---
_id: '14826'
abstract:
- lang: eng
text: The plant-signaling molecule auxin triggers fast and slow cellular responses
across land plants and algae. The nuclear auxin pathway mediates gene expression
and controls growth and development in land plants, but this pathway is absent
from algal sister groups. Several components of rapid responses have been identified
in Arabidopsis, but it is unknown if these are part of a conserved mechanism.
We recently identified a fast, proteome-wide phosphorylation response to auxin.
Here, we show that this response occurs across 5 land plant and algal species
and converges on a core group of shared targets. We found conserved rapid physiological
responses to auxin in the same species and identified rapidly accelerated fibrosarcoma
(RAF)-like protein kinases as central mediators of auxin-triggered phosphorylation
across species. Genetic analysis connects this kinase to both auxin-triggered
protein phosphorylation and rapid cellular response, thus identifying an ancient
mechanism for fast auxin responses in the green lineage.
acknowledgement: 'We are grateful to Asuka Shitaku and Eri Koide for generating and
sharing the Marchantia PRAF-mCitrine line and Peng-Cheng Wang for sharing the Arabidopsis
raf mutant. We are grateful to our team members for discussions and helpful advice.
This work was supported by funding from the Netherlands Organization for Scientific
Research (NWO): VICI grant 865.14.001 and ENW-KLEIN OCENW.KLEIN.027 grants to D.W.;
VENI grant VI.VENI.212.003 to A.K.; the European Research Council AdG DIRNDL (contract
number 833867) to D.W.; CoG CATCH to J.S.; StG CELLONGATE (contract 803048) to M.F.;
and AdG ETAP (contract 742985) to J.F.; MEXT KAKENHI grant number JP19H05675 to
T.K.; JSPS KAKENHI grant number JP20H03275 to R.N.; Takeda Science Foundation to
R.N.; and the Austrian Science Fund (FWF, P29988) to J.F.'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Andre
full_name: Kuhn, Andre
last_name: Kuhn
- first_name: Mark
full_name: Roosjen, Mark
last_name: Roosjen
- first_name: Sumanth
full_name: Mutte, Sumanth
last_name: Mutte
- first_name: Shiv Mani
full_name: Dubey, Shiv Mani
last_name: Dubey
- first_name: Vanessa Polet
full_name: Carrillo Carrasco, Vanessa Polet
last_name: Carrillo Carrasco
- first_name: Sjef
full_name: Boeren, Sjef
last_name: Boeren
- first_name: Aline
full_name: Monzer, Aline
id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425
last_name: Monzer
- first_name: Jasper
full_name: Koehorst, Jasper
last_name: Koehorst
- first_name: Takayuki
full_name: Kohchi, Takayuki
last_name: Kohchi
- first_name: Ryuichi
full_name: Nishihama, Ryuichi
last_name: Nishihama
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Joris
full_name: Sprakel, Joris
last_name: Sprakel
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
citation:
ama: Kuhn A, Roosjen M, Mutte S, et al. RAF-like protein kinases mediate a deeply
conserved, rapid auxin response. Cell. 2024;187(1):130-148.e17. doi:10.1016/j.cell.2023.11.021
apa: Kuhn, A., Roosjen, M., Mutte, S., Dubey, S. M., Carrillo Carrasco, V. P., Boeren,
S., … Weijers, D. (2024). RAF-like protein kinases mediate a deeply conserved,
rapid auxin response. Cell. Elsevier. https://doi.org/10.1016/j.cell.2023.11.021
chicago: Kuhn, Andre, Mark Roosjen, Sumanth Mutte, Shiv Mani Dubey, Vanessa Polet
Carrillo Carrasco, Sjef Boeren, Aline Monzer, et al. “RAF-like Protein Kinases
Mediate a Deeply Conserved, Rapid Auxin Response.” Cell. Elsevier, 2024.
https://doi.org/10.1016/j.cell.2023.11.021.
ieee: A. Kuhn et al., “RAF-like protein kinases mediate a deeply conserved,
rapid auxin response,” Cell, vol. 187, no. 1. Elsevier, p. 130–148.e17,
2024.
ista: Kuhn A, Roosjen M, Mutte S, Dubey SM, Carrillo Carrasco VP, Boeren S, Monzer
A, Koehorst J, Kohchi T, Nishihama R, Fendrych M, Sprakel J, Friml J, Weijers
D. 2024. RAF-like protein kinases mediate a deeply conserved, rapid auxin response.
Cell. 187(1), 130–148.e17.
mla: Kuhn, Andre, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid
Auxin Response.” Cell, vol. 187, no. 1, Elsevier, 2024, p. 130–148.e17,
doi:10.1016/j.cell.2023.11.021.
short: A. Kuhn, M. Roosjen, S. Mutte, S.M. Dubey, V.P. Carrillo Carrasco, S. Boeren,
A. Monzer, J. Koehorst, T. Kohchi, R. Nishihama, M. Fendrych, J. Sprakel, J. Friml,
D. Weijers, Cell 187 (2024) 130–148.e17.
date_created: 2024-01-17T12:45:40Z
date_published: 2024-01-04T00:00:00Z
date_updated: 2024-01-22T13:43:40Z
day: '04'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.cell.2023.11.021
ec_funded: 1
external_id:
pmid:
- '38128538'
file:
- access_level: open_access
checksum: 06fd236a9ee0b46ccb05f44695bfc34b
content_type: application/pdf
creator: dernst
date_created: 2024-01-22T13:41:41Z
date_updated: 2024-01-22T13:41:41Z
file_id: '14874'
file_name: 2024_Cell_Kuhn.pdf
file_size: 13194060
relation: main_file
success: 1
file_date_updated: 2024-01-22T13:41:41Z
has_accepted_license: '1'
intvolume: ' 187'
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '01'
oa: 1
oa_version: Published Version
page: 130-148.e17
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
- _id: 262EF96E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29988
name: RNA-directed DNA methylation in plant development
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: RAF-like protein kinases mediate a deeply conserved, rapid auxin response
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 187
year: '2024'
...
---
_id: '15033'
abstract:
- lang: eng
text: The GNOM (GN) Guanine nucleotide Exchange Factor for ARF small GTPases (ARF-GEF)
is among the best studied trafficking regulators in plants, playing crucial and
unique developmental roles in patterning and polarity. The current models place
GN at the Golgi apparatus (GA), where it mediates secretion/recycling, and at
the plasma membrane (PM) presumably contributing to clathrin-mediated endocytosis
(CME). The mechanistic basis of the developmental function of GN, distinct from
the other ARF-GEFs including its closest homologue GNOM-LIKE1 (GNL1), remains
elusive. Insights from this study largely extend the current notions of GN function.
We show that GN, but not GNL1, localizes to the cell periphery at long-lived structures
distinct from clathrin-coated pits, while CME and secretion proceed normally in
gn knockouts. The functional GN mutant variant GNfewerroots,
absent from the GA, suggests that the cell periphery is the major site of GN action
responsible for its developmental function. Following inhibition by Brefeldin
A, GN, but not GNL1, relocates to the PM likely on exocytic vesicles, suggesting
selective molecular associations en route to the cell periphery. A study of GN-GNL1
chimeric ARF-GEFs indicates that all GN domains contribute to the specific GN
function in a partially redundant manner. Together, this study offers significant
steps toward the elucidation of the mechanism underlying unique cellular and development
functions of GNOM.
acknowledgement: "The authors would like to gratefully acknowledge Dr Xixi Zhang for
cloning the GNL1/pDONR221 construct and for useful discussions.H2020 European Research\r\nCouncil
Advanced Grant ETAP742985 to Jiří Friml, Austrian Science Fund I 3630-B25 to Jiří
Friml"
article_processing_charge: Yes
article_type: original
author:
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Ivana
full_name: Matijevic, Ivana
id: 83c17ce3-15b2-11ec-abd3-f486545870bd
last_name: Matijevic
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Adamowski M, Matijevic I, Friml J. Developmental patterning function of GNOM
ARF-GEF mediated from the cell periphery. eLife. 2024;13. doi:10.7554/elife.68993
apa: Adamowski, M., Matijevic, I., & Friml, J. (2024). Developmental patterning
function of GNOM ARF-GEF mediated from the cell periphery. ELife. eLife
Sciences Publications. https://doi.org/10.7554/elife.68993
chicago: Adamowski, Maciek, Ivana Matijevic, and Jiří Friml. “Developmental Patterning
Function of GNOM ARF-GEF Mediated from the Cell Periphery.” ELife. eLife
Sciences Publications, 2024. https://doi.org/10.7554/elife.68993.
ieee: M. Adamowski, I. Matijevic, and J. Friml, “Developmental patterning function
of GNOM ARF-GEF mediated from the cell periphery,” eLife, vol. 13. eLife
Sciences Publications, 2024.
ista: Adamowski M, Matijevic I, Friml J. 2024. Developmental patterning function
of GNOM ARF-GEF mediated from the cell periphery. eLife. 13.
mla: Adamowski, Maciek, et al. “Developmental Patterning Function of GNOM ARF-GEF
Mediated from the Cell Periphery.” ELife, vol. 13, eLife Sciences Publications,
2024, doi:10.7554/elife.68993.
short: M. Adamowski, I. Matijevic, J. Friml, ELife 13 (2024).
date_created: 2024-02-27T07:10:11Z
date_published: 2024-02-21T00:00:00Z
date_updated: 2024-02-28T12:29:43Z
day: '21'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.7554/elife.68993
ec_funded: 1
has_accepted_license: '1'
intvolume: ' 13'
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.7554/eLife.68993
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: epub_ahead
publisher: eLife Sciences Publications
quality_controlled: '1'
status: public
title: Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2024'
...
---
_id: '13989'
abstract:
- lang: eng
text: Characterizing and controlling entanglement in quantum materials is crucial
for the development of next-generation quantum technologies. However, defining
a quantifiable figure of merit for entanglement in macroscopic solids is theoretically
and experimentally challenging. At equilibrium the presence of entanglement can
be diagnosed by extracting entanglement witnesses from spectroscopic observables
and a nonequilibrium extension of this method could lead to the discovery of novel
dynamical phenomena. Here, we propose a systematic approach to quantify the time-dependent
quantum Fisher information and entanglement depth of transient states of quantum
materials with time-resolved resonant inelastic x-ray scattering. Using a quarter-filled
extended Hubbard model as an example, we benchmark the efficiency of this approach
and predict a light-enhanced many-body entanglement due to the proximity to a
phase boundary. Our work sets the stage for experimentally witnessing and controlling
entanglement in light-driven quantum materials via ultrafast spectroscopic measurements.
article_number: '3512'
article_processing_charge: No
article_type: original
author:
- first_name: Jordyn
full_name: Hales, Jordyn
last_name: Hales
- first_name: Utkarsh
full_name: Bajpai, Utkarsh
last_name: Bajpai
- first_name: Tongtong
full_name: Liu, Tongtong
last_name: Liu
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Mingda
full_name: Li, Mingda
last_name: Li
- first_name: Matteo
full_name: Mitrano, Matteo
last_name: Mitrano
- first_name: Yao
full_name: Wang, Yao
last_name: Wang
citation:
ama: Hales J, Bajpai U, Liu T, et al. Witnessing light-driven entanglement using
time-resolved resonant inelastic X-ray scattering. Nature Communications.
2023;14. doi:10.1038/s41467-023-38540-3
apa: Hales, J., Bajpai, U., Liu, T., Baykusheva, D. R., Li, M., Mitrano, M., &
Wang, Y. (2023). Witnessing light-driven entanglement using time-resolved resonant
inelastic X-ray scattering. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38540-3
chicago: Hales, Jordyn, Utkarsh Bajpai, Tongtong Liu, Denitsa Rangelova Baykusheva,
Mingda Li, Matteo Mitrano, and Yao Wang. “Witnessing Light-Driven Entanglement
Using Time-Resolved Resonant Inelastic X-Ray Scattering.” Nature Communications.
Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38540-3.
ieee: J. Hales et al., “Witnessing light-driven entanglement using time-resolved
resonant inelastic X-ray scattering,” Nature Communications, vol. 14. Springer
Nature, 2023.
ista: Hales J, Bajpai U, Liu T, Baykusheva DR, Li M, Mitrano M, Wang Y. 2023. Witnessing
light-driven entanglement using time-resolved resonant inelastic X-ray scattering.
Nature Communications. 14, 3512.
mla: Hales, Jordyn, et al. “Witnessing Light-Driven Entanglement Using Time-Resolved
Resonant Inelastic X-Ray Scattering.” Nature Communications, vol. 14, 3512,
Springer Nature, 2023, doi:10.1038/s41467-023-38540-3.
short: J. Hales, U. Bajpai, T. Liu, D.R. Baykusheva, M. Li, M. Mitrano, Y. Wang,
Nature Communications 14 (2023).
date_created: 2023-08-09T13:06:59Z
date_published: 2023-06-14T00:00:00Z
date_updated: 2023-08-22T06:50:04Z
day: '14'
doi: 10.1038/s41467-023-38540-3
extern: '1'
external_id:
arxiv:
- '2209.02283'
pmid:
- '37316515'
intvolume: ' 14'
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/s41467-023-38540-3
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Witnessing light-driven entanglement using time-resolved resonant inelastic
X-ray scattering
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '14683'
abstract:
- lang: eng
text: "Mosaic analysis with double markers (MADM) technology enables the generation
of genetic mosaic tissue in mice and high-resolution phenotyping at the individual
cell level. Here, we present a protocol for isolating MADM-labeled cells with
high yield for downstream molecular analyses using fluorescence-activated cell
sorting (FACS). We describe steps for generating MADM-labeled mice, perfusion,
single-cell suspension, and debris removal. We then detail procedures for cell
sorting by FACS and downstream analysis. This protocol is suitable for embryonic
to adult mice.\r\nFor complete details on the use and execution of this protocol,
please refer to Contreras et al. (2021).1"
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: This research was supported by the Scientific Service Units (SSU)
at IST Austria through resources provided by the Imaging & Optics Facility (IOF)
and Preclinical Facilities (PCF). N.A. received support from FWF Firnberg-Programme
(T 1031). G.C. received support from the European Union’s Horizon 2020 research
and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411
as an ISTplus postdoctoral fellow. This work was also supported by IST Austria institutional
funds, FWF SFB F78 to S.H., and the European Research Council (ERC) under the European
Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780
LinPro) to S.H.
article_number: '102771'
article_processing_charge: No
article_type: review
author:
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Giselle T
full_name: Cheung, Giselle T
id: 471195F6-F248-11E8-B48F-1D18A9856A87
last_name: Cheung
orcid: 0000-0001-8457-2572
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Amberg N, Cheung GT, Hippenmeyer S. Protocol for sorting cells from mouse brains
labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols.
2023;5(1). doi:10.1016/j.xpro.2023.102771
apa: Amberg, N., Cheung, G. T., & Hippenmeyer, S. (2023). Protocol for sorting
cells from mouse brains labeled with mosaic analysis with double markers by flow
cytometry. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2023.102771
chicago: Amberg, Nicole, Giselle T Cheung, and Simon Hippenmeyer. “Protocol for
Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers
by Flow Cytometry.” STAR Protocols. Elsevier, 2023. https://doi.org/10.1016/j.xpro.2023.102771.
ieee: N. Amberg, G. T. Cheung, and S. Hippenmeyer, “Protocol for sorting cells from
mouse brains labeled with mosaic analysis with double markers by flow cytometry,”
STAR Protocols, vol. 5, no. 1. Elsevier, 2023.
ista: Amberg N, Cheung GT, Hippenmeyer S. 2023. Protocol for sorting cells from
mouse brains labeled with mosaic analysis with double markers by flow cytometry.
STAR Protocols. 5(1), 102771.
mla: Amberg, Nicole, et al. “Protocol for Sorting Cells from Mouse Brains Labeled
with Mosaic Analysis with Double Markers by Flow Cytometry.” STAR Protocols,
vol. 5, no. 1, 102771, Elsevier, 2023, doi:10.1016/j.xpro.2023.102771.
short: N. Amberg, G.T. Cheung, S. Hippenmeyer, STAR Protocols 5 (2023).
date_created: 2023-12-13T11:48:05Z
date_published: 2023-12-08T00:00:00Z
date_updated: 2023-12-18T08:06:14Z
day: '08'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.xpro.2023.102771
ec_funded: 1
external_id:
pmid:
- '38070137'
intvolume: ' 5'
issue: '1'
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Neuroscience
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.xpro.2023.102771
month: '12'
oa: 1
oa_version: Submitted Version
pmid: 1
project:
- _id: 268F8446-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: T0101031
name: Role of Eed in neural stem cell lineage progression
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
grant_number: F07805
name: Molecular Mechanisms of Neural Stem Cell Lineage Progression
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: STAR Protocols
publication_identifier:
issn:
- 2666-1667
publication_status: epub_ahead
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Protocol for sorting cells from mouse brains labeled with mosaic analysis with
double markers by flow cytometry
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: 5
year: '2023'
...
---
_id: '14742'
abstract:
- lang: eng
text: "Chromosomal rearrangements (CRs) have been known since almost the beginning
of genetics.\r\nWhile an important role for CRs in speciation has been suggested,
evidence primarily stems\r\nfrom theoretical and empirical studies focusing on
the microevolutionary level (i.e., on taxon\r\npairs where speciation is often
incomplete). Although the role of CRs in eukaryotic speciation at\r\na macroevolutionary
level has been supported by associations between species diversity and\r\nrates
of evolution of CRs across phylogenies, these findings are limited to a restricted
range of\r\nCRs and taxa. Now that more broadly applicable and precise CR detection
approaches have\r\nbecome available, we address the challenges in filling some
of the conceptual and empirical\r\ngaps between micro- and macroevolutionary studies
on the role of CRs in speciation. We\r\nsynthesize what is known about the macroevolutionary
impact of CRs and suggest new research avenues to overcome the pitfalls of previous
studies to gain a more comprehensive understanding of the evolutionary significance
of CRs in speciation across the tree of life."
acknowledgement: "K.L. was funded by a Swiss National Science Foundation Eccellenza
project: The evolution of strong reproductive barriers towards the completion of
speciation (PCEFP3_202869). R.F.\r\nwas funded by an FCT CEEC (Fundação para a Ciênca
e a Tecnologia, Concurso Estímulo ao\r\nEmprego Científico) contract (2020.00275.
CEECIND) and by an FCT research project\r\n(PTDC/BIA-EVL/1614/2021). M.R. was funded
by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243). A.M.W.
was partly funded by the Norwegian Research Council RCN. We thank Luis Silva for
his help preparing Figure 1. We are grateful to Maren Wellenreuther, Daniel Bolnick,
and two anonymous reviewers for their constructive feedback on an earlier version
of this paper."
article_number: a041447
article_processing_charge: No
article_type: original
author:
- first_name: Kay
full_name: Lucek, Kay
last_name: Lucek
- first_name: Mabel D.
full_name: Giménez, Mabel D.
last_name: Giménez
- first_name: Mathieu
full_name: Joron, Mathieu
last_name: Joron
- first_name: Marina
full_name: Rafajlović, Marina
last_name: Rafajlović
- first_name: Jeremy B.
full_name: Searle, Jeremy B.
last_name: Searle
- first_name: Nora
full_name: Walden, Nora
last_name: Walden
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
citation:
ama: 'Lucek K, Giménez MD, Joron M, et al. The impact of chromosomal rearrangements
in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives
in Biology. 2023;15(11). doi:10.1101/cshperspect.a041447'
apa: 'Lucek, K., Giménez, M. D., Joron, M., Rafajlović, M., Searle, J. B., Walden,
N., … Faria, R. (2023). The impact of chromosomal rearrangements in speciation:
From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology.
Cold Spring Harbor Laboratory. https://doi.org/10.1101/cshperspect.a041447'
chicago: 'Lucek, Kay, Mabel D. Giménez, Mathieu Joron, Marina Rafajlović, Jeremy
B. Searle, Nora Walden, Anja M Westram, and Rui Faria. “The Impact of Chromosomal
Rearrangements in Speciation: From Micro- to Macroevolution.” Cold Spring Harbor
Perspectives in Biology. Cold Spring Harbor Laboratory, 2023. https://doi.org/10.1101/cshperspect.a041447.'
ieee: 'K. Lucek et al., “The impact of chromosomal rearrangements in speciation:
From micro- to macroevolution,” Cold Spring Harbor Perspectives in Biology,
vol. 15, no. 11. Cold Spring Harbor Laboratory, 2023.'
ista: 'Lucek K, Giménez MD, Joron M, Rafajlović M, Searle JB, Walden N, Westram
AM, Faria R. 2023. The impact of chromosomal rearrangements in speciation: From
micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. 15(11),
a041447.'
mla: 'Lucek, Kay, et al. “The Impact of Chromosomal Rearrangements in Speciation:
From Micro- to Macroevolution.” Cold Spring Harbor Perspectives in Biology,
vol. 15, no. 11, a041447, Cold Spring Harbor Laboratory, 2023, doi:10.1101/cshperspect.a041447.'
short: K. Lucek, M.D. Giménez, M. Joron, M. Rafajlović, J.B. Searle, N. Walden,
A.M. Westram, R. Faria, Cold Spring Harbor Perspectives in Biology 15 (2023).
date_created: 2024-01-08T12:43:48Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2024-01-08T12:52:29Z
day: '01'
department:
- _id: NiBa
- _id: BeVi
doi: 10.1101/cshperspect.a041447
external_id:
pmid:
- '37604585'
intvolume: ' 15'
issue: '11'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/cshperspect.a041447
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Cold Spring Harbor Perspectives in Biology
publication_identifier:
issn:
- 1943-0264
publication_status: published
publisher: Cold Spring Harbor Laboratory
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The impact of chromosomal rearrangements in speciation: From micro- to macroevolution'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2023'
...
---
_id: '14781'
abstract:
- lang: eng
text: Germ granules, condensates of phase-separated RNA and protein, are organelles
that are essential for germline development in different organisms. The patterning
of the granules and their relevance for germ cell fate are not fully understood.
Combining three-dimensional in vivo structural and functional analyses, we study
the dynamic spatial organization of molecules within zebrafish germ granules.
We find that the localization of RNA molecules to the periphery of the granules,
where ribosomes are localized, depends on translational activity at this location.
In addition, we find that the vertebrate-specific Dead end (Dnd1) protein is essential
for nanos3 RNA localization at the condensates’ periphery. Accordingly, in the
absence of Dnd1, or when translation is inhibited, nanos3 RNA translocates into
the granule interior, away from the ribosomes, a process that is correlated with
the loss of germ cell fate. These findings highlight the relevance of sub-granule
compartmentalization for post-transcriptional control and its importance for preserving
germ cell totipotency.
acknowledgement: We thank Celeste Brennecka for editing and Michal Reichman-Fried
for critical comments on the manuscript. We thank Ursula Jordan, Esther Messerschmidt,
and Ines Sandbote for technical assistance. This work was supported by funding from
the University of Münster (K.J.W., K.T., E.R., A.G., T.G.-T., J.S., and M.G.), the
Max Planck Institute for Molecular Biomedicine (D.Z.), the German Research Foundation
grant CRU 326 (P2) RA863/12-2 (E.R.), Baylor University (K.H. and D.R.), and the
National Institutes of Health grant R35 GM 134910 (D.R.). We thank the referees
for insightful comments that helped improve the manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Kim Joana
full_name: Westerich, Kim Joana
last_name: Westerich
- first_name: Katsiaryna
full_name: Tarbashevich, Katsiaryna
last_name: Tarbashevich
- first_name: Jan
full_name: Schick, Jan
last_name: Schick
- first_name: Antra
full_name: Gupta, Antra
last_name: Gupta
- first_name: Mingzhao
full_name: Zhu, Mingzhao
last_name: Zhu
- first_name: Kenneth
full_name: Hull, Kenneth
last_name: Hull
- first_name: Daniel
full_name: Romo, Daniel
last_name: Romo
- first_name: Dagmar
full_name: Zeuschner, Dagmar
last_name: Zeuschner
- first_name: Mohammad
full_name: Goudarzi, Mohammad
id: 3384113A-F248-11E8-B48F-1D18A9856A87
last_name: Goudarzi
- first_name: Theresa
full_name: Gross-Thebing, Theresa
last_name: Gross-Thebing
- first_name: Erez
full_name: Raz, Erez
last_name: Raz
citation:
ama: Westerich KJ, Tarbashevich K, Schick J, et al. Spatial organization and function
of RNA molecules within phase-separated condensates in zebrafish are controlled
by Dnd1. Developmental Cell. 2023;58(17):1578-1592.e5. doi:10.1016/j.devcel.2023.06.009
apa: Westerich, K. J., Tarbashevich, K., Schick, J., Gupta, A., Zhu, M., Hull, K.,
… Raz, E. (2023). Spatial organization and function of RNA molecules within phase-separated
condensates in zebrafish are controlled by Dnd1. Developmental Cell. Elsevier.
https://doi.org/10.1016/j.devcel.2023.06.009
chicago: Westerich, Kim Joana, Katsiaryna Tarbashevich, Jan Schick, Antra Gupta,
Mingzhao Zhu, Kenneth Hull, Daniel Romo, et al. “Spatial Organization and Function
of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled
by Dnd1.” Developmental Cell. Elsevier, 2023. https://doi.org/10.1016/j.devcel.2023.06.009.
ieee: K. J. Westerich et al., “Spatial organization and function of RNA molecules
within phase-separated condensates in zebrafish are controlled by Dnd1,” Developmental
Cell, vol. 58, no. 17. Elsevier, p. 1578–1592.e5, 2023.
ista: Westerich KJ, Tarbashevich K, Schick J, Gupta A, Zhu M, Hull K, Romo D, Zeuschner
D, Goudarzi M, Gross-Thebing T, Raz E. 2023. Spatial organization and function
of RNA molecules within phase-separated condensates in zebrafish are controlled
by Dnd1. Developmental Cell. 58(17), 1578–1592.e5.
mla: Westerich, Kim Joana, et al. “Spatial Organization and Function of RNA Molecules
within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” Developmental
Cell, vol. 58, no. 17, Elsevier, 2023, p. 1578–1592.e5, doi:10.1016/j.devcel.2023.06.009.
short: K.J. Westerich, K. Tarbashevich, J. Schick, A. Gupta, M. Zhu, K. Hull, D.
Romo, D. Zeuschner, M. Goudarzi, T. Gross-Thebing, E. Raz, Developmental Cell
58 (2023) 1578–1592.e5.
date_created: 2024-01-10T09:41:21Z
date_published: 2023-09-11T00:00:00Z
date_updated: 2024-01-16T08:56:36Z
day: '11'
department:
- _id: Bio
doi: 10.1016/j.devcel.2023.06.009
external_id:
pmid:
- '37463577'
intvolume: ' 58'
issue: '17'
keyword:
- Developmental Biology
- Cell Biology
- General Biochemistry
- Genetics and Molecular Biology
- Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2023.07.09.548244
month: '09'
oa: 1
oa_version: Preprint
page: 1578-1592.e5
pmid: 1
publication: Developmental Cell
publication_identifier:
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Spatial organization and function of RNA molecules within phase-separated condensates
in zebrafish are controlled by Dnd1
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 58
year: '2023'
...
---
_id: '12802'
abstract:
- lang: eng
text: Little is known about the critical metabolic changes that neural cells have
to undergo during development and how temporary shifts in this program can influence
brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5,
a transporter of metabolically essential large neutral amino acids (LNAAs), lead
to autism, we employed metabolomic profiling to study the metabolic states of
the cerebral cortex across different developmental stages. We found that the forebrain
undergoes significant metabolic remodeling throughout development, with certain
groups of metabolites showing stage-specific changes, but what are the consequences
of perturbing this metabolic program? By manipulating Slc7a5 expression in neural
cells, we found that the metabolism of LNAAs and lipids are interconnected in
the cortex. Deletion of Slc7a5 in neurons affects the postnatal metabolic state,
leading to a shift in lipid metabolism. Additionally, it causes stage- and cell-type-specific
alterations in neuronal activity patterns, resulting in a long-term circuit dysfunction.
acknowledged_ssus:
- _id: PreCl
- _id: EM-Fac
- _id: Bio
- _id: LifeSc
acknowledgement: We thank A. Freeman and V. Voronin for technical assistance, S. Deixler,
A. Stichelberger, M. Schunn, and the Preclinical Facility for managing our animal
colony. We thank L. Andersen and J. Sonntag, who were involved in generating the
MADM lines. We thank the ISTA LSF Mass Spectrometry Core Facility for assistance
with the proteomic analysis, as well as the ISTA electron microscopy and Imaging
and Optics facility for technical support. Metabolomics LC-MS/MS analysis was performed
by the Metabolomics Facility at Vienna BioCenter Core Facilities (VBCF). We acknowledge
the support of the EMBL Metabolomics Core Facility (MCF) for lipidomics and intracellular
metabolomics mass spectrometry data acquisition and analysis. RNA sequencing was
performed by the Next Generation Sequencing Facility at VBCF. Schematics were generated
using Biorender.com. This work was supported by the Austrian Science Fund (FWF,
DK W1232-B24) and by the European Union’s Horizon 2020 research and innovation program
(ERC) grant 725780 (LinPro) to S.H. and 715508 (REVERSEAUTISM) to G.N.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Lisa
full_name: Knaus, Lisa
id: 3B2ABCF4-F248-11E8-B48F-1D18A9856A87
last_name: Knaus
- first_name: Bernadette
full_name: Basilico, Bernadette
id: 36035796-5ACA-11E9-A75E-7AF2E5697425
last_name: Basilico
orcid: 0000-0003-1843-3173
- first_name: Daniel
full_name: Malzl, Daniel
last_name: Malzl
- first_name: Maria
full_name: Gerykova Bujalkova, Maria
last_name: Gerykova Bujalkova
- first_name: Mateja
full_name: Smogavec, Mateja
last_name: Smogavec
- first_name: Lena A.
full_name: Schwarz, Lena A.
last_name: Schwarz
- first_name: Sarah
full_name: Gorkiewicz, Sarah
id: f141a35d-15a9-11ec-9fb2-fef6becc7b6f
last_name: Gorkiewicz
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Christian
full_name: Knittl-Frank, Christian
last_name: Knittl-Frank
- first_name: Marianna
full_name: Tassinari, Marianna
id: 7af593f1-d44a-11ed-bf94-a3646a6bb35e
last_name: Tassinari
- first_name: Nuno
full_name: Maulide, Nuno
last_name: Maulide
- first_name: Thomas
full_name: Rülicke, Thomas
last_name: Rülicke
- first_name: Jörg
full_name: Menche, Jörg
last_name: Menche
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Knaus L, Basilico B, Malzl D, et al. Large neutral amino acid levels tune perinatal
neuronal excitability and survival. Cell. 2023;186(9):1950-1967.e25. doi:10.1016/j.cell.2023.02.037
apa: Knaus, L., Basilico, B., Malzl, D., Gerykova Bujalkova, M., Smogavec, M., Schwarz,
L. A., … Novarino, G. (2023). Large neutral amino acid levels tune perinatal neuronal
excitability and survival. Cell. Elsevier. https://doi.org/10.1016/j.cell.2023.02.037
chicago: Knaus, Lisa, Bernadette Basilico, Daniel Malzl, Maria Gerykova Bujalkova,
Mateja Smogavec, Lena A. Schwarz, Sarah Gorkiewicz, et al. “Large Neutral Amino
Acid Levels Tune Perinatal Neuronal Excitability and Survival.” Cell. Elsevier,
2023. https://doi.org/10.1016/j.cell.2023.02.037.
ieee: L. Knaus et al., “Large neutral amino acid levels tune perinatal neuronal
excitability and survival,” Cell, vol. 186, no. 9. Elsevier, p. 1950–1967.e25,
2023.
ista: Knaus L, Basilico B, Malzl D, Gerykova Bujalkova M, Smogavec M, Schwarz LA,
Gorkiewicz S, Amberg N, Pauler F, Knittl-Frank C, Tassinari M, Maulide N, Rülicke
T, Menche J, Hippenmeyer S, Novarino G. 2023. Large neutral amino acid levels
tune perinatal neuronal excitability and survival. Cell. 186(9), 1950–1967.e25.
mla: Knaus, Lisa, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal
Excitability and Survival.” Cell, vol. 186, no. 9, Elsevier, 2023, p. 1950–1967.e25,
doi:10.1016/j.cell.2023.02.037.
short: L. Knaus, B. Basilico, D. Malzl, M. Gerykova Bujalkova, M. Smogavec, L.A.
Schwarz, S. Gorkiewicz, N. Amberg, F. Pauler, C. Knittl-Frank, M. Tassinari, N.
Maulide, T. Rülicke, J. Menche, S. Hippenmeyer, G. Novarino, Cell 186 (2023) 1950–1967.e25.
date_created: 2023-04-05T08:15:40Z
date_published: 2023-04-27T00:00:00Z
date_updated: 2024-02-07T08:03:32Z
day: '27'
ddc:
- '570'
department:
- _id: SiHi
- _id: GaNo
doi: 10.1016/j.cell.2023.02.037
ec_funded: 1
external_id:
isi:
- '000991468700001'
file:
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checksum: 47e94fbe19e86505b429cb7a5b503ce6
content_type: application/pdf
creator: dernst
date_created: 2023-05-02T09:26:21Z
date_updated: 2023-05-02T09:26:21Z
file_id: '12889'
file_name: 2023_Cell_Knaus.pdf
file_size: 15712841
relation: main_file
success: 1
file_date_updated: 2023-05-02T09:26:21Z
has_accepted_license: '1'
intvolume: ' 186'
isi: 1
issue: '9'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1950-1967.e25
project:
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
- _id: 25444568-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715508'
name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo
and in vitro Models
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/feed-them-or-lose-them/
record:
- id: '13107'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Large neutral amino acid levels tune perinatal neuronal excitability and survival
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: 186
year: '2023'
...
---
_id: '11713'
abstract:
- lang: eng
text: "Objective: MazF is a sequence-specific endoribonuclease-toxin of the MazEF
toxin–antitoxin system. MazF cleaves single-stranded ribonucleic acid (RNA) regions
at adenine–cytosine–adenine (ACA) sequences in the bacterium Escherichia coli.
The MazEF system has been used in various biotechnology and synthetic biology
applications. In this study, we infer how ectopic mazF overexpression affects
production of heterologous proteins. To this end, we quantified the levels of
fluorescent proteins expressed in E. coli from reporters translated from the ACA-containing
or ACA-less messenger RNAs (mRNAs). Additionally, we addressed the impact of the
5′-untranslated region of these reporter mRNAs under the same conditions by comparing
expression from mRNAs that comprise (canonical mRNA) or lack this region (leaderless
mRNA).\r\nResults: Flow cytometry analysis indicates that during mazF overexpression,
fluorescent proteins are translated from the canonical as well as leaderless mRNAs.
Our analysis further indicates that longer mazF overexpression generally increases
the concentration of fluorescent proteins translated from ACA-less mRNAs, however
it also substantially increases bacterial population heterogeneity. Finally, our
results suggest that the strength and duration of mazF overexpression should be
optimized for each experimental setup, to maximize the heterologous protein production
and minimize the amount of phenotypic heterogeneity in bacterial populations,
which is unfavorable in biotechnological processes."
acknowledgement: "We acknowledge the Max Perutz Labs FACS Facility together with Thomas
Sauer. NN is grateful to Călin C. Guet for his support.\r\nThis work was funded
by the Elise Richter grant V738 of the Austrian Science Fund (FWF), and the FWF
Lise Meitner grant M1697, to NN; and by the FWF grant P22249, FWF Special Research
Program RNA-REG F43 (subproject F4316), and FWF doctoral program RNA Biology (W1207),
to IM. Open access funding provided by the Austrian Science Fund."
article_number: '173'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
- first_name: Martina
full_name: Sauert, Martina
last_name: Sauert
- first_name: Tanino G.
full_name: Albanese, Tanino G.
last_name: Albanese
- first_name: Isabella
full_name: Moll, Isabella
last_name: Moll
citation:
ama: Nikolic N, Sauert M, Albanese TG, Moll I. Quantifying heterologous gene expression
during ectopic MazF production in Escherichia coli. BMC Research Notes.
2022;15. doi:10.1186/s13104-022-06061-9
apa: Nikolic, N., Sauert, M., Albanese, T. G., & Moll, I. (2022). Quantifying
heterologous gene expression during ectopic MazF production in Escherichia coli.
BMC Research Notes. Springer Nature. https://doi.org/10.1186/s13104-022-06061-9
chicago: Nikolic, Nela, Martina Sauert, Tanino G. Albanese, and Isabella Moll. “Quantifying
Heterologous Gene Expression during Ectopic MazF Production in Escherichia Coli.”
BMC Research Notes. Springer Nature, 2022. https://doi.org/10.1186/s13104-022-06061-9.
ieee: N. Nikolic, M. Sauert, T. G. Albanese, and I. Moll, “Quantifying heterologous
gene expression during ectopic MazF production in Escherichia coli,” BMC Research
Notes, vol. 15. Springer Nature, 2022.
ista: Nikolic N, Sauert M, Albanese TG, Moll I. 2022. Quantifying heterologous gene
expression during ectopic MazF production in Escherichia coli. BMC Research Notes.
15, 173.
mla: Nikolic, Nela, et al. “Quantifying Heterologous Gene Expression during Ectopic
MazF Production in Escherichia Coli.” BMC Research Notes, vol. 15, 173,
Springer Nature, 2022, doi:10.1186/s13104-022-06061-9.
short: N. Nikolic, M. Sauert, T.G. Albanese, I. Moll, BMC Research Notes 15 (2022).
date_created: 2022-08-01T09:04:27Z
date_published: 2022-05-13T00:00:00Z
date_updated: 2022-08-01T09:27:40Z
day: '13'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1186/s13104-022-06061-9
external_id:
pmid:
- '35562780'
file:
- access_level: open_access
checksum: 008156e5340e9789f0f6d82bde4d347a
content_type: application/pdf
creator: dernst
date_created: 2022-08-01T09:24:42Z
date_updated: 2022-08-01T09:24:42Z
file_id: '11714'
file_name: 2022_BMCResearchNotes_Nikolic.pdf
file_size: 1545310
relation: main_file
success: 1
file_date_updated: 2022-08-01T09:24:42Z
has_accepted_license: '1'
intvolume: ' 15'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26956E74-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: V00738
name: Bacterial toxin-antitoxin systems as antiphage defense mechanisms
publication: BMC Research Notes
publication_identifier:
issn:
- 1756-0500
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1186/s13104-022-06152-7
scopus_import: '1'
status: public
title: Quantifying heterologous gene expression during ectopic MazF production in
Escherichia coli
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: '2022'
...
---
_id: '12156'
abstract:
- lang: eng
text: Models of transcriptional regulation that assume equilibrium binding of transcription
factors have been less successful at predicting gene expression from sequence
in eukaryotes than in bacteria. This could be due to the non-equilibrium nature
of eukaryotic regulation. Unfortunately, the space of possible non-equilibrium
mechanisms is vast and predominantly uninteresting. The key question is therefore
how this space can be navigated efficiently, to focus on mechanisms and models
that are biologically relevant. In this review, we advocate for the normative
role of theory—theory that prescribes rather than just describes—in providing
such a focus. Theory should expand its remit beyond inferring mechanistic models
from data, towards identifying non-equilibrium gene regulatory schemes that may
have been evolutionarily selected, despite their energy consumption, because they
are precise, reliable, fast, or otherwise outperform regulation at equilibrium.
We illustrate our reasoning by toy examples for which we provide simulation code.
acknowledgement: 'This work was supported through the Center for the Physics of Biological
Function (PHYe1734030) and by National Institutes of Health Grants R01GM097275 and
U01DK127429 (TG). GT acknowledges the support of the Austrian Science Fund grant
FWF P28844 and the Human Frontiers Science Program. '
article_number: '100435'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Benjamin
full_name: Zoller, Benjamin
last_name: Zoller
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: '1'
citation:
ama: Zoller B, Gregor T, Tkačik G. Eukaryotic gene regulation at equilibrium, or
non? Current Opinion in Systems Biology. 2022;31(9). doi:10.1016/j.coisb.2022.100435
apa: Zoller, B., Gregor, T., & Tkačik, G. (2022). Eukaryotic gene regulation
at equilibrium, or non? Current Opinion in Systems Biology. Elsevier. https://doi.org/10.1016/j.coisb.2022.100435
chicago: Zoller, Benjamin, Thomas Gregor, and Gašper Tkačik. “Eukaryotic Gene Regulation
at Equilibrium, or Non?” Current Opinion in Systems Biology. Elsevier,
2022. https://doi.org/10.1016/j.coisb.2022.100435.
ieee: B. Zoller, T. Gregor, and G. Tkačik, “Eukaryotic gene regulation at equilibrium,
or non?,” Current Opinion in Systems Biology, vol. 31, no. 9. Elsevier,
2022.
ista: Zoller B, Gregor T, Tkačik G. 2022. Eukaryotic gene regulation at equilibrium,
or non? Current Opinion in Systems Biology. 31(9), 100435.
mla: Zoller, Benjamin, et al. “Eukaryotic Gene Regulation at Equilibrium, or Non?”
Current Opinion in Systems Biology, vol. 31, no. 9, 100435, Elsevier, 2022,
doi:10.1016/j.coisb.2022.100435.
short: B. Zoller, T. Gregor, G. Tkačik, Current Opinion in Systems Biology 31 (2022).
date_created: 2023-01-12T12:08:51Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2023-02-13T09:20:34Z
day: '01'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1016/j.coisb.2022.100435
file:
- access_level: open_access
checksum: 97ef01e0cc60cdc84f45640a0f248fb0
content_type: application/pdf
creator: dernst
date_created: 2023-01-24T12:14:10Z
date_updated: 2023-01-24T12:14:10Z
file_id: '12362'
file_name: 2022_CurrentBiology_Zoller.pdf
file_size: 2214944
relation: main_file
success: 1
file_date_updated: 2023-01-24T12:14:10Z
has_accepted_license: '1'
intvolume: ' 31'
issue: '9'
keyword:
- Applied Mathematics
- Computer Science Applications
- Drug Discovery
- General Biochemistry
- Genetics and Molecular Biology
- Modeling and Simulation
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Current Opinion in Systems Biology
publication_identifier:
issn:
- 2452-3100
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Eukaryotic gene regulation at equilibrium, or non?
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: 31
year: '2022'
...
---
_id: '12670'
abstract:
- lang: eng
text: DNA methylation plays essential homeostatic functions in eukaryotic genomes.
In animals, DNA methylation is also developmentally regulated and, in turn, regulates
development. In the past two decades, huge research effort has endorsed the understanding
that DNA methylation plays a similar role in plant development, especially during
sexual reproduction. The power of whole-genome sequencing and cell isolation techniques,
as well as bioinformatics tools, have enabled recent studies to reveal dynamic
changes in DNA methylation during germline development. Furthermore, the combination
of these technological advances with genetics, developmental biology and cell
biology tools has revealed functional methylation reprogramming events that control
gene and transposon activities in flowering plant germlines. In this review, we
discuss the major advances in our knowledge of DNA methylation dynamics during
male and female germline development in flowering plants.
article_processing_charge: No
article_type: review
author:
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: He S, Feng X. DNA methylation dynamics during germline development. Journal
of Integrative Plant Biology. 2022;64(12):2240-2251. doi:10.1111/jipb.13422
apa: He, S., & Feng, X. (2022). DNA methylation dynamics during germline development.
Journal of Integrative Plant Biology. Wiley. https://doi.org/10.1111/jipb.13422
chicago: He, Shengbo, and Xiaoqi Feng. “DNA Methylation Dynamics during Germline
Development.” Journal of Integrative Plant Biology. Wiley, 2022. https://doi.org/10.1111/jipb.13422.
ieee: S. He and X. Feng, “DNA methylation dynamics during germline development,”
Journal of Integrative Plant Biology, vol. 64, no. 12. Wiley, pp. 2240–2251,
2022.
ista: He S, Feng X. 2022. DNA methylation dynamics during germline development.
Journal of Integrative Plant Biology. 64(12), 2240–2251.
mla: He, Shengbo, and Xiaoqi Feng. “DNA Methylation Dynamics during Germline Development.”
Journal of Integrative Plant Biology, vol. 64, no. 12, Wiley, 2022, pp.
2240–51, doi:10.1111/jipb.13422.
short: S. He, X. Feng, Journal of Integrative Plant Biology 64 (2022) 2240–2251.
date_created: 2023-02-23T09:15:57Z
date_published: 2022-12-07T00:00:00Z
date_updated: 2023-05-08T10:59:00Z
day: '07'
department:
- _id: XiFe
doi: 10.1111/jipb.13422
extern: '1'
external_id:
pmid:
- '36478632'
intvolume: ' 64'
issue: '12'
keyword:
- Plant Science
- General Biochemistry
- Genetics and Molecular Biology
- Biochemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jipb.13422
month: '12'
oa: 1
oa_version: Published Version
page: 2240-2251
pmid: 1
publication: Journal of Integrative Plant Biology
publication_identifier:
eissn:
- 1744-7909
issn:
- 1672-9072
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation dynamics during germline development
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 64
year: '2022'
...
---
_id: '11351'
abstract:
- lang: eng
text: 'One hallmark of plant cells is their cell wall. They protect cells against
the environment and high turgor and mediate morphogenesis through the dynamics
of their mechanical and chemical properties. The walls are a complex polysaccharidic
structure. Although their biochemical composition is well known, how the different
components organize in the volume of the cell wall and interact with each other
is not well understood and yet is key to the wall’s mechanical properties. To
investigate the ultrastructure of the plant cell wall, we imaged the walls of
onion (Allium cepa) bulbs in a near-native state via cryo-focused ion beam milling
(cryo-FIB milling) and cryo-electron tomography (cryo-ET). This allowed the high-resolution
visualization of cellulose fibers in situ. We reveal the coexistence of dense
fiber fields bathed in a reticulated matrix we termed “meshing,” which is more
abundant at the inner surface of the cell wall. The fibers adopted a regular bimodal
angular distribution at all depths in the cell wall and bundled according to their
orientation, creating layers within the cell wall. Concomitantly, employing homogalacturonan
(HG)-specific enzymatic digestion, we observed changes in the meshing, suggesting
that it is—at least in part—composed of HG pectins. We propose the following model
for the construction of the abaxial epidermal primary cell wall: the cell deposits
successive layers of cellulose fibers at −45° and +45° relative to the cell’s
long axis and secretes the surrounding HG-rich meshing proximal to the plasma
membrane, which then migrates to more distal regions of the cell wall.'
acknowledgement: This work was supported by the Howard Hughes Medical Institute (HHMI)
and grant R35 GM122588 to G.J. and the Austrian Science Fund (FWF) P33367 to F.K.M.S.
We thank Noé Cochetel for his guidance and great help in data analysis, discovery,
and representation with the R software. We thank Hans-Ulrich Endress for graciously
providing us with the purified citrus pectin and Jozef Mravec for generating and
providing the COS488 probe. Cryo-EM work was done in the Beckman Institute Resource
Center for Transmission Electron Microscopy at Caltech. This article is subject
to HHMI’s Open Access to Publications policy. HHMI lab heads have previously granted
a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI
in their research articles. Pursuant to those licenses, the author accepted manuscript
of this article can be made freely available under a CC BY 4.0 license immediately
upon publication.
article_processing_charge: No
article_type: original
author:
- first_name: William J.
full_name: Nicolas, William J.
last_name: Nicolas
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Przemysław
full_name: Dutka, Przemysław
last_name: Dutka
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Grant
full_name: Jensen, Grant
last_name: Jensen
- first_name: Elliot
full_name: Meyerowitz, Elliot
last_name: Meyerowitz
citation:
ama: Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. Cryo-electron
tomography of the onion cell wall shows bimodally oriented cellulose fibers and
reticulated homogalacturonan networks. Current Biology. 2022;32(11):P2375-2389.
doi:10.1016/j.cub.2022.04.024
apa: Nicolas, W. J., Fäßler, F., Dutka, P., Schur, F. K., Jensen, G., & Meyerowitz,
E. (2022). Cryo-electron tomography of the onion cell wall shows bimodally oriented
cellulose fibers and reticulated homogalacturonan networks. Current Biology.
Elsevier. https://doi.org/10.1016/j.cub.2022.04.024
chicago: Nicolas, William J., Florian Fäßler, Przemysław Dutka, Florian KM Schur,
Grant Jensen, and Elliot Meyerowitz. “Cryo-Electron Tomography of the Onion Cell
Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan
Networks.” Current Biology. Elsevier, 2022. https://doi.org/10.1016/j.cub.2022.04.024.
ieee: W. J. Nicolas, F. Fäßler, P. Dutka, F. K. Schur, G. Jensen, and E. Meyerowitz,
“Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose
fibers and reticulated homogalacturonan networks,” Current Biology, vol.
32, no. 11. Elsevier, pp. P2375-2389, 2022.
ista: Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. 2022. Cryo-electron
tomography of the onion cell wall shows bimodally oriented cellulose fibers and
reticulated homogalacturonan networks. Current Biology. 32(11), P2375-2389.
mla: Nicolas, William J., et al. “Cryo-Electron Tomography of the Onion Cell Wall
Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.”
Current Biology, vol. 32, no. 11, Elsevier, 2022, pp. P2375-2389, doi:10.1016/j.cub.2022.04.024.
short: W.J. Nicolas, F. Fäßler, P. Dutka, F.K. Schur, G. Jensen, E. Meyerowitz,
Current Biology 32 (2022) P2375-2389.
date_created: 2022-05-04T06:22:06Z
date_published: 2022-06-06T00:00:00Z
date_updated: 2023-08-03T07:05:36Z
day: '06'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1016/j.cub.2022.04.024
external_id:
isi:
- '000822399200019'
pmid:
- '35508170'
file:
- access_level: open_access
checksum: af3f24d97c016d844df237abef987639
content_type: application/pdf
creator: dernst
date_created: 2022-08-05T06:29:18Z
date_updated: 2022-08-05T06:29:18Z
file_id: '11730'
file_name: 2022_CurrentBiology_Nicolas.pdf
file_size: 12827717
relation: main_file
success: 1
file_date_updated: 2022-08-05T06:29:18Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
issue: '11'
keyword:
- General Agricultural and Biological Sciences
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: P2375-2389
pmid: 1
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose
fibers and reticulated homogalacturonan networks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 32
year: '2022'
...
---
_id: '11448'
abstract:
- lang: eng
text: Studies of protein fitness landscapes reveal biophysical constraints guiding
protein evolution and empower prediction of functional proteins. However, generalisation
of these findings is limited due to scarceness of systematic data on fitness landscapes
of proteins with a defined evolutionary relationship. We characterized the fitness
peaks of four orthologous fluorescent proteins with a broad range of sequence
divergence. While two of the four studied fitness peaks were sharp, the other
two were considerably flatter, being almost entirely free of epistatic interactions.
Mutationally robust proteins, characterized by a flat fitness peak, were not optimal
templates for machine-learning-driven protein design – instead, predictions were
more accurate for fragile proteins with epistatic landscapes. Our work paves insights
for practical application of fitness landscape heterogeneity in protein engineering.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
acknowledgement: "We thank Ondřej Draganov, Rodrigo Redondo, Bor Kavčič, Mia Juračić
and Andrea Pauli for discussion and technical advice. We thank Anita Testa Salmazo
for advice on resin protein purification, Dmitry Bolotin and the Milaboratory (milaboratory.com)
for access to computing and storage infrastructure, and Josef Houser and Eva Fujdiarova
for technical assistance and data interpretation. Core facility Biomolecular Interactions
and Crystallization of CEITEC Masaryk University is gratefully acknowledged for
the obtaining of the scientific data presented in this paper. This research was
supported by the Scientific Service Units (SSU) of IST-Austria\r\nthrough resources
provided by the Bioimaging Facility (BIF), and the Life Science Facility (LSF).
MiSeq and HiSeq NGS sequencing was performed by the Next Generation Sequencing Facility
at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC),
Austria. FACS was performed at the BioOptics Facility of the Institute of Molecular
Pathology (IMP), Austria. We also thank the Biomolecular Crystallography Facility
in the Vanderbilt University Center for Structural Biology. We are grateful to Joel
M Harp for help with X-ray data collection. This work was supported by the ERC Consolidator
grant to FAK (771209—CharFL). KSS acknowledges support by President’s Grant МК–5405.2021.1.4,
the Imperial College Research Fellowship and the MRC London Institute of Medical
Sciences (UKRI MC-A658-5QEA0).\r\nAF is supported by the Marie Skłodowska-Curie
Fellowship (H2020-MSCA-IF-2019, Grant Agreement No. 898203, Project acronym \"FLINDIP\").
Experiments were partially carried out using equipment provided by the Institute
of Bioorganic Chemistry of the Russian Academy of Sciences Сore Facility (CKP IBCH).
This work was supported by a Russian Science Foundation grant 19-74-10102.This project
has received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 665,385."
article_number: '75842'
article_processing_charge: No
article_type: original
author:
- first_name: Louisa
full_name: Gonzalez Somermeyer, Louisa
id: 4720D23C-F248-11E8-B48F-1D18A9856A87
last_name: Gonzalez Somermeyer
orcid: 0000-0001-9139-5383
- first_name: Aubin
full_name: Fleiss, Aubin
last_name: Fleiss
- first_name: Alexander S
full_name: Mishin, Alexander S
last_name: Mishin
- first_name: Nina G
full_name: Bozhanova, Nina G
last_name: Bozhanova
- first_name: Anna A
full_name: Igolkina, Anna A
last_name: Igolkina
- first_name: Jens
full_name: Meiler, Jens
last_name: Meiler
- first_name: Maria-Elisenda
full_name: Alaball Pujol, Maria-Elisenda
last_name: Alaball Pujol
- first_name: Ekaterina V
full_name: Putintseva, Ekaterina V
last_name: Putintseva
- first_name: Karen S
full_name: Sarkisyan, Karen S
last_name: Sarkisyan
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Gonzalez Somermeyer L, Fleiss A, Mishin AS, et al. Heterogeneity of the GFP
fitness landscape and data-driven protein design. eLife. 2022;11. doi:10.7554/elife.75842
apa: Gonzalez Somermeyer, L., Fleiss, A., Mishin, A. S., Bozhanova, N. G., Igolkina,
A. A., Meiler, J., … Kondrashov, F. (2022). Heterogeneity of the GFP fitness landscape
and data-driven protein design. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.75842
chicago: Gonzalez Somermeyer, Louisa, Aubin Fleiss, Alexander S Mishin, Nina G Bozhanova,
Anna A Igolkina, Jens Meiler, Maria-Elisenda Alaball Pujol, Ekaterina V Putintseva,
Karen S Sarkisyan, and Fyodor Kondrashov. “Heterogeneity of the GFP Fitness Landscape
and Data-Driven Protein Design.” ELife. eLife Sciences Publications, 2022.
https://doi.org/10.7554/elife.75842.
ieee: L. Gonzalez Somermeyer et al., “Heterogeneity of the GFP fitness landscape
and data-driven protein design,” eLife, vol. 11. eLife Sciences Publications,
2022.
ista: Gonzalez Somermeyer L, Fleiss A, Mishin AS, Bozhanova NG, Igolkina AA, Meiler
J, Alaball Pujol M-E, Putintseva EV, Sarkisyan KS, Kondrashov F. 2022. Heterogeneity
of the GFP fitness landscape and data-driven protein design. eLife. 11, 75842.
mla: Gonzalez Somermeyer, Louisa, et al. “Heterogeneity of the GFP Fitness Landscape
and Data-Driven Protein Design.” ELife, vol. 11, 75842, eLife Sciences
Publications, 2022, doi:10.7554/elife.75842.
short: L. Gonzalez Somermeyer, A. Fleiss, A.S. Mishin, N.G. Bozhanova, A.A. Igolkina,
J. Meiler, M.-E. Alaball Pujol, E.V. Putintseva, K.S. Sarkisyan, F. Kondrashov,
ELife 11 (2022).
date_created: 2022-06-18T09:06:59Z
date_published: 2022-05-05T00:00:00Z
date_updated: 2023-08-03T07:20:15Z
day: '05'
ddc:
- '570'
department:
- _id: GradSch
- _id: FyKo
doi: 10.7554/elife.75842
ec_funded: 1
external_id:
isi:
- '000799197200001'
file:
- access_level: open_access
checksum: 7573c28f44028ab0cc81faef30039e44
content_type: application/pdf
creator: dernst
date_created: 2022-06-20T07:44:19Z
date_updated: 2022-06-20T07:44:19Z
file_id: '11454'
file_name: 2022_eLife_Somermeyer.pdf
file_size: 5297213
relation: main_file
success: 1
file_date_updated: 2022-06-20T07:44:19Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Heterogeneity of the GFP fitness landscape and data-driven protein design
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2022'
...
---
_id: '11447'
abstract:
- lang: eng
text: Empirical essays of fitness landscapes suggest that they may be rugged, that
is having multiple fitness peaks. Such fitness landscapes, those that have multiple
peaks, necessarily have special local structures, called reciprocal sign epistasis
(Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the
quantitative relationship between the number of fitness peaks and the number of
reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk
et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis
is a necessary but not sufficient condition for the existence of multiple peaks.
Applying discrete Morse theory, which to our knowledge has never been used in
this context, we extend this result by giving the minimal number of reciprocal
sign epistatic interactions required to create a given number of peaks.
acknowledgement: We are grateful to Herbert Edelsbrunner and Jeferson Zapata for helpful
discussions. Open access funding provided by Austrian Science Fund (FWF). Partially
supported by the ERC Consolidator (771209–CharFL) and the FWF Austrian Science Fund
(I5127-B) grants to FAK.
article_number: '74'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Raimundo J
full_name: Saona Urmeneta, Raimundo J
id: BD1DF4C4-D767-11E9-B658-BC13E6697425
last_name: Saona Urmeneta
orcid: 0000-0001-5103-038X
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
citation:
ama: Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number
of peaks and the number of reciprocal sign epistatic interactions. Bulletin
of Mathematical Biology. 2022;84(8). doi:10.1007/s11538-022-01029-z
apa: Saona Urmeneta, R. J., Kondrashov, F., & Khudiakova, K. (2022). Relation
between the number of peaks and the number of reciprocal sign epistatic interactions.
Bulletin of Mathematical Biology. Springer Nature. https://doi.org/10.1007/s11538-022-01029-z
chicago: Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova.
“Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic
Interactions.” Bulletin of Mathematical Biology. Springer Nature, 2022.
https://doi.org/10.1007/s11538-022-01029-z.
ieee: R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between
the number of peaks and the number of reciprocal sign epistatic interactions,”
Bulletin of Mathematical Biology, vol. 84, no. 8. Springer Nature, 2022.
ista: Saona Urmeneta RJ, Kondrashov F, Khudiakova K. 2022. Relation between the
number of peaks and the number of reciprocal sign epistatic interactions. Bulletin
of Mathematical Biology. 84(8), 74.
mla: Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and
the Number of Reciprocal Sign Epistatic Interactions.” Bulletin of Mathematical
Biology, vol. 84, no. 8, 74, Springer Nature, 2022, doi:10.1007/s11538-022-01029-z.
short: R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical
Biology 84 (2022).
date_created: 2022-06-17T16:16:15Z
date_published: 2022-06-17T00:00:00Z
date_updated: 2023-08-03T07:20:53Z
day: '17'
ddc:
- '510'
- '570'
department:
- _id: GradSch
- _id: NiBa
- _id: JaMa
doi: 10.1007/s11538-022-01029-z
ec_funded: 1
external_id:
isi:
- '000812509800001'
file:
- access_level: open_access
checksum: 05a1fe7d10914a00c2bca9b447993a65
content_type: application/pdf
creator: dernst
date_created: 2022-06-20T07:51:32Z
date_updated: 2022-06-20T07:51:32Z
file_id: '11455'
file_name: 2022_BulletinMathBiology_Saona.pdf
file_size: 463025
relation: main_file
success: 1
file_date_updated: 2022-06-20T07:51:32Z
has_accepted_license: '1'
intvolume: ' 84'
isi: 1
issue: '8'
keyword:
- Computational Theory and Mathematics
- General Agricultural and Biological Sciences
- Pharmacology
- General Environmental Science
- General Biochemistry
- Genetics and Molecular Biology
- General Mathematics
- Immunology
- General Neuroscience
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
- _id: c098eddd-5a5b-11eb-8a69-abe27170a68f
grant_number: I05127
name: Evolutionary analysis of gene regulation
publication: Bulletin of Mathematical Biology
publication_identifier:
eissn:
- 1522-9602
issn:
- 0092-8240
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1007/s11538-022-01118-z
scopus_import: '1'
status: public
title: Relation between the number of peaks and the number of reciprocal sign epistatic
interactions
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: 84
year: '2022'
...
---
_id: '11546'
abstract:
- lang: eng
text: Local adaptation leads to differences between populations within a species.
In many systems, similar environmental contrasts occur repeatedly, sometimes driving
parallel phenotypic evolution. Understanding the genomic basis of local adaptation
and parallel evolution is a major goal of evolutionary genomics. It is now known
that by preventing the break-up of favourable combinations of alleles across multiple
loci, genetic architectures that reduce recombination, like chromosomal inversions,
can make an important contribution to local adaptation. However, little is known
about whether inversions also contribute disproportionately to parallel evolution.
Our aim here is to highlight this knowledge gap, to showcase existing studies,
and to illustrate the differences between genomic architectures with and without
inversions using simple models. We predict that by generating stronger effective
selection, inversions can sometimes speed up the parallel adaptive process or
enable parallel adaptation where it would be impossible otherwise, but this is
highly dependent on the spatial setting. We highlight that further empirical work
is needed, in particular to cover a broader taxonomic range and to understand
the relative importance of inversions compared to genomic regions without inversions.
acknowledgement: We thank the editor and two anonymous reviewers for their helpful
and interesting comments on this manuscript.
article_number: '20210203'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. Inversions and parallel
evolution. Philosophical Transactions of the Royal Society B: Biological Sciences.
2022;377(1856). doi:10.1098/rstb.2021.0203'
apa: 'Westram, A. M., Faria, R., Johannesson, K., Butlin, R., & Barton, N. H.
(2022). Inversions and parallel evolution. Philosophical Transactions of the
Royal Society B: Biological Sciences. Royal Society of London. https://doi.org/10.1098/rstb.2021.0203'
chicago: 'Westram, Anja M, Rui Faria, Kerstin Johannesson, Roger Butlin, and Nicholas
H Barton. “Inversions and Parallel Evolution.” Philosophical Transactions of
the Royal Society B: Biological Sciences. Royal Society of London, 2022. https://doi.org/10.1098/rstb.2021.0203.'
ieee: 'A. M. Westram, R. Faria, K. Johannesson, R. Butlin, and N. H. Barton, “Inversions
and parallel evolution,” Philosophical Transactions of the Royal Society B:
Biological Sciences, vol. 377, no. 1856. Royal Society of London, 2022.'
ista: 'Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. 2022. Inversions
and parallel evolution. Philosophical Transactions of the Royal Society B: Biological
Sciences. 377(1856), 20210203.'
mla: 'Westram, Anja M., et al. “Inversions and Parallel Evolution.” Philosophical
Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1856,
20210203, Royal Society of London, 2022, doi:10.1098/rstb.2021.0203.'
short: 'A.M. Westram, R. Faria, K. Johannesson, R. Butlin, N.H. Barton, Philosophical
Transactions of the Royal Society B: Biological Sciences 377 (2022).'
date_created: 2022-07-08T11:41:56Z
date_published: 2022-08-01T00:00:00Z
date_updated: 2023-08-03T11:55:42Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1098/rstb.2021.0203
external_id:
isi:
- '000812317300005'
file:
- access_level: open_access
checksum: 49f69428f3dcf5ce3ff281f7d199e9df
content_type: application/pdf
creator: dernst
date_created: 2023-02-02T08:20:29Z
date_updated: 2023-02-02T08:20:29Z
file_id: '12479'
file_name: 2022_PhilosophicalTransactionsB_Westram.pdf
file_size: 920304
relation: main_file
success: 1
file_date_updated: 2023-02-02T08:20:29Z
has_accepted_license: '1'
intvolume: ' 377'
isi: 1
issue: '1856'
keyword:
- General Agricultural and Biological Sciences
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: The maintenance of alternative adaptive peaks in snapdragons
publication: 'Philosophical Transactions of the Royal Society B: Biological Sciences'
publication_identifier:
eissn:
- 1471-2970
issn:
- 0962-8436
publication_status: published
publisher: Royal Society of London
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inversions and parallel evolution
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 377
year: '2022'
...
---
_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).
date_created: 2022-08-24T08:25:50Z
date_published: 2022-08-16T00:00:00Z
date_updated: 2023-08-03T13:01:19Z
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'
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
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
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic 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: The Wittgenstein Prize
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13
year: '2022'
...
---
_id: '12130'
abstract:
- lang: eng
text: Germline determination is essential for species survival and evolution in
multicellular organisms. In most flowering plants, formation of the female germline
is initiated with specification of one megaspore mother cell (MMC) in each ovule;
however, the molecular mechanism underlying this key event remains unclear. Here
we report that spatially restricted auxin signaling promotes MMC fate in Arabidopsis.
Our results show that the microRNA160 (miR160) targeted gene ARF17 (AUXIN RESPONSE
FACTOR17) is required for promoting MMC specification by genetically interacting
with the SPL/NZZ (SPOROCYTELESS/NOZZLE) gene. Alterations of auxin signaling cause
formation of supernumerary MMCs in an ARF17- and SPL/NZZ-dependent manner. Furthermore,
miR160 and ARF17 are indispensable for attaining a normal auxin maximum at the
ovule apex via modulating the expression domain of PIN1 (PIN-FORMED1) auxin transporter.
Our findings elucidate the mechanism by which auxin signaling promotes the acquisition
of female germline cell fate in plants.
acknowledgement: "We thank A. Cheung,W. Lukowitz, V.Walbot, D.Weijers, and R. Yadegari
for critically reading the manuscript; E. Xiong and G. Zhang for preparing some
experiments, T. Schuck, J. Gonnering, and P. Engevold for plant care, the Arabidopsis
Biological Resource Center (ABRC) for ARF10,ARF16, ARF17, EMS1,MIR160a BAC clones
and cDNAs, the SALK_090804 seed, T. Nakagawa for pGBW vectors, Y. Zhao for the YUC1
cDNA, Q. Chen for the pHEE401E vector, R. Yadegari for pAT5G01860::n1GFP, pAT5G45980:n1GFP,
pAT5G50490::n1GFP, pAT5G56200:n1GFP vectors, and D.Weijers for the pGreenII KAN
SV40-3×GFP and R2D2 vectors, W. Yang for the splmutant, Y. Qin for the pKNU::KNU-VENUS
vector and seed, G. Tang for the STTM160/160-48 vector, and L. Colombo for pPIN1::PIN1-GFP
spl and pin1-5 seeds. This work was supported by the US National Science Foundation
(NSF)-Israel Binational Science Foundation (BSF) research grant to D.Z. (IOS-1322796)
and T.A. (2012756). D.Z. also\r\ngratefully acknowledges supports of the Shaw Scientist
Award from the Greater Milwaukee Foundation, USDA National Institute of Food and
Agriculture (NIFA, 2022-67013-36294), the UWM Discovery and Innovation Grant, the
Bradley Catalyst Award from the UWM Research\r\nFoundation, and WiSys and UW System
Applied Research Funding Programs."
article_number: '6960'
article_processing_charge: No
article_type: original
author:
- first_name: Jian
full_name: Huang, Jian
last_name: Huang
- first_name: Lei
full_name: Zhao, Lei
last_name: Zhao
- first_name: Shikha
full_name: Malik, Shikha
last_name: Malik
- first_name: Benjamin R.
full_name: Gentile, Benjamin R.
last_name: Gentile
- first_name: Va
full_name: Xiong, Va
last_name: Xiong
- first_name: Tzahi
full_name: Arazi, Tzahi
last_name: Arazi
- first_name: Heather A.
full_name: Owen, Heather A.
last_name: Owen
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Dazhong
full_name: Zhao, Dazhong
last_name: Zhao
citation:
ama: Huang J, Zhao L, Malik S, et al. Specification of female germline by microRNA
orchestrated auxin signaling in Arabidopsis. Nature Communications. 2022;13.
doi:10.1038/s41467-022-34723-6
apa: Huang, J., Zhao, L., Malik, S., Gentile, B. R., Xiong, V., Arazi, T., … Zhao,
D. (2022). Specification of female germline by microRNA orchestrated auxin signaling
in Arabidopsis. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-34723-6
chicago: Huang, Jian, Lei Zhao, Shikha Malik, Benjamin R. Gentile, Va Xiong, Tzahi
Arazi, Heather A. Owen, Jiří Friml, and Dazhong Zhao. “Specification of Female
Germline by MicroRNA Orchestrated Auxin Signaling in Arabidopsis.” Nature Communications.
Springer Nature, 2022. https://doi.org/10.1038/s41467-022-34723-6.
ieee: J. Huang et al., “Specification of female germline by microRNA orchestrated
auxin signaling in Arabidopsis,” Nature Communications, vol. 13. Springer
Nature, 2022.
ista: Huang J, Zhao L, Malik S, Gentile BR, Xiong V, Arazi T, Owen HA, Friml J,
Zhao D. 2022. Specification of female germline by microRNA orchestrated auxin
signaling in Arabidopsis. Nature Communications. 13, 6960.
mla: Huang, Jian, et al. “Specification of Female Germline by MicroRNA Orchestrated
Auxin Signaling in Arabidopsis.” Nature Communications, vol. 13, 6960,
Springer Nature, 2022, doi:10.1038/s41467-022-34723-6.
short: J. Huang, L. Zhao, S. Malik, B.R. Gentile, V. Xiong, T. Arazi, H.A. Owen,
J. Friml, D. Zhao, Nature Communications 13 (2022).
date_created: 2023-01-12T12:02:41Z
date_published: 2022-11-15T00:00:00Z
date_updated: 2023-08-04T08:52:01Z
day: '15'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41467-022-34723-6
external_id:
isi:
- '000884426700001'
pmid:
- '36379956'
file:
- access_level: open_access
checksum: 233922a7b9507d9d48591e6799e4526e
content_type: application/pdf
creator: dernst
date_created: 2023-01-23T11:17:33Z
date_updated: 2023-01-23T11:17:33Z
file_id: '12346'
file_name: 2022_NatureCommunications_Huang.pdf
file_size: 3375249
relation: main_file
success: 1
file_date_updated: 2023-01-23T11:17:33Z
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: '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: Specification of female germline by microRNA orchestrated auxin signaling in
Arabidopsis
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: '12157'
abstract:
- lang: eng
text: 'Polygenic adaptation is thought to be ubiquitous, yet remains poorly understood.
Here, we model this process analytically, in the plausible setting of a highly
polygenic, quantitative trait that experiences a sudden shift in the fitness optimum.
We show how the mean phenotype changes over time, depending on the effect sizes
of loci that contribute to variance in the trait, and characterize the allele
dynamics at these loci. Notably, we describe the two phases of the allele dynamics:
The first is a rapid phase, in which directional selection introduces small frequency
differences between alleles whose effects are aligned with or opposed to the shift,
ultimately leading to small differences in their probability of fixation during
a second, longer phase, governed by stabilizing selection. As we discuss, key
results should hold in more general settings and have important implications for
efforts to identify the genetic basis of adaptation in humans and other species.'
acknowledgement: "We thank Guy Amster, Jeremy Berg, Nick Barton, Yuval Simons and
Molly Przeworski for many helpful discussions, and Jeremy Berg, Graham Coop, Joachim
Hermisson, Guillaume Martin, Will Milligan, Peter Ralph, Yuval Simons, Leo Speidel
and Molly Przeworski for comments on the manuscript.\r\nNational Institutes of Health
GM115889 Laura Katharine Hayward Guy Sella \r\nNational Institutes of Health GM121372
Laura Katharine Hayward"
article_number: '66697'
article_processing_charge: No
article_type: original
author:
- first_name: Laura
full_name: Hayward, Laura
id: fc885ee5-24bf-11eb-ad7b-bcc5104c0c1b
last_name: Hayward
- first_name: Guy
full_name: Sella, Guy
last_name: Sella
citation:
ama: Hayward L, Sella G. Polygenic adaptation after a sudden change in environment.
eLife. 2022;11. doi:10.7554/elife.66697
apa: Hayward, L., & Sella, G. (2022). Polygenic adaptation after a sudden change
in environment. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.66697
chicago: Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change
in Environment.” ELife. eLife Sciences Publications, 2022. https://doi.org/10.7554/elife.66697.
ieee: L. Hayward and G. Sella, “Polygenic adaptation after a sudden change in environment,”
eLife, vol. 11. eLife Sciences Publications, 2022.
ista: Hayward L, Sella G. 2022. Polygenic adaptation after a sudden change in environment.
eLife. 11, 66697.
mla: Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change
in Environment.” ELife, vol. 11, 66697, eLife Sciences Publications, 2022,
doi:10.7554/elife.66697.
short: L. Hayward, G. Sella, ELife 11 (2022).
date_created: 2023-01-12T12:09:00Z
date_published: 2022-09-26T00:00:00Z
date_updated: 2023-08-04T09:04:58Z
day: '26'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.7554/elife.66697
external_id:
isi:
- '000890735600001'
file:
- access_level: open_access
checksum: 28de155b231ac1c8d4501c98b2fb359a
content_type: application/pdf
creator: dernst
date_created: 2023-01-24T12:21:32Z
date_updated: 2023-01-24T12:21:32Z
file_id: '12363'
file_name: 2022_eLife_Hayward.pdf
file_size: 18935612
relation: main_file
success: 1
file_date_updated: 2023-01-24T12:21:32Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Polygenic adaptation after a sudden change in environment
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
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).
date_created: 2023-01-16T09:45:09Z
date_published: 2022-10-24T00:00:00Z
date_updated: 2023-08-04T09:15:31Z
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
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: 2023-08-04T09:25:23Z
day: '05'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1038/s41467-022-32806-y
ec_funded: 1
external_id:
isi:
- '000850348400025'
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
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
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13
year: '2022'
...
---
_id: '12224'
abstract:
- lang: eng
text: Muskelin (Mkln1) is implicated in neuronal function, regulating plasma membrane
receptor trafficking. However, its influence on intrinsic brain activity and corresponding
behavioral processes remains unclear. Here we show that murine Mkln1
knockout causes non-habituating locomotor activity, increased exploratory drive,
and decreased locomotor response to amphetamine. Muskelin deficiency impairs social
novelty detection while promoting the retention of spatial reference memory and
fear extinction recall. This is strongly mirrored in either weaker or stronger
resting-state functional connectivity between critical circuits mediating locomotor
exploration and cognition. We show that Mkln1 deletion
alters dendrite branching and spine structure, coinciding with enhanced AMPAR-mediated
synaptic transmission but selective impairment in synaptic potentiation maintenance.
We identify muskelin at excitatory synapses and highlight its role in regulating
dendritic spine actin stability. Our findings point to aberrant spine actin modulation
and changes in glutamatergic synaptic function as critical mechanisms that contribute
to the neurobehavioral phenotype arising from Mkln1
ablation.
acknowledgement: "The authors are grateful to the UKE Animal Facilities (Hamburg)
for animal husbandry and Dr. Bastian Tiemann for his veterinary expertise and supervision
of animal care. We thank Dr. Franco Lombino for critically reading the manuscript
and for helpful discussion. This work was supported by grants from the Deutsche
Forschungsgemeinschaft (DFG) (FOR2419-KN556/11-1, FOR2419-KN556/11-2, KN556/12-1)
and the Landesforschungsförderung Hamburg (LFF-FV76) to M.K.\r\nOpen Access funding
enabled and organized by Projekt DEAL."
article_number: '589'
article_processing_charge: No
article_type: original
author:
- first_name: Mary W
full_name: Muhia, Mary W
id: ab7ed20f-09f7-11eb-909c-d5d0b443ee9d
last_name: Muhia
- first_name: PingAn
full_name: YuanXiang, PingAn
last_name: YuanXiang
- first_name: Jan
full_name: Sedlacik, Jan
last_name: Sedlacik
- first_name: Jürgen R.
full_name: Schwarz, Jürgen R.
last_name: Schwarz
- first_name: Frank F.
full_name: Heisler, Frank F.
last_name: Heisler
- first_name: Kira V.
full_name: Gromova, Kira V.
last_name: Gromova
- first_name: Edda
full_name: Thies, Edda
last_name: Thies
- first_name: Petra
full_name: Breiden, Petra
last_name: Breiden
- first_name: Yvonne
full_name: Pechmann, Yvonne
last_name: Pechmann
- first_name: Michael R.
full_name: Kreutz, Michael R.
last_name: Kreutz
- first_name: Matthias
full_name: Kneussel, Matthias
last_name: Kneussel
citation:
ama: Muhia MW, YuanXiang P, Sedlacik J, et al. Muskelin regulates actin-dependent
synaptic changes and intrinsic brain activity relevant to behavioral and cognitive
processes. Communications Biology. 2022;5. doi:10.1038/s42003-022-03446-1
apa: Muhia, M. W., YuanXiang, P., Sedlacik, J., Schwarz, J. R., Heisler, F. F.,
Gromova, K. V., … Kneussel, M. (2022). Muskelin regulates actin-dependent synaptic
changes and intrinsic brain activity relevant to behavioral and cognitive processes.
Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-022-03446-1
chicago: Muhia, Mary W, PingAn YuanXiang, Jan Sedlacik, Jürgen R. Schwarz, Frank
F. Heisler, Kira V. Gromova, Edda Thies, et al. “Muskelin Regulates Actin-Dependent
Synaptic Changes and Intrinsic Brain Activity Relevant to Behavioral and Cognitive
Processes.” Communications Biology. Springer Nature, 2022. https://doi.org/10.1038/s42003-022-03446-1.
ieee: M. W. Muhia et al., “Muskelin regulates actin-dependent synaptic changes
and intrinsic brain activity relevant to behavioral and cognitive processes,”
Communications Biology, vol. 5. Springer Nature, 2022.
ista: Muhia MW, YuanXiang P, Sedlacik J, Schwarz JR, Heisler FF, Gromova KV, Thies
E, Breiden P, Pechmann Y, Kreutz MR, Kneussel M. 2022. Muskelin regulates actin-dependent
synaptic changes and intrinsic brain activity relevant to behavioral and cognitive
processes. Communications Biology. 5, 589.
mla: Muhia, Mary W., et al. “Muskelin Regulates Actin-Dependent Synaptic Changes
and Intrinsic Brain Activity Relevant to Behavioral and Cognitive Processes.”
Communications Biology, vol. 5, 589, Springer Nature, 2022, doi:10.1038/s42003-022-03446-1.
short: M.W. Muhia, P. YuanXiang, J. Sedlacik, J.R. Schwarz, F.F. Heisler, K.V. Gromova,
E. Thies, P. Breiden, Y. Pechmann, M.R. Kreutz, M. Kneussel, Communications Biology
5 (2022).
date_created: 2023-01-16T09:48:19Z
date_published: 2022-06-15T00:00:00Z
date_updated: 2023-08-04T09:25:59Z
day: '15'
ddc:
- '570'
department:
- _id: PreCl
doi: 10.1038/s42003-022-03446-1
external_id:
isi:
- '000811777900003'
file:
- access_level: open_access
checksum: bd95be1e77090208b79bc45ea8785d0b
content_type: application/pdf
creator: dernst
date_created: 2023-01-27T08:23:46Z
date_updated: 2023-01-27T08:23:46Z
file_id: '12417'
file_name: 2022_CommBiology_Muhia.pdf
file_size: 3968356
relation: main_file
success: 1
file_date_updated: 2023-01-27T08:23:46Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
keyword:
- General Agricultural and Biological Sciences
- General Biochemistry
- Genetics and Molecular Biology
- Medicine (miscellaneous)
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Communications Biology
publication_identifier:
issn:
- 2399-3642
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity
relevant to behavioral and cognitive processes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 5
year: '2022'
...
---
_id: '12238'
abstract:
- lang: eng
text: Upon the initiation of collective cell migration, the cells at the free edge
are specified as leader cells; however, the mechanism underlying the leader cell
specification remains elusive. Here, we show that lamellipodial extension after
the release from mechanical confinement causes sustained extracellular signal-regulated
kinase (ERK) activation and underlies the leader cell specification. Live-imaging
of Madin-Darby canine kidney (MDCK) cells and mouse epidermis through the use
of Förster resonance energy transfer (FRET)-based biosensors showed that leader
cells exhibit sustained ERK activation in a hepatocyte growth factor (HGF)-dependent
manner. Meanwhile, follower cells exhibit oscillatory ERK activation waves in
an epidermal growth factor (EGF) signaling-dependent manner. Lamellipodial extension
at the free edge increases the cellular sensitivity to HGF. The HGF-dependent
ERK activation, in turn, promotes lamellipodial extension, thereby forming a positive
feedback loop between cell extension and ERK activation and specifying the cells
at the free edge as the leader cells. Our findings show that the integration of
physical and biochemical cues underlies the leader cell specification during collective
cell migration.
acknowledgement: We thank the members of the Matsuda Laboratory for their helpful
discussion and encouragement, and we thank K. Hirano and K. Takakura for their technical
assistance. This work was supported by the Kyoto University Live Imaging Center.
Financial support was provided in the form of JSPS KAKENHI grants (nos. 17J02107
and 20K22653 to N.H., and 20H05898 and 19H00993 to M.M.), a JST CREST grant (no.
JPMJCR1654 to M.M.), a Moonshot R&D grant (no. JPMJPS2022-11 to M.M.), Generalitat
de Catalunya and the CERCA Programme (no. SGR-2017-01602 to X.T.), MICCINN/FEDER
(no. PGC2018-099645-B-I00 to X.T.), and European Research Council (no. Adv-883739
to X.T.). IBEC is a recipient of a Severo Ochoa Award of Excellence from the MINECO.
This work was partly supported by an Extramural Collaborative Research Grant of
Cancer Research Institute, Kanazawa University.
article_processing_charge: No
article_type: original
author:
- first_name: Naoya
full_name: Hino, Naoya
id: 5299a9ce-7679-11eb-a7bc-d1e62b936307
last_name: Hino
- first_name: Kimiya
full_name: Matsuda, Kimiya
last_name: Matsuda
- first_name: Yuya
full_name: Jikko, Yuya
last_name: Jikko
- first_name: Gembu
full_name: Maryu, Gembu
last_name: Maryu
- first_name: Katsuya
full_name: Sakai, Katsuya
last_name: Sakai
- first_name: Ryu
full_name: Imamura, Ryu
last_name: Imamura
- first_name: Shinya
full_name: Tsukiji, Shinya
last_name: Tsukiji
- first_name: Kazuhiro
full_name: Aoki, Kazuhiro
last_name: Aoki
- first_name: Kenta
full_name: Terai, Kenta
last_name: Terai
- first_name: Tsuyoshi
full_name: Hirashima, Tsuyoshi
last_name: Hirashima
- first_name: Xavier
full_name: Trepat, Xavier
last_name: Trepat
- first_name: Michiyuki
full_name: Matsuda, Michiyuki
last_name: Matsuda
citation:
ama: Hino N, Matsuda K, Jikko Y, et al. A feedback loop between lamellipodial extension
and HGF-ERK signaling specifies leader cells during collective cell migration.
Developmental Cell. 2022;57(19):2290-2304.e7. doi:10.1016/j.devcel.2022.09.003
apa: Hino, N., Matsuda, K., Jikko, Y., Maryu, G., Sakai, K., Imamura, R., … Matsuda,
M. (2022). A feedback loop between lamellipodial extension and HGF-ERK signaling
specifies leader cells during collective cell migration. Developmental Cell.
Elsevier. https://doi.org/10.1016/j.devcel.2022.09.003
chicago: Hino, Naoya, Kimiya Matsuda, Yuya Jikko, Gembu Maryu, Katsuya Sakai, Ryu
Imamura, Shinya Tsukiji, et al. “A Feedback Loop between Lamellipodial Extension
and HGF-ERK Signaling Specifies Leader Cells during Collective Cell Migration.”
Developmental Cell. Elsevier, 2022. https://doi.org/10.1016/j.devcel.2022.09.003.
ieee: N. Hino et al., “A feedback loop between lamellipodial extension and
HGF-ERK signaling specifies leader cells during collective cell migration,” Developmental
Cell, vol. 57, no. 19. Elsevier, p. 2290–2304.e7, 2022.
ista: Hino N, Matsuda K, Jikko Y, Maryu G, Sakai K, Imamura R, Tsukiji S, Aoki K,
Terai K, Hirashima T, Trepat X, Matsuda M. 2022. A feedback loop between lamellipodial
extension and HGF-ERK signaling specifies leader cells during collective cell
migration. Developmental Cell. 57(19), 2290–2304.e7.
mla: Hino, Naoya, et al. “A Feedback Loop between Lamellipodial Extension and HGF-ERK
Signaling Specifies Leader Cells during Collective Cell Migration.” Developmental
Cell, vol. 57, no. 19, Elsevier, 2022, p. 2290–2304.e7, doi:10.1016/j.devcel.2022.09.003.
short: N. Hino, K. Matsuda, Y. Jikko, G. Maryu, K. Sakai, R. Imamura, S. Tsukiji,
K. Aoki, K. Terai, T. Hirashima, X. Trepat, M. Matsuda, Developmental Cell 57
(2022) 2290–2304.e7.
date_created: 2023-01-16T09:51:39Z
date_published: 2022-10-01T00:00:00Z
date_updated: 2023-08-04T09:38:53Z
day: '01'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2022.09.003
external_id:
isi:
- '000898428700006'
pmid:
- '36174555'
intvolume: ' 57'
isi: 1
issue: '19'
keyword:
- Developmental Biology
- Cell Biology
- General Biochemistry
- Genetics and Molecular Biology
- Molecular Biology
language:
- iso: eng
month: '10'
oa_version: None
page: 2290-2304.e7
pmid: 1
publication: Developmental Cell
publication_identifier:
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: A feedback loop between lamellipodial extension and HGF-ERK signaling specifies
leader cells during collective cell migration
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 57
year: '2022'
...
---
_id: '12261'
abstract:
- lang: eng
text: 'Dose–response relationships are a general concept for quantitatively describing
biological systems across multiple scales, from the molecular to the whole-cell
level. A clinically relevant example is the bacterial growth response to antibiotics,
which is routinely characterized by dose–response curves. The shape of the dose–response
curve varies drastically between antibiotics and plays a key role in treatment,
drug interactions, and resistance evolution. However, the mechanisms shaping the
dose–response curve remain largely unclear. Here, we show in Escherichia coli
that the distinctively shallow dose–response curve of the antibiotic trimethoprim
is caused by a negative growth-mediated feedback loop: Trimethoprim slows growth,
which in turn weakens the effect of this antibiotic. At the molecular level, this
feedback is caused by the upregulation of the drug target dihydrofolate reductase
(FolA/DHFR). We show that this upregulation is not a specific response to trimethoprim
but follows a universal trend line that depends primarily on the growth rate,
irrespective of its cause. Rewiring the feedback loop alters the dose–response
curve in a predictable manner, which we corroborate using a mathematical model
of cellular resource allocation and growth. Our results indicate that growth-mediated
feedback loops may shape drug responses more generally and could be exploited
to design evolutionary traps that enable selection against drug resistance.'
acknowledged_ssus:
- _id: M-Shop
acknowledgement: This work was in part supported by Human Frontier Science Program
GrantRGP0042/2013, Marie Curie Career Integration Grant303507, AustrianScience Fund
(FWF) Grant P27201-B22, and German Research Foundation(DFG) Collaborative Research
Center (SFB)1310to TB. SAA was supportedby the European Union’s Horizon2020Research
and Innovation Programunder the Marie Skłodowska-Curie Grant agreement No707352.
We wouldlike to thank the Bollenbach group for regular fruitful discussions. We
areparticularly thankful for the technical assistance of Booshini Fernando andfor
discussions of the theoretical aspects with Gerrit Ansmann. We areindebted to Bor
Kavˇciˇc for invaluable advice, help with setting up theluciferase-based growth
monitoring system, and for sharing plasmids. Weacknowledge the IST Austria Miba
Machine Shop for their support inbuilding a housing for the stacker of the plate
reader, which enabled thehigh-throughput luciferase-based experiments. We are grateful
to RosalindAllen, Bor Kavˇciˇc and Dor Russ for feedback on the manuscript. Open
Accessfunding enabled and organized by Projekt DEAL.
article_number: e10490
article_processing_charge: No
article_type: original
author:
- first_name: Andreas
full_name: Angermayr, Andreas
id: 4677C796-F248-11E8-B48F-1D18A9856A87
last_name: Angermayr
orcid: 0000-0001-8619-2223
- first_name: Tin Yau
full_name: Pang, Tin Yau
last_name: Pang
- first_name: Guillaume
full_name: Chevereau, Guillaume
last_name: Chevereau
- first_name: Karin
full_name: Mitosch, Karin
id: 39B66846-F248-11E8-B48F-1D18A9856A87
last_name: Mitosch
- first_name: Martin J
full_name: Lercher, Martin J
last_name: Lercher
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. Growth‐mediated
negative feedback shapes quantitative antibiotic response. Molecular Systems
Biology. 2022;18(9). doi:10.15252/msb.202110490
apa: Angermayr, A., Pang, T. Y., Chevereau, G., Mitosch, K., Lercher, M. J., &
Bollenbach, M. T. (2022). Growth‐mediated negative feedback shapes quantitative
antibiotic response. Molecular Systems Biology. Embo Press. https://doi.org/10.15252/msb.202110490
chicago: Angermayr, Andreas, Tin Yau Pang, Guillaume Chevereau, Karin Mitosch, Martin
J Lercher, and Mark Tobias Bollenbach. “Growth‐mediated Negative Feedback Shapes
Quantitative Antibiotic Response.” Molecular Systems Biology. Embo Press,
2022. https://doi.org/10.15252/msb.202110490.
ieee: A. Angermayr, T. Y. Pang, G. Chevereau, K. Mitosch, M. J. Lercher, and M.
T. Bollenbach, “Growth‐mediated negative feedback shapes quantitative antibiotic
response,” Molecular Systems Biology, vol. 18, no. 9. Embo Press, 2022.
ista: Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. 2022.
Growth‐mediated negative feedback shapes quantitative antibiotic response. Molecular
Systems Biology. 18(9), e10490.
mla: Angermayr, Andreas, et al. “Growth‐mediated Negative Feedback Shapes Quantitative
Antibiotic Response.” Molecular Systems Biology, vol. 18, no. 9, e10490,
Embo Press, 2022, doi:10.15252/msb.202110490.
short: A. Angermayr, T.Y. Pang, G. Chevereau, K. Mitosch, M.J. Lercher, M.T. Bollenbach,
Molecular Systems Biology 18 (2022).
date_created: 2023-01-16T09:58:34Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2023-08-04T09:51:49Z
day: '01'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.15252/msb.202110490
external_id:
isi:
- '000856482800001'
file:
- access_level: open_access
checksum: 8b1d8f5ea20c8408acf466435fb6ae01
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T09:49:55Z
date_updated: 2023-01-30T09:49:55Z
file_id: '12446'
file_name: 2022_MolecularSystemsBio_Angermayr.pdf
file_size: 1098812
relation: main_file
success: 1
file_date_updated: 2023-01-30T09:49:55Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '9'
keyword:
- Applied Mathematics
- Computational Theory and Mathematics
- General Agricultural and Biological Sciences
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- Information Systems
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Molecular Systems Biology
publication_identifier:
eissn:
- 1744-4292
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Growth‐mediated negative feedback shapes quantitative antibiotic response
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 18
year: '2022'
...
---
_id: '12288'
abstract:
- lang: eng
text: To understand the function of neuronal circuits, it is crucial to disentangle
the connectivity patterns within the network. However, most tools currently used
to explore connectivity have low throughput, low selectivity, or limited accessibility.
Here, we report the development of an improved packaging system for the production
of the highly neurotropic RVdGenvA-CVS-N2c rabies viral vectors, yielding titers
orders of magnitude higher with no background contamination, at a fraction of
the production time, while preserving the efficiency of transsynaptic labeling.
Along with the production pipeline, we developed suites of ‘starter’ AAV and bicistronic
RVdG-CVS-N2c vectors, enabling retrograde labeling from a wide range of neuronal
populations, tailored for diverse experimental requirements. We demonstrate the
power and flexibility of the new system by uncovering hidden local and distal
inhibitory connections in the mouse hippocampal formation and by imaging the functional
properties of a cortical microcircuit across weeks. Our novel production pipeline
provides a convenient approach to generate new rabies vectors, while our toolkit
flexibly and efficiently expands the current capacity to label, manipulate and
image the neuronal activity of interconnected neuronal circuits in vitro and in
vivo.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: We thank F Marr for technical assistance, A Murray for RVdG-CVS-N2c
viruses and Neuro2A packaging cell-lines and J Watson for reading the manuscript.
This research was supported by the Scientific Service Units (SSU) of IST-Austria
through resources provided by the Imaging and Optics Facility (IOF) and the Preclinical
Facility (PCF). This project was funded by the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation programme (ERC advanced
grant No 692692, PJ, ERC starting grant No 756502, MJ), the Fond zur Förderung der
Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award, PJ), the Human Frontier
Science Program (LT000256/2018-L, AS) and EMBO (ALTF 1098-2017, AS).
article_number: '79848'
article_processing_charge: No
article_type: original
author:
- first_name: Anton L
full_name: Sumser, Anton L
id: 3320A096-F248-11E8-B48F-1D18A9856A87
last_name: Sumser
orcid: 0000-0002-4792-1881
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Yoav
full_name: Ben Simon, Yoav
id: 43DF3136-F248-11E8-B48F-1D18A9856A87
last_name: Ben Simon
citation:
ama: Sumser AL, Jösch MA, Jonas PM, Ben Simon Y. Fast, high-throughput production
of improved rabies viral vectors for specific, efficient and versatile transsynaptic
retrograde labeling. eLife. 2022;11. doi:10.7554/elife.79848
apa: Sumser, A. L., Jösch, M. A., Jonas, P. M., & Ben Simon, Y. (2022). Fast,
high-throughput production of improved rabies viral vectors for specific, efficient
and versatile transsynaptic retrograde labeling. ELife. eLife Sciences
Publications. https://doi.org/10.7554/elife.79848
chicago: Sumser, Anton L, Maximilian A Jösch, Peter M Jonas, and Yoav Ben Simon.
“Fast, High-Throughput Production of Improved Rabies Viral Vectors for Specific,
Efficient and Versatile Transsynaptic Retrograde Labeling.” ELife. eLife
Sciences Publications, 2022. https://doi.org/10.7554/elife.79848.
ieee: A. L. Sumser, M. A. Jösch, P. M. Jonas, and Y. Ben Simon, “Fast, high-throughput
production of improved rabies viral vectors for specific, efficient and versatile
transsynaptic retrograde labeling,” eLife, vol. 11. eLife Sciences Publications,
2022.
ista: Sumser AL, Jösch MA, Jonas PM, Ben Simon Y. 2022. Fast, high-throughput production
of improved rabies viral vectors for specific, efficient and versatile transsynaptic
retrograde labeling. eLife. 11, 79848.
mla: Sumser, Anton L., et al. “Fast, High-Throughput Production of Improved Rabies
Viral Vectors for Specific, Efficient and Versatile Transsynaptic Retrograde Labeling.”
ELife, vol. 11, 79848, eLife Sciences Publications, 2022, doi:10.7554/elife.79848.
short: A.L. Sumser, M.A. Jösch, P.M. Jonas, Y. Ben Simon, ELife 11 (2022).
date_created: 2023-01-16T10:04:15Z
date_published: 2022-09-15T00:00:00Z
date_updated: 2023-08-04T10:29:48Z
day: '15'
ddc:
- '570'
department:
- _id: MaJö
- _id: PeJo
doi: 10.7554/elife.79848
ec_funded: 1
external_id:
isi:
- '000892204300001'
pmid:
- '36040301'
file:
- access_level: open_access
checksum: 5a2a65e3e7225090c3d8199f3bbd7b7b
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T11:50:53Z
date_updated: 2023-01-30T11:50:53Z
file_id: '12463'
file_name: 2022_eLife_Sumser.pdf
file_size: 8506811
relation: main_file
success: 1
file_date_updated: 2023-01-30T11:50:53Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 2634E9D2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '756502'
name: Circuits of Visual Attention
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
- _id: 266D407A-B435-11E9-9278-68D0E5697425
grant_number: LT000256
name: Neuronal networks of salience and spatial detection in the murine superior
colliculus
- _id: 264FEA02-B435-11E9-9278-68D0E5697425
grant_number: ALTF 1098-2017
name: Connecting sensory with motor processing in the superior colliculus
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fast, high-throughput production of improved rabies viral vectors for specific,
efficient and versatile transsynaptic retrograde labeling
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2022'
...
---
_id: '12120'
abstract:
- lang: eng
text: Plant root architecture flexibly adapts to changing nitrate (NO3−) availability
in the soil; however, the underlying molecular mechanism of this adaptive development
remains under-studied. To explore the regulation of NO3−-mediated root growth,
we screened for low-nitrate-resistant mutant (lonr) and identified mutants that
were defective in the NAC transcription factor NAC075 (lonr1) as being less sensitive
to low NO3− in terms of primary root growth. We show that NAC075 is a mobile transcription
factor relocating from the root stele tissues to the endodermis based on NO3−
availability. Under low-NO3− availability, the kinase CBL-interacting protein
kinase 1 (CIPK1) is activated, and it phosphorylates NAC075, restricting its movement
from the stele, which leads to the transcriptional regulation of downstream target
WRKY53, consequently leading to adapted root architecture. Our work thus identifies
an adaptive mechanism involving translocation of transcription factor based on
nutrient availability and leading to cell-specific reprogramming of plant root
growth.
acknowledgement: The authors are grateful to Jörg Kudla, Ying Miao, Yu Zheng, Gang
Li, and Jun Zheng for providing published materials and to Wenkun Zhou and Caifu
Jiang for helpful discussions. This work was supported by grants from the National
Key Research and Development Program of China (2021YFF1000500), the National Natural
Science Foundation of China (32170265 and 32022007), the Beijing Municipal Natural
Science Foundation (5192011), and the Chinese Universities Scientific Fund (2022TC153).
article_processing_charge: No
article_type: original
author:
- first_name: Huixin
full_name: Xiao, Huixin
last_name: Xiao
- first_name: Yumei
full_name: Hu, Yumei
last_name: Hu
- first_name: Yaping
full_name: Wang, Yaping
last_name: Wang
- first_name: Jinkui
full_name: Cheng, Jinkui
last_name: Cheng
- first_name: Jinyi
full_name: Wang, Jinyi
last_name: Wang
- first_name: Guojingwei
full_name: Chen, Guojingwei
last_name: Chen
- first_name: Qian
full_name: Li, Qian
last_name: Li
- first_name: Shuwei
full_name: Wang, Shuwei
last_name: Wang
- first_name: Yalu
full_name: Wang, Yalu
last_name: Wang
- first_name: Shao-Shuai
full_name: Wang, Shao-Shuai
last_name: Wang
- first_name: Yi
full_name: Wang, Yi
last_name: Wang
- first_name: Wei
full_name: Xuan, Wei
last_name: Xuan
- first_name: Zhen
full_name: Li, Zhen
last_name: Li
- first_name: Yan
full_name: Guo, Yan
last_name: Guo
- first_name: Zhizhong
full_name: Gong, Zhizhong
last_name: Gong
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jing
full_name: Zhang, Jing
last_name: Zhang
citation:
ama: Xiao H, Hu Y, Wang Y, et al. Nitrate availability controls translocation of
the transcription factor NAC075 for cell-type-specific reprogramming of root growth.
Developmental Cell. 2022;57(23):2638-2651.e6. doi:10.1016/j.devcel.2022.11.006
apa: Xiao, H., Hu, Y., Wang, Y., Cheng, J., Wang, J., Chen, G., … Zhang, J. (2022).
Nitrate availability controls translocation of the transcription factor NAC075
for cell-type-specific reprogramming of root growth. Developmental Cell.
Elsevier. https://doi.org/10.1016/j.devcel.2022.11.006
chicago: Xiao, Huixin, Yumei Hu, Yaping Wang, Jinkui Cheng, Jinyi Wang, Guojingwei
Chen, Qian Li, et al. “Nitrate Availability Controls Translocation of the Transcription
Factor NAC075 for Cell-Type-Specific Reprogramming of Root Growth.” Developmental
Cell. Elsevier, 2022. https://doi.org/10.1016/j.devcel.2022.11.006.
ieee: H. Xiao et al., “Nitrate availability controls translocation of the
transcription factor NAC075 for cell-type-specific reprogramming of root growth,”
Developmental Cell, vol. 57, no. 23. Elsevier, p. 2638–2651.e6, 2022.
ista: Xiao H, Hu Y, Wang Y, Cheng J, Wang J, Chen G, Li Q, Wang S, Wang Y, Wang
S-S, Wang Y, Xuan W, Li Z, Guo Y, Gong Z, Friml J, Zhang J. 2022. Nitrate availability
controls translocation of the transcription factor NAC075 for cell-type-specific
reprogramming of root growth. Developmental Cell. 57(23), 2638–2651.e6.
mla: Xiao, Huixin, et al. “Nitrate Availability Controls Translocation of the Transcription
Factor NAC075 for Cell-Type-Specific Reprogramming of Root Growth.” Developmental
Cell, vol. 57, no. 23, Elsevier, 2022, p. 2638–2651.e6, doi:10.1016/j.devcel.2022.11.006.
short: H. Xiao, Y. Hu, Y. Wang, J. Cheng, J. Wang, G. Chen, Q. Li, S. Wang, Y. Wang,
S.-S. Wang, Y. Wang, W. Xuan, Z. Li, Y. Guo, Z. Gong, J. Friml, J. Zhang, Developmental
Cell 57 (2022) 2638–2651.e6.
date_created: 2023-01-12T11:57:00Z
date_published: 2022-12-05T00:00:00Z
date_updated: 2023-10-04T08:23:20Z
day: '05'
department:
- _id: JiFr
doi: 10.1016/j.devcel.2022.11.006
external_id:
isi:
- '000919603800005'
pmid:
- '36473460'
intvolume: ' 57'
isi: 1
issue: '23'
keyword:
- Developmental Biology
- Cell Biology
- General Biochemistry
- Genetics and Molecular Biology
- Molecular Biology
language:
- iso: eng
month: '12'
oa_version: None
page: 2638-2651.e6
pmid: 1
publication: Developmental Cell
publication_identifier:
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nitrate availability controls translocation of the transcription factor NAC075
for cell-type-specific reprogramming of root growth
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2022'
...
---
_id: '12117'
abstract:
- lang: eng
text: "To understand how potential gene manipulations affect in vitro microglia,
we provide a set of short protocols to evaluate microglia identity and function.
We detail steps for immunostaining to determine microglia identity. We describe
three functional assays for microglia: phagocytosis, calcium response following
ATP stimulation, and cytokine expression upon inflammatory stimuli. We apply these
protocols to human induced-pluripotent-stem-cell (hiPSC)-derived microglia, but
they can be also applied to other in vitro microglial models including primary
mouse microglia.\r\nFor complete details on the use and execution of this protocol,
please refer to Bartalska et al. (2022).1"
acknowledged_ssus:
- _id: Bio
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation program (grant
No. 715571 to S.S.) and from the Gesellschaft für Forschungsförderung Niederösterreich
(grant No. Sc19-017 to V.H.). We thank Rouven Schulz and Alessandro Venturino for
their insights into functional assays and data analysis, Verena Seiboth for insights
into necessary institutional permission, and ISTA imaging & optics facility (IOF)
especially Bernhard Hochreiter for their support.
article_number: '101866'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Verena
full_name: Hübschmann, Verena
id: 32B7C918-F248-11E8-B48F-1D18A9856A87
last_name: Hübschmann
- first_name: Medina
full_name: Korkut, Medina
id: 4B51CE74-F248-11E8-B48F-1D18A9856A87
last_name: Korkut
orcid: 0000-0003-4309-2251
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
citation:
ama: Hübschmann V, Korkut M, Siegert S. Assessing human iPSC-derived microglia identity
and function by immunostaining, phagocytosis, calcium activity, and inflammation
assay. STAR Protocols. 2022;3(4). doi:10.1016/j.xpro.2022.101866
apa: Hübschmann, V., Korkut, M., & Siegert, S. (2022). Assessing human iPSC-derived
microglia identity and function by immunostaining, phagocytosis, calcium activity,
and inflammation assay. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2022.101866
chicago: Hübschmann, Verena, Medina Korkut, and Sandra Siegert. “Assessing Human
IPSC-Derived Microglia Identity and Function by Immunostaining, Phagocytosis,
Calcium Activity, and Inflammation Assay.” STAR Protocols. Elsevier, 2022.
https://doi.org/10.1016/j.xpro.2022.101866.
ieee: V. Hübschmann, M. Korkut, and S. Siegert, “Assessing human iPSC-derived microglia
identity and function by immunostaining, phagocytosis, calcium activity, and inflammation
assay,” STAR Protocols, vol. 3, no. 4. Elsevier, 2022.
ista: Hübschmann V, Korkut M, Siegert S. 2022. Assessing human iPSC-derived microglia
identity and function by immunostaining, phagocytosis, calcium activity, and inflammation
assay. STAR Protocols. 3(4), 101866.
mla: Hübschmann, Verena, et al. “Assessing Human IPSC-Derived Microglia Identity
and Function by Immunostaining, Phagocytosis, Calcium Activity, and Inflammation
Assay.” STAR Protocols, vol. 3, no. 4, 101866, Elsevier, 2022, doi:10.1016/j.xpro.2022.101866.
short: V. Hübschmann, M. Korkut, S. Siegert, STAR Protocols 3 (2022).
date_created: 2023-01-12T11:56:38Z
date_published: 2022-12-16T00:00:00Z
date_updated: 2023-11-02T12:21:32Z
day: '16'
ddc:
- '570'
department:
- _id: SaSi
- _id: GradSch
doi: 10.1016/j.xpro.2022.101866
ec_funded: 1
file:
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checksum: 3c71b8a60633d42c2f77c49025d5559b
content_type: application/pdf
creator: dernst
date_created: 2023-01-23T09:50:51Z
date_updated: 2023-01-23T09:50:51Z
file_id: '12340'
file_name: 2022_STARProtocols_Huebschmann.pdf
file_size: 6251945
relation: main_file
success: 1
file_date_updated: 2023-01-23T09:50:51Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '4'
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Neuroscience
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25D4A630-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715571'
name: Microglia action towards neuronal circuit formation and function in health
and disease
- _id: 9B99D380-BA93-11EA-9121-9846C619BF3A
grant_number: SC19-017
name: How human microglia shape developing neurons during health and inflammation
publication: STAR Protocols
publication_identifier:
issn:
- 2666-1667
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '11478'
relation: other
status: public
scopus_import: '1'
status: public
title: Assessing human iPSC-derived microglia identity and function by immunostaining,
phagocytosis, calcium activity, and inflammation assay
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: 3
year: '2022'
...
---
_id: '10787'
abstract:
- lang: eng
text: "A species distributed across diverse environments may adapt to local conditions.
We ask how quickly such a species changes its range in response to changed conditions.
Szép et al. (Szép E, Sachdeva H, Barton NH. 2021 Polygenic local adaptation in
metapopulations: a stochastic eco-evolutionary model. Evolution75, 1030–1045 (doi:10.1111/evo.14210))
used the infinite island model to find the stationary distribution of allele frequencies
and deme sizes. We extend this to find how a metapopulation responds to changes
in carrying capacity, selection strength, or migration rate when deme sizes are
fixed. We further develop a ‘fixed-state’ approximation. Under this approximation,
polymorphism is only possible for a narrow range of habitat proportions when selection
is weak compared to drift, but for a much wider range otherwise. When rates of
selection or migration relative to drift change in a single deme of the metapopulation,
the population takes a time of order m−1 to reach the new equilibrium. However,
even with many loci, there can be substantial fluctuations in net adaptation,
because at each locus, alleles randomly get lost or fixed. Thus, in a finite metapopulation,
variation may gradually be lost by chance, even if it would persist in an infinite
metapopulation. When conditions change across the whole metapopulation, there
can be rapid change, which is predicted well by the fixed-state approximation.
This work helps towards an understanding of how metapopulations extend their range
across diverse environments.\r\nThis article is part of the theme issue ‘Species’
ranges in the face of changing environments (Part II)’."
acknowledgement: This research was partly funded by the Austrian Science Fund (FWF)
[FWF P-32896B].
article_processing_charge: No
article_type: original
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Oluwafunmilola O
full_name: Olusanya, Oluwafunmilola O
id: 41AD96DC-F248-11E8-B48F-1D18A9856A87
last_name: Olusanya
orcid: 0000-0003-1971-8314
citation:
ama: 'Barton NH, Olusanya OO. The response of a metapopulation to a changing environment.
Philosophical Transactions of the Royal Society B: Biological Sciences.
2022;377(1848). doi:10.1098/rstb.2021.0009'
apa: 'Barton, N. H., & Olusanya, O. O. (2022). The response of a metapopulation
to a changing environment. Philosophical Transactions of the Royal Society
B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2021.0009'
chicago: 'Barton, Nicholas H, and Oluwafunmilola O Olusanya. “The Response of a
Metapopulation to a Changing Environment.” Philosophical Transactions of the
Royal Society B: Biological Sciences. The Royal Society, 2022. https://doi.org/10.1098/rstb.2021.0009.'
ieee: 'N. H. Barton and O. O. Olusanya, “The response of a metapopulation to a changing
environment,” Philosophical Transactions of the Royal Society B: Biological
Sciences, vol. 377, no. 1848. The Royal Society, 2022.'
ista: 'Barton NH, Olusanya OO. 2022. The response of a metapopulation to a changing
environment. Philosophical Transactions of the Royal Society B: Biological Sciences.
377(1848).'
mla: 'Barton, Nicholas H., and Oluwafunmilola O. Olusanya. “The Response of a Metapopulation
to a Changing Environment.” Philosophical Transactions of the Royal Society
B: Biological Sciences, vol. 377, no. 1848, The Royal Society, 2022, doi:10.1098/rstb.2021.0009.'
short: 'N.H. Barton, O.O. Olusanya, Philosophical Transactions of the Royal Society
B: Biological Sciences 377 (2022).'
date_created: 2022-02-21T16:08:10Z
date_published: 2022-04-11T00:00:00Z
date_updated: 2024-01-26T12:00:53Z
day: '11'
ddc:
- '570'
department:
- _id: GradSch
- _id: NiBa
doi: 10.1098/rstb.2021.0009
external_id:
isi:
- '000758140300001'
pmid:
- '35184588'
file:
- access_level: open_access
checksum: 3b0243738f01bf3c07e0d7e8dc64f71d
content_type: application/pdf
creator: dernst
date_created: 2022-08-02T06:14:32Z
date_updated: 2022-08-02T06:14:32Z
file_id: '11719'
file_name: 2022_PhilosophicalTransactionsRSB_Barton.pdf
file_size: 1349672
relation: main_file
success: 1
file_date_updated: 2022-08-02T06:14:32Z
has_accepted_license: '1'
intvolume: ' 377'
isi: 1
issue: '1848'
keyword:
- General Agricultural and Biological Sciences
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: c08d3278-5a5b-11eb-8a69-fdb09b55f4b8
grant_number: P32896
name: Causes and consequences of population fragmentation
publication: 'Philosophical Transactions of the Royal Society B: Biological Sciences'
publication_identifier:
eissn:
- 1471-2970
issn:
- 0962-8436
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
related_material:
record:
- id: '14711'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The response of a metapopulation to a changing environment
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 377
year: '2022'
...
---
_id: '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).
date_created: 2022-05-13T09:06:28Z
date_published: 2022-05-12T00:00:00Z
date_updated: 2024-02-21T12:35:18Z
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
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: "Understanding bacterial cell division by in vitro\r\nreconstitution"
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:
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relation: dissertation_contains
status: public
- id: '10934'
relation: research_data
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: '11160'
abstract:
- lang: eng
text: Mutations in the chromodomain helicase DNA-binding 8 (CHD8) gene are a frequent
cause of autism spectrum disorder (ASD). While its phenotypic spectrum often encompasses
macrocephaly, implicating cortical abnormalities, how CHD8 haploinsufficiency
affects neurodevelopmental is unclear. Here, employing human cerebral organoids,
we find that CHD8 haploinsufficiency disrupted neurodevelopmental trajectories
with an accelerated and delayed generation of, respectively, inhibitory and excitatory
neurons that yields, at days 60 and 120, symmetrically opposite expansions in
their proportions. This imbalance is consistent with an enlargement of cerebral
organoids as an in vitro correlate of patients’ macrocephaly. Through an isogenic
design of patient-specific mutations and mosaic organoids, we define genotype-phenotype
relationships and uncover their cell-autonomous nature. Our results define cell-type-specific
CHD8-dependent molecular defects related to an abnormal program of proliferation
and alternative splicing. By identifying cell-type-specific effects of CHD8 mutations,
our study uncovers reproducible developmental alterations that may be employed
for neurodevelopmental disease modeling.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: We thank Farnaz Freeman for technical assistance. This research was
supported by the Scientific Service Units (SSU) of IST Austria through resources
provided by the Bioimaging Facility (BIF) and the Life Science Facility (LSF). This
work supported by the European Union’s Horizon 2020 research and innovation program
(ERC) grant 715508 to G.N. (REVERSEAUTISM) and grant 825759 to G.T. (ENDpoiNTs);
the Fondazione Cariplo 2017-0886 to A.L.T.; E-Rare-3 JTC 2018 IMPACT to M. Gabriele;
and the Austrian Science Fund FWF I 4205-B to G.N. Graphical abstract and figures
were created using BioRender.com.
article_number: '110615'
article_processing_charge: Yes
article_type: original
author:
- first_name: Carlo Emanuele
full_name: Villa, Carlo Emanuele
last_name: Villa
- first_name: Cristina
full_name: Cheroni, Cristina
last_name: Cheroni
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
orcid: 0000-0002-9033-9096
- first_name: Alejandro
full_name: López-Tóbon, Alejandro
last_name: López-Tóbon
- first_name: Bárbara
full_name: Oliveira, Bárbara
id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87
last_name: Oliveira
- first_name: Roberto
full_name: Sacco, Roberto
id: 42C9F57E-F248-11E8-B48F-1D18A9856A87
last_name: Sacco
- first_name: Aysan Çerağ
full_name: Yahya, Aysan Çerağ
id: 365A65F8-F248-11E8-B48F-1D18A9856A87
last_name: Yahya
- first_name: Jasmin
full_name: Morandell, Jasmin
id: 4739D480-F248-11E8-B48F-1D18A9856A87
last_name: Morandell
- first_name: Michele
full_name: Gabriele, Michele
last_name: Gabriele
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Mariano
full_name: Gabitto, Mariano
last_name: Gabitto
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Giuseppe
full_name: Testa, Giuseppe
last_name: Testa
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Villa CE, Cheroni C, Dotter C, et al. CHD8 haploinsufficiency links autism
to transient alterations in excitatory and inhibitory trajectories. Cell Reports.
2022;39(1). doi:10.1016/j.celrep.2022.110615
apa: Villa, C. E., Cheroni, C., Dotter, C., López-Tóbon, A., Oliveira, B., Sacco,
R., … Novarino, G. (2022). CHD8 haploinsufficiency links autism to transient alterations
in excitatory and inhibitory trajectories. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2022.110615
chicago: Villa, Carlo Emanuele, Cristina Cheroni, Christoph Dotter, Alejandro López-Tóbon,
Bárbara Oliveira, Roberto Sacco, Aysan Çerağ Yahya, et al. “CHD8 Haploinsufficiency
Links Autism to Transient Alterations in Excitatory and Inhibitory Trajectories.”
Cell Reports. Elsevier, 2022. https://doi.org/10.1016/j.celrep.2022.110615.
ieee: C. E. Villa et al., “CHD8 haploinsufficiency links autism to transient
alterations in excitatory and inhibitory trajectories,” Cell Reports, vol.
39, no. 1. Elsevier, 2022.
ista: Villa CE, Cheroni C, Dotter C, López-Tóbon A, Oliveira B, Sacco R, Yahya AÇ,
Morandell J, Gabriele M, Tavakoli M, Lyudchik J, Sommer CM, Gabitto M, Danzl JG,
Testa G, Novarino G. 2022. CHD8 haploinsufficiency links autism to transient alterations
in excitatory and inhibitory trajectories. Cell Reports. 39(1), 110615.
mla: Villa, Carlo Emanuele, et al. “CHD8 Haploinsufficiency Links Autism to Transient
Alterations in Excitatory and Inhibitory Trajectories.” Cell Reports, vol.
39, no. 1, 110615, Elsevier, 2022, doi:10.1016/j.celrep.2022.110615.
short: C.E. Villa, C. Cheroni, C. Dotter, A. López-Tóbon, B. Oliveira, R. Sacco,
A.Ç. Yahya, J. Morandell, M. Gabriele, M. Tavakoli, J. Lyudchik, C.M. Sommer,
M. Gabitto, J.G. Danzl, G. Testa, G. Novarino, Cell Reports 39 (2022).
date_created: 2022-04-15T09:03:10Z
date_published: 2022-04-05T00:00:00Z
date_updated: 2024-03-27T23:30:44Z
day: '05'
ddc:
- '570'
department:
- _id: JoDa
- _id: GaNo
doi: 10.1016/j.celrep.2022.110615
ec_funded: 1
external_id:
isi:
- '000785983900003'
pmid:
- '35385734'
file:
- access_level: open_access
checksum: b4e8d68f0268dec499af333e6fd5d8e1
content_type: application/pdf
creator: dernst
date_created: 2022-04-15T09:06:25Z
date_updated: 2022-04-15T09:06:25Z
file_id: '11164'
file_name: 2022_CellReports_Villa.pdf
file_size: '7808644'
relation: main_file
success: 1
file_date_updated: 2022-04-15T09:06:25Z
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25444568-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715508'
name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo
and in vitro Models
- _id: 2690FEAC-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I04205
name: Identification of converging Molecular Pathways Across Chromatinopathies as
Targets for Therapy
publication: Cell Reports
publication_identifier:
issn:
- 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '12364'
relation: dissertation_contains
status: public
status: public
title: CHD8 haploinsufficiency links autism to transient alterations in excitatory
and inhibitory trajectories
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 39
year: '2022'
...
---
_id: '11052'
abstract:
- lang: eng
text: In order to combat molecular damage, most cellular proteins undergo rapid
turnover. We have previously identified large nuclear protein assemblies that
can persist for years in post-mitotic tissues and are subject to age-related decline.
Here, we report that mitochondria can be long lived in the mouse brain and reveal
that specific mitochondrial proteins have half-lives longer than the average proteome.
These mitochondrial long-lived proteins (mitoLLPs) are core components of the
electron transport chain (ETC) and display increased longevity in respiratory
supercomplexes. We find that COX7C, a mitoLLP that forms a stable contact site
between complexes I and IV, is required for complex IV and supercomplex assembly.
Remarkably, even upon depletion of COX7C transcripts, ETC function is maintained
for days, effectively uncoupling mitochondrial function from ongoing transcription
of its mitoLLPs. Our results suggest that modulating protein longevity within
the ETC is critical for mitochondrial proteome maintenance and the robustness
of mitochondrial function.
article_processing_charge: No
article_type: original
author:
- first_name: Shefali
full_name: Krishna, Shefali
last_name: Krishna
- first_name: Rafael
full_name: Arrojo e Drigo, Rafael
last_name: Arrojo e Drigo
- first_name: Juliana S.
full_name: Capitanio, Juliana S.
last_name: Capitanio
- first_name: Ranjan
full_name: Ramachandra, Ranjan
last_name: Ramachandra
- first_name: Mark
full_name: Ellisman, Mark
last_name: Ellisman
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Krishna S, Arrojo e Drigo R, Capitanio JS, Ramachandra R, Ellisman M, Hetzer
M. Identification of long-lived proteins in the mitochondria reveals increased
stability of the electron transport chain. Developmental Cell. 2021;56(21):P2952-2965.e9.
doi:10.1016/j.devcel.2021.10.008
apa: Krishna, S., Arrojo e Drigo, R., Capitanio, J. S., Ramachandra, R., Ellisman,
M., & Hetzer, M. (2021). Identification of long-lived proteins in the mitochondria
reveals increased stability of the electron transport chain. Developmental
Cell. Elsevier. https://doi.org/10.1016/j.devcel.2021.10.008
chicago: Krishna, Shefali, Rafael Arrojo e Drigo, Juliana S. Capitanio, Ranjan Ramachandra,
Mark Ellisman, and Martin Hetzer. “Identification of Long-Lived Proteins in the
Mitochondria Reveals Increased Stability of the Electron Transport Chain.” Developmental
Cell. Elsevier, 2021. https://doi.org/10.1016/j.devcel.2021.10.008.
ieee: S. Krishna, R. Arrojo e Drigo, J. S. Capitanio, R. Ramachandra, M. Ellisman,
and M. Hetzer, “Identification of long-lived proteins in the mitochondria reveals
increased stability of the electron transport chain,” Developmental Cell,
vol. 56, no. 21. Elsevier, p. P2952–2965.e9, 2021.
ista: Krishna S, Arrojo e Drigo R, Capitanio JS, Ramachandra R, Ellisman M, Hetzer
M. 2021. Identification of long-lived proteins in the mitochondria reveals increased
stability of the electron transport chain. Developmental Cell. 56(21), P2952–2965.e9.
mla: Krishna, Shefali, et al. “Identification of Long-Lived Proteins in the Mitochondria
Reveals Increased Stability of the Electron Transport Chain.” Developmental
Cell, vol. 56, no. 21, Elsevier, 2021, p. P2952–2965.e9, doi:10.1016/j.devcel.2021.10.008.
short: S. Krishna, R. Arrojo e Drigo, J.S. Capitanio, R. Ramachandra, M. Ellisman,
M. Hetzer, Developmental Cell 56 (2021) P2952–2965.e9.
date_created: 2022-04-07T07:43:14Z
date_published: 2021-11-08T00:00:00Z
date_updated: 2022-07-18T08:26:38Z
day: '08'
doi: 10.1016/j.devcel.2021.10.008
extern: '1'
external_id:
pmid:
- '34715012'
intvolume: ' 56'
issue: '21'
keyword:
- Developmental Biology
- Cell Biology
- General Biochemistry
- Genetics and Molecular Biology
- Molecular Biology
language:
- iso: eng
month: '11'
oa_version: None
page: P2952-2965.e9
pmid: 1
publication: Developmental Cell
publication_identifier:
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Identification of long-lived proteins in the mitochondria reveals increased
stability of the electron transport chain
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 56
year: '2021'
...
---
_id: '12585'
abstract:
- lang: eng
text: Glaciers in High Mountain Asia generate meltwater that supports the water
needs of 250 million people, but current knowledge of annual accumulation and
ablation is limited to sparse field measurements biased in location and glacier
size. Here, we present altitudinally-resolved specific mass balances (surface,
internal, and basal combined) for 5527 glaciers in High Mountain Asia for 2000–2016,
derived by correcting observed glacier thinning patterns for mass redistribution
due to ice flow. We find that 41% of glaciers accumulated mass over less than
20% of their area, and only 60% ± 10% of regional annual ablation was compensated
by accumulation. Even without 21st century warming, 21% ± 1% of ice volume will
be lost by 2100 due to current climatic-geometric imbalance, representing a reduction
in glacier ablation into rivers of 28% ± 1%. The ablation of glaciers in the Himalayas
and Tien Shan was mostly unsustainable and ice volume in these regions will reduce
by at least 30% by 2100. The most important and vulnerable glacier-fed river basins
(Amu Darya, Indus, Syr Darya, Tarim Interior) were supplied with >50% sustainable
glacier ablation but will see long-term reductions in ice mass and glacier meltwater
supply regardless of the Karakoram Anomaly.
article_number: '2868'
article_processing_charge: No
article_type: original
author:
- first_name: Evan
full_name: Miles, Evan
last_name: Miles
- first_name: Michael
full_name: McCarthy, Michael
last_name: McCarthy
- first_name: Amaury
full_name: Dehecq, Amaury
last_name: Dehecq
- first_name: Marin
full_name: Kneib, Marin
last_name: Kneib
- first_name: Stefan
full_name: Fugger, Stefan
last_name: Fugger
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
citation:
ama: Miles E, McCarthy M, Dehecq A, Kneib M, Fugger S, Pellicciotti F. Health and
sustainability of glaciers in High Mountain Asia. Nature Communications.
2021;12. doi:10.1038/s41467-021-23073-4
apa: Miles, E., McCarthy, M., Dehecq, A., Kneib, M., Fugger, S., & Pellicciotti,
F. (2021). Health and sustainability of glaciers in High Mountain Asia. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23073-4
chicago: Miles, Evan, Michael McCarthy, Amaury Dehecq, Marin Kneib, Stefan Fugger,
and Francesca Pellicciotti. “Health and Sustainability of Glaciers in High Mountain
Asia.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23073-4.
ieee: E. Miles, M. McCarthy, A. Dehecq, M. Kneib, S. Fugger, and F. Pellicciotti,
“Health and sustainability of glaciers in High Mountain Asia,” Nature Communications,
vol. 12. Springer Nature, 2021.
ista: Miles E, McCarthy M, Dehecq A, Kneib M, Fugger S, Pellicciotti F. 2021. Health
and sustainability of glaciers in High Mountain Asia. Nature Communications. 12,
2868.
mla: Miles, Evan, et al. “Health and Sustainability of Glaciers in High Mountain
Asia.” Nature Communications, vol. 12, 2868, Springer Nature, 2021, doi:10.1038/s41467-021-23073-4.
short: E. Miles, M. McCarthy, A. Dehecq, M. Kneib, S. Fugger, F. Pellicciotti, Nature
Communications 12 (2021).
date_created: 2023-02-20T08:11:29Z
date_published: 2021-05-17T00:00:00Z
date_updated: 2023-02-28T13:21:51Z
day: '17'
doi: 10.1038/s41467-021-23073-4
extern: '1'
intvolume: ' 12'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-021-23073-4
month: '05'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Health and sustainability of glaciers in High Mountain Asia
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2021'
...
---
_id: '13356'
abstract:
- lang: eng
text: 'Self-assembly of nanoparticles can be mediated by polymers, but has so far
led almost exclusively to nanoparticle aggregates that are amorphous. Here, we
employed Coulombic interactions to generate a range of composite materials from
mixtures of charged nanoparticles and oppositely charged polymers. The assembly
behavior of these nanoparticle/polymer composites depends on their order of addition:
polymers added to nanoparticles give rise to stable aggregates, but nanoparticles
added to polymers disassemble the initially formed aggregates. The amorphous aggregates
were transformed into crystalline ones by transiently increasing the ionic strength
of the solution. The morphology of the resulting crystals depended on the length
of the polymer: short polymer chains mediated the self-assembly of nanoparticles
into strongly faceted crystals, whereas long chains led to pseudospherical nanoparticle/polymer
assemblies, within which the crystalline order of nanoparticles was retained.'
article_processing_charge: No
article_type: original
author:
- first_name: Tong
full_name: Bian, Tong
last_name: Bian
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Bian T, Klajn R. Morphology control in crystalline nanoparticle–polymer aggregates.
Annals of the New York Academy of Sciences. 2021;1505(1):191-201. doi:10.1111/nyas.14674
apa: Bian, T., & Klajn, R. (2021). Morphology control in crystalline nanoparticle–polymer
aggregates. Annals of the New York Academy of Sciences. Wiley. https://doi.org/10.1111/nyas.14674
chicago: Bian, Tong, and Rafal Klajn. “Morphology Control in Crystalline Nanoparticle–Polymer
Aggregates.” Annals of the New York Academy of Sciences. Wiley, 2021. https://doi.org/10.1111/nyas.14674.
ieee: T. Bian and R. Klajn, “Morphology control in crystalline nanoparticle–polymer
aggregates,” Annals of the New York Academy of Sciences, vol. 1505, no.
1. Wiley, pp. 191–201, 2021.
ista: Bian T, Klajn R. 2021. Morphology control in crystalline nanoparticle–polymer
aggregates. Annals of the New York Academy of Sciences. 1505(1), 191–201.
mla: Bian, Tong, and Rafal Klajn. “Morphology Control in Crystalline Nanoparticle–Polymer
Aggregates.” Annals of the New York Academy of Sciences, vol. 1505, no.
1, Wiley, 2021, pp. 191–201, doi:10.1111/nyas.14674.
short: T. Bian, R. Klajn, Annals of the New York Academy of Sciences 1505 (2021)
191–201.
date_created: 2023-08-01T09:33:39Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2023-08-07T10:01:10Z
day: '01'
ddc:
- '540'
doi: 10.1111/nyas.14674
extern: '1'
external_id:
pmid:
- '34427923'
intvolume: ' 1505'
issue: '1'
keyword:
- History and Philosophy of Science
- General Biochemistry
- Genetics and Molecular Biology
- General Neuroscience
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/nyas.14674
month: '12'
oa: 1
oa_version: Published Version
page: 191-201
pmid: 1
publication: Annals of the New York Academy of Sciences
publication_identifier:
eissn:
- 1749-6632
issn:
- 0077-8923
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Morphology control in crystalline nanoparticle–polymer aggregates
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1505
year: '2021'
...
---
_id: '9387'
abstract:
- lang: eng
text: We report the complete analysis of a deterministic model of deleterious mutations
and negative selection against them at two haploid loci without recombination.
As long as mutation is a weaker force than selection, mutant alleles remain rare
at the only stable equilibrium, and otherwise, a variety of dynamics are possible.
If the mutation-free genotype is absent, generally the only stable equilibrium
is the one that corresponds to fixation of the mutant allele at the locus where
it is less deleterious. This result suggests that fixation of a deleterious allele
that follows a click of the Muller’s ratchet is governed by natural selection,
instead of random drift.
acknowledgement: This work was supported by the Russian Science Foundation grant N
16-14-10173.
article_number: '110729'
article_processing_charge: No
article_type: original
author:
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
- first_name: Tatiana Yu.
full_name: Neretina, Tatiana Yu.
last_name: Neretina
- first_name: Alexey S.
full_name: Kondrashov, Alexey S.
last_name: Kondrashov
citation:
ama: Khudiakova K, Neretina TY, Kondrashov AS. Two linked loci under mutation-selection
balance and Muller’s ratchet. Journal of Theoretical Biology. 2021;524.
doi:10.1016/j.jtbi.2021.110729
apa: Khudiakova, K., Neretina, T. Y., & Kondrashov, A. S. (2021). Two linked
loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical
Biology. Elsevier . https://doi.org/10.1016/j.jtbi.2021.110729
chicago: Khudiakova, Kseniia, Tatiana Yu. Neretina, and Alexey S. Kondrashov. “Two
Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” Journal
of Theoretical Biology. Elsevier , 2021. https://doi.org/10.1016/j.jtbi.2021.110729.
ieee: K. Khudiakova, T. Y. Neretina, and A. S. Kondrashov, “Two linked loci under
mutation-selection balance and Muller’s ratchet,” Journal of Theoretical Biology,
vol. 524. Elsevier , 2021.
ista: Khudiakova K, Neretina TY, Kondrashov AS. 2021. Two linked loci under mutation-selection
balance and Muller’s ratchet. Journal of Theoretical Biology. 524, 110729.
mla: Khudiakova, Kseniia, et al. “Two Linked Loci under Mutation-Selection Balance
and Muller’s Ratchet.” Journal of Theoretical Biology, vol. 524, 110729,
Elsevier , 2021, doi:10.1016/j.jtbi.2021.110729.
short: K. Khudiakova, T.Y. Neretina, A.S. Kondrashov, Journal of Theoretical Biology
524 (2021).
date_created: 2021-05-12T05:58:42Z
date_published: 2021-04-24T00:00:00Z
date_updated: 2023-08-08T13:32:40Z
day: '24'
department:
- _id: GradSch
doi: 10.1016/j.jtbi.2021.110729
external_id:
isi:
- '000659161500002'
intvolume: ' 524'
isi: 1
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- Modelling and Simulation
- Statistics and Probability
- General Immunology and Microbiology
- Applied Mathematics
- General Agricultural and Biological Sciences
- General Medicine
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/477489v1
month: '04'
oa: 1
oa_version: Preprint
publication: Journal of Theoretical Biology
publication_identifier:
issn:
- 0022-5193
publication_status: published
publisher: 'Elsevier '
quality_controlled: '1'
status: public
title: Two linked loci under mutation-selection balance and Muller’s ratchet
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 524
year: '2021'
...
---
_id: '9431'
abstract:
- lang: eng
text: Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report
here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus
from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid
protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces
infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram
averaging, mature capsid-like particles show an IP6-like density in the CA hexamer,
coordinated by rings of six lysines and six arginines. Phosphate and IP6 have
opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons
and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer
formation. Subtomogram averaging and classification optimized for analysis of
pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA
polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast,
the CA pentamer forms rigid units organizing the local architecture. These different
features of hexamers and pentamers determine the structural mechanism to form
CA polyhedrons of variable shape in mature RSV particles.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: EM-Fac
acknowledgement: This work was funded by the National Institute of Allergy and Infectious
Diseases under awards R01AI147890 to R.A.D., R01AI150454 to V.M.V, R35GM136258 in
support of J-P.R.F, and the Austrian Science Fund (FWF) grant P31445 to F.K.M.S.
Access to high-resolution cryo-ET data acquisition at EMBL Heidelberg was supported
by iNEXT (grant no. 653706), funded by the Horizon 2020 program of the European
Union (PID 4246). We thank Wim Hagen and Felix Weis at EMBL Heidelberg for support
in cryo-ET data acquisition. This work made use of the Cornell Center for Materials
Research Shared Facilities, which are supported through the NSF MRSEC program (DMR-179875).
This research was also supported by the Scientific Service Units (SSUs) of IST Austria
through resources provided by Scientific Computing (SciComp), the Life Science Facility
(LSF), and the Electron Microscopy Facility (EMF).
article_number: '3226'
article_processing_charge: No
article_type: original
author:
- first_name: Martin
full_name: Obr, Martin
id: 4741CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Obr
- first_name: Clifton L.
full_name: Ricana, Clifton L.
last_name: Ricana
- first_name: Nadia
full_name: Nikulin, Nadia
last_name: Nikulin
- first_name: Jon-Philip R.
full_name: Feathers, Jon-Philip R.
last_name: Feathers
- first_name: Marco
full_name: Klanschnig, Marco
last_name: Klanschnig
- first_name: Andreas
full_name: Thader, Andreas
id: 3A18A7B8-F248-11E8-B48F-1D18A9856A87
last_name: Thader
- first_name: Marc C.
full_name: Johnson, Marc C.
last_name: Johnson
- first_name: Volker M.
full_name: Vogt, Volker M.
last_name: Vogt
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Robert A.
full_name: Dick, Robert A.
last_name: Dick
citation:
ama: Obr M, Ricana CL, Nikulin N, et al. Structure of the mature Rous sarcoma virus
lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature
Communications. 2021;12(1). doi:10.1038/s41467-021-23506-0
apa: Obr, M., Ricana, C. L., Nikulin, N., Feathers, J.-P. R., Klanschnig, M., Thader,
A., … Dick, R. A. (2021). Structure of the mature Rous sarcoma virus lattice reveals
a role for IP6 in the formation of the capsid hexamer. Nature Communications.
Nature Research. https://doi.org/10.1038/s41467-021-23506-0
chicago: Obr, Martin, Clifton L. Ricana, Nadia Nikulin, Jon-Philip R. Feathers,
Marco Klanschnig, Andreas Thader, Marc C. Johnson, Volker M. Vogt, Florian KM
Schur, and Robert A. Dick. “Structure of the Mature Rous Sarcoma Virus Lattice
Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications.
Nature Research, 2021. https://doi.org/10.1038/s41467-021-23506-0.
ieee: M. Obr et al., “Structure of the mature Rous sarcoma virus lattice
reveals a role for IP6 in the formation of the capsid hexamer,” Nature Communications,
vol. 12, no. 1. Nature Research, 2021.
ista: Obr M, Ricana CL, Nikulin N, Feathers J-PR, Klanschnig M, Thader A, Johnson
MC, Vogt VM, Schur FK, Dick RA. 2021. Structure of the mature Rous sarcoma virus
lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature
Communications. 12(1), 3226.
mla: Obr, Martin, et al. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals
a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications,
vol. 12, no. 1, 3226, Nature Research, 2021, doi:10.1038/s41467-021-23506-0.
short: M. Obr, C.L. Ricana, N. Nikulin, J.-P.R. Feathers, M. Klanschnig, A. Thader,
M.C. Johnson, V.M. Vogt, F.K. Schur, R.A. Dick, Nature Communications 12 (2021).
date_created: 2021-05-28T14:25:50Z
date_published: 2021-05-28T00:00:00Z
date_updated: 2023-08-08T13:53:53Z
day: '28'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1038/s41467-021-23506-0
external_id:
isi:
- '000659145000011'
file:
- access_level: open_access
checksum: 53ccc53d09a9111143839dbe7784e663
content_type: application/pdf
creator: kschuh
date_created: 2021-06-09T15:21:14Z
date_updated: 2021-06-09T15:21:14Z
file_id: '9538'
file_name: 2021_NatureCommunications_Obr.pdf
file_size: 6166295
relation: main_file
success: 1
file_date_updated: 2021-06-09T15:21:14Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 26736D6A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31445
name: Structural conservation and diversity in retroviral capsid
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Nature Research
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/how-retroviruses-become-infectious/
scopus_import: '1'
status: public
title: Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in
the formation of the capsid hexamer
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '9540'
abstract:
- lang: eng
text: The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis
and initiates cytoplasmic maturation of the large ribosomal subunit by releasing
the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1
and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug
diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown.
Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism.
Diazaborine forms a covalent bond to the 2′-OH of the nucleotide in D2, explaining
its specificity for this site. As a consequence, the D2 domain is locked in a
rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms
identified include abolished drug binding and altered positioning of the nucleotide.
Our results suggest nucleotide-modifying compounds as potential novel inhibitors
for AAA-ATPases.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: We are deeply grateful to the late Gregor Högenauer who built the
foundation for this study with his visionary work on the inhibitor diazaborine and
its bacterial target. We thank Rolf Breinbauer for insightful discussions on boron
chemistry. We thank Anton Meinhart and Tim Clausen for the valuable discussion of
the manuscript. We are indebted to Thomas Köcher for the MS measurement of the diazaborine-ATPγS
adduct. We thank the team of the VBCF for support during early phases of this work
and the IST Austria Electron Microscopy Facility for providing equipment. The lab
of D.H. is supported by Boehringer Ingelheim. The work was funded by FWF projects
P32536 and P32977 (to H.B.).
article_number: '3483'
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Prattes, Michael
last_name: Prattes
- first_name: Irina
full_name: Grishkovskaya, Irina
last_name: Grishkovskaya
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: Ingrid
full_name: Rössler, Ingrid
last_name: Rössler
- first_name: Isabella
full_name: Klein, Isabella
last_name: Klein
- first_name: Christina
full_name: Hetzmannseder, Christina
last_name: Hetzmannseder
- first_name: Gertrude
full_name: Zisser, Gertrude
last_name: Zisser
- first_name: Christian C.
full_name: Gruber, Christian C.
last_name: Gruber
- first_name: Karl
full_name: Gruber, Karl
last_name: Gruber
- first_name: David
full_name: Haselbach, David
last_name: Haselbach
- first_name: Helmut
full_name: Bergler, Helmut
last_name: Bergler
citation:
ama: Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Structural basis for inhibition
of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 2021;12(1).
doi:10.1038/s41467-021-23854-x
apa: Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Rössler, I., Klein, I., Hetzmannseder,
C., … Bergler, H. (2021). Structural basis for inhibition of the AAA-ATPase Drg1
by diazaborine. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23854-x
chicago: Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Ingrid
Rössler, Isabella Klein, Christina Hetzmannseder, Gertrude Zisser, et al. “Structural
Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” Nature Communications.
Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23854-x.
ieee: M. Prattes et al., “Structural basis for inhibition of the AAA-ATPase
Drg1 by diazaborine,” Nature Communications, vol. 12, no. 1. Springer Nature,
2021.
ista: Prattes M, Grishkovskaya I, Hodirnau V-V, Rössler I, Klein I, Hetzmannseder
C, Zisser G, Gruber CC, Gruber K, Haselbach D, Bergler H. 2021. Structural basis
for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 12(1),
3483.
mla: Prattes, Michael, et al. “Structural Basis for Inhibition of the AAA-ATPase
Drg1 by Diazaborine.” Nature Communications, vol. 12, no. 1, 3483, Springer
Nature, 2021, doi:10.1038/s41467-021-23854-x.
short: M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, I. Rössler, I. Klein, C. Hetzmannseder,
G. Zisser, C.C. Gruber, K. Gruber, D. Haselbach, H. Bergler, Nature Communications
12 (2021).
date_created: 2021-06-10T14:57:45Z
date_published: 2021-06-09T00:00:00Z
date_updated: 2023-08-08T14:05:26Z
day: '09'
ddc:
- '570'
department:
- _id: EM-Fac
doi: 10.1038/s41467-021-23854-x
external_id:
isi:
- '000664874700014'
pmid:
- '34108481'
file:
- access_level: open_access
checksum: 40fc24c1310930990b52a8ad1142ee97
content_type: application/pdf
creator: cziletti
date_created: 2021-06-15T18:55:59Z
date_updated: 2021-06-15T18:55:59Z
file_id: '9556'
file_name: 2021_NatureComm_Prattes.pdf
file_size: 3397292
relation: main_file
success: 1
file_date_updated: 2021-06-15T18:55:59Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_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: No
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).
date_created: 2021-08-06T07:22:55Z
date_published: 2021-05-18T00:00:00Z
date_updated: 2023-08-10T14:16:16Z
day: '18'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1038/s41467-021-23153-5
ec_funded: 1
external_id:
isi:
- '000655481800014'
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
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
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '10163'
abstract:
- lang: eng
text: The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol
II) is a regulatory hub for transcription and RNA processing. Here, we identify
PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability
that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a
CTD reader domain that preferentially binds two phosphorylated Serine-2 marks
in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated
Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length
of genes. PHF3 knock-out or SPOC deletion in human cells results in increased
Pol II stalling, reduced elongation rate and an increase in mRNA stability, with
marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed
in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation.
Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation
by bridging transcription with mRNA decay.
acknowledgement: 'D.S. thanks Claudine Kraft, Renée Schroeder, Verena Jantsch, Franz
Klein and Peter Schlögelhofer for support. We thank Anita Testa Salmazo for help
with purifying Pol II; Matthias Geyer and Robert Düster for sharing DYRK1A kinase;
Felix Hartmann and Clemens Plaschka for help with mass photometry; Goran Kokic for
design of the arrest assay sequences; Petra van der Lelij for help with generating
mESC KO; Maximilian Freilinger for help with the purification of mEGFP-CTD; Stefan
Ameres, Nina Fasching and Brian Reichholf for advice on SLAM-seq and for sharing
reagents; Laura Gallego Valle for advice regarding LLPS assays; Krzysztof Chylinski
for advice regarding CRISPR/Cas9 methodology; VBCF Protein Technologies facility
for purifying PHF3 and providing gRNAs and Cas9; VBCF NGS facility for sequencing;
Monoclonal antibody facility at the Helmholtz center for Pol II antibodies; Friedrich
Propst and Elzbieta Kowalska for advice and for sharing materials; Egon Ogris for
sharing materials; Martin Eilers for recommending a ChIP-grade TFIIS antibody; Susanne
Opravil, Otto Hudecz, Markus Hartl and Natascha Hartl for mass spectrometry analysis;
staff of the X-ray beamlines at the ESRF in Grenoble for their excellent support;
Christa Bücker, Anton Meinhart, Clemens Plaschka and members of the Slade lab for
critical comments on the manuscript; Life Science Editors for editing assistance.
M.B. and D.S. acknowledge support by the FWF-funded DK ‘Chromosome Dynamics’. T.K.
is a recipient of the DOC fellowship from the Austrian Academy of Sciences. U.S.
is supported by the L’Oreal for Women in Science Austria Fellowship and the Austrian
Science Fund (FWF T 795-B30). M.L is supported by the Vienna Science and Technology
Fund (WWTF, VRG14-006). R.S. is supported by the Czech Science Foundation (15-17670 S
and 21-24460 S), Ministry of Education, Youths and Sports of the Czech Republic
(CEITEC 2020 project (LQ1601)), and the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation programme (Grant agreement
no. 649030); this publication reflects only the author’s view and the Research Executive
Agency is not responsible for any use that may be made of the information it contains.
M.S. is supported by the Czech Science Foundation (GJ20-21581Y). K.D.C. research
is supported by the Austrian Science Fund (FWF) Projects I525 and I1593, P22276,
P19060, and W1221, Federal Ministry of Economy, Family and Youth through the initiative
‘Laura Bassi Centres of Expertise’, funding from the Centre of Optimized Structural
Studies No. 253275, the Wellcome Trust Collaborative Award (201543/Z/16), COST action
BM1405 Non-globular proteins - from sequence to structure, function and application
in molecular physiopathology (NGP-NET), the Vienna Science and Technology Fund (WWTF
LS17-008), and by the University of Vienna. This project was funded by the MFPL
start-up grant, the Vienna Science and Technology Fund (WWTF LS14-001), and the
Austrian Science Fund (P31546-B28 and W1258 “DK: Integrative Structural Biology”)
to D.S.'
article_number: '6078'
article_processing_charge: No
article_type: original
author:
- first_name: Lisa-Marie
full_name: Appel, Lisa-Marie
last_name: Appel
- first_name: Vedran
full_name: Franke, Vedran
last_name: Franke
- first_name: Melania
full_name: Bruno, Melania
last_name: Bruno
- first_name: Irina
full_name: Grishkovskaya, Irina
last_name: Grishkovskaya
- first_name: Aiste
full_name: Kasiliauskaite, Aiste
last_name: Kasiliauskaite
- first_name: Tanja
full_name: Kaufmann, Tanja
last_name: Kaufmann
- first_name: Ursula E.
full_name: Schoeberl, Ursula E.
last_name: Schoeberl
- first_name: Martin G.
full_name: Puchinger, Martin G.
last_name: Puchinger
- first_name: Sebastian
full_name: Kostrhon, Sebastian
last_name: Kostrhon
- first_name: Carmen
full_name: Ebenwaldner, Carmen
last_name: Ebenwaldner
- first_name: Marek
full_name: Sebesta, Marek
last_name: Sebesta
- first_name: Etienne
full_name: Beltzung, Etienne
last_name: Beltzung
- first_name: Karl
full_name: Mechtler, Karl
last_name: Mechtler
- first_name: Gen
full_name: Lin, Gen
last_name: Lin
- first_name: Anna
full_name: Vlasova, Anna
last_name: Vlasova
- first_name: Martin
full_name: Leeb, Martin
last_name: Leeb
- first_name: Rushad
full_name: Pavri, Rushad
last_name: Pavri
- first_name: Alexander
full_name: Stark, Alexander
last_name: Stark
- first_name: Altuna
full_name: Akalin, Altuna
last_name: Akalin
- first_name: Richard
full_name: Stefl, Richard
last_name: Stefl
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
- first_name: Kristina
full_name: Djinovic-Carugo, Kristina
last_name: Djinovic-Carugo
- first_name: Dea
full_name: Slade, Dea
last_name: Slade
citation:
ama: Appel L-M, Franke V, Bruno M, et al. PHF3 regulates neuronal gene expression
through the Pol II CTD reader domain SPOC. Nature Communications. 2021;12(1).
doi:10.1038/s41467-021-26360-2
apa: Appel, L.-M., Franke, V., Bruno, M., Grishkovskaya, I., Kasiliauskaite, A.,
Kaufmann, T., … Slade, D. (2021). PHF3 regulates neuronal gene expression through
the Pol II CTD reader domain SPOC. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-021-26360-2
chicago: Appel, Lisa-Marie, Vedran Franke, Melania Bruno, Irina Grishkovskaya, Aiste
Kasiliauskaite, Tanja Kaufmann, Ursula E. Schoeberl, et al. “PHF3 Regulates Neuronal
Gene Expression through the Pol II CTD Reader Domain SPOC.” Nature Communications.
Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26360-2.
ieee: L.-M. Appel et al., “PHF3 regulates neuronal gene expression through
the Pol II CTD reader domain SPOC,” Nature Communications, vol. 12, no.
1. Springer Nature, 2021.
ista: Appel L-M, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann
T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung
E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R,
Bernecky C, Djinovic-Carugo K, Slade D. 2021. PHF3 regulates neuronal gene expression
through the Pol II CTD reader domain SPOC. Nature Communications. 12(1), 6078.
mla: Appel, Lisa-Marie, et al. “PHF3 Regulates Neuronal Gene Expression through
the Pol II CTD Reader Domain SPOC.” Nature Communications, vol. 12, no.
1, 6078, Springer Nature, 2021, doi:10.1038/s41467-021-26360-2.
short: L.-M. Appel, V. Franke, M. Bruno, I. Grishkovskaya, A. Kasiliauskaite, T.
Kaufmann, U.E. Schoeberl, M.G. Puchinger, S. Kostrhon, C. Ebenwaldner, M. Sebesta,
E. Beltzung, K. Mechtler, G. Lin, A. Vlasova, M. Leeb, R. Pavri, A. Stark, A.
Akalin, R. Stefl, C. Bernecky, K. Djinovic-Carugo, D. Slade, Nature Communications
12 (2021).
date_created: 2021-10-20T14:40:32Z
date_published: 2021-10-19T00:00:00Z
date_updated: 2023-08-14T08:02:31Z
day: '19'
ddc:
- '610'
department:
- _id: CaBe
doi: 10.1038/s41467-021-26360-2
external_id:
isi:
- '000709050300001'
file:
- access_level: open_access
checksum: d99fcd51aebde19c21314e3de0148007
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-21T13:51:49Z
date_updated: 2021-10-21T13:51:49Z
file_id: '10169'
file_name: 2021_NatComm_Appel.pdf
file_size: 5111706
relation: main_file
success: 1
file_date_updated: 2021-10-21T13:51:49Z
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: '10'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: 'Preprint '
relation: earlier_version
url: https://www.biorxiv.org/content/10.1101/2020.02.11.943159
status: public
title: PHF3 regulates neuronal gene expression through the Pol II CTD reader domain
SPOC
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '10301'
abstract:
- lang: eng
text: De novo protein synthesis is required for synapse modifications underlying
stable memory encoding. Yet neurons are highly compartmentalized cells and how
protein synthesis can be regulated at the synapse level is unknown. Here, we characterize
neuronal signaling complexes formed by the postsynaptic scaffold GIT1, the mechanistic
target of rapamycin (mTOR) kinase, and Raptor that couple synaptic stimuli to
mTOR-dependent protein synthesis; and identify NMDA receptors containing GluN3A
subunits as key negative regulators of GIT1 binding to mTOR. Disruption of GIT1/mTOR
complexes by enhancing GluN3A expression or silencing GIT1 inhibits synaptic mTOR
activation and restricts the mTOR-dependent translation of specific activity-regulated
mRNAs. Conversely, GluN3A removal enables complex formation, potentiates mTOR-dependent
protein synthesis, and facilitates the consolidation of associative and spatial
memories in mice. The memory enhancement becomes evident with light or spaced
training, can be achieved by selectively deleting GluN3A from excitatory neurons
during adulthood, and does not compromise other aspects of cognition such as memory
flexibility or extinction. Our findings provide mechanistic insight into synaptic
translational control and reveal a potentially selective target for cognitive
enhancement.
acknowledgement: We thank Stuart Lipton and Nobuki Nakanishi for providing the Grin3a
knockout mice, Beverly Davidson for the AAV-caRheb, Jose Esteban for help with behavioral
and biochemical experiments, and Noelia Campillo, Rebeca Martínez-Turrillas, and
Ana Navarro for expert technical help. Work was funded by the UTE project CIMA;
fellowships from the Fundación Tatiana Pérez de Guzmán el Bueno, FEBS, and IBRO
(to M.J.C.D.), Generalitat Valenciana (to O.E.-Z.), Juan de la Cierva (to L.G.R.),
FPI-MINECO (to E.R.V., to S.N.) and Intertalentum postdoctoral program (to V.B.);
ANR (GluBrain3A) and ERC Advanced Grants (#693021) (to P.P.); Ramón y Cajal program
RYC2014-15784, RETOS-MINECO SAF2016-76565-R, ERANET-Neuron JTC 2019 ISCIII AC19/00077
FEDER funds (to R.A.); RETOS-MINECO SAF2017-87928-R (to A.B.); an NIH grant (NS76637)
and UTHSC College of Medicine funds (to S.J.T.); and NARSAD Independent Investigator
Award and grants from the MINECO (CSD2008-00005, SAF2013-48983R, SAF2016-80895-R),
Generalitat Valenciana (PROMETEO 2019/020)(to I.P.O.) and Severo-Ochoa Excellence
Awards (SEV-2013-0317, SEV-2017-0723).
article_number: e71575
article_processing_charge: No
article_type: original
author:
- first_name: María J
full_name: Conde-Dusman, María J
last_name: Conde-Dusman
- first_name: Partha N
full_name: Dey, Partha N
last_name: Dey
- first_name: Óscar
full_name: Elía-Zudaire, Óscar
last_name: Elía-Zudaire
- first_name: Luis E
full_name: Garcia Rabaneda, Luis E
id: 33D1B084-F248-11E8-B48F-1D18A9856A87
last_name: Garcia Rabaneda
- first_name: Carmen
full_name: García-Lira, Carmen
last_name: García-Lira
- first_name: Teddy
full_name: Grand, Teddy
last_name: Grand
- first_name: Victor
full_name: Briz, Victor
last_name: Briz
- first_name: Eric R
full_name: Velasco, Eric R
last_name: Velasco
- first_name: Raül
full_name: Andero Galí, Raül
last_name: Andero Galí
- first_name: Sergio
full_name: Niñerola, Sergio
last_name: Niñerola
- first_name: Angel
full_name: Barco, Angel
last_name: Barco
- first_name: Pierre
full_name: Paoletti, Pierre
last_name: Paoletti
- first_name: John F
full_name: Wesseling, John F
last_name: Wesseling
- first_name: Fabrizio
full_name: Gardoni, Fabrizio
last_name: Gardoni
- first_name: Steven J
full_name: Tavalin, Steven J
last_name: Tavalin
- first_name: Isabel
full_name: Perez-Otaño, Isabel
last_name: Perez-Otaño
citation:
ama: Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, et al. Control of protein synthesis
and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly.
eLife. 2021;10. doi:10.7554/elife.71575
apa: Conde-Dusman, M. J., Dey, P. N., Elía-Zudaire, Ó., Garcia Rabaneda, L. E.,
García-Lira, C., Grand, T., … Perez-Otaño, I. (2021). Control of protein synthesis
and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly.
ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.71575
chicago: Conde-Dusman, María J, Partha N Dey, Óscar Elía-Zudaire, Luis E Garcia
Rabaneda, Carmen García-Lira, Teddy Grand, Victor Briz, et al. “Control of Protein
Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1
Assembly.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.71575.
ieee: M. J. Conde-Dusman et al., “Control of protein synthesis and memory
by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly,” eLife,
vol. 10. eLife Sciences Publications, 2021.
ista: Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, Garcia Rabaneda LE, García-Lira C,
Grand T, Briz V, Velasco ER, Andero Galí R, Niñerola S, Barco A, Paoletti P, Wesseling
JF, Gardoni F, Tavalin SJ, Perez-Otaño I. 2021. Control of protein synthesis and
memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. eLife.
10, e71575.
mla: Conde-Dusman, María J., et al. “Control of Protein Synthesis and Memory by
GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” ELife,
vol. 10, e71575, eLife Sciences Publications, 2021, doi:10.7554/elife.71575.
short: M.J. Conde-Dusman, P.N. Dey, Ó. Elía-Zudaire, L.E. Garcia Rabaneda, C. García-Lira,
T. Grand, V. Briz, E.R. Velasco, R. Andero Galí, S. Niñerola, A. Barco, P. Paoletti,
J.F. Wesseling, F. Gardoni, S.J. Tavalin, I. Perez-Otaño, ELife 10 (2021).
date_created: 2021-11-18T06:59:45Z
date_published: 2021-11-17T00:00:00Z
date_updated: 2023-08-14T11:50:50Z
day: '17'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.7554/elife.71575
external_id:
isi:
- '000720945900001'
file:
- access_level: open_access
checksum: 59318e9e41507cec83c2f4070e6ad540
content_type: application/pdf
creator: lgarciar
date_created: 2021-11-18T07:02:02Z
date_updated: 2021-11-18T07:02:02Z
file_id: '10302'
file_name: elife-71575-v1.pdf
file_size: 2477302
relation: main_file
success: 1
file_date_updated: 2021-11-18T07:02:02Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
keyword:
- general immunology and microbiology
- general biochemistry
- genetics and molecular biology
- general medicine
- general neuroscience
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
status: public
title: Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition
of GIT1/mTORC1 assembly
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: 10
year: '2021'
...
---
_id: '10310'
abstract:
- lang: eng
text: A high-resolution structure of trimeric cyanobacterial Photosystem I (PSI)
from Thermosynechococcus elongatus was reported as the first atomic model of PSI
almost 20 years ago. However, the monomeric PSI structure has not yet been reported
despite long-standing interest in its structure and extensive spectroscopic characterization
of the loss of red chlorophylls upon monomerization. Here, we describe the structure
of monomeric PSI from Thermosynechococcus elongatus BP-1. Comparison with the
trimer structure gave detailed insights into monomerization-induced changes in
both the central trimerization domain and the peripheral regions of the complex.
Monomerization-induced loss of red chlorophylls is assigned to a cluster of chlorophylls
adjacent to PsaX. Based on our findings, we propose a role of PsaX in the stabilization
of red chlorophylls and that lipids of the surrounding membrane present a major
source of thermal energy for uphill excitation energy transfer from red chlorophylls
to P700.
acknowledgement: We are grateful for additional support and valuable scientific input
for this project by Yuko Misumi, Jiannan Li, Hisako Kubota-Kawai, Takeshi Kawabata,
Mian Wu, Eiki Yamashita, Atsushi Nakagawa, Volker Hartmann, Melanie Völkel and Matthias
Rögner. Parts of this research were funded by the German Research Council (DFG)
within the framework of GRK 2341 (Microbial Substrate Conversion) to M.M.N., the
Platform Project for Supporting Drug Discovery and Life Science Research [Basis
for Supporting Innovative Drug Discovery and Life Science Research (BINDS)] from
AMED under grant number JP20am0101117 (K.N.), JP16K07266 to Atsunori Oshima and
C.G., a Grants-in-Aid for Scientific Research under grant number JP 25000013 (K.N.),
17H03647 (C.G.) and 16H06560 (G.K.) from MEXT-KAKENHI, the International Joint Research
Promotion Program from Osaka University to M.M.N., C.G. and G.K., and the Cyclic
Innovation for Clinical Empowerment (CiCLE) Grant Number JP17pc0101020 from AMED
to K.N. and G.K.
article_number: '304'
article_processing_charge: No
article_type: original
author:
- first_name: Mehmet Orkun
full_name: Çoruh, Mehmet Orkun
id: d25163e5-8d53-11eb-a251-e6dd8ea1b8ef
last_name: Çoruh
orcid: 0000-0002-3219-2022
- first_name: Anna
full_name: Frank, Anna
last_name: Frank
- first_name: Hideaki
full_name: Tanaka, Hideaki
last_name: Tanaka
- first_name: Akihiro
full_name: Kawamoto, Akihiro
last_name: Kawamoto
- first_name: Eithar
full_name: El-Mohsnawy, Eithar
last_name: El-Mohsnawy
- first_name: Takayuki
full_name: Kato, Takayuki
last_name: Kato
- first_name: Keiichi
full_name: Namba, Keiichi
last_name: Namba
- first_name: Christoph
full_name: Gerle, Christoph
last_name: Gerle
- first_name: Marc M.
full_name: Nowaczyk, Marc M.
last_name: Nowaczyk
- first_name: Genji
full_name: Kurisu, Genji
last_name: Kurisu
citation:
ama: Çoruh MO, Frank A, Tanaka H, et al. Cryo-EM structure of a functional monomeric
Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster.
Communications Biology. 2021;4(1). doi:10.1038/s42003-021-01808-9
apa: Çoruh, M. O., Frank, A., Tanaka, H., Kawamoto, A., El-Mohsnawy, E., Kato, T.,
… Kurisu, G. (2021). Cryo-EM structure of a functional monomeric Photosystem I
from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications
Biology. Springer . https://doi.org/10.1038/s42003-021-01808-9
chicago: Çoruh, Mehmet Orkun, Anna Frank, Hideaki Tanaka, Akihiro Kawamoto, Eithar
El-Mohsnawy, Takayuki Kato, Keiichi Namba, Christoph Gerle, Marc M. Nowaczyk,
and Genji Kurisu. “Cryo-EM Structure of a Functional Monomeric Photosystem I from
Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” Communications
Biology. Springer , 2021. https://doi.org/10.1038/s42003-021-01808-9.
ieee: M. O. Çoruh et al., “Cryo-EM structure of a functional monomeric Photosystem
I from Thermosynechococcus elongatus reveals red chlorophyll cluster,” Communications
Biology, vol. 4, no. 1. Springer , 2021.
ista: Çoruh MO, Frank A, Tanaka H, Kawamoto A, El-Mohsnawy E, Kato T, Namba K, Gerle
C, Nowaczyk MM, Kurisu G. 2021. Cryo-EM structure of a functional monomeric Photosystem
I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications
Biology. 4(1), 304.
mla: Çoruh, Mehmet Orkun, et al. “Cryo-EM Structure of a Functional Monomeric Photosystem
I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” Communications
Biology, vol. 4, no. 1, 304, Springer , 2021, doi:10.1038/s42003-021-01808-9.
short: M.O. Çoruh, A. Frank, H. Tanaka, A. Kawamoto, E. El-Mohsnawy, T. Kato, K.
Namba, C. Gerle, M.M. Nowaczyk, G. Kurisu, Communications Biology 4 (2021).
date_created: 2021-11-19T11:37:29Z
date_published: 2021-03-08T00:00:00Z
date_updated: 2023-08-14T11:51:19Z
day: '08'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1038/s42003-021-01808-9
external_id:
isi:
- '000627440700001'
pmid:
- '33686186'
file:
- access_level: open_access
checksum: 8ffd39f2bba7152a2441802ff313bf0b
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-19T15:09:18Z
date_updated: 2021-11-19T15:09:18Z
file_id: '10318'
file_name: 2021_CommBio_Çoruh.pdf
file_size: 6030261
relation: main_file
success: 1
file_date_updated: 2021-11-19T15:09:18Z
has_accepted_license: '1'
intvolume: ' 4'
isi: 1
issue: '1'
keyword:
- general agricultural and biological Sciences
- general biochemistry
- genetics and molecular biology
- medicine (miscellaneous)
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Communications Biology
publication_identifier:
issn:
- 2399-3642
publication_status: published
publisher: 'Springer '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus
elongatus reveals red chlorophyll cluster
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: 4
year: '2021'
...
---
_id: '10834'
abstract:
- lang: eng
text: Hematopoietic-specific protein 1 (Hem1) is an essential subunit of the WAVE
regulatory complex (WRC) in immune cells. WRC is crucial for Arp2/3 complex activation
and the protrusion of branched actin filament networks. Moreover, Hem1 loss of
function in immune cells causes autoimmune diseases in humans. Here, we show that
genetic removal of Hem1 in macrophages diminishes frequency and efficacy of phagocytosis
as well as phagocytic cup formation in addition to defects in lamellipodial protrusion
and migration. Moreover, Hem1-null macrophages displayed strong defects in cell
adhesion despite unaltered podosome formation and concomitant extracellular matrix
degradation. Specifically, dynamics of both adhesion and de-adhesion as well as
concomitant phosphorylation of paxillin and focal adhesion kinase (FAK) were significantly
compromised. Accordingly, disruption of WRC function in non-hematopoietic cells
coincided with both defects in adhesion turnover and altered FAK and paxillin
phosphorylation. Consistently, platelets exhibited reduced adhesion and diminished
integrin αIIbβ3 activation upon WRC removal. Interestingly, adhesion phenotypes,
but not lamellipodia formation, were partially rescued by small molecule activation
of FAK. A full rescue of the phenotype, including lamellipodia formation, required
not only the presence of WRCs but also their binding to and activation by Rac.
Collectively, our results uncover that WRC impacts on integrin-dependent processes
in a FAK-dependent manner, controlling formation and dismantling of adhesions,
relevant for properly grabbing onto extracellular surfaces and particles during
cell edge expansion, like in migration or phagocytosis.
acknowledgement: We are grateful to Silvia Prettin, Ina Schleicher, and Petra Hagendorff
for expert technical assistance; David Dettbarn for animal keeping and breeding;
and Lothar Gröbe and Maria Höxter for cell sorting. We also thank Werner Tegge for
peptides and Giorgio Scita for antibodies. This work was supported, in part, by
the Deutsche Forschungsgemeinschaft (DFG), Priority Programm SPP1150 (to T.E.B.S.,
K.R., and M. Sixt), and by DFG grant GRK2223/1 (to K.R.). T.E.B.S. acknowledges
support by the Helmholtz Society through HGF impulse fund W2/W3-066 and M. Schnoor
by the Mexican Council for Science and Technology (CONACyT, 284292 ), Fund SEP-Cinvestav
( 108 ), and the Royal Society, UK (Newton Advanced Fellowship, NAF/R1/180017 ).
article_processing_charge: No
article_type: original
author:
- first_name: Stephanie
full_name: Stahnke, Stephanie
last_name: Stahnke
- first_name: Hermann
full_name: Döring, Hermann
last_name: Döring
- first_name: Charly
full_name: Kusch, Charly
last_name: Kusch
- first_name: David J.J.
full_name: de Gorter, David J.J.
last_name: de Gorter
- first_name: Sebastian
full_name: Dütting, Sebastian
last_name: Dütting
- first_name: Aleks
full_name: Guledani, Aleks
last_name: Guledani
- first_name: Irina
full_name: Pleines, Irina
last_name: Pleines
- first_name: Michael
full_name: Schnoor, Michael
last_name: Schnoor
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Robert
full_name: Geffers, Robert
last_name: Geffers
- first_name: Manfred
full_name: Rohde, Manfred
last_name: Rohde
- first_name: Mathias
full_name: Müsken, Mathias
last_name: Müsken
- first_name: Frieda
full_name: Kage, Frieda
last_name: Kage
- first_name: Anika
full_name: Steffen, Anika
last_name: Steffen
- first_name: Jan
full_name: Faix, Jan
last_name: Faix
- first_name: Bernhard
full_name: Nieswandt, Bernhard
last_name: Nieswandt
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
- first_name: Theresia E.B.
full_name: Stradal, Theresia E.B.
last_name: Stradal
citation:
ama: Stahnke S, Döring H, Kusch C, et al. Loss of Hem1 disrupts macrophage function
and impacts migration, phagocytosis, and integrin-mediated adhesion. Current
Biology. 2021;31(10):2051-2064.e8. doi:10.1016/j.cub.2021.02.043
apa: Stahnke, S., Döring, H., Kusch, C., de Gorter, D. J. J., Dütting, S., Guledani,
A., … Stradal, T. E. B. (2021). Loss of Hem1 disrupts macrophage function and
impacts migration, phagocytosis, and integrin-mediated adhesion. Current Biology.
Elsevier. https://doi.org/10.1016/j.cub.2021.02.043
chicago: Stahnke, Stephanie, Hermann Döring, Charly Kusch, David J.J. de Gorter,
Sebastian Dütting, Aleks Guledani, Irina Pleines, et al. “Loss of Hem1 Disrupts
Macrophage Function and Impacts Migration, Phagocytosis, and Integrin-Mediated
Adhesion.” Current Biology. Elsevier, 2021. https://doi.org/10.1016/j.cub.2021.02.043.
ieee: S. Stahnke et al., “Loss of Hem1 disrupts macrophage function and impacts
migration, phagocytosis, and integrin-mediated adhesion,” Current Biology,
vol. 31, no. 10. Elsevier, p. 2051–2064.e8, 2021.
ista: Stahnke S, Döring H, Kusch C, de Gorter DJJ, Dütting S, Guledani A, Pleines
I, Schnoor M, Sixt MK, Geffers R, Rohde M, Müsken M, Kage F, Steffen A, Faix J,
Nieswandt B, Rottner K, Stradal TEB. 2021. Loss of Hem1 disrupts macrophage function
and impacts migration, phagocytosis, and integrin-mediated adhesion. Current Biology.
31(10), 2051–2064.e8.
mla: Stahnke, Stephanie, et al. “Loss of Hem1 Disrupts Macrophage Function and Impacts
Migration, Phagocytosis, and Integrin-Mediated Adhesion.” Current Biology,
vol. 31, no. 10, Elsevier, 2021, p. 2051–2064.e8, doi:10.1016/j.cub.2021.02.043.
short: S. Stahnke, H. Döring, C. Kusch, D.J.J. de Gorter, S. Dütting, A. Guledani,
I. Pleines, M. Schnoor, M.K. Sixt, R. Geffers, M. Rohde, M. Müsken, F. Kage, A.
Steffen, J. Faix, B. Nieswandt, K. Rottner, T.E.B. Stradal, Current Biology 31
(2021) 2051–2064.e8.
date_created: 2022-03-08T07:51:04Z
date_published: 2021-05-24T00:00:00Z
date_updated: 2023-08-17T07:01:14Z
day: '24'
department:
- _id: MiSi
doi: 10.1016/j.cub.2021.02.043
external_id:
isi:
- '000654652200002'
pmid:
- '33711252'
intvolume: ' 31'
isi: 1
issue: '10'
keyword:
- General Agricultural and Biological Sciences
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2020.03.24.005835
month: '05'
oa: 1
oa_version: Preprint
page: 2051-2064.e8
pmid: 1
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis,
and integrin-mediated adhesion
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 31
year: '2021'
...
---
_id: '15151'
abstract:
- lang: eng
text: Eukaryotic DNA-binding proteins operate in the context of chromatin, where
nucleosomes are the elementary building blocks. Nucleosomal DNA is wrapped around
a histone core, thereby rendering a large fraction of the DNA surface inaccessible
to DNA-binding proteins. Nevertheless, first responders in DNA repair and sequence-specific
transcription factors bind DNA target sites obstructed by chromatin. While early
studies examined protein binding to histone-free DNA, it is only now beginning
to emerge how DNA sequences are interrogated on nucleosomes. These readout strategies
range from the release of nucleosomal DNA from histones, to rotational/translation
register shifts of the DNA motif, and nucleosome-specific DNA binding modes that
differ from those observed on naked DNA. Since DNA motif engagement on nucleosomes
strongly depends on position and orientation, we argue that motif location and
nucleosome positioning co-determine protein access to DNA in transcription and
DNA repair.
article_processing_charge: No
article_type: review
author:
- first_name: Alicia
full_name: Michael, Alicia
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
orcid: 0000-0002-6080-839X
- first_name: Nicolas H.
full_name: Thomä, Nicolas H.
last_name: Thomä
citation:
ama: Michael AK, Thomä NH. Reading the chromatinized genome. Cell. 2021;184(14):3599-3611.
doi:10.1016/j.cell.2021.05.029
apa: Michael, A. K., & Thomä, N. H. (2021). Reading the chromatinized genome.
Cell. Elsevier. https://doi.org/10.1016/j.cell.2021.05.029
chicago: Michael, Alicia K., and Nicolas H. Thomä. “Reading the Chromatinized Genome.”
Cell. Elsevier, 2021. https://doi.org/10.1016/j.cell.2021.05.029.
ieee: A. K. Michael and N. H. Thomä, “Reading the chromatinized genome,” Cell,
vol. 184, no. 14. Elsevier, pp. 3599–3611, 2021.
ista: Michael AK, Thomä NH. 2021. Reading the chromatinized genome. Cell. 184(14),
3599–3611.
mla: Michael, Alicia K., and Nicolas H. Thomä. “Reading the Chromatinized Genome.”
Cell, vol. 184, no. 14, Elsevier, 2021, pp. 3599–611, doi:10.1016/j.cell.2021.05.029.
short: A.K. Michael, N.H. Thomä, Cell 184 (2021) 3599–3611.
date_created: 2024-03-21T07:54:19Z
date_published: 2021-07-08T00:00:00Z
date_updated: 2024-03-25T12:31:39Z
day: '08'
doi: 10.1016/j.cell.2021.05.029
extern: '1'
intvolume: ' 184'
issue: '14'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2021.05.029
month: '07'
oa: 1
oa_version: Published Version
page: 3599-3611
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reading the chromatinized genome
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 184
year: '2021'
...
---
_id: '9429'
abstract:
- lang: eng
text: De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3
lead to autism spectrum disorder (ASD). In mouse, constitutive haploinsufficiency
leads to motor coordination deficits as well as ASD-relevant social and cognitive
impairments. However, induction of Cul3 haploinsufficiency later in life does
not lead to ASD-relevant behaviors, pointing to an important role of Cul3 during
a critical developmental window. Here we show that Cul3 is essential to regulate
neuronal migration and, therefore, constitutive Cul3 heterozygous mutant mice
display cortical lamination abnormalities. At the molecular level, we found that
Cul3 controls neuronal migration by tightly regulating the amount of Plastin3
(Pls3), a previously unrecognized player of neural migration. Furthermore, we
found that Pls3 cell-autonomously regulates cell migration by regulating actin
cytoskeleton organization, and its levels are inversely proportional to neural
migration speed. Finally, we provide evidence that cellular phenotypes associated
with autism-linked gene haploinsufficiency can be rescued by transcriptional activation
of the intact allele in vitro, offering a proof of concept for a potential therapeutic
approach for ASDs.
acknowledged_ssus:
- _id: PreCl
acknowledgement: We thank A. Coll Manzano, F. Freeman, M. Ladron de Guevara, and A.
Ç. Yahya for technical assistance, S. Deixler, A. Lepold, and A. Schlerka for the
management of our animal colony, as well as M. Schunn and the Preclinical Facility
team for technical assistance. We thank K. Heesom and her team at the University
of Bristol Proteomics Facility for the proteomics sample preparation, data generation,
and analysis support. We thank Y. B. Simon for kindly providing the plasmid for
lentiviral labeling. Further, we thank M. Sixt for his advice regarding cell migration
and the fruitful discussions. This work was supported by the ISTPlus postdoctoral
fellowship (Grant Agreement No. 754411) to B.B., by the European Union’s Horizon
2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM), and by
the Austrian Science Fund (FWF) to G.N. (DK W1232-B24 and SFB F7807-B) and to J.G.D
(I3600-B27).
article_number: '3058'
article_processing_charge: No
article_type: original
author:
- first_name: Jasmin
full_name: Morandell, Jasmin
id: 4739D480-F248-11E8-B48F-1D18A9856A87
last_name: Morandell
- first_name: Lena A
full_name: Schwarz, Lena A
id: 29A8453C-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Bernadette
full_name: Basilico, Bernadette
id: 36035796-5ACA-11E9-A75E-7AF2E5697425
last_name: Basilico
orcid: 0000-0003-1843-3173
- first_name: Saren
full_name: Tasciyan, Saren
id: 4323B49C-F248-11E8-B48F-1D18A9856A87
last_name: Tasciyan
orcid: 0000-0003-1671-393X
- first_name: Georgi A
full_name: Dimchev, Georgi A
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
orcid: 0000-0001-8370-6161
- first_name: Armel
full_name: Nicolas, Armel
id: 2A103192-F248-11E8-B48F-1D18A9856A87
last_name: Nicolas
- 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: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
orcid: 0000-0002-9033-9096
- first_name: Lisa
full_name: Knaus, Lisa
id: 3B2ABCF4-F248-11E8-B48F-1D18A9856A87
last_name: Knaus
- first_name: Zoe
full_name: Dobler, Zoe
id: D23090A2-9057-11EA-883A-A8396FC7A38F
last_name: Dobler
- first_name: Emanuele
full_name: Cacci, Emanuele
last_name: Cacci
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- 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: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein
homeostasis and cell migration during a critical window of brain development.
Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23123-x
apa: Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Dimchev, G. A.,
Nicolas, A., … Novarino, G. (2021). Cul3 regulates cytoskeleton protein homeostasis
and cell migration during a critical window of brain development. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-021-23123-x
chicago: Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan,
Georgi A Dimchev, Armel Nicolas, Christoph M Sommer, et al. “Cul3 Regulates Cytoskeleton
Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.”
Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23123-x.
ieee: J. Morandell et al., “Cul3 regulates cytoskeleton protein homeostasis
and cell migration during a critical window of brain development,” Nature Communications,
vol. 12, no. 1. Springer Nature, 2021.
ista: Morandell J, Schwarz LA, Basilico B, Tasciyan S, Dimchev GA, Nicolas A, Sommer
CM, Kreuzinger C, Dotter C, Knaus L, Dobler Z, Cacci E, Schur FK, Danzl JG, Novarino
G. 2021. Cul3 regulates cytoskeleton protein homeostasis and cell migration during
a critical window of brain development. Nature Communications. 12(1), 3058.
mla: Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis
and Cell Migration during a Critical Window of Brain Development.” Nature Communications,
vol. 12, no. 1, 3058, Springer Nature, 2021, doi:10.1038/s41467-021-23123-x.
short: J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, G.A. Dimchev, A. Nicolas,
C.M. Sommer, C. Kreuzinger, C. Dotter, L. Knaus, Z. Dobler, E. Cacci, F.K. Schur,
J.G. Danzl, G. Novarino, Nature Communications 12 (2021).
date_created: 2021-05-28T11:49:46Z
date_published: 2021-05-24T00:00:00Z
date_updated: 2024-03-27T23:30:23Z
day: '24'
ddc:
- '572'
department:
- _id: GaNo
- _id: JoDa
- _id: FlSc
- _id: MiSi
- _id: LifeSc
- _id: Bio
doi: 10.1038/s41467-021-23123-x
ec_funded: 1
external_id:
isi:
- '000658769900010'
file:
- access_level: open_access
checksum: 337e0f7959c35ec959984cacdcb472ba
content_type: application/pdf
creator: kschuh
date_created: 2021-05-28T12:39:43Z
date_updated: 2021-05-28T12:39:43Z
file_id: '9430'
file_name: 2021_NatureCommunications_Morandell.pdf
file_size: 9358599
relation: main_file
success: 1
file_date_updated: 2021-05-28T12:39:43Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 25444568-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715508'
name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo
and in vitro Models
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
- _id: 05A0D778-7A3F-11EA-A408-12923DDC885E
grant_number: F07807
name: Neural stem cells in autism and epilepsy
- _id: 265CB4D0-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03600
name: Optical control of synaptic function via adhesion molecules
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: press_release
url: https://ist.ac.at/en/news/defective-gene-slows-down-brain-cells/
record:
- id: '7800'
relation: earlier_version
status: public
- id: '12401'
relation: dissertation_contains
status: public
status: public
title: Cul3 regulates cytoskeleton protein homeostasis and cell migration during a
critical window of brain development
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '10348'
abstract:
- lang: eng
text: The endosomal sorting complex required for transport-III (ESCRT-III) catalyzes
membrane fission from within membrane necks, a process that is essential for many
cellular functions, from cell division to lysosome degradation and autophagy.
How it breaks membranes, though, remains unknown. Here, we characterize a sequential
polymerization of ESCRT-III subunits that, driven by a recruitment cascade and
by continuous subunit-turnover powered by the ATPase Vps4, induces membrane deformation
and fission. During this process, the exchange of Vps24 for Did2 induces a tilt
in the polymer-membrane interface, which triggers transition from flat spiral
polymers to helical filament to drive the formation of membrane protrusions, and
ends with the formation of a highly constricted Did2-Ist1 co-polymer that we show
is competent to promote fission when bound on the inside of membrane necks. Overall,
our results suggest a mechanism of stepwise changes in ESCRT-III filament structure
and mechanical properties via exchange of the filament subunits to catalyze ESCRT-III
activity.
acknowledgement: The authors thank Nicolas Chiaruttini, Jean Gruenberg, and Lena Harker-Kirschneck
for careful correction of this manuscript and helpful discussions. The authors want
to thank the NCCR Chemical Biology for constant support during this project. A.R.
acknowledges funding from the Swiss National Fund for Research (31003A_130520, 31003A_149975,
and 31003A_173087) and the European Research Council Consolidator (311536). A.Š.
acknowledges the European Research Council (802960). B.B. thanks the BBSRC (BB/K009001/1)
and Wellcome Trust (203276/Z/16/Z) for support. J.M.v.F. acknowledges funding through
an EMBO Long-Term Fellowship (ALTF 1065-2015), the European Commission FP7 (Marie
Curie Actions, LTFCOFUND2013, and GA-2013-609409), and a Transitional Postdoc fellowship
(2015/345) from the Swiss SystemsX.ch initiative, evaluated by the Swiss National
Science Foundation and Swiss National Science Foundation Research (SNSF SINERGIA
160728/1 [leader, Sophie Martin]).
article_processing_charge: No
article_type: original
author:
- first_name: Anna-Katharina
full_name: Pfitzner, Anna-Katharina
last_name: Pfitzner
- first_name: Vincent
full_name: Mercier, Vincent
last_name: Mercier
- first_name: Xiuyun
full_name: Jiang, Xiuyun
last_name: Jiang
- first_name: Joachim
full_name: Moser von Filseck, Joachim
last_name: Moser von Filseck
- first_name: Buzz
full_name: Baum, Buzz
last_name: Baum
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Aurélien
full_name: Roux, Aurélien
last_name: Roux
citation:
ama: Pfitzner A-K, Mercier V, Jiang X, et al. An ESCRT-III polymerization sequence
drives membrane deformation and fission. Cell. 2020;182(5):1140-1155.e18.
doi:10.1016/j.cell.2020.07.021
apa: Pfitzner, A.-K., Mercier, V., Jiang, X., Moser von Filseck, J., Baum, B., Šarić,
A., & Roux, A. (2020). An ESCRT-III polymerization sequence drives membrane
deformation and fission. Cell. Elsevier. https://doi.org/10.1016/j.cell.2020.07.021
chicago: Pfitzner, Anna-Katharina, Vincent Mercier, Xiuyun Jiang, Joachim Moser
von Filseck, Buzz Baum, Anđela Šarić, and Aurélien Roux. “An ESCRT-III Polymerization
Sequence Drives Membrane Deformation and Fission.” Cell. Elsevier, 2020.
https://doi.org/10.1016/j.cell.2020.07.021.
ieee: A.-K. Pfitzner et al., “An ESCRT-III polymerization sequence drives
membrane deformation and fission,” Cell, vol. 182, no. 5. Elsevier, p.
1140–1155.e18, 2020.
ista: Pfitzner A-K, Mercier V, Jiang X, Moser von Filseck J, Baum B, Šarić A, Roux
A. 2020. An ESCRT-III polymerization sequence drives membrane deformation and
fission. Cell. 182(5), 1140–1155.e18.
mla: Pfitzner, Anna-Katharina, et al. “An ESCRT-III Polymerization Sequence Drives
Membrane Deformation and Fission.” Cell, vol. 182, no. 5, Elsevier, 2020,
p. 1140–1155.e18, doi:10.1016/j.cell.2020.07.021.
short: A.-K. Pfitzner, V. Mercier, X. Jiang, J. Moser von Filseck, B. Baum, A. Šarić,
A. Roux, Cell 182 (2020) 1140–1155.e18.
date_created: 2021-11-26T08:02:27Z
date_published: 2020-08-18T00:00:00Z
date_updated: 2021-11-26T08:58:37Z
day: '18'
doi: 10.1016/j.cell.2020.07.021
extern: '1'
external_id:
pmid:
- '32814015'
intvolume: ' 182'
issue: '5'
keyword:
- general biochemistry
- genetics and molecular biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.sciencedirect.com/science/article/pii/S0092867420309296
month: '08'
oa: 1
oa_version: Published Version
page: 1140-1155.e18
pmid: 1
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: An ESCRT-III polymerization sequence drives membrane deformation and fission
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 182
year: '2020'
...
---
_id: '11056'
abstract:
- lang: eng
text: Aging of the circulatory system correlates with the pathogenesis of a large
spectrum of diseases. However, it is largely unknown which factors drive the age-dependent
or pathological decline of the vasculature and how vascular defects relate to
tissue aging. The goal of the study is to design a multianalytical approach to
identify how the cellular microenvironment (i.e., fibroblasts) and serum from
healthy donors of different ages or Alzheimer disease (AD) patients can modulate
the functionality of organ-specific vascular endothelial cells (VECs). Long-living
human microvascular networks embedding VECs and fibroblasts from skin biopsies
are generated. RNA-seq, secretome analyses, and microfluidic assays demonstrate
that fibroblasts from young donors restore the functionality of aged endothelial
cells, an effect also achieved by serum from young donors. New biomarkers of vascular
aging are validated in human biopsies and it is shown that young serum induces
angiopoietin-like-4, which can restore compromised vascular barriers. This strategy
is then employed to characterize transcriptional/functional changes induced on
the blood–brain barrier by AD serum, demonstrating the importance of PTP4A3 in
the regulation of permeability. Features of vascular degeneration during aging
and AD are recapitulated, and a tool to identify novel biomarkers that can be
exploited to develop future therapeutics modulating vascular function is established.
article_number: '2000044'
article_processing_charge: No
article_type: original
author:
- first_name: Simone
full_name: Bersini, Simone
last_name: Bersini
- first_name: Rafael
full_name: Arrojo e Drigo, Rafael
last_name: Arrojo e Drigo
- first_name: Ling
full_name: Huang, Ling
last_name: Huang
- first_name: Maxim N.
full_name: Shokhirev, Maxim N.
last_name: Shokhirev
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Bersini S, Arrojo e Drigo R, Huang L, Shokhirev MN, Hetzer M. Transcriptional
and functional changes of the human microvasculature during physiological aging
and Alzheimer disease. Advanced Biosystems. 2020;4(5). doi:10.1002/adbi.202000044
apa: Bersini, S., Arrojo e Drigo, R., Huang, L., Shokhirev, M. N., & Hetzer,
M. (2020). Transcriptional and functional changes of the human microvasculature
during physiological aging and Alzheimer disease. Advanced Biosystems.
Wiley. https://doi.org/10.1002/adbi.202000044
chicago: Bersini, Simone, Rafael Arrojo e Drigo, Ling Huang, Maxim N. Shokhirev,
and Martin Hetzer. “Transcriptional and Functional Changes of the Human Microvasculature
during Physiological Aging and Alzheimer Disease.” Advanced Biosystems.
Wiley, 2020. https://doi.org/10.1002/adbi.202000044.
ieee: S. Bersini, R. Arrojo e Drigo, L. Huang, M. N. Shokhirev, and M. Hetzer, “Transcriptional
and functional changes of the human microvasculature during physiological aging
and Alzheimer disease,” Advanced Biosystems, vol. 4, no. 5. Wiley, 2020.
ista: Bersini S, Arrojo e Drigo R, Huang L, Shokhirev MN, Hetzer M. 2020. Transcriptional
and functional changes of the human microvasculature during physiological aging
and Alzheimer disease. Advanced Biosystems. 4(5), 2000044.
mla: Bersini, Simone, et al. “Transcriptional and Functional Changes of the Human
Microvasculature during Physiological Aging and Alzheimer Disease.” Advanced
Biosystems, vol. 4, no. 5, 2000044, Wiley, 2020, doi:10.1002/adbi.202000044.
short: S. Bersini, R. Arrojo e Drigo, L. Huang, M.N. Shokhirev, M. Hetzer, Advanced
Biosystems 4 (2020).
date_created: 2022-04-07T07:43:57Z
date_published: 2020-05-01T00:00:00Z
date_updated: 2022-07-18T08:30:48Z
day: '01'
ddc:
- '570'
doi: 10.1002/adbi.202000044
extern: '1'
external_id:
pmid:
- '32402127'
file:
- access_level: open_access
checksum: 5584d9a1609812dc75c02ce1e35d2ec0
content_type: application/pdf
creator: dernst
date_created: 2022-04-08T07:06:05Z
date_updated: 2022-04-08T07:06:05Z
file_id: '11134'
file_name: 2020_AdvancedBiosystems_Bersini.pdf
file_size: 2490829
relation: main_file
success: 1
file_date_updated: 2022-04-08T07:06:05Z
has_accepted_license: '1'
intvolume: ' 4'
issue: '5'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- Biomedical Engineering
- Biomaterials
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Advanced Biosystems
publication_identifier:
issn:
- 2366-7478
- 2366-7478
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Transcriptional and functional changes of the human microvasculature during
physiological aging and Alzheimer disease
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: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 4
year: '2020'
...
---
_id: '11055'
abstract:
- lang: eng
text: Vascular dysfunctions are a common feature of multiple age-related diseases.
However, modeling healthy and pathological aging of the human vasculature represents
an unresolved experimental challenge. Here, we generated induced vascular endothelial
cells (iVECs) and smooth muscle cells (iSMCs) by direct reprogramming of healthy
human fibroblasts from donors of different ages and Hutchinson-Gilford Progeria
Syndrome (HGPS) patients. iVECs induced from old donors revealed upregulation
of GSTM1 and PALD1, genes linked to oxidative stress, inflammation and endothelial
junction stability, as vascular aging markers. A functional assay performed on
PALD1 KD VECs demonstrated a recovery in vascular permeability. We found that
iSMCs from HGPS donors overexpressed bone morphogenetic protein (BMP)−4, which
plays a key role in both vascular calcification and endothelial barrier damage
observed in HGPS. Strikingly, BMP4 concentrations are higher in serum from HGPS
vs. age-matched mice. Furthermore, targeting BMP4 with blocking antibody recovered
the functionality of the vascular barrier in vitro, hence representing a potential
future therapeutic strategy to limit cardiovascular dysfunction in HGPS. These
results show that iVECs and iSMCs retain disease-related signatures, allowing
modeling of vascular aging and HGPS in vitro.
article_number: e54383
article_processing_charge: No
article_type: original
author:
- first_name: Simone
full_name: Bersini, Simone
last_name: Bersini
- first_name: Roberta
full_name: Schulte, Roberta
last_name: Schulte
- first_name: Ling
full_name: Huang, Ling
last_name: Huang
- first_name: Hannah
full_name: Tsai, Hannah
last_name: Tsai
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Bersini S, Schulte R, Huang L, Tsai H, Hetzer M. Direct reprogramming of human
smooth muscle and vascular endothelial cells reveals defects associated with aging
and Hutchinson-Gilford progeria syndrome. eLife. 2020;9. doi:10.7554/elife.54383
apa: Bersini, S., Schulte, R., Huang, L., Tsai, H., & Hetzer, M. (2020). Direct
reprogramming of human smooth muscle and vascular endothelial cells reveals defects
associated with aging and Hutchinson-Gilford progeria syndrome. ELife.
eLife Sciences Publications. https://doi.org/10.7554/elife.54383
chicago: Bersini, Simone, Roberta Schulte, Ling Huang, Hannah Tsai, and Martin Hetzer.
“Direct Reprogramming of Human Smooth Muscle and Vascular Endothelial Cells Reveals
Defects Associated with Aging and Hutchinson-Gilford Progeria Syndrome.” ELife.
eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.54383.
ieee: S. Bersini, R. Schulte, L. Huang, H. Tsai, and M. Hetzer, “Direct reprogramming
of human smooth muscle and vascular endothelial cells reveals defects associated
with aging and Hutchinson-Gilford progeria syndrome,” eLife, vol. 9. eLife
Sciences Publications, 2020.
ista: Bersini S, Schulte R, Huang L, Tsai H, Hetzer M. 2020. Direct reprogramming
of human smooth muscle and vascular endothelial cells reveals defects associated
with aging and Hutchinson-Gilford progeria syndrome. eLife. 9, e54383.
mla: Bersini, Simone, et al. “Direct Reprogramming of Human Smooth Muscle and Vascular
Endothelial Cells Reveals Defects Associated with Aging and Hutchinson-Gilford
Progeria Syndrome.” ELife, vol. 9, e54383, eLife Sciences Publications,
2020, doi:10.7554/elife.54383.
short: S. Bersini, R. Schulte, L. Huang, H. Tsai, M. Hetzer, ELife 9 (2020).
date_created: 2022-04-07T07:43:48Z
date_published: 2020-09-08T00:00:00Z
date_updated: 2022-07-18T08:30:37Z
day: '08'
ddc:
- '570'
doi: 10.7554/elife.54383
extern: '1'
external_id:
pmid:
- '32896271'
file:
- access_level: open_access
checksum: f8b3821349a194050be02570d8fe7d4b
content_type: application/pdf
creator: dernst
date_created: 2022-04-08T06:53:10Z
date_updated: 2022-04-08T06:53:10Z
file_id: '11132'
file_name: 2020_eLife_Bersini.pdf
file_size: 4399825
relation: main_file
success: 1
file_date_updated: 2022-04-08T06:53:10Z
has_accepted_license: '1'
intvolume: ' 9'
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Direct reprogramming of human smooth muscle and vascular endothelial cells
reveals defects associated with aging and Hutchinson-Gilford progeria syndrome
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: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 9
year: '2020'
...
---
_id: '8402'
abstract:
- lang: eng
text: "Background: The mitochondrial pyruvate carrier (MPC) plays a central role
in energy metabolism by transporting pyruvate across the inner mitochondrial membrane.
Its heterodimeric composition and homology to SWEET and semiSWEET transporters
set the MPC apart from the canonical mitochondrial carrier family (named MCF or
SLC25). The import of the canonical carriers is mediated by the carrier translocase
of the inner membrane (TIM22) pathway and is dependent on their structure, which
features an even number of transmembrane segments and both termini in the intermembrane
space. The import pathway of MPC proteins has not been elucidated. The odd number
of transmembrane segments and positioning of the N-terminus in the matrix argues
against an import via the TIM22 carrier pathway but favors an import via the flexible
presequence pathway.\r\nResults: Here, we systematically analyzed the import pathways
of Mpc2 and Mpc3 and report that, contrary to an expected import via the flexible
presequence pathway, yeast MPC proteins with an odd number of transmembrane segments
and matrix-exposed N-terminus are imported by the carrier pathway, using the receptor
Tom70, small TIM chaperones, and the TIM22 complex. The TIM9·10 complex chaperones
MPC proteins through the mitochondrial intermembrane space using conserved hydrophobic
motifs that are also required for the interaction with canonical carrier proteins.\r\nConclusions:
The carrier pathway can import paired and non-paired transmembrane helices and
translocate N-termini to either side of the mitochondrial inner membrane, revealing
an unexpected versatility of the mitochondrial import pathway for non-cleavable
inner membrane proteins."
article_number: '2'
article_processing_charge: No
article_type: original
author:
- first_name: Heike
full_name: Rampelt, Heike
last_name: Rampelt
- first_name: Iva
full_name: Sucec, Iva
last_name: Sucec
- first_name: Beate
full_name: Bersch, Beate
last_name: Bersch
- first_name: Patrick
full_name: Horten, Patrick
last_name: Horten
- first_name: Inge
full_name: Perschil, Inge
last_name: Perschil
- first_name: Jean-Claude
full_name: Martinou, Jean-Claude
last_name: Martinou
- first_name: Martin
full_name: van der Laan, Martin
last_name: van der Laan
- first_name: Nils
full_name: Wiedemann, Nils
last_name: Wiedemann
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Nikolaus
full_name: Pfanner, Nikolaus
last_name: Pfanner
citation:
ama: Rampelt H, Sucec I, Bersch B, et al. The mitochondrial carrier pathway transports
non-canonical substrates with an odd number of transmembrane segments. BMC
Biology. 2020;18. doi:10.1186/s12915-019-0733-6
apa: Rampelt, H., Sucec, I., Bersch, B., Horten, P., Perschil, I., Martinou, J.-C.,
… Pfanner, N. (2020). The mitochondrial carrier pathway transports non-canonical
substrates with an odd number of transmembrane segments. BMC Biology. Springer
Nature. https://doi.org/10.1186/s12915-019-0733-6
chicago: Rampelt, Heike, Iva Sucec, Beate Bersch, Patrick Horten, Inge Perschil,
Jean-Claude Martinou, Martin van der Laan, Nils Wiedemann, Paul Schanda, and Nikolaus
Pfanner. “The Mitochondrial Carrier Pathway Transports Non-Canonical Substrates
with an Odd Number of Transmembrane Segments.” BMC Biology. Springer Nature,
2020. https://doi.org/10.1186/s12915-019-0733-6.
ieee: H. Rampelt et al., “The mitochondrial carrier pathway transports non-canonical
substrates with an odd number of transmembrane segments,” BMC Biology,
vol. 18. Springer Nature, 2020.
ista: Rampelt H, Sucec I, Bersch B, Horten P, Perschil I, Martinou J-C, van der
Laan M, Wiedemann N, Schanda P, Pfanner N. 2020. The mitochondrial carrier pathway
transports non-canonical substrates with an odd number of transmembrane segments.
BMC Biology. 18, 2.
mla: Rampelt, Heike, et al. “The Mitochondrial Carrier Pathway Transports Non-Canonical
Substrates with an Odd Number of Transmembrane Segments.” BMC Biology,
vol. 18, 2, Springer Nature, 2020, doi:10.1186/s12915-019-0733-6.
short: H. Rampelt, I. Sucec, B. Bersch, P. Horten, I. Perschil, J.-C. Martinou,
M. van der Laan, N. Wiedemann, P. Schanda, N. Pfanner, BMC Biology 18 (2020).
date_created: 2020-09-17T10:26:53Z
date_published: 2020-01-06T00:00:00Z
date_updated: 2021-01-12T08:19:02Z
day: '06'
doi: 10.1186/s12915-019-0733-6
extern: '1'
external_id:
pmid:
- '31907035'
intvolume: ' 18'
keyword:
- Biotechnology
- Plant Science
- General Biochemistry
- Genetics and Molecular Biology
- Developmental Biology
- Cell Biology
- Physiology
- Ecology
- Evolution
- Behavior and Systematics
- Structural Biology
- General Agricultural and Biological Sciences
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1186/s12915-019-0733-6
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: BMC Biology
publication_identifier:
issn:
- 1741-7007
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: The mitochondrial carrier pathway transports non-canonical substrates with
an odd number of transmembrane segments
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2020'
...
---
_id: '8529'
abstract:
- lang: eng
text: Practical quantum networks require low-loss and noise-resilient optical interconnects
as well as non-Gaussian resources for entanglement distillation and distributed
quantum computation. The latter could be provided by superconducting circuits
but existing solutions to interface the microwave and optical domains lack either
scalability or efficiency, and in most cases the conversion noise is not known.
In this work we utilize the unique opportunities of silicon photonics, cavity
optomechanics and superconducting circuits to demonstrate a fully integrated,
coherent transducer interfacing the microwave X and the telecom S bands with a
total (internal) bidirectional transduction efficiency of 1.2% (135%) at millikelvin
temperatures. The coupling relies solely on the radiation pressure interaction
mediated by the femtometer-scale motion of two silicon nanobeams reaching a Vπ
as low as 16 μV for sub-nanowatt pump powers. Without the associated optomechanical
gain, we achieve a total (internal) pure conversion efficiency of up to 0.019%
(1.6%), relevant for future noise-free operation on this qubit-compatible platform.
acknowledged_ssus:
- _id: NanoFab
acknowledgement: We thank Yuan Chen for performing supplementary FEM simulations and
Andrew Higginbotham, Ralf Riedinger, Sungkun Hong, and Lorenzo Magrini for valuable
discussions. This work was supported by IST Austria, the IST nanofabrication facility
(NFF), the European Union’s Horizon 2020 research and innovation program under grant
agreement no. 732894 (FET Proactive HOT) and the European Research Council under
grant agreement no. 758053 (ERC StG QUNNECT). G.A. is the recipient of a DOC fellowship
of the Austrian Academy of Sciences at IST Austria. W.H. is the recipient of an
ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020
research and innovation program under the Marie Sklodowska-Curie grant agreement
no. 754411. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through
BeyondC (F71), a NOMIS foundation research grant, and the EU’s Horizon 2020 research
and innovation program under grant agreement no. 862644 (FET Open QUARTET).
article_number: '4460'
article_processing_charge: No
article_type: original
author:
- first_name: Georg M
full_name: Arnold, Georg M
id: 3770C838-F248-11E8-B48F-1D18A9856A87
last_name: Arnold
orcid: 0000-0003-1397-7876
- first_name: Matthias
full_name: Wulf, Matthias
id: 45598606-F248-11E8-B48F-1D18A9856A87
last_name: Wulf
orcid: 0000-0001-6613-1378
- first_name: Shabir
full_name: Barzanjeh, Shabir
id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
last_name: Barzanjeh
orcid: 0000-0003-0415-1423
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
- first_name: Alfredo R
full_name: Rueda Sanchez, Alfredo R
id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87
last_name: Rueda Sanchez
orcid: 0000-0001-6249-5860
- first_name: William J
full_name: Hease, William J
id: 29705398-F248-11E8-B48F-1D18A9856A87
last_name: Hease
orcid: 0000-0001-9868-2166
- first_name: Farid
full_name: Hassani, Farid
id: 2AED110C-F248-11E8-B48F-1D18A9856A87
last_name: Hassani
orcid: 0000-0001-6937-5773
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons
with a silicon photonic nanomechanical interface. Nature Communications.
2020;11. doi:10.1038/s41467-020-18269-z
apa: Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R.,
Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with
a silicon photonic nanomechanical interface. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-020-18269-z
chicago: Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo
R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting
Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.”
Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18269-z.
ieee: G. M. Arnold et al., “Converting microwave and telecom photons with
a silicon photonic nanomechanical interface,” Nature Communications, vol.
11. Springer Nature, 2020.
ista: Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani
F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic
nanomechanical interface. Nature Communications. 11, 4460.
mla: Arnold, Georg M., et al. “Converting Microwave and Telecom Photons with a Silicon
Photonic Nanomechanical Interface.” Nature Communications, vol. 11, 4460,
Springer Nature, 2020, doi:10.1038/s41467-020-18269-z.
short: G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J.
Hease, F. Hassani, J.M. Fink, Nature Communications 11 (2020).
date_created: 2020-09-18T10:56:20Z
date_published: 2020-09-08T00:00:00Z
date_updated: 2023-08-22T09:27:12Z
day: '08'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.1038/s41467-020-18269-z
ec_funded: 1
external_id:
isi:
- '000577280200001'
file:
- access_level: open_access
checksum: 88f92544889eb18bb38e25629a422a86
content_type: application/pdf
creator: dernst
date_created: 2020-09-18T13:02:37Z
date_updated: 2020-09-18T13:02:37Z
file_id: '8530'
file_name: 2020_NatureComm_Arnold.pdf
file_size: 1002818
relation: main_file
success: 1
file_date_updated: 2020-09-18T13:02:37Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 257EB838-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '732894'
name: Hybrid Optomechanical Technologies
- _id: 26336814-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '758053'
name: A Fiber Optic Transceiver for Superconducting Qubits
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 237CBA6C-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '862644'
name: Quantum readout techniques and technologies
- _id: 2671EB66-B435-11E9-9278-68D0E5697425
name: Coherent on-chip conversion of superconducting qubit signals from microwaves
to optical frequencies
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/s41467-020-18912-9
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/how-to-transport-microwave-quantum-information-via-optical-fiber/
record:
- id: '13056'
relation: research_data
status: public
status: public
title: Converting microwave and telecom photons with a silicon photonic nanomechanical
interface
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: '8568'
abstract:
- lang: eng
text: Aqueous iodine based electrochemical energy storage is considered a potential
candidate to improve sustainability and performance of current battery and supercapacitor
technology. It harnesses the redox activity of iodide, iodine, and polyiodide
species in the confined geometry of nanoporous carbon electrodes. However, current
descriptions of the electrochemical reaction mechanism to interconvert these species
are elusive. Here we show that electrochemical oxidation of iodide in nanoporous
carbons forms persistent solid iodine deposits. Confinement slows down dissolution
into triiodide and pentaiodide, responsible for otherwise significant self-discharge
via shuttling. The main tools for these insights are in situ Raman spectroscopy
and in situ small and wide-angle X-ray scattering (in situ SAXS/WAXS). In situ
Raman confirms the reversible formation of triiodide and pentaiodide. In situ
SAXS/WAXS indicates remarkable amounts of solid iodine deposited in the carbon
nanopores. Combined with stochastic modeling, in situ SAXS allows quantifying
the solid iodine volume fraction and visualizing the iodine structure on 3D lattice
models at the sub-nanometer scale. Based on the derived mechanism, we demonstrate
strategies for improved iodine pore filling capacity and prevention of self-discharge,
applicable to hybrid supercapacitors and batteries.
article_number: '4838'
article_processing_charge: No
article_type: original
author:
- first_name: Christian
full_name: Prehal, Christian
last_name: Prehal
- first_name: Harald
full_name: Fitzek, Harald
last_name: Fitzek
- first_name: Gerald
full_name: Kothleitner, Gerald
last_name: Kothleitner
- first_name: Volker
full_name: Presser, Volker
last_name: Presser
- first_name: Bernhard
full_name: Gollas, Bernhard
last_name: Gollas
- 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: Qamar
full_name: Abbas, Qamar
last_name: Abbas
citation:
ama: Prehal C, Fitzek H, Kothleitner G, et al. Persistent and reversible solid iodine
electrodeposition in nanoporous carbons. Nature Communications. 2020;11.
doi:10.1038/s41467-020-18610-6
apa: Prehal, C., Fitzek, H., Kothleitner, G., Presser, V., Gollas, B., Freunberger,
S. A., & Abbas, Q. (2020). Persistent and reversible solid iodine electrodeposition
in nanoporous carbons. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18610-6
chicago: Prehal, Christian, Harald Fitzek, Gerald Kothleitner, Volker Presser, Bernhard
Gollas, Stefan Alexander Freunberger, and Qamar Abbas. “Persistent and Reversible
Solid Iodine Electrodeposition in Nanoporous Carbons.” Nature Communications.
Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18610-6.
ieee: C. Prehal et al., “Persistent and reversible solid iodine electrodeposition
in nanoporous carbons,” Nature Communications, vol. 11. Springer Nature,
2020.
ista: Prehal C, Fitzek H, Kothleitner G, Presser V, Gollas B, Freunberger SA, Abbas
Q. 2020. Persistent and reversible solid iodine electrodeposition in nanoporous
carbons. Nature Communications. 11, 4838.
mla: Prehal, Christian, et al. “Persistent and Reversible Solid Iodine Electrodeposition
in Nanoporous Carbons.” Nature Communications, vol. 11, 4838, Springer
Nature, 2020, doi:10.1038/s41467-020-18610-6.
short: C. Prehal, H. Fitzek, G. Kothleitner, V. Presser, B. Gollas, S.A. Freunberger,
Q. Abbas, Nature Communications 11 (2020).
date_created: 2020-09-25T07:23:13Z
date_published: 2020-09-24T00:00:00Z
date_updated: 2023-08-22T09:37:24Z
day: '24'
ddc:
- '530'
department:
- _id: StFr
doi: 10.1038/s41467-020-18610-6
external_id:
isi:
- '000573756600004'
file:
- access_level: open_access
checksum: eada7bc8dd16a49390137cff882ef328
content_type: application/pdf
creator: dernst
date_created: 2020-09-28T13:16:15Z
date_updated: 2020-09-28T13:16:15Z
file_id: '8585'
file_name: 2020_NatureComm_Prehal.pdf
file_size: 1822469
relation: main_file
success: 1
file_date_updated: 2020-09-28T13:16:15Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
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/s41467-020-19720-x
status: public
title: Persistent and reversible solid iodine electrodeposition in nanoporous carbons
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: '8744'
abstract:
- lang: eng
text: Understanding the conformational sampling of translation-arrested ribosome
nascent chain complexes is key to understand co-translational folding. Up to now,
coupling of cysteine oxidation, disulfide bond formation and structure formation
in nascent chains has remained elusive. Here, we investigate the eye-lens protein
γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical
simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic
resonance and cryo-electron microscopy, we show that thiol groups of cysteine
residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide
bonds. Thus, covalent modification chemistry occurs already prior to nascent chain
release as the ribosome exit tunnel provides sufficient space even for disulfide
bond formation which can guide protein folding.
acknowledgement: 'We acknowledge help from Anja Seybert, Margot Frangakis, Diana Grewe,
Mikhail Eltsov, Utz Ermel, and Shintaro Aibara. The work was supported by Deutsche
Forschungsgemeinschaft in the CLiC graduate school. Work at the Center for Biomolecular
Magnetic Resonance (BMRZ) is supported by the German state of Hesse. The work at
BMRZ has been supported by the state of Hesse. L.S. has been supported by the DFG
graduate college: CLiC.'
article_number: '5569'
article_processing_charge: No
article_type: original
author:
- first_name: Linda
full_name: Schulte, Linda
last_name: Schulte
- first_name: Jiafei
full_name: Mao, Jiafei
last_name: Mao
- first_name: Julian
full_name: Reitz, Julian
last_name: Reitz
- first_name: Sridhar
full_name: Sreeramulu, Sridhar
last_name: Sreeramulu
- first_name: Denis
full_name: Kudlinzki, Denis
last_name: Kudlinzki
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: Jakob
full_name: Meier-Credo, Jakob
last_name: Meier-Credo
- first_name: Krishna
full_name: Saxena, Krishna
last_name: Saxena
- first_name: Florian
full_name: Buhr, Florian
last_name: Buhr
- first_name: Julian D.
full_name: Langer, Julian D.
last_name: Langer
- first_name: Martin
full_name: Blackledge, Martin
last_name: Blackledge
- first_name: Achilleas S.
full_name: Frangakis, Achilleas S.
last_name: Frangakis
- first_name: Clemens
full_name: Glaubitz, Clemens
last_name: Glaubitz
- first_name: Harald
full_name: Schwalbe, Harald
last_name: Schwalbe
citation:
ama: Schulte L, Mao J, Reitz J, et al. Cysteine oxidation and disulfide formation
in the ribosomal exit tunnel. Nature Communications. 2020;11. doi:10.1038/s41467-020-19372-x
apa: Schulte, L., Mao, J., Reitz, J., Sreeramulu, S., Kudlinzki, D., Hodirnau, V.-V.,
… Schwalbe, H. (2020). Cysteine oxidation and disulfide formation in the ribosomal
exit tunnel. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-19372-x
chicago: Schulte, Linda, Jiafei Mao, Julian Reitz, Sridhar Sreeramulu, Denis Kudlinzki,
Victor-Valentin Hodirnau, Jakob Meier-Credo, et al. “Cysteine Oxidation and Disulfide
Formation in the Ribosomal Exit Tunnel.” Nature Communications. Springer
Nature, 2020. https://doi.org/10.1038/s41467-020-19372-x.
ieee: L. Schulte et al., “Cysteine oxidation and disulfide formation in the
ribosomal exit tunnel,” Nature Communications, vol. 11. Springer Nature,
2020.
ista: Schulte L, Mao J, Reitz J, Sreeramulu S, Kudlinzki D, Hodirnau V-V, Meier-Credo
J, Saxena K, Buhr F, Langer JD, Blackledge M, Frangakis AS, Glaubitz C, Schwalbe
H. 2020. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel.
Nature Communications. 11, 5569.
mla: Schulte, Linda, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal
Exit Tunnel.” Nature Communications, vol. 11, 5569, Springer Nature, 2020,
doi:10.1038/s41467-020-19372-x.
short: L. Schulte, J. Mao, J. Reitz, S. Sreeramulu, D. Kudlinzki, V.-V. Hodirnau,
J. Meier-Credo, K. Saxena, F. Buhr, J.D. Langer, M. Blackledge, A.S. Frangakis,
C. Glaubitz, H. Schwalbe, Nature Communications 11 (2020).
date_created: 2020-11-09T07:49:36Z
date_published: 2020-11-04T00:00:00Z
date_updated: 2023-08-22T12:36:07Z
day: '04'
ddc:
- '570'
department:
- _id: EM-Fac
doi: 10.1038/s41467-020-19372-x
external_id:
isi:
- '000592028600001'
file:
- access_level: open_access
checksum: b2688f0347e69e6629bba582077278c5
content_type: application/pdf
creator: dernst
date_created: 2020-11-09T07:56:24Z
date_updated: 2020-11-09T07:56:24Z
file_id: '8745'
file_name: 2020_NatureComm_Schulte.pdf
file_size: 1670898
relation: main_file
success: 1
file_date_updated: 2020-11-09T07:56:24Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
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: Cysteine oxidation and disulfide formation in the ribosomal exit tunnel
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: '8971'
abstract:
- lang: eng
text: The actin-related protein (Arp)2/3 complex nucleates branched actin filament
networks pivotal for cell migration, endocytosis and pathogen infection. Its activation
is tightly regulated and involves complex structural rearrangements and actin
filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution
structure of the actin filament Arp2/3 complex branch junction in cells using
cryo-electron tomography and subtomogram averaging. This allows us to generate
an accurate model of the active Arp2/3 complex in the branch junction and its
interaction with actin filaments. Notably, our model reveals a previously undescribed
set of interactions of the Arp2/3 complex with the mother filament, significantly
different to the previous branch junction model. Our structure also indicates
a central role for the ArpC3 subunit in stabilizing the active conformation.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: Bio
- _id: EM-Fac
acknowledgement: "This research was supported by the Scientific Service Units (SSUs)
of IST Austria through resources provided by Scientific Computing (SciComp), the
Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy
Facility (EMF). We also thank Dimitry Tegunov (MPI for Biophysical Chemistry) for
helpful discussions\r\nabout the M software, and Michael Sixt (IST Austria) and
Klemens Rottner (Technical University Braunschweig, HZI Braunschweig) for critical
reading of the manuscript. We also thank Gregory Voth (University of Chicago) for
providing us the MD-derived branch junction model for comparison. The authors acknowledge
support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D.
and Austrian Science Fund (FWF): P33367 to F.K.M.S. "
article_number: '6437'
article_processing_charge: No
article_type: original
author:
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Georgi A
full_name: Dimchev, Georgi A
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
orcid: 0000-0001-8370-6161
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: William
full_name: Wan, William
last_name: Wan
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. Cryo-electron tomography
structure of Arp2/3 complex in cells reveals new insights into the branch junction.
Nature Communications. 2020;11. doi:10.1038/s41467-020-20286-x
apa: Fäßler, F., Dimchev, G. A., Hodirnau, V.-V., Wan, W., & Schur, F. K. (2020).
Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights
into the branch junction. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-20286-x
chicago: Fäßler, Florian, Georgi A Dimchev, Victor-Valentin Hodirnau, William Wan,
and Florian KM Schur. “Cryo-Electron Tomography Structure of Arp2/3 Complex in
Cells Reveals New Insights into the Branch Junction.” Nature Communications.
Springer Nature, 2020. https://doi.org/10.1038/s41467-020-20286-x.
ieee: F. Fäßler, G. A. Dimchev, V.-V. Hodirnau, W. Wan, and F. K. Schur, “Cryo-electron
tomography structure of Arp2/3 complex in cells reveals new insights into the
branch junction,” Nature Communications, vol. 11. Springer Nature, 2020.
ista: Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. 2020. Cryo-electron tomography
structure of Arp2/3 complex in cells reveals new insights into the branch junction.
Nature Communications. 11, 6437.
mla: Fäßler, Florian, et al. “Cryo-Electron Tomography Structure of Arp2/3 Complex
in Cells Reveals New Insights into the Branch Junction.” Nature Communications,
vol. 11, 6437, Springer Nature, 2020, doi:10.1038/s41467-020-20286-x.
short: F. Fäßler, G.A. Dimchev, V.-V. Hodirnau, W. Wan, F.K. Schur, Nature Communications
11 (2020).
date_created: 2020-12-23T08:25:45Z
date_published: 2020-12-22T00:00:00Z
date_updated: 2023-08-24T11:01:50Z
day: '22'
ddc:
- '570'
department:
- _id: FlSc
- _id: EM-Fac
doi: 10.1038/s41467-020-20286-x
external_id:
isi:
- '000603078000003'
file:
- access_level: open_access
checksum: 55d43ea0061cc4027ba45e966e1db8cc
content_type: application/pdf
creator: dernst
date_created: 2020-12-28T08:16:10Z
date_updated: 2020-12-28T08:16:10Z
file_id: '8975'
file_name: 2020_NatureComm_Faessler.pdf
file_size: 3958727
relation: main_file
success: 1
file_date_updated: 2020-12-28T08:16:10Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
- _id: 2674F658-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02495
name: Protein structure and function in filopodia across scales
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/cutting-edge-technology-reveals-structures-within-cells/
scopus_import: '1'
status: public
title: Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights
into the branch junction
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: '15153'
abstract:
- lang: eng
text: Mammalian circadian rhythms are generated by a transcription-based feedback
loop in which CLOCK:BMAL1 drives transcription of its repressors (PER1/2, CRY1/2),
which ultimately interact with CLOCK:BMAL1 to close the feedback loop with ~24
hr periodicity. Here we pinpoint a key difference between CRY1 and CRY2 that underlies
their differential strengths as transcriptional repressors. Both cryptochromes
bind the BMAL1 transactivation domain similarly to sequester it from coactivators
and repress CLOCK:BMAL1 activity. However, we find that CRY1 is recruited with
much higher affinity to the PAS domain core of CLOCK:BMAL1, allowing it to serve
as a stronger repressor that lengthens circadian period. We discovered a dynamic
serine-rich loop adjacent to the secondary pocket in the photolyase homology region
(PHR) domain that regulates differential binding of cryptochromes to the PAS domain
core of CLOCK:BMAL1. Notably, binding of the co-repressor PER2 remodels the serine
loop of CRY2, making it more CRY1-like and enhancing its affinity for CLOCK:BMAL1.
article_number: '55275'
article_processing_charge: No
article_type: original
author:
- first_name: Jennifer L
full_name: Fribourgh, Jennifer L
last_name: Fribourgh
- first_name: Ashutosh
full_name: Srivastava, Ashutosh
last_name: Srivastava
- first_name: Colby R
full_name: Sandate, Colby R
last_name: Sandate
- first_name: Alicia Kathleen
full_name: Michael, Alicia Kathleen
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
- first_name: Peter L
full_name: Hsu, Peter L
last_name: Hsu
- first_name: Christin
full_name: Rakers, Christin
last_name: Rakers
- first_name: Leslee T
full_name: Nguyen, Leslee T
last_name: Nguyen
- first_name: Megan R
full_name: Torgrimson, Megan R
last_name: Torgrimson
- first_name: Gian Carlo G
full_name: Parico, Gian Carlo G
last_name: Parico
- first_name: Sarvind
full_name: Tripathi, Sarvind
last_name: Tripathi
- first_name: Ning
full_name: Zheng, Ning
last_name: Zheng
- first_name: Gabriel C
full_name: Lander, Gabriel C
last_name: Lander
- first_name: Tsuyoshi
full_name: Hirota, Tsuyoshi
last_name: Hirota
- first_name: Florence
full_name: Tama, Florence
last_name: Tama
- first_name: Carrie L
full_name: Partch, Carrie L
last_name: Partch
citation:
ama: Fribourgh JL, Srivastava A, Sandate CR, et al. Dynamics at the serine loop
underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian
timing. eLife. 2020;9. doi:10.7554/elife.55275
apa: Fribourgh, J. L., Srivastava, A., Sandate, C. R., Michael, A. K., Hsu, P. L.,
Rakers, C., … Partch, C. L. (2020). Dynamics at the serine loop underlie differential
affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing. ELife.
eLife Sciences Publications. https://doi.org/10.7554/elife.55275
chicago: Fribourgh, Jennifer L, Ashutosh Srivastava, Colby R Sandate, Alicia K.
Michael, Peter L Hsu, Christin Rakers, Leslee T Nguyen, et al. “Dynamics at the
Serine Loop Underlie Differential Affinity of Cryptochromes for CLOCK:BMAL1 to
Control Circadian Timing.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.55275.
ieee: J. L. Fribourgh et al., “Dynamics at the serine loop underlie differential
affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing,” eLife,
vol. 9. eLife Sciences Publications, 2020.
ista: Fribourgh JL, Srivastava A, Sandate CR, Michael AK, Hsu PL, Rakers C, Nguyen
LT, Torgrimson MR, Parico GCG, Tripathi S, Zheng N, Lander GC, Hirota T, Tama
F, Partch CL. 2020. Dynamics at the serine loop underlie differential affinity
of cryptochromes for CLOCK:BMAL1 to control circadian timing. eLife. 9, 55275.
mla: Fribourgh, Jennifer L., et al. “Dynamics at the Serine Loop Underlie Differential
Affinity of Cryptochromes for CLOCK:BMAL1 to Control Circadian Timing.” ELife,
vol. 9, 55275, eLife Sciences Publications, 2020, doi:10.7554/elife.55275.
short: J.L. Fribourgh, A. Srivastava, C.R. Sandate, A.K. Michael, P.L. Hsu, C. Rakers,
L.T. Nguyen, M.R. Torgrimson, G.C.G. Parico, S. Tripathi, N. Zheng, G.C. Lander,
T. Hirota, F. Tama, C.L. Partch, ELife 9 (2020).
date_created: 2024-03-21T07:55:12Z
date_published: 2020-02-26T00:00:00Z
date_updated: 2024-03-25T12:25:02Z
day: '26'
doi: 10.7554/elife.55275
extern: '1'
intvolume: ' 9'
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.7554/eLife.55275
month: '02'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamics at the serine loop underlie differential affinity of cryptochromes
for CLOCK:BMAL1 to control circadian timing
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2020'
...
---
_id: '8405'
abstract:
- lang: eng
text: Atomic-resolution structure determination is crucial for understanding protein
function. Cryo-EM and NMR spectroscopy both provide structural information, but
currently cryo-EM does not routinely give access to atomic-level structural data,
and, generally, NMR structure determination is restricted to small (<30 kDa) proteins.
We introduce an integrated structure determination approach that simultaneously
uses NMR and EM data to overcome the limits of each of these methods. The approach
enables structure determination of the 468 kDa large dodecameric aminopeptidase
TET2 to a precision and accuracy below 1 Å by combining secondary-structure information
obtained from near-complete magic-angle-spinning NMR assignments of the 39 kDa-large
subunits, distance restraints from backbone amides and ILV methyl groups, and
a 4.1 Å resolution EM map. The resulting structure exceeds current standards of
NMR and EM structure determination in terms of molecular weight and precision.
Importantly, the approach is successful even in cases where only medium-resolution
cryo-EM data are available.
article_number: '2697'
article_processing_charge: No
article_type: original
author:
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- first_name: Leandro F.
full_name: Estrozi, Leandro F.
last_name: Estrozi
- first_name: Charles D.
full_name: Schwieters, Charles D.
last_name: Schwieters
- first_name: Gregory
full_name: Effantin, Gregory
last_name: Effantin
- first_name: Pavel
full_name: Macek, Pavel
last_name: Macek
- first_name: Remy
full_name: Sounier, Remy
last_name: Sounier
- first_name: Astrid C.
full_name: Sivertsen, Astrid C.
last_name: Sivertsen
- first_name: Elena
full_name: Schmidt, Elena
last_name: Schmidt
- first_name: Rime
full_name: Kerfah, Rime
last_name: Kerfah
- first_name: Guillaume
full_name: Mas, Guillaume
last_name: Mas
- first_name: Jacques-Philippe
full_name: Colletier, Jacques-Philippe
last_name: Colletier
- first_name: Peter
full_name: Güntert, Peter
last_name: Güntert
- first_name: Adrien
full_name: Favier, Adrien
last_name: Favier
- first_name: Guy
full_name: Schoehn, Guy
last_name: Schoehn
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Jerome
full_name: Boisbouvier, Jerome
last_name: Boisbouvier
citation:
ama: Gauto DF, Estrozi LF, Schwieters CD, et al. Integrated NMR and cryo-EM atomic-resolution
structure determination of a half-megadalton enzyme complex. Nature Communications.
2019;10. doi:10.1038/s41467-019-10490-9
apa: Gauto, D. F., Estrozi, L. F., Schwieters, C. D., Effantin, G., Macek, P., Sounier,
R., … Boisbouvier, J. (2019). Integrated NMR and cryo-EM atomic-resolution structure
determination of a half-megadalton enzyme complex. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-019-10490-9
chicago: Gauto, Diego F., Leandro F. Estrozi, Charles D. Schwieters, Gregory Effantin,
Pavel Macek, Remy Sounier, Astrid C. Sivertsen, et al. “Integrated NMR and Cryo-EM
Atomic-Resolution Structure Determination of a Half-Megadalton Enzyme Complex.”
Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-10490-9.
ieee: D. F. Gauto et al., “Integrated NMR and cryo-EM atomic-resolution structure
determination of a half-megadalton enzyme complex,” Nature Communications,
vol. 10. Springer Nature, 2019.
ista: Gauto DF, Estrozi LF, Schwieters CD, Effantin G, Macek P, Sounier R, Sivertsen
AC, Schmidt E, Kerfah R, Mas G, Colletier J-P, Güntert P, Favier A, Schoehn G,
Schanda P, Boisbouvier J. 2019. Integrated NMR and cryo-EM atomic-resolution structure
determination of a half-megadalton enzyme complex. Nature Communications. 10,
2697.
mla: Gauto, Diego F., et al. “Integrated NMR and Cryo-EM Atomic-Resolution Structure
Determination of a Half-Megadalton Enzyme Complex.” Nature Communications,
vol. 10, 2697, Springer Nature, 2019, doi:10.1038/s41467-019-10490-9.
short: D.F. Gauto, L.F. Estrozi, C.D. Schwieters, G. Effantin, P. Macek, R. Sounier,
A.C. Sivertsen, E. Schmidt, R. Kerfah, G. Mas, J.-P. Colletier, P. Güntert, A.
Favier, G. Schoehn, P. Schanda, J. Boisbouvier, Nature Communications 10 (2019).
date_created: 2020-09-17T10:28:25Z
date_published: 2019-06-19T00:00:00Z
date_updated: 2021-01-12T08:19:03Z
day: '19'
doi: 10.1038/s41467-019-10490-9
extern: '1'
external_id:
pmid:
- '31217444'
intvolume: ' 10'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-019-10490-9
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'
status: public
title: Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton
enzyme complex
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2019'
...
---
_id: '9060'
abstract:
- lang: eng
text: Molecular motors are essential to the living, generating fluctuations that
boost transport and assist assembly. Active colloids, that consume energy to move,
hold similar potential for man-made materials controlled by forces generated from
within. Yet, their use as a powerhouse in materials science lacks. Here we show
a massive acceleration of the annealing of a monolayer of passive beads by moderate
addition of self-propelled microparticles. We rationalize our observations with
a model of collisions that drive active fluctuations and activate the annealing.
The experiment is quantitatively compared with Brownian dynamic simulations that
further unveil a dynamical transition in the mechanism of annealing. Active dopants
travel uniformly in the system or co-localize at the grain boundaries as a result
of the persistence of their motion. Our findings uncover the potential of internal
activity to control materials and lay the groundwork for the rise of materials
science beyond equilibrium.
article_number: '3380'
article_processing_charge: No
article_type: original
author:
- first_name: Sophie
full_name: Ramananarivo, Sophie
last_name: Ramananarivo
- first_name: Etienne
full_name: Ducrot, Etienne
last_name: Ducrot
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
citation:
ama: Ramananarivo S, Ducrot E, Palacci JA. Activity-controlled annealing of colloidal
monolayers. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-11362-y
apa: Ramananarivo, S., Ducrot, E., & Palacci, J. A. (2019). Activity-controlled
annealing of colloidal monolayers. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-019-11362-y
chicago: Ramananarivo, Sophie, Etienne Ducrot, and Jérémie A Palacci. “Activity-Controlled
Annealing of Colloidal Monolayers.” Nature Communications. Springer Nature,
2019. https://doi.org/10.1038/s41467-019-11362-y.
ieee: S. Ramananarivo, E. Ducrot, and J. A. Palacci, “Activity-controlled annealing
of colloidal monolayers,” Nature Communications, vol. 10, no. 1. Springer
Nature, 2019.
ista: Ramananarivo S, Ducrot E, Palacci JA. 2019. Activity-controlled annealing
of colloidal monolayers. Nature Communications. 10(1), 3380.
mla: Ramananarivo, Sophie, et al. “Activity-Controlled Annealing of Colloidal Monolayers.”
Nature Communications, vol. 10, no. 1, 3380, Springer Nature, 2019, doi:10.1038/s41467-019-11362-y.
short: S. Ramananarivo, E. Ducrot, J.A. Palacci, Nature Communications 10 (2019).
date_created: 2021-02-02T13:43:36Z
date_published: 2019-07-29T00:00:00Z
date_updated: 2023-02-23T13:47:59Z
day: '29'
ddc:
- '530'
doi: 10.1038/s41467-019-11362-y
extern: '1'
external_id:
arxiv:
- '1909.07382'
pmid:
- '31358762'
file:
- access_level: open_access
checksum: 70c6e5d6fbea0932b0669505ab6633ec
content_type: application/pdf
creator: cziletti
date_created: 2021-02-02T13:47:21Z
date_updated: 2021-02-02T13:47:21Z
file_id: '9061'
file_name: 2019_NatureComm_Ramananarivo.pdf
file_size: 2820337
relation: main_file
success: 1
file_date_updated: 2021-02-02T13:47:21Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
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: Activity-controlled annealing of colloidal monolayers
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: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 10
year: '2019'
...
---
_id: '12192'
abstract:
- lang: eng
text: Transposable elements (TEs), the movement of which can damage the genome,
are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in
the sperm companion cell – vegetative cell (VC) – of the flowering plant Arabidopsis
thaliana. However, the extent and mechanism of this activation are unknown. Here
we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed
DNA demethylation. We further demonstrate that DEMETER access to some of these
TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically
expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent
mechanism. We demonstrate that H1 is required for heterochromatin condensation
in plant cells and show that H1 overexpression creates heterochromatic foci in
the VC progenitor cell. Taken together, our results demonstrate that the natural
depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation,
heterochromatin relaxation, and TE activation.
acknowledgement: We thank David Twell for the pDONR-P4-P1R-pLAT52 and pDONR-P2R-P3-mRFP
vectors, the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder)
for their assistance with microscopy, and the Norwich BioScience Institute Partnership
Computing infrastructure for Science Group for High Performance Computing resources.
This work was funded by a Biotechnology and Biological Sciences Research Council
(BBSRC) David Phillips Fellowship (BB/L025043/1; SH, JZ and XF), a European Research
Council Starting Grant ('SexMeth' 804981; XF) and a Grant to Exceptional Researchers
by the Gatsby Charitable Foundation (SH and XF).
article_number: '42530'
article_processing_charge: No
article_type: original
author:
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: Jingyi
full_name: Zhang, Jingyi
last_name: Zhang
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: He S, Vickers M, Zhang J, Feng X. Natural depletion of histone H1 in sex cells
causes DNA demethylation, heterochromatin decondensation and transposon activation.
eLife. 2019;8. doi:10.7554/elife.42530
apa: He, S., Vickers, M., Zhang, J., & Feng, X. (2019). Natural depletion of
histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation
and transposon activation. ELife. eLife Sciences Publications, Ltd. https://doi.org/10.7554/elife.42530
chicago: He, Shengbo, Martin Vickers, Jingyi Zhang, and Xiaoqi Feng. “Natural Depletion
of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation
and Transposon Activation.” ELife. eLife Sciences Publications, Ltd, 2019.
https://doi.org/10.7554/elife.42530.
ieee: S. He, M. Vickers, J. Zhang, and X. Feng, “Natural depletion of histone H1
in sex cells causes DNA demethylation, heterochromatin decondensation and transposon
activation,” eLife, vol. 8. eLife Sciences Publications, Ltd, 2019.
ista: He S, Vickers M, Zhang J, Feng X. 2019. Natural depletion of histone H1 in
sex cells causes DNA demethylation, heterochromatin decondensation and transposon
activation. eLife. 8, 42530.
mla: He, Shengbo, et al. “Natural Depletion of Histone H1 in Sex Cells Causes DNA
Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife,
vol. 8, 42530, eLife Sciences Publications, Ltd, 2019, doi:10.7554/elife.42530.
short: S. He, M. Vickers, J. Zhang, X. Feng, ELife 8 (2019).
date_created: 2023-01-16T09:17:21Z
date_published: 2019-05-28T00:00:00Z
date_updated: 2023-05-08T10:54:12Z
day: '28'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.7554/elife.42530
extern: '1'
external_id:
unknown:
- '31135340'
file:
- access_level: open_access
checksum: ea6b89c20d59e5eb3646916fe5d568ad
content_type: application/pdf
creator: alisjak
date_created: 2023-02-07T09:42:46Z
date_updated: 2023-02-07T09:42:46Z
file_id: '12525'
file_name: 2019_elife_He.pdf
file_size: 2493837
relation: main_file
success: 1
file_date_updated: 2023-02-07T09:42:46Z
has_accepted_license: '1'
intvolume: ' 8'
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6594752/
month: '05'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications, Ltd
quality_controlled: '1'
scopus_import: '1'
status: public
title: Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin
decondensation and transposon 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2019'
...
---
_id: '12190'
abstract:
- lang: eng
text: Meiotic crossover frequency varies within genomes, which influences genetic
diversity and adaptation. In turn, genetic variation within populations can act
to modify crossover frequency in cis and trans. To identify genetic variation
that controls meiotic crossover frequency, we screened Arabidopsis accessions
using fluorescent recombination reporters. We mapped a genetic modifier of crossover
frequency in Col × Bur populations of Arabidopsis to a premature stop codon within
TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase
II general transcription factor TFIID. The Arabidopsis taf4b mutation is a rare
variant found in the British Isles, originating in South-West Ireland. Using genetics,
genomics, and immunocytology, we demonstrate a genome-wide decrease in taf4b crossovers,
with strongest reduction in the sub-telomeric regions. Using RNA sequencing (RNA-seq)
from purified meiocytes, we show that TAF4b expression is meiocyte enriched, whereas
its paralog TAF4 is broadly expressed. Consistent with the role of TFIID in promoting
gene expression, RNA-seq of wild-type and taf4b meiocytes identified widespread
transcriptional changes, including in genes that regulate the meiotic cell cycle
and recombination. Therefore, TAF4b duplication is associated with acquisition
of meiocyte-specific expression and promotion of germline transcription, which
act directly or indirectly to elevate crossovers. This identifies a novel mode
of meiotic recombination control via a general transcription factor.
acknowledgement: "We thank Gregory Copenhaver (University of North Carolina), Avraham
Levy (The Weizmann Institute), and Scott Poethig (University of Pennsylvania) for
FTLs; Piotr Ziolkowski for Col-420/Bur seed; Sureshkumar Balasubramanian\r\n(Monash
University) for providing British and Irish Arabidopsis accessions; Mathilde Grelon
(INRA, Versailles) for providing the MLH1 antibody; and the Gurdon Institute for
access to microscopes. This work was supported by a BBSRC DTP studentship (E.J.L.),
European Research Area Network for Coordinating Action in Plant Sciences/BBSRC ‘‘DeCOP’’
(BB/M004937/1; C.L.), a BBSRC David Phillips Fellowship (BB/L025043/1; H.G. and
X.F.), the European Research Council (CoG ‘‘SynthHotspot,’’ A.J.T., C.L., and I.R.H.;
StG ‘‘SexMeth,’’ X.F.), and a Sainsbury Charitable Foundation Studentship (A.R.B.)."
article_processing_charge: No
article_type: original
author:
- first_name: Emma J.
full_name: Lawrence, Emma J.
last_name: Lawrence
- first_name: Hongbo
full_name: Gao, Hongbo
last_name: Gao
- first_name: Andrew J.
full_name: Tock, Andrew J.
last_name: Tock
- first_name: Christophe
full_name: Lambing, Christophe
last_name: Lambing
- first_name: Alexander R.
full_name: Blackwell, Alexander R.
last_name: Blackwell
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Ian R.
full_name: Henderson, Ian R.
last_name: Henderson
citation:
ama: Lawrence EJ, Gao H, Tock AJ, et al. Natural variation in TBP-ASSOCIATED FACTOR
4b controls meiotic crossover and germline transcription in Arabidopsis. Current
Biology. 2019;29(16):2676-2686.e3. doi:10.1016/j.cub.2019.06.084
apa: Lawrence, E. J., Gao, H., Tock, A. J., Lambing, C., Blackwell, A. R., Feng,
X., & Henderson, I. R. (2019). Natural variation in TBP-ASSOCIATED FACTOR
4b controls meiotic crossover and germline transcription in Arabidopsis. Current
Biology. Elsevier BV. https://doi.org/10.1016/j.cub.2019.06.084
chicago: Lawrence, Emma J., Hongbo Gao, Andrew J. Tock, Christophe Lambing, Alexander
R. Blackwell, Xiaoqi Feng, and Ian R. Henderson. “Natural Variation in TBP-ASSOCIATED
FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.”
Current Biology. Elsevier BV, 2019. https://doi.org/10.1016/j.cub.2019.06.084.
ieee: E. J. Lawrence et al., “Natural variation in TBP-ASSOCIATED FACTOR
4b controls meiotic crossover and germline transcription in Arabidopsis,” Current
Biology, vol. 29, no. 16. Elsevier BV, p. 2676–2686.e3, 2019.
ista: Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR.
2019. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover
and germline transcription in Arabidopsis. Current Biology. 29(16), 2676–2686.e3.
mla: Lawrence, Emma J., et al. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls
Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology,
vol. 29, no. 16, Elsevier BV, 2019, p. 2676–2686.e3, doi:10.1016/j.cub.2019.06.084.
short: E.J. Lawrence, H. Gao, A.J. Tock, C. Lambing, A.R. Blackwell, X. Feng, I.R.
Henderson, Current Biology 29 (2019) 2676–2686.e3.
date_created: 2023-01-16T09:16:33Z
date_published: 2019-08-19T00:00:00Z
date_updated: 2023-05-08T10:54:54Z
day: '19'
department:
- _id: XiFe
doi: 10.1016/j.cub.2019.06.084
extern: '1'
external_id:
pmid:
- '31378616'
intvolume: ' 29'
issue: '16'
keyword:
- General Agricultural and Biological Sciences
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '08'
oa_version: None
page: 2676-2686.e3
pmid: 1
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Elsevier BV
quality_controlled: '1'
scopus_import: '1'
status: public
title: Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and
germline transcription in Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2019'
...
---
_id: '11060'
abstract:
- lang: eng
text: The inner nuclear membrane (INM) is a subdomain of the endoplasmic reticulum
(ER) that is gated by the nuclear pore complex. It is unknown whether proteins
of the INM and ER are degraded through shared or distinct pathways in mammalian
cells. We applied dynamic proteomics to profile protein half-lives and report
that INM and ER residents turn over at similar rates, indicating that the INM’s
unique topology is not a barrier to turnover. Using a microscopy approach, we
observed that the proteasome can degrade INM proteins in situ. However, we also
uncovered evidence for selective, vesicular transport-mediated turnover of a single
INM protein, emerin, that is potentiated by ER stress. Emerin is rapidly cleared
from the INM by a mechanism that requires emerin’s LEM domain to mediate vesicular
trafficking to lysosomes. This work demonstrates that the INM can be dynamically
remodeled in response to environmental inputs.
article_number: e49796
article_processing_charge: No
article_type: original
author:
- first_name: Abigail
full_name: Buchwalter, Abigail
last_name: Buchwalter
- first_name: Roberta
full_name: Schulte, Roberta
last_name: Schulte
- first_name: Hsiao
full_name: Tsai, Hsiao
last_name: Tsai
- first_name: Juliana
full_name: Capitanio, Juliana
last_name: Capitanio
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. Selective clearance
of the inner nuclear membrane protein emerin by vesicular transport during ER
stress. eLife. 2019;8. doi:10.7554/elife.49796
apa: Buchwalter, A., Schulte, R., Tsai, H., Capitanio, J., & Hetzer, M. (2019).
Selective clearance of the inner nuclear membrane protein emerin by vesicular
transport during ER stress. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.49796
chicago: Buchwalter, Abigail, Roberta Schulte, Hsiao Tsai, Juliana Capitanio, and
Martin Hetzer. “Selective Clearance of the Inner Nuclear Membrane Protein Emerin
by Vesicular Transport during ER Stress.” ELife. eLife Sciences Publications,
2019. https://doi.org/10.7554/elife.49796.
ieee: A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, and M. Hetzer, “Selective
clearance of the inner nuclear membrane protein emerin by vesicular transport
during ER stress,” eLife, vol. 8. eLife Sciences Publications, 2019.
ista: Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. 2019. Selective clearance
of the inner nuclear membrane protein emerin by vesicular transport during ER
stress. eLife. 8, e49796.
mla: Buchwalter, Abigail, et al. “Selective Clearance of the Inner Nuclear Membrane
Protein Emerin by Vesicular Transport during ER Stress.” ELife, vol. 8,
e49796, eLife Sciences Publications, 2019, doi:10.7554/elife.49796.
short: A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, M. Hetzer, ELife 8 (2019).
date_created: 2022-04-07T07:45:02Z
date_published: 2019-10-10T00:00:00Z
date_updated: 2023-05-31T06:36:22Z
day: '10'
ddc:
- '570'
doi: 10.7554/elife.49796
extern: '1'
external_id:
pmid:
- '31599721'
file:
- access_level: open_access
checksum: 1e8672a1e9c3dc0a2d3d0dad89673616
content_type: application/pdf
creator: dernst
date_created: 2022-04-08T08:18:01Z
date_updated: 2022-04-08T08:18:01Z
file_id: '11138'
file_name: 2019_eLife_Buchwalter.pdf
file_size: 6984654
relation: main_file
success: 1
file_date_updated: 2022-04-08T08:18:01Z
has_accepted_license: '1'
intvolume: ' 8'
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
record:
- id: '13079'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Selective clearance of the inner nuclear membrane protein emerin by vesicular
transport during ER stress
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: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 8
year: '2019'
...
---
_id: '8436'
abstract:
- lang: eng
text: The exchange of metabolites between the mitochondrial matrix and the cytosol
depends on β-barrel channels in the outer membrane and α-helical carrier proteins
in the inner membrane. The essential translocase of the inner membrane (TIM) chaperones
escort these proteins through the intermembrane space, but the structural and
mechanistic details remain elusive. We have used an integrated structural biology
approach to reveal the functional principle of TIM chaperones. Multiple clamp-like
binding sites hold the mitochondrial membrane proteins in a translocation-competent
elongated form, thus mimicking characteristics of co-translational membrane insertion.
The bound preprotein undergoes conformational dynamics within the chaperone binding
clefts, pointing to a multitude of dynamic local binding events. Mutations in
these binding sites cause cell death or growth defects associated with impairment
of carrier and β-barrel protein biogenesis. Our work reveals how a single mitochondrial
“transfer-chaperone” system is able to guide α-helical and β-barrel membrane proteins
in a “nascent chain-like” conformation through a ribosome-free compartment.
article_processing_charge: No
article_type: original
author:
- first_name: Katharina
full_name: Weinhäupl, Katharina
last_name: Weinhäupl
- first_name: Caroline
full_name: Lindau, Caroline
last_name: Lindau
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: Yong
full_name: Wang, Yong
last_name: Wang
- first_name: Conny
full_name: Schütze, Conny
last_name: Schütze
- first_name: Tobias
full_name: Jores, Tobias
last_name: Jores
- first_name: Laura
full_name: Melchionda, Laura
last_name: Melchionda
- first_name: Birgit
full_name: Schönfisch, Birgit
last_name: Schönfisch
- first_name: Hubert
full_name: Kalbacher, Hubert
last_name: Kalbacher
- first_name: Beate
full_name: Bersch, Beate
last_name: Bersch
- first_name: Doron
full_name: Rapaport, Doron
last_name: Rapaport
- first_name: Martha
full_name: Brennich, Martha
last_name: Brennich
- first_name: Kresten
full_name: Lindorff-Larsen, Kresten
last_name: Lindorff-Larsen
- first_name: Nils
full_name: Wiedemann, Nils
last_name: Wiedemann
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Weinhäupl K, Lindau C, Hessel A, et al. Structural basis of membrane protein
chaperoning through the mitochondrial intermembrane space. Cell. 2018;175(5):1365-1379.e25.
doi:10.1016/j.cell.2018.10.039
apa: Weinhäupl, K., Lindau, C., Hessel, A., Wang, Y., Schütze, C., Jores, T., …
Schanda, P. (2018). Structural basis of membrane protein chaperoning through the
mitochondrial intermembrane space. Cell. Elsevier. https://doi.org/10.1016/j.cell.2018.10.039
chicago: Weinhäupl, Katharina, Caroline Lindau, Audrey Hessel, Yong Wang, Conny
Schütze, Tobias Jores, Laura Melchionda, et al. “Structural Basis of Membrane
Protein Chaperoning through the Mitochondrial Intermembrane Space.” Cell.
Elsevier, 2018. https://doi.org/10.1016/j.cell.2018.10.039.
ieee: K. Weinhäupl et al., “Structural basis of membrane protein chaperoning
through the mitochondrial intermembrane space,” Cell, vol. 175, no. 5.
Elsevier, p. 1365–1379.e25, 2018.
ista: Weinhäupl K, Lindau C, Hessel A, Wang Y, Schütze C, Jores T, Melchionda L,
Schönfisch B, Kalbacher H, Bersch B, Rapaport D, Brennich M, Lindorff-Larsen K,
Wiedemann N, Schanda P. 2018. Structural basis of membrane protein chaperoning
through the mitochondrial intermembrane space. Cell. 175(5), 1365–1379.e25.
mla: Weinhäupl, Katharina, et al. “Structural Basis of Membrane Protein Chaperoning
through the Mitochondrial Intermembrane Space.” Cell, vol. 175, no. 5,
Elsevier, 2018, p. 1365–1379.e25, doi:10.1016/j.cell.2018.10.039.
short: K. Weinhäupl, C. Lindau, A. Hessel, Y. Wang, C. Schütze, T. Jores, L. Melchionda,
B. Schönfisch, H. Kalbacher, B. Bersch, D. Rapaport, M. Brennich, K. Lindorff-Larsen,
N. Wiedemann, P. Schanda, Cell 175 (2018) 1365–1379.e25.
date_created: 2020-09-18T10:04:39Z
date_published: 2018-11-15T00:00:00Z
date_updated: 2021-01-12T08:19:15Z
day: '15'
doi: 10.1016/j.cell.2018.10.039
extern: '1'
intvolume: ' 175'
issue: '5'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '11'
oa_version: None
page: 1365-1379.e25
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Structural basis of membrane protein chaperoning through the mitochondrial
intermembrane space
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 175
year: '2018'
...
---
_id: '13374'
abstract:
- lang: eng
text: Confining molecules to volumes only slightly larger than the molecules themselves
can profoundly alter their properties. Molecular switches—entities that can be
toggled between two or more forms upon exposure to an external stimulus—often
require conformational freedom to isomerize. Therefore, placing these switches
in confined spaces can render them non-operational. To preserve the switchability
of these species under confinement, we work with a water-soluble coordination
cage that is flexible enough to adapt its shape to the conformation of the encapsulated
guest. We show that owing to its flexibility, the cage is not only capable of
accommodating—and solubilizing in water—several light-responsive spiropyran-based
molecular switches, but, more importantly, it also provides an environment suitable
for the efficient, reversible photoisomerization of the bound guests. Our findings
pave the way towards studying various molecular switching processes in confined
environments.
article_number: '641'
article_processing_charge: No
article_type: original
author:
- first_name: Dipak
full_name: Samanta, Dipak
last_name: Samanta
- first_name: Daria
full_name: Galaktionova, Daria
last_name: Galaktionova
- first_name: Julius
full_name: Gemen, Julius
last_name: Gemen
- first_name: Linda J. W.
full_name: Shimon, Linda J. W.
last_name: Shimon
- first_name: Yael
full_name: Diskin-Posner, Yael
last_name: Diskin-Posner
- first_name: Liat
full_name: Avram, Liat
last_name: Avram
- first_name: Petr
full_name: Král, Petr
last_name: Král
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Samanta D, Galaktionova D, Gemen J, et al. Reversible chromism of spiropyran
in the cavity of a flexible coordination cage. Nature Communications. 2018;9.
doi:10.1038/s41467-017-02715-6
apa: Samanta, D., Galaktionova, D., Gemen, J., Shimon, L. J. W., Diskin-Posner,
Y., Avram, L., … Klajn, R. (2018). Reversible chromism of spiropyran in the cavity
of a flexible coordination cage. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-017-02715-6
chicago: Samanta, Dipak, Daria Galaktionova, Julius Gemen, Linda J. W. Shimon, Yael
Diskin-Posner, Liat Avram, Petr Král, and Rafal Klajn. “Reversible Chromism of
Spiropyran in the Cavity of a Flexible Coordination Cage.” Nature Communications.
Springer Nature, 2018. https://doi.org/10.1038/s41467-017-02715-6.
ieee: D. Samanta et al., “Reversible chromism of spiropyran in the cavity
of a flexible coordination cage,” Nature Communications, vol. 9. Springer
Nature, 2018.
ista: Samanta D, Galaktionova D, Gemen J, Shimon LJW, Diskin-Posner Y, Avram L,
Král P, Klajn R. 2018. Reversible chromism of spiropyran in the cavity of a flexible
coordination cage. Nature Communications. 9, 641.
mla: Samanta, Dipak, et al. “Reversible Chromism of Spiropyran in the Cavity of
a Flexible Coordination Cage.” Nature Communications, vol. 9, 641, Springer
Nature, 2018, doi:10.1038/s41467-017-02715-6.
short: D. Samanta, D. Galaktionova, J. Gemen, L.J.W. Shimon, Y. Diskin-Posner, L.
Avram, P. Král, R. Klajn, Nature Communications 9 (2018).
date_created: 2023-08-01T09:39:32Z
date_published: 2018-02-13T00:00:00Z
date_updated: 2023-08-07T10:54:05Z
day: '13'
doi: 10.1038/s41467-017-02715-6
extern: '1'
external_id:
pmid:
- '29440687'
intvolume: ' 9'
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/s41467-017-02715-6
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41467-018-03701-2
scopus_import: '1'
status: public
title: Reversible chromism of spiropyran in the cavity of a flexible coordination
cage
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2018'
...
---
_id: '14284'
abstract:
- lang: eng
text: Pore-forming toxins (PFT) are virulence factors that transform from soluble
to membrane-bound states. The Yersinia YaxAB system represents a family of binary
α-PFTs with orthologues in human, insect, and plant pathogens, with unknown structures.
YaxAB was shown to be cytotoxic and likely involved in pathogenesis, though the
molecular basis for its two-component lytic mechanism remains elusive. Here, we
present crystal structures of YaxA and YaxB, together with a cryo-electron microscopy
map of the YaxAB complex. Our structures reveal a pore predominantly composed
of decamers of YaxA–YaxB heterodimers. Both subunits bear membrane-active moieties,
but only YaxA is capable of binding to membranes by itself. YaxB can subsequently
be recruited to membrane-associated YaxA and induced to present its lytic transmembrane
helices. Pore formation can progress by further oligomerization of YaxA–YaxB dimers.
Our results allow for a comparison between pore assemblies belonging to the wider
ClyA-like family of α-PFTs, highlighting diverse pore architectures.
article_number: '1806'
article_processing_charge: No
article_type: original
author:
- first_name: Bastian
full_name: Bräuning, Bastian
last_name: Bräuning
- first_name: Eva
full_name: Bertosin, Eva
last_name: Bertosin
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Christian
full_name: Ihling, Christian
last_name: Ihling
- first_name: Alexandra
full_name: Schatt, Alexandra
last_name: Schatt
- first_name: Agnes
full_name: Adler, Agnes
last_name: Adler
- first_name: Klaus
full_name: Richter, Klaus
last_name: Richter
- first_name: Andrea
full_name: Sinz, Andrea
last_name: Sinz
- first_name: Hendrik
full_name: Dietz, Hendrik
last_name: Dietz
- first_name: Michael
full_name: Groll, Michael
last_name: Groll
citation:
ama: Bräuning B, Bertosin E, Praetorius FM, et al. Structure and mechanism of the
two-component α-helical pore-forming toxin YaxAB. Nature Communications.
2018;9. doi:10.1038/s41467-018-04139-2
apa: Bräuning, B., Bertosin, E., Praetorius, F. M., Ihling, C., Schatt, A., Adler,
A., … Groll, M. (2018). Structure and mechanism of the two-component α-helical
pore-forming toxin YaxAB. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-04139-2
chicago: Bräuning, Bastian, Eva Bertosin, Florian M Praetorius, Christian Ihling,
Alexandra Schatt, Agnes Adler, Klaus Richter, Andrea Sinz, Hendrik Dietz, and
Michael Groll. “Structure and Mechanism of the Two-Component α-Helical Pore-Forming
Toxin YaxAB.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-04139-2.
ieee: B. Bräuning et al., “Structure and mechanism of the two-component α-helical
pore-forming toxin YaxAB,” Nature Communications, vol. 9. Springer Nature,
2018.
ista: Bräuning B, Bertosin E, Praetorius FM, Ihling C, Schatt A, Adler A, Richter
K, Sinz A, Dietz H, Groll M. 2018. Structure and mechanism of the two-component
α-helical pore-forming toxin YaxAB. Nature Communications. 9, 1806.
mla: Bräuning, Bastian, et al. “Structure and Mechanism of the Two-Component α-Helical
Pore-Forming Toxin YaxAB.” Nature Communications, vol. 9, 1806, Springer
Nature, 2018, doi:10.1038/s41467-018-04139-2.
short: B. Bräuning, E. Bertosin, F.M. Praetorius, C. Ihling, A. Schatt, A. Adler,
K. Richter, A. Sinz, H. Dietz, M. Groll, Nature Communications 9 (2018).
date_created: 2023-09-06T12:07:33Z
date_published: 2018-05-04T00:00:00Z
date_updated: 2023-11-07T11:46:12Z
day: '04'
doi: 10.1038/s41467-018-04139-2
extern: '1'
external_id:
pmid:
- '29728606'
intvolume: ' 9'
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/s41467-018-04139-2
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: Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2018'
...
---
_id: '10370'
abstract:
- lang: eng
text: Eukaryotic cells are densely packed with macromolecular complexes and intertwining
organelles, continually transported and reshaped. Intriguingly, organelles avoid
clashing and entangling with each other in such limited space. Mitochondria form
extensive networks constantly remodeled by fission and fusion. Here, we show that
mitochondrial fission is triggered by mechanical forces. Mechano-stimulation of
mitochondria – via encounter with motile intracellular pathogens, via external
pressure applied by an atomic force microscope, or via cell migration across uneven
microsurfaces – results in the recruitment of the mitochondrial fission machinery,
and subsequent division. We propose that MFF, owing to affinity for narrow mitochondria,
acts as a membrane-bound force sensor to recruit the fission machinery to mechanically
strained sites. Thus, mitochondria adapt to the environment by sensing and responding
to biomechanical cues. Our findings that mechanical triggers can be coupled to
biochemical responses in membrane dynamics may explain how organelles orderly
cohabit in the crowded cytoplasm.
article_number: e30292
article_processing_charge: No
article_type: original
author:
- first_name: Sebastian Carsten Johannes
full_name: Helle, Sebastian Carsten Johannes
last_name: Helle
- first_name: Qian
full_name: Feng, Qian
last_name: Feng
- first_name: Mathias J
full_name: Aebersold, Mathias J
last_name: Aebersold
- first_name: Luca
full_name: Hirt, Luca
last_name: Hirt
- first_name: Raphael R
full_name: Grüter, Raphael R
last_name: Grüter
- first_name: Afshin
full_name: Vahid, Afshin
last_name: Vahid
- first_name: Andrea
full_name: Sirianni, Andrea
last_name: Sirianni
- first_name: Serge
full_name: Mostowy, Serge
last_name: Mostowy
- first_name: Jess G
full_name: Snedeker, Jess G
last_name: Snedeker
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Timon
full_name: Idema, Timon
last_name: Idema
- first_name: Tomaso
full_name: Zambelli, Tomaso
last_name: Zambelli
- first_name: Benoît
full_name: Kornmann, Benoît
last_name: Kornmann
citation:
ama: Helle SCJ, Feng Q, Aebersold MJ, et al. Mechanical force induces mitochondrial
fission. eLife. 2017;6. doi:10.7554/elife.30292
apa: Helle, S. C. J., Feng, Q., Aebersold, M. J., Hirt, L., Grüter, R. R., Vahid,
A., … Kornmann, B. (2017). Mechanical force induces mitochondrial fission. ELife.
eLife Sciences Publications. https://doi.org/10.7554/elife.30292
chicago: Helle, Sebastian Carsten Johannes, Qian Feng, Mathias J Aebersold, Luca
Hirt, Raphael R Grüter, Afshin Vahid, Andrea Sirianni, et al. “Mechanical Force
Induces Mitochondrial Fission.” ELife. eLife Sciences Publications, 2017.
https://doi.org/10.7554/elife.30292.
ieee: S. C. J. Helle et al., “Mechanical force induces mitochondrial fission,”
eLife, vol. 6. eLife Sciences Publications, 2017.
ista: Helle SCJ, Feng Q, Aebersold MJ, Hirt L, Grüter RR, Vahid A, Sirianni A, Mostowy
S, Snedeker JG, Šarić A, Idema T, Zambelli T, Kornmann B. 2017. Mechanical force
induces mitochondrial fission. eLife. 6, e30292.
mla: Helle, Sebastian Carsten Johannes, et al. “Mechanical Force Induces Mitochondrial
Fission.” ELife, vol. 6, e30292, eLife Sciences Publications, 2017, doi:10.7554/elife.30292.
short: S.C.J. Helle, Q. Feng, M.J. Aebersold, L. Hirt, R.R. Grüter, A. Vahid, A.
Sirianni, S. Mostowy, J.G. Snedeker, A. Šarić, T. Idema, T. Zambelli, B. Kornmann,
ELife 6 (2017).
date_created: 2021-11-29T08:51:38Z
date_published: 2017-11-09T00:00:00Z
date_updated: 2021-11-29T09:28:14Z
day: '09'
ddc:
- '572'
doi: 10.7554/elife.30292
extern: '1'
external_id:
pmid:
- '29119945'
file:
- access_level: open_access
checksum: c35f42dcfb007f6d6c761a27e24c26d3
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-29T09:07:41Z
date_updated: 2021-11-29T09:07:41Z
file_id: '10372'
file_name: 2017_eLife_Helle.pdf
file_size: 6120157
relation: main_file
success: 1
file_date_updated: 2021-11-29T09:07:41Z
has_accepted_license: '1'
intvolume: ' 6'
keyword:
- general immunology and microbiology
- general biochemistry
- genetics and molecular biology
- general medicine
- general neuroscience
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://elifesciences.org/articles/30292
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanical force induces mitochondrial fission
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 6
year: '2017'
...
---
_id: '11065'
abstract:
- lang: eng
text: Premature aging disorders provide an opportunity to study the mechanisms that
drive aging. In Hutchinson-Gilford progeria syndrome (HGPS), a mutant form of
the nuclear scaffold protein lamin A distorts nuclei and sequesters nuclear proteins.
We sought to investigate protein homeostasis in this disease. Here, we report
a widespread increase in protein turnover in HGPS-derived cells compared to normal
cells. We determine that global protein synthesis is elevated as a consequence
of activated nucleoli and enhanced ribosome biogenesis in HGPS-derived fibroblasts.
Depleting normal lamin A or inducing mutant lamin A expression are each sufficient
to drive nucleolar expansion. We further show that nucleolar size correlates with
donor age in primary fibroblasts derived from healthy individuals and that ribosomal
RNA production increases with age, indicating that nucleolar size and activity
can serve as aging biomarkers. While limiting ribosome biogenesis extends lifespan
in several systems, we show that increased ribosome biogenesis and activity are
a hallmark of premature aging.
article_number: '328'
article_processing_charge: No
article_type: original
author:
- first_name: Abigail
full_name: Buchwalter, Abigail
last_name: Buchwalter
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Buchwalter A, Hetzer M. Nucleolar expansion and elevated protein translation
in premature aging. Nature Communications. 2017;8. doi:10.1038/s41467-017-00322-z
apa: Buchwalter, A., & Hetzer, M. (2017). Nucleolar expansion and elevated protein
translation in premature aging. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-017-00322-z
chicago: Buchwalter, Abigail, and Martin Hetzer. “Nucleolar Expansion and Elevated
Protein Translation in Premature Aging.” Nature Communications. Springer
Nature, 2017. https://doi.org/10.1038/s41467-017-00322-z.
ieee: A. Buchwalter and M. Hetzer, “Nucleolar expansion and elevated protein translation
in premature aging,” Nature Communications, vol. 8. Springer Nature, 2017.
ista: Buchwalter A, Hetzer M. 2017. Nucleolar expansion and elevated protein translation
in premature aging. Nature Communications. 8, 328.
mla: Buchwalter, Abigail, and Martin Hetzer. “Nucleolar Expansion and Elevated Protein
Translation in Premature Aging.” Nature Communications, vol. 8, 328, Springer
Nature, 2017, doi:10.1038/s41467-017-00322-z.
short: A. Buchwalter, M. Hetzer, Nature Communications 8 (2017).
date_created: 2022-04-07T07:45:50Z
date_published: 2017-08-30T00:00:00Z
date_updated: 2022-07-18T08:33:03Z
day: '30'
doi: 10.1038/s41467-017-00322-z
extern: '1'
external_id:
pmid:
- '28855503'
intvolume: ' 8'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-017-00322-z
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: Nucleolar expansion and elevated protein translation in premature aging
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 8
year: '2017'
...
---
_id: '14005'
abstract:
- lang: eng
text: Strong-field photoelectron holography and laser-induced electron diffraction
(LIED) are two powerful emerging methods for probing the ultrafast dynamics of
molecules. However, both of them have remained restricted to static systems and
to nuclear dynamics induced by strong-field ionization. Here we extend these promising
methods to image purely electronic valence-shell dynamics in molecules using photoelectron
holography. In the same experiment, we use LIED and photoelectron holography simultaneously,
to observe coupled electronic-rotational dynamics taking place on similar timescales.
These results offer perspectives for imaging ultrafast dynamics of molecules on
femtosecond to attosecond timescales.
article_number: '15651'
article_processing_charge: No
article_type: original
author:
- first_name: Samuel G.
full_name: Walt, Samuel G.
last_name: Walt
- first_name: Niraghatam
full_name: Bhargava Ram, Niraghatam
last_name: Bhargava Ram
- first_name: Marcos
full_name: Atala, Marcos
last_name: Atala
- first_name: Nikolay I
full_name: Shvetsov-Shilovski, Nikolay I
last_name: Shvetsov-Shilovski
- first_name: Aaron
full_name: von Conta, Aaron
last_name: von Conta
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Manfred
full_name: Lein, Manfred
last_name: Lein
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
citation:
ama: Walt SG, Bhargava Ram N, Atala M, et al. Dynamics of valence-shell electrons
and nuclei probed by strong-field holography and rescattering. Nature Communications.
2017;8. doi:10.1038/ncomms15651
apa: Walt, S. G., Bhargava Ram, N., Atala, M., Shvetsov-Shilovski, N. I., von Conta,
A., Baykusheva, D. R., … Wörner, H. J. (2017). Dynamics of valence-shell electrons
and nuclei probed by strong-field holography and rescattering. Nature Communications.
Springer Nature. https://doi.org/10.1038/ncomms15651
chicago: Walt, Samuel G., Niraghatam Bhargava Ram, Marcos Atala, Nikolay I Shvetsov-Shilovski,
Aaron von Conta, Denitsa Rangelova Baykusheva, Manfred Lein, and Hans Jakob Wörner.
“Dynamics of Valence-Shell Electrons and Nuclei Probed by Strong-Field Holography
and Rescattering.” Nature Communications. Springer Nature, 2017. https://doi.org/10.1038/ncomms15651.
ieee: S. G. Walt et al., “Dynamics of valence-shell electrons and nuclei
probed by strong-field holography and rescattering,” Nature Communications,
vol. 8. Springer Nature, 2017.
ista: Walt SG, Bhargava Ram N, Atala M, Shvetsov-Shilovski NI, von Conta A, Baykusheva
DR, Lein M, Wörner HJ. 2017. Dynamics of valence-shell electrons and nuclei probed
by strong-field holography and rescattering. Nature Communications. 8, 15651.
mla: Walt, Samuel G., et al. “Dynamics of Valence-Shell Electrons and Nuclei Probed
by Strong-Field Holography and Rescattering.” Nature Communications, vol.
8, 15651, Springer Nature, 2017, doi:10.1038/ncomms15651.
short: S.G. Walt, N. Bhargava Ram, M. Atala, N.I. Shvetsov-Shilovski, A. von Conta,
D.R. Baykusheva, M. Lein, H.J. Wörner, Nature Communications 8 (2017).
date_created: 2023-08-10T06:36:09Z
date_published: 2017-06-15T00:00:00Z
date_updated: 2023-08-22T08:26:06Z
day: '15'
doi: 10.1038/ncomms15651
extern: '1'
external_id:
pmid:
- '28643771'
intvolume: ' 8'
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/ncomms15651
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamics of valence-shell electrons and nuclei probed by strong-field holography
and rescattering
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '15154'
abstract:
- lang: eng
text: Biofilm formation is critical for the infection cycle of Vibrio cholerae.
Vibrio exopolysaccharides (VPS) and the matrix proteins RbmA, Bap1 and RbmC are
required for the development of biofilm architecture. We demonstrate that RbmA
binds VPS directly and uses a binary structural switch within its first fibronectin
type III (FnIII-1) domain to control RbmA structural dynamics and the formation
of VPS-dependent higher-order structures. The structural switch in FnIII-1 regulates
interactions in trans with the FnIII-2 domain, leading to open (monomeric) or
closed (dimeric) interfaces. The ability of RbmA to switch between open and closed
states is important for V. cholerae biofilm formation, as RbmA variants with switches
that are locked in either of the two states lead to biofilms with altered architecture
and structural integrity.
article_number: '26163'
article_processing_charge: Yes
article_type: original
author:
- first_name: Jiunn CN
full_name: Fong, Jiunn CN
last_name: Fong
- first_name: Andrew
full_name: Rogers, Andrew
last_name: Rogers
- first_name: Alicia Kathleen
full_name: Michael, Alicia Kathleen
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
- first_name: Nicole C
full_name: Parsley, Nicole C
last_name: Parsley
- first_name: William-Cole
full_name: Cornell, William-Cole
last_name: Cornell
- first_name: Yu-Cheng
full_name: Lin, Yu-Cheng
last_name: Lin
- first_name: Praveen K
full_name: Singh, Praveen K
last_name: Singh
- first_name: Raimo
full_name: Hartmann, Raimo
last_name: Hartmann
- first_name: Knut
full_name: Drescher, Knut
last_name: Drescher
- first_name: Evgeny
full_name: Vinogradov, Evgeny
last_name: Vinogradov
- first_name: Lars EP
full_name: Dietrich, Lars EP
last_name: Dietrich
- first_name: Carrie L
full_name: Partch, Carrie L
last_name: Partch
- first_name: Fitnat H
full_name: Yildiz, Fitnat H
last_name: Yildiz
citation:
ama: Fong JC, Rogers A, Michael AK, et al. Structural dynamics of RbmA governs plasticity
of Vibrio cholerae biofilms. eLife. 2017;6. doi:10.7554/elife.26163
apa: Fong, J. C., Rogers, A., Michael, A. K., Parsley, N. C., Cornell, W.-C., Lin,
Y.-C., … Yildiz, F. H. (2017). Structural dynamics of RbmA governs plasticity
of Vibrio cholerae biofilms. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.26163
chicago: Fong, Jiunn CN, Andrew Rogers, Alicia K. Michael, Nicole C Parsley, William-Cole
Cornell, Yu-Cheng Lin, Praveen K Singh, et al. “Structural Dynamics of RbmA Governs
Plasticity of Vibrio Cholerae Biofilms.” ELife. eLife Sciences Publications,
2017. https://doi.org/10.7554/elife.26163.
ieee: J. C. Fong et al., “Structural dynamics of RbmA governs plasticity
of Vibrio cholerae biofilms,” eLife, vol. 6. eLife Sciences Publications,
2017.
ista: Fong JC, Rogers A, Michael AK, Parsley NC, Cornell W-C, Lin Y-C, Singh PK,
Hartmann R, Drescher K, Vinogradov E, Dietrich LE, Partch CL, Yildiz FH. 2017.
Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms. eLife.
6, 26163.
mla: Fong, Jiunn CN, et al. “Structural Dynamics of RbmA Governs Plasticity of Vibrio
Cholerae Biofilms.” ELife, vol. 6, 26163, eLife Sciences Publications,
2017, doi:10.7554/elife.26163.
short: J.C. Fong, A. Rogers, A.K. Michael, N.C. Parsley, W.-C. Cornell, Y.-C. Lin,
P.K. Singh, R. Hartmann, K. Drescher, E. Vinogradov, L.E. Dietrich, C.L. Partch,
F.H. Yildiz, ELife 6 (2017).
date_created: 2024-03-21T07:55:36Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2024-03-25T12:22:54Z
day: '01'
doi: 10.7554/elife.26163
extern: '1'
external_id:
pmid:
- '28762945'
intvolume: ' 6'
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.7554/eLife.26163
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2017'
...
---
_id: '11072'
abstract:
- lang: eng
text: "Spatiotemporal activation of RhoA and actomyosin contraction underpins cellular
adhesion and division. Loss of cell–cell adhesion and chromosomal instability
are cardinal events that drive tumour progression. Here, we show that p120-catenin
(p120) not only controls cell–cell adhesion, but also acts as a critical regulator
of cytokinesis. We find that p120 regulates actomyosin contractility through concomitant
binding to RhoA and the centralspindlin component MKLP1, independent of cadherin
association. In anaphase, p120 is enriched at the cleavage furrow where it binds
MKLP1 to spatially control RhoA GTPase cycling. Binding of p120 to MKLP1 during
cytokinesis depends on the N-terminal coiled-coil domain of p120 isoform 1A. Importantly,
clinical data show that loss of p120 expression is a common event in breast cancer
that strongly correlates with multinucleation and adverse patient survival. In
summary, our study identifies p120 loss as a driver event of chromosomal instability
in cancer.\r\n"
article_number: '13874'
article_processing_charge: No
article_type: original
author:
- first_name: Robert A.H.
full_name: van de Ven, Robert A.H.
last_name: van de Ven
- first_name: Jolien S.
full_name: de Groot, Jolien S.
last_name: de Groot
- first_name: Danielle
full_name: Park, Danielle
last_name: Park
- first_name: Robert
full_name: van Domselaar, Robert
last_name: van Domselaar
- first_name: Danielle
full_name: de Jong, Danielle
last_name: de Jong
- first_name: Karoly
full_name: Szuhai, Karoly
last_name: Szuhai
- first_name: Elsken
full_name: van der Wall, Elsken
last_name: van der Wall
- first_name: Oscar M.
full_name: Rueda, Oscar M.
last_name: Rueda
- first_name: H. Raza
full_name: Ali, H. Raza
last_name: Ali
- first_name: Carlos
full_name: Caldas, Carlos
last_name: Caldas
- first_name: Paul J.
full_name: van Diest, Paul J.
last_name: van Diest
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
- first_name: Erik
full_name: Sahai, Erik
last_name: Sahai
- first_name: Patrick W.B.
full_name: Derksen, Patrick W.B.
last_name: Derksen
citation:
ama: van de Ven RAH, de Groot JS, Park D, et al. p120-catenin prevents multinucleation
through control of MKLP1-dependent RhoA activity during cytokinesis. Nature
Communications. 2016;7. doi:10.1038/ncomms13874
apa: van de Ven, R. A. H., de Groot, J. S., Park, D., van Domselaar, R., de Jong,
D., Szuhai, K., … Derksen, P. W. B. (2016). p120-catenin prevents multinucleation
through control of MKLP1-dependent RhoA activity during cytokinesis. Nature
Communications. Springer Nature. https://doi.org/10.1038/ncomms13874
chicago: Ven, Robert A.H. van de, Jolien S. de Groot, Danielle Park, Robert van
Domselaar, Danielle de Jong, Karoly Szuhai, Elsken van der Wall, et al. “P120-Catenin
Prevents Multinucleation through Control of MKLP1-Dependent RhoA Activity during
Cytokinesis.” Nature Communications. Springer Nature, 2016. https://doi.org/10.1038/ncomms13874.
ieee: R. A. H. van de Ven et al., “p120-catenin prevents multinucleation
through control of MKLP1-dependent RhoA activity during cytokinesis,” Nature
Communications, vol. 7. Springer Nature, 2016.
ista: van de Ven RAH, de Groot JS, Park D, van Domselaar R, de Jong D, Szuhai K,
van der Wall E, Rueda OM, Ali HR, Caldas C, van Diest PJ, Hetzer M, Sahai E, Derksen
PWB. 2016. p120-catenin prevents multinucleation through control of MKLP1-dependent
RhoA activity during cytokinesis. Nature Communications. 7, 13874.
mla: van de Ven, Robert A. H., et al. “P120-Catenin Prevents Multinucleation through
Control of MKLP1-Dependent RhoA Activity during Cytokinesis.” Nature Communications,
vol. 7, 13874, Springer Nature, 2016, doi:10.1038/ncomms13874.
short: R.A.H. van de Ven, J.S. de Groot, D. Park, R. van Domselaar, D. de Jong,
K. Szuhai, E. van der Wall, O.M. Rueda, H.R. Ali, C. Caldas, P.J. van Diest, M.
Hetzer, E. Sahai, P.W.B. Derksen, Nature Communications 7 (2016).
date_created: 2022-04-07T07:48:34Z
date_published: 2016-12-22T00:00:00Z
date_updated: 2022-07-18T08:34:32Z
day: '22'
doi: 10.1038/ncomms13874
extern: '1'
external_id:
pmid:
- '28004812'
intvolume: ' 7'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/ncomms13874
month: '12'
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/ncomms16030
scopus_import: '1'
status: public
title: p120-catenin prevents multinucleation through control of MKLP1-dependent RhoA
activity during cytokinesis
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 7
year: '2016'
...
---
_id: '11073'
abstract:
- lang: eng
text: Human cancer cells bear complex chromosome rearrangements that can be potential
drivers of cancer development. However, the molecular mechanisms underlying these
rearrangements have been unclear. Zhang et al. use a new technique combining live-cell
imaging and single-cell sequencing to demonstrate that chromosomes mis-segregated
to micronuclei frequently undergo chromothripsis-like rearrangements in the subsequent
cell cycle.
article_processing_charge: No
article_type: original
author:
- first_name: Emily M.
full_name: Hatch, Emily M.
last_name: Hatch
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Hatch EM, Hetzer M. Linking micronuclei to chromosome fragmentation. Cell.
2015;161(7):1502-1504. doi:10.1016/j.cell.2015.06.005
apa: Hatch, E. M., & Hetzer, M. (2015). Linking micronuclei to chromosome fragmentation.
Cell. Elsevier. https://doi.org/10.1016/j.cell.2015.06.005
chicago: Hatch, Emily M., and Martin Hetzer. “Linking Micronuclei to Chromosome
Fragmentation.” Cell. Elsevier, 2015. https://doi.org/10.1016/j.cell.2015.06.005.
ieee: E. M. Hatch and M. Hetzer, “Linking micronuclei to chromosome fragmentation,”
Cell, vol. 161, no. 7. Elsevier, pp. 1502–1504, 2015.
ista: Hatch EM, Hetzer M. 2015. Linking micronuclei to chromosome fragmentation.
Cell. 161(7), 1502–1504.
mla: Hatch, Emily M., and Martin Hetzer. “Linking Micronuclei to Chromosome Fragmentation.”
Cell, vol. 161, no. 7, Elsevier, 2015, pp. 1502–04, doi:10.1016/j.cell.2015.06.005.
short: E.M. Hatch, M. Hetzer, Cell 161 (2015) 1502–1504.
date_created: 2022-04-07T07:48:49Z
date_published: 2015-06-18T00:00:00Z
date_updated: 2022-07-18T08:34:33Z
day: '18'
doi: 10.1016/j.cell.2015.06.005
extern: '1'
external_id:
pmid:
- '26091034'
intvolume: ' 161'
issue: '7'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2015.06.005
month: '06'
oa: 1
oa_version: Published Version
page: 1502-1504
pmid: 1
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Linking micronuclei to chromosome fragmentation
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 161
year: '2015'
...
---
_id: '11074'
article_processing_charge: No
article_type: original
author:
- first_name: Emily M.
full_name: Hatch, Emily M.
last_name: Hatch
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Hatch EM, Hetzer M. Chromothripsis. Current Biology. 2015;25(10):PR397-R399.
doi:10.1016/j.cub.2015.02.033
apa: Hatch, E. M., & Hetzer, M. (2015). Chromothripsis. Current Biology.
Elsevier. https://doi.org/10.1016/j.cub.2015.02.033
chicago: Hatch, Emily M., and Martin Hetzer. “Chromothripsis.” Current Biology.
Elsevier, 2015. https://doi.org/10.1016/j.cub.2015.02.033.
ieee: E. M. Hatch and M. Hetzer, “Chromothripsis,” Current Biology, vol.
25, no. 10. Elsevier, pp. PR397-R399, 2015.
ista: Hatch EM, Hetzer M. 2015. Chromothripsis. Current Biology. 25(10), PR397-R399.
mla: Hatch, Emily M., and Martin Hetzer. “Chromothripsis.” Current Biology,
vol. 25, no. 10, Elsevier, 2015, pp. PR397-R399, doi:10.1016/j.cub.2015.02.033.
short: E.M. Hatch, M. Hetzer, Current Biology 25 (2015) PR397-R399.
date_created: 2022-04-07T07:49:00Z
date_published: 2015-05-18T00:00:00Z
date_updated: 2022-07-18T08:34:34Z
day: '18'
doi: 10.1016/j.cub.2015.02.033
extern: '1'
external_id:
pmid:
- '25989073'
intvolume: ' 25'
issue: '10'
keyword:
- General Agricultural and Biological Sciences
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2015.02.033
month: '05'
oa: 1
oa_version: Published Version
page: PR397-R399
pmid: 1
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chromothripsis
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 25
year: '2015'
...
---
_id: '8456'
abstract:
- lang: eng
text: The large majority of three-dimensional structures of biological macromolecules
have been determined by X-ray diffraction of crystalline samples. High-resolution
structure determination crucially depends on the homogeneity of the protein crystal.
Overall ‘rocking’ motion of molecules in the crystal is expected to influence
diffraction quality, and such motion may therefore affect the process of solving
crystal structures. Yet, so far overall molecular motion has not directly been
observed in protein crystals, and the timescale of such dynamics remains unclear.
Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics
simulations to directly characterize the rigid-body motion of a protein in different
crystal forms. For ubiquitin crystals investigated in this study we determine
the range of possible correlation times of rocking motion, 0.1–100 μs. The amplitude
of rocking varies from one crystal form to another and is correlated with the
resolution obtainable in X-ray diffraction experiments.
article_number: '8361'
article_processing_charge: No
article_type: original
author:
- first_name: Peixiang
full_name: Ma, Peixiang
last_name: Ma
- first_name: Yi
full_name: Xue, Yi
last_name: Xue
- first_name: Nicolas
full_name: Coquelle, Nicolas
last_name: Coquelle
- first_name: Jens D.
full_name: Haller, Jens D.
last_name: Haller
- first_name: Tairan
full_name: Yuwen, Tairan
last_name: Yuwen
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Oleg
full_name: Mikhailovskii, Oleg
last_name: Mikhailovskii
- first_name: Dieter
full_name: Willbold, Dieter
last_name: Willbold
- first_name: Jacques-Philippe
full_name: Colletier, Jacques-Philippe
last_name: Colletier
- first_name: Nikolai R.
full_name: Skrynnikov, Nikolai R.
last_name: Skrynnikov
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Ma P, Xue Y, Coquelle N, et al. Observing the overall rocking motion of a protein
in a crystal. Nature Communications. 2015;6. doi:10.1038/ncomms9361
apa: Ma, P., Xue, Y., Coquelle, N., Haller, J. D., Yuwen, T., Ayala, I., … Schanda,
P. (2015). Observing the overall rocking motion of a protein in a crystal. Nature
Communications. Springer Nature. https://doi.org/10.1038/ncomms9361
chicago: Ma, Peixiang, Yi Xue, Nicolas Coquelle, Jens D. Haller, Tairan Yuwen, Isabel
Ayala, Oleg Mikhailovskii, et al. “Observing the Overall Rocking Motion of a Protein
in a Crystal.” Nature Communications. Springer Nature, 2015. https://doi.org/10.1038/ncomms9361.
ieee: P. Ma et al., “Observing the overall rocking motion of a protein in
a crystal,” Nature Communications, vol. 6. Springer Nature, 2015.
ista: Ma P, Xue Y, Coquelle N, Haller JD, Yuwen T, Ayala I, Mikhailovskii O, Willbold
D, Colletier J-P, Skrynnikov NR, Schanda P. 2015. Observing the overall rocking
motion of a protein in a crystal. Nature Communications. 6, 8361.
mla: Ma, Peixiang, et al. “Observing the Overall Rocking Motion of a Protein in
a Crystal.” Nature Communications, vol. 6, 8361, Springer Nature, 2015,
doi:10.1038/ncomms9361.
short: P. Ma, Y. Xue, N. Coquelle, J.D. Haller, T. Yuwen, I. Ayala, O. Mikhailovskii,
D. Willbold, J.-P. Colletier, N.R. Skrynnikov, P. Schanda, Nature Communications
6 (2015).
date_created: 2020-09-18T10:07:36Z
date_published: 2015-10-05T00:00:00Z
date_updated: 2021-01-12T08:19:24Z
day: '05'
doi: 10.1038/ncomms9361
extern: '1'
intvolume: ' 6'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '10'
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Observing the overall rocking motion of a protein in a crystal
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2015'
...
---
_id: '14016'
abstract:
- lang: eng
text: All attosecond time-resolved measurements have so far relied on the use of
intense near-infrared laser pulses. In particular, attosecond streaking, laser-induced
electron diffraction and high-harmonic generation all make use of non-perturbative
light–matter interactions. Remarkably, the effect of the strong laser field on
the studied sample has often been neglected in previous studies. Here we use high-harmonic
spectroscopy to measure laser-induced modifications of the electronic structure
of molecules. We study high-harmonic spectra of spatially oriented CH3F and CH3Br
as generic examples of polar polyatomic molecules. We accurately measure intensity
ratios of even and odd-harmonic orders, and of the emission from aligned and unaligned
molecules. We show that these robust observables reveal a substantial modification
of the molecular electronic structure by the external laser field. Our insights
offer new challenges and opportunities for a range of emerging strong-field attosecond
spectroscopies.
article_number: '7039'
article_processing_charge: No
article_type: original
author:
- first_name: P. M.
full_name: Kraus, P. M.
last_name: Kraus
- first_name: O. I.
full_name: Tolstikhin, O. I.
last_name: Tolstikhin
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: A.
full_name: Rupenyan, A.
last_name: Rupenyan
- first_name: J.
full_name: Schneider, J.
last_name: Schneider
- first_name: C. Z.
full_name: Bisgaard, C. Z.
last_name: Bisgaard
- first_name: T.
full_name: Morishita, T.
last_name: Morishita
- first_name: F.
full_name: Jensen, F.
last_name: Jensen
- first_name: L. B.
full_name: Madsen, L. B.
last_name: Madsen
- first_name: H. J.
full_name: Wörner, H. J.
last_name: Wörner
citation:
ama: Kraus PM, Tolstikhin OI, Baykusheva DR, et al. Observation of laser-induced
electronic structure in oriented polyatomic molecules. Nature Communications.
2015;6. doi:10.1038/ncomms8039
apa: Kraus, P. M., Tolstikhin, O. I., Baykusheva, D. R., Rupenyan, A., Schneider,
J., Bisgaard, C. Z., … Wörner, H. J. (2015). Observation of laser-induced electronic
structure in oriented polyatomic molecules. Nature Communications. Springer
Nature. https://doi.org/10.1038/ncomms8039
chicago: Kraus, P. M., O. I. Tolstikhin, Denitsa Rangelova Baykusheva, A. Rupenyan,
J. Schneider, C. Z. Bisgaard, T. Morishita, F. Jensen, L. B. Madsen, and H. J.
Wörner. “Observation of Laser-Induced Electronic Structure in Oriented Polyatomic
Molecules.” Nature Communications. Springer Nature, 2015. https://doi.org/10.1038/ncomms8039.
ieee: P. M. Kraus et al., “Observation of laser-induced electronic structure
in oriented polyatomic molecules,” Nature Communications, vol. 6. Springer
Nature, 2015.
ista: Kraus PM, Tolstikhin OI, Baykusheva DR, Rupenyan A, Schneider J, Bisgaard
CZ, Morishita T, Jensen F, Madsen LB, Wörner HJ. 2015. Observation of laser-induced
electronic structure in oriented polyatomic molecules. Nature Communications.
6, 7039.
mla: Kraus, P. M., et al. “Observation of Laser-Induced Electronic Structure in
Oriented Polyatomic Molecules.” Nature Communications, vol. 6, 7039, Springer
Nature, 2015, doi:10.1038/ncomms8039.
short: P.M. Kraus, O.I. Tolstikhin, D.R. Baykusheva, A. Rupenyan, J. Schneider,
C.Z. Bisgaard, T. Morishita, F. Jensen, L.B. Madsen, H.J. Wörner, Nature Communications
6 (2015).
date_created: 2023-08-10T06:38:01Z
date_published: 2015-05-05T00:00:00Z
date_updated: 2023-08-22T08:52:56Z
day: '05'
doi: 10.1038/ncomms8039
extern: '1'
external_id:
pmid:
- '25940229'
intvolume: ' 6'
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/ncomms8039
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Observation of laser-induced electronic structure in oriented polyatomic molecules
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2015'
...
---
_id: '11080'
abstract:
- lang: eng
text: The spindle assembly checkpoint prevents separation of sister chromatids until
each kinetochore is attached to the mitotic spindle. Rodriguez-Bravo et al. report
that the nuclear pore complex scaffolds spindle assembly checkpoint signaling
in interphase, providing a store of inhibitory signals that limits the speed of
the subsequent mitosis.
article_processing_charge: No
article_type: original
author:
- first_name: Abigail
full_name: Buchwalter, Abigail
last_name: Buchwalter
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Buchwalter A, Hetzer M. Nuclear pores set the speed limit for mitosis. Cell.
2014;156(5):868-869. doi:10.1016/j.cell.2014.02.004
apa: Buchwalter, A., & Hetzer, M. (2014). Nuclear pores set the speed limit
for mitosis. Cell. Elsevier. https://doi.org/10.1016/j.cell.2014.02.004
chicago: Buchwalter, Abigail, and Martin Hetzer. “Nuclear Pores Set the Speed Limit
for Mitosis.” Cell. Elsevier, 2014. https://doi.org/10.1016/j.cell.2014.02.004.
ieee: A. Buchwalter and M. Hetzer, “Nuclear pores set the speed limit for mitosis,”
Cell, vol. 156, no. 5. Elsevier, pp. 868–869, 2014.
ista: Buchwalter A, Hetzer M. 2014. Nuclear pores set the speed limit for mitosis.
Cell. 156(5), 868–869.
mla: Buchwalter, Abigail, and Martin Hetzer. “Nuclear Pores Set the Speed Limit
for Mitosis.” Cell, vol. 156, no. 5, Elsevier, 2014, pp. 868–69, doi:10.1016/j.cell.2014.02.004.
short: A. Buchwalter, M. Hetzer, Cell 156 (2014) 868–869.
date_created: 2022-04-07T07:50:04Z
date_published: 2014-02-27T00:00:00Z
date_updated: 2022-07-18T08:44:33Z
day: '27'
doi: 10.1016/j.cell.2014.02.004
extern: '1'
external_id:
pmid:
- '24581486'
intvolume: ' 156'
issue: '5'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2014.02.004
month: '02'
oa: 1
oa_version: Published Version
page: 868-869
pmid: 1
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nuclear pores set the speed limit for mitosis
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 156
year: '2014'
...
---
_id: '13402'
abstract:
- lang: eng
text: Nanoporous frameworks are polymeric materials built from rigid molecules,
which give rise to their nanoporous structures with applications in gas sorption
and storage, catalysis and others. Conceptually new applications could emerge,
should these beneficial properties be manipulated by external stimuli in a reversible
manner. One approach to render nanoporous frameworks responsive to external signals
would be to immobilize molecular switches within their nanopores. Although the
majority of molecular switches require conformational freedom to isomerize, and
switching in the solid state is prohibited, the nanopores may provide enough room
for the switches to efficiently isomerize. Here we describe two families of nanoporous
materials incorporating the spiropyran molecular switch. These materials exhibit
a variety of interesting properties, including reversible photochromism and acidochromism
under solvent-free conditions, light-controlled capture and release of metal ions,
as well reversible chromism induced by solvation/desolvation.
article_number: '3588'
article_processing_charge: No
article_type: original
author:
- first_name: Pintu K.
full_name: Kundu, Pintu K.
last_name: Kundu
- first_name: Gregory L.
full_name: Olsen, Gregory L.
last_name: Olsen
- first_name: Vladimir
full_name: Kiss, Vladimir
last_name: Kiss
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Kundu PK, Olsen GL, Kiss V, Klajn R. Nanoporous frameworks exhibiting multiple
stimuli responsiveness. Nature Communications. 2014;5. doi:10.1038/ncomms4588
apa: Kundu, P. K., Olsen, G. L., Kiss, V., & Klajn, R. (2014). Nanoporous frameworks
exhibiting multiple stimuli responsiveness. Nature Communications. Springer
Nature. https://doi.org/10.1038/ncomms4588
chicago: Kundu, Pintu K., Gregory L. Olsen, Vladimir Kiss, and Rafal Klajn. “Nanoporous
Frameworks Exhibiting Multiple Stimuli Responsiveness.” Nature Communications.
Springer Nature, 2014. https://doi.org/10.1038/ncomms4588.
ieee: P. K. Kundu, G. L. Olsen, V. Kiss, and R. Klajn, “Nanoporous frameworks exhibiting
multiple stimuli responsiveness,” Nature Communications, vol. 5. Springer
Nature, 2014.
ista: Kundu PK, Olsen GL, Kiss V, Klajn R. 2014. Nanoporous frameworks exhibiting
multiple stimuli responsiveness. Nature Communications. 5, 3588.
mla: Kundu, Pintu K., et al. “Nanoporous Frameworks Exhibiting Multiple Stimuli
Responsiveness.” Nature Communications, vol. 5, 3588, Springer Nature,
2014, doi:10.1038/ncomms4588.
short: P.K. Kundu, G.L. Olsen, V. Kiss, R. Klajn, Nature Communications 5 (2014).
date_created: 2023-08-01T09:46:27Z
date_published: 2014-04-07T00:00:00Z
date_updated: 2023-08-08T07:28:10Z
day: '07'
doi: 10.1038/ncomms4588
extern: '1'
external_id:
pmid:
- '24709950'
intvolume: ' 5'
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/ncomms4588
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nanoporous frameworks exhibiting multiple stimuli responsiveness
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2014'
...
---
_id: '11087'
abstract:
- lang: eng
text: Intracellular proteins with long lifespans have recently been linked to age-dependent
defects, ranging from decreased fertility to the functional decline of neurons.
Why long-lived proteins exist in metabolically active cellular environments and
how they are maintained over time remains poorly understood. Here, we provide
a system-wide identification of proteins with exceptional lifespans in the rat
brain. These proteins are inefficiently replenished despite being translated robustly
throughout adulthood. Using nucleoporins as a paradigm for long-term protein persistence,
we found that nuclear pore complexes (NPCs) are maintained over a cell’s life
through slow but finite exchange of even its most stable subcomplexes. This maintenance
is limited, however, as some nucleoporin levels decrease during aging, providing
a rationale for the previously observed age-dependent deterioration of NPC function.
Our identification of a long-lived proteome reveals cellular components that are
at increased risk for damage accumulation, linking long-term protein persistence
to the cellular aging process.
article_processing_charge: No
article_type: original
author:
- first_name: Brandon H.
full_name: Toyama, Brandon H.
last_name: Toyama
- first_name: Jeffrey N.
full_name: Savas, Jeffrey N.
last_name: Savas
- first_name: Sung Kyu
full_name: Park, Sung Kyu
last_name: Park
- first_name: Michael S.
full_name: Harris, Michael S.
last_name: Harris
- first_name: Nicholas T.
full_name: Ingolia, Nicholas T.
last_name: Ingolia
- first_name: John R.
full_name: Yates, John R.
last_name: Yates
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Toyama BH, Savas JN, Park SK, et al. Identification of long-lived proteins
reveals exceptional stability of essential cellular structures. Cell. 2013;154(5):971-982.
doi:10.1016/j.cell.2013.07.037
apa: Toyama, B. H., Savas, J. N., Park, S. K., Harris, M. S., Ingolia, N. T., Yates,
J. R., & Hetzer, M. (2013). Identification of long-lived proteins reveals
exceptional stability of essential cellular structures. Cell. Elsevier.
https://doi.org/10.1016/j.cell.2013.07.037
chicago: Toyama, Brandon H., Jeffrey N. Savas, Sung Kyu Park, Michael S. Harris,
Nicholas T. Ingolia, John R. Yates, and Martin Hetzer. “Identification of Long-Lived
Proteins Reveals Exceptional Stability of Essential Cellular Structures.” Cell.
Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.07.037.
ieee: B. H. Toyama et al., “Identification of long-lived proteins reveals
exceptional stability of essential cellular structures,” Cell, vol. 154,
no. 5. Elsevier, pp. 971–982, 2013.
ista: Toyama BH, Savas JN, Park SK, Harris MS, Ingolia NT, Yates JR, Hetzer M. 2013.
Identification of long-lived proteins reveals exceptional stability of essential
cellular structures. Cell. 154(5), 971–982.
mla: Toyama, Brandon H., et al. “Identification of Long-Lived Proteins Reveals Exceptional
Stability of Essential Cellular Structures.” Cell, vol. 154, no. 5, Elsevier,
2013, pp. 971–82, doi:10.1016/j.cell.2013.07.037.
short: B.H. Toyama, J.N. Savas, S.K. Park, M.S. Harris, N.T. Ingolia, J.R. Yates,
M. Hetzer, Cell 154 (2013) 971–982.
date_created: 2022-04-07T07:51:08Z
date_published: 2013-08-29T00:00:00Z
date_updated: 2022-07-18T08:50:47Z
day: '29'
doi: 10.1016/j.cell.2013.07.037
extern: '1'
external_id:
pmid:
- '23993091'
intvolume: ' 154'
issue: '5'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2013.07.037
month: '08'
oa: 1
oa_version: Published Version
page: 971-982
pmid: 1
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Identification of long-lived proteins reveals exceptional stability of essential
cellular structures
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 154
year: '2013'
...
---
_id: '11085'
abstract:
- lang: eng
text: During mitotic exit, missegregated chromosomes can recruit their own nuclear
envelope (NE) to form micronuclei (MN). MN have reduced functioning compared to
primary nuclei in the same cell, although the two compartments appear to be structurally
comparable. Here we show that over 60% of MN undergo an irreversible loss of compartmentalization
during interphase due to NE collapse. This disruption of the MN, which is induced
by defects in nuclear lamina assembly, drastically reduces nuclear functions and
can trigger massive DNA damage. MN disruption is associated with chromatin compaction
and invasion of endoplasmic reticulum (ER) tubules into the chromatin. We identified
disrupted MN in both major subtypes of human non-small-cell lung cancer, suggesting
that disrupted MN could be a useful objective biomarker for genomic instability
in solid tumors. Our study shows that NE collapse is a key event underlying MN
dysfunction and establishes a link between aberrant NE organization and aneuploidy.
article_processing_charge: No
article_type: original
author:
- first_name: Emily M.
full_name: Hatch, Emily M.
last_name: Hatch
- first_name: Andrew H.
full_name: Fischer, Andrew H.
last_name: Fischer
- first_name: Thomas J.
full_name: Deerinck, Thomas J.
last_name: Deerinck
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Hatch EM, Fischer AH, Deerinck TJ, Hetzer M. Catastrophic nuclear envelope
collapse in cancer cell micronuclei. Cell. 2013;154(1):47-60. doi:10.1016/j.cell.2013.06.007
apa: Hatch, E. M., Fischer, A. H., Deerinck, T. J., & Hetzer, M. (2013). Catastrophic
nuclear envelope collapse in cancer cell micronuclei. Cell. Elsevier. https://doi.org/10.1016/j.cell.2013.06.007
chicago: Hatch, Emily M., Andrew H. Fischer, Thomas J. Deerinck, and Martin Hetzer.
“Catastrophic Nuclear Envelope Collapse in Cancer Cell Micronuclei.” Cell.
Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.06.007.
ieee: E. M. Hatch, A. H. Fischer, T. J. Deerinck, and M. Hetzer, “Catastrophic nuclear
envelope collapse in cancer cell micronuclei,” Cell, vol. 154, no. 1. Elsevier,
pp. 47–60, 2013.
ista: Hatch EM, Fischer AH, Deerinck TJ, Hetzer M. 2013. Catastrophic nuclear envelope
collapse in cancer cell micronuclei. Cell. 154(1), 47–60.
mla: Hatch, Emily M., et al. “Catastrophic Nuclear Envelope Collapse in Cancer Cell
Micronuclei.” Cell, vol. 154, no. 1, Elsevier, 2013, pp. 47–60, doi:10.1016/j.cell.2013.06.007.
short: E.M. Hatch, A.H. Fischer, T.J. Deerinck, M. Hetzer, Cell 154 (2013) 47–60.
date_created: 2022-04-07T07:50:51Z
date_published: 2013-07-03T00:00:00Z
date_updated: 2022-07-18T08:45:47Z
day: '03'
doi: 10.1016/j.cell.2013.06.007
extern: '1'
external_id:
pmid:
- '23827674'
intvolume: ' 154'
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2013.06.007
month: '07'
oa: 1
oa_version: Published Version
page: 47-60
pmid: 1
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Catastrophic nuclear envelope collapse in cancer cell micronuclei
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 154
year: '2013'
...
---
_id: '11093'
abstract:
- lang: eng
text: Nuclear pore complexes (NPCs) are built from ∼30 different proteins called
nucleoporins or Nups. Previous studies have shown that several Nups exhibit cell-type-specific
expression and that mutations in NPC components result in tissue-specific diseases.
Here we show that a specific change in NPC composition is required for both myogenic
and neuronal differentiation. The transmembrane nucleoporin Nup210 is absent in
proliferating myoblasts and embryonic stem cells (ESCs) but becomes expressed
and incorporated into NPCs during cell differentiation. Preventing Nup210 production
by RNAi blocks myogenesis and the differentiation of ESCs into neuroprogenitors.
We found that the addition of Nup210 to NPCs does not affect nuclear transport
but is required for the induction of genes that are essential for cell differentiation.
Our results identify a single change in NPC composition as an essential step in
cell differentiation and establish a role for Nup210 in gene expression regulation
and cell fate determination.
article_processing_charge: No
article_type: original
author:
- first_name: Maximiliano A.
full_name: D'Angelo, Maximiliano A.
last_name: D'Angelo
- first_name: J. Sebastian
full_name: Gomez-Cavazos, J. Sebastian
last_name: Gomez-Cavazos
- first_name: Arianna
full_name: Mei, Arianna
last_name: Mei
- first_name: Daniel H.
full_name: Lackner, Daniel H.
last_name: Lackner
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: D’Angelo MA, Gomez-Cavazos JS, Mei A, Lackner DH, Hetzer M. A change in nuclear
pore complex composition regulates cell differentiation. Developmental Cell.
2012;22(2):446-458. doi:10.1016/j.devcel.2011.11.021
apa: D’Angelo, M. A., Gomez-Cavazos, J. S., Mei, A., Lackner, D. H., & Hetzer,
M. (2012). A change in nuclear pore complex composition regulates cell differentiation.
Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2011.11.021
chicago: D’Angelo, Maximiliano A., J. Sebastian Gomez-Cavazos, Arianna Mei, Daniel H.
Lackner, and Martin Hetzer. “A Change in Nuclear Pore Complex Composition Regulates
Cell Differentiation.” Developmental Cell. Elsevier, 2012. https://doi.org/10.1016/j.devcel.2011.11.021.
ieee: M. A. D’Angelo, J. S. Gomez-Cavazos, A. Mei, D. H. Lackner, and M. Hetzer,
“A change in nuclear pore complex composition regulates cell differentiation,”
Developmental Cell, vol. 22, no. 2. Elsevier, pp. 446–458, 2012.
ista: D’Angelo MA, Gomez-Cavazos JS, Mei A, Lackner DH, Hetzer M. 2012. A change
in nuclear pore complex composition regulates cell differentiation. Developmental
Cell. 22(2), 446–458.
mla: D’Angelo, Maximiliano A., et al. “A Change in Nuclear Pore Complex Composition
Regulates Cell Differentiation.” Developmental Cell, vol. 22, no. 2, Elsevier,
2012, pp. 446–58, doi:10.1016/j.devcel.2011.11.021.
short: M.A. D’Angelo, J.S. Gomez-Cavazos, A. Mei, D.H. Lackner, M. Hetzer, Developmental
Cell 22 (2012) 446–458.
date_created: 2022-04-07T07:52:10Z
date_published: 2012-01-19T00:00:00Z
date_updated: 2022-07-18T08:53:16Z
day: '19'
doi: 10.1016/j.devcel.2011.11.021
extern: '1'
external_id:
pmid:
- '22264802'
intvolume: ' 22'
issue: '2'
keyword:
- Developmental Biology
- Cell Biology
- General Biochemistry
- Genetics and Molecular Biology
- Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.devcel.2011.11.021
month: '01'
oa: 1
oa_version: Published Version
page: 446-458
pmid: 1
publication: Developmental Cell
publication_identifier:
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: A change in nuclear pore complex composition regulates cell differentiation
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 22
year: '2012'
...
---
_id: '11090'
abstract:
- lang: eng
text: Nuclear export of mRNAs is thought to occur exclusively through nuclear pore
complexes. In this issue of Cell, Speese et al. identify an alternate pathway
for mRNA export in muscle cells where ribonucleoprotein complexes involved in
forming neuromuscular junctions transit the nuclear envelope by fusing with and
budding through the nuclear membrane.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Emily M.
full_name: Hatch, Emily M.
last_name: Hatch
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Hatch EM, Hetzer M. RNP export by nuclear envelope budding. Cell. 2012;149(4):733-735.
doi:10.1016/j.cell.2012.04.018
apa: Hatch, E. M., & Hetzer, M. (2012). RNP export by nuclear envelope budding.
Cell. Elsevier. https://doi.org/10.1016/j.cell.2012.04.018
chicago: Hatch, Emily M., and Martin Hetzer. “RNP Export by Nuclear Envelope Budding.”
Cell. Elsevier, 2012. https://doi.org/10.1016/j.cell.2012.04.018.
ieee: E. M. Hatch and M. Hetzer, “RNP export by nuclear envelope budding,” Cell,
vol. 149, no. 4. Elsevier, pp. 733–735, 2012.
ista: Hatch EM, Hetzer M. 2012. RNP export by nuclear envelope budding. Cell. 149(4),
733–735.
mla: Hatch, Emily M., and Martin Hetzer. “RNP Export by Nuclear Envelope Budding.”
Cell, vol. 149, no. 4, Elsevier, 2012, pp. 733–35, doi:10.1016/j.cell.2012.04.018.
short: E.M. Hatch, M. Hetzer, Cell 149 (2012) 733–735.
date_created: 2022-04-07T07:51:45Z
date_published: 2012-05-11T00:00:00Z
date_updated: 2022-07-18T08:58:48Z
day: '11'
doi: 10.1016/j.cell.2012.04.018
extern: '1'
external_id:
pmid:
- '22579277'
intvolume: ' 149'
issue: '4'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2012.04.018
month: '05'
oa: 1
oa_version: Published Version
page: 733-735
pmid: 1
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: RNP export by nuclear envelope budding
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 149
year: '2012'
...
---
_id: '11097'
abstract:
- lang: eng
text: The nuclear envelope (NE) is a highly regulated membrane barrier that separates
the nucleus from the cytoplasm in eukaryotic cells. It contains a large number
of different proteins that have been implicated in chromatin organization and
gene regulation. Although the nuclear membrane enables complex levels of gene
expression, it also poses a challenge when it comes to cell division. To allow
access of the mitotic spindle to chromatin, the nucleus of metazoans must completely
disassemble during mitosis, generating the need to re-establish the nuclear compartment
at the end of each cell division. Here, I summarize our current understanding
of the dynamic remodeling of the NE during the cell cycle.
article_processing_charge: No
article_type: original
author:
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Hetzer M. The nuclear envelope. Cold Spring Harbor Perspectives in Biology.
2010;2(3):a000539-a000539. doi:10.1101/cshperspect.a000539
apa: Hetzer, M. (2010). The nuclear envelope. Cold Spring Harbor Perspectives
in Biology. Cold Spring Harbor Laboratory. https://doi.org/10.1101/cshperspect.a000539
chicago: Hetzer, Martin. “The Nuclear Envelope.” Cold Spring Harbor Perspectives
in Biology. Cold Spring Harbor Laboratory, 2010. https://doi.org/10.1101/cshperspect.a000539.
ieee: M. Hetzer, “The nuclear envelope,” Cold Spring Harbor Perspectives in Biology,
vol. 2, no. 3. Cold Spring Harbor Laboratory, pp. a000539–a000539, 2010.
ista: Hetzer M. 2010. The nuclear envelope. Cold Spring Harbor Perspectives in Biology.
2(3), a000539–a000539.
mla: Hetzer, Martin. “The Nuclear Envelope.” Cold Spring Harbor Perspectives
in Biology, vol. 2, no. 3, Cold Spring Harbor Laboratory, 2010, pp. a000539–a000539,
doi:10.1101/cshperspect.a000539.
short: M. Hetzer, Cold Spring Harbor Perspectives in Biology 2 (2010) a000539–a000539.
date_created: 2022-04-07T07:52:49Z
date_published: 2010-02-03T00:00:00Z
date_updated: 2022-07-18T08:53:50Z
day: '03'
doi: 10.1101/cshperspect.a000539
extern: '1'
external_id:
pmid:
- '20300205'
intvolume: ' 2'
issue: '3'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '02'
oa_version: None
page: a000539-a000539
pmid: 1
publication: Cold Spring Harbor Perspectives in Biology
publication_identifier:
issn:
- 1943-0264
publication_status: published
publisher: Cold Spring Harbor Laboratory
quality_controlled: '1'
scopus_import: '1'
status: public
title: The nuclear envelope
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 2
year: '2010'
...
---
_id: '11102'
abstract:
- lang: eng
text: Nuclear pore complexes have recently been shown to play roles in gene activation;
however their potential involvement in metazoan transcription remains unclear.
Here we show that the nucleoporins Sec13, Nup98, and Nup88, as well as a group
of FG-repeat nucleoporins, bind to the Drosophila genome at functionally distinct
loci that often do not represent nuclear envelope contact sites. Whereas Nup88
localizes to silent loci, Sec13, Nup98, and a subset of FG-repeat nucleoporins
bind to developmentally regulated genes undergoing transcription induction. Strikingly,
RNAi-mediated knockdown of intranuclear Sec13 and Nup98 specifically inhibits
transcription of their target genes and prevents efficient reactivation of transcription
after heat shock, suggesting an essential role of NPC components in regulating
complex gene expression programs of multicellular organisms.
article_processing_charge: No
article_type: original
author:
- first_name: Maya
full_name: Capelson, Maya
last_name: Capelson
- first_name: Yun
full_name: Liang, Yun
last_name: Liang
- first_name: Roberta
full_name: Schulte, Roberta
last_name: Schulte
- first_name: William
full_name: Mair, William
last_name: Mair
- first_name: Ulrich
full_name: Wagner, Ulrich
last_name: Wagner
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Capelson M, Liang Y, Schulte R, Mair W, Wagner U, Hetzer M. Chromatin-bound
nuclear pore components regulate gene expression in higher eukaryotes. Cell.
2010;140(3):372-383. doi:10.1016/j.cell.2009.12.054
apa: Capelson, M., Liang, Y., Schulte, R., Mair, W., Wagner, U., & Hetzer, M.
(2010). Chromatin-bound nuclear pore components regulate gene expression in higher
eukaryotes. Cell. Elsevier. https://doi.org/10.1016/j.cell.2009.12.054
chicago: Capelson, Maya, Yun Liang, Roberta Schulte, William Mair, Ulrich Wagner,
and Martin Hetzer. “Chromatin-Bound Nuclear Pore Components Regulate Gene Expression
in Higher Eukaryotes.” Cell. Elsevier, 2010. https://doi.org/10.1016/j.cell.2009.12.054.
ieee: M. Capelson, Y. Liang, R. Schulte, W. Mair, U. Wagner, and M. Hetzer, “Chromatin-bound
nuclear pore components regulate gene expression in higher eukaryotes,” Cell,
vol. 140, no. 3. Elsevier, pp. 372–383, 2010.
ista: Capelson M, Liang Y, Schulte R, Mair W, Wagner U, Hetzer M. 2010. Chromatin-bound
nuclear pore components regulate gene expression in higher eukaryotes. Cell. 140(3),
372–383.
mla: Capelson, Maya, et al. “Chromatin-Bound Nuclear Pore Components Regulate Gene
Expression in Higher Eukaryotes.” Cell, vol. 140, no. 3, Elsevier, 2010,
pp. 372–83, doi:10.1016/j.cell.2009.12.054.
short: M. Capelson, Y. Liang, R. Schulte, W. Mair, U. Wagner, M. Hetzer, Cell 140
(2010) 372–383.
date_created: 2022-04-07T07:53:36Z
date_published: 2010-02-05T00:00:00Z
date_updated: 2022-07-18T08:55:03Z
day: '05'
doi: 10.1016/j.cell.2009.12.054
extern: '1'
external_id:
pmid:
- '20144761'
intvolume: ' 140'
issue: '3'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2009.12.054
month: '02'
oa: 1
oa_version: Published Version
page: 372-383
pmid: 1
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chromatin-bound nuclear pore components regulate gene expression in higher
eukaryotes
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 140
year: '2010'
...
---
_id: '11101'
abstract:
- lang: eng
text: In metazoa, nuclear pore complexes (NPCs) assemble from disassembled precursors
into a reforming nuclear envelope (NE) at the end of mitosis and into growing
intact NEs during interphase. Here, we show via RNAi-mediated knockdown that ELYS,
a nucleoporin critical for the recruitment of the essential Nup107/160 complex
to chromatin, is required for NPC assembly at the end of mitosis but not during
interphase. Conversely, the transmembrane nucleoporin POM121 is critical for the
incorporation of the Nup107/160 complex into new assembly sites specifically during
interphase. Strikingly, recruitment of the Nup107/160 complex to an intact NE
involves a membrane curvature-sensing domain of its constituent Nup133, which
is not required for postmitotic NPC formation. Our results suggest that in organisms
with open mitosis, NPCs assemble via two distinct mechanisms to accommodate cell
cycle-dependent differences in NE topology.
article_processing_charge: No
article_type: original
author:
- first_name: Christine M.
full_name: Doucet, Christine M.
last_name: Doucet
- first_name: Jessica A.
full_name: Talamas, Jessica A.
last_name: Talamas
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Doucet CM, Talamas JA, Hetzer M. Cell cycle-dependent differences in nuclear
pore complex assembly in metazoa. Cell. 2010;141(6):1030-1041. doi:10.1016/j.cell.2010.04.036
apa: Doucet, C. M., Talamas, J. A., & Hetzer, M. (2010). Cell cycle-dependent
differences in nuclear pore complex assembly in metazoa. Cell. Elsevier.
https://doi.org/10.1016/j.cell.2010.04.036
chicago: Doucet, Christine M., Jessica A. Talamas, and Martin Hetzer. “Cell Cycle-Dependent
Differences in Nuclear Pore Complex Assembly in Metazoa.” Cell. Elsevier,
2010. https://doi.org/10.1016/j.cell.2010.04.036.
ieee: C. M. Doucet, J. A. Talamas, and M. Hetzer, “Cell cycle-dependent differences
in nuclear pore complex assembly in metazoa,” Cell, vol. 141, no. 6. Elsevier,
pp. 1030–1041, 2010.
ista: Doucet CM, Talamas JA, Hetzer M. 2010. Cell cycle-dependent differences in
nuclear pore complex assembly in metazoa. Cell. 141(6), 1030–1041.
mla: Doucet, Christine M., et al. “Cell Cycle-Dependent Differences in Nuclear Pore
Complex Assembly in Metazoa.” Cell, vol. 141, no. 6, Elsevier, 2010, pp.
1030–41, doi:10.1016/j.cell.2010.04.036.
short: C.M. Doucet, J.A. Talamas, M. Hetzer, Cell 141 (2010) 1030–1041.
date_created: 2022-04-07T07:53:29Z
date_published: 2010-06-11T00:00:00Z
date_updated: 2022-07-18T08:54:52Z
day: '11'
doi: 10.1016/j.cell.2010.04.036
extern: '1'
external_id:
pmid:
- '20550937'
intvolume: ' 141'
issue: '6'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2010.04.036
month: '06'
oa: 1
oa_version: Published Version
page: 1030-1041
pmid: 1
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cell cycle-dependent differences in nuclear pore complex assembly in metazoa
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 141
year: '2010'
...
---
_id: '11103'
abstract:
- lang: eng
text: Over the last decade, the nuclear envelope (NE) has emerged as a key component
in the organization and function of the nuclear genome. As many as 100 different
proteins are thought to specifically localize to this double membrane that separates
the cytoplasm and the nucleoplasm of eukaryotic cells. Selective portals through
the NE are formed at sites where the inner and outer nuclear membranes are fused,
and the coincident assembly of ∼30 proteins into nuclear pore complexes occurs.
These nuclear pore complexes are essential for the control of nucleocytoplasmic
exchange. Many of the NE and nuclear pore proteins are thought to play crucial
roles in gene regulation and thus are increasingly linked to human diseases.
article_processing_charge: No
article_type: review
author:
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
- first_name: Susan R.
full_name: Wente, Susan R.
last_name: Wente
citation:
ama: 'Hetzer M, Wente SR. Border control at the nucleus: Biogenesis and organization
of the nuclear membrane and pore complexes. Developmental Cell. 2009;17(5):606-616.
doi:10.1016/j.devcel.2009.10.007'
apa: 'Hetzer, M., & Wente, S. R. (2009). Border control at the nucleus: Biogenesis
and organization of the nuclear membrane and pore complexes. Developmental
Cell. Elsevier. https://doi.org/10.1016/j.devcel.2009.10.007'
chicago: 'Hetzer, Martin, and Susan R. Wente. “Border Control at the Nucleus: Biogenesis
and Organization of the Nuclear Membrane and Pore Complexes.” Developmental
Cell. Elsevier, 2009. https://doi.org/10.1016/j.devcel.2009.10.007.'
ieee: 'M. Hetzer and S. R. Wente, “Border control at the nucleus: Biogenesis and
organization of the nuclear membrane and pore complexes,” Developmental Cell,
vol. 17, no. 5. Elsevier, pp. 606–616, 2009.'
ista: 'Hetzer M, Wente SR. 2009. Border control at the nucleus: Biogenesis and organization
of the nuclear membrane and pore complexes. Developmental Cell. 17(5), 606–616.'
mla: 'Hetzer, Martin, and Susan R. Wente. “Border Control at the Nucleus: Biogenesis
and Organization of the Nuclear Membrane and Pore Complexes.” Developmental
Cell, vol. 17, no. 5, Elsevier, 2009, pp. 606–16, doi:10.1016/j.devcel.2009.10.007.'
short: M. Hetzer, S.R. Wente, Developmental Cell 17 (2009) 606–616.
date_created: 2022-04-07T07:53:45Z
date_published: 2009-11-17T00:00:00Z
date_updated: 2022-07-18T08:55:01Z
day: '17'
doi: 10.1016/j.devcel.2009.10.007
extern: '1'
external_id:
pmid:
- '19922866'
intvolume: ' 17'
issue: '5'
keyword:
- Developmental Biology
- Cell Biology
- General Biochemistry
- Genetics and Molecular Biology
- Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.devcel.2009.10.007
month: '11'
oa: 1
oa_version: Published Version
page: 606-616
pmid: 1
publication: Developmental Cell
publication_identifier:
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Border control at the nucleus: Biogenesis and organization of the nuclear
membrane and pore complexes'
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 17
year: '2009'
...
---
_id: '11108'
abstract:
- lang: eng
text: In dividing cells, nuclear pore complexes (NPCs) disassemble during mitosis
and reassemble into the newly forming nuclei. However, the fate of nuclear pores
in postmitotic cells is unknown. Here, we show that NPCs, unlike other nuclear
structures, do not turn over in differentiated cells. While a subset of NPC components,
like Nup153 and Nup50, are continuously exchanged, scaffold nucleoporins, like
the Nup107/160 complex, are extremely long-lived and remain incorporated in the
nuclear membrane during the entire cellular life span. Besides the lack of nucleoporin
expression and NPC turnover, we discovered an age-related deterioration of NPCs,
leading to an increase in nuclear permeability and the leaking of cytoplasmic
proteins into the nucleus. Our finding that nuclear “leakiness” is dramatically
accelerated during aging and that a subset of nucleoporins is oxidatively damaged
in old cells suggests that the accumulation of damage at the NPC might be a crucial
aging event.
article_processing_charge: No
article_type: original
author:
- first_name: Maximiliano A.
full_name: D'Angelo, Maximiliano A.
last_name: D'Angelo
- first_name: Marcela
full_name: Raices, Marcela
last_name: Raices
- first_name: Siler H.
full_name: Panowski, Siler H.
last_name: Panowski
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: D’Angelo MA, Raices M, Panowski SH, Hetzer M. Age-dependent deterioration of
nuclear pore complexes causes a loss of nuclear integrity in postmitotic cells.
Cell. 2009;136(2):284-295. doi:10.1016/j.cell.2008.11.037
apa: D’Angelo, M. A., Raices, M., Panowski, S. H., & Hetzer, M. (2009). Age-dependent
deterioration of nuclear pore complexes causes a loss of nuclear integrity in
postmitotic cells. Cell. Elsevier. https://doi.org/10.1016/j.cell.2008.11.037
chicago: D’Angelo, Maximiliano A., Marcela Raices, Siler H. Panowski, and Martin
Hetzer. “Age-Dependent Deterioration of Nuclear Pore Complexes Causes a Loss of
Nuclear Integrity in Postmitotic Cells.” Cell. Elsevier, 2009. https://doi.org/10.1016/j.cell.2008.11.037.
ieee: M. A. D’Angelo, M. Raices, S. H. Panowski, and M. Hetzer, “Age-dependent deterioration
of nuclear pore complexes causes a loss of nuclear integrity in postmitotic cells,”
Cell, vol. 136, no. 2. Elsevier, pp. 284–295, 2009.
ista: D’Angelo MA, Raices M, Panowski SH, Hetzer M. 2009. Age-dependent deterioration
of nuclear pore complexes causes a loss of nuclear integrity in postmitotic cells.
Cell. 136(2), 284–295.
mla: D’Angelo, Maximiliano A., et al. “Age-Dependent Deterioration of Nuclear Pore
Complexes Causes a Loss of Nuclear Integrity in Postmitotic Cells.” Cell,
vol. 136, no. 2, Elsevier, 2009, pp. 284–95, doi:10.1016/j.cell.2008.11.037.
short: M.A. D’Angelo, M. Raices, S.H. Panowski, M. Hetzer, Cell 136 (2009) 284–295.
date_created: 2022-04-07T07:54:52Z
date_published: 2009-01-23T00:00:00Z
date_updated: 2022-07-18T08:55:29Z
day: '23'
doi: 10.1016/j.cell.2008.11.037
extern: '1'
external_id:
pmid:
- '19167330'
intvolume: ' 136'
issue: '2'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2008.11.037
month: '01'
oa: 1
oa_version: Published Version
page: 284-295
pmid: 1
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Age-dependent deterioration of nuclear pore complexes causes a loss of nuclear
integrity in postmitotic cells
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 136
year: '2009'
...
---
_id: '11122'
abstract:
- lang: eng
text: Nuclear pore complexes (NPCs) are large multiprotein assemblies that allow
traffic between the cytoplasm and the nucleus. During mitosis in higher eukaryotes,
the Nuclear Envelope (NE) breaks down and NPCs disassemble. How NPCs reassemble
and incorporate into the NE upon mitotic exit is poorly understood. We demonstrate
a function for the conserved Nup107-160 complex in this process. Partial in vivo
depletion of Nup133 or Nup107 via RNAi in HeLa cells resulted in reduced levels
of multiple nucleoporins and decreased NPC density in the NE. Immunodepletion
of the entire Nup107-160 complex from in vitro nuclear assembly reactions produced
nuclei with a continuous NE but no NPCs. This phenotype was reversible only if
Nup107-160 complex was readded before closed NE formation. Depletion also prevented
association of FG-repeat nucleoporins with chromatin. We propose a stepwise model
in which postmitotic NPC assembly initiates on chromatin via early recruitment
of the Nup107-160 complex.
article_processing_charge: No
article_type: original
author:
- first_name: Tobias C.
full_name: Walther, Tobias C.
last_name: Walther
- first_name: Annabelle
full_name: Alves, Annabelle
last_name: Alves
- first_name: Helen
full_name: Pickersgill, Helen
last_name: Pickersgill
- first_name: Isabelle
full_name: Loı̈odice, Isabelle
last_name: Loı̈odice
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
- first_name: Vincent
full_name: Galy, Vincent
last_name: Galy
- first_name: Bastian B.
full_name: Hülsmann, Bastian B.
last_name: Hülsmann
- first_name: Thomas
full_name: Köcher, Thomas
last_name: Köcher
- first_name: Matthias
full_name: Wilm, Matthias
last_name: Wilm
- first_name: Terry
full_name: Allen, Terry
last_name: Allen
- first_name: Iain W.
full_name: Mattaj, Iain W.
last_name: Mattaj
- first_name: Valérie
full_name: Doye, Valérie
last_name: Doye
citation:
ama: Walther TC, Alves A, Pickersgill H, et al. The conserved Nup107-160 complex
is critical for nuclear pore complex assembly. Cell. 2003;113(2):195-206.
doi:10.1016/s0092-8674(03)00235-6
apa: Walther, T. C., Alves, A., Pickersgill, H., Loı̈odice, I., Hetzer, M., Galy,
V., … Doye, V. (2003). The conserved Nup107-160 complex is critical for nuclear
pore complex assembly. Cell. Elsevier. https://doi.org/10.1016/s0092-8674(03)00235-6
chicago: Walther, Tobias C., Annabelle Alves, Helen Pickersgill, Isabelle Loı̈odice,
Martin Hetzer, Vincent Galy, Bastian B. Hülsmann, et al. “The Conserved Nup107-160
Complex Is Critical for Nuclear Pore Complex Assembly.” Cell. Elsevier,
2003. https://doi.org/10.1016/s0092-8674(03)00235-6.
ieee: T. C. Walther et al., “The conserved Nup107-160 complex is critical
for nuclear pore complex assembly,” Cell, vol. 113, no. 2. Elsevier, pp.
195–206, 2003.
ista: Walther TC, Alves A, Pickersgill H, Loı̈odice I, Hetzer M, Galy V, Hülsmann
BB, Köcher T, Wilm M, Allen T, Mattaj IW, Doye V. 2003. The conserved Nup107-160
complex is critical for nuclear pore complex assembly. Cell. 113(2), 195–206.
mla: Walther, Tobias C., et al. “The Conserved Nup107-160 Complex Is Critical for
Nuclear Pore Complex Assembly.” Cell, vol. 113, no. 2, Elsevier, 2003,
pp. 195–206, doi:10.1016/s0092-8674(03)00235-6.
short: T.C. Walther, A. Alves, H. Pickersgill, I. Loı̈odice, M. Hetzer, V. Galy,
B.B. Hülsmann, T. Köcher, M. Wilm, T. Allen, I.W. Mattaj, V. Doye, Cell 113 (2003)
195–206.
date_created: 2022-04-07T07:57:10Z
date_published: 2003-04-17T00:00:00Z
date_updated: 2022-07-18T08:57:42Z
day: '17'
doi: 10.1016/s0092-8674(03)00235-6
extern: '1'
external_id:
pmid:
- '12705868'
intvolume: ' 113'
issue: '2'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '04'
oa_version: Published Version
page: 195-206
pmid: 1
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The conserved Nup107-160 complex is critical for nuclear pore complex assembly
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 113
year: '2003'
...
---
_id: '11124'
abstract:
- lang: eng
text: Ran GTPase plays important roles in nucleocytoplasmic transport in interphase
[1, 2] and in both spindle formation and nuclear envelope (NE) assembly during
mitosis [3, 4, 5]. The latter functions rely on the presence of high local concentrations
of GTP-bound Ran near mitotic chromatin [3, 4, 5]. RanGTP localization has been
proposed to result from the association of Ran's GDP/GTP exchange factor, RCC1,
with chromatin [6, 7, 8, 9], but Ran is shown here to bind directly to chromatin
in two modes, either dependent or independent of RCC1, and, where bound, to increase
the affinity of chromatin for NE membranes. We propose that the Ran binding capacity
of chromatin contributes to localized spindle and NE assembly.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Daniel
full_name: Bilbao-Cortés, Daniel
last_name: Bilbao-Cortés
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
- first_name: Gernot
full_name: Längst, Gernot
last_name: Längst
- first_name: Peter B.
full_name: Becker, Peter B.
last_name: Becker
- first_name: Iain W.
full_name: Mattaj, Iain W.
last_name: Mattaj
citation:
ama: Bilbao-Cortés D, Hetzer M, Längst G, Becker PB, Mattaj IW. Ran binds to chromatin
by two distinct mechanisms. Current Biology. 2002;12(13):1151-1156. doi:10.1016/s0960-9822(02)00927-2
apa: Bilbao-Cortés, D., Hetzer, M., Längst, G., Becker, P. B., & Mattaj, I.
W. (2002). Ran binds to chromatin by two distinct mechanisms. Current Biology.
Elsevier BV. https://doi.org/10.1016/s0960-9822(02)00927-2
chicago: Bilbao-Cortés, Daniel, Martin Hetzer, Gernot Längst, Peter B. Becker, and
Iain W. Mattaj. “Ran Binds to Chromatin by Two Distinct Mechanisms.” Current
Biology. Elsevier BV, 2002. https://doi.org/10.1016/s0960-9822(02)00927-2.
ieee: D. Bilbao-Cortés, M. Hetzer, G. Längst, P. B. Becker, and I. W. Mattaj, “Ran
binds to chromatin by two distinct mechanisms,” Current Biology, vol. 12,
no. 13. Elsevier BV, pp. 1151–1156, 2002.
ista: Bilbao-Cortés D, Hetzer M, Längst G, Becker PB, Mattaj IW. 2002. Ran binds
to chromatin by two distinct mechanisms. Current Biology. 12(13), 1151–1156.
mla: Bilbao-Cortés, Daniel, et al. “Ran Binds to Chromatin by Two Distinct Mechanisms.”
Current Biology, vol. 12, no. 13, Elsevier BV, 2002, pp. 1151–56, doi:10.1016/s0960-9822(02)00927-2.
short: D. Bilbao-Cortés, M. Hetzer, G. Längst, P.B. Becker, I.W. Mattaj, Current
Biology 12 (2002) 1151–1156.
date_created: 2022-04-07T07:57:31Z
date_published: 2002-07-09T00:00:00Z
date_updated: 2022-07-18T08:58:05Z
day: '09'
doi: 10.1016/s0960-9822(02)00927-2
extern: '1'
external_id:
pmid:
- '12121625'
intvolume: ' 12'
issue: '13'
keyword:
- General Agricultural and Biological Sciences
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/S0960-9822(02)00927-2
month: '07'
oa: 1
oa_version: Published Version
page: 1151-1156
pmid: 1
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Elsevier BV
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ran binds to chromatin by two distinct mechanisms
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 12
year: '2002'
...