bao
- first_name: Amrit
full_name: Cassim, Amrit
last_name: Cassim
- first_name: Shih Wei
full_name: Fang, Shih Wei
last_name: Fang
- first_name: Diego
full_name: Jimenez-De La Cuesta, Diego
last_name: Jimenez-De La Cuesta
- first_name: Paul
full_name: Keil, Paul
last_name: Keil
- first_name: Lukas
full_name: Kluft, Lukas
last_name: Kluft
- first_name: Clarissa
full_name: Kroll, Clarissa
last_name: Kroll
- first_name: Theresa
full_name: Lang, Theresa
last_name: Lang
- first_name: Ulrike
full_name: Niemeier, Ulrike
last_name: Niemeier
- first_name: Andrea
full_name: Schneidereit, Andrea
last_name: Schneidereit
- first_name: Andrew I.L.
full_name: Williams, Andrew I.L.
last_name: Williams
- first_name: Bjorn
full_name: Stevens, Bjorn
last_name: Stevens
citation:
ama: Schmidt H, Rast S, Bao J, et al. Effects of vertical grid spacing on the climate
simulated in the ICON-Sapphire global storm-resolving model. Geoscientific
Model Development. 2024;17(4):1563-1584. doi:10.5194/gmd-17-1563-2024
apa: Schmidt, H., Rast, S., Bao, J., Cassim, A., Fang, S. W., Jimenez-De La Cuesta,
D., … Stevens, B. (2024). Effects of vertical grid spacing on the climate simulated
in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development.
European Geosciences Union. https://doi.org/10.5194/gmd-17-1563-2024
chicago: Schmidt, Hauke, Sebastian Rast, Jiawei Bao, Amrit Cassim, Shih Wei Fang,
Diego Jimenez-De La Cuesta, Paul Keil, et al. “Effects of Vertical Grid Spacing
on the Climate Simulated in the ICON-Sapphire Global Storm-Resolving Model.” Geoscientific
Model Development. European Geosciences Union, 2024. https://doi.org/10.5194/gmd-17-1563-2024.
ieee: H. Schmidt et al., “Effects of vertical grid spacing on the climate
simulated in the ICON-Sapphire global storm-resolving model,” Geoscientific
Model Development, vol. 17, no. 4. European Geosciences Union, pp. 1563–1584,
2024.
ista: Schmidt H, Rast S, Bao J, Cassim A, Fang SW, Jimenez-De La Cuesta D, Keil
P, Kluft L, Kroll C, Lang T, Niemeier U, Schneidereit A, Williams AIL, Stevens
B. 2024. Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire
global storm-resolving model. Geoscientific Model Development. 17(4), 1563–1584.
mla: Schmidt, Hauke, et al. “Effects of Vertical Grid Spacing on the Climate Simulated
in the ICON-Sapphire Global Storm-Resolving Model.” Geoscientific Model Development,
vol. 17, no. 4, European Geosciences Union, 2024, pp. 1563–84, doi:10.5194/gmd-17-1563-2024.
short: H. Schmidt, S. Rast, J. Bao, A. Cassim, S.W. Fang, D. Jimenez-De La Cuesta,
P. Keil, L. Kluft, C. Kroll, T. Lang, U. Niemeier, A. Schneidereit, A.I.L. Williams,
B. Stevens, Geoscientific Model Development 17 (2024) 1563–1584.
date_created: 2024-03-10T23:00:53Z
date_published: 2024-02-22T00:00:00Z
date_updated: 2024-03-13T09:01:20Z
day: '22'
ddc:
- '550'
department:
- _id: CaMu
doi: 10.5194/gmd-17-1563-2024
file:
- access_level: open_access
checksum: 270d2340402729b0532f7072ea914cae
content_type: application/pdf
creator: dernst
date_created: 2024-03-13T08:59:21Z
date_updated: 2024-03-13T08:59:21Z
file_id: '15111'
file_name: 2024_GeoscientificModelDev_Schmidt.pdf
file_size: 13364601
relation: main_file
success: 1
file_date_updated: 2024-03-13T08:59:21Z
has_accepted_license: '1'
intvolume: ' 17'
issue: '4'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 1563-1584
publication: Geoscientific Model Development
publication_identifier:
eissn:
- 1991-9603
issn:
- 1991-959X
publication_status: published
publisher: European Geosciences Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire
global storm-resolving model
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2024'
...
---
_id: '12311'
abstract:
- lang: eng
text: In this note, we prove a formula for the cancellation exponent kv,n between
division polynomials ψn and ϕn associated with a sequence {nP}n∈N of points
on an elliptic curve E defined over a discrete valuation field K. The formula
greatly generalizes the previously known special cases and treats also the case
of non-standard Kodaira types for non-perfect residue fields.
acknowledgement: Silverman, and Paul Voutier for the comments on the earlier version
of this paper. The first author acknowledges the support by Dioscuri programme initiated
by the Max Planck Society, jointly managed with the National Science Centre (Poland),
and mutually funded by the Polish Ministry of Science and Higher Education and the
German Federal Ministry of Education and Research. The second author has been supported
by MIUR (Italy) through PRIN 2017 ‘Geometric, algebraic and analytic methods in
arithmetic’ and has received funding from the European Union's Horizon 2020 research
and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.
article_number: '2203.02015'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Bartosz
full_name: Naskręcki, Bartosz
last_name: Naskręcki
- first_name: Matteo
full_name: Verzobio, Matteo
id: 7aa8f170-131e-11ed-88e1-a9efd01027cb
last_name: Verzobio
orcid: 0000-0002-0854-0306
citation:
ama: 'Naskręcki B, Verzobio M. Common valuations of division polynomials. Proceedings
of the Royal Society of Edinburgh Section A: Mathematics. 2024. doi:10.1017/prm.2024.7'
apa: 'Naskręcki, B., & Verzobio, M. (2024). Common valuations of division polynomials.
Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge
University Press. https://doi.org/10.1017/prm.2024.7'
chicago: 'Naskręcki, Bartosz, and Matteo Verzobio. “Common Valuations of Division
Polynomials.” Proceedings of the Royal Society of Edinburgh Section A: Mathematics.
Cambridge University Press, 2024. https://doi.org/10.1017/prm.2024.7.'
ieee: 'B. Naskręcki and M. Verzobio, “Common valuations of division polynomials,”
Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge
University Press, 2024.'
ista: 'Naskręcki B, Verzobio M. 2024. Common valuations of division polynomials.
Proceedings of the Royal Society of Edinburgh Section A: Mathematics., 2203.02015.'
mla: 'Naskręcki, Bartosz, and Matteo Verzobio. “Common Valuations of Division Polynomials.”
Proceedings of the Royal Society of Edinburgh Section A: Mathematics, 2203.02015,
Cambridge University Press, 2024, doi:10.1017/prm.2024.7.'
short: 'B. Naskręcki, M. Verzobio, Proceedings of the Royal Society of Edinburgh
Section A: Mathematics (2024).'
date_created: 2023-01-16T11:45:22Z
date_published: 2024-02-26T00:00:00Z
date_updated: 2024-03-13T11:55:21Z
day: '26'
ddc:
- '510'
department:
- _id: TiBr
doi: 10.1017/prm.2024.7
ec_funded: 1
external_id:
arxiv:
- '2203.02015'
has_accepted_license: '1'
keyword:
- Elliptic curves
- Néron models
- division polynomials
- height functions
- discrete valuation rings
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1017/prm.2024.7
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: 'Proceedings of the Royal Society of Edinburgh Section A: Mathematics'
publication_identifier:
eissn:
- 1473-7124
issn:
- 0308-2105
publication_status: epub_ahead
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Common valuations of division polynomials
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_id: '15099'
abstract:
- lang: eng
text: Speciation is a key evolutionary process that is not yet fully understood.
Combining population genomic and ecological data from multiple diverging pairs
of marine snails (Littorina) supports the search for speciation mechanisms. Placing
pairs on a one-dimensional speciation continuum, from undifferentiated populations
to species, obscured the complexity of speciation. Adding multiple axes helped
to describe either speciation routes or reproductive isolation in the snails.
Divergent ecological selection repeatedly generated barriers between ecotypes,
but appeared less important in completing speciation while genetic incompatibilities
played a key role. Chromosomal inversions contributed to genomic barriers, but
with variable impact. A multidimensional (hypercube) approach supported framing
of questions and identification of knowledge gaps and can be useful to understand
speciation in many other systems.
acknowledgement: KJ, MR, and RKB were supported by grants from the Swedish Research
Council (2021-0419, 2021-05243, and 2018-03695, respectively). RKB was also supported
by the Leverhulme Trust (RPG-2021-141), RF by FCT- Portuguese Science Foundation
(PTDC/BIA-EVL/1614/2021 and 2020.00275.CEECIND), and AMW by Norwegian Research Council
RCN (Project number 315287). We thank the members of the Integration of Speciation
Research network for stimulating discussions, the Littorina research community for
important contributions of data and analyses, and Cynthia Riginos for useful comments
on an earlier draft.
article_processing_charge: Yes (in subscription journal)
article_type: review
author:
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Alan
full_name: Le Moan, Alan
last_name: Le Moan
- first_name: Marina
full_name: Rafajlović, Marina
last_name: Rafajlović
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
citation:
ama: Johannesson K, Faria R, Le Moan A, et al. Diverse pathways to speciation revealed
by marine snails. Trends in Genetics. 2024. doi:10.1016/j.tig.2024.01.002
apa: Johannesson, K., Faria, R., Le Moan, A., Rafajlović, M., Westram, A. M., Butlin,
R. K., & Stankowski, S. (2024). Diverse pathways to speciation revealed by
marine snails. Trends in Genetics. Cell Press. https://doi.org/10.1016/j.tig.2024.01.002
chicago: Johannesson, Kerstin, Rui Faria, Alan Le Moan, Marina Rafajlović, Anja
M Westram, Roger K. Butlin, and Sean Stankowski. “Diverse Pathways to Speciation
Revealed by Marine Snails.” Trends in Genetics. Cell Press, 2024. https://doi.org/10.1016/j.tig.2024.01.002.
ieee: K. Johannesson et al., “Diverse pathways to speciation revealed by
marine snails,” Trends in Genetics. Cell Press, 2024.
ista: Johannesson K, Faria R, Le Moan A, Rafajlović M, Westram AM, Butlin RK, Stankowski
S. 2024. Diverse pathways to speciation revealed by marine snails. Trends in Genetics.
mla: Johannesson, Kerstin, et al. “Diverse Pathways to Speciation Revealed by Marine
Snails.” Trends in Genetics, Cell Press, 2024, doi:10.1016/j.tig.2024.01.002.
short: K. Johannesson, R. Faria, A. Le Moan, M. Rafajlović, A.M. Westram, R.K. Butlin,
S. Stankowski, Trends in Genetics (2024).
date_created: 2024-03-10T23:00:54Z
date_published: 2024-02-22T00:00:00Z
date_updated: 2024-03-13T12:08:57Z
day: '22'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1016/j.tig.2024.01.002
external_id:
pmid:
- '38395682'
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.tig.2024.01.002
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Trends in Genetics
publication_identifier:
eissn:
- 1362-4555
issn:
- 0168-9525
publication_status: epub_ahead
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diverse pathways to speciation revealed by marine snails
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...