---
_id: '17113'
abstract:
- lang: eng
text: CRISPR-Cas9 is a powerful tool for genome editing, but the strict requirement
for an NGG protospacer-adjacent motif (PAM) sequence immediately next to the DNA
target limits the number of editable genes. Recently developed Cas9 variants have
been engineered with relaxed PAM requirements, including SpG-Cas9 (SpG) and the
nearly PAM-less SpRY-Cas9 (SpRY). However, the molecular mechanisms of how SpRY
recognizes all potential PAM sequences remains unclear. Here, we combine structural
and biochemical approaches to determine how SpRY interrogates DNA and recognizes
target sites. Divergent PAM sequences can be accommodated through conformational
flexibility within the PAM-interacting region, which facilitates tight binding
to off-target DNA sequences. Nuclease activation occurs ~1000-fold slower than
for Streptococcus pyogenes Cas9, enabling us to directly
visualize multiple on-pathway intermediate states. Experiments with SpG position
it as an intermediate enzyme between Cas9 and SpRY. Our findings shed light on
the molecular mechanisms of PAMless genome editing.
article_number: '3663'
article_processing_charge: Yes
article_type: original
author:
- first_name: Grace N.
full_name: Hibshman, Grace N.
last_name: Hibshman
- 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: Matthew M.
full_name: Hooper, Matthew M.
last_name: Hooper
- first_name: Tyler L.
full_name: Dangerfield, Tyler L.
last_name: Dangerfield
- first_name: Hongshan
full_name: Zhang, Hongshan
last_name: Zhang
- first_name: Ilya J.
full_name: Finkelstein, Ilya J.
last_name: Finkelstein
- first_name: Kenneth A.
full_name: Johnson, Kenneth A.
last_name: Johnson
- first_name: David W.
full_name: Taylor, David W.
last_name: Taylor
citation:
ama: Hibshman GN, Bravo JPK, Hooper MM, et al. Unraveling the mechanisms of PAMless
DNA interrogation by SpRY-Cas9. Nature Communications. 2024;15. doi:10.1038/s41467-024-47830-3
apa: Hibshman, G. N., Bravo, J. P. K., Hooper, M. M., Dangerfield, T. L., Zhang,
H., Finkelstein, I. J., … Taylor, D. W. (2024). Unraveling the mechanisms of PAMless
DNA interrogation by SpRY-Cas9. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-024-47830-3
chicago: Hibshman, Grace N., Jack Peter Kelly Bravo, Matthew M. Hooper, Tyler L.
Dangerfield, Hongshan Zhang, Ilya J. Finkelstein, Kenneth A. Johnson, and David
W. Taylor. “Unraveling the Mechanisms of PAMless DNA Interrogation by SpRY-Cas9.”
Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-47830-3.
ieee: G. N. Hibshman et al., “Unraveling the mechanisms of PAMless DNA interrogation
by SpRY-Cas9,” Nature Communications, vol. 15. Springer Nature, 2024.
ista: Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ,
Johnson KA, Taylor DW. 2024. Unraveling the mechanisms of PAMless DNA interrogation
by SpRY-Cas9. Nature Communications. 15, 3663.
mla: Hibshman, Grace N., et al. “Unraveling the Mechanisms of PAMless DNA Interrogation
by SpRY-Cas9.” Nature Communications, vol. 15, 3663, Springer Nature, 2024,
doi:10.1038/s41467-024-47830-3.
short: G.N. Hibshman, J.P.K. Bravo, M.M. Hooper, T.L. Dangerfield, H. Zhang, I.J.
Finkelstein, K.A. Johnson, D.W. Taylor, Nature Communications 15 (2024).
date_created: 2024-06-04T06:42:07Z
date_published: 2024-04-30T00:00:00Z
date_updated: 2024-10-14T12:34:26Z
day: '30'
doi: 10.1038/s41467-024-47830-3
extern: '1'
external_id:
pmid:
- '38688943'
fulldoi: https://doi.org/10.1038/s41467-024-47830-3
intvolume: ' 15'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-024-47830-3
month: '04'
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: Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2024'
...
---
_id: '17114'
abstract:
- lang: eng
text: CRISPR-Cas are adaptive immune systems in bacteria and archaea that utilize
CRISPR RNA-guided surveillance complexes to target complementary RNA or DNA for
destruction1–5. Target RNA cleavage at regular intervals
is characteristic of type III effector complexes6–8. Here,
we determine the structures of the Synechocystis type
III-Dv complex, an apparent evolutionary intermediate from multi-protein to single-protein
type III effectors9,10, in pre- and post-cleavage states.
The structures show how multi-subunit fusion proteins in the effector are tethered
together in an unusual arrangement to assemble into an active and programmable
RNA endonuclease and how the effector utilizes a distinct mechanism for target
RNA seeding from other type III effectors. Using structural, biochemical, and
quantum/classical molecular dynamics simulation, we study the structure and dynamics
of the three catalytic sites, where a 2′-OH of the ribose on the target RNA acts
as a nucleophile for in line self-cleavage of the upstream scissile phosphate.
Strikingly, the arrangement at the catalytic residues of most type III complexes
resembles the active site of ribozymes, including the hammerhead, pistol, and
Varkud satellite ribozymes. Our work provides detailed molecular insight into
the mechanisms of RNA targeting and cleavage by an important intermediate in the
evolution of type III effector complexes.
article_number: '3324'
article_processing_charge: Yes
article_type: original
author:
- first_name: Evan A.
full_name: Schwartz, Evan A.
last_name: Schwartz
- 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: Mohd
full_name: Ahsan, Mohd
last_name: Ahsan
- first_name: Luis A.
full_name: Macias, Luis A.
last_name: Macias
- first_name: Caitlyn L.
full_name: McCafferty, Caitlyn L.
last_name: McCafferty
- first_name: Tyler L.
full_name: Dangerfield, Tyler L.
last_name: Dangerfield
- first_name: Jada N.
full_name: Walker, Jada N.
last_name: Walker
- first_name: Jennifer S.
full_name: Brodbelt, Jennifer S.
last_name: Brodbelt
- first_name: Giulia
full_name: Palermo, Giulia
last_name: Palermo
- 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, Bravo JPK, Ahsan M, et al. RNA targeting and cleavage by the type
III-Dv CRISPR effector complex. Nature Communications. 2024;15. doi:10.1038/s41467-024-47506-y
apa: Schwartz, E. A., Bravo, J. P. K., Ahsan, M., Macias, L. A., McCafferty, C.
L., Dangerfield, T. L., … Taylor, D. W. (2024). RNA targeting and cleavage by
the type III-Dv CRISPR effector complex. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-024-47506-y
chicago: Schwartz, Evan A., Jack Peter Kelly Bravo, Mohd Ahsan, Luis A. Macias,
Caitlyn L. McCafferty, Tyler L. Dangerfield, Jada N. Walker, et al. “RNA Targeting
and Cleavage by the Type III-Dv CRISPR Effector Complex.” Nature Communications.
Springer Nature, 2024. https://doi.org/10.1038/s41467-024-47506-y.
ieee: E. A. Schwartz et al., “RNA targeting and cleavage by the type III-Dv
CRISPR effector complex,” Nature Communications, vol. 15. Springer Nature,
2024.
ista: Schwartz EA, Bravo JPK, Ahsan M, Macias LA, McCafferty CL, Dangerfield TL,
Walker JN, Brodbelt JS, Palermo G, Fineran PC, Fagerlund RD, Taylor DW. 2024.
RNA targeting and cleavage by the type III-Dv CRISPR effector complex. Nature
Communications. 15, 3324.
mla: Schwartz, Evan A., et al. “RNA Targeting and Cleavage by the Type III-Dv CRISPR
Effector Complex.” Nature Communications, vol. 15, 3324, Springer Nature,
2024, doi:10.1038/s41467-024-47506-y.
short: E.A. Schwartz, J.P.K. Bravo, M. Ahsan, L.A. Macias, C.L. McCafferty, T.L.
Dangerfield, J.N. Walker, J.S. Brodbelt, G. Palermo, P.C. Fineran, R.D. Fagerlund,
D.W. Taylor, Nature Communications 15 (2024).
date_created: 2024-06-04T06:43:02Z
date_published: 2024-04-18T00:00:00Z
date_updated: 2024-06-04T07:05:26Z
day: '18'
doi: 10.1038/s41467-024-47506-y
extern: '1'
external_id:
pmid:
- '38637512'
fulldoi: https://doi.org/10.1038/s41467-024-47506-y
intvolume: ' 15'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-024-47506-y
month: '04'
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: RNA targeting and cleavage by the type III-Dv CRISPR effector complex
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18545'
abstract:
- lang: eng
text: Clinical implementation of therapeutic genome editing relies on efficient
in vivo delivery and the safety of CRISPR-Cas tools. Previously, we identified
PsCas9 as a Type II-B family enzyme capable of editing mouse liver genome upon
adenoviral delivery without detectable off-targets and reduced chromosomal translocations.
Yet, its efficacy remains insufficient with non-viral delivery, a common challenge
for many Cas9 orthologues. Here, we sought to redesign PsCas9 for in vivo editing
using lipid nanoparticles. We solve the PsCas9 ribonucleoprotein structure with
cryo-EM and characterize it biochemically, providing a basis for its rational
engineering. Screening over numerous guide RNA and protein variants lead us to
develop engineered PsCas9 (ePsCas9) with up to 20-fold increased activity across
various targets and preserved safety advantages. We apply the same design principles
to boost the activity of FnCas9, an enzyme phylogenetically relevant to PsCas9.
Remarkably, a single administration of mRNA encoding ePsCas9 and its guide formulated
with lipid nanoparticles results in high levels of editing in the Pcsk9 gene in
mouse liver, a clinically relevant target for hypercholesterolemia treatment.
Collectively, our findings introduce ePsCas9 as a highly efficient, and precise
tool for therapeutic genome editing, in addition to the engineering strategy applicable
to other Cas9 orthologues.
article_number: '9173'
article_processing_charge: Yes
article_type: original
author:
- first_name: Dmitrii
full_name: Degtev, Dmitrii
last_name: Degtev
- 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: Aikaterini
full_name: Emmanouilidi, Aikaterini
last_name: Emmanouilidi
- first_name: Aleksandar
full_name: Zdravković, Aleksandar
last_name: Zdravković
- first_name: Oi Kuan
full_name: Choong, Oi Kuan
last_name: Choong
- first_name: Julia
full_name: Liz Touza, Julia
last_name: Liz Touza
- first_name: Niklas
full_name: Selfjord, Niklas
last_name: Selfjord
- first_name: Isabel
full_name: Weisheit, Isabel
last_name: Weisheit
- first_name: Margherita
full_name: Francescatto, Margherita
last_name: Francescatto
- first_name: Pinar
full_name: Akcakaya, Pinar
last_name: Akcakaya
- first_name: Michelle
full_name: Porritt, Michelle
last_name: Porritt
- first_name: Marcello
full_name: Maresca, Marcello
last_name: Maresca
- first_name: David
full_name: Taylor, David
last_name: Taylor
- first_name: Grzegorz
full_name: Sienski, Grzegorz
last_name: Sienski
citation:
ama: Degtev D, Bravo JPK, Emmanouilidi A, et al. Engineered PsCas9 enables therapeutic
genome editing in mouse liver with lipid nanoparticles. Nature Communications.
2024;15. doi:10.1038/s41467-024-53418-8
apa: Degtev, D., Bravo, J. P. K., Emmanouilidi, A., Zdravković, A., Choong, O. K.,
Liz Touza, J., … Sienski, G. (2024). Engineered PsCas9 enables therapeutic genome
editing in mouse liver with lipid nanoparticles. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-024-53418-8
chicago: Degtev, Dmitrii, Jack Peter Kelly Bravo, Aikaterini Emmanouilidi, Aleksandar
Zdravković, Oi Kuan Choong, Julia Liz Touza, Niklas Selfjord, et al. “Engineered
PsCas9 Enables Therapeutic Genome Editing in Mouse Liver with Lipid Nanoparticles.”
Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-53418-8.
ieee: D. Degtev et al., “Engineered PsCas9 enables therapeutic genome editing
in mouse liver with lipid nanoparticles,” Nature Communications, vol. 15.
Springer Nature, 2024.
ista: Degtev D, Bravo JPK, Emmanouilidi A, Zdravković A, Choong OK, Liz Touza J,
Selfjord N, Weisheit I, Francescatto M, Akcakaya P, Porritt M, Maresca M, Taylor
D, Sienski G. 2024. Engineered PsCas9 enables therapeutic genome editing in mouse
liver with lipid nanoparticles. Nature Communications. 15, 9173.
mla: Degtev, Dmitrii, et al. “Engineered PsCas9 Enables Therapeutic Genome Editing
in Mouse Liver with Lipid Nanoparticles.” Nature Communications, vol. 15,
9173, Springer Nature, 2024, doi:10.1038/s41467-024-53418-8.
short: D. Degtev, J.P.K. Bravo, A. Emmanouilidi, A. Zdravković, O.K. Choong, J.
Liz Touza, N. Selfjord, I. Weisheit, M. Francescatto, P. Akcakaya, M. Porritt,
M. Maresca, D. Taylor, G. Sienski, Nature Communications 15 (2024).
date_created: 2024-11-12T10:18:04Z
date_published: 2024-11-07T00:00:00Z
date_updated: 2024-11-13T08:19:50Z
day: '07'
ddc:
- '572'
doi: 10.1038/s41467-024-53418-8
extern: '1'
file:
- access_level: open_access
checksum: dcfadc806f4144d065eb8e2032554782
content_type: application/pdf
creator: jbravo
date_created: 2024-11-12T10:18:32Z
date_updated: 2024-11-12T10:18:32Z
file_id: '18546'
file_name: s41467-024-53418-8.pdf
file_size: 2967001
relation: main_file
success: 1
file_date_updated: 2024-11-12T10:18:32Z
fulldoi: https://doi.org/10.1038/s41467-024-53418-8
has_accepted_license: '1'
intvolume: ' 15'
language:
- iso: eng
month: '11'
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: Engineered PsCas9 enables therapeutic genome editing in mouse liver with lipid
nanoparticles
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '17852'
abstract:
- lang: eng
text: Metal-metal contacts, though not yet widely realized, may provide exciting
opportunities to serve as tunable and functional interfaces in single-molecule
devices. One of the simplest components which might facilitate such binding interactions
is the ferrocene group. Notably, direct bonds between the ferrocene iron center
and metals such as Pd or Co have been demonstrated in molecular complexes comprising
coordinating ligands attached to the cyclopentadienyl rings. Here, we demonstrate
that ferrocene-based single-molecule devices with Fe-Au interfacial contact geometries
form at room temperature in the absence of supporting coordinating ligands. Applying
a photoredox reaction, we propose that ferrocene only functions effectively as
a contact group when oxidized, binding to gold through a formal Fe3+
center. This observation is further supported by a series of control measurements
and density functional theory calculations. Our findings extend the scope of junction
contact chemistries beyond those involving main group elements, lay the foundation
for light switchable ferrocene-based single-molecule devices, and highlight new
potential mechanistic function(s) of unsubstituted ferrocenium groups in synthetic
processes.
article_number: '1439'
article_processing_charge: Yes
article_type: original
author:
- first_name: Woojung
full_name: Lee, Woojung
last_name: Lee
- first_name: Liang
full_name: Li, Liang
last_name: Li
- first_name: María
full_name: Camarasa-Gómez, María
last_name: Camarasa-Gómez
- first_name: Daniel
full_name: Hernangómez-Pérez, Daniel
last_name: Hernangómez-Pérez
- first_name: Xavier
full_name: Roy, Xavier
last_name: Roy
- first_name: Ferdinand
full_name: Evers, Ferdinand
last_name: Evers
- first_name: Michael S.
full_name: Inkpen, Michael S.
last_name: Inkpen
- first_name: Latha
full_name: Venkataraman, Latha
id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
last_name: Venkataraman
orcid: 0000-0002-6957-6089
citation:
ama: Lee W, Li L, Camarasa-Gómez M, et al. Photooxidation driven formation of Fe-Au
linked ferrocene-based single-molecule junctions. Nature Communications.
2024;15. doi:10.1038/s41467-024-45707-z
apa: Lee, W., Li, L., Camarasa-Gómez, M., Hernangómez-Pérez, D., Roy, X., Evers,
F., … Venkataraman, L. (2024). Photooxidation driven formation of Fe-Au linked
ferrocene-based single-molecule junctions. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-024-45707-z
chicago: Lee, Woojung, Liang Li, María Camarasa-Gómez, Daniel Hernangómez-Pérez,
Xavier Roy, Ferdinand Evers, Michael S. Inkpen, and Latha Venkataraman. “Photooxidation
Driven Formation of Fe-Au Linked Ferrocene-Based Single-Molecule Junctions.” Nature
Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-45707-z.
ieee: W. Lee et al., “Photooxidation driven formation of Fe-Au linked ferrocene-based
single-molecule junctions,” Nature Communications, vol. 15. Springer Nature,
2024.
ista: Lee W, Li L, Camarasa-Gómez M, Hernangómez-Pérez D, Roy X, Evers F, Inkpen
MS, Venkataraman L. 2024. Photooxidation driven formation of Fe-Au linked ferrocene-based
single-molecule junctions. Nature Communications. 15, 1439.
mla: Lee, Woojung, et al. “Photooxidation Driven Formation of Fe-Au Linked Ferrocene-Based
Single-Molecule Junctions.” Nature Communications, vol. 15, 1439, Springer
Nature, 2024, doi:10.1038/s41467-024-45707-z.
short: W. Lee, L. Li, M. Camarasa-Gómez, D. Hernangómez-Pérez, X. Roy, F. Evers,
M.S. Inkpen, L. Venkataraman, Nature Communications 15 (2024).
date_created: 2024-09-06T12:38:44Z
date_published: 2024-02-16T00:00:00Z
date_updated: 2024-11-18T10:47:10Z
day: '16'
doi: 10.1038/s41467-024-45707-z
extern: '1'
external_id:
pmid:
- '38365892'
fulldoi: https://doi.org/10.1038/s41467-024-45707-z
intvolume: ' 15'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-024-45707-z
month: '02'
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: Photooxidation driven formation of Fe-Au linked ferrocene-based single-molecule
junctions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2024'
...
---
_id: '18153'
abstract:
- lang: eng
text: Attention supports decision making by selecting the features that are relevant
for decisions. Selective enhancement of the relevant features and inhibition of
distractors has been proposed as potential neural mechanisms driving this selection
process. Yet, how attention operates when relevance cannot be directly determined,
and the attention signal needs to be internally constructed is less understood.
Here we recorded from populations of neurons in the anterior cingulate cortex
(ACC) of mice in an attention-shifting task where relevance of stimulus modalities
changed across blocks of trials. In contrast with V1 recordings, decoding of the
irrelevant modality gradually declined in ACC after an initial transient. Our
analytical proof and a recurrent neural network model of the task revealed mutually
inhibiting connections that produced context-gated suppression as observed in
mice. Using this RNN model we predicted a correlation between contextual modulation
of individual neurons and their stimulus drive, which we confirmed in ACC but
not in V1.
article_number: '5559'
article_processing_charge: Yes
article_type: original
author:
- first_name: Márton Albert
full_name: Hajnal, Márton Albert
last_name: Hajnal
- first_name: Duy
full_name: Tran, Duy
last_name: Tran
- first_name: Zsombor
full_name: Szabó, Zsombor
id: 47757b1e-3f56-11ef-9908-8ddefb4d05eb
last_name: Szabó
orcid: 0009-0003-8524-4994
- first_name: Andrea
full_name: Albert, Andrea
last_name: Albert
- first_name: Karen
full_name: Safaryan, Karen
last_name: Safaryan
- first_name: Michael
full_name: Einstein, Michael
last_name: Einstein
- first_name: Mauricio
full_name: Vallejo Martelo, Mauricio
last_name: Vallejo Martelo
- first_name: Pierre-Olivier
full_name: Polack, Pierre-Olivier
last_name: Polack
- first_name: Peyman
full_name: Golshani, Peyman
last_name: Golshani
- first_name: Gergő
full_name: Orbán, Gergő
last_name: Orbán
citation:
ama: Hajnal MA, Tran D, Szabó Z, et al. Shifts in attention drive context-dependent
subspace encoding in anterior cingulate cortex in mice during decision making.
Nature Communications. 2024;15. doi:10.1038/s41467-024-49845-2
apa: Hajnal, M. A., Tran, D., Szabó, Z., Albert, A., Safaryan, K., Einstein, M.,
… Orbán, G. (2024). Shifts in attention drive context-dependent subspace encoding
in anterior cingulate cortex in mice during decision making. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-024-49845-2
chicago: Hajnal, Márton Albert, Duy Tran, Zsombor Szabó, Andrea Albert, Karen Safaryan,
Michael Einstein, Mauricio Vallejo Martelo, Pierre-Olivier Polack, Peyman Golshani,
and Gergő Orbán. “Shifts in Attention Drive Context-Dependent Subspace Encoding
in Anterior Cingulate Cortex in Mice during Decision Making.” Nature Communications.
Springer Nature, 2024. https://doi.org/10.1038/s41467-024-49845-2.
ieee: M. A. Hajnal et al., “Shifts in attention drive context-dependent subspace
encoding in anterior cingulate cortex in mice during decision making,” Nature
Communications, vol. 15. Springer Nature, 2024.
ista: Hajnal MA, Tran D, Szabó Z, Albert A, Safaryan K, Einstein M, Vallejo Martelo
M, Polack P-O, Golshani P, Orbán G. 2024. Shifts in attention drive context-dependent
subspace encoding in anterior cingulate cortex in mice during decision making.
Nature Communications. 15, 5559.
mla: Hajnal, Márton Albert, et al. “Shifts in Attention Drive Context-Dependent
Subspace Encoding in Anterior Cingulate Cortex in Mice during Decision Making.”
Nature Communications, vol. 15, 5559, Springer Nature, 2024, doi:10.1038/s41467-024-49845-2.
short: M.A. Hajnal, D. Tran, Z. Szabó, A. Albert, K. Safaryan, M. Einstein, M. Vallejo
Martelo, P.-O. Polack, P. Golshani, G. Orbán, Nature Communications 15 (2024).
date_created: 2024-09-28T06:59:03Z
date_published: 2024-07-02T00:00:00Z
date_updated: 2024-10-01T07:14:56Z
day: '02'
ddc:
- '570'
doi: 10.1038/s41467-024-49845-2
extern: '1'
external_id:
pmid:
- '37873364'
file:
- access_level: open_access
checksum: 22caa17a6691884c66c650c61227e903
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creator: dernst
date_created: 2024-10-01T07:13:36Z
date_updated: 2024-10-01T07:13:36Z
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file_date_updated: 2024-10-01T07:13:36Z
fulldoi: https://doi.org/10.1038/s41467-024-49845-2
has_accepted_license: '1'
intvolume: ' 15'
language:
- iso: eng
month: '07'
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: Shifts in attention drive context-dependent subspace encoding in anterior cingulate
cortex in mice during decision making
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: 15
year: '2024'
...
---
_id: '11951'
abstract:
- lang: eng
text: The mammalian hippocampal formation (HF) plays a key role in several higher
brain functions, such as spatial coding, learning and memory. Its simple circuit
architecture is often viewed as a trisynaptic loop, processing input originating
from the superficial layers of the entorhinal cortex (EC) and sending it back
to its deeper layers. Here, we show that excitatory neurons in layer 6b of the
mouse EC project to all sub-regions comprising the HF and receive input from the
CA1, thalamus and claustrum. Furthermore, their output is characterized by unique
slow-decaying excitatory postsynaptic currents capable of driving plateau-like
potentials in their postsynaptic targets. Optogenetic inhibition of the EC-6b
pathway affects spatial coding in CA1 pyramidal neurons, while cell ablation impairs
not only acquisition of new spatial memories, but also degradation of previously
acquired ones. Our results provide evidence of a functional role for cortical
layer 6b neurons in the adult brain.
acknowledged_ssus:
- _id: Bio
- _id: SSU
acknowledgement: We thank F. Marr and A. Schlögl for technical assistance, E. Kralli-Beller
for manuscript editing, as well as C. Sommer and the Imaging and Optics Facility
of the Institute of Science and Technology Austria (ISTA) for image analysis scripts
and microscopy support. We extend our gratitude to J. Wallenschus and D. Rangel
Guerrero for technical assistance acquiring single-unit data and I. Gridchyn for
help with single-unit clustering. Finally, we also thank B. Suter for discussions,
A. Saunders, M. Jösch, and H. Monyer for critically reading earlier versions of
the manuscript, C. Petersen for sharing clearing protocols, and the Scientific Service
Units of ISTA for efficient support. 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 to P.J.) and the Fond zur Förderung der Wissenschaftlichen
Forschung (Z 312-B27, Wittgenstein award for P.J. and I3600-B27 for J.G.D. and P.V.).
article_number: '4826'
article_processing_charge: No
article_type: original
author:
- first_name: Yoav
full_name: Ben Simon, Yoav
id: 43DF3136-F248-11E8-B48F-1D18A9856A87
last_name: Ben Simon
- first_name: Karola
full_name: Käfer, Karola
id: 2DAA49AA-F248-11E8-B48F-1D18A9856A87
last_name: Käfer
- first_name: Philipp
full_name: Velicky, Philipp
id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
last_name: Velicky
orcid: 0000-0002-2340-7431
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- 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: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Ben Simon Y, Käfer K, Velicky P, Csicsvari JL, Danzl JG, Jonas PM. A direct
excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes
to spatial coding and memory. Nature Communications. 2022;13. doi:10.1038/s41467-022-32559-8
apa: Ben Simon, Y., Käfer, K., Velicky, P., Csicsvari, J. L., Danzl, J. G., &
Jonas, P. M. (2022). A direct excitatory projection from entorhinal layer 6b neurons
to the hippocampus contributes to spatial coding and memory. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-022-32559-8
chicago: Ben Simon, Yoav, Karola Käfer, Philipp Velicky, Jozsef L Csicsvari, Johann
G Danzl, and Peter M Jonas. “A Direct Excitatory Projection from Entorhinal Layer
6b Neurons to the Hippocampus Contributes to Spatial Coding and Memory.” Nature
Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-32559-8.
ieee: Y. Ben Simon, K. Käfer, P. Velicky, J. L. Csicsvari, J. G. Danzl, and P. M.
Jonas, “A direct excitatory projection from entorhinal layer 6b neurons to the
hippocampus contributes to spatial coding and memory,” Nature Communications,
vol. 13. Springer Nature, 2022.
ista: Ben Simon Y, Käfer K, Velicky P, Csicsvari JL, Danzl JG, Jonas PM. 2022. A
direct excitatory projection from entorhinal layer 6b neurons to the hippocampus
contributes to spatial coding and memory. Nature Communications. 13, 4826.
mla: Ben Simon, Yoav, et al. “A Direct Excitatory Projection from Entorhinal Layer
6b Neurons to the Hippocampus Contributes to Spatial Coding and Memory.” Nature
Communications, vol. 13, 4826, Springer Nature, 2022, doi:10.1038/s41467-022-32559-8.
short: Y. Ben Simon, K. Käfer, P. Velicky, J.L. Csicsvari, J.G. Danzl, P.M. Jonas,
Nature Communications 13 (2022).
corr_author: '1'
date_created: 2022-08-24T08:25:50Z
date_published: 2022-08-16T00:00:00Z
date_updated: 2025-06-12T06:10:44Z
day: '16'
ddc:
- '570'
department:
- _id: JoCs
- _id: PeJo
- _id: JoDa
doi: 10.1038/s41467-022-32559-8
ec_funded: 1
external_id:
isi:
- '000841396400008'
pmid:
- '35974109'
file:
- access_level: open_access
checksum: 405936d9e4d33625d80c093c9713a91f
content_type: application/pdf
creator: dernst
date_created: 2022-08-26T11:51:40Z
date_updated: 2022-08-26T11:51:40Z
file_id: '11990'
file_name: 2022_NatureCommunications_BenSimon.pdf
file_size: 5910357
relation: main_file
success: 1
file_date_updated: 2022-08-26T11:51:40Z
fulldoi: https://doi.org/10.1038/s41467-022-32559-8
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
month: '08'
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: 265CB4D0-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03600
name: Optical control of synaptic function via adhesion molecules
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus
contributes to spatial coding and memory
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2022'
...
---
_id: '12052'
abstract:
- lang: eng
text: Directionality in the intercellular transport of the plant hormone auxin is
determined by polar plasma membrane localization of PIN-FORMED (PIN) auxin transport
proteins. However, apart from PIN phosphorylation at conserved motifs, no further
determinants explicitly controlling polar PIN sorting decisions have been identified.
Here we present Arabidopsis WAVY GROWTH 3 (WAV3) and closely related RING-finger
E3 ubiquitin ligases, whose loss-of-function mutants show a striking apical-to-basal
polarity switch in PIN2 localization in root meristem cells. WAV3 E3 ligases function
as essential determinants for PIN polarity, acting independently from PINOID/WAG-dependent
PIN phosphorylation. They antagonize ectopic deposition of de novo synthesized
PIN proteins already immediately following completion of cell division, presumably
via preventing PIN sorting into basal, ARF GEF-mediated trafficking. Our findings
reveal an involvement of E3 ligases in the selective targeting of apically localized
PINs in higher plants.
acknowledgement: We would like to thank Tatsuo Sakai, Marcus Heisler, Toru Fujiwara,
Lucia Strader, Christian Hardtke, Malcolm Bennett, Claus Schwechheimer, Gerd Jürgens
and Remko Offringa for sharing published materials and Alba Grau Gimeno for support.
We are greatly indebted to Bert de Rybel for supporting N.K. and M.G. to work on
the final stages of manuscript preparation as postdocs in his laboratory. A full-length
SOR1 cDNA clone (J090099M14) was obtained from the National Agriculture and Food
Research Organization (NARO, Japan). Support by the Multiscale Imaging Core Facility
at the BOKU is greatly acknowledged. This work has been supported by grants from
the Austrian Science Fund (FWF P25931-B16; P31493-B25 to Christian Luschnig; I3630-B25
to Jiří Friml; P30850-B32 to Barbara Korbei) and from the Swiss National Funds (31003A-165877/1
to Markus Geisler) and the European Union’s Horizon 2020 research and innovation
program (Marie Skłodowska-Curie grant agreement No 885979 to Matouš Glanc).
article_number: '5147'
article_processing_charge: No
article_type: original
author:
- first_name: N
full_name: Konstantinova, N
last_name: Konstantinova
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
orcid: 0000-0001-8295-2926
- first_name: Matous
full_name: Glanc, Matous
id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2
last_name: Glanc
orcid: 0000-0003-0619-7783
- first_name: R
full_name: Keshkeih, R
last_name: Keshkeih
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: M
full_name: Di Donato, M
last_name: Di Donato
- first_name: K
full_name: Retzer, K
last_name: Retzer
- first_name: J
full_name: Moulinier-Anzola, J
last_name: Moulinier-Anzola
- first_name: M
full_name: Schwihla, M
last_name: Schwihla
- first_name: B
full_name: Korbei, B
last_name: Korbei
- first_name: M
full_name: Geisler, M
last_name: Geisler
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: C
full_name: Luschnig, C
last_name: Luschnig
citation:
ama: Konstantinova N, Hörmayer L, Glanc M, et al. WAVY GROWTH Arabidopsis E3 ubiquitin
ligases affect apical PIN sorting decisions. Nature Communications. 2022;13.
doi:10.1038/s41467-022-32888-8
apa: Konstantinova, N., Hörmayer, L., Glanc, M., Keshkeih, R., Tan, S., Di Donato,
M., … Luschnig, C. (2022). WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect
apical PIN sorting decisions. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-32888-8
chicago: Konstantinova, N, Lukas Hörmayer, Matous Glanc, R Keshkeih, Shutang Tan,
M Di Donato, K Retzer, et al. “WAVY GROWTH Arabidopsis E3 Ubiquitin Ligases Affect
Apical PIN Sorting Decisions.” Nature Communications. Springer Nature,
2022. https://doi.org/10.1038/s41467-022-32888-8.
ieee: N. Konstantinova et al., “WAVY GROWTH Arabidopsis E3 ubiquitin ligases
affect apical PIN sorting decisions,” Nature Communications, vol. 13. Springer
Nature, 2022.
ista: Konstantinova N, Hörmayer L, Glanc M, Keshkeih R, Tan S, Di Donato M, Retzer
K, Moulinier-Anzola J, Schwihla M, Korbei B, Geisler M, Friml J, Luschnig C. 2022.
WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions.
Nature Communications. 13, 5147.
mla: Konstantinova, N., et al. “WAVY GROWTH Arabidopsis E3 Ubiquitin Ligases Affect
Apical PIN Sorting Decisions.” Nature Communications, vol. 13, 5147, Springer
Nature, 2022, doi:10.1038/s41467-022-32888-8.
short: N. Konstantinova, L. Hörmayer, M. Glanc, R. Keshkeih, S. Tan, M. Di Donato,
K. Retzer, J. Moulinier-Anzola, M. Schwihla, B. Korbei, M. Geisler, J. Friml,
C. Luschnig, Nature Communications 13 (2022).
date_created: 2022-09-07T14:19:26Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2025-04-15T07:32:09Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41467-022-32888-8
external_id:
isi:
- '000848744900004'
pmid:
- '36050482'
file:
- access_level: open_access
checksum: 43336758c89cd6c045839089af070afe
content_type: application/pdf
creator: dernst
date_created: 2022-09-08T07:46:16Z
date_updated: 2022-09-08T07:46:16Z
file_id: '12063'
file_name: 2022_NatureCommunications_Konstantinova.pdf
file_size: 6678579
relation: main_file
success: 1
file_date_updated: 2022-09-08T07:46:16Z
fulldoi: https://doi.org/10.1038/s41467-022-32888-8
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
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/s41467-022-33198-9
scopus_import: '1'
status: public
title: WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions
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: '12208'
abstract:
- lang: eng
text: The inadequate understanding of the mechanisms that reversibly convert molecular
sulfur (S) into lithium sulfide (Li2S) via soluble polysulfides
(PSs) formation impedes the development of high-performance lithium-sulfur (Li-S)
batteries with non-aqueous electrolyte solutions. Here, we use operando small
and wide angle X-ray scattering and operando small angle neutron scattering (SANS)
measurements to track the nucleation, growth and dissolution of solid deposits
from atomic to sub-micron scales during real-time Li-S cell operation. In particular,
stochastic modelling based on the SANS data allows quantifying the nanoscale phase
evolution during battery cycling. We show that next to nano-crystalline Li2S
the deposit comprises solid short-chain PSs particles. The analysis of the experimental
data suggests that initially, Li2S2
precipitates from the solution and then is partially converted via solid-state
electroreduction to Li2S. We further demonstrate that mass
transport, rather than electron transport through a thin passivating film, limits
the discharge capacity and rate performance in Li-S cells.
acknowledgement: "This project has received funding from the European Union’s Horizon
2020 research and innovation program under the Marie Skłodowska-Curie grant NanoEvolution,
grant agreement No 894042. The authors acknowledge the CERIC-ERIC Consortium for
the access to the Austrian SAXS beamline and TU Graz for support through the Lead
Project LP-03.\r\nLikewise, the use of SOMAPP Lab, a core facility supported by
the Austrian Federal Ministry of Education, Science and Research, the Graz University
of Technology, the University of Graz, and Anton Paar GmbH is acknowledged. In addition,
the authors acknowledge access to the D-22SANS beamline at the ILL neutron source.
Electron microscopy measurements were performed at the Scientific Scenter for Optical
and Electron Microscopy (ScopeM) of the Swiss Federal Institute of Technology. C.P.
and J.M.M. thank A. Senol for her support with the SANS\r\nbeamtime preparation.
S.D.T, A.V. and R.D. acknowledge the financial support by the Slovenian Research
Agency (ARRS) research core funding P2-0393 and P2-0423. Furthermore, A.V. acknowledge
the funding from the Slovenian Research Agency, research project Z2−1863.\r\nS.A.F.
is indebted to IST Austria for support. "
article_number: '6326'
article_processing_charge: No
article_type: original
author:
- first_name: Christian
full_name: Prehal, Christian
last_name: Prehal
- first_name: Jean-Marc
full_name: von Mentlen, Jean-Marc
last_name: von Mentlen
- first_name: Sara
full_name: Drvarič Talian, Sara
last_name: Drvarič Talian
- first_name: Alen
full_name: Vizintin, Alen
last_name: Vizintin
- first_name: Robert
full_name: Dominko, Robert
last_name: Dominko
- first_name: Heinz
full_name: Amenitsch, Heinz
last_name: Amenitsch
- first_name: Lionel
full_name: Porcar, Lionel
last_name: Porcar
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Vanessa
full_name: Wood, Vanessa
last_name: Wood
citation:
ama: Prehal C, von Mentlen J-M, Drvarič Talian S, et al. On the nanoscale structural
evolution of solid discharge products in lithium-sulfur batteries using operando
scattering. Nature Communications. 2022;13. doi:10.1038/s41467-022-33931-4
apa: Prehal, C., von Mentlen, J.-M., Drvarič Talian, S., Vizintin, A., Dominko,
R., Amenitsch, H., … Wood, V. (2022). On the nanoscale structural evolution of
solid discharge products in lithium-sulfur batteries using operando scattering.
Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-33931-4
chicago: Prehal, Christian, Jean-Marc von Mentlen, Sara Drvarič Talian, Alen Vizintin,
Robert Dominko, Heinz Amenitsch, Lionel Porcar, Stefan Alexander Freunberger,
and Vanessa Wood. “On the Nanoscale Structural Evolution of Solid Discharge Products
in Lithium-Sulfur Batteries Using Operando Scattering.” Nature Communications.
Springer Nature, 2022. https://doi.org/10.1038/s41467-022-33931-4.
ieee: C. Prehal et al., “On the nanoscale structural evolution of solid discharge
products in lithium-sulfur batteries using operando scattering,” Nature Communications,
vol. 13. Springer Nature, 2022.
ista: Prehal C, von Mentlen J-M, Drvarič Talian S, Vizintin A, Dominko R, Amenitsch
H, Porcar L, Freunberger SA, Wood V. 2022. On the nanoscale structural evolution
of solid discharge products in lithium-sulfur batteries using operando scattering.
Nature Communications. 13, 6326.
mla: Prehal, Christian, et al. “On the Nanoscale Structural Evolution of Solid Discharge
Products in Lithium-Sulfur Batteries Using Operando Scattering.” Nature Communications,
vol. 13, 6326, Springer Nature, 2022, doi:10.1038/s41467-022-33931-4.
short: C. Prehal, J.-M. von Mentlen, S. Drvarič Talian, A. Vizintin, R. Dominko,
H. Amenitsch, L. Porcar, S.A. Freunberger, V. Wood, Nature Communications 13 (2022).
corr_author: '1'
date_created: 2023-01-16T09:45:09Z
date_published: 2022-10-24T00:00:00Z
date_updated: 2024-10-09T21:03:47Z
day: '24'
ddc:
- '540'
department:
- _id: StFr
doi: 10.1038/s41467-022-33931-4
external_id:
isi:
- '000871563700006'
pmid:
- '36280671'
file:
- access_level: open_access
checksum: 5034336dbf0f860030ef745c08df9e0e
content_type: application/pdf
creator: dernst
date_created: 2023-01-27T07:19:11Z
date_updated: 2023-01-27T07:19:11Z
file_id: '12411'
file_name: 2022_NatureCommunications_Prehal.pdf
file_size: 4216931
relation: main_file
success: 1
file_date_updated: 2023-01-27T07:19:11Z
fulldoi: https://doi.org/10.1038/s41467-022-33931-4
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
month: '10'
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: On the nanoscale structural evolution of solid discharge products in lithium-sulfur
batteries using operando scattering
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: '12217'
abstract:
- lang: eng
text: The development dynamics and self-organization of glandular branched epithelia
is of utmost importance for our understanding of diverse processes ranging from
normal tissue growth to the growth of cancerous tissues. Using single primary
murine pancreatic ductal adenocarcinoma (PDAC) cells embedded in a collagen matrix
and adapted media supplementation, we generate organoids that self-organize into
highly branched structures displaying a seamless lumen connecting terminal end
buds, replicating in vivo PDAC architecture. We identify distinct morphogenesis
phases, each characterized by a unique pattern of cell invasion, matrix deformation,
protein expression, and respective molecular dependencies. We propose a minimal
theoretical model of a branching and proliferating tissue, capturing the dynamics
of the first phases. Observing the interaction of morphogenesis, mechanical environment
and gene expression in vitro sets a benchmark for the understanding of self-organization
processes governing complex organoid structure formation processes and branching
morphogenesis.
acknowledgement: "A.R.B. acknowledges the financial support of the European Research
Council (ERC) through the funding of the grant Principles of Integrin Mechanics
and Adhesion (PoINT) and the German Research Foundation (DFG, SFB 1032, project
ID 201269156). E.H. was supported by the European Union (European Research Council
Starting Grant 851288). D.S., M.R., and R.R. acknowledge the support by the German
Research Foundation (DFG, SFB1321 Modeling and Targeting Pancreatic Cancer, Project
S01, project ID 329628492). C.S. and M.R. acknowledge the support by the German
Research Foundation (DFG, SFB1321 Modeling and Targeting Pancreatic Cancer, Project
12, project ID 329628492). M.R. was supported by the German Research Foundation
(DFG RE 3723/4-1). A.P. and M.R. were supported by the German Cancer Aid (Max-Eder
Program 111273 and 70114328).\r\nOpen Access funding enabled and organized by Projekt
DEAL."
article_number: '5219'
article_processing_charge: No
article_type: original
author:
- first_name: S.
full_name: Randriamanantsoa, S.
last_name: Randriamanantsoa
- first_name: A.
full_name: Papargyriou, A.
last_name: Papargyriou
- first_name: H. C.
full_name: Maurer, H. C.
last_name: Maurer
- first_name: K.
full_name: Peschke, K.
last_name: Peschke
- first_name: M.
full_name: Schuster, M.
last_name: Schuster
- first_name: G.
full_name: Zecchin, G.
last_name: Zecchin
- first_name: K.
full_name: Steiger, K.
last_name: Steiger
- first_name: R.
full_name: Öllinger, R.
last_name: Öllinger
- first_name: D.
full_name: Saur, D.
last_name: Saur
- first_name: C.
full_name: Scheel, C.
last_name: Scheel
- first_name: R.
full_name: Rad, R.
last_name: Rad
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: M.
full_name: Reichert, M.
last_name: Reichert
- first_name: A. R.
full_name: Bausch, A. R.
last_name: Bausch
citation:
ama: Randriamanantsoa S, Papargyriou A, Maurer HC, et al. Spatiotemporal dynamics
of self-organized branching in pancreas-derived organoids. Nature Communications.
2022;13. doi:10.1038/s41467-022-32806-y
apa: Randriamanantsoa, S., Papargyriou, A., Maurer, H. C., Peschke, K., Schuster,
M., Zecchin, G., … Bausch, A. R. (2022). Spatiotemporal dynamics of self-organized
branching in pancreas-derived organoids. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-022-32806-y
chicago: Randriamanantsoa, S., A. Papargyriou, H. C. Maurer, K. Peschke, M. Schuster,
G. Zecchin, K. Steiger, et al. “Spatiotemporal Dynamics of Self-Organized Branching
in Pancreas-Derived Organoids.” Nature Communications. Springer Nature,
2022. https://doi.org/10.1038/s41467-022-32806-y.
ieee: S. Randriamanantsoa et al., “Spatiotemporal dynamics of self-organized
branching in pancreas-derived organoids,” Nature Communications, vol. 13.
Springer Nature, 2022.
ista: Randriamanantsoa S, Papargyriou A, Maurer HC, Peschke K, Schuster M, Zecchin
G, Steiger K, Öllinger R, Saur D, Scheel C, Rad R, Hannezo EB, Reichert M, Bausch
AR. 2022. Spatiotemporal dynamics of self-organized branching in pancreas-derived
organoids. Nature Communications. 13, 5219.
mla: Randriamanantsoa, S., et al. “Spatiotemporal Dynamics of Self-Organized Branching
in Pancreas-Derived Organoids.” Nature Communications, vol. 13, 5219, Springer
Nature, 2022, doi:10.1038/s41467-022-32806-y.
short: S. Randriamanantsoa, A. Papargyriou, H.C. Maurer, K. Peschke, M. Schuster,
G. Zecchin, K. Steiger, R. Öllinger, D. Saur, C. Scheel, R. Rad, E.B. Hannezo,
M. Reichert, A.R. Bausch, Nature Communications 13 (2022).
date_created: 2023-01-16T09:46:53Z
date_published: 2022-09-05T00:00:00Z
date_updated: 2025-06-11T13:53:55Z
day: '05'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1038/s41467-022-32806-y
ec_funded: 1
external_id:
isi:
- '000850348400025'
pmid:
- '36064947'
file:
- access_level: open_access
checksum: 295261b5172274fd5b8f85a6a6058828
content_type: application/pdf
creator: dernst
date_created: 2023-01-27T08:14:48Z
date_updated: 2023-01-27T08:14:48Z
file_id: '12416'
file_name: 2022_NatureCommunications_Randriamanantsoa.pdf
file_size: 22645149
relation: main_file
success: 1
file_date_updated: 2023-01-27T08:14:48Z
fulldoi: https://doi.org/10.1038/s41467-022-32806-y
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '13068'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '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'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18221'
abstract:
- lang: eng
text: Synonymous codons translate into chemically identical amino acids. Once considered
inconsequential to the formation of the protein product, there is evidence to
suggest that codon usage affects co-translational protein folding and the final
structure of the expressed protein. Here we develop a method for computing and
comparing codon-specific Ramachandran plots and demonstrate that the backbone
dihedral angle distributions of some synonymous codons are distinguishable with
statistical significance for some secondary structures. This shows that there
exists a dependence between codon identity and backbone torsion of the translated
amino acid. Although these findings cannot pinpoint the causal direction of this
dependence, we discuss the vast biological implications should coding be shown
to directly shape protein conformation and demonstrate the usefulness of this
method as a tool for probing associations between codon usage and protein structure.
Finally, we urge for the inclusion of exact genetic information into structural
databases.
article_number: '2815'
article_processing_charge: Yes
article_type: original
author:
- first_name: Aviv A.
full_name: Rosenberg, Aviv A.
last_name: Rosenberg
- first_name: Ailie
full_name: Marx, Ailie
last_name: Marx
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
citation:
ama: Rosenberg AA, Marx A, Bronstein AM. Codon-specific Ramachandran plots show
amino acid backbone conformation depends on identity of the translated codon.
Nature Communications. 2022;13. doi:10.1038/s41467-022-30390-9
apa: Rosenberg, A. A., Marx, A., & Bronstein, A. M. (2022). Codon-specific Ramachandran
plots show amino acid backbone conformation depends on identity of the translated
codon. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-30390-9
chicago: Rosenberg, Aviv A., Ailie Marx, and Alex M. Bronstein. “Codon-Specific
Ramachandran Plots Show Amino Acid Backbone Conformation Depends on Identity of
the Translated Codon.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-30390-9.
ieee: A. A. Rosenberg, A. Marx, and A. M. Bronstein, “Codon-specific Ramachandran
plots show amino acid backbone conformation depends on identity of the translated
codon,” Nature Communications, vol. 13. Springer Nature, 2022.
ista: Rosenberg AA, Marx A, Bronstein AM. 2022. Codon-specific Ramachandran plots
show amino acid backbone conformation depends on identity of the translated codon.
Nature Communications. 13, 2815.
mla: Rosenberg, Aviv A., et al. “Codon-Specific Ramachandran Plots Show Amino Acid
Backbone Conformation Depends on Identity of the Translated Codon.” Nature
Communications, vol. 13, 2815, Springer Nature, 2022, doi:10.1038/s41467-022-30390-9.
short: A.A. Rosenberg, A. Marx, A.M. Bronstein, Nature Communications 13 (2022).
date_created: 2024-10-08T12:53:01Z
date_published: 2022-05-20T00:00:00Z
date_updated: 2024-10-14T09:49:02Z
day: '20'
doi: 10.1038/s41467-022-30390-9
extern: '1'
external_id:
pmid:
- '35595777'
fulldoi: https://doi.org/10.1038/s41467-022-30390-9
intvolume: ' 13'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-022-30390-9
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: Codon-specific Ramachandran plots show amino acid backbone conformation depends
on identity of the translated codon
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
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: 2026-11-12T23:30:04Z
day: '12'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1038/s41467-022-30301-y
ec_funded: 1
external_id:
isi:
- '000795171100037'
file:
- access_level: open_access
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: '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: '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'
...
---
OA_place: publisher
OA_type: gold
_id: '9778'
abstract:
- lang: eng
text: The hippocampal mossy fiber synapse is a key synapse of the trisynaptic circuit.
Post-tetanic potentiation (PTP) is the most powerful form of plasticity at this
synaptic connection. It is widely believed that mossy fiber PTP is an entirely
presynaptic phenomenon, implying that PTP induction is input-specific, and requires
neither activity of multiple inputs nor stimulation of postsynaptic neurons. To
directly test cooperativity and associativity, we made paired recordings between
single mossy fiber terminals and postsynaptic CA3 pyramidal neurons in rat brain
slices. By stimulating non-overlapping mossy fiber inputs converging onto single
CA3 neurons, we confirm that PTP is input-specific and non-cooperative. Unexpectedly,
mossy fiber PTP exhibits anti-associative induction properties. EPSCs show only
minimal PTP after combined pre- and postsynaptic high-frequency stimulation with
intact postsynaptic Ca2+ signaling, but marked PTP in the absence of postsynaptic
spiking and after suppression of postsynaptic Ca2+ signaling (10 mM EGTA). PTP
is largely recovered by inhibitors of voltage-gated R- and L-type Ca2+ channels,
group II mGluRs, and vacuolar-type H+-ATPase, suggesting the involvement of retrograde
vesicular glutamate signaling. Transsynaptic regulation of PTP extends the repertoire
of synaptic computations, implementing a brake on mossy fiber detonation and a
“smart teacher” function of hippocampal mossy fiber synapses.
acknowledged_ssus:
- _id: SSU
acknowledgement: We thank Drs. Carolina Borges-Merjane and Jose Guzman for critically
reading the manuscript, and Pablo Castillo for discussions. We are grateful to Alois
Schlögl for help with analysis, Florian Marr for excellent technical assistance
and cell reconstruction, Christina Altmutter for technical help, Eleftheria Kralli-Beller
for manuscript editing, and the Scientific Service Units of IST Austria for support.
This project received funding from the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation program (grant agreement No
692692) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27,
Wittgenstein award), both to P.J.
article_number: '2912'
article_processing_charge: Yes
article_type: original
author:
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Yuji
full_name: Okamoto, Yuji
id: 3337E116-F248-11E8-B48F-1D18A9856A87
last_name: Okamoto
orcid: 0000-0003-0408-6094
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Vandael DH, Okamoto Y, Jonas PM. Transsynaptic modulation of presynaptic short-term
plasticity in hippocampal mossy fiber synapses. Nature Communications.
2021;12(1). doi:10.1038/s41467-021-23153-5
apa: Vandael, D. H., Okamoto, Y., & Jonas, P. M. (2021). Transsynaptic modulation
of presynaptic short-term plasticity in hippocampal mossy fiber synapses. Nature
Communications. Springer. https://doi.org/10.1038/s41467-021-23153-5
chicago: Vandael, David H, Yuji Okamoto, and Peter M Jonas. “Transsynaptic Modulation
of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” Nature
Communications. Springer, 2021. https://doi.org/10.1038/s41467-021-23153-5.
ieee: D. H. Vandael, Y. Okamoto, and P. M. Jonas, “Transsynaptic modulation of presynaptic
short-term plasticity in hippocampal mossy fiber synapses,” Nature Communications,
vol. 12, no. 1. Springer, 2021.
ista: Vandael DH, Okamoto Y, Jonas PM. 2021. Transsynaptic modulation of presynaptic
short-term plasticity in hippocampal mossy fiber synapses. Nature Communications.
12(1), 2912.
mla: Vandael, David H., et al. “Transsynaptic Modulation of Presynaptic Short-Term
Plasticity in Hippocampal Mossy Fiber Synapses.” Nature Communications,
vol. 12, no. 1, 2912, Springer, 2021, doi:10.1038/s41467-021-23153-5.
short: D.H. Vandael, Y. Okamoto, P.M. Jonas, Nature Communications 12 (2021).
corr_author: '1'
date_created: 2021-08-06T07:22:55Z
date_published: 2021-05-18T00:00:00Z
date_updated: 2025-06-12T06:28:45Z
day: '18'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1038/s41467-021-23153-5
ec_funded: 1
external_id:
isi:
- '000655481800014'
pmid:
- '34006874'
file:
- access_level: open_access
checksum: 6036a8cdae95e1707c2a04d54e325ff4
content_type: application/pdf
creator: kschuh
date_created: 2021-12-17T11:34:50Z
date_updated: 2021-12-17T11:34:50Z
file_id: '10563'
file_name: 2021_NatureCommunications_Vandael.pdf
file_size: 3108845
relation: main_file
success: 1
file_date_updated: 2021-12-17T11:34:50Z
fulldoi: https://doi.org/10.1038/s41467-021-23153-5
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '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
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: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/synaptic-transmission-not-a-one-way-street/
scopus_import: '1'
status: public
title: Transsynaptic modulation of presynaptic short-term plasticity in hippocampal
mossy fiber synapses
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2021'
...
---
_id: '15142'
abstract:
- lang: eng
text: Bacteria and archaea employ CRISPR (clustered, regularly, interspaced, short
palindromic repeats)-Cas (CRISPR-associated) systems as a type of adaptive immunity
to target and degrade foreign nucleic acids. While a myriad of CRISPR-Cas systems
have been identified to date, type I-C is one of the most commonly found subtypes
in nature. Interestingly, the type I-C system employs a minimal Cascade effector
complex, which encodes only three unique subunits in its operon. Here, we present
a 3.1 Å resolution cryo-EM structure of the Desulfovibrio vulgaris
type I-C Cascade, revealing the molecular mechanisms that underlie RNA-directed
complex assembly. We demonstrate how this minimal Cascade utilizes previously
overlooked, non-canonical small subunits to stabilize R-loop formation. Furthermore,
we describe putative PAM and Cas3 binding sites. These findings provide the structural
basis for harnessing the type I-C Cascade as a genome-engineering tool.
article_number: '5931'
article_processing_charge: Yes
article_type: original
author:
- first_name: Roisin E.
full_name: O’Brien, Roisin E.
last_name: O’Brien
- first_name: Inês C.
full_name: Santos, Inês C.
last_name: Santos
- first_name: Daniel
full_name: Wrapp, Daniel
last_name: Wrapp
- 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: Evan A.
full_name: Schwartz, Evan A.
last_name: Schwartz
- first_name: Jennifer S.
full_name: Brodbelt, Jennifer S.
last_name: Brodbelt
- first_name: David W.
full_name: Taylor, David W.
last_name: Taylor
citation:
ama: O’Brien RE, Santos IC, Wrapp D, et al. Structural basis for assembly of non-canonical
small subunits into type I-C Cascade. Nature Communications. 2020;11. doi:10.1038/s41467-020-19785-8
apa: O’Brien, R. E., Santos, I. C., Wrapp, D., Bravo, J. P. K., Schwartz, E. A.,
Brodbelt, J. S., & Taylor, D. W. (2020). Structural basis for assembly of
non-canonical small subunits into type I-C Cascade. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-020-19785-8
chicago: O’Brien, Roisin E., Inês C. Santos, Daniel Wrapp, Jack Peter Kelly Bravo,
Evan A. Schwartz, Jennifer S. Brodbelt, and David W. Taylor. “Structural Basis
for Assembly of Non-Canonical Small Subunits into Type I-C Cascade.” Nature
Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-19785-8.
ieee: R. E. O’Brien et al., “Structural basis for assembly of non-canonical
small subunits into type I-C Cascade,” Nature Communications, vol. 11.
Springer Nature, 2020.
ista: O’Brien RE, Santos IC, Wrapp D, Bravo JPK, Schwartz EA, Brodbelt JS, Taylor
DW. 2020. Structural basis for assembly of non-canonical small subunits into type
I-C Cascade. Nature Communications. 11, 5931.
mla: O’Brien, Roisin E., et al. “Structural Basis for Assembly of Non-Canonical
Small Subunits into Type I-C Cascade.” Nature Communications, vol. 11,
5931, Springer Nature, 2020, doi:10.1038/s41467-020-19785-8.
short: R.E. O’Brien, I.C. Santos, D. Wrapp, J.P.K. Bravo, E.A. Schwartz, J.S. Brodbelt,
D.W. Taylor, Nature Communications 11 (2020).
date_created: 2024-03-20T10:43:07Z
date_published: 2020-11-23T00:00:00Z
date_updated: 2024-06-04T05:52:51Z
day: '23'
doi: 10.1038/s41467-020-19785-8
extern: '1'
external_id:
pmid:
- '33230133'
fulldoi: https://doi.org/10.1038/s41467-020-19785-8
intvolume: ' 11'
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/s41467-020-19785-8
month: '11'
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 assembly of non-canonical small subunits into type I-C
Cascade
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2020'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '7707'
abstract:
- lang: eng
text: The growing sample size of genome-wide association studies has facilitated
the discovery of gene-environment interactions (GxE). Here we propose a maximum
likelihood method to estimate the contribution of GxE to continuous traits taking
into account all interacting environmental variables, without the need to measure
any. Extensive simulations demonstrate that our method provides unbiased interaction
estimates and excellent coverage. We also offer strategies to distinguish specific
GxE from general scale effects. Applying our method to 32 traits in the UK Biobank
reveals that while the genetic risk score (GRS) of 376 variants explains 5.2%
of body mass index (BMI) variance, GRSxE explains an additional 1.9%. Nevertheless,
this interaction holds for any variable with identical correlation to BMI as the
GRS, hence may not be GRS-specific. Still, we observe that the global contribution
of specific GRSxE to complex traits is substantial for nine obesity-related measures
(including leg impedance and trunk fat-free mass).
article_number: '1385'
article_processing_charge: No
article_type: original
author:
- first_name: Jonathan
full_name: Sulc, Jonathan
last_name: Sulc
- first_name: Ninon
full_name: Mounier, Ninon
last_name: Mounier
- first_name: Felix
full_name: Günther, Felix
last_name: Günther
- first_name: Thomas
full_name: Winkler, Thomas
last_name: Winkler
- first_name: Andrew R.
full_name: Wood, Andrew R.
last_name: Wood
- first_name: Timothy M.
full_name: Frayling, Timothy M.
last_name: Frayling
- first_name: Iris M.
full_name: Heid, Iris M.
last_name: Heid
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Zoltán
full_name: Kutalik, Zoltán
last_name: Kutalik
citation:
ama: Sulc J, Mounier N, Günther F, et al. Quantification of the overall contribution
of gene-environment interaction for obesity-related traits. Nature Communications.
2020;11. doi:10.1038/s41467-020-15107-0
apa: Sulc, J., Mounier, N., Günther, F., Winkler, T., Wood, A. R., Frayling, T.
M., … Kutalik, Z. (2020). Quantification of the overall contribution of gene-environment
interaction for obesity-related traits. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-020-15107-0
chicago: Sulc, Jonathan, Ninon Mounier, Felix Günther, Thomas Winkler, Andrew R.
Wood, Timothy M. Frayling, Iris M. Heid, Matthew Richard Robinson, and Zoltán
Kutalik. “Quantification of the Overall Contribution of Gene-Environment Interaction
for Obesity-Related Traits.” Nature Communications. Springer Nature, 2020.
https://doi.org/10.1038/s41467-020-15107-0.
ieee: J. Sulc et al., “Quantification of the overall contribution of gene-environment
interaction for obesity-related traits,” Nature Communications, vol. 11.
Springer Nature, 2020.
ista: Sulc J, Mounier N, Günther F, Winkler T, Wood AR, Frayling TM, Heid IM, Robinson
MR, Kutalik Z. 2020. Quantification of the overall contribution of gene-environment
interaction for obesity-related traits. Nature Communications. 11, 1385.
mla: Sulc, Jonathan, et al. “Quantification of the Overall Contribution of Gene-Environment
Interaction for Obesity-Related Traits.” Nature Communications, vol. 11,
1385, Springer Nature, 2020, doi:10.1038/s41467-020-15107-0.
short: J. Sulc, N. Mounier, F. Günther, T. Winkler, A.R. Wood, T.M. Frayling, I.M.
Heid, M.R. Robinson, Z. Kutalik, Nature Communications 11 (2020).
date_created: 2020-04-30T10:39:33Z
date_published: 2020-03-20T00:00:00Z
date_updated: 2024-10-15T12:43:32Z
day: '20'
doi: 10.1038/s41467-020-15107-0
extern: '1'
fulldoi: https://doi.org/10.1038/s41467-020-15107-0
intvolume: ' 11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-020-15107-0
month: '03'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Quantification of the overall contribution of gene-environment interaction
for obesity-related traits
type: journal_article
user_id: 0043cee0-e5fc-11ee-9736-f83bc23afbf0
volume: 11
year: '2020'
...
---
_id: '7999'
abstract:
- lang: eng
text: 'Linking epigenetic marks to clinical outcomes improves insight into molecular
processes, disease prediction, and therapeutic target identification. Here, a
statistical approach is presented to infer the epigenetic architecture of complex
disease, determine the variation captured by epigenetic effects, and estimate
phenotype-epigenetic probe associations jointly. Implicitly adjusting for probe
correlations, data structure (cell-count or relatedness), and single-nucleotide
polymorphism (SNP) marker effects, improves association estimates and in 9,448
individuals, 75.7% (95% CI 71.70–79.3) of body mass index (BMI) variation and
45.6% (95% CI 37.3–51.9) of cigarette consumption variation was captured by whole
blood methylation array data. Pathway-linked probes of blood cholesterol, lipid
transport and sterol metabolism for BMI, and xenobiotic stimuli response for smoking,
showed >1.5 times larger associations with >95% posterior inclusion probability.
Prediction accuracy improved by 28.7% for BMI and 10.2% for smoking over a LASSO
model, with age-, and tissue-specificity, implying associations are a phenotypic
consequence rather than causal. '
article_number: '2865'
article_processing_charge: No
article_type: original
author:
- first_name: D
full_name: Trejo Banos, D
last_name: Trejo Banos
- first_name: DL
full_name: McCartney, DL
last_name: McCartney
- first_name: M
full_name: Patxot, M
last_name: Patxot
- first_name: L
full_name: Anchieri, L
last_name: Anchieri
- first_name: T
full_name: Battram, T
last_name: Battram
- first_name: C
full_name: Christiansen, C
last_name: Christiansen
- first_name: R
full_name: Costeira, R
last_name: Costeira
- first_name: RM
full_name: Walker, RM
last_name: Walker
- first_name: SW
full_name: Morris, SW
last_name: Morris
- first_name: A
full_name: Campbell, A
last_name: Campbell
- first_name: Q
full_name: Zhang, Q
last_name: Zhang
- first_name: DJ
full_name: Porteous, DJ
last_name: Porteous
- first_name: AF
full_name: McRae, AF
last_name: McRae
- first_name: NR
full_name: Wray, NR
last_name: Wray
- first_name: PM
full_name: Visscher, PM
last_name: Visscher
- first_name: CS
full_name: Haley, CS
last_name: Haley
- first_name: KL
full_name: Evans, KL
last_name: Evans
- first_name: IJ
full_name: Deary, IJ
last_name: Deary
- first_name: AM
full_name: McIntosh, AM
last_name: McIntosh
- first_name: G
full_name: Hemani, G
last_name: Hemani
- first_name: JT
full_name: Bell, JT
last_name: Bell
- first_name: RE
full_name: Marioni, RE
last_name: Marioni
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
citation:
ama: Trejo Banos D, McCartney D, Patxot M, et al. Bayesian reassessment of the epigenetic
architecture of complex traits. Nature Communications. 2020;11. doi:10.1038/s41467-020-16520-1
apa: Trejo Banos, D., McCartney, D., Patxot, M., Anchieri, L., Battram, T., Christiansen,
C., … Robinson, M. R. (2020). Bayesian reassessment of the epigenetic architecture
of complex traits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-16520-1
chicago: Trejo Banos, D, DL McCartney, M Patxot, L Anchieri, T Battram, C Christiansen,
R Costeira, et al. “Bayesian Reassessment of the Epigenetic Architecture of Complex
Traits.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-16520-1.
ieee: D. Trejo Banos et al., “Bayesian reassessment of the epigenetic architecture
of complex traits,” Nature Communications, vol. 11. Springer Nature, 2020.
ista: Trejo Banos D, McCartney D, Patxot M, Anchieri L, Battram T, Christiansen
C, Costeira R, Walker R, Morris S, Campbell A, Zhang Q, Porteous D, McRae A, Wray
N, Visscher P, Haley C, Evans K, Deary I, McIntosh A, Hemani G, Bell J, Marioni
R, Robinson MR. 2020. Bayesian reassessment of the epigenetic architecture of
complex traits. Nature Communications. 11, 2865.
mla: Trejo Banos, D., et al. “Bayesian Reassessment of the Epigenetic Architecture
of Complex Traits.” Nature Communications, vol. 11, 2865, Springer Nature,
2020, doi:10.1038/s41467-020-16520-1.
short: D. Trejo Banos, D. McCartney, M. Patxot, L. Anchieri, T. Battram, C. Christiansen,
R. Costeira, R. Walker, S. Morris, A. Campbell, Q. Zhang, D. Porteous, A. McRae,
N. Wray, P. Visscher, C. Haley, K. Evans, I. Deary, A. McIntosh, G. Hemani, J.
Bell, R. Marioni, M.R. Robinson, Nature Communications 11 (2020).
corr_author: '1'
date_created: 2020-06-22T11:18:25Z
date_published: 2020-06-08T00:00:00Z
date_updated: 2024-10-09T20:59:38Z
day: '08'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.1038/s41467-020-16520-1
external_id:
isi:
- '000541702400004'
pmid:
- '32513961'
file:
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creator: dernst
date_created: 2020-06-22T11:24:32Z
date_updated: 2020-07-14T12:48:07Z
file_id: '8000'
file_name: 2020_NatureComm_Bayesian.pdf
file_size: 1475657
relation: main_file
file_date_updated: 2020-07-14T12:48:07Z
fulldoi: https://doi.org/10.1038/s41467-020-16520-1
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '06'
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'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41467-020-19099-9
scopus_import: '1'
status: public
title: Bayesian reassessment of the epigenetic architecture of complex traits
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: '2020'
...
---
_id: '8138'
abstract:
- lang: eng
text: Directional transport of the phytohormone auxin is a versatile, plant-specific
mechanism regulating many aspects of plant development. The recently identified
plant hormones, strigolactones (SLs), are implicated in many plant traits; among
others, they modify the phenotypic output of PIN-FORMED (PIN) auxin transporters
for fine-tuning of growth and developmental responses. Here, we show in pea and
Arabidopsis that SLs target processes dependent on the canalization of auxin flow,
which involves auxin feedback on PIN subcellular distribution. D14 receptor- and
MAX2 F-box-mediated SL signaling inhibits the formation of auxin-conducting channels
after wounding or from artificial auxin sources, during vasculature de novo formation
and regeneration. At the cellular level, SLs interfere with auxin effects on PIN
polar targeting, constitutive PIN trafficking as well as clathrin-mediated endocytosis.
Our results identify a non-transcriptional mechanism of SL action, uncoupling
auxin feedback on PIN polarity and trafficking, thereby regulating vascular tissue
formation and regeneration.
acknowledgement: We are grateful to David Nelson for providing published materials
and extremely helpful comments, and Elizabeth Dun and Christine Beveridge for helpful
discussions. The research leading to these results has received funding from the
European Research Council (ERC) under the European Union's Horizon 2020 research
and innovation programme (742985). This work was also supported by the Beijing Municipal
Natural Science Foundation (5192011), Beijing Outstanding University Discipline
Program, the National Natural Science Foundation of China (31370309), CEITEC 2020
(LQ1601) project with financial contribution made by the Ministry of Education,
Youth and Sports of the Czech Republic within special support paid from the National
Program of Sustainability II funds, Australian Research Council (FT180100081), and
China Postdoctoral Science Foundation (2019M660864).
article_processing_charge: No
article_type: original
author:
- first_name: J
full_name: Zhang, J
last_name: Zhang
- first_name: E
full_name: Mazur, E
last_name: Mazur
- first_name: J
full_name: Balla, J
last_name: Balla
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- first_name: P
full_name: Kalousek, P
last_name: Kalousek
- first_name: Z
full_name: Medveďová, Z
last_name: Medveďová
- first_name: Y
full_name: Li, Y
last_name: Li
- first_name: Y
full_name: Wang, Y
last_name: Wang
- first_name: Tomas
full_name: Prat, Tomas
id: 3DA3BFEE-F248-11E8-B48F-1D18A9856A87
last_name: Prat
- first_name: Mina K
full_name: Vasileva, Mina K
id: 3407EB18-F248-11E8-B48F-1D18A9856A87
last_name: Vasileva
- first_name: V
full_name: Reinöhl, V
last_name: Reinöhl
- first_name: S
full_name: Procházka, S
last_name: Procházka
- first_name: R
full_name: Halouzka, R
last_name: Halouzka
- first_name: P
full_name: Tarkowski, P
last_name: Tarkowski
- first_name: C
full_name: Luschnig, C
last_name: Luschnig
- first_name: PB
full_name: Brewer, PB
last_name: Brewer
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Zhang J, Mazur E, Balla J, et al. Strigolactones inhibit auxin feedback on
PIN-dependent auxin transport canalization. Nature Communications. 2020;11(1):3508.
doi:10.1038/s41467-020-17252-y
apa: Zhang, J., Mazur, E., Balla, J., Gallei, M. C., Kalousek, P., Medveďová, Z.,
… Friml, J. (2020). Strigolactones inhibit auxin feedback on PIN-dependent auxin
transport canalization. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17252-y
chicago: Zhang, J, E Mazur, J Balla, Michelle C Gallei, P Kalousek, Z Medveďová,
Y Li, et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin Transport
Canalization.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17252-y.
ieee: J. Zhang et al., “Strigolactones inhibit auxin feedback on PIN-dependent
auxin transport canalization,” Nature Communications, vol. 11, no. 1. Springer
Nature, p. 3508, 2020.
ista: Zhang J, Mazur E, Balla J, Gallei MC, Kalousek P, Medveďová Z, Li Y, Wang
Y, Prat T, Vasileva MK, Reinöhl V, Procházka S, Halouzka R, Tarkowski P, Luschnig
C, Brewer P, Friml J. 2020. Strigolactones inhibit auxin feedback on PIN-dependent
auxin transport canalization. Nature Communications. 11(1), 3508.
mla: Zhang, J., et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin
Transport Canalization.” Nature Communications, vol. 11, no. 1, Springer
Nature, 2020, p. 3508, doi:10.1038/s41467-020-17252-y.
short: J. Zhang, E. Mazur, J. Balla, M.C. Gallei, P. Kalousek, Z. Medveďová, Y.
Li, Y. Wang, T. Prat, M.K. Vasileva, V. Reinöhl, S. Procházka, R. Halouzka, P.
Tarkowski, C. Luschnig, P. Brewer, J. Friml, Nature Communications 11 (2020) 3508.
corr_author: '1'
date_created: 2020-07-21T08:58:07Z
date_published: 2020-07-14T00:00:00Z
date_updated: 2026-04-07T14:18:57Z
day: '14'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41467-020-17252-y
ec_funded: 1
external_id:
isi:
- '000550062200004'
pmid:
- '32665554'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-07-22T08:32:55Z
date_updated: 2020-07-22T08:32:55Z
file_id: '8148'
file_name: 2020_NatureComm_Zhang.pdf
file_size: 1759490
relation: main_file
success: 1
file_date_updated: 2020-07-22T08:32:55Z
fulldoi: https://doi.org/10.1038/s41467-020-17252-y
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '3508'
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '11626'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization
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: '2020'
...