---
_id: '11551'
abstract:
- lang: eng
text: Imbalanced mitochondrial dNTP pools are known players in the pathogenesis
of multiple human diseases. Here we show that, even under physiological conditions,
dGTP is largely overrepresented among other dNTPs in mitochondria of mouse tissues
and human cultured cells. In addition, a vast majority of mitochondrial dGTP is
tightly bound to NDUFA10, an accessory subunit of complex I of the mitochondrial
respiratory chain. NDUFA10 shares a deoxyribonucleoside kinase (dNK) domain with
deoxyribonucleoside kinases in the nucleotide salvage pathway, though no specific
function beyond stabilizing the complex I holoenzyme has been described for this
subunit. We mutated the dNK domain of NDUFA10 in human HEK-293T cells while preserving
complex I assembly and activity. The NDUFA10E160A/R161A shows reduced dGTP binding
capacity in vitro and leads to a 50% reduction in mitochondrial dGTP content,
proving that most dGTP is directly bound to the dNK domain of NDUFA10. This interaction
may represent a hitherto unknown mechanism regulating mitochondrial dNTP availability
and linking oxidative metabolism to DNA maintenance.
acknowledgement: "We thank Dr, Luke Formosa (Department of Biochemistry and Molecular
Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia)
for his valuable advice and assistance on NDUFA10 molecular studies and Dr. Francesc
Canals and his team (Proteomics Laboratory, Vall d’Hebron Institute of Oncology
[VHIO], Universitat Autònoma de Barcelona, Barcelona, Spain) for their assistance
with LC-MS/MS analyses. This work was supported by the Spanish Ministry of Industry,
Economy and Competitiveness [grants BFU2014-52618-R, SAF2017-87506, and PID2020-112929RB-I00
to Y.C.], by the Spanish Instituto de Salud Carlos III [grants PI21/00554 and PMP15/00025
to R.M.], co-financed by the European Regional Development Fund (ERDF), and by an
NHMRC Project grant to M.R. (GNT1164459).\r\n"
article_number: '620'
article_processing_charge: No
author:
- first_name: David
full_name: Molina-Granada, David
last_name: Molina-Granada
- first_name: Emiliano
full_name: González-Vioque, Emiliano
last_name: González-Vioque
- first_name: Marris G.
full_name: Dibley, Marris G.
last_name: Dibley
- first_name: Raquel
full_name: Cabrera-Pérez, Raquel
last_name: Cabrera-Pérez
- first_name: Antoni
full_name: Vallbona-Garcia, Antoni
last_name: Vallbona-Garcia
- first_name: Javier
full_name: Torres-Torronteras, Javier
last_name: Torres-Torronteras
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
- first_name: Michael T.
full_name: Ryan, Michael T.
last_name: Ryan
- first_name: Yolanda
full_name: Cámara, Yolanda
last_name: Cámara
- first_name: Ramon
full_name: Martí, Ramon
last_name: Martí
citation:
ama: Molina-Granada D, González-Vioque E, Dibley MG, et al. Most mitochondrial dGTP
is tightly bound to respiratory complex I through the NDUFA10 subunit. Communications
Biology. 2022;5(1). doi:10.1038/s42003-022-03568-6
apa: Molina-Granada, D., González-Vioque, E., Dibley, M. G., Cabrera-Pérez, R.,
Vallbona-Garcia, A., Torres-Torronteras, J., … Martí, R. (2022). Most mitochondrial
dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. Communications
Biology. Springer Nature. https://doi.org/10.1038/s42003-022-03568-6
chicago: Molina-Granada, David, Emiliano González-Vioque, Marris G. Dibley, Raquel
Cabrera-Pérez, Antoni Vallbona-Garcia, Javier Torres-Torronteras, Leonid A Sazanov,
Michael T. Ryan, Yolanda Cámara, and Ramon Martí. “Most Mitochondrial DGTP Is
Tightly Bound to Respiratory Complex I through the NDUFA10 Subunit.” Communications
Biology. Springer Nature, 2022. https://doi.org/10.1038/s42003-022-03568-6.
ieee: D. Molina-Granada et al., “Most mitochondrial dGTP is tightly bound
to respiratory complex I through the NDUFA10 subunit,” Communications Biology,
vol. 5, no. 1. Springer Nature, 2022.
ista: Molina-Granada D, González-Vioque E, Dibley MG, Cabrera-Pérez R, Vallbona-Garcia
A, Torres-Torronteras J, Sazanov LA, Ryan MT, Cámara Y, Martí R. 2022. Most mitochondrial
dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. Communications
Biology. 5(1), 620.
mla: Molina-Granada, David, et al. “Most Mitochondrial DGTP Is Tightly Bound to
Respiratory Complex I through the NDUFA10 Subunit.” Communications Biology,
vol. 5, no. 1, 620, Springer Nature, 2022, doi:10.1038/s42003-022-03568-6.
short: D. Molina-Granada, E. González-Vioque, M.G. Dibley, R. Cabrera-Pérez, A.
Vallbona-Garcia, J. Torres-Torronteras, L.A. Sazanov, M.T. Ryan, Y. Cámara, R.
Martí, Communications Biology 5 (2022).
date_created: 2022-07-10T22:01:52Z
date_published: 2022-06-23T00:00:00Z
date_updated: 2023-08-03T11:51:58Z
day: '23'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1038/s42003-022-03568-6
external_id:
isi:
- '000815098500002'
pmid:
- ' 35739187'
file:
- access_level: open_access
checksum: 965f88bbcef3fd0c3e121340555c4467
content_type: application/pdf
creator: kschuh
date_created: 2022-07-13T07:44:58Z
date_updated: 2022-07-13T07:44:58Z
file_id: '11571'
file_name: 2022_communicationsbiology_Molina-Granada.pdf
file_size: 2335369
relation: main_file
success: 1
file_date_updated: 2022-07-13T07:44:58Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Communications Biology
publication_identifier:
eissn:
- '23993642'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Most mitochondrial dGTP is tightly bound to respiratory complex I through the
NDUFA10 subunit
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: 5
year: '2022'
...
---
_id: '11552'
abstract:
- lang: eng
text: Rotational dynamics of D2 molecules inside helium nanodroplets is induced
by a moderately intense femtosecond pump pulse and measured as a function of time
by recording the yield of HeD+ ions, created through strong-field dissociative
ionization with a delayed femtosecond probe pulse. The yield oscillates with a
period of 185 fs, reflecting field-free rotational wave packet dynamics, and the
oscillation persists for more than 500 periods. Within the experimental uncertainty,
the rotational constant BHe of the in-droplet D2 molecule, determined by Fourier
analysis, is the same as Bgas for an isolated D2 molecule. Our observations show
that the D2 molecules inside helium nanodroplets essentially rotate as free D2
molecules.
article_number: '243201'
article_processing_charge: No
arxiv: 1
author:
- first_name: Junjie
full_name: Qiang, Junjie
last_name: Qiang
- first_name: Lianrong
full_name: Zhou, Lianrong
last_name: Zhou
- first_name: Peifen
full_name: Lu, Peifen
last_name: Lu
- first_name: Kang
full_name: Lin, Kang
last_name: Lin
- first_name: Yongzhe
full_name: Ma, Yongzhe
last_name: Ma
- first_name: Shengzhe
full_name: Pan, Shengzhe
last_name: Pan
- first_name: Chenxu
full_name: Lu, Chenxu
last_name: Lu
- first_name: Wenyu
full_name: Jiang, Wenyu
last_name: Jiang
- first_name: Fenghao
full_name: Sun, Fenghao
last_name: Sun
- first_name: Wenbin
full_name: Zhang, Wenbin
last_name: Zhang
- first_name: Hui
full_name: Li, Hui
last_name: Li
- first_name: Xiaochun
full_name: Gong, Xiaochun
last_name: Gong
- first_name: Ilya Sh
full_name: Averbukh, Ilya Sh
last_name: Averbukh
- first_name: Yehiam
full_name: Prior, Yehiam
last_name: Prior
- first_name: Constant A.
full_name: Schouder, Constant A.
last_name: Schouder
- first_name: Henrik
full_name: Stapelfeldt, Henrik
last_name: Stapelfeldt
- first_name: Igor
full_name: Cherepanov, Igor
id: 339C7E5A-F248-11E8-B48F-1D18A9856A87
last_name: Cherepanov
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Wolfgang
full_name: Jäger, Wolfgang
last_name: Jäger
- first_name: Jian
full_name: Wu, Jian
last_name: Wu
citation:
ama: Qiang J, Zhou L, Lu P, et al. Femtosecond rotational dynamics of D2 molecules
in superfluid helium nanodroplets. Physical Review Letters. 2022;128(24).
doi:10.1103/PhysRevLett.128.243201
apa: Qiang, J., Zhou, L., Lu, P., Lin, K., Ma, Y., Pan, S., … Wu, J. (2022). Femtosecond
rotational dynamics of D2 molecules in superfluid helium nanodroplets. Physical
Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.128.243201
chicago: Qiang, Junjie, Lianrong Zhou, Peifen Lu, Kang Lin, Yongzhe Ma, Shengzhe
Pan, Chenxu Lu, et al. “Femtosecond Rotational Dynamics of D2 Molecules in Superfluid
Helium Nanodroplets.” Physical Review Letters. American Physical Society,
2022. https://doi.org/10.1103/PhysRevLett.128.243201.
ieee: J. Qiang et al., “Femtosecond rotational dynamics of D2 molecules in
superfluid helium nanodroplets,” Physical Review Letters, vol. 128, no.
24. American Physical Society, 2022.
ista: Qiang J, Zhou L, Lu P, Lin K, Ma Y, Pan S, Lu C, Jiang W, Sun F, Zhang W,
Li H, Gong X, Averbukh IS, Prior Y, Schouder CA, Stapelfeldt H, Cherepanov I,
Lemeshko M, Jäger W, Wu J. 2022. Femtosecond rotational dynamics of D2 molecules
in superfluid helium nanodroplets. Physical Review Letters. 128(24), 243201.
mla: Qiang, Junjie, et al. “Femtosecond Rotational Dynamics of D2 Molecules in Superfluid
Helium Nanodroplets.” Physical Review Letters, vol. 128, no. 24, 243201,
American Physical Society, 2022, doi:10.1103/PhysRevLett.128.243201.
short: J. Qiang, L. Zhou, P. Lu, K. Lin, Y. Ma, S. Pan, C. Lu, W. Jiang, F. Sun,
W. Zhang, H. Li, X. Gong, I.S. Averbukh, Y. Prior, C.A. Schouder, H. Stapelfeldt,
I. Cherepanov, M. Lemeshko, W. Jäger, J. Wu, Physical Review Letters 128 (2022).
date_created: 2022-07-10T22:01:52Z
date_published: 2022-06-16T00:00:00Z
date_updated: 2023-08-03T11:54:14Z
day: '16'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.128.243201
ec_funded: 1
external_id:
arxiv:
- '2201.09281'
isi:
- '000820659700002'
intvolume: ' 128'
isi: 1
issue: '24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2201.09281
month: '06'
oa: 1
oa_version: Submitted Version
project:
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Physical Review Letters
publication_identifier:
eissn:
- '10797114'
issn:
- '00319007'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 128
year: '2022'
...
---
_id: '11553'
abstract:
- lang: eng
text: "In holomorphic dynamics, complex box mappings arise as first return maps
to wellchosen domains. They are a generalization of polynomial-like mapping, where
the domain of the return map can have infinitely many components. They turned
out to be extremely useful in tackling diverse problems. The purpose of this paper
is:\r\n• To illustrate some pathologies that can occur when a complex box mapping
is not induced by a globally defined map and when its domain has infinitely many
components, and to give conditions to avoid these issues.\r\n• To show that once
one has a box mapping for a rational map, these conditions can be assumed to hold
in a very natural setting. Thus, we call such complex box mappings dynamically
natural. Having such box mappings is the first step in tackling many problems
in one-dimensional dynamics.\r\n• Many results in holomorphic dynamics rely on
an interplay between combinatorial and analytic techniques. In this setting, some
of these tools are:\r\n • the Enhanced Nest (a nest of puzzle pieces around critical
points) from Kozlovski, Shen, van Strien (AnnMath 165:749–841, 2007), referred
to below as KSS;\r\n • the Covering Lemma (which controls the moduli of pullbacks
of annuli) from Kahn and Lyubich (Ann Math 169(2):561–593, 2009);\r\n • the
QC-Criterion and the Spreading Principle from KSS.\r\nThe purpose of this paper
is to make these tools more accessible so that they can be used as a ‘black box’,
so one does not have to redo the proofs in new settings.\r\n• To give an intuitive,
but also rather detailed, outline of the proof from KSS and Kozlovski and van
Strien (Proc Lond Math Soc (3) 99:275–296, 2009) of the following results for
non-renormalizable dynamically natural complex box mappings:\r\n • puzzle pieces
shrink to points,\r\n • (under some assumptions) topologically conjugate non-renormalizable
polynomials and box mappings are quasiconformally conjugate.\r\n• We prove the
fundamental ergodic properties for dynamically natural box mappings. This leads
to some necessary conditions for when such a box mapping supports a measurable
invariant line field on its filled Julia set. These mappings\r\nare the analogues
of Lattès maps in this setting.\r\n• We prove a version of Mañé’s Theorem for
complex box mappings concerning expansion along orbits of points that avoid a
neighborhood of the set of critical points."
acknowledgement: We would also like to thank Dzmitry Dudko and Dierk Schleicher for
many stimulating discussions and encouragement during our work on this project,
and Weixiao Shen, Mikhail Hlushchanka and the referee for helpful comments. We are
grateful to Leon Staresinic who carefully read the revised version of the manuscript
and provided many helpful suggestions.
article_processing_charge: No
article_type: original
author:
- first_name: Trevor
full_name: Clark, Trevor
last_name: Clark
- first_name: Kostiantyn
full_name: Drach, Kostiantyn
id: fe8209e2-906f-11eb-847d-950f8fc09115
last_name: Drach
orcid: 0000-0002-9156-8616
- first_name: Oleg
full_name: Kozlovski, Oleg
last_name: Kozlovski
- first_name: Sebastian Van
full_name: Strien, Sebastian Van
last_name: Strien
citation:
ama: Clark T, Drach K, Kozlovski O, Strien SV. The dynamics of complex box mappings.
Arnold Mathematical Journal. 2022;8(2):319-410. doi:10.1007/s40598-022-00200-7
apa: Clark, T., Drach, K., Kozlovski, O., & Strien, S. V. (2022). The dynamics
of complex box mappings. Arnold Mathematical Journal. Springer Nature.
https://doi.org/10.1007/s40598-022-00200-7
chicago: Clark, Trevor, Kostiantyn Drach, Oleg Kozlovski, and Sebastian Van Strien.
“The Dynamics of Complex Box Mappings.” Arnold Mathematical Journal. Springer
Nature, 2022. https://doi.org/10.1007/s40598-022-00200-7.
ieee: T. Clark, K. Drach, O. Kozlovski, and S. V. Strien, “The dynamics of complex
box mappings,” Arnold Mathematical Journal, vol. 8, no. 2. Springer Nature,
pp. 319–410, 2022.
ista: Clark T, Drach K, Kozlovski O, Strien SV. 2022. The dynamics of complex box
mappings. Arnold Mathematical Journal. 8(2), 319–410.
mla: Clark, Trevor, et al. “The Dynamics of Complex Box Mappings.” Arnold Mathematical
Journal, vol. 8, no. 2, Springer Nature, 2022, pp. 319–410, doi:10.1007/s40598-022-00200-7.
short: T. Clark, K. Drach, O. Kozlovski, S.V. Strien, Arnold Mathematical Journal
8 (2022) 319–410.
date_created: 2022-07-10T22:01:53Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2023-02-16T10:02:12Z
day: '01'
ddc:
- '500'
department:
- _id: VaKa
doi: 10.1007/s40598-022-00200-7
ec_funded: 1
file:
- access_level: open_access
checksum: 16e7c659dee9073c6c8aeb87316ef201
content_type: application/pdf
creator: kschuh
date_created: 2022-07-12T10:04:55Z
date_updated: 2022-07-12T10:04:55Z
file_id: '11559'
file_name: 2022_ArnoldMathematicalJournal_Clark.pdf
file_size: 2509915
relation: main_file
success: 1
file_date_updated: 2022-07-12T10:04:55Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '2'
language:
- iso: eng
month: '06'
oa: 1
oa_version: None
page: 319-410
project:
- _id: 9B8B92DE-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '885707'
name: Spectral rigidity and integrability for billiards and geodesic flows
publication: Arnold Mathematical Journal
publication_identifier:
eissn:
- 2199-6806
issn:
- 2199-6792
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1007/s40598-022-00209-y
- relation: erratum
url: https://doi.org/10.1007/s40598-022-00218-x
scopus_import: '1'
status: public
title: The dynamics of complex box mappings
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: 8
year: '2022'
...
---
_id: '11556'
abstract:
- lang: eng
text: "We revisit two basic Direct Simulation Monte Carlo Methods to model aggregation
kinetics and extend them for aggregation processes with collisional fragmentation
(shattering). We test the performance and accuracy of the extended methods and
compare their performance with efficient deterministic finite-difference method
applied to the same model. We validate the stochastic methods on the test problems
and apply them to verify the existence of oscillating regimes in the aggregation-fragmentation
kinetics recently detected in deterministic simulations. We confirm the emergence
of steady oscillations of densities in such systems and prove the stability of
the\r\noscillations with respect to fluctuations and noise."
acknowledgement: Zhores supercomputer of Skolkovo Institute of Science and Technology
[68] has been used in the present research. S.A.M. was supported by Moscow Center
for Fundamental and Applied Mathematics (the agreement with the Ministry of Education
and Science of the Russian Federation No. 075-15-2019-1624). A.I.O. acknowledges
RFBR project No. 20-31-90022. N.V.B. acknowledges the support of the Analytical
Center (subsidy agreement 000000D730321P5Q0002, Grant No. 70-2021-00145 02.11.2021).
article_number: '111439'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Aleksei
full_name: Kalinov, Aleksei
id: 44b7120e-eb97-11eb-a6c2-e1557aa81d02
last_name: Kalinov
orcid: 0000-0003-2189-3904
- first_name: A.I.
full_name: Osinskiy, A.I.
last_name: Osinskiy
- first_name: S.A.
full_name: Matveev, S.A.
last_name: Matveev
- first_name: W.
full_name: Otieno, W.
last_name: Otieno
- first_name: N.V.
full_name: Brilliantov, N.V.
last_name: Brilliantov
citation:
ama: Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. Direct simulation
Monte Carlo for new regimes in aggregation-fragmentation kinetics. Journal
of Computational Physics. 2022;467. doi:10.1016/j.jcp.2022.111439
apa: Kalinov, A., Osinskiy, A. I., Matveev, S. A., Otieno, W., & Brilliantov,
N. V. (2022). Direct simulation Monte Carlo for new regimes in aggregation-fragmentation
kinetics. Journal of Computational Physics. Elsevier. https://doi.org/10.1016/j.jcp.2022.111439
chicago: Kalinov, Aleksei, A.I. Osinskiy, S.A. Matveev, W. Otieno, and N.V. Brilliantov.
“Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.”
Journal of Computational Physics. Elsevier, 2022. https://doi.org/10.1016/j.jcp.2022.111439.
ieee: A. Kalinov, A. I. Osinskiy, S. A. Matveev, W. Otieno, and N. V. Brilliantov,
“Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics,”
Journal of Computational Physics, vol. 467. Elsevier, 2022.
ista: Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. 2022. Direct
simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics.
Journal of Computational Physics. 467, 111439.
mla: Kalinov, Aleksei, et al. “Direct Simulation Monte Carlo for New Regimes in
Aggregation-Fragmentation Kinetics.” Journal of Computational Physics,
vol. 467, 111439, Elsevier, 2022, doi:10.1016/j.jcp.2022.111439.
short: A. Kalinov, A.I. Osinskiy, S.A. Matveev, W. Otieno, N.V. Brilliantov, Journal
of Computational Physics 467 (2022).
date_created: 2022-07-11T12:19:59Z
date_published: 2022-10-15T00:00:00Z
date_updated: 2023-08-03T11:55:06Z
day: '15'
ddc:
- '518'
department:
- _id: GradSch
- _id: ChWo
doi: 10.1016/j.jcp.2022.111439
external_id:
arxiv:
- '2103.09481'
isi:
- '000917225500013'
intvolume: ' 467'
isi: 1
keyword:
- Computer Science Applications
- Physics and Astronomy (miscellaneous)
- Applied Mathematics
- Computational Mathematics
- Modeling and Simulation
- Numerical Analysis
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2103.09481
month: '10'
oa: 1
oa_version: Preprint
publication: Journal of Computational Physics
publication_identifier:
issn:
- 0021-9991
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Direct simulation Monte Carlo for new regimes in aggregation-fragmentation
kinetics
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 467
year: '2022'
...
---
_id: '11587'
abstract:
- lang: eng
text: "Background: Accurate and comprehensive annotation of transcript sequences
is essential for transcript quantification and differential gene and transcript
expression analysis. Single-molecule long-read sequencing technologies provide
improved integrity of transcript structures including alternative splicing, and
transcription start and polyadenylation sites. However, accuracy is significantly
affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis.\r\nResults:
We present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset
3 (AtRTD3). AtRTD3 contains over 169,000 transcripts—twice that of the best current
Arabidopsis transcriptome and including over 1500 novel genes. Seventy-eight percent
of transcripts are from Iso-seq with accurately defined splice junctions and transcription
start and end sites. We develop novel methods to determine splice junctions and
transcription start and end sites accurately. Mismatch profiles around splice
junctions provide a powerful feature to distinguish correct splice junctions and
remove false splice junctions. Stratified approaches identify high-confidence
transcription start and end sites and remove fragmentary transcripts due to degradation.
AtRTD3 is a major improvement over existing transcriptomes as demonstrated by
analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provides
higher resolution of transcript expression profiling and identifies cold-induced
differential transcription start and polyadenylation site usage.\r\nConclusions:
AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves
the precision of differential gene and transcript expression, differential alternative
splicing, and transcription start/end site usage analysis from RNA-seq data. The
novel methods for identifying accurate splice junctions and transcription start/end
sites are widely applicable and will improve single-molecule sequencing analysis
from any species."
acknowledgement: "This work was jointly supported by funding from the Biotechnology
and Biological Sciences Research Council (BBSRC) BB/P009751/1 to JB; BB/R014582/1
to RW and RZ; BB/S020160/1 to RZ; BB/S004610/1 (16 ERA-CAPS BARN) to RW; the Scottish
Government Rural and Environment Science and Analytical Services division (RESAS)
[to RZ, RW, and JB]; the\r\nNational Science Foundation (MCB-2014408) and the National
Institute of Health (NIH) (GM-114297) to E.H.; S. H. was supported by funding to
K.D. from the University of York; the Austrian Science Fund (FWF) SFB F43 to AB
and MJ and [P26333] to MK; The French Agence Nationale de la Recherche grant ANR-16-CE12-0032
to MC; the Japan Science and\r\nTechnology Agency (JST), the Core Research for Evolutionary
Science and Technology (CREST; Grant Number JPMJCR13B4) to M.S.; the National Science
Foundation (Grant No. DBI1949036 to A.b.H and A.S.N.R, and Grant No. MCB 2014542
to E.H. and A.S.N.R.); and the DOE Office of Science, Office of Biological and Environmental
Research (Grant\r\nNo. DE-SC0010733) to A.S.N.R and A.b.H.; the Deutsche Forschungsgemeinschaft
(DFG) STA653/14-1 and STA653/15-1 to DS; the National Science Foundation grant (IOS-154173)
to Q.Q.L.; the German Research Foundation (DFG) WA2167/8-1 to AW and SFB1101/C03
to AW and TWK; the Research Grants Council (RGC) of Hong Kong (GRF 12103020) to
LX. NSF grant IOS-1849708 and NSF EPSCoR grant 1826836 to RS; the Academia Sinica
to S.-L. T."
article_number: '149'
article_processing_charge: No
article_type: original
author:
- first_name: Runxuan
full_name: Zhang, Runxuan
last_name: Zhang
- first_name: Richard
full_name: Kuo, Richard
last_name: Kuo
- first_name: Max
full_name: Coulter, Max
last_name: Coulter
- first_name: Cristiane P.G.
full_name: Calixto, Cristiane P.G.
last_name: Calixto
- first_name: Juan Carlos
full_name: Entizne, Juan Carlos
last_name: Entizne
- first_name: Wenbin
full_name: Guo, Wenbin
last_name: Guo
- first_name: Yamile
full_name: Marquez, Yamile
last_name: Marquez
- first_name: Linda
full_name: Milne, Linda
last_name: Milne
- first_name: Stefan
full_name: Riegler, Stefan
id: FF6018E0-D806-11E9-8E43-0B14E6697425
last_name: Riegler
orcid: 0000-0003-3413-1343
- first_name: Akihiro
full_name: Matsui, Akihiro
last_name: Matsui
- first_name: Maho
full_name: Tanaka, Maho
last_name: Tanaka
- first_name: Sarah
full_name: Harvey, Sarah
last_name: Harvey
- first_name: Yubang
full_name: Gao, Yubang
last_name: Gao
- first_name: Theresa
full_name: Wießner-Kroh, Theresa
last_name: Wießner-Kroh
- first_name: Alejandro
full_name: Paniagua, Alejandro
last_name: Paniagua
- first_name: Martin
full_name: Crespi, Martin
last_name: Crespi
- first_name: Katherine
full_name: Denby, Katherine
last_name: Denby
- first_name: Asa Ben
full_name: Hur, Asa Ben
last_name: Hur
- first_name: Enamul
full_name: Huq, Enamul
last_name: Huq
- first_name: Michael
full_name: Jantsch, Michael
last_name: Jantsch
- first_name: Artur
full_name: Jarmolowski, Artur
last_name: Jarmolowski
- first_name: Tino
full_name: Koester, Tino
last_name: Koester
- first_name: Sascha
full_name: Laubinger, Sascha
last_name: Laubinger
- first_name: Qingshun Quinn
full_name: Li, Qingshun Quinn
last_name: Li
- first_name: Lianfeng
full_name: Gu, Lianfeng
last_name: Gu
- first_name: Motoaki
full_name: Seki, Motoaki
last_name: Seki
- first_name: Dorothee
full_name: Staiger, Dorothee
last_name: Staiger
- first_name: Ramanjulu
full_name: Sunkar, Ramanjulu
last_name: Sunkar
- first_name: Zofia
full_name: Szweykowska-Kulinska, Zofia
last_name: Szweykowska-Kulinska
- first_name: Shih Long
full_name: Tu, Shih Long
last_name: Tu
- first_name: Andreas
full_name: Wachter, Andreas
last_name: Wachter
- first_name: Robbie
full_name: Waugh, Robbie
last_name: Waugh
- first_name: Liming
full_name: Xiong, Liming
last_name: Xiong
- first_name: Xiao Ning
full_name: Zhang, Xiao Ning
last_name: Zhang
- first_name: Ana
full_name: Conesa, Ana
last_name: Conesa
- first_name: Anireddy S.N.
full_name: Reddy, Anireddy S.N.
last_name: Reddy
- first_name: Andrea
full_name: Barta, Andrea
last_name: Barta
- first_name: Maria
full_name: Kalyna, Maria
last_name: Kalyna
- first_name: John W.S.
full_name: Brown, John W.S.
last_name: Brown
citation:
ama: Zhang R, Kuo R, Coulter M, et al. A high-resolution single-molecule sequencing-based
Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biology.
2022;23. doi:10.1186/s13059-022-02711-0
apa: Zhang, R., Kuo, R., Coulter, M., Calixto, C. P. G., Entizne, J. C., Guo, W.,
… Brown, J. W. S. (2022). A high-resolution single-molecule sequencing-based Arabidopsis
transcriptome using novel methods of Iso-seq analysis. Genome Biology.
BioMed Central. https://doi.org/10.1186/s13059-022-02711-0
chicago: Zhang, Runxuan, Richard Kuo, Max Coulter, Cristiane P.G. Calixto, Juan
Carlos Entizne, Wenbin Guo, Yamile Marquez, et al. “A High-Resolution Single-Molecule
Sequencing-Based Arabidopsis Transcriptome Using Novel Methods of Iso-Seq Analysis.”
Genome Biology. BioMed Central, 2022. https://doi.org/10.1186/s13059-022-02711-0.
ieee: R. Zhang et al., “A high-resolution single-molecule sequencing-based
Arabidopsis transcriptome using novel methods of Iso-seq analysis,” Genome
Biology, vol. 23. BioMed Central, 2022.
ista: Zhang R, Kuo R, Coulter M, Calixto CPG, Entizne JC, Guo W, Marquez Y, Milne
L, Riegler S, Matsui A, Tanaka M, Harvey S, Gao Y, Wießner-Kroh T, Paniagua A,
Crespi M, Denby K, Hur AB, Huq E, Jantsch M, Jarmolowski A, Koester T, Laubinger
S, Li QQ, Gu L, Seki M, Staiger D, Sunkar R, Szweykowska-Kulinska Z, Tu SL, Wachter
A, Waugh R, Xiong L, Zhang XN, Conesa A, Reddy ASN, Barta A, Kalyna M, Brown JWS.
2022. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome
using novel methods of Iso-seq analysis. Genome Biology. 23, 149.
mla: Zhang, Runxuan, et al. “A High-Resolution Single-Molecule Sequencing-Based
Arabidopsis Transcriptome Using Novel Methods of Iso-Seq Analysis.” Genome
Biology, vol. 23, 149, BioMed Central, 2022, doi:10.1186/s13059-022-02711-0.
short: R. Zhang, R. Kuo, M. Coulter, C.P.G. Calixto, J.C. Entizne, W. Guo, Y. Marquez,
L. Milne, S. Riegler, A. Matsui, M. Tanaka, S. Harvey, Y. Gao, T. Wießner-Kroh,
A. Paniagua, M. Crespi, K. Denby, A.B. Hur, E. Huq, M. Jantsch, A. Jarmolowski,
T. Koester, S. Laubinger, Q.Q. Li, L. Gu, M. Seki, D. Staiger, R. Sunkar, Z. Szweykowska-Kulinska,
S.L. Tu, A. Wachter, R. Waugh, L. Xiong, X.N. Zhang, A. Conesa, A.S.N. Reddy,
A. Barta, M. Kalyna, J.W.S. Brown, Genome Biology 23 (2022).
date_created: 2022-07-17T22:01:53Z
date_published: 2022-07-07T00:00:00Z
date_updated: 2023-08-03T12:04:18Z
day: '07'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1186/s13059-022-02711-0
external_id:
isi:
- '000821915500002'
file:
- access_level: open_access
checksum: 2c30ef84151d257a6b835b4e069b70ac
content_type: application/pdf
creator: dernst
date_created: 2022-07-18T08:15:24Z
date_updated: 2022-07-18T08:15:24Z
file_id: '11597'
file_name: 2022_GenomeBiology_Zhang.pdf
file_size: 3146207
relation: main_file
success: 1
file_date_updated: 2022-07-18T08:15:24Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Genome Biology
publication_identifier:
eissn:
- 1474-760X
publication_status: published
publisher: BioMed Central
quality_controlled: '1'
scopus_import: '1'
status: public
title: A high-resolution single-molecule sequencing-based Arabidopsis transcriptome
using novel methods of Iso-seq analysis
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: 23
year: '2022'
...
---
_id: '11588'
abstract:
- lang: eng
text: Visualizing cell behavior and effector function on a single cell level has
been crucial for understanding key aspects of mammalian biology. Due to their
small size, large number and rapid recruitment into thrombi, there is a lack of
data on fate and behavior of individual platelets in thrombosis and hemostasis.
Here we report the use of platelet lineage restricted multi-color reporter mouse
strains to delineate platelet function on a single cell level. We show that genetic
labeling allows for single platelet and megakaryocyte (MK) tracking and morphological
analysis in vivo and in vitro, while not affecting lineage functions. Using Cre-driven
Confetti expression, we provide insights into temporal gene expression patterns
as well as spatial clustering of MK in the bone marrow. In the vasculature, shape
analysis of activated platelets recruited to thrombi identifies ubiquitous filopodia
formation with no evidence of lamellipodia formation. Single cell tracking in
complex thrombi reveals prominent myosin-dependent motility of platelets and highlights
thrombus formation as a highly dynamic process amenable to modification and intervention
of the acto-myosin cytoskeleton. Platelet function assays combining flow cytrometry,
as well as in vivo, ex vivo and in vitro imaging show unaltered platelet functions
of multicolor reporter mice compared to wild-type controls. In conclusion, platelet
lineage multicolor reporter mice prove useful in furthering our understanding
of platelet and MK biology on a single cell level.
acknowledgement: "This study was supported by the Deutsche Forschungsgemeinschaft
(DFG) SFB 914 ( to SM [B02 and Z01]), the DFG SFB 1123 (to SM [B06]), the DFG FOR
2033 (to SM), the German\r\nCenter for Cardiovascular Research (DZHK) (Clinician
Scientist Programme), MHA 1.4VD (to SM), Postdoc Start-up Grant, 81X3600213 (to
FG), 81X3600222 (to LN), the FP7 program\r\n(project 260309, PRESTIGE [to SM]).
This project has received funding from the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation programme (grant agreement
No. 83344, ERC-2018-ADG “IMMUNOTHROMBOSIS” [to SM] and the Marie Skłodowska Curie
Individual Fellowship (EU project 747687, LamelliActin [to FG]). "
article_processing_charge: No
article_type: original
author:
- first_name: Leo
full_name: Nicolai, Leo
last_name: Nicolai
- first_name: Rainer
full_name: Kaiser, Rainer
last_name: Kaiser
- first_name: Raphael
full_name: Escaig, Raphael
last_name: Escaig
- first_name: Marie Louise
full_name: Hoffknecht, Marie Louise
last_name: Hoffknecht
- first_name: Afra
full_name: Anjum, Afra
last_name: Anjum
- first_name: Alexander
full_name: Leunig, Alexander
last_name: Leunig
- first_name: Joachim
full_name: Pircher, Joachim
last_name: Pircher
- first_name: Andreas
full_name: Ehrlich, Andreas
last_name: Ehrlich
- first_name: Michael
full_name: Lorenz, Michael
last_name: Lorenz
- first_name: Hellen
full_name: Ishikawa-Ankerhold, Hellen
last_name: Ishikawa-Ankerhold
- first_name: William C.
full_name: Aird, William C.
last_name: Aird
- first_name: Steffen
full_name: Massberg, Steffen
last_name: Massberg
- first_name: Florian R
full_name: Gärtner, Florian R
id: 397A88EE-F248-11E8-B48F-1D18A9856A87
last_name: Gärtner
orcid: 0000-0001-6120-3723
citation:
ama: Nicolai L, Kaiser R, Escaig R, et al. Single platelet and megakaryocyte morpho-dynamics
uncovered by multicolor reporter mouse strains in vitro and in vivo. Haematologica.
2022;107(7):1669-1680. doi:10.3324/haematol.2021.278896
apa: Nicolai, L., Kaiser, R., Escaig, R., Hoffknecht, M. L., Anjum, A., Leunig,
A., … Gärtner, F. R. (2022). Single platelet and megakaryocyte morpho-dynamics
uncovered by multicolor reporter mouse strains in vitro and in vivo. Haematologica.
Ferrata Storti Foundation. https://doi.org/10.3324/haematol.2021.278896
chicago: Nicolai, Leo, Rainer Kaiser, Raphael Escaig, Marie Louise Hoffknecht, Afra
Anjum, Alexander Leunig, Joachim Pircher, et al. “Single Platelet and Megakaryocyte
Morpho-Dynamics Uncovered by Multicolor Reporter Mouse Strains in Vitro and in
Vivo.” Haematologica. Ferrata Storti Foundation, 2022. https://doi.org/10.3324/haematol.2021.278896.
ieee: L. Nicolai et al., “Single platelet and megakaryocyte morpho-dynamics
uncovered by multicolor reporter mouse strains in vitro and in vivo,” Haematologica,
vol. 107, no. 7. Ferrata Storti Foundation, pp. 1669–1680, 2022.
ista: Nicolai L, Kaiser R, Escaig R, Hoffknecht ML, Anjum A, Leunig A, Pircher J,
Ehrlich A, Lorenz M, Ishikawa-Ankerhold H, Aird WC, Massberg S, Gärtner FR. 2022.
Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter
mouse strains in vitro and in vivo. Haematologica. 107(7), 1669–1680.
mla: Nicolai, Leo, et al. “Single Platelet and Megakaryocyte Morpho-Dynamics Uncovered
by Multicolor Reporter Mouse Strains in Vitro and in Vivo.” Haematologica,
vol. 107, no. 7, Ferrata Storti Foundation, 2022, pp. 1669–80, doi:10.3324/haematol.2021.278896.
short: L. Nicolai, R. Kaiser, R. Escaig, M.L. Hoffknecht, A. Anjum, A. Leunig, J.
Pircher, A. Ehrlich, M. Lorenz, H. Ishikawa-Ankerhold, W.C. Aird, S. Massberg,
F.R. Gärtner, Haematologica 107 (2022) 1669–1680.
date_created: 2022-07-17T22:01:54Z
date_published: 2022-07-01T00:00:00Z
date_updated: 2023-08-03T12:01:01Z
day: '01'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.3324/haematol.2021.278896
ec_funded: 1
external_id:
isi:
- '000823746100018'
file:
- access_level: open_access
checksum: 9b47830945f3c30428fe9cfee2dc4a8a
content_type: application/pdf
creator: dernst
date_created: 2022-07-18T07:51:55Z
date_updated: 2022-07-18T07:51:55Z
file_id: '11595'
file_name: 2022_Haematologica_Nicolai.pdf
file_size: 1722094
relation: main_file
success: 1
file_date_updated: 2022-07-18T07:51:55Z
has_accepted_license: '1'
intvolume: ' 107'
isi: 1
issue: '7'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '07'
oa: 1
oa_version: Published Version
page: 1669-1680
project:
- _id: 260AA4E2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '747687'
name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells
publication: Haematologica
publication_identifier:
eissn:
- 1592-8721
issn:
- 0390-6078
publication_status: published
publisher: Ferrata Storti Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter
mouse strains in vitro and in vivo
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2022'
...
---
_id: '11589'
abstract:
- lang: eng
text: Calcium-dependent protein kinases (CPK) are key components of a wide array
of signaling pathways, translating stress and nutrient signaling into the modulation
of cellular processes such as ion transport and transcription. However, not much
is known about CPKs in endomembrane trafficking. Here, we screened for CPKs that
impact on root growth and gravitropism, by overexpressing constitutively active
forms of CPKs under the control of an inducible promoter in Arabidopsis thaliana.
We found that inducible overexpression of an constitutive active CPK30 (CA-CPK30)
resulted in a loss of root gravitropism and ectopic auxin accumulation in the
root tip. Immunolocalization revealed that CA-CPK30 roots have reduced PIN protein
levels, PIN1 polarity defects and impaired Brefeldin A (BFA)-sensitive trafficking.
Moreover, FM4-64 uptake was reduced, indicative of a defect in endocytosis. The
effects on BFA-sensitive trafficking were not specific to PINs, as BFA could not
induce aggregation of ARF1- and CHC-labeled endosomes in CA-CPK30. Interestingly,
the interference with BFA-body formation, could be reverted by increasing the
extracellular pH, indicating a pH-dependence of this CA-CPK30 effect. Altogether,
our data reveal an important role for CPK30 in root growth regulation and endomembrane
trafficking in Arabidopsis thaliana.
acknowledgement: "RW and JC predoctoral fellows that were supported by the Chinese
Science Counsil. The IPS2 benefits from the support of the LabEx Saclay Plant Sciences-SPS
(ANR-10-LABX-0040-SPS).\r\nWe thank Jen Sheen for establishing and generously sharing
the CKP family clone sets, and for providing useful feedback on the manuscript."
article_number: '862398'
article_processing_charge: No
article_type: original
author:
- first_name: Ren
full_name: Wang, Ren
last_name: Wang
- first_name: Ellie
full_name: Himschoot, Ellie
last_name: Himschoot
- first_name: Jian
full_name: Chen, Jian
last_name: Chen
- first_name: Marie
full_name: Boudsocq, Marie
last_name: Boudsocq
- first_name: Danny
full_name: Geelen, Danny
last_name: Geelen
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
citation:
ama: Wang R, Himschoot E, Chen J, et al. Constitutive active CPK30 interferes with
root growth and endomembrane trafficking in Arabidopsis thaliana. Frontiers
in Plant Science. 2022;13. doi:10.3389/fpls.2022.862398
apa: Wang, R., Himschoot, E., Chen, J., Boudsocq, M., Geelen, D., Friml, J., … Vanneste,
S. (2022). Constitutive active CPK30 interferes with root growth and endomembrane
trafficking in Arabidopsis thaliana. Frontiers in Plant Science. Frontiers.
https://doi.org/10.3389/fpls.2022.862398
chicago: Wang, Ren, Ellie Himschoot, Jian Chen, Marie Boudsocq, Danny Geelen, Jiří
Friml, Tom Beeckman, and Steffen Vanneste. “Constitutive Active CPK30 Interferes
with Root Growth and Endomembrane Trafficking in Arabidopsis Thaliana.” Frontiers
in Plant Science. Frontiers, 2022. https://doi.org/10.3389/fpls.2022.862398.
ieee: R. Wang et al., “Constitutive active CPK30 interferes with root growth
and endomembrane trafficking in Arabidopsis thaliana,” Frontiers in Plant Science,
vol. 13. Frontiers, 2022.
ista: Wang R, Himschoot E, Chen J, Boudsocq M, Geelen D, Friml J, Beeckman T, Vanneste
S. 2022. Constitutive active CPK30 interferes with root growth and endomembrane
trafficking in Arabidopsis thaliana. Frontiers in Plant Science. 13, 862398.
mla: Wang, Ren, et al. “Constitutive Active CPK30 Interferes with Root Growth and
Endomembrane Trafficking in Arabidopsis Thaliana.” Frontiers in Plant Science,
vol. 13, 862398, Frontiers, 2022, doi:10.3389/fpls.2022.862398.
short: R. Wang, E. Himschoot, J. Chen, M. Boudsocq, D. Geelen, J. Friml, T. Beeckman,
S. Vanneste, Frontiers in Plant Science 13 (2022).
date_created: 2022-07-17T22:01:54Z
date_published: 2022-06-16T00:00:00Z
date_updated: 2023-08-03T12:01:47Z
day: '16'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.3389/fpls.2022.862398
external_id:
isi:
- '000819250500001'
pmid:
- '35783951'
file:
- access_level: open_access
checksum: 95313515637c0f84de591d204375d764
content_type: application/pdf
creator: dernst
date_created: 2022-07-18T08:05:15Z
date_updated: 2022-07-18T08:05:15Z
file_id: '11596'
file_name: 2022_FrontiersPlantScience_Wang.pdf
file_size: 5040638
relation: main_file
success: 1
file_date_updated: 2022-07-18T08:05:15Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Plant Science
publication_identifier:
eissn:
- 1664-462X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.3389/fpls.2022.1100792
scopus_import: '1'
status: public
title: Constitutive active CPK30 interferes with root growth and endomembrane trafficking
in Arabidopsis thaliana
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13
year: '2022'
...
---
_id: '11590'
abstract:
- lang: eng
text: 'We investigate the ground-state properties of weakly repulsive one-dimensional
bosons in the presence of an attractive zero-range impurity potential. First,
we derive mean-field solutions to the problem on a finite ring for the two asymptotic
cases: (i) all bosons are bound to the impurity and (ii) all bosons are in a scattering
state. Moreover, we derive the critical line that separates these regimes in the
parameter space. In the thermodynamic limit, this critical line determines the
maximum number of bosons that can be bound by the impurity potential, forming
an artificial atom. Second, we validate the mean-field results using the flow
equation approach and the multi-layer multi-configuration time-dependent Hartree
method for atomic mixtures. While beyond-mean-field effects destroy long-range
order in the Bose gas, the critical boson number is unaffected. Our findings are
important for understanding such artificial atoms in low-density Bose gases with
static and mobile impurities.'
acknowledgement: This work has received funding from the DFG Project No. 413495248
[VO 2437/1-1] (FB, H-WH, AGV) and European Union's Horizon 2020 research and innovation
programme under the Marie Skĺodowska-Curie Grant Agreement No. 754411 (AGV). ML
acknowledges support by the European Research Council (ERC) Starting Grant No. 801770
(ANGULON). SIM acknowledges support from the NSF through a grant for ITAMP at Harvard
University.
article_number: '063036'
article_processing_charge: No
article_type: original
author:
- first_name: Fabian
full_name: Brauneis, Fabian
last_name: Brauneis
- first_name: Timothy G.
full_name: Backert, Timothy G.
last_name: Backert
- first_name: Simeon I.
full_name: Mistakidis, Simeon I.
last_name: Mistakidis
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Hans Werner
full_name: Hammer, Hans Werner
last_name: Hammer
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Brauneis F, Backert TG, Mistakidis SI, Lemeshko M, Hammer HW, Volosniev A.
Artificial atoms from cold bosons in one dimension. New Journal of Physics.
2022;24(6). doi:10.1088/1367-2630/ac78d8
apa: Brauneis, F., Backert, T. G., Mistakidis, S. I., Lemeshko, M., Hammer, H. W.,
& Volosniev, A. (2022). Artificial atoms from cold bosons in one dimension.
New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/ac78d8
chicago: Brauneis, Fabian, Timothy G. Backert, Simeon I. Mistakidis, Mikhail Lemeshko,
Hans Werner Hammer, and Artem Volosniev. “Artificial Atoms from Cold Bosons in
One Dimension.” New Journal of Physics. IOP Publishing, 2022. https://doi.org/10.1088/1367-2630/ac78d8.
ieee: F. Brauneis, T. G. Backert, S. I. Mistakidis, M. Lemeshko, H. W. Hammer, and
A. Volosniev, “Artificial atoms from cold bosons in one dimension,” New Journal
of Physics, vol. 24, no. 6. IOP Publishing, 2022.
ista: Brauneis F, Backert TG, Mistakidis SI, Lemeshko M, Hammer HW, Volosniev A.
2022. Artificial atoms from cold bosons in one dimension. New Journal of Physics.
24(6), 063036.
mla: Brauneis, Fabian, et al. “Artificial Atoms from Cold Bosons in One Dimension.”
New Journal of Physics, vol. 24, no. 6, 063036, IOP Publishing, 2022, doi:10.1088/1367-2630/ac78d8.
short: F. Brauneis, T.G. Backert, S.I. Mistakidis, M. Lemeshko, H.W. Hammer, A.
Volosniev, New Journal of Physics 24 (2022).
date_created: 2022-07-17T22:01:55Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2023-08-03T11:57:41Z
day: '01'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1088/1367-2630/ac78d8
ec_funded: 1
external_id:
isi:
- '000818530000001'
file:
- access_level: open_access
checksum: dc67b60f2e50e9ef2bd820ca0d7333d2
content_type: application/pdf
creator: dernst
date_created: 2022-07-18T06:33:13Z
date_updated: 2022-07-18T06:33:13Z
file_id: '11594'
file_name: 2022_NewJournalPhysics_Brauneis.pdf
file_size: 3415721
relation: main_file
success: 1
file_date_updated: 2022-07-18T06:33:13Z
has_accepted_license: '1'
intvolume: ' 24'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: New Journal of Physics
publication_identifier:
issn:
- 1367-2630
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Artificial atoms from cold bosons in one dimension
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: 24
year: '2022'
...
---
_id: '11591'
abstract:
- lang: eng
text: We investigate the deterministic generation and distribution of entanglement
in large quantum networks by driving distant qubits with the output fields of
a nondegenerate parametric amplifier. In this setting, the amplifier produces
a continuous Gaussian two-mode squeezed state, which acts as a quantum-correlated
reservoir for the qubits and relaxes them into a highly entangled steady state.
Here we are interested in the maximal amount of entanglement and the optimal entanglement
generation rates that can be achieved with this scheme under realistic conditions
taking, in particular, the finite amplifier bandwidth, waveguide losses, and propagation
delays into account. By combining exact numerical simulations of the full network
with approximate analytic results, we predict the optimal working point for the
amplifier and the corresponding qubit-qubit entanglement under various conditions.
Our findings show that this passive conversion of Gaussian into discrete-variable
entanglement offers a robust and experimentally very attractive approach for operating
large optical, microwave, or hybrid quantum networks, for which efficient parametric
amplifiers are currently developed.
acknowledgement: We thank T. Mavrogordatos and D. Zhu for initial contribution on
the presented topic and K. Fedorov for stimulating discussions on entangled microwave
beams. This work was supported by the Austrian Science Fund (FWF) through Grant
No. P32299 (PHONED) and the European Union’s Horizon 2020 research and innovation
programme under Grant Agreement No. 899354 (SuperQuLAN). Most of the computational
results presented were obtained using the CLIP cluster [65].
article_number: '062454'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: J.
full_name: Agustí, J.
last_name: Agustí
- first_name: Y.
full_name: Minoguchi, Y.
last_name: Minoguchi
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: P.
full_name: Rabl, P.
last_name: Rabl
citation:
ama: Agustí J, Minoguchi Y, Fink JM, Rabl P. Long-distance distribution of qubit-qubit
entanglement using Gaussian-correlated photonic beams. Physical Review A.
2022;105(6). doi:10.1103/PhysRevA.105.062454
apa: Agustí, J., Minoguchi, Y., Fink, J. M., & Rabl, P. (2022). Long-distance
distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams.
Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.105.062454
chicago: Agustí, J., Y. Minoguchi, Johannes M Fink, and P. Rabl. “Long-Distance
Distribution of Qubit-Qubit Entanglement Using Gaussian-Correlated Photonic Beams.”
Physical Review A. American Physical Society, 2022. https://doi.org/10.1103/PhysRevA.105.062454.
ieee: J. Agustí, Y. Minoguchi, J. M. Fink, and P. Rabl, “Long-distance distribution
of qubit-qubit entanglement using Gaussian-correlated photonic beams,” Physical
Review A, vol. 105, no. 6. American Physical Society, 2022.
ista: Agustí J, Minoguchi Y, Fink JM, Rabl P. 2022. Long-distance distribution of
qubit-qubit entanglement using Gaussian-correlated photonic beams. Physical Review
A. 105(6), 062454.
mla: Agustí, J., et al. “Long-Distance Distribution of Qubit-Qubit Entanglement
Using Gaussian-Correlated Photonic Beams.” Physical Review A, vol. 105,
no. 6, 062454, American Physical Society, 2022, doi:10.1103/PhysRevA.105.062454.
short: J. Agustí, Y. Minoguchi, J.M. Fink, P. Rabl, Physical Review A 105 (2022).
date_created: 2022-07-17T22:01:55Z
date_published: 2022-06-29T00:00:00Z
date_updated: 2023-08-03T11:58:16Z
day: '29'
department:
- _id: JoFi
doi: 10.1103/PhysRevA.105.062454
ec_funded: 1
external_id:
arxiv:
- '2204.02993'
isi:
- '000824330200003'
intvolume: ' 105'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2204.02993'
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 9B868D20-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '899354'
name: Quantum Local Area Networks with Superconducting Qubits
publication: Physical Review A
publication_identifier:
eissn:
- 2469-9934
issn:
- 2469-9926
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated
photonic beams
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 105
year: '2022'
...
---
_id: '11592'
abstract:
- lang: eng
text: 'We compare recent experimental results [Science 375, 528 (2022)] of the superfluid
unitary Fermi gas near the critical temperature with a thermodynamic model based
on the elementary excitations of the system. We find good agreement between experimental
data and our theory for several quantities such as first sound, second sound,
and superfluid fraction. We also show that mode mixing between first and second
sound occurs. Finally, we characterize the response amplitude to a density perturbation:
Close to the critical temperature both first and second sound can be excited through
a density perturbation, whereas at lower temperatures only the first sound mode
exhibits a significant response.'
acknowledgement: The authors gratefully acknowledge stimulating discussions with T.
Enss, and thank an anonymous referee for suggestions and remarks that allowed us
to improve the original manuscript. This work is supported by the Deutsche Forschungsgemeinschaft
(DFG, German Research Foundation) under Germany’s Excellence Strategy EXC2181/1-390900948
(the Heidelberg STRUCTURES Excellence Cluster).
article_number: '063329'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Alberto
full_name: Cappellaro, Alberto
id: 9d13b3cb-30a2-11eb-80dc-f772505e8660
last_name: Cappellaro
orcid: 0000-0001-6110-2359
- first_name: L.
full_name: Salasnich, L.
last_name: Salasnich
citation:
ama: 'Bighin G, Cappellaro A, Salasnich L. Unitary Fermi superfluid near the critical
temperature: Thermodynamics and sound modes from elementary excitations. Physical
Review A. 2022;105(6). doi:10.1103/PhysRevA.105.063329'
apa: 'Bighin, G., Cappellaro, A., & Salasnich, L. (2022). Unitary Fermi superfluid
near the critical temperature: Thermodynamics and sound modes from elementary
excitations. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.105.063329'
chicago: 'Bighin, Giacomo, Alberto Cappellaro, and L. Salasnich. “Unitary Fermi
Superfluid near the Critical Temperature: Thermodynamics and Sound Modes from
Elementary Excitations.” Physical Review A. American Physical Society,
2022. https://doi.org/10.1103/PhysRevA.105.063329.'
ieee: 'G. Bighin, A. Cappellaro, and L. Salasnich, “Unitary Fermi superfluid near
the critical temperature: Thermodynamics and sound modes from elementary excitations,”
Physical Review A, vol. 105, no. 6. American Physical Society, 2022.'
ista: 'Bighin G, Cappellaro A, Salasnich L. 2022. Unitary Fermi superfluid near
the critical temperature: Thermodynamics and sound modes from elementary excitations.
Physical Review A. 105(6), 063329.'
mla: 'Bighin, Giacomo, et al. “Unitary Fermi Superfluid near the Critical Temperature:
Thermodynamics and Sound Modes from Elementary Excitations.” Physical Review
A, vol. 105, no. 6, 063329, American Physical Society, 2022, doi:10.1103/PhysRevA.105.063329.'
short: G. Bighin, A. Cappellaro, L. Salasnich, Physical Review A 105 (2022).
date_created: 2022-07-17T22:01:55Z
date_published: 2022-06-30T00:00:00Z
date_updated: 2023-08-03T12:00:11Z
day: '30'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.105.063329
external_id:
arxiv:
- '2206.03924'
isi:
- '000829758500010'
intvolume: ' 105'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2206.03924'
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review A
publication_identifier:
eissn:
- 2469-9934
issn:
- 2469-9926
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Unitary Fermi superfluid near the critical temperature: Thermodynamics and
sound modes from elementary excitations'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 105
year: '2022'
...
---
_id: '11593'
abstract:
- lang: eng
text: 'A drawing of a graph on a surface is independently even if every pair of
nonadjacent edges in the drawing crosses an even number of times. The Z2 -genus
of a graph G is the minimum g such that G has an independently even drawing on
the orientable surface of genus g. An unpublished result by Robertson and Seymour
implies that for every t, every graph of sufficiently large genus contains as
a minor a projective t×t grid or one of the following so-called t -Kuratowski
graphs: K3,t, or t copies of K5 or K3,3 sharing at most two common vertices. We
show that the Z2-genus of graphs in these families is unbounded in t; in fact,
equal to their genus. Together, this implies that the genus of a graph is bounded
from above by a function of its Z2-genus, solving a problem posed by Schaefer
and Štefankovič, and giving an approximate version of the Hanani–Tutte theorem
on orientable surfaces. We also obtain an analogous result for Euler genus and
Euler Z2-genus of graphs.'
acknowledgement: "We thank Zdeněk Dvořák, Xavier Goaoc, and Pavel Paták for helpful
discussions. We also thank Bojan Mohar, Paul Seymour, Gelasio Salazar, Jim Geelen,
and John Maharry for information about their unpublished results related to Conjecture
3.1. Finally we thank the reviewers for corrections and suggestions for improving
the presentation.\r\nSupported by Austrian Science Fund (FWF): M2281-N35. Supported
by project 19-04113Y of the Czech Science Foundation (GAČR), by the Czech-French
collaboration project EMBEDS II (CZ: 7AMB17FR029, FR: 38087RM), and by Charles University
project UNCE/SCI/004."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Jan
full_name: Kynčl, Jan
last_name: Kynčl
citation:
ama: Fulek R, Kynčl J. The Z2-Genus of Kuratowski minors. Discrete and Computational
Geometry. 2022;68:425-447. doi:10.1007/s00454-022-00412-w
apa: Fulek, R., & Kynčl, J. (2022). The Z2-Genus of Kuratowski minors. Discrete
and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00412-w
chicago: Fulek, Radoslav, and Jan Kynčl. “The Z2-Genus of Kuratowski Minors.” Discrete
and Computational Geometry. Springer Nature, 2022. https://doi.org/10.1007/s00454-022-00412-w.
ieee: R. Fulek and J. Kynčl, “The Z2-Genus of Kuratowski minors,” Discrete and
Computational Geometry, vol. 68. Springer Nature, pp. 425–447, 2022.
ista: Fulek R, Kynčl J. 2022. The Z2-Genus of Kuratowski minors. Discrete and Computational
Geometry. 68, 425–447.
mla: Fulek, Radoslav, and Jan Kynčl. “The Z2-Genus of Kuratowski Minors.” Discrete
and Computational Geometry, vol. 68, Springer Nature, 2022, pp. 425–47, doi:10.1007/s00454-022-00412-w.
short: R. Fulek, J. Kynčl, Discrete and Computational Geometry 68 (2022) 425–447.
date_created: 2022-07-17T22:01:56Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2023-08-14T12:43:52Z
day: '01'
department:
- _id: UlWa
doi: 10.1007/s00454-022-00412-w
external_id:
arxiv:
- '1803.05085'
isi:
- '000825014500001'
intvolume: ' 68'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1803.05085
month: '09'
oa: 1
oa_version: Preprint
page: 425-447
project:
- _id: 261FA626-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02281
name: Eliminating intersections in drawings of graphs
publication: Discrete and Computational Geometry
publication_identifier:
eissn:
- 1432-0444
issn:
- 0179-5376
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
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- id: '186'
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status: public
scopus_import: '1'
status: public
title: The Z2-Genus of Kuratowski minors
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 68
year: '2022'
...
---
_id: '11626'
abstract:
- lang: eng
text: Plant growth and development is well known to be both, flexible and dynamic.
The high capacity for post-embryonic organ formation and tissue regeneration requires
tightly regulated intercellular communication and coordinated tissue polarization.
One of the most important drivers for patterning and polarity in plant development
is the phytohormone auxin. Auxin has the unique characteristic to establish polarized
channels for its own active directional cell to cell transport. This fascinating
phenomenon is called auxin canalization. Those auxin transport channels are characterized
by the expression and polar, subcellular localization of PIN auxin efflux carriers.
PIN proteins have the ability to dynamically change their localization and auxin
itself can affect this by interfering with trafficking. Most of the underlying
molecular mechanisms of canalization still remain enigmatic. What is known so
far is that canonical auxin signaling is indispensable but also other non-canonical
signaling components are thought to play a role. In order to shed light into the
mysteries auf auxin canalization this study revisits the branches of auxin signaling
in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like
responses but does not directly activate canonical transcriptional auxin signaling.
We revisit the direct auxin effect on PIN trafficking where we found that, contradictory
to previous observations, auxin is very specifically promoting endocytosis of
PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular
processes related to PIN subcellular dynamics are involved in the establishment
of auxin conducting channels and the formation of vascular tissue. We are re-evaluating
the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture
about its developmental phneotypes and involvement in auxin signaling and canalization.
Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL)
and auxin and found that SL is interfering with essentially all processes involved
in auxin canalization in a non-transcriptional manner. Lastly we identify a new
way of SL perception and signaling which is emanating from mitochondria, is independent
of canonical SL signaling and is modulating primary root growth.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
citation:
ama: Gallei MC. Auxin and strigolactone non-canonical signaling regulating development
in Arabidopsis thaliana. 2022. doi:10.15479/at:ista:11626
apa: Gallei, M. C. (2022). Auxin and strigolactone non-canonical signaling regulating
development in Arabidopsis thaliana. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:11626
chicago: Gallei, Michelle C. “Auxin and Strigolactone Non-Canonical Signaling Regulating
Development in Arabidopsis Thaliana.” Institute of Science and Technology Austria,
2022. https://doi.org/10.15479/at:ista:11626.
ieee: M. C. Gallei, “Auxin and strigolactone non-canonical signaling regulating
development in Arabidopsis thaliana,” Institute of Science and Technology Austria,
2022.
ista: Gallei MC. 2022. Auxin and strigolactone non-canonical signaling regulating
development in Arabidopsis thaliana. Institute of Science and Technology Austria.
mla: Gallei, Michelle C. Auxin and Strigolactone Non-Canonical Signaling Regulating
Development in Arabidopsis Thaliana. Institute of Science and Technology Austria,
2022, doi:10.15479/at:ista:11626.
short: M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development
in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022.
date_created: 2022-07-20T11:21:53Z
date_published: 2022-07-20T00:00:00Z
date_updated: 2024-10-29T10:22:45Z
day: '20'
ddc:
- '575'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JiFr
doi: 10.15479/at:ista:11626
ec_funded: 1
file:
- access_level: open_access
checksum: bd7ac35403cf5b4b2607287d2a104b3a
content_type: application/pdf
creator: mgallei
date_created: 2022-07-25T09:08:47Z
date_updated: 2022-07-25T09:08:47Z
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file_size: 19560720
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content_type: application/pdf
creator: mgallei
date_created: 2022-07-25T09:09:32Z
date_updated: 2022-07-25T09:39:58Z
description: This is the print version of the thesis including the full appendix
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creator: mgallei
date_created: 2022-07-25T11:48:45Z
date_updated: 2022-07-25T11:48:45Z
file_id: '11650'
file_name: Thesis_Gallei_Appendix.pdf
file_size: 15435966
relation: main_file
file_date_updated: 2022-07-25T11:48:45Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '248'
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication_identifier:
isbn:
- 978-3-99078-019-0
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9287'
relation: part_of_dissertation
status: public
- id: '7142'
relation: part_of_dissertation
status: public
- id: '7465'
relation: part_of_dissertation
status: public
- id: '8138'
relation: part_of_dissertation
status: public
- id: '6260'
relation: part_of_dissertation
status: public
- id: '8931'
relation: part_of_dissertation
status: public
- id: '10411'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Eilon
full_name: Shani, Eilon
last_name: Shani
title: Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis
thaliana
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '11636'
abstract:
- lang: eng
text: In [3], Poonen and Slavov recently developed a novel approach to Bertini irreducibility
theorems over an arbitrary field, based on random hyperplane slicing. In this
paper, we extend their work by proving an analogous bound for the dimension of
the exceptional locus in the setting of linear subspaces of higher codimensions.
article_number: '102085'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Philip
full_name: Kmentt, Philip
id: c90670c9-0bf0-11ed-86f5-ed522ece2fac
last_name: Kmentt
- first_name: Alec L
full_name: Shute, Alec L
id: 440EB050-F248-11E8-B48F-1D18A9856A87
last_name: Shute
orcid: 0000-0002-1812-2810
citation:
ama: Kmentt P, Shute AL. The Bertini irreducibility theorem for higher codimensional
slices. Finite Fields and their Applications. 2022;83(10). doi:10.1016/j.ffa.2022.102085
apa: Kmentt, P., & Shute, A. L. (2022). The Bertini irreducibility theorem for
higher codimensional slices. Finite Fields and Their Applications. Elsevier.
https://doi.org/10.1016/j.ffa.2022.102085
chicago: Kmentt, Philip, and Alec L Shute. “The Bertini Irreducibility Theorem for
Higher Codimensional Slices.” Finite Fields and Their Applications. Elsevier,
2022. https://doi.org/10.1016/j.ffa.2022.102085.
ieee: P. Kmentt and A. L. Shute, “The Bertini irreducibility theorem for higher
codimensional slices,” Finite Fields and their Applications, vol. 83, no.
10. Elsevier, 2022.
ista: Kmentt P, Shute AL. 2022. The Bertini irreducibility theorem for higher codimensional
slices. Finite Fields and their Applications. 83(10), 102085.
mla: Kmentt, Philip, and Alec L. Shute. “The Bertini Irreducibility Theorem for
Higher Codimensional Slices.” Finite Fields and Their Applications, vol.
83, no. 10, 102085, Elsevier, 2022, doi:10.1016/j.ffa.2022.102085.
short: P. Kmentt, A.L. Shute, Finite Fields and Their Applications 83 (2022).
date_created: 2022-07-24T22:01:41Z
date_published: 2022-10-01T00:00:00Z
date_updated: 2023-08-03T12:12:57Z
day: '01'
ddc:
- '510'
department:
- _id: TiBr
doi: 10.1016/j.ffa.2022.102085
external_id:
arxiv:
- '2111.06697'
isi:
- '000835490600001'
file:
- access_level: open_access
checksum: 3ca88decb1011180dc6de7e0862153e1
content_type: application/pdf
creator: dernst
date_created: 2023-02-02T07:56:34Z
date_updated: 2023-02-02T07:56:34Z
file_id: '12475'
file_name: 2022_FiniteFields_Kmentt.pdf
file_size: 247615
relation: main_file
success: 1
file_date_updated: 2023-02-02T07:56:34Z
has_accepted_license: '1'
intvolume: ' 83'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Finite Fields and their Applications
publication_identifier:
eissn:
- '10902465'
issn:
- '10715797'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Bertini irreducibility theorem for higher codimensional slices
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: 83
year: '2022'
...
---
_id: '11637'
abstract:
- lang: eng
text: The ability to detect and respond to acute oxygen (O2) shortages is indispensable
to aerobic life. The molecular mechanisms and circuits underlying this capacity
are poorly understood. Here, we characterize the behavioral responses of feeding
Caenorhabditis elegans to approximately 1% O2. Acute hypoxia triggers a bout of
turning maneuvers followed by a persistent switch to rapid forward movement as
animals seek to avoid and escape hypoxia. While the behavioral responses to 1%
O2 closely resemble those evoked by 21% O2, they have distinct molecular and circuit
underpinnings. Disrupting phosphodiesterases (PDEs), specific G proteins, or BBSome
function inhibits escape from 1% O2 due to increased cGMP signaling. A primary
source of cGMP is GCY-28, the ortholog of the atrial natriuretic peptide (ANP)
receptor. cGMP activates the protein kinase G EGL-4 and enhances neuroendocrine
secretion to inhibit acute responses to 1% O2. Triggering a rise in cGMP optogenetically
in multiple neurons, including AIA interneurons, rapidly and reversibly inhibits
escape from 1% O2. Ca2+ imaging reveals that a 7% to 1% O2 stimulus evokes a Ca2+
decrease in several neurons. Defects in mitochondrial complex I (MCI) and mitochondrial
complex I (MCIII), which lead to persistently high reactive oxygen species (ROS),
abrogate acute hypoxia responses. In particular, repressing the expression of
isp-1, which encodes the iron sulfur protein of MCIII, inhibits escape from 1%
O2 without affecting responses to 21% O2. Both genetic and pharmacological up-regulation
of mitochondrial ROS increase cGMP levels, which contribute to the reduced hypoxia
responses. Our results implicate ROS and precise regulation of intracellular cGMP
in the modulation of acute responses to hypoxia by C. elegans.
acknowledgement: ' This work was funded by H2020 European Research Council (ERC Advanced
grant, 269058 ACMO, https://erc.europa.eu/funding/advanced-grants) and Wellcome
Trust UK (Wellcome Investigator Award, 209504/Z/17/Z, https://wellcome.org/grant-funding/people-and-projects/grants-awarded/molecular-mechanisms-neural-circuit-function-0)
to M.d.B, and by H2020 European Research Council (ERC starting grant, 802653 OXYGEN
SENSING, https://erc.europa.eu/funding/starting-grants) and Vetenskapsrådet (VR
starting grant, 2018-02216, https://www.vr.se/english.html) to C.C. The funders
had no role in study design, data collection and analysis, decision to publish,
or preparation of the manuscript.'
article_number: e3001684
article_processing_charge: No
article_type: original
author:
- first_name: Lina
full_name: Zhao, Lina
last_name: Zhao
- first_name: Lorenz A.
full_name: Fenk, Lorenz A.
last_name: Fenk
- first_name: Lars
full_name: Nilsson, Lars
last_name: Nilsson
- first_name: Niko Paresh
full_name: Amin-Wetzel, Niko Paresh
id: E95D3014-9D8C-11E9-9C80-D2F8E5697425
last_name: Amin-Wetzel
- first_name: Nelson
full_name: Ramirez, Nelson
id: 39831956-E4FE-11E9-85DE-0DC7E5697425
last_name: Ramirez
- first_name: Mario
full_name: De Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: De Bono
orcid: 0000-0001-8347-0443
- first_name: Changchun
full_name: Chen, Changchun
last_name: Chen
citation:
ama: Zhao L, Fenk LA, Nilsson L, et al. ROS and cGMP signaling modulate persistent
escape from hypoxia in Caenorhabditis elegans. PLoS Biology. 2022;20(6).
doi:10.1371/journal.pbio.3001684
apa: Zhao, L., Fenk, L. A., Nilsson, L., Amin-Wetzel, N. P., Ramirez, N., de Bono,
M., & Chen, C. (2022). ROS and cGMP signaling modulate persistent escape from
hypoxia in Caenorhabditis elegans. PLoS Biology. Public Library of Science.
https://doi.org/10.1371/journal.pbio.3001684
chicago: Zhao, Lina, Lorenz A. Fenk, Lars Nilsson, Niko Paresh Amin-Wetzel, Nelson
Ramirez, Mario de Bono, and Changchun Chen. “ROS and CGMP Signaling Modulate Persistent
Escape from Hypoxia in Caenorhabditis Elegans.” PLoS Biology. Public Library
of Science, 2022. https://doi.org/10.1371/journal.pbio.3001684.
ieee: L. Zhao et al., “ROS and cGMP signaling modulate persistent escape
from hypoxia in Caenorhabditis elegans,” PLoS Biology, vol. 20, no. 6.
Public Library of Science, 2022.
ista: Zhao L, Fenk LA, Nilsson L, Amin-Wetzel NP, Ramirez N, de Bono M, Chen C.
2022. ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis
elegans. PLoS Biology. 20(6), e3001684.
mla: Zhao, Lina, et al. “ROS and CGMP Signaling Modulate Persistent Escape from
Hypoxia in Caenorhabditis Elegans.” PLoS Biology, vol. 20, no. 6, e3001684,
Public Library of Science, 2022, doi:10.1371/journal.pbio.3001684.
short: L. Zhao, L.A. Fenk, L. Nilsson, N.P. Amin-Wetzel, N. Ramirez, M. de Bono,
C. Chen, PLoS Biology 20 (2022).
date_created: 2022-07-24T22:01:42Z
date_published: 2022-06-21T00:00:00Z
date_updated: 2023-08-03T12:11:44Z
day: '21'
ddc:
- '570'
department:
- _id: MaDe
doi: 10.1371/journal.pbio.3001684
external_id:
isi:
- '000828679600001'
pmid:
- '35727855'
file:
- access_level: open_access
checksum: df4902f854ad76769d3203bfdc69f16c
content_type: application/pdf
creator: dernst
date_created: 2022-07-25T07:38:49Z
date_updated: 2022-07-25T07:38:49Z
file_id: '11643'
file_name: 2022_PLoSBiology_Zhao.pdf
file_size: 3721585
relation: main_file
success: 1
file_date_updated: 2022-07-25T07:38:49Z
has_accepted_license: '1'
intvolume: ' 20'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 23870BE8-32DE-11EA-91FC-C7463DDC885E
grant_number: 209504/A/17/Z
name: Molecular mechanisms of neural circuit function
publication: PLoS Biology
publication_identifier:
eissn:
- 1545-7885
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis
elegans
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: 20
year: '2022'
...
---
_id: '11638'
abstract:
- lang: eng
text: 'Statistical inference is central to many scientific endeavors, yet how it
works remains unresolved. Answering this requires a quantitative understanding
of the intrinsic interplay between statistical models, inference methods, and
the structure in the data. To this end, we characterize the efficacy of direct
coupling analysis (DCA)—a highly successful method for analyzing amino acid sequence
data—in inferring pairwise interactions from samples of ferromagnetic Ising models
on random graphs. Our approach allows for physically motivated exploration of
qualitatively distinct data regimes separated by phase transitions. We show that
inference quality depends strongly on the nature of data-generating distributions:
optimal accuracy occurs at an intermediate temperature where the detrimental effects
from macroscopic order and thermal noise are minimal. Importantly our results
indicate that DCA does not always outperform its local-statistics-based predecessors;
while DCA excels at low temperatures, it becomes inferior to simple correlation
thresholding at virtually all temperatures when data are limited. Our findings
offer insights into the regime in which DCA operates so successfully, and more
broadly, how inference interacts with the structure in the data.'
acknowledgement: This work was supported in part by the Alfred P. Sloan Foundation,
the Simons Foundation, the National Institutes of Health under Award No. R01EB026943,
and the National Science Foundation, through the Center for the Physics of Biological
Function (PHY-1734030).
article_number: '023240'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Vudtiwat
full_name: Ngampruetikorn, Vudtiwat
last_name: Ngampruetikorn
- first_name: Vedant
full_name: Sachdeva, Vedant
last_name: Sachdeva
- first_name: Johanna
full_name: Torrence, Johanna
last_name: Torrence
- first_name: Jan
full_name: Humplik, Jan
id: 2E9627A8-F248-11E8-B48F-1D18A9856A87
last_name: Humplik
- first_name: David J.
full_name: Schwab, David J.
last_name: Schwab
- first_name: Stephanie E.
full_name: Palmer, Stephanie E.
last_name: Palmer
citation:
ama: Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE.
Inferring couplings in networks across order-disorder phase transitions. Physical
Review Research. 2022;4(2). doi:10.1103/PhysRevResearch.4.023240
apa: Ngampruetikorn, V., Sachdeva, V., Torrence, J., Humplik, J., Schwab, D. J.,
& Palmer, S. E. (2022). Inferring couplings in networks across order-disorder
phase transitions. Physical Review Research. American Physical Society.
https://doi.org/10.1103/PhysRevResearch.4.023240
chicago: Ngampruetikorn, Vudtiwat, Vedant Sachdeva, Johanna Torrence, Jan Humplik,
David J. Schwab, and Stephanie E. Palmer. “Inferring Couplings in Networks across
Order-Disorder Phase Transitions.” Physical Review Research. American Physical
Society, 2022. https://doi.org/10.1103/PhysRevResearch.4.023240.
ieee: V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D. J. Schwab, and
S. E. Palmer, “Inferring couplings in networks across order-disorder phase transitions,”
Physical Review Research, vol. 4, no. 2. American Physical Society, 2022.
ista: Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE.
2022. Inferring couplings in networks across order-disorder phase transitions.
Physical Review Research. 4(2), 023240.
mla: Ngampruetikorn, Vudtiwat, et al. “Inferring Couplings in Networks across Order-Disorder
Phase Transitions.” Physical Review Research, vol. 4, no. 2, 023240, American
Physical Society, 2022, doi:10.1103/PhysRevResearch.4.023240.
short: V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D.J. Schwab, S.E.
Palmer, Physical Review Research 4 (2022).
date_created: 2022-07-24T22:01:42Z
date_published: 2022-06-24T00:00:00Z
date_updated: 2022-07-25T07:52:35Z
day: '24'
ddc:
- '530'
department:
- _id: GaTk
doi: 10.1103/PhysRevResearch.4.023240
external_id:
arxiv:
- '2106.02349'
file:
- access_level: open_access
checksum: ed6fdc2a3a096df785fa5f7b17b716c6
content_type: application/pdf
creator: dernst
date_created: 2022-07-25T07:47:23Z
date_updated: 2022-07-25T07:47:23Z
file_id: '11644'
file_name: 2022_PhysicalReviewResearch_Ngampruetikorn.pdf
file_size: 1379683
relation: main_file
success: 1
file_date_updated: 2022-07-25T07:47:23Z
funded_apc: '1'
has_accepted_license: '1'
intvolume: ' 4'
issue: '2'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Physical Review Research
publication_identifier:
issn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inferring couplings in networks across order-disorder phase transitions
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: 4
year: '2022'
...
---
_id: '11639'
abstract:
- lang: eng
text: We study the list decodability of different ensembles of codes over the real
alphabet under the assumption of an omniscient adversary. It is a well-known result
that when the source and the adversary have power constraints P and N respectively,
the list decoding capacity is equal to 1/2logP/N. Random spherical codes achieve
constant list sizes, and the goal of the present paper is to obtain a better understanding
of the smallest achievable list size as a function of the gap to capacity. We
show a reduction from arbitrary codes to spherical codes, and derive a lower bound
on the list size of typical random spherical codes. We also give an upper bound
on the list size achievable using nested Construction-A lattices and infinite
Construction-A lattices. We then define and study a class of infinite constellations
that generalize Construction-A lattices and prove upper and lower bounds for the
same. Other goodness properties such as packing goodness and AWGN goodness of
infinite constellations are proved along the way. Finally, we consider random
lattices sampled from the Haar distribution and show that if a certain conjecture
that originates in analytic number theory is true, then the list size grows as
a polynomial function of the gap-to-capacity.
acknowledgement: "This work was done when Shashank Vatedka was at the Chinese University
of Hong Kong, where he was supported in part by CUHK Direct Grants 4055039 and 4055077.
He would like to acknowledge funding from a seed grant offered by IIT Hyderabad
and the Start-up Research Grant (SRG/2020/000910) from the Science and Engineering
Board, India. Yihan Zhang has received funding from the European Union’s Horizon
2020 research and innovation programme\r\nunder grant agreement No 682203-ERC-[Inf-Speed-Tradeoff]."
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
citation:
ama: Zhang Y, Vatedka S. List decoding random Euclidean codes and Infinite constellations.
IEEE Transactions on Information Theory. 2022;68(12):7753-7786. doi:10.1109/TIT.2022.3189542
apa: Zhang, Y., & Vatedka, S. (2022). List decoding random Euclidean codes and
Infinite constellations. IEEE Transactions on Information Theory. IEEE.
https://doi.org/10.1109/TIT.2022.3189542
chicago: Zhang, Yihan, and Shashank Vatedka. “List Decoding Random Euclidean Codes
and Infinite Constellations.” IEEE Transactions on Information Theory.
IEEE, 2022. https://doi.org/10.1109/TIT.2022.3189542.
ieee: Y. Zhang and S. Vatedka, “List decoding random Euclidean codes and Infinite
constellations,” IEEE Transactions on Information Theory, vol. 68, no.
12. IEEE, pp. 7753–7786, 2022.
ista: Zhang Y, Vatedka S. 2022. List decoding random Euclidean codes and Infinite
constellations. IEEE Transactions on Information Theory. 68(12), 7753–7786.
mla: Zhang, Yihan, and Shashank Vatedka. “List Decoding Random Euclidean Codes and
Infinite Constellations.” IEEE Transactions on Information Theory, vol.
68, no. 12, IEEE, 2022, pp. 7753–86, doi:10.1109/TIT.2022.3189542.
short: Y. Zhang, S. Vatedka, IEEE Transactions on Information Theory 68 (2022) 7753–7786.
date_created: 2022-07-24T22:01:42Z
date_published: 2022-12-01T00:00:00Z
date_updated: 2023-08-03T12:12:19Z
day: '01'
department:
- _id: MaMo
doi: 10.1109/TIT.2022.3189542
external_id:
arxiv:
- '1901.03790'
isi:
- '000891796100007'
intvolume: ' 68'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1901.03790
month: '12'
oa: 1
oa_version: Preprint
page: 7753-7786
publication: IEEE Transactions on Information Theory
publication_identifier:
eissn:
- 1557-9654
issn:
- 0018-9448
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: List decoding random Euclidean codes and Infinite constellations
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 68
year: '2022'
...
---
_id: '11640'
abstract:
- lang: eng
text: Spatially explicit population genetic models have long been developed, yet
have rarely been used to test hypotheses about the spatial distribution of genetic
diversity or the genetic divergence between populations. Here, we use spatially
explicit coalescence simulations to explore the properties of the island and the
two-dimensional stepping stone models under a wide range of scenarios with spatio-temporal
variation in deme size. We avoid the simulation of genetic data, using the fact
that under the studied models, summary statistics of genetic diversity and divergence
can be approximated from coalescence times. We perform the simulations using gridCoal,
a flexible spatial wrapper for the software msprime (Kelleher et al., 2016, Theoretical
Population Biology, 95, 13) developed herein. In gridCoal, deme sizes can change
arbitrarily across space and time, as well as migration rates between individual
demes. We identify different factors that can cause a deviation from theoretical
expectations, such as the simulation time in comparison to the effective deme
size and the spatio-temporal autocorrelation across the grid. Our results highlight
that FST, a measure of the strength of population structure, principally depends
on recent demography, which makes it robust to temporal variation in deme size.
In contrast, the amount of genetic diversity is dependent on the distant past
when Ne is large, therefore longer run times are needed to estimate Ne than FST.
Finally, we illustrate the use of gridCoal on a real-world example, the range
expansion of silver fir (Abies alba Mill.) since the last glacial maximum, using
different degrees of spatio-temporal variation in deme size.
acknowledgement: ES was supported by an IST studentship provided by IST Austria. BT
was funded by the European Union's Horizon 2020 research and innovation programme
under the Marie Sklodowska-Curie Independent Fellowship (704172, RACE). This project
received further funding awarded to KC from the Swiss National Science Foundation
(SNSF CRSK-3_190288) and the Swiss Federal Research Institute WSL. We thank Nick
Barton for many invaluable discussions and his comments on the thesis chapter and
this manuscript. We thank Peter Ralph and Jerome Kelleher for useful discussions
and Bisschop Gertjan for comments on this manuscript. We thank Fortunat Joos for
providing us with the raw data from the LPX-Bern model for silver fir, and Willy
Tinner for helpful insights about the demographic history of silver fir. We also
thank the editor Alana Alexander for useful comments and advice on the manuscript.
Open access funding provided by Eidgenossische Technische Hochschule Zurich.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Eniko
full_name: Szep, Eniko
id: 485BB5A4-F248-11E8-B48F-1D18A9856A87
last_name: Szep
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Katalin
full_name: Csilléry, Katalin
last_name: Csilléry
citation:
ama: Szep E, Trubenova B, Csilléry K. Using gridCoal to assess whether standard
population genetic theory holds in the presence of spatio-temporal heterogeneity
in population size. Molecular Ecology Resources. 2022;22(8):2941-2955.
doi:10.1111/1755-0998.13676
apa: Szep, E., Trubenova, B., & Csilléry, K. (2022). Using gridCoal to assess
whether standard population genetic theory holds in the presence of spatio-temporal
heterogeneity in population size. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13676
chicago: Szep, Eniko, Barbora Trubenova, and Katalin Csilléry. “Using GridCoal to
Assess Whether Standard Population Genetic Theory Holds in the Presence of Spatio-Temporal
Heterogeneity in Population Size.” Molecular Ecology Resources. Wiley,
2022. https://doi.org/10.1111/1755-0998.13676.
ieee: E. Szep, B. Trubenova, and K. Csilléry, “Using gridCoal to assess whether
standard population genetic theory holds in the presence of spatio-temporal heterogeneity
in population size,” Molecular Ecology Resources, vol. 22, no. 8. Wiley,
pp. 2941–2955, 2022.
ista: Szep E, Trubenova B, Csilléry K. 2022. Using gridCoal to assess whether standard
population genetic theory holds in the presence of spatio-temporal heterogeneity
in population size. Molecular Ecology Resources. 22(8), 2941–2955.
mla: Szep, Eniko, et al. “Using GridCoal to Assess Whether Standard Population Genetic
Theory Holds in the Presence of Spatio-Temporal Heterogeneity in Population Size.”
Molecular Ecology Resources, vol. 22, no. 8, Wiley, 2022, pp. 2941–55,
doi:10.1111/1755-0998.13676.
short: E. Szep, B. Trubenova, K. Csilléry, Molecular Ecology Resources 22 (2022)
2941–2955.
date_created: 2022-07-24T22:01:43Z
date_published: 2022-11-01T00:00:00Z
date_updated: 2023-08-03T12:11:01Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/1755-0998.13676
ec_funded: 1
external_id:
isi:
- '000825873600001'
file:
- access_level: open_access
checksum: 3102e203e77b884bffffdbe8e548da88
content_type: application/pdf
creator: dernst
date_created: 2023-02-02T08:11:23Z
date_updated: 2023-02-02T08:11:23Z
file_id: '12477'
file_name: 2022_MolecularEcologyRes_Szep.pdf
file_size: 6431779
relation: main_file
success: 1
file_date_updated: 2023-02-02T08:11:23Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
issue: '8'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 2941-2955
project:
- _id: 25AEDD42-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '704172'
name: Rate of Adaptation in Changing Environment
publication: Molecular Ecology Resources
publication_identifier:
eissn:
- 1755-0998
issn:
- 1755-098X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Using gridCoal to assess whether standard population genetic theory holds in
the presence of spatio-temporal heterogeneity in population size
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 22
year: '2022'
...
---
_id: '11648'
abstract:
- lang: eng
text: 'Progress in structural membrane biology has been significantly accelerated
by the ongoing ''Resolution Revolution'' in cryo electron microscopy (cryo-EM).
In particular, structure determination by single particle analysis has evolved
into the most powerful method for atomic model building of multisubunit membrane
protein complexes. This has created an ever increasing demand in cryo-EM machine
time, which to satisfy is in need of new and affordable cryo electron microscopes.
Here, we review our experience in using the JEOL CRYO ARM 200 prototype for the
structure determination by single particle analysis of three different multisubunit
membrane complexes: the Thermus thermophilus V-type ATPase VO complex, the Thermosynechococcus
elongatus photosystem I monomer and the flagellar motor LP-ring from Salmonella
enterica.'
acknowledgement: "Cyclic Innovation for Clinical Empowerment (JP17pc0101020 from Japan
Agency for Medical Research and Development (AMED) to K.N. and G.K.); Platform Project
for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative
Drug Discovery and Life Science Research) from AMED (JP20am0101117 to K.N., JP16K07266
to Atsunori Oshima and C.G., JP22ama121001j0001 to Masaki Yamamoto, G.K., T.K. and
C.G.); a JSPS KAHKENHI\r\ngrant (20K06514 to J.K.) and a Grant-in-aid for JSPS fellows
(20J00162 to A.N.).\r\nWe are grateful for initiation and scientific support from
Matthias Rogner, Marc M. Nowaczyk, Anna Frank and ̈Yuko Misumi for the PSI monomer
project and also would like to thank Hideki Shigematsu for critical reading of the
manuscript. And we are indebted to the two anonymous reviewers who helped us to
improve our manuscript."
article_processing_charge: No
article_type: original
author:
- first_name: Christoph
full_name: Gerle, Christoph
last_name: Gerle
- first_name: Jun-ichi
full_name: Kishikawa, Jun-ichi
last_name: Kishikawa
- first_name: Tomoko
full_name: Yamaguchi, Tomoko
last_name: Yamaguchi
- first_name: Atsuko
full_name: Nakanishi, Atsuko
last_name: Nakanishi
- first_name: Mehmet Orkun
full_name: Çoruh, Mehmet Orkun
id: d25163e5-8d53-11eb-a251-e6dd8ea1b8ef
last_name: Çoruh
orcid: 0000-0002-3219-2022
- first_name: Fumiaki
full_name: Makino, Fumiaki
last_name: Makino
- first_name: Tomoko
full_name: Miyata, Tomoko
last_name: Miyata
- first_name: Akihiro
full_name: Kawamoto, Akihiro
last_name: Kawamoto
- first_name: Ken
full_name: Yokoyama, Ken
last_name: Yokoyama
- first_name: Keiichi
full_name: Namba, Keiichi
last_name: Namba
- first_name: Genji
full_name: Kurisu, Genji
last_name: Kurisu
- first_name: Takayuki
full_name: Kato, Takayuki
last_name: Kato
citation:
ama: Gerle C, Kishikawa J, Yamaguchi T, et al. Structures of multisubunit membrane
complexes with the CRYO ARM 200. Microscopy. 2022;71(5):249-261. doi:10.1093/jmicro/dfac037
apa: Gerle, C., Kishikawa, J., Yamaguchi, T., Nakanishi, A., Çoruh, M. O., Makino,
F., … Kato, T. (2022). Structures of multisubunit membrane complexes with the
CRYO ARM 200. Microscopy. Oxford University Press. https://doi.org/10.1093/jmicro/dfac037
chicago: Gerle, Christoph, Jun-ichi Kishikawa, Tomoko Yamaguchi, Atsuko Nakanishi,
Mehmet Orkun Çoruh, Fumiaki Makino, Tomoko Miyata, et al. “Structures of Multisubunit
Membrane Complexes with the CRYO ARM 200.” Microscopy. Oxford University
Press, 2022. https://doi.org/10.1093/jmicro/dfac037.
ieee: C. Gerle et al., “Structures of multisubunit membrane complexes with
the CRYO ARM 200,” Microscopy, vol. 71, no. 5. Oxford University Press,
pp. 249–261, 2022.
ista: Gerle C, Kishikawa J, Yamaguchi T, Nakanishi A, Çoruh MO, Makino F, Miyata
T, Kawamoto A, Yokoyama K, Namba K, Kurisu G, Kato T. 2022. Structures of multisubunit
membrane complexes with the CRYO ARM 200. Microscopy. 71(5), 249–261.
mla: Gerle, Christoph, et al. “Structures of Multisubunit Membrane Complexes with
the CRYO ARM 200.” Microscopy, vol. 71, no. 5, Oxford University Press,
2022, pp. 249–61, doi:10.1093/jmicro/dfac037.
short: C. Gerle, J. Kishikawa, T. Yamaguchi, A. Nakanishi, M.O. Çoruh, F. Makino,
T. Miyata, A. Kawamoto, K. Yokoyama, K. Namba, G. Kurisu, T. Kato, Microscopy
71 (2022) 249–261.
date_created: 2022-07-25T10:04:58Z
date_published: 2022-10-01T00:00:00Z
date_updated: 2023-08-03T12:13:37Z
day: '01'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1093/jmicro/dfac037
external_id:
isi:
- '000837950900001'
pmid:
- '35861182'
file:
- access_level: open_access
checksum: 23b51c163636bf9313f7f0818312e67e
content_type: application/pdf
creator: dernst
date_created: 2023-02-03T08:34:48Z
date_updated: 2023-02-03T08:34:48Z
file_id: '12498'
file_name: 2022_Microscopy_Gerle.pdf
file_size: 7812696
relation: main_file
success: 1
file_date_updated: 2023-02-03T08:34:48Z
has_accepted_license: '1'
intvolume: ' 71'
isi: 1
issue: '5'
keyword:
- Radiology
- Nuclear Medicine and imaging
- Instrumentation
- Structural Biology
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 249-261
pmid: 1
publication: Microscopy
publication_identifier:
eissn:
- 2050-5701
issn:
- 2050-5698
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structures of multisubunit membrane complexes with the CRYO ARM 200
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: 71
year: '2022'
...
---
_id: '11653'
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 A. 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 A. sp. Kazakhstan and several
asexual lineages of A. 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.
article_processing_charge: No
author:
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
citation:
ama: Elkrewi MN. Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome
evolution and contagious parthenogenesis in Artemia brine shrimp.” 2022. doi:10.15479/AT:ISTA:11653
apa: Elkrewi, M. N. (2022). Data from Elkrewi, Khauratovich, Toups et al. 2022,
“ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.”
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:11653
chicago: Elkrewi, Marwan N. “Data from Elkrewi, Khauratovich, Toups et Al. 2022,
‘ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.’”
Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:11653.
ieee: M. N. Elkrewi, “Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome
evolution and contagious parthenogenesis in Artemia brine shrimp.’” Institute
of Science and Technology Austria, 2022.
ista: Elkrewi MN. 2022. Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW
sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp’,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:11653.
mla: Elkrewi, Marwan N. Data from Elkrewi, Khauratovich, Toups et Al. 2022, “ZW
Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.”
Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:11653.
short: M.N. Elkrewi, (2022).
contributor:
- first_name: Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
- first_name: Uladzislava
last_name: Khauratovich
- first_name: Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
- first_name: Vincent K
id: 57854184-AAE0-11E9-8D04-98D6E5697425
last_name: Bett
- first_name: Andrea
id: 353FAC84-AE61-11E9-8BFC-00D3E5697425
last_name: Mrnjavac
- first_name: Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Luca
last_name: Sax
- first_name: Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
- first_name: Francisco
last_name: 'Hontoria '
- first_name: Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
date_created: 2022-07-26T11:01:47Z
date_published: 2022-08-05T00:00:00Z
date_updated: 2024-02-21T12:35:53Z
day: '05'
ddc:
- '570'
department:
- _id: GradSch
- _id: BeVi
doi: 10.15479/AT:ISTA:11653
file:
- access_level: open_access
checksum: 5f1d7c6d7ab5375ed2564521432bed0c
content_type: application/x-zip-compressed
creator: melkrewi
date_created: 2022-07-26T12:37:52Z
date_updated: 2022-08-08T22:30:04Z
description: |
The folder contains the following datasets (fasta files, and text files):
Sup. Dataset 1: Genome assemblies: A. sinica male high quality assembly, A. sp. Kazakhstan
male draft assembly
Sup. Dataset 2: Male transcriptome assemblies for A. sinica and A. franciscana
Sup. Dataset 3: Male and female coverage for A. sinica, A. sp. Kazakhstan, A. urmiana, and
A. parthenogenetica females and rare male.
Sup. Dataset 4: Artemia sinica Male:female FST per 1Kb window
Sup. Dataset 5: FASTA file with candidate W scaffolds
Sup. Dataset 6: Candidate W-derived transcripts and alignments
Sup. Dataset 7: Gene expression with genomic location
Sup. Dataset 8: VCF for asexual female and rare male
Sup. Dataset 9: FST between backcrossed asexual and control females (pooled analysis)
Sup. Dataset 10: VCF of backcrossed asexual and control females (individual analysis using
A. sp. Kazakhstan as the reference), and inferred ancestry
Sup. Dataset 11: GO and DE annotations of all the Artemia sinica transcripts and their
locations in the Artemia sinica male genome.
embargo: 2022-08-07
file_id: '11655'
file_name: Data.zip
file_size: 2209382998
relation: main_file
title: Supplementary Datasets
file_date_updated: 2022-08-08T22:30:04Z
has_accepted_license: '1'
month: '08'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12248'
relation: used_in_publication
status: public
status: public
title: Data from Elkrewi, Khauratovich, Toups et al. 2022, "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: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '11658'
abstract:
- lang: eng
text: The depth of a cell in an arrangement of n (non-vertical) great-spheres in
Sd is the number of great-spheres that pass above the cell. We prove Euler-type
relations, which imply extensions of the classic Dehn–Sommerville relations for
convex polytopes to sublevel sets of the depth function, and we use the relations
to extend the expressions for the number of faces of neighborly polytopes to the
number of cells of levels in neighborly arrangements.
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme,
grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant
no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization
in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35.
article_processing_charge: No
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Sebastiano
full_name: Cultrera di Montesano, Sebastiano
id: 34D2A09C-F248-11E8-B48F-1D18A9856A87
last_name: Cultrera di Montesano
orcid: 0000-0001-6249-0832
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Morteza
full_name: Saghafian, Morteza
id: f86f7148-b140-11ec-9577-95435b8df824
last_name: Saghafian
citation:
ama: 'Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Depth in arrangements:
Dehn–Sommerville–Euler relations with applications. Leibniz International Proceedings
on Mathematics.'
apa: 'Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., & Saghafian,
M. (n.d.). Depth in arrangements: Dehn–Sommerville–Euler relations with applications.
Leibniz International Proceedings on Mathematics. Schloss Dagstuhl - Leibniz
Zentrum für Informatik.'
chicago: 'Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner,
and Morteza Saghafian. “Depth in Arrangements: Dehn–Sommerville–Euler Relations
with Applications.” Leibniz International Proceedings on Mathematics. Schloss
Dagstuhl - Leibniz Zentrum für Informatik, n.d.'
ieee: 'R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “Depth
in arrangements: Dehn–Sommerville–Euler relations with applications,” Leibniz
International Proceedings on Mathematics. Schloss Dagstuhl - Leibniz Zentrum
für Informatik.'
ista: 'Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Depth in
arrangements: Dehn–Sommerville–Euler relations with applications. Leibniz International
Proceedings on Mathematics.'
mla: 'Biswas, Ranita, et al. “Depth in Arrangements: Dehn–Sommerville–Euler Relations
with Applications.” Leibniz International Proceedings on Mathematics, Schloss
Dagstuhl - Leibniz Zentrum für Informatik.'
short: R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, Leibniz
International Proceedings on Mathematics (n.d.).
date_created: 2022-07-27T09:27:34Z
date_published: 2022-07-27T00:00:00Z
date_updated: 2022-07-28T07:57:48Z
day: '27'
ddc:
- '510'
department:
- _id: GradSch
- _id: HeEd
ec_funded: 1
file:
- access_level: open_access
checksum: b2f511e8b1cae5f1892b0cdec341acac
content_type: application/pdf
creator: scultrer
date_created: 2022-07-27T09:25:53Z
date_updated: 2022-07-27T09:25:53Z
file_id: '11659'
file_name: D-S-E.pdf
file_size: 639266
relation: main_file
file_date_updated: 2022-07-27T09:25:53Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: The Wittgenstein Prize
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: Leibniz International Proceedings on Mathematics
publication_status: submitted
publisher: Schloss Dagstuhl - Leibniz Zentrum für Informatik
quality_controlled: '1'
status: public
title: 'Depth in arrangements: Dehn–Sommerville–Euler relations with applications'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...