---
_id: '12248'
abstract:
- lang: eng
text: Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual
lineages of parthenogenetic females, which produce rare males at low frequencies.
Although they are known to have ZW chromosomes, these are not well characterized,
and it is unclear whether they are shared across the clade. Furthermore, the underlying
genetic architecture of the transmission of asexuality, which can occur when rare
males mate with closely related sexual females, is not well understood. We produced
a chromosome-level assembly for the sexual Eurasian species Artemia sinica and
characterized in detail the pair of sex chromosomes of this species. We combined
this new assembly with short-read genomic data for the sexual species Artemia
sp. Kazakhstan and several asexual lineages of Artemia parthenogenetica, allowing
us to perform an in-depth characterization of sex-chromosome evolution across
the genus. We identified a small differentiated region of the ZW pair that is
shared by all sexual and asexual lineages, supporting the shared ancestry of the
sex chromosomes. We also inferred that recombination suppression has spread to
larger sections of the chromosome independently in the American and Eurasian lineages.
Finally, we took advantage of a rare male, which we backcrossed to sexual females,
to explore the genetic basis of asexuality. Our results suggest that parthenogenesis
is likely partly controlled by a locus on the Z chromosome, highlighting the interplay
between sex determination and asexuality.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "This work was supported by the European Research Council under the
European Union’s Horizon 2020 research and innovation program (grant agreement no.
715257) and by the Austrian Science Foundation (FWF SFB F88-10).\r\nWe thank the
Vicoso group for comments on the manuscript and the ISTA Scientific computing team
and the Vienna Biocenter Sequencing facility for technical support."
article_number: iyac123
article_processing_charge: No
article_type: original
author:
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
- first_name: Uladzislava
full_name: Khauratovich, Uladzislava
id: 5eba06f4-97d8-11ed-9f8f-d826ebdd9434
last_name: Khauratovich
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Vincent K
full_name: Bett, Vincent K
id: 57854184-AAE0-11E9-8D04-98D6E5697425
last_name: Bett
- first_name: Andrea
full_name: Mrnjavac, Andrea
id: 353FAC84-AE61-11E9-8BFC-00D3E5697425
last_name: Mrnjavac
- first_name: Ariana
full_name: Macon, Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Luca
full_name: Sax, Luca
id: 701c5602-97d8-11ed-96b5-b52773c70189
last_name: Sax
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Francisco
full_name: Hontoria, Francisco
last_name: Hontoria
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Elkrewi MN, Khauratovich U, Toups MA, et al. ZW sex-chromosome evolution and
contagious parthenogenesis in Artemia brine shrimp. Genetics. 2022;222(2).
doi:10.1093/genetics/iyac123
apa: Elkrewi, M. N., Khauratovich, U., Toups, M. A., Bett, V. K., Mrnjavac, A.,
Macon, A., … Vicoso, B. (2022). ZW sex-chromosome evolution and contagious parthenogenesis
in Artemia brine shrimp. Genetics. Oxford University Press. https://doi.org/10.1093/genetics/iyac123
chicago: Elkrewi, Marwan N, Uladzislava Khauratovich, Melissa A Toups, Vincent K
Bett, Andrea Mrnjavac, Ariana Macon, Christelle Fraisse, et al. “ZW Sex-Chromosome
Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” Genetics.
Oxford University Press, 2022. https://doi.org/10.1093/genetics/iyac123.
ieee: M. N. Elkrewi et al., “ZW sex-chromosome evolution and contagious parthenogenesis
in Artemia brine shrimp,” Genetics, vol. 222, no. 2. Oxford University
Press, 2022.
ista: Elkrewi MN, Khauratovich U, Toups MA, Bett VK, Mrnjavac A, Macon A, Fraisse
C, Sax L, Huylmans AK, Hontoria F, Vicoso B. 2022. ZW sex-chromosome evolution
and contagious parthenogenesis in Artemia brine shrimp. Genetics. 222(2), iyac123.
mla: Elkrewi, Marwan N., et al. “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis
in Artemia Brine Shrimp.” Genetics, vol. 222, no. 2, iyac123, Oxford University
Press, 2022, doi:10.1093/genetics/iyac123.
short: M.N. Elkrewi, U. Khauratovich, M.A. Toups, V.K. Bett, A. Mrnjavac, A. Macon,
C. Fraisse, L. Sax, A.K. Huylmans, F. Hontoria, B. Vicoso, Genetics 222 (2022).
date_created: 2023-01-16T09:56:10Z
date_published: 2022-10-01T00:00:00Z
date_updated: 2024-03-25T23:30:26Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/genetics/iyac123
ec_funded: 1
external_id:
isi:
- '000850270300001'
pmid:
- '35977389'
file:
- access_level: open_access
checksum: f79ff5383e882ea3f95f3da47a78029d
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T08:59:58Z
date_updated: 2023-01-30T08:59:58Z
file_id: '12440'
file_name: 2022_Genetics_Elkrewi.pdf
file_size: 1347136
relation: main_file
success: 1
file_date_updated: 2023-01-30T08:59:58Z
has_accepted_license: '1'
intvolume: ' 222'
isi: 1
issue: '2'
keyword:
- Genetics
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
- _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396
grant_number: F8810
name: The highjacking of meiosis for asexual reproduction
publication: Genetics
publication_identifier:
issn:
- 1943-2631
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '11653'
relation: research_data
status: public
scopus_import: '1'
status: public
title: ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine
shrimp
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 222
year: '2022'
...
---
_id: '12249'
abstract:
- lang: eng
text: 'The chemical potential of a component in a solution is defined as the free
energy change as the amount of that component changes. Computing this fundamental
thermodynamic property from atomistic simulations is notoriously difficult because
of the convergence issues involved in free energy methods and finite size effects.
This Communication presents the so-called S0 method, which can be used to obtain
chemical potentials from static structure factors computed from equilibrium molecular
dynamics simulations under the isothermal–isobaric ensemble. This new method is
demonstrated on the systems of binary Lennard-Jones particles, urea–water mixtures,
a NaCl aqueous solution, and a high-pressure carbon–hydrogen mixture. '
acknowledgement: I thank Daan Frenkel for providing feedback on an early draft and
for stimulating discussions, Debashish Mukherji and Robinson Cortes-Huerto for sharing
the trajectories for urea–water mixtures, and Aleks Reinhardt for useful suggestions
on the manuscript.
article_number: '121101'
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Cheng B. Computing chemical potentials of solutions from structure factors.
The Journal of Chemical Physics. 2022;157(12). doi:10.1063/5.0107059
apa: Cheng, B. (2022). Computing chemical potentials of solutions from structure
factors. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0107059
chicago: Cheng, Bingqing. “Computing Chemical Potentials of Solutions from Structure
Factors.” The Journal of Chemical Physics. AIP Publishing, 2022. https://doi.org/10.1063/5.0107059.
ieee: B. Cheng, “Computing chemical potentials of solutions from structure factors,”
The Journal of Chemical Physics, vol. 157, no. 12. AIP Publishing, 2022.
ista: Cheng B. 2022. Computing chemical potentials of solutions from structure factors.
The Journal of Chemical Physics. 157(12), 121101.
mla: Cheng, Bingqing. “Computing Chemical Potentials of Solutions from Structure
Factors.” The Journal of Chemical Physics, vol. 157, no. 12, 121101, AIP
Publishing, 2022, doi:10.1063/5.0107059.
short: B. Cheng, The Journal of Chemical Physics 157 (2022).
date_created: 2023-01-16T09:56:20Z
date_published: 2022-09-30T00:00:00Z
date_updated: 2023-08-04T09:43:11Z
day: '30'
ddc:
- '530'
- '540'
department:
- _id: BiCh
doi: 10.1063/5.0107059
external_id:
isi:
- '000862856000003'
file:
- access_level: open_access
checksum: b0915b706568a663a9a372fca24adf35
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T09:07:00Z
date_updated: 2023-01-30T09:07:00Z
file_id: '12441'
file_name: 2022_JourChemPhysics_Cheng.pdf
file_size: 4402384
relation: main_file
success: 1
file_date_updated: 2023-01-30T09:07:00Z
has_accepted_license: '1'
intvolume: ' 157'
isi: 1
issue: '12'
keyword:
- Physical and Theoretical Chemistry
- General Physics and Astronomy
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/ BingqingCheng/S0
scopus_import: '1'
status: public
title: Computing chemical potentials of solutions from structure factors
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 157
year: '2022'
...
---
_id: '12251'
abstract:
- lang: eng
text: Amyloid formation is linked to devastating neurodegenerative diseases, motivating
detailed studies of the mechanisms of amyloid formation. For Aβ, the peptide associated
with Alzheimer’s disease, the mechanism and rate of aggregation have been established
for a range of variants and conditions in vitro and
in bodily fluids. A key outstanding question is how the relative stabilities of
monomers, fibrils and intermediates affect each step in the fibril formation process.
By monitoring the kinetics of aggregation of Aβ42, in the presence of urea or
guanidinium hydrochloride (GuHCl), we here determine the rates of the underlying
microscopic steps and establish the importance of changes in relative stability
induced by the presence of denaturant for each individual step. Denaturants shift
the equilibrium towards the unfolded state of each species. We find that a non-ionic
denaturant, urea, reduces the overall aggregation rate, and that the effect on
nucleation is stronger than the effect on elongation. Urea reduces the rate of
secondary nucleation by decreasing the coverage of fibril surfaces and the rate
of nucleus formation. It also reduces the rate of primary nucleation, increasing
its reaction order. The ionic denaturant, GuHCl, accelerates the aggregation at
low denaturant concentrations and decelerates the aggregation at high denaturant
concentrations. Below approximately 0.25 M GuHCl, the screening of repulsive electrostatic
interactions between peptides by the charged denaturant dominates, leading to
an increased aggregation rate. At higher GuHCl concentrations, the electrostatic
repulsion is completely screened, and the denaturing effect dominates. The results
illustrate how the differential effects of denaturants on stability of monomer,
oligomer and fibril translate to differential effects on microscopic steps, with
the rate of nucleation being most strongly reduced.
acknowledgement: This work was supported by grants from the Swedish Research Council
(grant no. 2015-00143) and the European Research Council (grant no. 340890).
article_number: '943355'
article_processing_charge: No
article_type: original
author:
- first_name: Tanja
full_name: Weiffert, Tanja
last_name: Weiffert
- first_name: Georg
full_name: Meisl, Georg
last_name: Meisl
- first_name: Samo
full_name: Curk, Samo
last_name: Curk
- first_name: Risto
full_name: Cukalevski, Risto
last_name: Cukalevski
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
- first_name: Sara
full_name: Linse, Sara
last_name: Linse
citation:
ama: Weiffert T, Meisl G, Curk S, et al. Influence of denaturants on amyloid β42
aggregation kinetics. Frontiers in Neuroscience. 2022;16. doi:10.3389/fnins.2022.943355
apa: Weiffert, T., Meisl, G., Curk, S., Cukalevski, R., Šarić, A., Knowles, T. P.
J., & Linse, S. (2022). Influence of denaturants on amyloid β42 aggregation
kinetics. Frontiers in Neuroscience. Frontiers Media. https://doi.org/10.3389/fnins.2022.943355
chicago: Weiffert, Tanja, Georg Meisl, Samo Curk, Risto Cukalevski, Anđela Šarić,
Tuomas P. J. Knowles, and Sara Linse. “Influence of Denaturants on Amyloid Β42
Aggregation Kinetics.” Frontiers in Neuroscience. Frontiers Media, 2022.
https://doi.org/10.3389/fnins.2022.943355.
ieee: T. Weiffert et al., “Influence of denaturants on amyloid β42 aggregation
kinetics,” Frontiers in Neuroscience, vol. 16. Frontiers Media, 2022.
ista: Weiffert T, Meisl G, Curk S, Cukalevski R, Šarić A, Knowles TPJ, Linse S.
2022. Influence of denaturants on amyloid β42 aggregation kinetics. Frontiers
in Neuroscience. 16, 943355.
mla: Weiffert, Tanja, et al. “Influence of Denaturants on Amyloid Β42 Aggregation
Kinetics.” Frontiers in Neuroscience, vol. 16, 943355, Frontiers Media,
2022, doi:10.3389/fnins.2022.943355.
short: T. Weiffert, G. Meisl, S. Curk, R. Cukalevski, A. Šarić, T.P.J. Knowles,
S. Linse, Frontiers in Neuroscience 16 (2022).
date_created: 2023-01-16T09:56:43Z
date_published: 2022-09-20T00:00:00Z
date_updated: 2023-08-04T09:48:56Z
day: '20'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.3389/fnins.2022.943355
external_id:
isi:
- '000866287100001'
file:
- access_level: open_access
checksum: e67d16113ffb4fb4fa38a183d169f210
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T09:15:13Z
date_updated: 2023-01-30T09:15:13Z
file_id: '12442'
file_name: 2022_FrontiersNeuroscience_Weiffert2.pdf
file_size: 19798610
relation: main_file
success: 1
file_date_updated: 2023-01-30T09:15:13Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
keyword:
- General Neuroscience
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Frontiers in Neuroscience
publication_identifier:
issn:
- 1662-453X
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
scopus_import: '1'
status: public
title: Influence of denaturants on amyloid β42 aggregation kinetics
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 16
year: '2022'
...
---
_id: '12252'
abstract:
- lang: eng
text: The COVID−19 pandemic not only resulted in a global crisis, but also accelerated
vaccine development and antibody discovery. Herein we report a synthetic humanized
VHH library development pipeline for nanomolar-range affinity VHH binders to SARS-CoV-2
variants of concern (VoC) receptor binding domains (RBD) isolation. Trinucleotide-based
randomization of CDRs by Kunkel mutagenesis with the subsequent rolling-cycle
amplification resulted in more than 1011 diverse phage display
library in a manageable for a single person number of electroporation reactions.
We identified a number of nanomolar-range affinity VHH binders to SARS-CoV-2 variants
of concern (VoC) receptor binding domains (RBD) by screening a novel synthetic
humanized antibody library. In order to explore the most robust and fast method
for affinity improvement, we performed affinity maturation by CDR1 and CDR2 shuffling
and avidity engineering by multivalent trimeric VHH fusion protein construction.
As a result, H7-Fc and G12x3-Fc binders were developed with the affinities in
nM and pM range respectively. Importantly, these affinities are weakly influenced
by most of SARS-CoV-2 VoC mutations and they retain moderate binding to BA.4\5.
The plaque reduction neutralization test (PRNT) resulted in IC50 = 100 ng\ml and
9.6 ng\ml for H7-Fc and G12x3-Fc antibodies, respectively, for the emerging Omicron
BA.1 variant. Therefore, these VHH could expand the present landscape of SARS-CoV-2
neutralization binders with the therapeutic potential for present and future SARS-CoV-2
variants.
acknowledgement: The authors declare that this study received funding from Immunofusion.
The funder was not involved in the study design, collection, analysis, interpretation
of data, the writing of this article or the decision to submit it for publication.
article_number: '965446'
article_processing_charge: No
article_type: original
author:
- first_name: Dmitri
full_name: Dormeshkin, Dmitri
last_name: Dormeshkin
- first_name: Michail
full_name: Shapira, Michail
last_name: Shapira
- first_name: Simon
full_name: Dubovik, Simon
last_name: Dubovik
- first_name: Anton
full_name: Kavaleuski, Anton
id: 4968f7ad-eb97-11eb-a6c2-8ed382e8912c
last_name: Kavaleuski
orcid: 0000-0003-2091-526X
- first_name: Mikalai
full_name: Katsin, Mikalai
last_name: Katsin
- first_name: Alexandr
full_name: Migas, Alexandr
last_name: Migas
- first_name: Alexander
full_name: Meleshko, Alexander
last_name: Meleshko
- first_name: Sergei
full_name: Semyonov, Sergei
last_name: Semyonov
citation:
ama: Dormeshkin D, Shapira M, Dubovik S, et al. Isolation of an escape-resistant
SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library. Frontiers
in Immunology. 2022;13. doi:10.3389/fimmu.2022.965446
apa: Dormeshkin, D., Shapira, M., Dubovik, S., Kavaleuski, A., Katsin, M., Migas,
A., … Semyonov, S. (2022). Isolation of an escape-resistant SARS-CoV-2 neutralizing
nanobody from a novel synthetic nanobody library. Frontiers in Immunology.
Frontiers Media. https://doi.org/10.3389/fimmu.2022.965446
chicago: Dormeshkin, Dmitri, Michail Shapira, Simon Dubovik, Anton Kavaleuski, Mikalai
Katsin, Alexandr Migas, Alexander Meleshko, and Sergei Semyonov. “Isolation of
an Escape-Resistant SARS-CoV-2 Neutralizing Nanobody from a Novel Synthetic Nanobody
Library.” Frontiers in Immunology. Frontiers Media, 2022. https://doi.org/10.3389/fimmu.2022.965446.
ieee: D. Dormeshkin et al., “Isolation of an escape-resistant SARS-CoV-2
neutralizing nanobody from a novel synthetic nanobody library,” Frontiers in
Immunology, vol. 13. Frontiers Media, 2022.
ista: Dormeshkin D, Shapira M, Dubovik S, Kavaleuski A, Katsin M, Migas A, Meleshko
A, Semyonov S. 2022. Isolation of an escape-resistant SARS-CoV-2 neutralizing
nanobody from a novel synthetic nanobody library. Frontiers in Immunology. 13,
965446.
mla: Dormeshkin, Dmitri, et al. “Isolation of an Escape-Resistant SARS-CoV-2 Neutralizing
Nanobody from a Novel Synthetic Nanobody Library.” Frontiers in Immunology,
vol. 13, 965446, Frontiers Media, 2022, doi:10.3389/fimmu.2022.965446.
short: D. Dormeshkin, M. Shapira, S. Dubovik, A. Kavaleuski, M. Katsin, A. Migas,
A. Meleshko, S. Semyonov, Frontiers in Immunology 13 (2022).
date_created: 2023-01-16T09:56:57Z
date_published: 2022-09-16T00:00:00Z
date_updated: 2023-08-04T09:49:24Z
day: '16'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.3389/fimmu.2022.965446
external_id:
isi:
- '000862479100001'
file:
- access_level: open_access
checksum: f8f5d8110710033d0532e7e08bf9dad4
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T09:22:26Z
date_updated: 2023-01-30T09:22:26Z
file_id: '12443'
file_name: 2022_FrontiersImmunology_Dormeshkin.pdf
file_size: 5695892
relation: main_file
success: 1
file_date_updated: 2023-01-30T09:22:26Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
keyword:
- Immunology
- Immunology and Allergy
- COVID-19
- SARS-CoV-2
- synthetic library
- RBD
- neutralization nanobody
- VHH
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Frontiers in Immunology
publication_identifier:
issn:
- 1664-3224
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
scopus_import: '1'
status: public
title: Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel
synthetic nanobody library
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13
year: '2022'
...
---
_id: '12253'
abstract:
- lang: eng
text: The sculpting of germ layers during gastrulation relies on the coordinated
migration of progenitor cells, yet the cues controlling these long-range directed
movements remain largely unknown. While directional migration often relies on
a chemokine gradient generated from a localized source, we find that zebrafish
ventrolateral mesoderm is guided by a self-generated gradient of the initially
uniformly expressed and secreted protein Toddler/ELABELA/Apela. We show that the
Apelin receptor, which is specifically expressed in mesodermal cells, has a dual
role during gastrulation, acting as a scavenger receptor to generate a Toddler
gradient, and as a chemokine receptor to sense this guidance cue. Thus, we uncover
a single receptor–based self-generated gradient as the enigmatic guidance cue
that can robustly steer the directional migration of mesoderm through the complex
and continuously changing environment of the gastrulating embryo.
acknowledgement: 'We thank K. Aumayer and the team of the biooptics facility at the
Vienna Biocenter, particularly P. Pasierbek and T. Müller, for support with microscopy;
K. Panser, C. Pribitzer, and the animal facility personnel for taking care of zebrafish;
M. Binner and A. Bandura for help with genotyping; M. Codina Tobias for help with
establishing the conditions for the Toddler overexpression compensation experiment;
T. Lubiana Alves for sharing the code for scRNA-Seq analyses; the Heisenberg laboratory,
particularly D. Pinheiro, for joint laboratory meetings, discussions on the project,
and providing the tg(gsc:CAAX-GFP) fish line; the Raz laboratory for providing the
Lifeact-GFP plasmid; A. Andersen, A. Schier, C.-P. Heisenberg, and E. Tanaka for
comments on the manuscript; and the entire Pauli laboratory, particularly K. Gert
and V. Deneke, for valuable discussions and feedback on the manuscript. Funding:
Work in A.P.’s laboratory has been supported by the IMP, which receives institutional
funding from Boehringer Ingelheim and the Austrian Research Promotion Agency (Headquarter
grant FFG-852936), as well as the FWF START program (Y 1031-B28 to A.P.), the Human
Frontier Science Program (HFSP) Career Development Award (CDA00066/2015 to A.P.)
and Young Investigator Grant (RGY0079/2020 to A.P.), the SFB RNA-Deco (project number
F 80 to A.P.), a Whitman Center Fellowship from the Marine Biological Laboratory
(to A.P.), and EMBO-YIP funds (to A.P.). This work was supported by the European
Union (European Research Council Starting Grant 851288 to E.H.). For the purpose
of Open Access, the authors have applied a CC BY public copyright license to any
Author Accepted Manuscript (AAM) version arising from this submission.'
article_number: eadd2488
article_processing_charge: No
article_type: original
author:
- first_name: Jessica
full_name: Stock, Jessica
last_name: Stock
- first_name: Tomas
full_name: Kazmar, Tomas
last_name: Kazmar
- first_name: Friederike
full_name: Schlumm, Friederike
last_name: Schlumm
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Andrea
full_name: Pauli, Andrea
last_name: Pauli
citation:
ama: Stock J, Kazmar T, Schlumm F, Hannezo EB, Pauli A. A self-generated Toddler
gradient guides mesodermal cell migration. Science Advances. 2022;8(37).
doi:10.1126/sciadv.add2488
apa: Stock, J., Kazmar, T., Schlumm, F., Hannezo, E. B., & Pauli, A. (2022).
A self-generated Toddler gradient guides mesodermal cell migration. Science
Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.add2488
chicago: Stock, Jessica, Tomas Kazmar, Friederike Schlumm, Edouard B Hannezo, and
Andrea Pauli. “A Self-Generated Toddler Gradient Guides Mesodermal Cell Migration.”
Science Advances. American Association for the Advancement of Science,
2022. https://doi.org/10.1126/sciadv.add2488.
ieee: J. Stock, T. Kazmar, F. Schlumm, E. B. Hannezo, and A. Pauli, “A self-generated
Toddler gradient guides mesodermal cell migration,” Science Advances, vol.
8, no. 37. American Association for the Advancement of Science, 2022.
ista: Stock J, Kazmar T, Schlumm F, Hannezo EB, Pauli A. 2022. A self-generated
Toddler gradient guides mesodermal cell migration. Science Advances. 8(37), eadd2488.
mla: Stock, Jessica, et al. “A Self-Generated Toddler Gradient Guides Mesodermal
Cell Migration.” Science Advances, vol. 8, no. 37, eadd2488, American Association
for the Advancement of Science, 2022, doi:10.1126/sciadv.add2488.
short: J. Stock, T. Kazmar, F. Schlumm, E.B. Hannezo, A. Pauli, Science Advances
8 (2022).
date_created: 2023-01-16T09:57:10Z
date_published: 2022-09-14T00:00:00Z
date_updated: 2023-08-04T09:49:59Z
day: '14'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1126/sciadv.add2488
ec_funded: 1
external_id:
isi:
- '000888875000009'
pmid:
- '36103529'
file:
- access_level: open_access
checksum: f59cdb824e5d4221045def81f46f6c65
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T09:27:49Z
date_updated: 2023-01-30T09:27:49Z
file_id: '12444'
file_name: 2022_ScienceAdvances_Stock.pdf
file_size: 1636732
relation: main_file
success: 1
file_date_updated: 2023-01-30T09:27:49Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '37'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: A self-generated Toddler gradient guides mesodermal cell migration
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 8
year: '2022'
...
---
_id: '12257'
abstract:
- lang: eng
text: Structural balance theory is an established framework for studying social
relationships of friendship and enmity. These relationships are modeled by a signed
network whose energy potential measures the level of imbalance, while stochastic
dynamics drives the network toward a state of minimum energy that captures social
balance. It is known that this energy landscape has local minima that can trap
socially aware dynamics, preventing it from reaching balance. Here we first study
the robustness and attractor properties of these local minima. We show that a
stochastic process can reach them from an abundance of initial states and that
some local minima cannot be escaped by mild perturbations of the network. Motivated
by these anomalies, we introduce best-edge dynamics (BED), a new plausible stochastic
process. We prove that BED always reaches balance and that it does so fast in
various interesting settings.
acknowledgement: "K.C. acknowledges support from ERC Start Grant No. (279307: Graph
Games), ERC Consolidator Grant No. (863818: ForM-SMart), and Austrian Science Fund
(FWF)\r\nGrants No. P23499-N23 and No. S11407-N23 (RiSE). This project has received
funding from the European Union’s Horizon 2020 research and innovation programme
under the Marie\r\nSkłodowska-Curie Grant Agreement No. 665385."
article_number: '034321'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Jakub
full_name: Svoboda, Jakub
id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
last_name: Svoboda
orcid: 0000-0002-1419-3267
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
citation:
ama: 'Chatterjee K, Svoboda J, Zikelic D, Pavlogiannis A, Tkadlec J. Social balance
on networks: Local minima and best-edge dynamics. Physical Review E. 2022;106(3).
doi:10.1103/physreve.106.034321'
apa: 'Chatterjee, K., Svoboda, J., Zikelic, D., Pavlogiannis, A., & Tkadlec,
J. (2022). Social balance on networks: Local minima and best-edge dynamics. Physical
Review E. American Physical Society. https://doi.org/10.1103/physreve.106.034321'
chicago: 'Chatterjee, Krishnendu, Jakub Svoboda, Dorde Zikelic, Andreas Pavlogiannis,
and Josef Tkadlec. “Social Balance on Networks: Local Minima and Best-Edge Dynamics.”
Physical Review E. American Physical Society, 2022. https://doi.org/10.1103/physreve.106.034321.'
ieee: 'K. Chatterjee, J. Svoboda, D. Zikelic, A. Pavlogiannis, and J. Tkadlec, “Social
balance on networks: Local minima and best-edge dynamics,” Physical Review
E, vol. 106, no. 3. American Physical Society, 2022.'
ista: 'Chatterjee K, Svoboda J, Zikelic D, Pavlogiannis A, Tkadlec J. 2022. Social
balance on networks: Local minima and best-edge dynamics. Physical Review E. 106(3),
034321.'
mla: 'Chatterjee, Krishnendu, et al. “Social Balance on Networks: Local Minima and
Best-Edge Dynamics.” Physical Review E, vol. 106, no. 3, 034321, American
Physical Society, 2022, doi:10.1103/physreve.106.034321.'
short: K. Chatterjee, J. Svoboda, D. Zikelic, A. Pavlogiannis, J. Tkadlec, Physical
Review E 106 (2022).
date_created: 2023-01-16T09:57:57Z
date_published: 2022-09-29T00:00:00Z
date_updated: 2025-07-14T09:09:49Z
day: '29'
department:
- _id: KrCh
doi: 10.1103/physreve.106.034321
ec_funded: 1
external_id:
arxiv:
- '2210.02394'
isi:
- '000870243100001'
intvolume: ' 106'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2210.02394
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Physical Review E
publication_identifier:
eissn:
- 2470-0053
issn:
- 2470-0045
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Social balance on networks: Local minima and best-edge dynamics'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 106
year: '2022'
...
---
_id: '12259'
abstract:
- lang: eng
text: 'Theoretical foundations of chaos have been predominantly laid out for finite-dimensional
dynamical systems, such as the three-body problem in classical mechanics and the
Lorenz model in dissipative systems. In contrast, many real-world chaotic phenomena,
e.g., weather, arise in systems with many (formally infinite) degrees of freedom,
which limits direct quantitative analysis of such systems using chaos theory.
In the present work, we demonstrate that the hydrodynamic pilot-wave systems offer
a bridge between low- and high-dimensional chaotic phenomena by allowing for a
systematic study of how the former connects to the latter. Specifically, we present
experimental results, which show the formation of low-dimensional chaotic attractors
upon destabilization of regular dynamics and a final transition to high-dimensional
chaos via the merging of distinct chaotic regions through a crisis bifurcation.
Moreover, we show that the post-crisis dynamics of the system can be rationalized
as consecutive scatterings from the nonattracting chaotic sets with lifetimes
following exponential distributions. '
acknowledgement: 'This work was partially funded by the Institute of Science and Technology
Austria Interdisciplinary Project Committee Grant “Pilot-Wave Hydrodynamics: Chaos
and Quantum Analogies.”'
article_number: '093138'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: George H
full_name: Choueiri, George H
id: 448BD5BC-F248-11E8-B48F-1D18A9856A87
last_name: Choueiri
- first_name: Balachandra
full_name: Suri, Balachandra
id: 47A5E706-F248-11E8-B48F-1D18A9856A87
last_name: Suri
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
citation:
ama: 'Choueiri GH, Suri B, Merrin J, Serbyn M, Hof B, Budanur NB. Crises and chaotic
scattering in hydrodynamic pilot-wave experiments. Chaos: An Interdisciplinary
Journal of Nonlinear Science. 2022;32(9). doi:10.1063/5.0102904'
apa: 'Choueiri, G. H., Suri, B., Merrin, J., Serbyn, M., Hof, B., & Budanur,
N. B. (2022). Crises and chaotic scattering in hydrodynamic pilot-wave experiments.
Chaos: An Interdisciplinary Journal of Nonlinear Science. AIP Publishing.
https://doi.org/10.1063/5.0102904'
chicago: 'Choueiri, George H, Balachandra Suri, Jack Merrin, Maksym Serbyn, Björn
Hof, and Nazmi B Budanur. “Crises and Chaotic Scattering in Hydrodynamic Pilot-Wave
Experiments.” Chaos: An Interdisciplinary Journal of Nonlinear Science.
AIP Publishing, 2022. https://doi.org/10.1063/5.0102904.'
ieee: 'G. H. Choueiri, B. Suri, J. Merrin, M. Serbyn, B. Hof, and N. B. Budanur,
“Crises and chaotic scattering in hydrodynamic pilot-wave experiments,” Chaos:
An Interdisciplinary Journal of Nonlinear Science, vol. 32, no. 9. AIP Publishing,
2022.'
ista: 'Choueiri GH, Suri B, Merrin J, Serbyn M, Hof B, Budanur NB. 2022. Crises
and chaotic scattering in hydrodynamic pilot-wave experiments. Chaos: An Interdisciplinary
Journal of Nonlinear Science. 32(9), 093138.'
mla: 'Choueiri, George H., et al. “Crises and Chaotic Scattering in Hydrodynamic
Pilot-Wave Experiments.” Chaos: An Interdisciplinary Journal of Nonlinear Science,
vol. 32, no. 9, 093138, AIP Publishing, 2022, doi:10.1063/5.0102904.'
short: 'G.H. Choueiri, B. Suri, J. Merrin, M. Serbyn, B. Hof, N.B. Budanur, Chaos:
An Interdisciplinary Journal of Nonlinear Science 32 (2022).'
date_created: 2023-01-16T09:58:16Z
date_published: 2022-09-26T00:00:00Z
date_updated: 2023-08-04T09:51:17Z
day: '26'
ddc:
- '530'
department:
- _id: MaSe
- _id: BjHo
- _id: NanoFab
doi: 10.1063/5.0102904
external_id:
arxiv:
- '2206.01531'
isi:
- '000861009600005'
file:
- access_level: open_access
checksum: 17881eff8b21969359a2dd64620120ba
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T09:41:12Z
date_updated: 2023-01-30T09:41:12Z
file_id: '12445'
file_name: 2022_Chaos_Choueiri.pdf
file_size: 3209644
relation: main_file
success: 1
file_date_updated: 2023-01-30T09:41:12Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
issue: '9'
keyword:
- Applied Mathematics
- General Physics and Astronomy
- Mathematical Physics
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: 'Chaos: An Interdisciplinary Journal of Nonlinear Science'
publication_identifier:
eissn:
- 1089-7682
issn:
- 1054-1500
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Crises and chaotic scattering in hydrodynamic pilot-wave experiments
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 32
year: '2022'
...
---
_id: '12261'
abstract:
- lang: eng
text: 'Dose–response relationships are a general concept for quantitatively describing
biological systems across multiple scales, from the molecular to the whole-cell
level. A clinically relevant example is the bacterial growth response to antibiotics,
which is routinely characterized by dose–response curves. The shape of the dose–response
curve varies drastically between antibiotics and plays a key role in treatment,
drug interactions, and resistance evolution. However, the mechanisms shaping the
dose–response curve remain largely unclear. Here, we show in Escherichia coli
that the distinctively shallow dose–response curve of the antibiotic trimethoprim
is caused by a negative growth-mediated feedback loop: Trimethoprim slows growth,
which in turn weakens the effect of this antibiotic. At the molecular level, this
feedback is caused by the upregulation of the drug target dihydrofolate reductase
(FolA/DHFR). We show that this upregulation is not a specific response to trimethoprim
but follows a universal trend line that depends primarily on the growth rate,
irrespective of its cause. Rewiring the feedback loop alters the dose–response
curve in a predictable manner, which we corroborate using a mathematical model
of cellular resource allocation and growth. Our results indicate that growth-mediated
feedback loops may shape drug responses more generally and could be exploited
to design evolutionary traps that enable selection against drug resistance.'
acknowledged_ssus:
- _id: M-Shop
acknowledgement: This work was in part supported by Human Frontier Science Program
GrantRGP0042/2013, Marie Curie Career Integration Grant303507, AustrianScience Fund
(FWF) Grant P27201-B22, and German Research Foundation(DFG) Collaborative Research
Center (SFB)1310to TB. SAA was supportedby the European Union’s Horizon2020Research
and Innovation Programunder the Marie Skłodowska-Curie Grant agreement No707352.
We wouldlike to thank the Bollenbach group for regular fruitful discussions. We
areparticularly thankful for the technical assistance of Booshini Fernando andfor
discussions of the theoretical aspects with Gerrit Ansmann. We areindebted to Bor
Kavˇciˇc for invaluable advice, help with setting up theluciferase-based growth
monitoring system, and for sharing plasmids. Weacknowledge the IST Austria Miba
Machine Shop for their support inbuilding a housing for the stacker of the plate
reader, which enabled thehigh-throughput luciferase-based experiments. We are grateful
to RosalindAllen, Bor Kavˇciˇc and Dor Russ for feedback on the manuscript. Open
Accessfunding enabled and organized by Projekt DEAL.
article_number: e10490
article_processing_charge: No
article_type: original
author:
- first_name: Andreas
full_name: Angermayr, Andreas
id: 4677C796-F248-11E8-B48F-1D18A9856A87
last_name: Angermayr
orcid: 0000-0001-8619-2223
- first_name: Tin Yau
full_name: Pang, Tin Yau
last_name: Pang
- first_name: Guillaume
full_name: Chevereau, Guillaume
last_name: Chevereau
- first_name: Karin
full_name: Mitosch, Karin
id: 39B66846-F248-11E8-B48F-1D18A9856A87
last_name: Mitosch
- first_name: Martin J
full_name: Lercher, Martin J
last_name: Lercher
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. Growth‐mediated
negative feedback shapes quantitative antibiotic response. Molecular Systems
Biology. 2022;18(9). doi:10.15252/msb.202110490
apa: Angermayr, A., Pang, T. Y., Chevereau, G., Mitosch, K., Lercher, M. J., &
Bollenbach, M. T. (2022). Growth‐mediated negative feedback shapes quantitative
antibiotic response. Molecular Systems Biology. Embo Press. https://doi.org/10.15252/msb.202110490
chicago: Angermayr, Andreas, Tin Yau Pang, Guillaume Chevereau, Karin Mitosch, Martin
J Lercher, and Mark Tobias Bollenbach. “Growth‐mediated Negative Feedback Shapes
Quantitative Antibiotic Response.” Molecular Systems Biology. Embo Press,
2022. https://doi.org/10.15252/msb.202110490.
ieee: A. Angermayr, T. Y. Pang, G. Chevereau, K. Mitosch, M. J. Lercher, and M.
T. Bollenbach, “Growth‐mediated negative feedback shapes quantitative antibiotic
response,” Molecular Systems Biology, vol. 18, no. 9. Embo Press, 2022.
ista: Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. 2022.
Growth‐mediated negative feedback shapes quantitative antibiotic response. Molecular
Systems Biology. 18(9), e10490.
mla: Angermayr, Andreas, et al. “Growth‐mediated Negative Feedback Shapes Quantitative
Antibiotic Response.” Molecular Systems Biology, vol. 18, no. 9, e10490,
Embo Press, 2022, doi:10.15252/msb.202110490.
short: A. Angermayr, T.Y. Pang, G. Chevereau, K. Mitosch, M.J. Lercher, M.T. Bollenbach,
Molecular Systems Biology 18 (2022).
date_created: 2023-01-16T09:58:34Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2023-08-04T09:51:49Z
day: '01'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.15252/msb.202110490
external_id:
isi:
- '000856482800001'
file:
- access_level: open_access
checksum: 8b1d8f5ea20c8408acf466435fb6ae01
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T09:49:55Z
date_updated: 2023-01-30T09:49:55Z
file_id: '12446'
file_name: 2022_MolecularSystemsBio_Angermayr.pdf
file_size: 1098812
relation: main_file
success: 1
file_date_updated: 2023-01-30T09:49:55Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '9'
keyword:
- Applied Mathematics
- Computational Theory and Mathematics
- General Agricultural and Biological Sciences
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- Information Systems
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Molecular Systems Biology
publication_identifier:
eissn:
- 1744-4292
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Growth‐mediated negative feedback shapes quantitative antibiotic response
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 18
year: '2022'
...
---
_id: '12262'
abstract:
- lang: eng
text: The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that
initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases
the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear
export, a strict requirement for downstream maturation. The molecular mechanism
of release remained elusive. Here, we report a series of cryo-EM structures that
captured the extraction of Rlp24 from pre-60S particles by Saccharomyces cerevisiae
Drg1. These structures reveal that Arx1 and the eukaryote-specific rRNA expansion
segment ES27 form a joint docking platform that positions Drg1 for efficient extraction
of Rlp24 from the pre-ribosome. The tips of the Drg1 N domains thereby guide the
Rlp24 C terminus into the central pore of the Drg1 hexamer, enabling extraction
by a hand-over-hand translocation mechanism. Our results uncover substrate recognition
and processing by Drg1 step by step and provide a comprehensive mechanistic picture
of the conserved modus operandi of AAA-ATPases.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: "We thank M. Fromont-Racine, A. Johnson, J. Woolford, S. Rospert,
J. P. G. Ballesta and\r\nE. Hurt for supplying antibodies. The work was supported
by Boehringer Ingelheim (to\r\nD. H.), the Austrian Science Foundation FWF (grants
32536 and 32977 to H. B.), the\r\nUK Medical Research Council (MR/T012412/1 to A.
J. W.) and the German Research\r\nFoundation (Emmy Noether Programme STE 2517/1-1
and STE 2517/5-1 to F.S.). We\r\nthank Norberto Escudero-Urquijo, Pablo Castro-Hartmann
and K. Dent, Cambridge\r\nInstitute for Medical Research, for their help in cryo-EM
during early phases of this\r\nproject. This research was supported by the Scientific
Service Units of IST Austria through\r\nresources provided by the Electron Microscopy
Facility. We thank S. Keller, Institute of\r\nMolecular Biosciences (Biophysics),
University Graz for support with the quantification of\r\nthe SPR particle release
assay. We thank I. Schaffner, University of Natural Resources and\r\nLife Sciences,
Vienna for her help in early stages of the SPR experiments."
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Prattes, Michael
last_name: Prattes
- first_name: Irina
full_name: Grishkovskaya, Irina
last_name: Grishkovskaya
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: Christina
full_name: Hetzmannseder, Christina
last_name: Hetzmannseder
- first_name: Gertrude
full_name: Zisser, Gertrude
last_name: Zisser
- first_name: Carolin
full_name: Sailer, Carolin
last_name: Sailer
- first_name: Vasileios
full_name: Kargas, Vasileios
last_name: Kargas
- first_name: Mathias
full_name: Loibl, Mathias
last_name: Loibl
- first_name: Magdalena
full_name: Gerhalter, Magdalena
last_name: Gerhalter
- first_name: Lisa
full_name: Kofler, Lisa
last_name: Kofler
- first_name: Alan J.
full_name: Warren, Alan J.
last_name: Warren
- first_name: Florian
full_name: Stengel, Florian
last_name: Stengel
- first_name: David
full_name: Haselbach, David
last_name: Haselbach
- first_name: Helmut
full_name: Bergler, Helmut
last_name: Bergler
citation:
ama: Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Visualizing maturation factor
extraction from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural
& Molecular Biology. 2022;29(9):942-953. doi:10.1038/s41594-022-00832-5
apa: Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Hetzmannseder, C., Zisser,
G., Sailer, C., … Bergler, H. (2022). Visualizing maturation factor extraction
from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural & Molecular
Biology. Springer Nature. https://doi.org/10.1038/s41594-022-00832-5
chicago: Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Christina
Hetzmannseder, Gertrude Zisser, Carolin Sailer, Vasileios Kargas, et al. “Visualizing
Maturation Factor Extraction from the Nascent Ribosome by the AAA-ATPase Drg1.”
Nature Structural & Molecular Biology. Springer Nature, 2022. https://doi.org/10.1038/s41594-022-00832-5.
ieee: M. Prattes et al., “Visualizing maturation factor extraction from the
nascent ribosome by the AAA-ATPase Drg1,” Nature Structural & Molecular
Biology, vol. 29, no. 9. Springer Nature, pp. 942–953, 2022.
ista: Prattes M, Grishkovskaya I, Hodirnau V-V, Hetzmannseder C, Zisser G, Sailer
C, Kargas V, Loibl M, Gerhalter M, Kofler L, Warren AJ, Stengel F, Haselbach D,
Bergler H. 2022. Visualizing maturation factor extraction from the nascent ribosome
by the AAA-ATPase Drg1. Nature Structural & Molecular Biology. 29(9), 942–953.
mla: Prattes, Michael, et al. “Visualizing Maturation Factor Extraction from the
Nascent Ribosome by the AAA-ATPase Drg1.” Nature Structural & Molecular
Biology, vol. 29, no. 9, Springer Nature, 2022, pp. 942–53, doi:10.1038/s41594-022-00832-5.
short: M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, C. Hetzmannseder, G. Zisser,
C. Sailer, V. Kargas, M. Loibl, M. Gerhalter, L. Kofler, A.J. Warren, F. Stengel,
D. Haselbach, H. Bergler, Nature Structural & Molecular Biology 29 (2022)
942–953.
date_created: 2023-01-16T09:59:06Z
date_published: 2022-09-12T00:00:00Z
date_updated: 2023-08-04T09:52:20Z
day: '12'
ddc:
- '570'
department:
- _id: EM-Fac
doi: 10.1038/s41594-022-00832-5
external_id:
isi:
- '000852942100004'
pmid:
- '36097293'
file:
- access_level: open_access
checksum: 2d5c3ec01718fefd7553052b0b8a0793
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T10:00:04Z
date_updated: 2023-01-30T10:00:04Z
file_id: '12447'
file_name: 2022_NatureStrucMolecBio_Prattes.pdf
file_size: 9935057
relation: main_file
success: 1
file_date_updated: 2023-01-30T10:00:04Z
has_accepted_license: '1'
intvolume: ' 29'
isi: 1
issue: '9'
keyword:
- Molecular Biology
- Structural Biology
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 942-953
pmid: 1
publication: Nature Structural & Molecular Biology
publication_identifier:
eissn:
- 1545-9985
issn:
- 1545-9993
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase
Drg1
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 29
year: '2022'
...
---
_id: '12264'
abstract:
- lang: eng
text: Reproductive isolation (RI) is a core concept in evolutionary biology. It
has been the central focus of speciation research since the modern synthesis and
is the basis by which biological species are defined. Despite this, the term is
used in seemingly different ways, and attempts to quantify RI have used very different
approaches. After showing that the field lacks a clear definition of the term,
we attempt to clarify key issues, including what RI is, how it can be quantified
in principle, and how it can be measured in practice. Following other definitions
with a genetic focus, we propose that RI is a quantitative measure of the effect
that genetic differences between populations have on gene flow. Specifically,
RI compares the flow of neutral alleles in the presence of these genetic differences
to the flow without any such differences. RI is thus greater than zero when genetic
differences between populations reduce the flow of neutral alleles between populations.
We show how RI can be quantified in a range of scenarios. A key conclusion is
that RI depends strongly on circumstances—including the spatial, temporal and
genomic context—making it difficult to compare across systems. After reviewing
methods for estimating RI from data, we conclude that it is difficult to measure
in practice. We discuss our findings in light of the goals of speciation research
and encourage the use of methods for estimating RI that integrate organismal and
genetic approaches.
acknowledgement: 'We are grateful to the participants of the ESEB satellite symposium
‘Understanding reproductive isolation: bridging conceptual barriers in speciation research’ in 2021 for the interesting discussions that helped us clarify the thoughts presented in this article. We thank Roger
Butlin, Michael Turelli and two anonymous reviewers for their thoughtful comments
on this manuscript. We are also very grateful to Roger Butlin and the Barton Group
for the continued conversa-tions about RI. In addition, we thank all participants
of the speciation survey. Part of this work was funded by the Austrian Science Fund
FWF (grant P 32166)'
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- 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: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Parvathy
full_name: Surendranadh, Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Westram AM, Stankowski S, Surendranadh P, Barton NH. What is reproductive isolation?
Journal of Evolutionary Biology. 2022;35(9):1143-1164. doi:10.1111/jeb.14005
apa: Westram, A. M., Stankowski, S., Surendranadh, P., & Barton, N. H. (2022).
What is reproductive isolation? Journal of Evolutionary Biology. Wiley.
https://doi.org/10.1111/jeb.14005
chicago: Westram, Anja M, Sean Stankowski, Parvathy Surendranadh, and Nicholas H
Barton. “What Is Reproductive Isolation?” Journal of Evolutionary Biology.
Wiley, 2022. https://doi.org/10.1111/jeb.14005.
ieee: A. M. Westram, S. Stankowski, P. Surendranadh, and N. H. Barton, “What is
reproductive isolation?,” Journal of Evolutionary Biology, vol. 35, no.
9. Wiley, pp. 1143–1164, 2022.
ista: Westram AM, Stankowski S, Surendranadh P, Barton NH. 2022. What is reproductive
isolation? Journal of Evolutionary Biology. 35(9), 1143–1164.
mla: Westram, Anja M., et al. “What Is Reproductive Isolation?” Journal of Evolutionary
Biology, vol. 35, no. 9, Wiley, 2022, pp. 1143–64, doi:10.1111/jeb.14005.
short: A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary
Biology 35 (2022) 1143–1164.
date_created: 2023-01-16T09:59:24Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2023-08-04T09:53:40Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/jeb.14005
external_id:
isi:
- '000849851100002'
pmid:
- '36063156'
file:
- access_level: open_access
checksum: f08de57112330a7ee88d2e1b20576a1e
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T10:05:31Z
date_updated: 2023-01-30T10:05:31Z
file_id: '12448'
file_name: 2022_JourEvoBiology_Westram.pdf
file_size: 3146793
relation: main_file
success: 1
file_date_updated: 2023-01-30T10:05:31Z
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '9'
keyword:
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1143-1164
pmid: 1
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: The maintenance of alternative adaptive peaks in snapdragons
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '12265'
relation: other
status: public
scopus_import: '1'
status: public
title: What is reproductive isolation?
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 35
year: '2022'
...
---
_id: '12265'
acknowledgement: We are very grateful to the authors of the commentaries for the interesting
discussion and to Luke Holman for handling this set of manuscripts. Part of this
work was funded by the Austrian Science Fund FWF (grant P 32166).
article_processing_charge: Yes (via OA deal)
article_type: letter_note
author:
- 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: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Parvathy
full_name: Surendranadh, Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Westram AM, Stankowski S, Surendranadh P, Barton NH. Reproductive isolation,
speciation, and the value of disagreement: A reply to the commentaries on ‘What
is reproductive isolation?’ Journal of Evolutionary Biology. 2022;35(9):1200-1205.
doi:10.1111/jeb.14082'
apa: 'Westram, A. M., Stankowski, S., Surendranadh, P., & Barton, N. H. (2022).
Reproductive isolation, speciation, and the value of disagreement: A reply to
the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary
Biology. Wiley. https://doi.org/10.1111/jeb.14082'
chicago: 'Westram, Anja M, Sean Stankowski, Parvathy Surendranadh, and Nicholas
H Barton. “Reproductive Isolation, Speciation, and the Value of Disagreement:
A Reply to the Commentaries on ‘What Is Reproductive Isolation?’” Journal of
Evolutionary Biology. Wiley, 2022. https://doi.org/10.1111/jeb.14082.'
ieee: 'A. M. Westram, S. Stankowski, P. Surendranadh, and N. H. Barton, “Reproductive
isolation, speciation, and the value of disagreement: A reply to the commentaries
on ‘What is reproductive isolation?,’” Journal of Evolutionary Biology,
vol. 35, no. 9. Wiley, pp. 1200–1205, 2022.'
ista: 'Westram AM, Stankowski S, Surendranadh P, Barton NH. 2022. Reproductive isolation,
speciation, and the value of disagreement: A reply to the commentaries on ‘What
is reproductive isolation?’ Journal of Evolutionary Biology. 35(9), 1200–1205.'
mla: 'Westram, Anja M., et al. “Reproductive Isolation, Speciation, and the Value
of Disagreement: A Reply to the Commentaries on ‘What Is Reproductive Isolation?’”
Journal of Evolutionary Biology, vol. 35, no. 9, Wiley, 2022, pp. 1200–05,
doi:10.1111/jeb.14082.'
short: A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary
Biology 35 (2022) 1200–1205.
date_created: 2023-01-16T09:59:37Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2023-08-04T09:53:41Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/jeb.14082
external_id:
isi:
- '000849851100009'
file:
- access_level: open_access
checksum: 27268009e5eec030bc10667a4ac5ed4c
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T10:14:09Z
date_updated: 2023-01-30T10:14:09Z
file_id: '12449'
file_name: 2022_JourEvoBiology_Westram_Response.pdf
file_size: 349603
relation: main_file
success: 1
file_date_updated: 2023-01-30T10:14:09Z
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '9'
keyword:
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1200-1205
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: The maintenance of alternative adaptive peaks in snapdragons
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '12264'
relation: other
status: public
scopus_import: '1'
status: public
title: 'Reproductive isolation, speciation, and the value of disagreement: A reply
to the commentaries on ‘What is reproductive isolation?’'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 35
year: '2022'
...
---
_id: '12268'
abstract:
- lang: eng
text: The complexity of the microenvironment effects on cell response, show accumulating
evidence that glioblastoma (GBM) migration and invasiveness are influenced by
the mechanical rigidity of their surroundings. The epithelial–mesenchymal transition
(EMT) is a well-recognized driving force of the invasive behavior of cancer. However,
the primary mechanisms of EMT initiation and progression remain unclear. We have
previously showed that certain substrate stiffness can selectively stimulate human
GBM U251-MG and GL15 glioblastoma cell lines motility. The present study unifies
several known EMT mediators to uncover the reason of the regulation and response
to these stiffnesses. Our results revealed that changing the rigidity of the mechanical
environment tuned the response of both cell lines through change in morphological
features, epithelial-mesenchymal markers (E-, N-Cadherin), EGFR and ROS expressions
in an interrelated manner. Specifically, a stiffer microenvironment induced a
mesenchymal cell shape, a more fragmented morphology, higher intracellular cytosolic
ROS expression and lower mitochondrial ROS. Finally, we observed that cells more
motile showed a more depolarized mitochondrial membrane potential. Unravelling
the process that regulates GBM cells’ infiltrative behavior could provide new
opportunities for identification of new targets and less invasive approaches for
treatment.
acknowledgement: "The research leading to these results has received funding from
AIRC under IG 2021 - ID. 26328 project – P.I. Cortese Barbara and AIRC under MFAG
2015 - ID. 16803 project – “P.I. Cortese Barbara”. The authors are also grateful
to the ”Tecnopolo per la medicina di precisione” (TecnoMed Puglia) - Regione Puglia:
DGR n.2117 del 21/11/2018, CUP: B84I18000540002 and “Tecnopolo di Nanotecnologia
e Fotonica per la medicina di precisione” (TECNOMED) - FISR/MIUR-CNR: delibera CIPE
n.3449 del 7-08-2017, CUP: B83B17000010001.\r\nWe thank Dr. Francesca Pagani for
useful technical support. We thank also Irene Iacuitto, Giovanna Loffredo and Manuela
Marchetti for practical administrative support."
article_number: '983507'
article_processing_charge: No
article_type: original
author:
- first_name: Bernadette
full_name: Basilico, Bernadette
id: 36035796-5ACA-11E9-A75E-7AF2E5697425
last_name: Basilico
orcid: 0000-0003-1843-3173
- first_name: Ilaria Elena
full_name: Palamà, Ilaria Elena
last_name: Palamà
- first_name: Stefania
full_name: D’Amone, Stefania
last_name: D’Amone
- first_name: Clotilde
full_name: Lauro, Clotilde
last_name: Lauro
- first_name: Maria
full_name: Rosito, Maria
last_name: Rosito
- first_name: Maddalena
full_name: Grieco, Maddalena
last_name: Grieco
- first_name: Patrizia
full_name: Ratano, Patrizia
last_name: Ratano
- first_name: Federica
full_name: Cordella, Federica
last_name: Cordella
- first_name: Caterina
full_name: Sanchini, Caterina
last_name: Sanchini
- first_name: Silvia
full_name: Di Angelantonio, Silvia
last_name: Di Angelantonio
- first_name: Davide
full_name: Ragozzino, Davide
last_name: Ragozzino
- first_name: Mariafrancesca
full_name: Cascione, Mariafrancesca
last_name: Cascione
- first_name: Giuseppe
full_name: Gigli, Giuseppe
last_name: Gigli
- first_name: Barbara
full_name: Cortese, Barbara
last_name: Cortese
citation:
ama: Basilico B, Palamà IE, D’Amone S, et al. Substrate stiffness effect on molecular
crosstalk of epithelial-mesenchymal transition mediators of human glioblastoma
cells. Frontiers in Oncology. 2022;12. doi:10.3389/fonc.2022.983507
apa: Basilico, B., Palamà, I. E., D’Amone, S., Lauro, C., Rosito, M., Grieco, M.,
… Cortese, B. (2022). Substrate stiffness effect on molecular crosstalk of epithelial-mesenchymal
transition mediators of human glioblastoma cells. Frontiers in Oncology.
Frontiers Media. https://doi.org/10.3389/fonc.2022.983507
chicago: Basilico, Bernadette, Ilaria Elena Palamà, Stefania D’Amone, Clotilde Lauro,
Maria Rosito, Maddalena Grieco, Patrizia Ratano, et al. “Substrate Stiffness Effect
on Molecular Crosstalk of Epithelial-Mesenchymal Transition Mediators of Human
Glioblastoma Cells.” Frontiers in Oncology. Frontiers Media, 2022. https://doi.org/10.3389/fonc.2022.983507.
ieee: B. Basilico et al., “Substrate stiffness effect on molecular crosstalk
of epithelial-mesenchymal transition mediators of human glioblastoma cells,” Frontiers
in Oncology, vol. 12. Frontiers Media, 2022.
ista: Basilico B, Palamà IE, D’Amone S, Lauro C, Rosito M, Grieco M, Ratano P, Cordella
F, Sanchini C, Di Angelantonio S, Ragozzino D, Cascione M, Gigli G, Cortese B.
2022. Substrate stiffness effect on molecular crosstalk of epithelial-mesenchymal
transition mediators of human glioblastoma cells. Frontiers in Oncology. 12, 983507.
mla: Basilico, Bernadette, et al. “Substrate Stiffness Effect on Molecular Crosstalk
of Epithelial-Mesenchymal Transition Mediators of Human Glioblastoma Cells.” Frontiers
in Oncology, vol. 12, 983507, Frontiers Media, 2022, doi:10.3389/fonc.2022.983507.
short: B. Basilico, I.E. Palamà, S. D’Amone, C. Lauro, M. Rosito, M. Grieco, P.
Ratano, F. Cordella, C. Sanchini, S. Di Angelantonio, D. Ragozzino, M. Cascione,
G. Gigli, B. Cortese, Frontiers in Oncology 12 (2022).
date_created: 2023-01-16T10:00:28Z
date_published: 2022-08-25T00:00:00Z
date_updated: 2023-08-04T09:54:16Z
day: '25'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.3389/fonc.2022.983507
external_id:
isi:
- '000856524900001'
pmid:
- '36091138'
file:
- access_level: open_access
checksum: efc7edf9f626af31853790c5b598a68c
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T10:25:21Z
date_updated: 2023-01-30T10:25:21Z
file_id: '12450'
file_name: 2022_FrontiersOntology_Basilico.pdf
file_size: 13588502
relation: main_file
success: 1
file_date_updated: 2023-01-30T10:25:21Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
keyword:
- Cancer Research
- Oncology
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Oncology
publication_identifier:
issn:
- 2234-943X
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
scopus_import: '1'
status: public
title: Substrate stiffness effect on molecular crosstalk of epithelial-mesenchymal
transition mediators of human glioblastoma cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2022'
...
---
_id: '12269'
abstract:
- lang: eng
text: We study the thermalization of a small XX chain coupled to long, gapped XXZ
leads at either side by observing the relaxation dynamics of the whole system.
Using extensive tensor network simulations, we show that such systems, although
not integrable, appear to show either extremely slow thermalization or even lack
thereof since the two cannot be distinguished within the accuracy of our numerics.
We show that the persistent oscillations observed in the spin current in the middle
of the XX chain are related to eigenstates of the entire system located within
the gap of the boundary chains. We find from exact diagonalization that some of
these states remain strictly localized within the XX chain and do not hybridize
with the rest of the system. The frequencies of the persistent oscillations determined
by numerical simulations of dynamics match the energy differences between these
states exactly. This has important implications for open systems, where the strongly
interacting leads are often assumed to thermalize the central system. Our results
suggest that, if we employ gapped systems for the leads, this assumption does
not hold.
acknowledgement: "M.L. and T.P. acknowledge support from the European Research Council
(ERC) through the advanced grant 694544 – OMNES and the grant P1-0402 of Slovenian
Research Agency (ARRS). M.L. acknowledges support from the European Research Council
(ERC) through the starting grant 850899 – NEQuM. D.R. acknowledges support from
the Ministry of Electronics & Information Technology (MeitY), India under the grant
for “Centre for Excellence in Quantum\r\nTechnologies” with Ref. No. 4(7)/2020-ITEA. "
article_number: '054314'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Marko
full_name: Ljubotina, Marko
id: F75EE9BE-5C90-11EA-905D-16643DDC885E
last_name: Ljubotina
- first_name: Dibyendu
full_name: Roy, Dibyendu
last_name: Roy
- first_name: Tomaž
full_name: Prosen, Tomaž
last_name: Prosen
citation:
ama: Ljubotina M, Roy D, Prosen T. Absence of thermalization of free systems coupled
to gapped interacting reservoirs. Physical Review B. 2022;106(5). doi:10.1103/physrevb.106.054314
apa: Ljubotina, M., Roy, D., & Prosen, T. (2022). Absence of thermalization
of free systems coupled to gapped interacting reservoirs. Physical Review B.
American Physical Society. https://doi.org/10.1103/physrevb.106.054314
chicago: Ljubotina, Marko, Dibyendu Roy, and Tomaž Prosen. “Absence of Thermalization
of Free Systems Coupled to Gapped Interacting Reservoirs.” Physical Review
B. American Physical Society, 2022. https://doi.org/10.1103/physrevb.106.054314.
ieee: M. Ljubotina, D. Roy, and T. Prosen, “Absence of thermalization of free systems
coupled to gapped interacting reservoirs,” Physical Review B, vol. 106,
no. 5. American Physical Society, 2022.
ista: Ljubotina M, Roy D, Prosen T. 2022. Absence of thermalization of free systems
coupled to gapped interacting reservoirs. Physical Review B. 106(5), 054314.
mla: Ljubotina, Marko, et al. “Absence of Thermalization of Free Systems Coupled
to Gapped Interacting Reservoirs.” Physical Review B, vol. 106, no. 5,
054314, American Physical Society, 2022, doi:10.1103/physrevb.106.054314.
short: M. Ljubotina, D. Roy, T. Prosen, Physical Review B 106 (2022).
date_created: 2023-01-16T10:00:39Z
date_published: 2022-08-31T00:00:00Z
date_updated: 2023-08-04T10:07:33Z
day: '31'
department:
- _id: MaSe
doi: 10.1103/physrevb.106.054314
ec_funded: 1
external_id:
arxiv:
- '2106.08373'
isi:
- '000861332900005'
intvolume: ' 106'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2106.08373
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review 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: Absence of thermalization of free systems coupled to gapped interacting reservoirs
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 106
year: '2022'
...
---
_id: '12272'
abstract:
- lang: eng
text: Reading, interpreting and crawling along gradients of chemotactic cues is
one of the most complex questions in cell biology. In this issue, Georgantzoglou
et al. (2022. J. Cell. Biol.https://doi.org/10.1083/jcb.202103207) use in vivo
models to map the temporal sequence of how neutrophils respond to an acutely arising
gradient of chemoattractant.
article_number: e202206127
article_processing_charge: No
article_type: original
author:
- first_name: Julian A
full_name: Stopp, Julian A
id: 489E3F00-F248-11E8-B48F-1D18A9856A87
last_name: Stopp
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: 'Stopp JA, Sixt MK. Plan your trip before you leave: The neutrophils’ search-and-run
journey. Journal of Cell Biology. 2022;221(8). doi:10.1083/jcb.202206127'
apa: 'Stopp, J. A., & Sixt, M. K. (2022). Plan your trip before you leave: The
neutrophils’ search-and-run journey. Journal of Cell Biology. Rockefeller
University Press. https://doi.org/10.1083/jcb.202206127'
chicago: 'Stopp, Julian A, and Michael K Sixt. “Plan Your Trip before You Leave:
The Neutrophils’ Search-and-Run Journey.” Journal of Cell Biology. Rockefeller
University Press, 2022. https://doi.org/10.1083/jcb.202206127.'
ieee: 'J. A. Stopp and M. K. Sixt, “Plan your trip before you leave: The neutrophils’
search-and-run journey,” Journal of Cell Biology, vol. 221, no. 8. Rockefeller
University Press, 2022.'
ista: 'Stopp JA, Sixt MK. 2022. Plan your trip before you leave: The neutrophils’
search-and-run journey. Journal of Cell Biology. 221(8), e202206127.'
mla: 'Stopp, Julian A., and Michael K. Sixt. “Plan Your Trip before You Leave: The
Neutrophils’ Search-and-Run Journey.” Journal of Cell Biology, vol. 221,
no. 8, e202206127, Rockefeller University Press, 2022, doi:10.1083/jcb.202206127.'
short: J.A. Stopp, M.K. Sixt, Journal of Cell Biology 221 (2022).
date_created: 2023-01-16T10:01:08Z
date_published: 2022-07-20T00:00:00Z
date_updated: 2023-12-21T14:30:01Z
day: '20'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1083/jcb.202206127
external_id:
isi:
- '000874717200001'
pmid:
- '35856919'
file:
- access_level: open_access
checksum: 6b1620743669679b48b9389bb40f5a11
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T10:39:34Z
date_updated: 2023-01-30T10:39:34Z
file_id: '12451'
file_name: 2022_JourCellBiology_Stopp.pdf
file_size: 969969
relation: main_file
success: 1
file_date_updated: 2023-01-30T10:39:34Z
has_accepted_license: '1'
intvolume: ' 221'
isi: 1
issue: '8'
keyword:
- Cell Biology
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Cell Biology
publication_identifier:
eissn:
- 1540-8140
issn:
- 0021-9525
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
related_material:
record:
- id: '14697'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Plan your trip before you leave: The neutrophils’ search-and-run journey'
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 221
year: '2022'
...
---
_id: '12273'
abstract:
- lang: eng
text: We study communication in the presence of a jamming adversary where quadratic
power constraints are imposed on the transmitter and the jammer. The jamming signal
is allowed to be a function of the codebook, and a noncausal but noisy observation
of the transmitted codeword. For a certain range of the noise-to-signal ratios
(NSRs) of the transmitter and the jammer, we are able to characterize the capacity
of this channel under deterministic encoding or stochastic encoding, i.e., with
no common randomness between the encoder/decoder pair. For the remaining NSR regimes,
we determine the capacity under the assumption of a small amount of common randomness
(at most 2log(n) bits in one sub-regime, and at most Ω(n) bits in the other sub-regime)
available to the encoder-decoder pair. Our proof techniques involve a novel myopic
list-decoding result for achievability, and a Plotkin-type push attack for the
converse in a subregion of the NSRs, both of which may be of independent interest.
We also give bounds on the strong secrecy capacity of this channel assuming that
the jammer is simultaneously eavesdropping.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Yihan
full_name: Zhang, Yihan
id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c
last_name: Zhang
- first_name: Shashank
full_name: Vatedka, Shashank
last_name: Vatedka
- first_name: Sidharth
full_name: Jaggi, Sidharth
last_name: Jaggi
- first_name: Anand D.
full_name: Sarwate, Anand D.
last_name: Sarwate
citation:
ama: Zhang Y, Vatedka S, Jaggi S, Sarwate AD. Quadratically constrained myopic adversarial
channels. IEEE Transactions on Information Theory. 2022;68(8):4901-4948.
doi:10.1109/tit.2022.3167554
apa: Zhang, Y., Vatedka, S., Jaggi, S., & Sarwate, A. D. (2022). Quadratically
constrained myopic adversarial channels. IEEE Transactions on Information Theory.
Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/tit.2022.3167554
chicago: Zhang, Yihan, Shashank Vatedka, Sidharth Jaggi, and Anand D. Sarwate. “Quadratically
Constrained Myopic Adversarial Channels.” IEEE Transactions on Information
Theory. Institute of Electrical and Electronics Engineers, 2022. https://doi.org/10.1109/tit.2022.3167554.
ieee: Y. Zhang, S. Vatedka, S. Jaggi, and A. D. Sarwate, “Quadratically constrained
myopic adversarial channels,” IEEE Transactions on Information Theory,
vol. 68, no. 8. Institute of Electrical and Electronics Engineers, pp. 4901–4948,
2022.
ista: Zhang Y, Vatedka S, Jaggi S, Sarwate AD. 2022. Quadratically constrained myopic
adversarial channels. IEEE Transactions on Information Theory. 68(8), 4901–4948.
mla: Zhang, Yihan, et al. “Quadratically Constrained Myopic Adversarial Channels.”
IEEE Transactions on Information Theory, vol. 68, no. 8, Institute of Electrical
and Electronics Engineers, 2022, pp. 4901–48, doi:10.1109/tit.2022.3167554.
short: Y. Zhang, S. Vatedka, S. Jaggi, A.D. Sarwate, IEEE Transactions on Information
Theory 68 (2022) 4901–4948.
date_created: 2023-01-16T10:01:19Z
date_published: 2022-08-01T00:00:00Z
date_updated: 2023-08-04T10:08:49Z
day: '01'
department:
- _id: MaMo
doi: 10.1109/tit.2022.3167554
external_id:
arxiv:
- '1801.05951'
isi:
- '000838527100004'
intvolume: ' 68'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1801.05951
month: '08'
oa: 1
oa_version: Preprint
page: 4901-4948
publication: IEEE Transactions on Information Theory
publication_identifier:
eissn:
- 1557-9654
issn:
- 0018-9448
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quadratically constrained myopic adversarial channels
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 68
year: '2022'
...
---
_id: '12274'
abstract:
- lang: eng
text: The morphology and functionality of the epithelial lining differ along the
intestinal tract, but tissue renewal at all sites is driven by stem cells at the
base of crypts1,2,3. Whether stem cell numbers and behaviour vary at different
sites is unknown. Here we show using intravital microscopy that, despite similarities
in the number and distribution of proliferative cells with an Lgr5 signature in
mice, small intestinal crypts contain twice as many effective stem cells as large
intestinal crypts. We find that, although passively displaced by a conveyor-belt-like
upward movement, small intestinal cells positioned away from the crypt base can
function as long-term effective stem cells owing to Wnt-dependent retrograde cellular
movement. By contrast, the near absence of retrograde movement in the large intestine
restricts cell repositioning, leading to a reduction in effective stem cell number.
Moreover, after suppression of the retrograde movement in the small intestine,
the number of effective stem cells is reduced, and the rate of monoclonal conversion
of crypts is accelerated. Together, these results show that the number of effective
stem cells is determined by active retrograde movement, revealing a new channel
of stem cell regulation that can be experimentally and pharmacologically manipulated.
acknowledgement: We thank the members of the van Rheenen laboratory for reading the
manuscript, and the members of the bioimaging, FACS and animal facility of the NKI
for experimental support. We acknowledge the staff at the MedH Flow Cytometry core
facility, Karolinska Institutet, and LCI facility/Nikon Center of Excellence, Karolinska
Institutet. This work was financially supported by the Netherlands Organization
of Scientific Research NWO (Veni grant 863.15.011 to S.I.J.E. and Vici grant 09150182110004
to J.v.R.) and the CancerGenomics.nl (Netherlands Organisation for Scientific Research)
program (to J.v.R.) the Doctor Josef Steiner Foundation (to J.v.R). B.D.S. acknowledges
funding from the Royal Society E.P. Abraham Research Professorship (RP\R1\180165)
and the Wellcome Trust (098357/Z/12/Z and 219478/Z/19/Z). B.C.-M. acknowledges the
support of the field of excellence ‘Complexity of life in basic research and innovation’
of the University of Graz. O.J.S. and their laboratory acknowledge CRUK core funding
to the CRUK Beatson Institute (A17196 and A31287) and CRUK core funding to the Sansom
laboratory (A21139). P.K. and their laboratory are supported by grants from the
Swedish Research Council (2018-03078), Cancerfonden (190634), Academy of Finland
Centre of Excellence (266869, 304591 and 320185) and the Jane and Aatos Erkko Foundation.
P.L. has received funding from the European Research Council (ERC) under the European
Union’s Horizon 2020 research and innovation programme (grant agreement no. 758617).
E.H. acknowledges funding from the European Research Council (ERC) under the European
Union’s Horizon 2020 research and innovation programme (grant agreement no. 851288).
article_processing_charge: No
article_type: original
author:
- first_name: Maria
full_name: Azkanaz, Maria
last_name: Azkanaz
- first_name: Bernat
full_name: Corominas-Murtra, Bernat
id: 43BE2298-F248-11E8-B48F-1D18A9856A87
last_name: Corominas-Murtra
orcid: 0000-0001-9806-5643
- first_name: Saskia I. J.
full_name: Ellenbroek, Saskia I. J.
last_name: Ellenbroek
- first_name: Lotte
full_name: Bruens, Lotte
last_name: Bruens
- first_name: Anna T.
full_name: Webb, Anna T.
last_name: Webb
- first_name: Dimitrios
full_name: Laskaris, Dimitrios
last_name: Laskaris
- first_name: Koen C.
full_name: Oost, Koen C.
last_name: Oost
- first_name: Simona J. A.
full_name: Lafirenze, Simona J. A.
last_name: Lafirenze
- first_name: Karl
full_name: Annusver, Karl
last_name: Annusver
- first_name: Hendrik A.
full_name: Messal, Hendrik A.
last_name: Messal
- first_name: Sharif
full_name: Iqbal, Sharif
last_name: Iqbal
- first_name: Dustin J.
full_name: Flanagan, Dustin J.
last_name: Flanagan
- first_name: David J.
full_name: Huels, David J.
last_name: Huels
- first_name: Felipe
full_name: Rojas-Rodríguez, Felipe
last_name: Rojas-Rodríguez
- first_name: Miguel
full_name: Vizoso, Miguel
last_name: Vizoso
- first_name: Maria
full_name: Kasper, Maria
last_name: Kasper
- first_name: Owen J.
full_name: Sansom, Owen J.
last_name: Sansom
- first_name: Hugo J.
full_name: Snippert, Hugo J.
last_name: Snippert
- first_name: Prisca
full_name: Liberali, Prisca
last_name: Liberali
- first_name: Benjamin D.
full_name: Simons, Benjamin D.
last_name: Simons
- first_name: Pekka
full_name: Katajisto, Pekka
last_name: Katajisto
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Jacco
full_name: van Rheenen, Jacco
last_name: van Rheenen
citation:
ama: Azkanaz M, Corominas-Murtra B, Ellenbroek SIJ, et al. Retrograde movements
determine effective stem cell numbers in the intestine. Nature. 2022;607(7919):548-554.
doi:10.1038/s41586-022-04962-0
apa: Azkanaz, M., Corominas-Murtra, B., Ellenbroek, S. I. J., Bruens, L., Webb,
A. T., Laskaris, D., … van Rheenen, J. (2022). Retrograde movements determine
effective stem cell numbers in the intestine. Nature. Springer Nature.
https://doi.org/10.1038/s41586-022-04962-0
chicago: Azkanaz, Maria, Bernat Corominas-Murtra, Saskia I. J. Ellenbroek, Lotte
Bruens, Anna T. Webb, Dimitrios Laskaris, Koen C. Oost, et al. “Retrograde Movements
Determine Effective Stem Cell Numbers in the Intestine.” Nature. Springer
Nature, 2022. https://doi.org/10.1038/s41586-022-04962-0.
ieee: M. Azkanaz et al., “Retrograde movements determine effective stem cell
numbers in the intestine,” Nature, vol. 607, no. 7919. Springer Nature,
pp. 548–554, 2022.
ista: Azkanaz M, Corominas-Murtra B, Ellenbroek SIJ, Bruens L, Webb AT, Laskaris
D, Oost KC, Lafirenze SJA, Annusver K, Messal HA, Iqbal S, Flanagan DJ, Huels
DJ, Rojas-Rodríguez F, Vizoso M, Kasper M, Sansom OJ, Snippert HJ, Liberali P,
Simons BD, Katajisto P, Hannezo EB, van Rheenen J. 2022. Retrograde movements
determine effective stem cell numbers in the intestine. Nature. 607(7919), 548–554.
mla: Azkanaz, Maria, et al. “Retrograde Movements Determine Effective Stem Cell
Numbers in the Intestine.” Nature, vol. 607, no. 7919, Springer Nature,
2022, pp. 548–54, doi:10.1038/s41586-022-04962-0.
short: M. Azkanaz, B. Corominas-Murtra, S.I.J. Ellenbroek, L. Bruens, A.T. Webb,
D. Laskaris, K.C. Oost, S.J.A. Lafirenze, K. Annusver, H.A. Messal, S. Iqbal,
D.J. Flanagan, D.J. Huels, F. Rojas-Rodríguez, M. Vizoso, M. Kasper, O.J. Sansom,
H.J. Snippert, P. Liberali, B.D. Simons, P. Katajisto, E.B. Hannezo, J. van Rheenen,
Nature 607 (2022) 548–554.
date_created: 2023-01-16T10:01:29Z
date_published: 2022-07-13T00:00:00Z
date_updated: 2023-10-03T11:16:30Z
day: '13'
department:
- _id: EdHa
doi: 10.1038/s41586-022-04962-0
ec_funded: 1
external_id:
isi:
- '000824430000004'
pmid:
- '35831497'
intvolume: ' 607'
isi: 1
issue: '7919'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://helda.helsinki.fi/items/94433455-4854-45c0-9de8-7326caea8780
month: '07'
oa: 1
oa_version: Submitted Version
page: 548-554
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/JaccovanRheenenLab/Retrograde_movement_Azkanaz_Nature_2022
scopus_import: '1'
status: public
title: Retrograde movements determine effective stem cell numbers in the intestine
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 607
year: '2022'
...
---
_id: '12275'
abstract:
- lang: eng
text: N-glycans are molecularly diverse sugars borne by over 70% of proteins transiting
the secretory pathway and have been implicated in protein folding, stability,
and localization. Mutations in genes important for N-glycosylation result in congenital
disorders of glycosylation that are often associated with intellectual disability.
Here, we show that structurally distinct N-glycans regulate an extracellular protein
complex involved in the patterning of somatosensory dendrites in Caenorhabditis
elegans. Specifically, aman-2/Golgi alpha-mannosidase II, a conserved key enzyme
in the biosynthesis of specific N-glycans, regulates the activity of the Menorin
adhesion complex without obviously affecting the protein stability and localization
of its components. AMAN-2 functions cell-autonomously to allow for decoration
of the neuronal transmembrane receptor DMA-1/LRR-TM with the correct set of high-mannose/hybrid/paucimannose
N-glycans. Moreover, distinct types of N-glycans on specific N-glycosylation sites
regulate DMA-1/LRR-TM receptor function, which, together with three other extracellular
proteins, forms the Menorin adhesion complex. In summary, specific N-glycan structures
regulate dendrite patterning by coordinating the activity of an extracellular
adhesion complex, suggesting that the molecular diversity of N-glycans can contribute
to developmental specificity in the nervous system.
acknowledgement: 'We thank Scott Garforth, Sarah Garrett, Peri Kurshan, Yehuda Salzberg,
PamelaStanley, Robert Townley, and members of the B€ulow laboratory for commentson
the manuscript or helpful discussions during the course of this work. Wethank David
Miller, Shohei Mitani, Kang Shen, and Iain Wilson for reagents,and Yuji Kohara for
theyk11g705cDNA clone. We are grateful to MeeraTrivedi for sharing thedzIs117strain
prior to publication. Some strains wereprovided by the Caenorhabditis Genome Center
(funded by the NIH Office ofResearch Infrastructure Programs P40OD010440). This
work was supportedby grants from the National Institute of Health (NIH): R01NS096672andR21NS111145to
HEB; F31NS100370to MR; T32GM007288and F31HD066967to CADB; P30HD071593to Albert Einstein
College of Medicine. We acknowl-edge support to MR by the Department of Neuroscience.
NJRS was the recipi-ent of a Colciencias-Fulbright Fellowship and HEB of an Irma
T. Hirschl/Monique Weill-Caulier research fellowship'
article_number: e54163
article_processing_charge: No
article_type: original
author:
- first_name: Maisha
full_name: Rahman, Maisha
last_name: Rahman
- first_name: Nelson
full_name: Ramirez, Nelson
id: 39831956-E4FE-11E9-85DE-0DC7E5697425
last_name: Ramirez
- first_name: Carlos A
full_name: Diaz‐Balzac, Carlos A
last_name: Diaz‐Balzac
- first_name: Hannes E
full_name: Bülow, Hannes E
last_name: Bülow
citation:
ama: Rahman M, Ramirez N, Diaz‐Balzac CA, Bülow HE. Specific N-glycans regulate
an extracellular adhesion complex during somatosensory dendrite patterning. EMBO
Reports. 2022;23(7). doi:10.15252/embr.202154163
apa: Rahman, M., Ramirez, N., Diaz‐Balzac, C. A., & Bülow, H. E. (2022). Specific
N-glycans regulate an extracellular adhesion complex during somatosensory dendrite
patterning. EMBO Reports. Embo Press. https://doi.org/10.15252/embr.202154163
chicago: Rahman, Maisha, Nelson Ramirez, Carlos A Diaz‐Balzac, and Hannes E Bülow.
“Specific N-Glycans Regulate an Extracellular Adhesion Complex during Somatosensory
Dendrite Patterning.” EMBO Reports. Embo Press, 2022. https://doi.org/10.15252/embr.202154163.
ieee: M. Rahman, N. Ramirez, C. A. Diaz‐Balzac, and H. E. Bülow, “Specific N-glycans
regulate an extracellular adhesion complex during somatosensory dendrite patterning,”
EMBO Reports, vol. 23, no. 7. Embo Press, 2022.
ista: Rahman M, Ramirez N, Diaz‐Balzac CA, Bülow HE. 2022. Specific N-glycans regulate
an extracellular adhesion complex during somatosensory dendrite patterning. EMBO
Reports. 23(7), e54163.
mla: Rahman, Maisha, et al. “Specific N-Glycans Regulate an Extracellular Adhesion
Complex during Somatosensory Dendrite Patterning.” EMBO Reports, vol. 23,
no. 7, e54163, Embo Press, 2022, doi:10.15252/embr.202154163.
short: M. Rahman, N. Ramirez, C.A. Diaz‐Balzac, H.E. Bülow, EMBO Reports 23 (2022).
date_created: 2023-01-16T10:01:44Z
date_published: 2022-07-05T00:00:00Z
date_updated: 2023-10-03T11:25:54Z
day: '05'
department:
- _id: MaDe
doi: 10.15252/embr.202154163
external_id:
isi:
- '000797302700001'
pmid:
- '35586945'
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
issue: '7'
keyword:
- Genetics
- Molecular Biology
- Biochemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.15252/embr.202154163
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: EMBO Reports
publication_identifier:
eissn:
- 1469-3178
issn:
- 1469-221X
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Specific N-glycans regulate an extracellular adhesion complex during somatosensory
dendrite patterning
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2022'
...
---
_id: '12276'
abstract:
- lang: eng
text: Ongoing development of quantum simulators allows for a progressively finer
degree of control of quantum many-body systems. This motivates the development
of efficient approaches to facilitate the control of such systems and enable the
preparation of nontrivial quantum states. Here we formulate an approach to control
quantum systems based on matrix product states (MPSs). We compare counterdiabatic
and leakage minimization approaches to the so-called local steering problem that
consists in finding the best value of the control parameters for generating a
unitary evolution of the specific MPS in a given direction. In order to benchmark
the different approaches, we apply them to the generalization of the PXP model
known to exhibit coherent quantum dynamics due to quantum many-body scars. We
find that the leakage-based approach generally outperforms the counterdiabatic
framework and use it to construct a Floquet model with quantum scars. We perform
the first steps towards global trajectory optimization and demonstrate entanglement
steering capabilities in the generalized PXP model. Finally, we apply our leakage
minimization approach to construct quantum scars in the periodically driven nonintegrable
Ising model.
acknowledgement: We thank A. A. Michailidis for insightful discussions. M.L. and M.S.
acknowledge support from the European Research Council (ERC) under the European
Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 850899).
D.A. is supported by the European Research Council (ERC) under the European Union’s
Horizon 2020 research and innovation programme (Grant Agreement No. 864597) and
by the Swiss National Science Foundation. The infinite TEBD simulations were performed
using the ITensor library [67].
article_number: '030343'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Marko
full_name: Ljubotina, Marko
id: F75EE9BE-5C90-11EA-905D-16643DDC885E
last_name: Ljubotina
- first_name: Barbara
full_name: Roos, Barbara
id: 5DA90512-D80F-11E9-8994-2E2EE6697425
last_name: Roos
orcid: 0000-0002-9071-5880
- first_name: Dmitry A.
full_name: Abanin, Dmitry A.
last_name: Abanin
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Ljubotina M, Roos B, Abanin DA, Serbyn M. Optimal steering of matrix product
states and quantum many-body scars. PRX Quantum. 2022;3(3). doi:10.1103/prxquantum.3.030343
apa: Ljubotina, M., Roos, B., Abanin, D. A., & Serbyn, M. (2022). Optimal steering
of matrix product states and quantum many-body scars. PRX Quantum. American
Physical Society. https://doi.org/10.1103/prxquantum.3.030343
chicago: Ljubotina, Marko, Barbara Roos, Dmitry A. Abanin, and Maksym Serbyn. “Optimal
Steering of Matrix Product States and Quantum Many-Body Scars.” PRX Quantum.
American Physical Society, 2022. https://doi.org/10.1103/prxquantum.3.030343.
ieee: M. Ljubotina, B. Roos, D. A. Abanin, and M. Serbyn, “Optimal steering of matrix
product states and quantum many-body scars,” PRX Quantum, vol. 3, no. 3.
American Physical Society, 2022.
ista: Ljubotina M, Roos B, Abanin DA, Serbyn M. 2022. Optimal steering of matrix
product states and quantum many-body scars. PRX Quantum. 3(3), 030343.
mla: Ljubotina, Marko, et al. “Optimal Steering of Matrix Product States and Quantum
Many-Body Scars.” PRX Quantum, vol. 3, no. 3, 030343, American Physical
Society, 2022, doi:10.1103/prxquantum.3.030343.
short: M. Ljubotina, B. Roos, D.A. Abanin, M. Serbyn, PRX Quantum 3 (2022).
date_created: 2023-01-16T10:01:56Z
date_published: 2022-09-23T00:00:00Z
date_updated: 2023-01-30T11:05:23Z
day: '23'
ddc:
- '530'
department:
- _id: MaSe
- _id: RoSe
doi: 10.1103/prxquantum.3.030343
ec_funded: 1
external_id:
arxiv:
- '2204.02899'
file:
- access_level: open_access
checksum: ef8f0a1b5a019b3958009162de0fa4c3
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T11:02:50Z
date_updated: 2023-01-30T11:02:50Z
file_id: '12457'
file_name: 2022_PRXQuantum_Ljubotina.pdf
file_size: 7661905
relation: main_file
success: 1
file_date_updated: 2023-01-30T11:02:50Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '3'
keyword:
- General Medicine
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: PRX Quantum
publication_identifier:
eissn:
- 2691-3399
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimal steering of matrix product states and quantum many-body scars
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: 3
year: '2022'
...
---
_id: '12277'
abstract:
- lang: eng
text: Cell migration in confining physiological environments relies on the concerted
dynamics of several cellular components, including protrusions, adhesions with
the environment, and the cell nucleus. However, it remains poorly understood how
the dynamic interplay of these components and the cell polarity determine the
emergent migration behavior at the cellular scale. Here, we combine data-driven
inference with a mechanistic bottom-up approach to develop a model for protrusion
and polarity dynamics in confined cell migration, revealing how the cellular dynamics
adapt to confining geometries. Specifically, we use experimental data of joint
protrusion-nucleus migration trajectories of cells on confining micropatterns
to systematically determine a mechanistic model linking the stochastic dynamics
of cell polarity, protrusions, and nucleus. This model indicates that the cellular
dynamics adapt to confining constrictions through a switch in the polarity dynamics
from a negative to a positive self-reinforcing feedback loop. Our model further
reveals how this feedback loop leads to stereotypical cycles of protrusion-nucleus
dynamics that drive the migration of the cell through constrictions. These cycles
are disrupted upon perturbation of cytoskeletal components, indicating that the
positive feedback is controlled by cellular migration mechanisms. Our data-driven
theoretical approach therefore identifies polarity feedback adaptation as a key
mechanism in confined cell migration.
acknowledgement: "We thank Grzegorz Gradziuk, StevenRiedijk, Janni Harju, and M. R.
Schnucki for helpful discussions, and Andriy Goychuk for advice on the image segmentation.
This project\r\nwas funded by the Deutsche Forschungsgemeinschaft (DFG, German Research
Foundation), Project No. 201269156—SFB 1032 (Projects B01 and B12). D. B. B. is
supported by the NOMIS Foundation and in part by a DFG fellowship within the Graduate
School of Quantitative Biosciences Munich (QBM), as well as by the Joachim Herz
Stiftung."
article_number: '031041'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Matthew
full_name: Schmitt, Matthew
last_name: Schmitt
- first_name: Alexandra
full_name: Fink, Alexandra
last_name: Fink
- first_name: Georg
full_name: Ladurner, Georg
last_name: Ladurner
- first_name: Johannes
full_name: Flommersfeld, Johannes
last_name: Flommersfeld
- first_name: Nicolas
full_name: Arlt, Nicolas
last_name: Arlt
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Joachim O.
full_name: Rädler, Joachim O.
last_name: Rädler
- first_name: Chase P.
full_name: Broedersz, Chase P.
last_name: Broedersz
citation:
ama: Brückner D, Schmitt M, Fink A, et al. Geometry adaptation of protrusion and
polarity dynamics in confined cell migration. Physical Review X. 2022;12(3).
doi:10.1103/physrevx.12.031041
apa: Brückner, D., Schmitt, M., Fink, A., Ladurner, G., Flommersfeld, J., Arlt,
N., … Broedersz, C. P. (2022). Geometry adaptation of protrusion and polarity
dynamics in confined cell migration. Physical Review X. American Physical
Society. https://doi.org/10.1103/physrevx.12.031041
chicago: Brückner, David, Matthew Schmitt, Alexandra Fink, Georg Ladurner, Johannes
Flommersfeld, Nicolas Arlt, Edouard B Hannezo, Joachim O. Rädler, and Chase P.
Broedersz. “Geometry Adaptation of Protrusion and Polarity Dynamics in Confined
Cell Migration.” Physical Review X. American Physical Society, 2022. https://doi.org/10.1103/physrevx.12.031041.
ieee: D. Brückner et al., “Geometry adaptation of protrusion and polarity
dynamics in confined cell migration,” Physical Review X, vol. 12, no. 3.
American Physical Society, 2022.
ista: Brückner D, Schmitt M, Fink A, Ladurner G, Flommersfeld J, Arlt N, Hannezo
EB, Rädler JO, Broedersz CP. 2022. Geometry adaptation of protrusion and polarity
dynamics in confined cell migration. Physical Review X. 12(3), 031041.
mla: Brückner, David, et al. “Geometry Adaptation of Protrusion and Polarity Dynamics
in Confined Cell Migration.” Physical Review X, vol. 12, no. 3, 031041,
American Physical Society, 2022, doi:10.1103/physrevx.12.031041.
short: D. Brückner, M. Schmitt, A. Fink, G. Ladurner, J. Flommersfeld, N. Arlt,
E.B. Hannezo, J.O. Rädler, C.P. Broedersz, Physical Review X 12 (2022).
date_created: 2023-01-16T10:02:06Z
date_published: 2022-09-20T00:00:00Z
date_updated: 2023-08-04T10:25:49Z
day: '20'
ddc:
- '530'
- '570'
department:
- _id: EdHa
doi: 10.1103/physrevx.12.031041
external_id:
arxiv:
- '2106.01014'
isi:
- '000861534700001'
file:
- access_level: open_access
checksum: 40a8fbc3663bf07b37cb80020974d40d
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T11:07:27Z
date_updated: 2023-01-30T11:07:27Z
file_id: '12458'
file_name: 2022_PhysicalReviewX_Brueckner.pdf
file_size: 4686804
relation: main_file
success: 1
file_date_updated: 2023-01-30T11:07:27Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '3'
keyword:
- General Physics and Astronomy
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Physical Review X
publication_identifier:
issn:
- 2160-3308
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Geometry adaptation of protrusion and polarity dynamics in confined cell migration
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2022'
...
---
_id: '12278'
abstract:
- lang: eng
text: Mercury telluride (HgTe) thin films with a critical thickness of 6.5 nm are
predicted to possess a gapless Dirac-like band structure. We report a comprehensive
study on gated and optically doped samples by magnetooptical spectroscopy in the
THz range. The quasi-classical analysis of the cyclotron resonance allowed the
mapping of the band dispersion of Dirac charge carriers in a broad range of electron
and hole doping. A smooth transition through the charge neutrality point between
Dirac holes and electrons was observed. An additional peak coming from a second
type of holes with an almost density-independent mass of around 0.04m0 was detected
in the hole-doping range and attributed to an asymmetric spin splitting of the
Dirac cone. Spectroscopic evidence for disorder-induced band energy fluctuations
could not be detected in present cyclotron resonance experiments.
acknowledgement: "This work was supported by the Austrian Science Funds (W1243, I
3456-N27, I 5539-N).\r\nOpen Access Funding by the Austrian Science Fund (FWF)."
article_number: '2492'
article_processing_charge: Yes
article_type: original
author:
- first_name: Alexey
full_name: Shuvaev, Alexey
last_name: Shuvaev
- first_name: Uladzislau
full_name: Dziom, Uladzislau
id: 6A9A37C2-8C5C-11E9-AE53-F2FDE5697425
last_name: Dziom
orcid: 0000-0002-1648-0999
- first_name: Jan
full_name: Gospodarič, Jan
last_name: Gospodarič
- first_name: Elena G.
full_name: Novik, Elena G.
last_name: Novik
- first_name: Alena A.
full_name: Dobretsova, Alena A.
last_name: Dobretsova
- first_name: Nikolay N.
full_name: Mikhailov, Nikolay N.
last_name: Mikhailov
- first_name: Ze Don
full_name: Kvon, Ze Don
last_name: Kvon
- first_name: Andrei
full_name: Pimenov, Andrei
last_name: Pimenov
citation:
ama: Shuvaev A, Dziom U, Gospodarič J, et al. Band structure near the Dirac Point
in HgTe quantum wells with critical thickness. Nanomaterials. 2022;12(14).
doi:10.3390/nano12142492
apa: Shuvaev, A., Dziom, U., Gospodarič, J., Novik, E. G., Dobretsova, A. A., Mikhailov,
N. N., … Pimenov, A. (2022). Band structure near the Dirac Point in HgTe quantum
wells with critical thickness. Nanomaterials. MDPI. https://doi.org/10.3390/nano12142492
chicago: Shuvaev, Alexey, Uladzislau Dziom, Jan Gospodarič, Elena G. Novik, Alena
A. Dobretsova, Nikolay N. Mikhailov, Ze Don Kvon, and Andrei Pimenov. “Band Structure
near the Dirac Point in HgTe Quantum Wells with Critical Thickness.” Nanomaterials.
MDPI, 2022. https://doi.org/10.3390/nano12142492.
ieee: A. Shuvaev et al., “Band structure near the Dirac Point in HgTe quantum
wells with critical thickness,” Nanomaterials, vol. 12, no. 14. MDPI, 2022.
ista: Shuvaev A, Dziom U, Gospodarič J, Novik EG, Dobretsova AA, Mikhailov NN, Kvon
ZD, Pimenov A. 2022. Band structure near the Dirac Point in HgTe quantum wells
with critical thickness. Nanomaterials. 12(14), 2492.
mla: Shuvaev, Alexey, et al. “Band Structure near the Dirac Point in HgTe Quantum
Wells with Critical Thickness.” Nanomaterials, vol. 12, no. 14, 2492, MDPI,
2022, doi:10.3390/nano12142492.
short: A. Shuvaev, U. Dziom, J. Gospodarič, E.G. Novik, A.A. Dobretsova, N.N. Mikhailov,
Z.D. Kvon, A. Pimenov, Nanomaterials 12 (2022).
date_created: 2023-01-16T10:02:31Z
date_published: 2022-07-20T00:00:00Z
date_updated: 2023-10-17T11:41:28Z
day: '20'
ddc:
- '530'
department:
- _id: ZhAl
doi: 10.3390/nano12142492
external_id:
isi:
- '000834401600001'
file:
- access_level: open_access
checksum: efad6742f89f39a18bec63116dd689a0
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T11:16:54Z
date_updated: 2023-01-30T11:16:54Z
file_id: '12459'
file_name: 2022_Nanomaterials_Shuvaev.pdf
file_size: 464840
relation: main_file
success: 1
file_date_updated: 2023-01-30T11:16:54Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '14'
keyword:
- General Materials Science
- General Chemical Engineering
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Nanomaterials
publication_identifier:
issn:
- 2079-4991
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Band structure near the Dirac Point in HgTe quantum wells with critical thickness
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: 12
year: '2022'
...