---
_id: '12247'
abstract:
- lang: eng
text: Chromosomal inversions have been shown to play a major role in a local adaptation
by suppressing recombination between alternative arrangements and maintaining
beneficial allele combinations. However, so far, their importance relative to
the remaining genome remains largely unknown. Understanding the genetic architecture
of adaptation requires better estimates of how loci of different effect sizes
contribute to phenotypic variation. Here, we used three Swedish islands where
the marine snail Littorina saxatilis has repeatedly evolved into two distinct
ecotypes along a habitat transition. We estimated the contribution of inversion
polymorphisms to phenotypic divergence while controlling for polygenic effects
in the remaining genome using a quantitative genetics framework. We confirmed
the importance of inversions but showed that contributions of loci outside inversions
are of similar magnitude, with variable proportions dependent on the trait and
the population. Some inversions showed consistent effects across all sites, whereas
others exhibited site-specific effects, indicating that the genomic basis for
replicated phenotypic divergence is only partly shared. The contributions of sexual
dimorphism as well as environmental factors to phenotypic variation were significant
but minor compared to inversions and polygenic background. Overall, this integrated
approach provides insight into the multiple mechanisms contributing to parallel
phenotypic divergence.
acknowledgement: We thank everyone who helped with fieldwork, snail processing, and
DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise
Liabot, Irena Senčić, and Zuzanna Zagrodzka. We also thank Rui Faria and Jenny Larsson
for their contributions, with inversions and shell shape respectively. KJ was funded
by the Swedish research council Vetenskapsrådet, grant number 2017-03798. R.K.B.
and E.K. were funded by the European Research Council (ERC-2015-AdG-693030-BARRIERS).
R.K.B. was also funded by the Natural Environment Research Council and the Swedish
Research Council Vetenskapsrådet.
article_processing_charge: No
article_type: original
author:
- first_name: Eva L.
full_name: Koch, Eva L.
last_name: Koch
- first_name: Mark
full_name: Ravinet, Mark
last_name: Ravinet
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. Genetic architecture
of repeated phenotypic divergence in Littorina saxatilis evolution. Evolution.
2022;76(10):2332-2346. doi:10.1111/evo.14602
apa: Koch, E. L., Ravinet, M., Westram, A. M., Johannesson, K., & Butlin, R.
K. (2022). Genetic architecture of repeated phenotypic divergence in Littorina
saxatilis evolution. Evolution. Wiley. https://doi.org/10.1111/evo.14602
chicago: Koch, Eva L., Mark Ravinet, Anja M Westram, Kerstin Johannesson, and Roger
K. Butlin. “Genetic Architecture of Repeated Phenotypic Divergence in Littorina
Saxatilis Evolution.” Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14602.
ieee: E. L. Koch, M. Ravinet, A. M. Westram, K. Johannesson, and R. K. Butlin, “Genetic
architecture of repeated phenotypic divergence in Littorina saxatilis evolution,”
Evolution, vol. 76, no. 10. Wiley, pp. 2332–2346, 2022.
ista: Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. 2022. Genetic architecture
of repeated phenotypic divergence in Littorina saxatilis evolution. Evolution.
76(10), 2332–2346.
mla: Koch, Eva L., et al. “Genetic Architecture of Repeated Phenotypic Divergence
in Littorina Saxatilis Evolution.” Evolution, vol. 76, no. 10, Wiley, 2022,
pp. 2332–46, doi:10.1111/evo.14602.
short: E.L. Koch, M. Ravinet, A.M. Westram, K. Johannesson, R.K. Butlin, Evolution
76 (2022) 2332–2346.
date_created: 2023-01-16T09:54:15Z
date_published: 2022-10-01T00:00:00Z
date_updated: 2023-08-04T09:42:11Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/evo.14602
external_id:
isi:
- '000848449100001'
pmid:
- '35994296'
file:
- access_level: open_access
checksum: defd8a4bea61cf00a3c88d4a30e2728c
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T08:45:35Z
date_updated: 2023-01-30T08:45:35Z
file_id: '12439'
file_name: 2022_Evolution_Koch.pdf
file_size: 2990581
relation: main_file
success: 1
file_date_updated: 2023-01-30T08:45:35Z
fulldoi: https://doi.org/10.1111/evo.14602
has_accepted_license: '1'
intvolume: ' 76'
isi: 1
issue: '10'
keyword:
- General Agricultural and Biological Sciences
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 2332-2346
pmid: 1
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '13066'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis
evolution
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: 76
year: '2022'
...
---
_id: '12261'
abstract:
- lang: eng
text: 'Dose–response relationships are a general concept for quantitatively describing
biological systems across multiple scales, from the molecular to the whole-cell
level. A clinically relevant example is the bacterial growth response to antibiotics,
which is routinely characterized by dose–response curves. The shape of the dose–response
curve varies drastically between antibiotics and plays a key role in treatment,
drug interactions, and resistance evolution. However, the mechanisms shaping the
dose–response curve remain largely unclear. Here, we show in Escherichia coli
that the distinctively shallow dose–response curve of the antibiotic trimethoprim
is caused by a negative growth-mediated feedback loop: Trimethoprim slows growth,
which in turn weakens the effect of this antibiotic. At the molecular level, this
feedback is caused by the upregulation of the drug target dihydrofolate reductase
(FolA/DHFR). We show that this upregulation is not a specific response to trimethoprim
but follows a universal trend line that depends primarily on the growth rate,
irrespective of its cause. Rewiring the feedback loop alters the dose–response
curve in a predictable manner, which we corroborate using a mathematical model
of cellular resource allocation and growth. Our results indicate that growth-mediated
feedback loops may shape drug responses more generally and could be exploited
to design evolutionary traps that enable selection against drug resistance.'
acknowledged_ssus:
- _id: M-Shop
acknowledgement: This work was in part supported by Human Frontier Science Program
GrantRGP0042/2013, Marie Curie Career Integration Grant303507, AustrianScience Fund
(FWF) Grant P27201-B22, and German Research Foundation(DFG) Collaborative Research
Center (SFB)1310to TB. SAA was supportedby the European Union’s Horizon2020Research
and Innovation Programunder the Marie Skłodowska-Curie Grant agreement No707352.
We wouldlike to thank the Bollenbach group for regular fruitful discussions. We
areparticularly thankful for the technical assistance of Booshini Fernando andfor
discussions of the theoretical aspects with Gerrit Ansmann. We areindebted to Bor
Kavˇciˇc for invaluable advice, help with setting up theluciferase-based growth
monitoring system, and for sharing plasmids. Weacknowledge the IST Austria Miba
Machine Shop for their support inbuilding a housing for the stacker of the plate
reader, which enabled thehigh-throughput luciferase-based experiments. We are grateful
to RosalindAllen, Bor Kavˇciˇc and Dor Russ for feedback on the manuscript. Open
Accessfunding enabled and organized by Projekt DEAL.
article_number: e10490
article_processing_charge: No
article_type: original
author:
- first_name: Andreas
full_name: Angermayr, Andreas
id: 4677C796-F248-11E8-B48F-1D18A9856A87
last_name: Angermayr
orcid: 0000-0001-8619-2223
- first_name: Tin Yau
full_name: Pang, Tin Yau
last_name: Pang
- first_name: Guillaume
full_name: Chevereau, Guillaume
last_name: Chevereau
- first_name: Karin
full_name: Mitosch, Karin
id: 39B66846-F248-11E8-B48F-1D18A9856A87
last_name: Mitosch
- first_name: Martin J
full_name: Lercher, Martin J
last_name: Lercher
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. Growth‐mediated
negative feedback shapes quantitative antibiotic response. Molecular Systems
Biology. 2022;18(9). doi:10.15252/msb.202110490
apa: Angermayr, A., Pang, T. Y., Chevereau, G., Mitosch, K., Lercher, M. J., &
Bollenbach, M. T. (2022). Growth‐mediated negative feedback shapes quantitative
antibiotic response. Molecular Systems Biology. Embo Press. https://doi.org/10.15252/msb.202110490
chicago: Angermayr, Andreas, Tin Yau Pang, Guillaume Chevereau, Karin Mitosch, Martin
J Lercher, and Mark Tobias Bollenbach. “Growth‐mediated Negative Feedback Shapes
Quantitative Antibiotic Response.” Molecular Systems Biology. Embo Press,
2022. https://doi.org/10.15252/msb.202110490.
ieee: A. Angermayr, T. Y. Pang, G. Chevereau, K. Mitosch, M. J. Lercher, and M.
T. Bollenbach, “Growth‐mediated negative feedback shapes quantitative antibiotic
response,” Molecular Systems Biology, vol. 18, no. 9. Embo Press, 2022.
ista: Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. 2022.
Growth‐mediated negative feedback shapes quantitative antibiotic response. Molecular
Systems Biology. 18(9), e10490.
mla: Angermayr, Andreas, et al. “Growth‐mediated Negative Feedback Shapes Quantitative
Antibiotic Response.” Molecular Systems Biology, vol. 18, no. 9, e10490,
Embo Press, 2022, doi:10.15252/msb.202110490.
short: A. Angermayr, T.Y. Pang, G. Chevereau, K. Mitosch, M.J. Lercher, M.T. Bollenbach,
Molecular Systems Biology 18 (2022).
date_created: 2023-01-16T09:58:34Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2025-06-11T14:10:18Z
day: '01'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.15252/msb.202110490
external_id:
isi:
- '000856482800001'
pmid:
- '36124745'
file:
- access_level: open_access
checksum: 8b1d8f5ea20c8408acf466435fb6ae01
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T09:49:55Z
date_updated: 2023-01-30T09:49:55Z
file_id: '12446'
file_name: 2022_MolecularSystemsBio_Angermayr.pdf
file_size: 1098812
relation: main_file
success: 1
file_date_updated: 2023-01-30T09:49:55Z
fulldoi: https://doi.org/10.15252/msb.202110490
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '9'
keyword:
- Applied Mathematics
- Computational Theory and Mathematics
- General Agricultural and Biological Sciences
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- Information Systems
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Molecular Systems Biology
publication_identifier:
eissn:
- 1744-4292
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Growth‐mediated negative feedback shapes quantitative antibiotic response
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2022'
...
---
_id: '12275'
abstract:
- lang: eng
text: N-glycans are molecularly diverse sugars borne by over 70% of proteins transiting
the secretory pathway and have been implicated in protein folding, stability,
and localization. Mutations in genes important for N-glycosylation result in congenital
disorders of glycosylation that are often associated with intellectual disability.
Here, we show that structurally distinct N-glycans regulate an extracellular protein
complex involved in the patterning of somatosensory dendrites in Caenorhabditis
elegans. Specifically, aman-2/Golgi alpha-mannosidase II, a conserved key enzyme
in the biosynthesis of specific N-glycans, regulates the activity of the Menorin
adhesion complex without obviously affecting the protein stability and localization
of its components. AMAN-2 functions cell-autonomously to allow for decoration
of the neuronal transmembrane receptor DMA-1/LRR-TM with the correct set of high-mannose/hybrid/paucimannose
N-glycans. Moreover, distinct types of N-glycans on specific N-glycosylation sites
regulate DMA-1/LRR-TM receptor function, which, together with three other extracellular
proteins, forms the Menorin adhesion complex. In summary, specific N-glycan structures
regulate dendrite patterning by coordinating the activity of an extracellular
adhesion complex, suggesting that the molecular diversity of N-glycans can contribute
to developmental specificity in the nervous system.
acknowledgement: 'We thank Scott Garforth, Sarah Garrett, Peri Kurshan, Yehuda Salzberg,
PamelaStanley, Robert Townley, and members of the B€ulow laboratory for commentson
the manuscript or helpful discussions during the course of this work. Wethank David
Miller, Shohei Mitani, Kang Shen, and Iain Wilson for reagents,and Yuji Kohara for
theyk11g705cDNA clone. We are grateful to MeeraTrivedi for sharing thedzIs117strain
prior to publication. Some strains wereprovided by the Caenorhabditis Genome Center
(funded by the NIH Office ofResearch Infrastructure Programs P40OD010440). This
work was supportedby grants from the National Institute of Health (NIH): R01NS096672andR21NS111145to
HEB; F31NS100370to MR; T32GM007288and F31HD066967to CADB; P30HD071593to Albert Einstein
College of Medicine. We acknowl-edge support to MR by the Department of Neuroscience.
NJRS was the recipi-ent of a Colciencias-Fulbright Fellowship and HEB of an Irma
T. Hirschl/Monique Weill-Caulier research fellowship'
article_number: e54163
article_processing_charge: No
article_type: original
author:
- first_name: Maisha
full_name: Rahman, Maisha
last_name: Rahman
- first_name: Nelson
full_name: Ramirez, Nelson
id: 39831956-E4FE-11E9-85DE-0DC7E5697425
last_name: Ramirez
- first_name: Carlos A
full_name: Diaz‐Balzac, Carlos A
last_name: Diaz‐Balzac
- first_name: Hannes E
full_name: Bülow, Hannes E
last_name: Bülow
citation:
ama: Rahman M, Ramirez N, Diaz‐Balzac CA, Bülow HE. Specific N-glycans regulate
an extracellular adhesion complex during somatosensory dendrite patterning. EMBO
Reports. 2022;23(7). doi:10.15252/embr.202154163
apa: Rahman, M., Ramirez, N., Diaz‐Balzac, C. A., & Bülow, H. E. (2022). Specific
N-glycans regulate an extracellular adhesion complex during somatosensory dendrite
patterning. EMBO Reports. Embo Press. https://doi.org/10.15252/embr.202154163
chicago: Rahman, Maisha, Nelson Ramirez, Carlos A Diaz‐Balzac, and Hannes E Bülow.
“Specific N-Glycans Regulate an Extracellular Adhesion Complex during Somatosensory
Dendrite Patterning.” EMBO Reports. Embo Press, 2022. https://doi.org/10.15252/embr.202154163.
ieee: M. Rahman, N. Ramirez, C. A. Diaz‐Balzac, and H. E. Bülow, “Specific N-glycans
regulate an extracellular adhesion complex during somatosensory dendrite patterning,”
EMBO Reports, vol. 23, no. 7. Embo Press, 2022.
ista: Rahman M, Ramirez N, Diaz‐Balzac CA, Bülow HE. 2022. Specific N-glycans regulate
an extracellular adhesion complex during somatosensory dendrite patterning. EMBO
Reports. 23(7), e54163.
mla: Rahman, Maisha, et al. “Specific N-Glycans Regulate an Extracellular Adhesion
Complex during Somatosensory Dendrite Patterning.” EMBO Reports, vol. 23,
no. 7, e54163, Embo Press, 2022, doi:10.15252/embr.202154163.
short: M. Rahman, N. Ramirez, C.A. Diaz‐Balzac, H.E. Bülow, EMBO Reports 23 (2022).
date_created: 2023-01-16T10:01:44Z
date_published: 2022-07-05T00:00:00Z
date_updated: 2026-06-18T17:26:25Z
day: '05'
ddc:
- '570'
department:
- _id: MaDe
doi: 10.15252/embr.202154163
external_id:
isi:
- '000797302700001'
pmid:
- '35586945'
fulldoi: https://doi.org/10.15252/embr.202154163
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
issue: '7'
keyword:
- Genetics
- Molecular Biology
- Biochemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.15252/embr.202154163
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: EMBO Reports
publication_identifier:
eissn:
- 1469-3178
issn:
- 1469-221X
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Specific N-glycans regulate an extracellular adhesion complex during somatosensory
dendrite patterning
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2022'
...
---
_id: '12280'
abstract:
- lang: eng
text: 'In repeated interactions, players can use strategies that respond to the
outcome of previous rounds. Much of the existing literature on direct reciprocity
assumes that all competing individuals use the same strategy space. Here, we study
both learning and evolutionary dynamics of players that differ in the strategy
space they explore. We focus on the infinitely repeated donation game and compare
three natural strategy spaces: memory-1 strategies, which consider the last moves
of both players, reactive strategies, which respond to the last move of the co-player,
and unconditional strategies. These three strategy spaces differ in the memory
capacity that is needed. We compute the long term average payoff that is achieved
in a pairwise learning process. We find that smaller strategy spaces can dominate
larger ones. For weak selection, unconditional players dominate both reactive
and memory-1 players. For intermediate selection, reactive players dominate memory-1
players. Only for strong selection and low cost-to-benefit ratio, memory-1 players
dominate the others. We observe that the supergame between strategy spaces can
be a social dilemma: maximum payoff is achieved if both players explore a larger
strategy space, but smaller strategy spaces dominate.'
acknowledgement: "This work was supported by the European Research Council (https://erc.europa.eu/)\r\nCoG
863818 (ForM-SMArt) (to K.C.), and the European Research Council Starting Grant
850529: E-DIRECT (to C.H.). The funders had no role in study design, data collection
and analysis, decision to publish, or preparation of the manuscript."
article_number: e1010149
article_processing_charge: No
article_type: original
author:
- first_name: Laura
full_name: Schmid, Laura
id: 38B437DE-F248-11E8-B48F-1D18A9856A87
last_name: Schmid
orcid: 0000-0002-6978-7329
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Schmid L, Hilbe C, Chatterjee K, Nowak M. Direct reciprocity between individuals
that use different strategy spaces. PLOS Computational Biology. 2022;18(6).
doi:10.1371/journal.pcbi.1010149
apa: Schmid, L., Hilbe, C., Chatterjee, K., & Nowak, M. (2022). Direct reciprocity
between individuals that use different strategy spaces. PLOS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1010149
chicago: Schmid, Laura, Christian Hilbe, Krishnendu Chatterjee, and Martin Nowak.
“Direct Reciprocity between Individuals That Use Different Strategy Spaces.” PLOS
Computational Biology. Public Library of Science, 2022. https://doi.org/10.1371/journal.pcbi.1010149.
ieee: L. Schmid, C. Hilbe, K. Chatterjee, and M. Nowak, “Direct reciprocity between
individuals that use different strategy spaces,” PLOS Computational Biology,
vol. 18, no. 6. Public Library of Science, 2022.
ista: Schmid L, Hilbe C, Chatterjee K, Nowak M. 2022. Direct reciprocity between
individuals that use different strategy spaces. PLOS Computational Biology. 18(6),
e1010149.
mla: Schmid, Laura, et al. “Direct Reciprocity between Individuals That Use Different
Strategy Spaces.” PLOS Computational Biology, vol. 18, no. 6, e1010149,
Public Library of Science, 2022, doi:10.1371/journal.pcbi.1010149.
short: L. Schmid, C. Hilbe, K. Chatterjee, M. Nowak, PLOS Computational Biology
18 (2022).
corr_author: '1'
date_created: 2023-01-16T10:02:51Z
date_published: 2022-06-14T00:00:00Z
date_updated: 2025-04-14T07:52:47Z
day: '14'
ddc:
- '000'
- '570'
department:
- _id: KrCh
doi: 10.1371/journal.pcbi.1010149
ec_funded: 1
external_id:
isi:
- '000843626800031'
pmid:
- '35700167'
file:
- access_level: open_access
checksum: 31b6b311b6731f1658277a9dfff6632c
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T11:28:13Z
date_updated: 2023-01-30T11:28:13Z
file_id: '12460'
file_name: 2022_PlosCompBio_Schmid.pdf
file_size: 3143222
relation: main_file
success: 1
file_date_updated: 2023-01-30T11:28:13Z
fulldoi: https://doi.org/10.1371/journal.pcbi.1010149
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '6'
keyword:
- Computational Theory and Mathematics
- Cellular and Molecular Neuroscience
- Genetics
- Molecular Biology
- Ecology
- Modeling and Simulation
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: PLOS Computational Biology
publication_identifier:
eissn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Direct reciprocity between individuals that use different strategy spaces
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 18
year: '2022'
...
---
_id: '12288'
abstract:
- lang: eng
text: To understand the function of neuronal circuits, it is crucial to disentangle
the connectivity patterns within the network. However, most tools currently used
to explore connectivity have low throughput, low selectivity, or limited accessibility.
Here, we report the development of an improved packaging system for the production
of the highly neurotropic RVdGenvA-CVS-N2c rabies viral vectors, yielding titers
orders of magnitude higher with no background contamination, at a fraction of
the production time, while preserving the efficiency of transsynaptic labeling.
Along with the production pipeline, we developed suites of ‘starter’ AAV and bicistronic
RVdG-CVS-N2c vectors, enabling retrograde labeling from a wide range of neuronal
populations, tailored for diverse experimental requirements. We demonstrate the
power and flexibility of the new system by uncovering hidden local and distal
inhibitory connections in the mouse hippocampal formation and by imaging the functional
properties of a cortical microcircuit across weeks. Our novel production pipeline
provides a convenient approach to generate new rabies vectors, while our toolkit
flexibly and efficiently expands the current capacity to label, manipulate and
image the neuronal activity of interconnected neuronal circuits in vitro and in
vivo.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: We thank F Marr for technical assistance, A Murray for RVdG-CVS-N2c
viruses and Neuro2A packaging cell-lines and J Watson for reading the manuscript.
This research was supported by the Scientific Service Units (SSU) of IST-Austria
through resources provided by the Imaging and Optics Facility (IOF) and the Preclinical
Facility (PCF). This project was funded by the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation programme (ERC advanced
grant No 692692, PJ, ERC starting grant No 756502, MJ), the Fond zur Förderung der
Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award, PJ), the Human Frontier
Science Program (LT000256/2018-L, AS) and EMBO (ALTF 1098-2017, AS).
article_number: '79848'
article_processing_charge: No
article_type: original
author:
- first_name: Anton L
full_name: Sumser, Anton L
id: 3320A096-F248-11E8-B48F-1D18A9856A87
last_name: Sumser
orcid: 0000-0002-4792-1881
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Yoav
full_name: Ben Simon, Yoav
id: 43DF3136-F248-11E8-B48F-1D18A9856A87
last_name: Ben Simon
citation:
ama: Sumser AL, Jösch MA, Jonas PM, Ben Simon Y. Fast, high-throughput production
of improved rabies viral vectors for specific, efficient and versatile transsynaptic
retrograde labeling. eLife. 2022;11. doi:10.7554/elife.79848
apa: Sumser, A. L., Jösch, M. A., Jonas, P. M., & Ben Simon, Y. (2022). Fast,
high-throughput production of improved rabies viral vectors for specific, efficient
and versatile transsynaptic retrograde labeling. ELife. eLife Sciences
Publications. https://doi.org/10.7554/elife.79848
chicago: Sumser, Anton L, Maximilian A Jösch, Peter M Jonas, and Yoav Ben Simon.
“Fast, High-Throughput Production of Improved Rabies Viral Vectors for Specific,
Efficient and Versatile Transsynaptic Retrograde Labeling.” ELife. eLife
Sciences Publications, 2022. https://doi.org/10.7554/elife.79848.
ieee: A. L. Sumser, M. A. Jösch, P. M. Jonas, and Y. Ben Simon, “Fast, high-throughput
production of improved rabies viral vectors for specific, efficient and versatile
transsynaptic retrograde labeling,” eLife, vol. 11. eLife Sciences Publications,
2022.
ista: Sumser AL, Jösch MA, Jonas PM, Ben Simon Y. 2022. Fast, high-throughput production
of improved rabies viral vectors for specific, efficient and versatile transsynaptic
retrograde labeling. eLife. 11, 79848.
mla: Sumser, Anton L., et al. “Fast, High-Throughput Production of Improved Rabies
Viral Vectors for Specific, Efficient and Versatile Transsynaptic Retrograde Labeling.”
ELife, vol. 11, 79848, eLife Sciences Publications, 2022, doi:10.7554/elife.79848.
short: A.L. Sumser, M.A. Jösch, P.M. Jonas, Y. Ben Simon, ELife 11 (2022).
corr_author: '1'
date_created: 2023-01-16T10:04:15Z
date_published: 2022-09-15T00:00:00Z
date_updated: 2025-04-15T08:29:05Z
day: '15'
ddc:
- '570'
department:
- _id: MaJö
- _id: PeJo
doi: 10.7554/elife.79848
ec_funded: 1
external_id:
isi:
- '000892204300001'
pmid:
- '36040301'
file:
- access_level: open_access
checksum: 5a2a65e3e7225090c3d8199f3bbd7b7b
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T11:50:53Z
date_updated: 2023-01-30T11:50:53Z
file_id: '12463'
file_name: 2022_eLife_Sumser.pdf
file_size: 8506811
relation: main_file
success: 1
file_date_updated: 2023-01-30T11:50:53Z
fulldoi: https://doi.org/10.7554/elife.79848
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 2634E9D2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '756502'
name: Circuits of Visual Attention
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
- _id: 266D407A-B435-11E9-9278-68D0E5697425
grant_number: LT000256
name: Neuronal networks of salience and spatial detection in the murine superior
colliculus
- _id: 264FEA02-B435-11E9-9278-68D0E5697425
grant_number: ALTF 1098-2017
name: Connecting sensory with motor processing in the superior colliculus
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fast, high-throughput production of improved rabies viral vectors for specific,
efficient and versatile transsynaptic retrograde labeling
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: 11
year: '2022'
...
---
_id: '12670'
abstract:
- lang: eng
text: DNA methylation plays essential homeostatic functions in eukaryotic genomes.
In animals, DNA methylation is also developmentally regulated and, in turn, regulates
development. In the past two decades, huge research effort has endorsed the understanding
that DNA methylation plays a similar role in plant development, especially during
sexual reproduction. The power of whole-genome sequencing and cell isolation techniques,
as well as bioinformatics tools, have enabled recent studies to reveal dynamic
changes in DNA methylation during germline development. Furthermore, the combination
of these technological advances with genetics, developmental biology and cell
biology tools has revealed functional methylation reprogramming events that control
gene and transposon activities in flowering plant germlines. In this review, we
discuss the major advances in our knowledge of DNA methylation dynamics during
male and female germline development in flowering plants.
article_processing_charge: No
article_type: review
author:
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: He S, Feng X. DNA methylation dynamics during germline development. Journal
of Integrative Plant Biology. 2022;64(12):2240-2251. doi:10.1111/jipb.13422
apa: He, S., & Feng, X. (2022). DNA methylation dynamics during germline development.
Journal of Integrative Plant Biology. Wiley. https://doi.org/10.1111/jipb.13422
chicago: He, Shengbo, and Xiaoqi Feng. “DNA Methylation Dynamics during Germline
Development.” Journal of Integrative Plant Biology. Wiley, 2022. https://doi.org/10.1111/jipb.13422.
ieee: S. He and X. Feng, “DNA methylation dynamics during germline development,”
Journal of Integrative Plant Biology, vol. 64, no. 12. Wiley, pp. 2240–2251,
2022.
ista: He S, Feng X. 2022. DNA methylation dynamics during germline development.
Journal of Integrative Plant Biology. 64(12), 2240–2251.
mla: He, Shengbo, and Xiaoqi Feng. “DNA Methylation Dynamics during Germline Development.”
Journal of Integrative Plant Biology, vol. 64, no. 12, Wiley, 2022, pp.
2240–51, doi:10.1111/jipb.13422.
short: S. He, X. Feng, Journal of Integrative Plant Biology 64 (2022) 2240–2251.
date_created: 2023-02-23T09:15:57Z
date_published: 2022-12-07T00:00:00Z
date_updated: 2024-10-14T12:03:14Z
day: '07'
department:
- _id: XiFe
doi: 10.1111/jipb.13422
extern: '1'
external_id:
pmid:
- '36478632'
fulldoi: https://doi.org/10.1111/jipb.13422
intvolume: ' 64'
issue: '12'
keyword:
- Plant Science
- General Biochemistry
- Genetics and Molecular Biology
- Biochemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jipb.13422
month: '12'
oa: 1
oa_version: Published Version
page: 2240-2251
pmid: 1
publication: Journal of Integrative Plant Biology
publication_identifier:
eissn:
- 1744-7909
issn:
- 1672-9072
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation dynamics during germline development
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 64
year: '2022'
...
---
_id: '15133'
abstract:
- lang: eng
text: In the evolutionary arms race against phage, bacteria have assembled a diverse
arsenal of antiviral immune strategies. While the recently discovered DISARM (Defense
Island System Associated with Restriction-Modification) systems can provide protection
against a wide range of phage, the molecular mechanisms that underpin broad antiviral
targeting but avoiding autoimmunity remain enigmatic. Here, we report cryo-EM
structures of the core DISARM complex, DrmAB, both alone and in complex with an
unmethylated phage DNA mimetic. These structures reveal that DrmAB core complex
is autoinhibited by a trigger loop (TL) within DrmA and binding to DNA substrates
containing a 5′ overhang dislodges the TL, initiating a long-range structural
rearrangement for DrmAB activation. Together with structure-guided in vivo studies,
our work provides insights into the mechanism of phage DNA recognition and specific
activation of this widespread antiviral defense system.
article_number: '2987'
article_processing_charge: Yes
article_type: original
author:
- first_name: Jack Peter Kelly
full_name: Bravo, Jack Peter Kelly
id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e
last_name: Bravo
orcid: 0000-0003-0456-0753
- first_name: Cristian
full_name: Aparicio-Maldonado, Cristian
last_name: Aparicio-Maldonado
- first_name: Franklin L.
full_name: Nobrega, Franklin L.
last_name: Nobrega
- first_name: Stan J. J.
full_name: Brouns, Stan J. J.
last_name: Brouns
- first_name: David W.
full_name: Taylor, David W.
last_name: Taylor
citation:
ama: Bravo JPK, Aparicio-Maldonado C, Nobrega FL, Brouns SJJ, Taylor DW. Structural
basis for broad anti-phage immunity by DISARM. Nature Communications. 2022;13.
doi:10.1038/s41467-022-30673-1
apa: Bravo, J. P. K., Aparicio-Maldonado, C., Nobrega, F. L., Brouns, S. J. J.,
& Taylor, D. W. (2022). Structural basis for broad anti-phage immunity by
DISARM. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-30673-1
chicago: Bravo, Jack Peter Kelly, Cristian Aparicio-Maldonado, Franklin L. Nobrega,
Stan J. J. Brouns, and David W. Taylor. “Structural Basis for Broad Anti-Phage
Immunity by DISARM.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-30673-1.
ieee: J. P. K. Bravo, C. Aparicio-Maldonado, F. L. Nobrega, S. J. J. Brouns, and
D. W. Taylor, “Structural basis for broad anti-phage immunity by DISARM,” Nature
Communications, vol. 13. Springer Nature, 2022.
ista: Bravo JPK, Aparicio-Maldonado C, Nobrega FL, Brouns SJJ, Taylor DW. 2022.
Structural basis for broad anti-phage immunity by DISARM. Nature Communications.
13, 2987.
mla: Bravo, Jack Peter Kelly, et al. “Structural Basis for Broad Anti-Phage Immunity
by DISARM.” Nature Communications, vol. 13, 2987, Springer Nature, 2022,
doi:10.1038/s41467-022-30673-1.
short: J.P.K. Bravo, C. Aparicio-Maldonado, F.L. Nobrega, S.J.J. Brouns, D.W. Taylor,
Nature Communications 13 (2022).
date_created: 2024-03-20T10:41:59Z
date_published: 2022-05-27T00:00:00Z
date_updated: 2024-06-04T06:16:38Z
day: '27'
doi: 10.1038/s41467-022-30673-1
extern: '1'
external_id:
pmid:
- '35624106'
fulldoi: https://doi.org/10.1038/s41467-022-30673-1
intvolume: ' 13'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-022-30673-1
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structural basis for broad anti-phage immunity by DISARM
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2022'
...
---
_id: '15134'
abstract:
- lang: eng
text: CRISPR-Cas systems are adaptive immune systems that protect prokaryotes from
foreign nucleic acids, such as bacteriophages. Two of the most prevalent CRISPR-Cas
systems include type I and type III. Interestingly, the type I-D interference
proteins contain characteristic features of both type I and type III systems.
Here, we present the structures of type I-D Cascade bound to both a double-stranded
(ds)DNA and a single-stranded (ss)RNA target at 2.9 and 3.1 Å, respectively. We
show that type I-D Cascade is capable of specifically binding ssRNA and reveal
how PAM recognition of dsDNA targets initiates long-range structural rearrangements
that likely primes Cas10d for Cas3′ binding and subsequent non-target strand DNA
cleavage. These structures allow us to model how binding of the anti-CRISPR protein
AcrID1 likely blocks target dsDNA binding via competitive inhibition of the DNA
substrate engagement with the Cas10d active site. This work elucidates the unique
mechanisms used by type I-D Cascade for discrimination of single-stranded and
double stranded targets. Thus, our data supports a model for the hybrid nature
of this complex with features of type III and type I systems.
article_number: '2829'
article_processing_charge: Yes
article_type: original
author:
- first_name: Evan A.
full_name: Schwartz, Evan A.
last_name: Schwartz
- first_name: Tess M.
full_name: McBride, Tess M.
last_name: McBride
- first_name: Jack Peter Kelly
full_name: Bravo, Jack Peter Kelly
id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e
last_name: Bravo
orcid: 0000-0003-0456-0753
- first_name: Daniel
full_name: Wrapp, Daniel
last_name: Wrapp
- first_name: Peter C.
full_name: Fineran, Peter C.
last_name: Fineran
- first_name: Robert D.
full_name: Fagerlund, Robert D.
last_name: Fagerlund
- first_name: David W.
full_name: Taylor, David W.
last_name: Taylor
citation:
ama: Schwartz EA, McBride TM, Bravo JPK, et al. Structural rearrangements allow
nucleic acid discrimination by type I-D Cascade. Nature Communications.
2022;13. doi:10.1038/s41467-022-30402-8
apa: Schwartz, E. A., McBride, T. M., Bravo, J. P. K., Wrapp, D., Fineran, P. C.,
Fagerlund, R. D., & Taylor, D. W. (2022). Structural rearrangements allow
nucleic acid discrimination by type I-D Cascade. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-022-30402-8
chicago: Schwartz, Evan A., Tess M. McBride, Jack Peter Kelly Bravo, Daniel Wrapp,
Peter C. Fineran, Robert D. Fagerlund, and David W. Taylor. “Structural Rearrangements
Allow Nucleic Acid Discrimination by Type I-D Cascade.” Nature Communications.
Springer Nature, 2022. https://doi.org/10.1038/s41467-022-30402-8.
ieee: E. A. Schwartz et al., “Structural rearrangements allow nucleic acid
discrimination by type I-D Cascade,” Nature Communications, vol. 13. Springer
Nature, 2022.
ista: Schwartz EA, McBride TM, Bravo JPK, Wrapp D, Fineran PC, Fagerlund RD, Taylor
DW. 2022. Structural rearrangements allow nucleic acid discrimination by type
I-D Cascade. Nature Communications. 13, 2829.
mla: Schwartz, Evan A., et al. “Structural Rearrangements Allow Nucleic Acid Discrimination
by Type I-D Cascade.” Nature Communications, vol. 13, 2829, Springer Nature,
2022, doi:10.1038/s41467-022-30402-8.
short: E.A. Schwartz, T.M. McBride, J.P.K. Bravo, D. Wrapp, P.C. Fineran, R.D. Fagerlund,
D.W. Taylor, Nature Communications 13 (2022).
date_created: 2024-03-20T10:42:05Z
date_published: 2022-05-20T00:00:00Z
date_updated: 2024-06-04T06:14:28Z
day: '20'
doi: 10.1038/s41467-022-30402-8
extern: '1'
external_id:
pmid:
- '35595728'
fulldoi: https://doi.org/10.1038/s41467-022-30402-8
intvolume: ' 13'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-022-30402-8
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structural rearrangements allow nucleic acid discrimination by type I-D Cascade
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2022'
...
---
_id: '10604'
abstract:
- lang: eng
text: Maternally inherited Wolbachia transinfections are being introduced into natural
mosquito populations to reduce the transmission of dengue, Zika, and other arboviruses.
Wolbachia-induced cytoplasmic incompatibility provides a frequency-dependent reproductive
advantage to infected females that can spread transinfections within and among
populations. However, because transinfections generally reduce host fitness, they
tend to spread within populations only after their frequency exceeds a critical
threshold. This produces bistability with stable equilibrium frequencies at both
0 and 1, analogous to the bistability produced by underdominance between alleles
or karyotypes and by population dynamics under Allee effects. Here, we analyze
how stochastic frequency variation produced by finite population size can facilitate
the local spread of variants with bistable dynamics into areas where invasion
is unexpected from deterministic models. Our exemplar is the establishment of
wMel Wolbachia in the Aedes aegypti population of Pyramid Estates (PE), a small
community in far north Queensland, Australia. In 2011, wMel was stably introduced
into Gordonvale, separated from PE by barriers to A. aegypti dispersal. After
nearly 6 years during which wMel was observed only at low frequencies in PE, corresponding
to an apparent equilibrium between immigration and selection, wMel rose to fixation
by 2018. Using analytic approximations and statistical analyses, we demonstrate
that the observed fixation of wMel at PE is consistent with both stochastic transition
past an unstable threshold frequency and deterministic transformation produced
by steady immigration at a rate just above the threshold required for deterministic
invasion. The indeterminacy results from a delicate balance of parameters needed
to produce the delayed transition observed. Our analyses suggest that once Wolbachia
transinfections are established locally through systematic introductions, stochastic
“threshold crossing” is likely to only minimally enhance spatial spread, providing
a local ratchet that slightly—but systematically—aids area-wide transformation
of disease-vector populations in heterogeneous landscapes.
acknowledgement: We thank S. O'Neill, C. Simmons, and the World Mosquito Project for
providing access to unpublished data. S. Ritchie provided valuable insights into
Aedes aegypti biology and the literature describing A. aegypti populations near
Cairns. We thank B. Cooper for help with the figures and D. Shropshire, S. O'Neill,
S. Ritchie, A. Hoffmann, B. Cooper, and members of the Cooper lab for comments on
an earlier draft. Comments from three reviewers greatly improved our presentation.
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Turelli M, Barton NH. Why did the Wolbachia transinfection cross the road?
Drift, deterministic dynamics, and disease control. Evolution Letters.
2022;6(1):92-105. doi:10.1002/evl3.270
apa: Turelli, M., & Barton, N. H. (2022). Why did the Wolbachia transinfection
cross the road? Drift, deterministic dynamics, and disease control. Evolution
Letters. Wiley. https://doi.org/10.1002/evl3.270
chicago: Turelli, Michael, and Nicholas H Barton. “Why Did the Wolbachia Transinfection
Cross the Road? Drift, Deterministic Dynamics, and Disease Control.” Evolution
Letters. Wiley, 2022. https://doi.org/10.1002/evl3.270.
ieee: M. Turelli and N. H. Barton, “Why did the Wolbachia transinfection cross the
road? Drift, deterministic dynamics, and disease control,” Evolution Letters,
vol. 6, no. 1. Wiley, pp. 92–105, 2022.
ista: Turelli M, Barton NH. 2022. Why did the Wolbachia transinfection cross the
road? Drift, deterministic dynamics, and disease control. Evolution Letters. 6(1),
92–105.
mla: Turelli, Michael, and Nicholas H. Barton. “Why Did the Wolbachia Transinfection
Cross the Road? Drift, Deterministic Dynamics, and Disease Control.” Evolution
Letters, vol. 6, no. 1, Wiley, 2022, pp. 92–105, doi:10.1002/evl3.270.
short: M. Turelli, N.H. Barton, Evolution Letters 6 (2022) 92–105.
date_created: 2022-01-09T09:45:17Z
date_published: 2022-02-01T00:00:00Z
date_updated: 2025-06-11T13:45:56Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1002/evl3.270
external_id:
isi:
- '000754412600008'
pmid:
- '35127140'
file:
- access_level: open_access
checksum: 7e9a37e3b65b480cd7014a6a4a7e460a
content_type: application/pdf
creator: dernst
date_created: 2022-07-29T06:59:10Z
date_updated: 2022-07-29T06:59:10Z
file_id: '11689'
file_name: 2022_EvolutionLetters_Turelli.pdf
file_size: 2435185
relation: main_file
success: 1
file_date_updated: 2022-07-29T06:59:10Z
fulldoi: https://doi.org/10.1002/evl3.270
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '1'
keyword:
- genetics
- ecology
- evolution
- behavior and systematics
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 92-105
pmid: 1
publication: Evolution Letters
publication_identifier:
eissn:
- 2056-3744
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '11686'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics,
and disease control
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2022'
...
---
_id: '11448'
abstract:
- lang: eng
text: Studies of protein fitness landscapes reveal biophysical constraints guiding
protein evolution and empower prediction of functional proteins. However, generalisation
of these findings is limited due to scarceness of systematic data on fitness landscapes
of proteins with a defined evolutionary relationship. We characterized the fitness
peaks of four orthologous fluorescent proteins with a broad range of sequence
divergence. While two of the four studied fitness peaks were sharp, the other
two were considerably flatter, being almost entirely free of epistatic interactions.
Mutationally robust proteins, characterized by a flat fitness peak, were not optimal
templates for machine-learning-driven protein design – instead, predictions were
more accurate for fragile proteins with epistatic landscapes. Our work paves insights
for practical application of fitness landscape heterogeneity in protein engineering.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
acknowledgement: "We thank Ondřej Draganov, Rodrigo Redondo, Bor Kavčič, Mia Juračić
and Andrea Pauli for discussion and technical advice. We thank Anita Testa Salmazo
for advice on resin protein purification, Dmitry Bolotin and the Milaboratory (milaboratory.com)
for access to computing and storage infrastructure, and Josef Houser and Eva Fujdiarova
for technical assistance and data interpretation. Core facility Biomolecular Interactions
and Crystallization of CEITEC Masaryk University is gratefully acknowledged for
the obtaining of the scientific data presented in this paper. This research was
supported by the Scientific Service Units (SSU) of IST-Austria\r\nthrough resources
provided by the Bioimaging Facility (BIF), and the Life Science Facility (LSF).
MiSeq and HiSeq NGS sequencing was performed by the Next Generation Sequencing Facility
at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC),
Austria. FACS was performed at the BioOptics Facility of the Institute of Molecular
Pathology (IMP), Austria. We also thank the Biomolecular Crystallography Facility
in the Vanderbilt University Center for Structural Biology. We are grateful to Joel
M Harp for help with X-ray data collection. This work was supported by the ERC Consolidator
grant to FAK (771209—CharFL). KSS acknowledges support by President’s Grant МК–5405.2021.1.4,
the Imperial College Research Fellowship and the MRC London Institute of Medical
Sciences (UKRI MC-A658-5QEA0).\r\nAF is supported by the Marie Skłodowska-Curie
Fellowship (H2020-MSCA-IF-2019, Grant Agreement No. 898203, Project acronym \"FLINDIP\").
Experiments were partially carried out using equipment provided by the Institute
of Bioorganic Chemistry of the Russian Academy of Sciences Сore Facility (CKP IBCH).
This work was supported by a Russian Science Foundation grant 19-74-10102.This project
has received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 665,385."
article_number: '75842'
article_processing_charge: No
article_type: original
author:
- first_name: Louisa
full_name: Gonzalez Somermeyer, Louisa
id: 4720D23C-F248-11E8-B48F-1D18A9856A87
last_name: Gonzalez Somermeyer
orcid: 0000-0001-9139-5383
- first_name: Aubin
full_name: Fleiss, Aubin
last_name: Fleiss
- first_name: Alexander S
full_name: Mishin, Alexander S
last_name: Mishin
- first_name: Nina G
full_name: Bozhanova, Nina G
last_name: Bozhanova
- first_name: Anna A
full_name: Igolkina, Anna A
last_name: Igolkina
- first_name: Jens
full_name: Meiler, Jens
last_name: Meiler
- first_name: Maria-Elisenda
full_name: Alaball Pujol, Maria-Elisenda
last_name: Alaball Pujol
- first_name: Ekaterina V
full_name: Putintseva, Ekaterina V
last_name: Putintseva
- first_name: Karen S
full_name: Sarkisyan, Karen S
last_name: Sarkisyan
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Gonzalez Somermeyer L, Fleiss A, Mishin AS, et al. Heterogeneity of the GFP
fitness landscape and data-driven protein design. eLife. 2022;11. doi:10.7554/elife.75842
apa: Gonzalez Somermeyer, L., Fleiss, A., Mishin, A. S., Bozhanova, N. G., Igolkina,
A. A., Meiler, J., … Kondrashov, F. (2022). Heterogeneity of the GFP fitness landscape
and data-driven protein design. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.75842
chicago: Gonzalez Somermeyer, Louisa, Aubin Fleiss, Alexander S Mishin, Nina G Bozhanova,
Anna A Igolkina, Jens Meiler, Maria-Elisenda Alaball Pujol, Ekaterina V Putintseva,
Karen S Sarkisyan, and Fyodor Kondrashov. “Heterogeneity of the GFP Fitness Landscape
and Data-Driven Protein Design.” ELife. eLife Sciences Publications, 2022.
https://doi.org/10.7554/elife.75842.
ieee: L. Gonzalez Somermeyer et al., “Heterogeneity of the GFP fitness landscape
and data-driven protein design,” eLife, vol. 11. eLife Sciences Publications,
2022.
ista: Gonzalez Somermeyer L, Fleiss A, Mishin AS, Bozhanova NG, Igolkina AA, Meiler
J, Alaball Pujol M-E, Putintseva EV, Sarkisyan KS, Kondrashov F. 2022. Heterogeneity
of the GFP fitness landscape and data-driven protein design. eLife. 11, 75842.
mla: Gonzalez Somermeyer, Louisa, et al. “Heterogeneity of the GFP Fitness Landscape
and Data-Driven Protein Design.” ELife, vol. 11, 75842, eLife Sciences
Publications, 2022, doi:10.7554/elife.75842.
short: L. Gonzalez Somermeyer, A. Fleiss, A.S. Mishin, N.G. Bozhanova, A.A. Igolkina,
J. Meiler, M.-E. Alaball Pujol, E.V. Putintseva, K.S. Sarkisyan, F. Kondrashov,
ELife 11 (2022).
corr_author: '1'
date_created: 2022-06-18T09:06:59Z
date_published: 2022-05-05T00:00:00Z
date_updated: 2026-10-02T11:21:40Z
day: '05'
ddc:
- '570'
department:
- _id: GradSch
- _id: FyKo
doi: 10.7554/elife.75842
ec_funded: 1
external_id:
isi:
- '000799197200001'
pmid:
- '35510622'
file:
- access_level: open_access
checksum: 7573c28f44028ab0cc81faef30039e44
content_type: application/pdf
creator: dernst
date_created: 2022-06-20T07:44:19Z
date_updated: 2022-06-20T07:44:19Z
file_id: '11454'
file_name: 2022_eLife_Somermeyer.pdf
file_size: 5297213
relation: main_file
success: 1
file_date_updated: 2022-06-20T07:44:19Z
fulldoi: https://doi.org/10.7554/elife.75842
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/aequorea238/Orthologous_GFP_Fitness_Peaks
record:
- id: '17850'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Heterogeneity of the GFP fitness landscape and data-driven protein design
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: 11
year: '2022'
...
---
_id: '10787'
abstract:
- lang: eng
text: "A species distributed across diverse environments may adapt to local conditions.
We ask how quickly such a species changes its range in response to changed conditions.
Szép et al. (Szép E, Sachdeva H, Barton NH. 2021 Polygenic local adaptation in
metapopulations: a stochastic eco-evolutionary model. Evolution75, 1030–1045 (doi:10.1111/evo.14210))
used the infinite island model to find the stationary distribution of allele frequencies
and deme sizes. We extend this to find how a metapopulation responds to changes
in carrying capacity, selection strength, or migration rate when deme sizes are
fixed. We further develop a ‘fixed-state’ approximation. Under this approximation,
polymorphism is only possible for a narrow range of habitat proportions when selection
is weak compared to drift, but for a much wider range otherwise. When rates of
selection or migration relative to drift change in a single deme of the metapopulation,
the population takes a time of order m−1 to reach the new equilibrium. However,
even with many loci, there can be substantial fluctuations in net adaptation,
because at each locus, alleles randomly get lost or fixed. Thus, in a finite metapopulation,
variation may gradually be lost by chance, even if it would persist in an infinite
metapopulation. When conditions change across the whole metapopulation, there
can be rapid change, which is predicted well by the fixed-state approximation.
This work helps towards an understanding of how metapopulations extend their range
across diverse environments.\r\nThis article is part of the theme issue ‘Species’
ranges in the face of changing environments (Part II)’."
acknowledgement: This research was partly funded by the Austrian Science Fund (FWF)
[FWF P-32896B].
article_processing_charge: No
article_type: original
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Oluwafunmilola O
full_name: Olusanya, Oluwafunmilola O
id: 41AD96DC-F248-11E8-B48F-1D18A9856A87
last_name: Olusanya
orcid: 0000-0003-1971-8314
citation:
ama: 'Barton NH, Olusanya OO. The response of a metapopulation to a changing environment.
Philosophical Transactions of the Royal Society B: Biological Sciences.
2022;377(1848). doi:10.1098/rstb.2021.0009'
apa: 'Barton, N. H., & Olusanya, O. O. (2022). The response of a metapopulation
to a changing environment. Philosophical Transactions of the Royal Society
B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2021.0009'
chicago: 'Barton, Nicholas H, and Oluwafunmilola O Olusanya. “The Response of a
Metapopulation to a Changing Environment.” Philosophical Transactions of the
Royal Society B: Biological Sciences. The Royal Society, 2022. https://doi.org/10.1098/rstb.2021.0009.'
ieee: 'N. H. Barton and O. O. Olusanya, “The response of a metapopulation to a changing
environment,” Philosophical Transactions of the Royal Society B: Biological
Sciences, vol. 377, no. 1848. The Royal Society, 2022.'
ista: 'Barton NH, Olusanya OO. 2022. The response of a metapopulation to a changing
environment. Philosophical Transactions of the Royal Society B: Biological Sciences.
377(1848).'
mla: 'Barton, Nicholas H., and Oluwafunmilola O. Olusanya. “The Response of a Metapopulation
to a Changing Environment.” Philosophical Transactions of the Royal Society
B: Biological Sciences, vol. 377, no. 1848, The Royal Society, 2022, doi:10.1098/rstb.2021.0009.'
short: 'N.H. Barton, O.O. Olusanya, Philosophical Transactions of the Royal Society
B: Biological Sciences 377 (2022).'
corr_author: '1'
date_created: 2022-02-21T16:08:10Z
date_published: 2022-04-11T00:00:00Z
date_updated: 2026-10-21T08:24:47Z
day: '11'
ddc:
- '570'
department:
- _id: GradSch
- _id: NiBa
doi: 10.1098/rstb.2021.0009
external_id:
isi:
- '000758140300001'
pmid:
- '35184588'
file:
- access_level: open_access
checksum: 3b0243738f01bf3c07e0d7e8dc64f71d
content_type: application/pdf
creator: dernst
date_created: 2022-08-02T06:14:32Z
date_updated: 2022-08-02T06:14:32Z
file_id: '11719'
file_name: 2022_PhilosophicalTransactionsRSB_Barton.pdf
file_size: 1349672
relation: main_file
success: 1
file_date_updated: 2022-08-02T06:14:32Z
fulldoi: https://doi.org/10.1098/rstb.2021.0009
has_accepted_license: '1'
intvolume: ' 377'
isi: 1
issue: '1848'
keyword:
- General Agricultural and Biological Sciences
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: c08d3278-5a5b-11eb-8a69-fdb09b55f4b8
grant_number: P32896
name: Causes and consequences of population fragmentation
publication: 'Philosophical Transactions of the Royal Society B: Biological Sciences'
publication_identifier:
eissn:
- 1471-2970
issn:
- 0962-8436
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
related_material:
record:
- id: '14711'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The response of a metapopulation to a changing environment
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 377
year: '2022'
...
---
_id: '11160'
abstract:
- lang: eng
text: Mutations in the chromodomain helicase DNA-binding 8 (CHD8) gene are a frequent
cause of autism spectrum disorder (ASD). While its phenotypic spectrum often encompasses
macrocephaly, implicating cortical abnormalities, how CHD8 haploinsufficiency
affects neurodevelopmental is unclear. Here, employing human cerebral organoids,
we find that CHD8 haploinsufficiency disrupted neurodevelopmental trajectories
with an accelerated and delayed generation of, respectively, inhibitory and excitatory
neurons that yields, at days 60 and 120, symmetrically opposite expansions in
their proportions. This imbalance is consistent with an enlargement of cerebral
organoids as an in vitro correlate of patients’ macrocephaly. Through an isogenic
design of patient-specific mutations and mosaic organoids, we define genotype-phenotype
relationships and uncover their cell-autonomous nature. Our results define cell-type-specific
CHD8-dependent molecular defects related to an abnormal program of proliferation
and alternative splicing. By identifying cell-type-specific effects of CHD8 mutations,
our study uncovers reproducible developmental alterations that may be employed
for neurodevelopmental disease modeling.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: We thank Farnaz Freeman for technical assistance. This research was
supported by the Scientific Service Units (SSU) of IST Austria through resources
provided by the Bioimaging Facility (BIF) and the Life Science Facility (LSF). This
work supported by the European Union’s Horizon 2020 research and innovation program
(ERC) grant 715508 to G.N. (REVERSEAUTISM) and grant 825759 to G.T. (ENDpoiNTs);
the Fondazione Cariplo 2017-0886 to A.L.T.; E-Rare-3 JTC 2018 IMPACT to M. Gabriele;
and the Austrian Science Fund FWF I 4205-B to G.N. Graphical abstract and figures
were created using BioRender.com.
article_number: '110615'
article_processing_charge: Yes
article_type: original
author:
- first_name: Carlo Emanuele
full_name: Villa, Carlo Emanuele
last_name: Villa
- first_name: Cristina
full_name: Cheroni, Cristina
last_name: Cheroni
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
orcid: 0000-0002-9033-9096
- first_name: Alejandro
full_name: López-Tóbon, Alejandro
last_name: López-Tóbon
- first_name: Bárbara
full_name: Oliveira, Bárbara
id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87
last_name: Oliveira
- first_name: Roberto
full_name: Sacco, Roberto
id: 42C9F57E-F248-11E8-B48F-1D18A9856A87
last_name: Sacco
- first_name: Aysan Çerağ
full_name: Yahya, Aysan Çerağ
id: 365A65F8-F248-11E8-B48F-1D18A9856A87
last_name: Yahya
- first_name: Jasmin
full_name: Morandell, Jasmin
id: 4739D480-F248-11E8-B48F-1D18A9856A87
last_name: Morandell
- first_name: Michele
full_name: Gabriele, Michele
last_name: Gabriele
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Mariano
full_name: Gabitto, Mariano
last_name: Gabitto
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Giuseppe
full_name: Testa, Giuseppe
last_name: Testa
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Villa CE, Cheroni C, Dotter C, et al. CHD8 haploinsufficiency links autism
to transient alterations in excitatory and inhibitory trajectories. Cell Reports.
2022;39(1). doi:10.1016/j.celrep.2022.110615
apa: Villa, C. E., Cheroni, C., Dotter, C., López-Tóbon, A., Oliveira, B., Sacco,
R., … Novarino, G. (2022). CHD8 haploinsufficiency links autism to transient alterations
in excitatory and inhibitory trajectories. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2022.110615
chicago: Villa, Carlo Emanuele, Cristina Cheroni, Christoph Dotter, Alejandro López-Tóbon,
Bárbara Oliveira, Roberto Sacco, Aysan Çerağ Yahya, et al. “CHD8 Haploinsufficiency
Links Autism to Transient Alterations in Excitatory and Inhibitory Trajectories.”
Cell Reports. Elsevier, 2022. https://doi.org/10.1016/j.celrep.2022.110615.
ieee: C. E. Villa et al., “CHD8 haploinsufficiency links autism to transient
alterations in excitatory and inhibitory trajectories,” Cell Reports, vol.
39, no. 1. Elsevier, 2022.
ista: Villa CE, Cheroni C, Dotter C, López-Tóbon A, Oliveira B, Sacco R, Yahya AÇ,
Morandell J, Gabriele M, Tavakoli M, Lyudchik J, Sommer CM, Gabitto M, Danzl JG,
Testa G, Novarino G. 2022. CHD8 haploinsufficiency links autism to transient alterations
in excitatory and inhibitory trajectories. Cell Reports. 39(1), 110615.
mla: Villa, Carlo Emanuele, et al. “CHD8 Haploinsufficiency Links Autism to Transient
Alterations in Excitatory and Inhibitory Trajectories.” Cell Reports, vol.
39, no. 1, 110615, Elsevier, 2022, doi:10.1016/j.celrep.2022.110615.
short: C.E. Villa, C. Cheroni, C. Dotter, A. López-Tóbon, B. Oliveira, R. Sacco,
A.Ç. Yahya, J. Morandell, M. Gabriele, M. Tavakoli, J. Lyudchik, C.M. Sommer,
M. Gabitto, J.G. Danzl, G. Testa, G. Novarino, Cell Reports 39 (2022).
corr_author: '1'
date_created: 2022-04-15T09:03:10Z
date_published: 2022-04-05T00:00:00Z
date_updated: 2026-10-26T23:30:08Z
day: '05'
ddc:
- '570'
department:
- _id: JoDa
- _id: GaNo
doi: 10.1016/j.celrep.2022.110615
ec_funded: 1
external_id:
isi:
- '000785983900003'
pmid:
- '35385734'
file:
- access_level: open_access
checksum: b4e8d68f0268dec499af333e6fd5d8e1
content_type: application/pdf
creator: dernst
date_created: 2022-04-15T09:06:25Z
date_updated: 2022-04-15T09:06:25Z
file_id: '11164'
file_name: 2022_CellReports_Villa.pdf
file_size: '7808644'
relation: main_file
success: 1
file_date_updated: 2022-04-15T09:06:25Z
fulldoi: https://doi.org/10.1016/j.celrep.2022.110615
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25444568-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715508'
name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo
and in vitro Models
- _id: 2690FEAC-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I04205
name: Identification of converging Molecular Pathways Across Chromatinopathies as
Targets for Therapy
publication: Cell Reports
publication_identifier:
issn:
- 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '18674'
relation: dissertation_contains
status: public
- id: '18681'
relation: dissertation_contains
status: public
- id: '12364'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: CHD8 haploinsufficiency links autism to transient alterations in excitatory
and inhibitory trajectories
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 39
year: '2022'
...
---
_id: '11373'
abstract:
- lang: eng
text: The actin-homologue FtsA is essential for E. coli cell division, as it links
FtsZ filaments in the Z-ring to transmembrane proteins. FtsA is thought to initiate
cell constriction by switching from an inactive polymeric to an active monomeric
conformation, which recruits downstream proteins and stabilizes the Z-ring. However,
direct biochemical evidence for this mechanism is missing. Here, we use reconstitution
experiments and quantitative fluorescence microscopy to study divisome activation
in vitro. By comparing wild-type FtsA with FtsA R286W, we find that this hyperactive
mutant outperforms FtsA WT in replicating FtsZ treadmilling dynamics, FtsZ filament
stabilization and recruitment of FtsN. We could attribute these differences to
a faster exchange and denser packing of FtsA R286W below FtsZ filaments. Using
FRET microscopy, we also find that FtsN binding promotes FtsA self-interaction.
We propose that in the active divisome FtsA and FtsN exist as a dynamic copolymer
that follows treadmilling filaments of FtsZ.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: We acknowledge members of the Loose laboratory at IST Austria for
helpful discussions—in particular L. Lindorfer for his assistance with cloning and
purifications. We thank J. Löwe and T. Nierhaus (MRC-LMB Cambridge, UK) for sharing
unpublished work and helpful discussions, as well as D. Vavylonis and D. Rutkowski
(Lehigh University, Bethlehem, PA, USA) and S. Martin (University of Lausanne, Switzerland)
for sharing their code for FRAP analysis. We are also thankful for the support by
the Scientific Service Units (SSU) of IST Austria through resources provided by
the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). This work
was supported by the European Research Council through grant ERC 2015-StG-679239
and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L. and HFSP LT 000824/2016-L4
to N.B. For the purpose of open access, we have applied a CC BY public copyright
licence to any Author Accepted Manuscript version arising from this submission.
article_number: '2635'
article_processing_charge: No
article_type: original
author:
- first_name: Philipp
full_name: Radler, Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
- first_name: Natalia S.
full_name: Baranova, Natalia S.
id: 38661662-F248-11E8-B48F-1D18A9856A87
last_name: Baranova
orcid: 0000-0002-3086-9124
- first_name: Paulo R
full_name: Dos Santos Caldas, Paulo R
id: 38FCDB4C-F248-11E8-B48F-1D18A9856A87
last_name: Dos Santos Caldas
orcid: 0000-0001-6730-4461
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Maria D
full_name: Lopez Pelegrin, Maria D
id: 319AA9CE-F248-11E8-B48F-1D18A9856A87
last_name: Lopez Pelegrin
- first_name: David
full_name: Michalik, David
id: B9577E20-AA38-11E9-AC9A-0930E6697425
last_name: Michalik
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: Radler P, Baranova NS, Dos Santos Caldas PR, et al. In vitro reconstitution
of Escherichia coli divisome activation. Nature Communications. 2022;13.
doi:10.1038/s41467-022-30301-y
apa: Radler, P., Baranova, N. S., Dos Santos Caldas, P. R., Sommer, C. M., Lopez
Pelegrin, M. D., Michalik, D., & Loose, M. (2022). In vitro reconstitution
of Escherichia coli divisome activation. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-022-30301-y
chicago: Radler, Philipp, Natalia S. Baranova, Paulo R Dos Santos Caldas, Christoph
M Sommer, Maria D Lopez Pelegrin, David Michalik, and Martin Loose. “In Vitro
Reconstitution of Escherichia Coli Divisome Activation.” Nature Communications.
Springer Nature, 2022. https://doi.org/10.1038/s41467-022-30301-y.
ieee: P. Radler et al., “In vitro reconstitution of Escherichia coli divisome
activation,” Nature Communications, vol. 13. Springer Nature, 2022.
ista: Radler P, Baranova NS, Dos Santos Caldas PR, Sommer CM, Lopez Pelegrin MD,
Michalik D, Loose M. 2022. In vitro reconstitution of Escherichia coli divisome
activation. Nature Communications. 13, 2635.
mla: Radler, Philipp, et al. “In Vitro Reconstitution of Escherichia Coli Divisome
Activation.” Nature Communications, vol. 13, 2635, Springer Nature, 2022,
doi:10.1038/s41467-022-30301-y.
short: P. Radler, N.S. Baranova, P.R. Dos Santos Caldas, C.M. Sommer, M.D. Lopez
Pelegrin, D. Michalik, M. Loose, Nature Communications 13 (2022).
corr_author: '1'
date_created: 2022-05-13T09:06:28Z
date_published: 2022-05-12T00:00:00Z
date_updated: 2026-10-26T23:30:07Z
day: '12'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1038/s41467-022-30301-y
ec_funded: 1
external_id:
isi:
- '000795171100037'
file:
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checksum: 5af863ee1b95a0710f6ee864d68dc7a6
content_type: application/pdf
creator: dernst
date_created: 2022-05-13T09:10:51Z
date_updated: 2022-05-13T09:10:51Z
file_id: '11374'
file_name: 2022_NatureCommunications_Radler.pdf
file_size: 6945191
relation: main_file
success: 1
file_date_updated: 2022-05-13T09:10:51Z
fulldoi: https://doi.org/10.1038/s41467-022-30301-y
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
- _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d
grant_number: P34607
name: In vitro reconstitution of bacterial cell division
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41467-022-34485-1
record:
- id: '10934'
relation: research_data
status: public
- id: '14280'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: In vitro reconstitution of Escherichia coli divisome activation
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: '12248'
abstract:
- lang: eng
text: Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual
lineages of parthenogenetic females, which produce rare males at low frequencies.
Although they are known to have ZW chromosomes, these are not well characterized,
and it is unclear whether they are shared across the clade. Furthermore, the underlying
genetic architecture of the transmission of asexuality, which can occur when rare
males mate with closely related sexual females, is not well understood. We produced
a chromosome-level assembly for the sexual Eurasian species Artemia sinica and
characterized in detail the pair of sex chromosomes of this species. We combined
this new assembly with short-read genomic data for the sexual species Artemia
sp. Kazakhstan and several asexual lineages of Artemia parthenogenetica, allowing
us to perform an in-depth characterization of sex-chromosome evolution across
the genus. We identified a small differentiated region of the ZW pair that is
shared by all sexual and asexual lineages, supporting the shared ancestry of the
sex chromosomes. We also inferred that recombination suppression has spread to
larger sections of the chromosome independently in the American and Eurasian lineages.
Finally, we took advantage of a rare male, which we backcrossed to sexual females,
to explore the genetic basis of asexuality. Our results suggest that parthenogenesis
is likely partly controlled by a locus on the Z chromosome, highlighting the interplay
between sex determination and asexuality.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "This work was supported by the European Research Council under the
European Union’s Horizon 2020 research and innovation program (grant agreement no.
715257) and by the Austrian Science Foundation (FWF SFB F88-10).\r\nWe thank the
Vicoso group for comments on the manuscript and the ISTA Scientific computing team
and the Vienna Biocenter Sequencing facility for technical support."
article_number: iyac123
article_processing_charge: No
article_type: original
author:
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
- first_name: Uladzislava
full_name: Khauratovich, Uladzislava
id: 5eba06f4-97d8-11ed-9f8f-d826ebdd9434
last_name: Khauratovich
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Vincent K
full_name: Bett, Vincent K
id: 57854184-AAE0-11E9-8D04-98D6E5697425
last_name: Bett
- first_name: Andrea
full_name: Mrnjavac, Andrea
id: 353FAC84-AE61-11E9-8BFC-00D3E5697425
last_name: Mrnjavac
- first_name: Ariana
full_name: Macon, Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Luca
full_name: Sax, Luca
id: 701c5602-97d8-11ed-96b5-b52773c70189
last_name: Sax
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Francisco
full_name: Hontoria, Francisco
last_name: Hontoria
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Elkrewi MN, Khauratovich U, Toups MA, et al. ZW sex-chromosome evolution and
contagious parthenogenesis in Artemia brine shrimp. Genetics. 2022;222(2).
doi:10.1093/genetics/iyac123
apa: Elkrewi, M. N., Khauratovich, U., Toups, M. A., Bett, V. K., Mrnjavac, A.,
Macon, A., … Vicoso, B. (2022). ZW sex-chromosome evolution and contagious parthenogenesis
in Artemia brine shrimp. Genetics. Oxford University Press. https://doi.org/10.1093/genetics/iyac123
chicago: Elkrewi, Marwan N, Uladzislava Khauratovich, Melissa A Toups, Vincent K
Bett, Andrea Mrnjavac, Ariana Macon, Christelle Fraisse, et al. “ZW Sex-Chromosome
Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” Genetics.
Oxford University Press, 2022. https://doi.org/10.1093/genetics/iyac123.
ieee: M. N. Elkrewi et al., “ZW sex-chromosome evolution and contagious parthenogenesis
in Artemia brine shrimp,” Genetics, vol. 222, no. 2. Oxford University
Press, 2022.
ista: Elkrewi MN, Khauratovich U, Toups MA, Bett VK, Mrnjavac A, Macon A, Fraisse
C, Sax L, Huylmans AK, Hontoria F, Vicoso B. 2022. ZW sex-chromosome evolution
and contagious parthenogenesis in Artemia brine shrimp. Genetics. 222(2), iyac123.
mla: Elkrewi, Marwan N., et al. “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis
in Artemia Brine Shrimp.” Genetics, vol. 222, no. 2, iyac123, Oxford University
Press, 2022, doi:10.1093/genetics/iyac123.
short: M.N. Elkrewi, U. Khauratovich, M.A. Toups, V.K. Bett, A. Mrnjavac, A. Macon,
C. Fraisse, L. Sax, A.K. Huylmans, F. Hontoria, B. Vicoso, Genetics 222 (2022).
corr_author: '1'
date_created: 2023-01-16T09:56:10Z
date_published: 2022-10-01T00:00:00Z
date_updated: 2026-10-26T23:30:55Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/genetics/iyac123
ec_funded: 1
external_id:
isi:
- '000850270300001'
pmid:
- '35977389'
file:
- access_level: open_access
checksum: f79ff5383e882ea3f95f3da47a78029d
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T08:59:58Z
date_updated: 2023-01-30T08:59:58Z
file_id: '12440'
file_name: 2022_Genetics_Elkrewi.pdf
file_size: 1347136
relation: main_file
success: 1
file_date_updated: 2023-01-30T08:59:58Z
fulldoi: https://doi.org/10.1093/genetics/iyac123
has_accepted_license: '1'
intvolume: ' 222'
isi: 1
issue: '2'
keyword:
- Genetics
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
- _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396
grant_number: F8810
name: The highjacking of meiosis for asexual reproduction
publication: Genetics
publication_identifier:
issn:
- 1943-2631
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '11653'
relation: research_data
status: public
- id: '19386'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine
shrimp
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 222
year: '2022'
...
---
_id: '10834'
abstract:
- lang: eng
text: Hematopoietic-specific protein 1 (Hem1) is an essential subunit of the WAVE
regulatory complex (WRC) in immune cells. WRC is crucial for Arp2/3 complex activation
and the protrusion of branched actin filament networks. Moreover, Hem1 loss of
function in immune cells causes autoimmune diseases in humans. Here, we show that
genetic removal of Hem1 in macrophages diminishes frequency and efficacy of phagocytosis
as well as phagocytic cup formation in addition to defects in lamellipodial protrusion
and migration. Moreover, Hem1-null macrophages displayed strong defects in cell
adhesion despite unaltered podosome formation and concomitant extracellular matrix
degradation. Specifically, dynamics of both adhesion and de-adhesion as well as
concomitant phosphorylation of paxillin and focal adhesion kinase (FAK) were significantly
compromised. Accordingly, disruption of WRC function in non-hematopoietic cells
coincided with both defects in adhesion turnover and altered FAK and paxillin
phosphorylation. Consistently, platelets exhibited reduced adhesion and diminished
integrin αIIbβ3 activation upon WRC removal. Interestingly, adhesion phenotypes,
but not lamellipodia formation, were partially rescued by small molecule activation
of FAK. A full rescue of the phenotype, including lamellipodia formation, required
not only the presence of WRCs but also their binding to and activation by Rac.
Collectively, our results uncover that WRC impacts on integrin-dependent processes
in a FAK-dependent manner, controlling formation and dismantling of adhesions,
relevant for properly grabbing onto extracellular surfaces and particles during
cell edge expansion, like in migration or phagocytosis.
acknowledgement: We are grateful to Silvia Prettin, Ina Schleicher, and Petra Hagendorff
for expert technical assistance; David Dettbarn for animal keeping and breeding;
and Lothar Gröbe and Maria Höxter for cell sorting. We also thank Werner Tegge for
peptides and Giorgio Scita for antibodies. This work was supported, in part, by
the Deutsche Forschungsgemeinschaft (DFG), Priority Programm SPP1150 (to T.E.B.S.,
K.R., and M. Sixt), and by DFG grant GRK2223/1 (to K.R.). T.E.B.S. acknowledges
support by the Helmholtz Society through HGF impulse fund W2/W3-066 and M. Schnoor
by the Mexican Council for Science and Technology (CONACyT, 284292 ), Fund SEP-Cinvestav
( 108 ), and the Royal Society, UK (Newton Advanced Fellowship, NAF/R1/180017 ).
article_processing_charge: No
article_type: original
author:
- first_name: Stephanie
full_name: Stahnke, Stephanie
last_name: Stahnke
- first_name: Hermann
full_name: Döring, Hermann
last_name: Döring
- first_name: Charly
full_name: Kusch, Charly
last_name: Kusch
- first_name: David J.J.
full_name: de Gorter, David J.J.
last_name: de Gorter
- first_name: Sebastian
full_name: Dütting, Sebastian
last_name: Dütting
- first_name: Aleks
full_name: Guledani, Aleks
last_name: Guledani
- first_name: Irina
full_name: Pleines, Irina
last_name: Pleines
- first_name: Michael
full_name: Schnoor, Michael
last_name: Schnoor
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Robert
full_name: Geffers, Robert
last_name: Geffers
- first_name: Manfred
full_name: Rohde, Manfred
last_name: Rohde
- first_name: Mathias
full_name: Müsken, Mathias
last_name: Müsken
- first_name: Frieda
full_name: Kage, Frieda
last_name: Kage
- first_name: Anika
full_name: Steffen, Anika
last_name: Steffen
- first_name: Jan
full_name: Faix, Jan
last_name: Faix
- first_name: Bernhard
full_name: Nieswandt, Bernhard
last_name: Nieswandt
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
- first_name: Theresia E.B.
full_name: Stradal, Theresia E.B.
last_name: Stradal
citation:
ama: Stahnke S, Döring H, Kusch C, et al. Loss of Hem1 disrupts macrophage function
and impacts migration, phagocytosis, and integrin-mediated adhesion. Current
Biology. 2021;31(10):2051-2064.e8. doi:10.1016/j.cub.2021.02.043
apa: Stahnke, S., Döring, H., Kusch, C., de Gorter, D. J. J., Dütting, S., Guledani,
A., … Stradal, T. E. B. (2021). Loss of Hem1 disrupts macrophage function and
impacts migration, phagocytosis, and integrin-mediated adhesion. Current Biology.
Elsevier. https://doi.org/10.1016/j.cub.2021.02.043
chicago: Stahnke, Stephanie, Hermann Döring, Charly Kusch, David J.J. de Gorter,
Sebastian Dütting, Aleks Guledani, Irina Pleines, et al. “Loss of Hem1 Disrupts
Macrophage Function and Impacts Migration, Phagocytosis, and Integrin-Mediated
Adhesion.” Current Biology. Elsevier, 2021. https://doi.org/10.1016/j.cub.2021.02.043.
ieee: S. Stahnke et al., “Loss of Hem1 disrupts macrophage function and impacts
migration, phagocytosis, and integrin-mediated adhesion,” Current Biology,
vol. 31, no. 10. Elsevier, p. 2051–2064.e8, 2021.
ista: Stahnke S, Döring H, Kusch C, de Gorter DJJ, Dütting S, Guledani A, Pleines
I, Schnoor M, Sixt MK, Geffers R, Rohde M, Müsken M, Kage F, Steffen A, Faix J,
Nieswandt B, Rottner K, Stradal TEB. 2021. Loss of Hem1 disrupts macrophage function
and impacts migration, phagocytosis, and integrin-mediated adhesion. Current Biology.
31(10), 2051–2064.e8.
mla: Stahnke, Stephanie, et al. “Loss of Hem1 Disrupts Macrophage Function and Impacts
Migration, Phagocytosis, and Integrin-Mediated Adhesion.” Current Biology,
vol. 31, no. 10, Elsevier, 2021, p. 2051–2064.e8, doi:10.1016/j.cub.2021.02.043.
short: S. Stahnke, H. Döring, C. Kusch, D.J.J. de Gorter, S. Dütting, A. Guledani,
I. Pleines, M. Schnoor, M.K. Sixt, R. Geffers, M. Rohde, M. Müsken, F. Kage, A.
Steffen, J. Faix, B. Nieswandt, K. Rottner, T.E.B. Stradal, Current Biology 31
(2021) 2051–2064.e8.
date_created: 2022-03-08T07:51:04Z
date_published: 2021-05-24T00:00:00Z
date_updated: 2023-08-17T07:01:14Z
day: '24'
department:
- _id: MiSi
doi: 10.1016/j.cub.2021.02.043
external_id:
isi:
- '000654652200002'
pmid:
- '33711252'
fulldoi: https://doi.org/10.1016/j.cub.2021.02.043
intvolume: ' 31'
isi: 1
issue: '10'
keyword:
- General Agricultural and Biological Sciences
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2020.03.24.005835
month: '05'
oa: 1
oa_version: Preprint
page: 2051-2064.e8
pmid: 1
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis,
and integrin-mediated adhesion
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 31
year: '2021'
...
---
_id: '10838'
abstract:
- lang: eng
text: Combining hybrid zone analysis with genomic data is a promising approach to
understanding the genomic basis of adaptive divergence. It allows for the identification
of genomic regions underlying barriers to gene flow. It also provides insights
into spatial patterns of allele frequency change, informing about the interplay
between environmental factors, dispersal and selection. However, when only a single
hybrid zone is analysed, it is difficult to separate patterns generated by selection
from those resulting from chance. Therefore, it is beneficial to look for repeatable
patterns across replicate hybrid zones in the same system. We applied this approach
to the marine snail Littorina saxatilis, which contains two ecotypes, adapted
to wave-exposed rocks vs. high-predation boulder fields. The existence of numerous
hybrid zones between ecotypes offered the opportunity to test for the repeatability
of genomic architectures and spatial patterns of divergence. We sampled and phenotyped
snails from seven replicate hybrid zones on the Swedish west coast and genotyped
them for thousands of single nucleotide polymorphisms. Shell shape and size showed
parallel clines across all zones. Many genomic regions showing steep clines and/or
high differentiation were shared among hybrid zones, consistent with a common
evolutionary history and extensive gene flow between zones, and supporting the
importance of these regions for divergence. In particular, we found that several
large putative inversions contribute to divergence in all locations. Additionally,
we found evidence for consistent displacement of clines from the boulder–rock
transition. Our results demonstrate patterns of spatial variation that would not
be accessible without continuous spatial sampling, a large genomic data set and
replicate hybrid zones.
acknowledgement: "We thank everyone who helped with fieldwork, snail processing and
DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise
Liabot, Mark Ravinet, Irena Senčić and Zuzanna Zagrodzka. We are also grateful to
Edinburgh Genomics for library preparation and sequencing, to Stuart Baird and Mark
Ravinet for helpful discussions, and to three anonymous reviewers for their constructive
comments. This work was supported by the Natural Environment Research Council (NE/K014021/1),
the European Research Council (AdG-693030-BARRIERS), Swedish Research Councils Formas
and Vetenskapsrådet through a Linnaeus grant to the Centre for Marine Evolutionary
Biology (217-2008-1719), the European Regional Development Fund (POCI-01-0145-FEDER-030628),
and the Fundação para a iência e a Tecnologia,\r\nPortugal (PTDC/BIA-EVL/\r\n30628/2017).
A.M.W. and R.F. were\r\nfunded by the European Union’s Horizon 2020 research and
innovation\r\nprogramme under Marie Skłodowska-Curie\r\ngrant agreements\r\nno.
754411/797747 and no. 706376, respectively."
article_processing_charge: No
article_type: original
author:
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
citation:
ama: Westram AM, Faria R, Johannesson K, Butlin R. Using replicate hybrid zones
to understand the genomic basis of adaptive divergence. Molecular Ecology.
2021;30(15):3797-3814. doi:10.1111/mec.15861
apa: Westram, A. M., Faria, R., Johannesson, K., & Butlin, R. (2021). Using
replicate hybrid zones to understand the genomic basis of adaptive divergence.
Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15861
chicago: Westram, Anja M, Rui Faria, Kerstin Johannesson, and Roger Butlin. “Using
Replicate Hybrid Zones to Understand the Genomic Basis of Adaptive Divergence.”
Molecular Ecology. Wiley, 2021. https://doi.org/10.1111/mec.15861.
ieee: A. M. Westram, R. Faria, K. Johannesson, and R. Butlin, “Using replicate hybrid
zones to understand the genomic basis of adaptive divergence,” Molecular Ecology,
vol. 30, no. 15. Wiley, pp. 3797–3814, 2021.
ista: Westram AM, Faria R, Johannesson K, Butlin R. 2021. Using replicate hybrid
zones to understand the genomic basis of adaptive divergence. Molecular Ecology.
30(15), 3797–3814.
mla: Westram, Anja M., et al. “Using Replicate Hybrid Zones to Understand the Genomic
Basis of Adaptive Divergence.” Molecular Ecology, vol. 30, no. 15, Wiley,
2021, pp. 3797–814, doi:10.1111/mec.15861.
short: A.M. Westram, R. Faria, K. Johannesson, R. Butlin, Molecular Ecology 30 (2021)
3797–3814.
corr_author: '1'
date_created: 2022-03-08T11:28:32Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2024-10-09T21:01:47Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1111/mec.15861
external_id:
isi:
- '000669439700001'
pmid:
- '33638231'
file:
- access_level: open_access
checksum: d5611f243ceb63a0e091d6662ebd9cda
content_type: application/pdf
creator: dernst
date_created: 2022-03-08T11:31:30Z
date_updated: 2022-03-08T11:31:30Z
file_id: '10839'
file_name: 2021_MolecularEcology_Westram.pdf
file_size: 1726548
relation: main_file
success: 1
file_date_updated: 2022-03-08T11:31:30Z
fulldoi: https://doi.org/10.1111/mec.15861
has_accepted_license: '1'
intvolume: ' 30'
isi: 1
issue: '15'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 3797-3814
pmid: 1
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Using replicate hybrid zones to understand the genomic basis of adaptive divergence
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 30
year: '2021'
...
---
_id: '11052'
abstract:
- lang: eng
text: In order to combat molecular damage, most cellular proteins undergo rapid
turnover. We have previously identified large nuclear protein assemblies that
can persist for years in post-mitotic tissues and are subject to age-related decline.
Here, we report that mitochondria can be long lived in the mouse brain and reveal
that specific mitochondrial proteins have half-lives longer than the average proteome.
These mitochondrial long-lived proteins (mitoLLPs) are core components of the
electron transport chain (ETC) and display increased longevity in respiratory
supercomplexes. We find that COX7C, a mitoLLP that forms a stable contact site
between complexes I and IV, is required for complex IV and supercomplex assembly.
Remarkably, even upon depletion of COX7C transcripts, ETC function is maintained
for days, effectively uncoupling mitochondrial function from ongoing transcription
of its mitoLLPs. Our results suggest that modulating protein longevity within
the ETC is critical for mitochondrial proteome maintenance and the robustness
of mitochondrial function.
article_processing_charge: No
article_type: original
author:
- first_name: Shefali
full_name: Krishna, Shefali
last_name: Krishna
- first_name: Rafael
full_name: Arrojo e Drigo, Rafael
last_name: Arrojo e Drigo
- first_name: Juliana S.
full_name: Capitanio, Juliana S.
last_name: Capitanio
- first_name: Ranjan
full_name: Ramachandra, Ranjan
last_name: Ramachandra
- first_name: Mark
full_name: Ellisman, Mark
last_name: Ellisman
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Krishna S, Arrojo e Drigo R, Capitanio JS, Ramachandra R, Ellisman M, Hetzer
M. Identification of long-lived proteins in the mitochondria reveals increased
stability of the electron transport chain. Developmental Cell. 2021;56(21):P2952-2965.e9.
doi:10.1016/j.devcel.2021.10.008
apa: Krishna, S., Arrojo e Drigo, R., Capitanio, J. S., Ramachandra, R., Ellisman,
M., & Hetzer, M. (2021). Identification of long-lived proteins in the mitochondria
reveals increased stability of the electron transport chain. Developmental
Cell. Elsevier. https://doi.org/10.1016/j.devcel.2021.10.008
chicago: Krishna, Shefali, Rafael Arrojo e Drigo, Juliana S. Capitanio, Ranjan Ramachandra,
Mark Ellisman, and Martin Hetzer. “Identification of Long-Lived Proteins in the
Mitochondria Reveals Increased Stability of the Electron Transport Chain.” Developmental
Cell. Elsevier, 2021. https://doi.org/10.1016/j.devcel.2021.10.008.
ieee: S. Krishna, R. Arrojo e Drigo, J. S. Capitanio, R. Ramachandra, M. Ellisman,
and M. Hetzer, “Identification of long-lived proteins in the mitochondria reveals
increased stability of the electron transport chain,” Developmental Cell,
vol. 56, no. 21. Elsevier, p. P2952–2965.e9, 2021.
ista: Krishna S, Arrojo e Drigo R, Capitanio JS, Ramachandra R, Ellisman M, Hetzer
M. 2021. Identification of long-lived proteins in the mitochondria reveals increased
stability of the electron transport chain. Developmental Cell. 56(21), P2952–2965.e9.
mla: Krishna, Shefali, et al. “Identification of Long-Lived Proteins in the Mitochondria
Reveals Increased Stability of the Electron Transport Chain.” Developmental
Cell, vol. 56, no. 21, Elsevier, 2021, p. P2952–2965.e9, doi:10.1016/j.devcel.2021.10.008.
short: S. Krishna, R. Arrojo e Drigo, J.S. Capitanio, R. Ramachandra, M. Ellisman,
M. Hetzer, Developmental Cell 56 (2021) P2952–2965.e9.
date_created: 2022-04-07T07:43:14Z
date_published: 2021-11-08T00:00:00Z
date_updated: 2025-12-15T10:01:56Z
day: '08'
department:
- _id: MaHe
doi: 10.1016/j.devcel.2021.10.008
extern: '1'
external_id:
pmid:
- '34715012'
fulldoi: https://doi.org/10.1016/j.devcel.2021.10.008
intvolume: ' 56'
issue: '21'
keyword:
- Developmental Biology
- Cell Biology
- General Biochemistry
- Genetics and Molecular Biology
- Molecular Biology
language:
- iso: eng
month: '11'
oa_version: None
page: P2952-2965.e9
pmid: 1
publication: Developmental Cell
publication_identifier:
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Identification of long-lived proteins in the mitochondria reveals increased
stability of the electron transport chain
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 56
year: '2021'
...
---
_id: '12585'
abstract:
- lang: eng
text: Glaciers in High Mountain Asia generate meltwater that supports the water
needs of 250 million people, but current knowledge of annual accumulation and
ablation is limited to sparse field measurements biased in location and glacier
size. Here, we present altitudinally-resolved specific mass balances (surface,
internal, and basal combined) for 5527 glaciers in High Mountain Asia for 2000–2016,
derived by correcting observed glacier thinning patterns for mass redistribution
due to ice flow. We find that 41% of glaciers accumulated mass over less than
20% of their area, and only 60% ± 10% of regional annual ablation was compensated
by accumulation. Even without 21st century warming, 21% ± 1% of ice volume will
be lost by 2100 due to current climatic-geometric imbalance, representing a reduction
in glacier ablation into rivers of 28% ± 1%. The ablation of glaciers in the Himalayas
and Tien Shan was mostly unsustainable and ice volume in these regions will reduce
by at least 30% by 2100. The most important and vulnerable glacier-fed river basins
(Amu Darya, Indus, Syr Darya, Tarim Interior) were supplied with >50% sustainable
glacier ablation but will see long-term reductions in ice mass and glacier meltwater
supply regardless of the Karakoram Anomaly.
article_number: '2868'
article_processing_charge: No
article_type: original
author:
- first_name: Evan
full_name: Miles, Evan
last_name: Miles
- first_name: Michael
full_name: McCarthy, Michael
last_name: McCarthy
- first_name: Amaury
full_name: Dehecq, Amaury
last_name: Dehecq
- first_name: Marin
full_name: Kneib, Marin
last_name: Kneib
- first_name: Stefan
full_name: Fugger, Stefan
last_name: Fugger
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
citation:
ama: Miles E, McCarthy M, Dehecq A, Kneib M, Fugger S, Pellicciotti F. Health and
sustainability of glaciers in High Mountain Asia. Nature Communications.
2021;12. doi:10.1038/s41467-021-23073-4
apa: Miles, E., McCarthy, M., Dehecq, A., Kneib, M., Fugger, S., & Pellicciotti,
F. (2021). Health and sustainability of glaciers in High Mountain Asia. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23073-4
chicago: Miles, Evan, Michael McCarthy, Amaury Dehecq, Marin Kneib, Stefan Fugger,
and Francesca Pellicciotti. “Health and Sustainability of Glaciers in High Mountain
Asia.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23073-4.
ieee: E. Miles, M. McCarthy, A. Dehecq, M. Kneib, S. Fugger, and F. Pellicciotti,
“Health and sustainability of glaciers in High Mountain Asia,” Nature Communications,
vol. 12. Springer Nature, 2021.
ista: Miles E, McCarthy M, Dehecq A, Kneib M, Fugger S, Pellicciotti F. 2021. Health
and sustainability of glaciers in High Mountain Asia. Nature Communications. 12,
2868.
mla: Miles, Evan, et al. “Health and Sustainability of Glaciers in High Mountain
Asia.” Nature Communications, vol. 12, 2868, Springer Nature, 2021, doi:10.1038/s41467-021-23073-4.
short: E. Miles, M. McCarthy, A. Dehecq, M. Kneib, S. Fugger, F. Pellicciotti, Nature
Communications 12 (2021).
date_created: 2023-02-20T08:11:29Z
date_published: 2021-05-17T00:00:00Z
date_updated: 2023-02-28T13:21:51Z
day: '17'
doi: 10.1038/s41467-021-23073-4
extern: '1'
fulldoi: https://doi.org/10.1038/s41467-021-23073-4
intvolume: ' 12'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-021-23073-4
month: '05'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Health and sustainability of glaciers in High Mountain Asia
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2021'
...
---
_id: '13356'
abstract:
- lang: eng
text: 'Self-assembly of nanoparticles can be mediated by polymers, but has so far
led almost exclusively to nanoparticle aggregates that are amorphous. Here, we
employed Coulombic interactions to generate a range of composite materials from
mixtures of charged nanoparticles and oppositely charged polymers. The assembly
behavior of these nanoparticle/polymer composites depends on their order of addition:
polymers added to nanoparticles give rise to stable aggregates, but nanoparticles
added to polymers disassemble the initially formed aggregates. The amorphous aggregates
were transformed into crystalline ones by transiently increasing the ionic strength
of the solution. The morphology of the resulting crystals depended on the length
of the polymer: short polymer chains mediated the self-assembly of nanoparticles
into strongly faceted crystals, whereas long chains led to pseudospherical nanoparticle/polymer
assemblies, within which the crystalline order of nanoparticles was retained.'
article_processing_charge: No
article_type: original
author:
- first_name: Tong
full_name: Bian, Tong
last_name: Bian
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Bian T, Klajn R. Morphology control in crystalline nanoparticle–polymer aggregates.
Annals of the New York Academy of Sciences. 2021;1505(1):191-201. doi:10.1111/nyas.14674
apa: Bian, T., & Klajn, R. (2021). Morphology control in crystalline nanoparticle–polymer
aggregates. Annals of the New York Academy of Sciences. Wiley. https://doi.org/10.1111/nyas.14674
chicago: Bian, Tong, and Rafal Klajn. “Morphology Control in Crystalline Nanoparticle–Polymer
Aggregates.” Annals of the New York Academy of Sciences. Wiley, 2021. https://doi.org/10.1111/nyas.14674.
ieee: T. Bian and R. Klajn, “Morphology control in crystalline nanoparticle–polymer
aggregates,” Annals of the New York Academy of Sciences, vol. 1505, no.
1. Wiley, pp. 191–201, 2021.
ista: Bian T, Klajn R. 2021. Morphology control in crystalline nanoparticle–polymer
aggregates. Annals of the New York Academy of Sciences. 1505(1), 191–201.
mla: Bian, Tong, and Rafal Klajn. “Morphology Control in Crystalline Nanoparticle–Polymer
Aggregates.” Annals of the New York Academy of Sciences, vol. 1505, no.
1, Wiley, 2021, pp. 191–201, doi:10.1111/nyas.14674.
short: T. Bian, R. Klajn, Annals of the New York Academy of Sciences 1505 (2021)
191–201.
date_created: 2023-08-01T09:33:39Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2024-10-14T12:12:06Z
day: '01'
ddc:
- '540'
doi: 10.1111/nyas.14674
extern: '1'
external_id:
pmid:
- '34427923'
fulldoi: https://doi.org/10.1111/nyas.14674
intvolume: ' 1505'
issue: '1'
keyword:
- History and Philosophy of Science
- General Biochemistry
- Genetics and Molecular Biology
- General Neuroscience
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/nyas.14674
month: '12'
oa: 1
oa_version: Published Version
page: 191-201
pmid: 1
publication: Annals of the New York Academy of Sciences
publication_identifier:
eissn:
- 1749-6632
issn:
- 0077-8923
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Morphology control in crystalline nanoparticle–polymer aggregates
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1505
year: '2021'
...
---
_id: '15137'
abstract:
- lang: eng
text: Characteristic properties of type III CRISPR-Cas systems include recognition
of target RNA and the subsequent induction of a multifaceted immune response.
This involves sequence-specific cleavage of the target RNA and production of cyclic
oligoadenylate (cOA) molecules. Here we report that an exposed seed region at
the 3′ end of the crRNA is essential for target RNA binding and cleavage, whereas
cOA production requires base pairing at the 5′ end of the crRNA. Moreover, we
uncover that the variation in the size and composition of type III complexes within
a single host results in variable seed regions. This may prevent escape by invading
genetic elements, while controlling cOA production tightly to prevent unnecessary
damage to the host. Lastly, we use these findings to develop a new diagnostic
tool, SCOPE, for the specific detection of SARS-CoV-2 from human nasal swab samples,
revealing sensitivities in the atto-molar range.
article_number: '5033'
article_processing_charge: Yes
article_type: original
author:
- first_name: Jurre A.
full_name: Steens, Jurre A.
last_name: Steens
- first_name: Yifan
full_name: Zhu, Yifan
last_name: Zhu
- first_name: David W.
full_name: Taylor, David W.
last_name: Taylor
- first_name: Jack Peter Kelly
full_name: Bravo, Jack Peter Kelly
id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e
last_name: Bravo
orcid: 0000-0003-0456-0753
- first_name: Stijn H. P.
full_name: Prinsen, Stijn H. P.
last_name: Prinsen
- first_name: Cor D.
full_name: Schoen, Cor D.
last_name: Schoen
- first_name: Bart J. F.
full_name: Keijser, Bart J. F.
last_name: Keijser
- first_name: Michel
full_name: Ossendrijver, Michel
last_name: Ossendrijver
- first_name: L. Marije
full_name: Hofstra, L. Marije
last_name: Hofstra
- first_name: Stan J. J.
full_name: Brouns, Stan J. J.
last_name: Brouns
- first_name: Akeo
full_name: Shinkai, Akeo
last_name: Shinkai
- first_name: John
full_name: van der Oost, John
last_name: van der Oost
- first_name: Raymond H. J.
full_name: Staals, Raymond H. J.
last_name: Staals
citation:
ama: Steens JA, Zhu Y, Taylor DW, et al. SCOPE enables type III CRISPR-Cas diagnostics
using flexible targeting and stringent CARF ribonuclease activation. Nature
Communications. 2021;12. doi:10.1038/s41467-021-25337-5
apa: Steens, J. A., Zhu, Y., Taylor, D. W., Bravo, J. P. K., Prinsen, S. H. P.,
Schoen, C. D., … Staals, R. H. J. (2021). SCOPE enables type III CRISPR-Cas diagnostics
using flexible targeting and stringent CARF ribonuclease activation. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-021-25337-5
chicago: Steens, Jurre A., Yifan Zhu, David W. Taylor, Jack Peter Kelly Bravo, Stijn
H. P. Prinsen, Cor D. Schoen, Bart J. F. Keijser, et al. “SCOPE Enables Type III
CRISPR-Cas Diagnostics Using Flexible Targeting and Stringent CARF Ribonuclease
Activation.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-25337-5.
ieee: J. A. Steens et al., “SCOPE enables type III CRISPR-Cas diagnostics
using flexible targeting and stringent CARF ribonuclease activation,” Nature
Communications, vol. 12. Springer Nature, 2021.
ista: Steens JA, Zhu Y, Taylor DW, Bravo JPK, Prinsen SHP, Schoen CD, Keijser BJF,
Ossendrijver M, Hofstra LM, Brouns SJJ, Shinkai A, van der Oost J, Staals RHJ.
2021. SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and
stringent CARF ribonuclease activation. Nature Communications. 12, 5033.
mla: Steens, Jurre A., et al. “SCOPE Enables Type III CRISPR-Cas Diagnostics Using
Flexible Targeting and Stringent CARF Ribonuclease Activation.” Nature Communications,
vol. 12, 5033, Springer Nature, 2021, doi:10.1038/s41467-021-25337-5.
short: J.A. Steens, Y. Zhu, D.W. Taylor, J.P.K. Bravo, S.H.P. Prinsen, C.D. Schoen,
B.J.F. Keijser, M. Ossendrijver, L.M. Hofstra, S.J.J. Brouns, A. Shinkai, J. van
der Oost, R.H.J. Staals, Nature Communications 12 (2021).
date_created: 2024-03-20T10:42:33Z
date_published: 2021-08-19T00:00:00Z
date_updated: 2024-06-04T06:11:54Z
day: '19'
doi: 10.1038/s41467-021-25337-5
extern: '1'
external_id:
pmid:
- '34413302'
fulldoi: https://doi.org/10.1038/s41467-021-25337-5
intvolume: ' 12'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-021-25337-5
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and
stringent CARF ribonuclease activation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2021'
...