---
_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: '13347'
abstract:
- lang: eng
text: Confining molecules within well-defined nanosized spaces can profoundly alter
their physicochemical characteristics. For example, the controlled aggregation
of chromophores into discrete oligomers has been shown to tune their optical properties
whereas encapsulation of reactive species within molecular hosts can increase
their stability. The resazurin/resorufin pair has been widely used for detecting
redox processes in biological settings; yet, how tight confinement affects the
properties of these two dyes remains to be explored. Here, we show that a flexible
PdII6L4 coordination
cage can efficiently encapsulate both resorufin and resazurin in the form of dimers,
dramatically modulating their optical properties. Furthermore, binding within
the cage significantly decreases the reduction rate of resazurin to resorufin,
and the rate of the subsequent reduction of resorufin to dihydroresorufin. During
our studies, we also found that upon dilution, the PdII6L4
cage disassembles to afford PdII2L2
species, which lacks the ability to form inclusion complexes – a process that
can be reversed upon the addition of the strongly binding resorufin/resazurin
guests. We expect that the herein disclosed ability of a water-soluble cage to
reversibly modulate the optical and chemical properties of a molecular redox probe
will expand the versatility of synthetic fluorescent probes in biologically relevant
environments.
article_number: '44'
article_processing_charge: No
article_type: original
author:
- first_name: Oksana
full_name: Yanshyna, Oksana
last_name: Yanshyna
- first_name: Michał J.
full_name: Białek, Michał J.
last_name: Białek
- first_name: Oleg V.
full_name: Chashchikhin, Oleg V.
last_name: Chashchikhin
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Yanshyna O, Białek MJ, Chashchikhin OV, Klajn R. Encapsulation within a coordination
cage modulates the reactivity of redox-active dyes. Communications Chemistry.
2022;5. doi:10.1038/s42004-022-00658-8
apa: Yanshyna, O., Białek, M. J., Chashchikhin, O. V., & Klajn, R. (2022). Encapsulation
within a coordination cage modulates the reactivity of redox-active dyes. Communications
Chemistry. Springer Nature. https://doi.org/10.1038/s42004-022-00658-8
chicago: Yanshyna, Oksana, Michał J. Białek, Oleg V. Chashchikhin, and Rafal Klajn.
“Encapsulation within a Coordination Cage Modulates the Reactivity of Redox-Active
Dyes.” Communications Chemistry. Springer Nature, 2022. https://doi.org/10.1038/s42004-022-00658-8.
ieee: O. Yanshyna, M. J. Białek, O. V. Chashchikhin, and R. Klajn, “Encapsulation
within a coordination cage modulates the reactivity of redox-active dyes,” Communications
Chemistry, vol. 5. Springer Nature, 2022.
ista: Yanshyna O, Białek MJ, Chashchikhin OV, Klajn R. 2022. Encapsulation within
a coordination cage modulates the reactivity of redox-active dyes. Communications
Chemistry. 5, 44.
mla: Yanshyna, Oksana, et al. “Encapsulation within a Coordination Cage Modulates
the Reactivity of Redox-Active Dyes.” Communications Chemistry, vol. 5,
44, Springer Nature, 2022, doi:10.1038/s42004-022-00658-8.
short: O. Yanshyna, M.J. Białek, O.V. Chashchikhin, R. Klajn, Communications Chemistry
5 (2022).
date_created: 2023-08-01T09:30:47Z
date_published: 2022-03-30T00:00:00Z
date_updated: 2023-08-02T06:41:54Z
day: '30'
doi: 10.1038/s42004-022-00658-8
extern: '1'
intvolume: ' 5'
keyword:
- Materials Chemistry
- Biochemistry
- Environmental Chemistry
- General Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s42004-022-00658-8
month: '03'
oa: 1
oa_version: Published Version
publication: Communications Chemistry
publication_identifier:
eissn:
- 2399-3669
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Encapsulation within a coordination cage modulates the reactivity of redox-active
dyes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2022'
...
---
_id: '13348'
abstract:
- lang: eng
text: Molecular confinement effects can profoundly alter the physicochemical properties
of the confined species. A plethora of organic molecules were encapsulated within
the cavities of supramolecular hosts, and the impact of the cavity size and polarity
was widely investigated. However, the extent to which the properties of the confined
guests can be affected by the symmetry of the cage─which dictates the shape of
the cavity─remains to be understood. Here we show that cage symmetry has a dramatic
effect on the equilibrium between two isomers of the encapsulated spiropyran guests.
Working with two Pd-based coordination cages featuring similarly sized but differently
shaped hydrophobic cavities, we found a highly selective stabilization of the
isomer whose shape matches that of the cavity of the cage. A Td-symmetric cage
stabilized the spiropyrans’ colorless form and rendered them photochemically inert.
In contrast, a D2h-symmetric cage favored the colored isomer, while maintaining
reversible photoswitching between the two states of the encapsulated spiropyrans.
We also show that the switching kinetics strongly depend on the substitution pattern
on the spiropyran scaffold. This finding was used to fabricate a time-sensitive
information storage medium with tunable lifetimes of the encoded messages.
article_processing_charge: No
article_type: original
author:
- first_name: Jinhua
full_name: Wang, Jinhua
last_name: Wang
- first_name: Liat
full_name: Avram, Liat
last_name: Avram
- first_name: Yael
full_name: Diskin-Posner, Yael
last_name: Diskin-Posner
- first_name: Michał J.
full_name: Białek, Michał J.
last_name: Białek
- first_name: Wojciech
full_name: Stawski, Wojciech
last_name: Stawski
- first_name: Moran
full_name: Feller, Moran
last_name: Feller
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Wang J, Avram L, Diskin-Posner Y, et al. Altering the properties of spiropyran
switches using coordination cages with different symmetries. Journal of the
American Chemical Society. 2022;144(46):21244-21254. doi:10.1021/jacs.2c08901
apa: Wang, J., Avram, L., Diskin-Posner, Y., Białek, M. J., Stawski, W., Feller,
M., & Klajn, R. (2022). Altering the properties of spiropyran switches using
coordination cages with different symmetries. Journal of the American Chemical
Society. American Chemical Society. https://doi.org/10.1021/jacs.2c08901
chicago: Wang, Jinhua, Liat Avram, Yael Diskin-Posner, Michał J. Białek, Wojciech
Stawski, Moran Feller, and Rafal Klajn. “Altering the Properties of Spiropyran
Switches Using Coordination Cages with Different Symmetries.” Journal of the
American Chemical Society. American Chemical Society, 2022. https://doi.org/10.1021/jacs.2c08901.
ieee: J. Wang et al., “Altering the properties of spiropyran switches using
coordination cages with different symmetries,” Journal of the American Chemical
Society, vol. 144, no. 46. American Chemical Society, pp. 21244–21254, 2022.
ista: Wang J, Avram L, Diskin-Posner Y, Białek MJ, Stawski W, Feller M, Klajn R.
2022. Altering the properties of spiropyran switches using coordination cages
with different symmetries. Journal of the American Chemical Society. 144(46),
21244–21254.
mla: Wang, Jinhua, et al. “Altering the Properties of Spiropyran Switches Using
Coordination Cages with Different Symmetries.” Journal of the American Chemical
Society, vol. 144, no. 46, American Chemical Society, 2022, pp. 21244–54,
doi:10.1021/jacs.2c08901.
short: J. Wang, L. Avram, Y. Diskin-Posner, M.J. Białek, W. Stawski, M. Feller,
R. Klajn, Journal of the American Chemical Society 144 (2022) 21244–21254.
date_created: 2023-08-01T09:31:01Z
date_published: 2022-11-15T00:00:00Z
date_updated: 2023-08-02T06:39:50Z
day: '15'
doi: 10.1021/jacs.2c08901
extern: '1'
intvolume: ' 144'
issue: '46'
keyword:
- Colloid and Surface Chemistry
- Biochemistry
- General Chemistry
- Catalysis
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1021/jacs.2c08901
month: '11'
oa: 1
oa_version: Published Version
page: 21244-21254
publication: Journal of the American Chemical Society
publication_identifier:
eissn:
- 1520-5126
issn:
- 0002-7863
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Altering the properties of spiropyran switches using coordination cages with
different symmetries
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 144
year: '2022'
...
---
_id: '13350'
abstract:
- lang: eng
text: Confinement within molecular cages can dramatically modify the physicochemical
properties of the encapsulated guest molecules, but such host-guest complexes
have mainly been studied in a static context. Combining confinement effects with
fast guest exchange kinetics could pave the way toward stimuli-responsive supramolecular
systems—and ultimately materials—whose desired properties could be tailored “on
demand” rapidly and reversibly. Here, we demonstrate rapid guest exchange between
inclusion complexes of an open-window coordination cage that can simultaneously
accommodate two guest molecules. Working with two types of guests, anthracene
derivatives and BODIPY dyes, we show that the former can substantially modify
the optical properties of the latter upon noncovalent heterodimer formation. We
also studied the light-induced covalent dimerization of encapsulated anthracenes
and found large effects of confinement on reaction rates. By coupling the photodimerization
with the rapid guest exchange, we developed a new way to modulate fluorescence
using external irradiation.
article_processing_charge: No
article_type: original
author:
- first_name: Julius
full_name: Gemen, Julius
last_name: Gemen
- first_name: Michał J.
full_name: Białek, Michał J.
last_name: Białek
- first_name: Miri
full_name: Kazes, Miri
last_name: Kazes
- first_name: Linda J.W.
full_name: Shimon, Linda J.W.
last_name: Shimon
- first_name: Moran
full_name: Feller, Moran
last_name: Feller
- first_name: Sergey N.
full_name: Semenov, Sergey N.
last_name: Semenov
- first_name: Yael
full_name: Diskin-Posner, Yael
last_name: Diskin-Posner
- first_name: Dan
full_name: Oron, Dan
last_name: Oron
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Gemen J, Białek MJ, Kazes M, et al. Ternary host-guest complexes with rapid
exchange kinetics and photoswitchable fluorescence. Chem. 2022;8(9):2362-2379.
doi:10.1016/j.chempr.2022.05.008
apa: Gemen, J., Białek, M. J., Kazes, M., Shimon, L. J. W., Feller, M., Semenov,
S. N., … Klajn, R. (2022). Ternary host-guest complexes with rapid exchange kinetics
and photoswitchable fluorescence. Chem. Elsevier. https://doi.org/10.1016/j.chempr.2022.05.008
chicago: Gemen, Julius, Michał J. Białek, Miri Kazes, Linda J.W. Shimon, Moran Feller,
Sergey N. Semenov, Yael Diskin-Posner, Dan Oron, and Rafal Klajn. “Ternary Host-Guest
Complexes with Rapid Exchange Kinetics and Photoswitchable Fluorescence.” Chem.
Elsevier, 2022. https://doi.org/10.1016/j.chempr.2022.05.008.
ieee: J. Gemen et al., “Ternary host-guest complexes with rapid exchange
kinetics and photoswitchable fluorescence,” Chem, vol. 8, no. 9. Elsevier,
pp. 2362–2379, 2022.
ista: Gemen J, Białek MJ, Kazes M, Shimon LJW, Feller M, Semenov SN, Diskin-Posner
Y, Oron D, Klajn R. 2022. Ternary host-guest complexes with rapid exchange kinetics
and photoswitchable fluorescence. Chem. 8(9), 2362–2379.
mla: Gemen, Julius, et al. “Ternary Host-Guest Complexes with Rapid Exchange Kinetics
and Photoswitchable Fluorescence.” Chem, vol. 8, no. 9, Elsevier, 2022,
pp. 2362–79, doi:10.1016/j.chempr.2022.05.008.
short: J. Gemen, M.J. Białek, M. Kazes, L.J.W. Shimon, M. Feller, S.N. Semenov,
Y. Diskin-Posner, D. Oron, R. Klajn, Chem 8 (2022) 2362–2379.
date_created: 2023-08-01T09:32:14Z
date_published: 2022-09-08T00:00:00Z
date_updated: 2023-08-02T09:39:35Z
day: '08'
doi: 10.1016/j.chempr.2022.05.008
extern: '1'
external_id:
pmid:
- '36133801'
intvolume: ' 8'
issue: '9'
keyword:
- Materials Chemistry
- Biochemistry (medical)
- General Chemical Engineering
- Environmental Chemistry
- Biochemistry
- General Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.chempr.2022.05.008
month: '09'
oa: 1
oa_version: Published Version
page: 2362-2379
pmid: 1
publication: Chem
publication_identifier:
eissn:
- 2451-9294
issn:
- 2451-9308
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ternary host-guest complexes with rapid exchange kinetics and photoswitchable
fluorescence
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2022'
...
---
_id: '13351'
abstract:
- lang: eng
text: 'Molecular recognition is at the heart of the noncovalent synthesis of supramolecular
assemblies and, at higher length scales, supramolecular materials. In a recent
publication in Nature, Stoddart and co-workers demonstrate that the formation
of host-guest complexes can be catalyzed by one of the simplest possible catalysts:
the electron.'
article_processing_charge: No
article_type: original
author:
- first_name: Julius
full_name: Gemen, Julius
last_name: Gemen
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Gemen J, Klajn R. Electron catalysis expands the supramolecular chemist’s toolbox.
Chem. 2022;8(5):1183-1186. doi:10.1016/j.chempr.2022.04.022
apa: Gemen, J., & Klajn, R. (2022). Electron catalysis expands the supramolecular
chemist’s toolbox. Chem. Elsevier. https://doi.org/10.1016/j.chempr.2022.04.022
chicago: Gemen, Julius, and Rafal Klajn. “Electron Catalysis Expands the Supramolecular
Chemist’s Toolbox.” Chem. Elsevier, 2022. https://doi.org/10.1016/j.chempr.2022.04.022.
ieee: J. Gemen and R. Klajn, “Electron catalysis expands the supramolecular chemist’s
toolbox,” Chem, vol. 8, no. 5. Elsevier, pp. 1183–1186, 2022.
ista: Gemen J, Klajn R. 2022. Electron catalysis expands the supramolecular chemist’s
toolbox. Chem. 8(5), 1183–1186.
mla: Gemen, Julius, and Rafal Klajn. “Electron Catalysis Expands the Supramolecular
Chemist’s Toolbox.” Chem, vol. 8, no. 5, Elsevier, 2022, pp. 1183–86, doi:10.1016/j.chempr.2022.04.022.
short: J. Gemen, R. Klajn, Chem 8 (2022) 1183–1186.
date_created: 2023-08-01T09:32:27Z
date_published: 2022-05-12T00:00:00Z
date_updated: 2023-08-02T07:24:57Z
day: '12'
doi: 10.1016/j.chempr.2022.04.022
extern: '1'
intvolume: ' 8'
issue: '5'
keyword:
- Materials Chemistry
- Biochemistry (medical)
- General Chemical Engineering
- Environmental Chemistry
- Biochemistry
- General Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.chempr.2022.04.022
month: '05'
oa: 1
oa_version: Published Version
page: 1183-1186
publication: Chem
publication_identifier:
eissn:
- 2451-9294
issn:
- 2451-9308
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Electron catalysis expands the supramolecular chemist’s toolbox
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
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: '12051'
abstract:
- lang: eng
text: Transcription of the ribosomal RNA precursor by RNA polymerase (Pol) I is
a major determinant of cellular growth, and dysregulation is observed in many
cancer types. Here, we present the purification of human Pol I from cells carrying
a genomic GFP fusion on the largest subunit allowing the structural and functional
analysis of the enzyme across species. In contrast to yeast, human Pol I carries
a single-subunit stalk, and in vitro transcription indicates a reduced proofreading
activity. Determination of the human Pol I cryo-EM reconstruction in a close-to-native
state rationalizes the effects of disease-associated mutations and uncovers an
additional domain that is built into the sequence of Pol I subunit RPA1. This
“dock II” domain resembles a truncated HMG box incapable of DNA binding which
may serve as a downstream transcription factor–binding platform in metazoans.
Biochemical analysis, in situ modelling, and ChIP data indicate that Topoisomerase
2a can be recruited to Pol I via the domain and cooperates with the HMG box domain–containing
factor UBF. These adaptations of the metazoan Pol I transcription system may allow
efficient release of positive DNA supercoils accumulating downstream of the transcription
bubble.
acknowledgement: "The authors especially thank Philip Gunkel for his contribution.
We thank all\r\npast and present members of the Engel lab, Achim Griesenbeck, Colyn
Crane-\r\nRobinson, Christophe Lotz, Marlene Vayssieres, Klaus Grasser, Herbert
Tschochner, and Philipp Milkereit for help and discussion; Gerhard Lehmann and Nobert
Eichner for IT support; Joost Zomerdijk for UBF-constructs, Volker Cordes for the
Hela P2 cell line; Remco Sprangers for shared cell culture; Dina Grohmann and the
Archaea Center for fermentation; and Thomas\r\nDresselhaus for access to fluorescence
microscopes. This work was in part supported by the Emmy-Noether Programm (DFG grant
no. EN 1204/1-1 to C Engel) of the German Research Council and Collaborative Research
Center 960 (TP-A8 to C Engel)."
article_number: e202201568
article_processing_charge: No
article_type: original
author:
- first_name: Julia L
full_name: Daiß, Julia L
last_name: Daiß
- first_name: Michael
full_name: Pilsl, Michael
last_name: Pilsl
- first_name: Kristina
full_name: Straub, Kristina
last_name: Straub
- first_name: Andrea
full_name: Bleckmann, Andrea
last_name: Bleckmann
- first_name: Mona
full_name: Höcherl, Mona
last_name: Höcherl
- first_name: Florian B
full_name: Heiss, Florian B
last_name: Heiss
- first_name: Guillermo
full_name: Abascal-Palacios, Guillermo
last_name: Abascal-Palacios
- first_name: Ewan P
full_name: Ramsay, Ewan P
last_name: Ramsay
- first_name: Katarina
full_name: Tluckova, Katarina
id: 4AC7D980-F248-11E8-B48F-1D18A9856A87
last_name: Tluckova
- first_name: Jean-Clement
full_name: Mars, Jean-Clement
last_name: Mars
- first_name: Torben
full_name: Fürtges, Torben
last_name: Fürtges
- first_name: Astrid
full_name: Bruckmann, Astrid
last_name: Bruckmann
- first_name: Till
full_name: Rudack, Till
last_name: Rudack
- 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: Valérie
full_name: Lamour, Valérie
last_name: Lamour
- first_name: Konstantin
full_name: Panov, Konstantin
last_name: Panov
- first_name: Alessandro
full_name: Vannini, Alessandro
last_name: Vannini
- first_name: Tom
full_name: Moss, Tom
last_name: Moss
- first_name: Christoph
full_name: Engel, Christoph
last_name: Engel
citation:
ama: Daiß JL, Pilsl M, Straub K, et al. The human RNA polymerase I structure reveals
an HMG-like docking domain specific to metazoans. Life Science Alliance.
2022;5(11). doi:10.26508/lsa.202201568
apa: Daiß, J. L., Pilsl, M., Straub, K., Bleckmann, A., Höcherl, M., Heiss, F. B.,
… Engel, C. (2022). The human RNA polymerase I structure reveals an HMG-like docking
domain specific to metazoans. Life Science Alliance. Life Science Alliance.
https://doi.org/10.26508/lsa.202201568
chicago: Daiß, Julia L, Michael Pilsl, Kristina Straub, Andrea Bleckmann, Mona Höcherl,
Florian B Heiss, Guillermo Abascal-Palacios, et al. “The Human RNA Polymerase
I Structure Reveals an HMG-like Docking Domain Specific to Metazoans.” Life
Science Alliance. Life Science Alliance, 2022. https://doi.org/10.26508/lsa.202201568.
ieee: J. L. Daiß et al., “The human RNA polymerase I structure reveals an
HMG-like docking domain specific to metazoans,” Life Science Alliance,
vol. 5, no. 11. Life Science Alliance, 2022.
ista: Daiß JL, Pilsl M, Straub K, Bleckmann A, Höcherl M, Heiss FB, Abascal-Palacios
G, Ramsay EP, Tluckova K, Mars J-C, Fürtges T, Bruckmann A, Rudack T, Bernecky
C, Lamour V, Panov K, Vannini A, Moss T, Engel C. 2022. The human RNA polymerase
I structure reveals an HMG-like docking domain specific to metazoans. Life Science
Alliance. 5(11), e202201568.
mla: Daiß, Julia L., et al. “The Human RNA Polymerase I Structure Reveals an HMG-like
Docking Domain Specific to Metazoans.” Life Science Alliance, vol. 5, no.
11, e202201568, Life Science Alliance, 2022, doi:10.26508/lsa.202201568.
short: J.L. Daiß, M. Pilsl, K. Straub, A. Bleckmann, M. Höcherl, F.B. Heiss, G.
Abascal-Palacios, E.P. Ramsay, K. Tluckova, J.-C. Mars, T. Fürtges, A. Bruckmann,
T. Rudack, C. Bernecky, V. Lamour, K. Panov, A. Vannini, T. Moss, C. Engel, Life
Science Alliance 5 (2022).
date_created: 2022-09-06T18:45:23Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2023-08-03T13:39:36Z
day: '01'
ddc:
- '570'
department:
- _id: CaBe
doi: 10.26508/lsa.202201568
external_id:
isi:
- '000972702600001'
file:
- access_level: open_access
checksum: 4201d876a3e5e8b65e319d03300014ad
content_type: application/pdf
creator: dernst
date_created: 2022-09-08T06:41:14Z
date_updated: 2022-09-08T06:41:14Z
file_id: '12062'
file_name: 2022_LifeScienceAlliance_Daiss.pdf
file_size: 3183129
relation: main_file
success: 1
file_date_updated: 2022-09-08T06:41:14Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '11'
keyword:
- Health
- Toxicology and Mutagenesis
- Plant Science
- Biochemistry
- Genetics and Molecular Biology (miscellaneous)
- Ecology
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Life Science Alliance
publication_identifier:
issn:
- 2575-1077
publication_status: published
publisher: Life Science Alliance
quality_controlled: '1'
status: public
title: The human RNA polymerase I structure reveals an HMG-like docking domain specific
to metazoans
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: '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:
- access_level: open_access
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: '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: '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: '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: '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: '12275'
abstract:
- lang: eng
text: N-glycans are molecularly diverse sugars borne by over 70% of proteins transiting
the secretory pathway and have been implicated in protein folding, stability,
and localization. Mutations in genes important for N-glycosylation result in congenital
disorders of glycosylation that are often associated with intellectual disability.
Here, we show that structurally distinct N-glycans regulate an extracellular protein
complex involved in the patterning of somatosensory dendrites in Caenorhabditis
elegans. Specifically, aman-2/Golgi alpha-mannosidase II, a conserved key enzyme
in the biosynthesis of specific N-glycans, regulates the activity of the Menorin
adhesion complex without obviously affecting the protein stability and localization
of its components. AMAN-2 functions cell-autonomously to allow for decoration
of the neuronal transmembrane receptor DMA-1/LRR-TM with the correct set of high-mannose/hybrid/paucimannose
N-glycans. Moreover, distinct types of N-glycans on specific N-glycosylation sites
regulate DMA-1/LRR-TM receptor function, which, together with three other extracellular
proteins, forms the Menorin adhesion complex. In summary, specific N-glycan structures
regulate dendrite patterning by coordinating the activity of an extracellular
adhesion complex, suggesting that the molecular diversity of N-glycans can contribute
to developmental specificity in the nervous system.
acknowledgement: 'We thank Scott Garforth, Sarah Garrett, Peri Kurshan, Yehuda Salzberg,
PamelaStanley, Robert Townley, and members of the B€ulow laboratory for commentson
the manuscript or helpful discussions during the course of this work. Wethank David
Miller, Shohei Mitani, Kang Shen, and Iain Wilson for reagents,and Yuji Kohara for
theyk11g705cDNA clone. We are grateful to MeeraTrivedi for sharing thedzIs117strain
prior to publication. Some strains wereprovided by the Caenorhabditis Genome Center
(funded by the NIH Office ofResearch Infrastructure Programs P40OD010440). This
work was supportedby grants from the National Institute of Health (NIH): R01NS096672andR21NS111145to
HEB; F31NS100370to MR; T32GM007288and F31HD066967to CADB; P30HD071593to Albert Einstein
College of Medicine. We acknowl-edge support to MR by the Department of Neuroscience.
NJRS was the recipi-ent of a Colciencias-Fulbright Fellowship and HEB of an Irma
T. Hirschl/Monique Weill-Caulier research fellowship'
article_number: e54163
article_processing_charge: No
article_type: original
author:
- first_name: Maisha
full_name: Rahman, Maisha
last_name: Rahman
- first_name: Nelson
full_name: Ramirez, Nelson
id: 39831956-E4FE-11E9-85DE-0DC7E5697425
last_name: Ramirez
- first_name: Carlos A
full_name: Diaz‐Balzac, Carlos A
last_name: Diaz‐Balzac
- first_name: Hannes E
full_name: Bülow, Hannes E
last_name: Bülow
citation:
ama: Rahman M, Ramirez N, Diaz‐Balzac CA, Bülow HE. Specific N-glycans regulate
an extracellular adhesion complex during somatosensory dendrite patterning. EMBO
Reports. 2022;23(7). doi:10.15252/embr.202154163
apa: Rahman, M., Ramirez, N., Diaz‐Balzac, C. A., & Bülow, H. E. (2022). Specific
N-glycans regulate an extracellular adhesion complex during somatosensory dendrite
patterning. EMBO Reports. Embo Press. https://doi.org/10.15252/embr.202154163
chicago: Rahman, Maisha, Nelson Ramirez, Carlos A Diaz‐Balzac, and Hannes E Bülow.
“Specific N-Glycans Regulate an Extracellular Adhesion Complex during Somatosensory
Dendrite Patterning.” EMBO Reports. Embo Press, 2022. https://doi.org/10.15252/embr.202154163.
ieee: M. Rahman, N. Ramirez, C. A. Diaz‐Balzac, and H. E. Bülow, “Specific N-glycans
regulate an extracellular adhesion complex during somatosensory dendrite patterning,”
EMBO Reports, vol. 23, no. 7. Embo Press, 2022.
ista: Rahman M, Ramirez N, Diaz‐Balzac CA, Bülow HE. 2022. Specific N-glycans regulate
an extracellular adhesion complex during somatosensory dendrite patterning. EMBO
Reports. 23(7), e54163.
mla: Rahman, Maisha, et al. “Specific N-Glycans Regulate an Extracellular Adhesion
Complex during Somatosensory Dendrite Patterning.” EMBO Reports, vol. 23,
no. 7, e54163, Embo Press, 2022, doi:10.15252/embr.202154163.
short: M. Rahman, N. Ramirez, C.A. Diaz‐Balzac, H.E. Bülow, EMBO Reports 23 (2022).
date_created: 2023-01-16T10:01:44Z
date_published: 2022-07-05T00:00:00Z
date_updated: 2023-10-03T11:25:54Z
day: '05'
department:
- _id: MaDe
doi: 10.15252/embr.202154163
external_id:
isi:
- '000797302700001'
pmid:
- '35586945'
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
issue: '7'
keyword:
- Genetics
- Molecular Biology
- Biochemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.15252/embr.202154163
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: EMBO Reports
publication_identifier:
eissn:
- 1469-3178
issn:
- 1469-221X
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Specific N-glycans regulate an extracellular adhesion complex during somatosensory
dendrite patterning
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2022'
...
---
_id: '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: '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'
...