---
_id: '797'
abstract:
- lang: ger
  text: Phasenübergänge helfen beim Verständnis von Vielteilchensystemen in der Festkörperphysik
    und Fluiddynamik bis hin zur Teilchenphysik. Unserer internationalen Kollaboration
    ist es gelungen, einen neuartigen Phasenübergang in einem Quantensystem zu beobachten
    [1]. In einem Mikrowellenresonator konnte erstmals die spontane Zustandsänderung
    von undurchsichtig zu transparent nachgewiesen werden.
article_processing_charge: No
article_type: original
author:
- first_name: Johannes M
  full_name: Fink, Johannes M
  id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
  last_name: Fink
  orcid: 0000-0001-8112-028X
citation:
  ama: Fink JM. Photonenblockade aufgelöst. <i>Physik in unserer Zeit</i>. 2017;48(3):111-113.
    doi:<a href="https://doi.org/10.1002/piuz.201770305">10.1002/piuz.201770305</a>
  apa: Fink, J. M. (2017). Photonenblockade aufgelöst. <i>Physik in Unserer Zeit</i>.
    Wiley. <a href="https://doi.org/10.1002/piuz.201770305">https://doi.org/10.1002/piuz.201770305</a>
  chicago: Fink, Johannes M. “Photonenblockade Aufgelöst.” <i>Physik in Unserer Zeit</i>.
    Wiley, 2017. <a href="https://doi.org/10.1002/piuz.201770305">https://doi.org/10.1002/piuz.201770305</a>.
  ieee: J. M. Fink, “Photonenblockade aufgelöst,” <i>Physik in unserer Zeit</i>, vol.
    48, no. 3. Wiley, pp. 111–113, 2017.
  ista: Fink JM. 2017. Photonenblockade aufgelöst. Physik in unserer Zeit. 48(3),
    111–113.
  mla: Fink, Johannes M. “Photonenblockade Aufgelöst.” <i>Physik in Unserer Zeit</i>,
    vol. 48, no. 3, Wiley, 2017, pp. 111–13, doi:<a href="https://doi.org/10.1002/piuz.201770305">10.1002/piuz.201770305</a>.
  short: J.M. Fink, Physik in Unserer Zeit 48 (2017) 111–113.
corr_author: '1'
date_created: 2018-12-11T11:48:33Z
date_published: 2017-05-01T00:00:00Z
date_updated: 2024-10-09T20:57:34Z
day: '01'
department:
- _id: JoFi
doi: 10.1002/piuz.201770305
fulldoi: https://doi.org/10.1002/piuz.201770305
intvolume: '        48'
issue: '3'
language:
- iso: eng
month: '05'
oa_version: None
page: 111 - 113
publication: Physik in unserer Zeit
publication_status: published
publisher: Wiley
publist_id: '6856'
quality_controlled: '1'
status: public
title: Photonenblockade aufgelöst
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 48
year: '2017'
...
---
_id: '798'
abstract:
- lang: eng
  text: Nonreciprocal circuit elements form an integral part of modern measurement
    and communication systems. Mathematically they require breaking of time-reversal
    symmetry, typically achieved using magnetic materials and more recently using
    the quantum Hall effect, parametric permittivity modulation or Josephson nonlinearities.
    Here we demonstrate an on-chip magnetic-free circulator based on reservoir-engineered
    electromechanic interactions. Directional circulation is achieved with controlled
    phase-sensitive interference of six distinct electro-mechanical signal conversion
    paths. The presented circulator is compact, its silicon-on-insulator platform
    is compatible with both superconducting qubits and silicon photonics, and its
    noise performance is close to the quantum limit. With a high dynamic range, a
    tunable bandwidth of up to 30 MHz and an in situ reconfigurability as beam splitter
    or wavelength converter, it could pave the way for superconducting qubit processors
    with multiplexed on-chip signal processing and readout.
article_number: '1304'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Shabir
  full_name: Barzanjeh, Shabir
  id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
  last_name: Barzanjeh
  orcid: 0000-0003-0415-1423
- first_name: Matthias
  full_name: Wulf, Matthias
  id: 45598606-F248-11E8-B48F-1D18A9856A87
  last_name: Wulf
  orcid: 0000-0001-6613-1378
- first_name: Matilda
  full_name: Peruzzo, Matilda
  id: 3F920B30-F248-11E8-B48F-1D18A9856A87
  last_name: Peruzzo
  orcid: 0000-0002-3415-4628
- first_name: Mahmoud
  full_name: Kalaee, Mahmoud
  last_name: Kalaee
- first_name: Paul
  full_name: Dieterle, Paul
  last_name: Dieterle
- first_name: Oskar
  full_name: Painter, Oskar
  last_name: Painter
- first_name: Johannes M
  full_name: Fink, Johannes M
  id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
  last_name: Fink
  orcid: 0000-0001-8112-028X
citation:
  ama: Barzanjeh S, Wulf M, Peruzzo M, et al. Mechanical on chip microwave circulator.
    <i>Nature Communications</i>. 2017;8(1). doi:<a href="https://doi.org/10.1038/s41467-017-01304-x">10.1038/s41467-017-01304-x</a>
  apa: Barzanjeh, S., Wulf, M., Peruzzo, M., Kalaee, M., Dieterle, P., Painter, O.,
    &#38; Fink, J. M. (2017). Mechanical on chip microwave circulator. <i>Nature Communications</i>.
    Nature Publishing Group. <a href="https://doi.org/10.1038/s41467-017-01304-x">https://doi.org/10.1038/s41467-017-01304-x</a>
  chicago: Barzanjeh, Shabir, Matthias Wulf, Matilda Peruzzo, Mahmoud Kalaee, Paul
    Dieterle, Oskar Painter, and Johannes M Fink. “Mechanical on Chip Microwave Circulator.”
    <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href="https://doi.org/10.1038/s41467-017-01304-x">https://doi.org/10.1038/s41467-017-01304-x</a>.
  ieee: S. Barzanjeh <i>et al.</i>, “Mechanical on chip microwave circulator,” <i>Nature
    Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.
  ista: Barzanjeh S, Wulf M, Peruzzo M, Kalaee M, Dieterle P, Painter O, Fink JM.
    2017. Mechanical on chip microwave circulator. Nature Communications. 8(1), 1304.
  mla: Barzanjeh, Shabir, et al. “Mechanical on Chip Microwave Circulator.” <i>Nature
    Communications</i>, vol. 8, no. 1, 1304, Nature Publishing Group, 2017, doi:<a
    href="https://doi.org/10.1038/s41467-017-01304-x">10.1038/s41467-017-01304-x</a>.
  short: S. Barzanjeh, M. Wulf, M. Peruzzo, M. Kalaee, P. Dieterle, O. Painter, J.M.
    Fink, Nature Communications 8 (2017).
corr_author: '1'
date_created: 2018-12-11T11:48:33Z
date_published: 2017-10-16T00:00:00Z
date_updated: 2025-07-10T11:54:54Z
day: '16'
ddc:
- '539'
department:
- _id: JoFi
doi: 10.1038/s41467-017-01304-x
ec_funded: 1
external_id:
  isi:
  - '000412999700021'
file:
- access_level: open_access
  checksum: b68dafa71d1834c23b742cd9987a3d5f
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:15:25Z
  date_updated: 2020-07-14T12:48:06Z
  file_id: '5145'
  file_name: IST-2017-867-v1+1_s41467-017-01304-x.pdf
  file_size: 1467696
  relation: main_file
file_date_updated: 2020-07-14T12:48:06Z
fulldoi: https://doi.org/10.1038/s41467-017-01304-x
has_accepted_license: '1'
intvolume: '         8'
isi: 1
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 257EB838-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '732894'
  name: Hybrid Optomechanical Technologies
- _id: 258047B6-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '707438'
  name: 'Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination
    with cavity Optomechanics'
publication: Nature Communications
publication_identifier:
  issn:
  - 2041-1723
publication_status: published
publisher: Nature Publishing Group
publist_id: '6855'
pubrep_id: '867'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanical on chip microwave circulator
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '7980'
abstract:
- lang: eng
  text: In this part, the use of polysaccharides, either directly through composite
    approaches, or by carbonization will be described. In many cases, materials are
    obtained which are competitive in terms of capacitance and cycle lifetime. In
    this part, the use of polysaccharides, either directly through composite approaches,
    or by carbonization will be described. In many cases, materials are obtained which
    are competitive in terms of capacitance and cycle lifetime. The following part
    will focus mainly on cellulosic composites with conductive polymers since cellulose
    is most abundant and therefore has attracted much more research interest in this
    field whereas in the second part also other polysaccharides, such as chitin, xylans,
    alginates, pectins, dextrans and caragenaans have been used in carbonization experiments.
alternative_title:
- SpringerBriefs in Molecular Science
article_processing_charge: No
author:
- first_name: Soon
  full_name: Yee Liew, Soon
  last_name: Yee Liew
- first_name: Wim
  full_name: Thielemans, Wim
  last_name: Thielemans
- 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: Stefan
  full_name: Spirk, Stefan
  last_name: Spirk
citation:
  ama: 'Yee Liew S, Thielemans W, Freunberger SA, Spirk S. Polysaccharides in supercapacitors.
    In: Yee Liew S, Thielemans W, Freunberger SA, Spirk S, eds. <i>Polysaccharide
    Based Supercapacitors</i>. Springer Nature; 2017:15-53. doi:<a href="https://doi.org/10.1007/978-3-319-50754-5_2">10.1007/978-3-319-50754-5_2</a>'
  apa: Yee Liew, S., Thielemans, W., Freunberger, S. A., &#38; Spirk, S. (2017). Polysaccharides
    in supercapacitors. In S. Yee Liew, W. Thielemans, S. A. Freunberger, &#38; S.
    Spirk (Eds.), <i>Polysaccharide Based Supercapacitors</i> (pp. 15–53). Springer
    Nature. <a href="https://doi.org/10.1007/978-3-319-50754-5_2">https://doi.org/10.1007/978-3-319-50754-5_2</a>
  chicago: Yee Liew, Soon, Wim Thielemans, Stefan Alexander Freunberger, and Stefan
    Spirk. “Polysaccharides in Supercapacitors.” In <i>Polysaccharide Based Supercapacitors</i>,
    edited by Soon Yee Liew, Wim Thielemans, Stefan Alexander Freunberger, and Stefan
    Spirk, 15–53. Springer Nature, 2017. <a href="https://doi.org/10.1007/978-3-319-50754-5_2">https://doi.org/10.1007/978-3-319-50754-5_2</a>.
  ieee: S. Yee Liew, W. Thielemans, S. A. Freunberger, and S. Spirk, “Polysaccharides
    in supercapacitors,” in <i>Polysaccharide Based Supercapacitors</i>, S. Yee Liew,
    W. Thielemans, S. A. Freunberger, and S. Spirk, Eds. Springer Nature, 2017, pp.
    15–53.
  ista: 'Yee Liew S, Thielemans W, Freunberger SA, Spirk S. 2017.Polysaccharides in
    supercapacitors. In: Polysaccharide Based Supercapacitors. SpringerBriefs in Molecular
    Science, , 15–53.'
  mla: Yee Liew, Soon, et al. “Polysaccharides in Supercapacitors.” <i>Polysaccharide
    Based Supercapacitors</i>, edited by Soon Yee Liew et al., Springer Nature, 2017,
    pp. 15–53, doi:<a href="https://doi.org/10.1007/978-3-319-50754-5_2">10.1007/978-3-319-50754-5_2</a>.
  short: S. Yee Liew, W. Thielemans, S.A. Freunberger, S. Spirk, in:, S. Yee Liew,
    W. Thielemans, S.A. Freunberger, S. Spirk (Eds.), Polysaccharide Based Supercapacitors,
    Springer Nature, 2017, pp. 15–53.
date_created: 2020-06-19T08:11:08Z
date_published: 2017-03-26T00:00:00Z
date_updated: 2021-01-12T08:16:19Z
day: '26'
ddc:
- '540'
- '541'
doi: 10.1007/978-3-319-50754-5_2
editor:
- first_name: Soon
  full_name: Yee Liew, Soon
  last_name: Yee Liew
- first_name: Wim
  full_name: Thielemans, Wim
  last_name: Thielemans
- 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: Stefan
  full_name: Spirk, Stefan
  last_name: Spirk
extern: '1'
file:
- access_level: open_access
  checksum: 4182aeee32c9263a626a7e522f1934f5
  content_type: application/pdf
  creator: sfreunbe
  date_created: 2020-06-29T14:13:44Z
  date_updated: 2020-07-14T12:48:06Z
  file_id: '8048'
  file_name: Final_EPNOE.pdf
  file_size: 3339826
  relation: main_file
file_date_updated: 2020-07-14T12:48:06Z
fulldoi: https://doi.org/10.1007/978-3-319-50754-5_2
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 15-53
publication: Polysaccharide Based Supercapacitors
publication_identifier:
  isbn:
  - '9783319507538'
  - '9783319507545'
  issn:
  - 2191-5407
  - 2191-5415
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Polysaccharides in supercapacitors
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '7981'
abstract:
- lang: ger
  text: Aprotische Natrium‐O2‐Batterien basieren auf der reversiblen Bildung und Auflösung
    von Natriumsuperoxid (NaO2) während des Zellbetriebs. Nebenreaktionen des Elektrolyten
    und der Elektrode mit dem stark nukleophilen und basischen NaO2 führen zu mangelhafter
    Zyklenstabilität. Seine Reaktivität allein kann die Nebenreaktionen und schlechte
    Reversibilität jedoch nicht schlüssig erklären. Hier wird gezeigt, dass Singulett‐Sauerstoff
    (1O2) in allen Phasen des Betriebs entsteht und eine Hauptursache für Nebenreaktionen
    ist. 1O2 wurde in situ und ex situ mit einem 1O2‐Fänger detektiert, der schnell
    und selektiv ein Addukt mit 1O2 bildet. Mechanistisch betrachtet entsteht 1O2
    entweder durch protonenunterstützte Disproportionierung von Superoxid während
    des Entladens, Lagerns und Ladens unter ca. 3.3 V oder durch direkte elektrochemische
    1O2‐Entwicklung über ca. 3.3 V. Spuren von Wasser ermöglichen hohe Kapazitäten,
    beschleunigen aber auch Nebenreaktionen. Daher muss das hochreaktive 1O2 unbedingt
    kontrolliert werden, um die Zelle reversibel zu betreiben.
article_processing_charge: No
article_type: original
author:
- first_name: Lukas
  full_name: Schafzahl, Lukas
  last_name: Schafzahl
- first_name: Nika
  full_name: Mahne, Nika
  last_name: Mahne
- first_name: Bettina
  full_name: Schafzahl, Bettina
  last_name: Schafzahl
- first_name: Martin
  full_name: Wilkening, Martin
  last_name: Wilkening
- first_name: Christian
  full_name: Slugovc, Christian
  last_name: Slugovc
- first_name: Sergey M.
  full_name: Borisov, Sergey M.
  last_name: Borisov
- first_name: Stefan Alexander
  full_name: Freunberger, Stefan Alexander
  id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
  last_name: Freunberger
  orcid: 0000-0003-2902-5319
citation:
  ama: Schafzahl L, Mahne N, Schafzahl B, et al. Singulett-Sauerstoff in der aprotischen
    Natrium-O2-Batterie. <i>Angewandte Chemie</i>. 2017;129(49):15934-15938. doi:<a
    href="https://doi.org/10.1002/ange.201709351">10.1002/ange.201709351</a>
  apa: Schafzahl, L., Mahne, N., Schafzahl, B., Wilkening, M., Slugovc, C., Borisov,
    S. M., &#38; Freunberger, S. A. (2017). Singulett-Sauerstoff in der aprotischen
    Natrium-O2-Batterie. <i>Angewandte Chemie</i>. Wiley. <a href="https://doi.org/10.1002/ange.201709351">https://doi.org/10.1002/ange.201709351</a>
  chicago: Schafzahl, Lukas, Nika Mahne, Bettina Schafzahl, Martin Wilkening, Christian
    Slugovc, Sergey M. Borisov, and Stefan Alexander Freunberger. “Singulett-Sauerstoff
    in Der Aprotischen Natrium-O2-Batterie.” <i>Angewandte Chemie</i>. Wiley, 2017.
    <a href="https://doi.org/10.1002/ange.201709351">https://doi.org/10.1002/ange.201709351</a>.
  ieee: L. Schafzahl <i>et al.</i>, “Singulett-Sauerstoff in der aprotischen Natrium-O2-Batterie,”
    <i>Angewandte Chemie</i>, vol. 129, no. 49. Wiley, pp. 15934–15938, 2017.
  ista: Schafzahl L, Mahne N, Schafzahl B, Wilkening M, Slugovc C, Borisov SM, Freunberger
    SA. 2017. Singulett-Sauerstoff in der aprotischen Natrium-O2-Batterie. Angewandte
    Chemie. 129(49), 15934–15938.
  mla: Schafzahl, Lukas, et al. “Singulett-Sauerstoff in Der Aprotischen Natrium-O2-Batterie.”
    <i>Angewandte Chemie</i>, vol. 129, no. 49, Wiley, 2017, pp. 15934–38, doi:<a
    href="https://doi.org/10.1002/ange.201709351">10.1002/ange.201709351</a>.
  short: L. Schafzahl, N. Mahne, B. Schafzahl, M. Wilkening, C. Slugovc, S.M. Borisov,
    S.A. Freunberger, Angewandte Chemie 129 (2017) 15934–15938.
date_created: 2020-06-19T08:22:06Z
date_published: 2017-12-04T00:00:00Z
date_updated: 2021-01-12T08:16:20Z
day: '04'
ddc:
- '540'
doi: 10.1002/ange.201709351
extern: '1'
file:
- access_level: open_access
  checksum: 38f2c2383bc9573f6770c1dba72d7a9a
  content_type: application/pdf
  creator: dernst
  date_created: 2020-06-19T11:39:09Z
  date_updated: 2020-07-14T12:48:06Z
  file_id: '7987'
  file_name: 2017_AngChemieDT_Schafzahl.pdf
  file_size: 988125
  relation: main_file
file_date_updated: 2020-07-14T12:48:06Z
fulldoi: https://doi.org/10.1002/ange.201709351
has_accepted_license: '1'
intvolume: '       129'
issue: '49'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '12'
oa: 1
oa_version: Published Version
page: 15934-15938
publication: Angewandte Chemie
publication_identifier:
  issn:
  - 0044-8249
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Singulett-Sauerstoff in der aprotischen Natrium-O2-Batterie
tmp:
  image: /images/cc_by_nc.png
  legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
  short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 129
year: '2017'
...
---
_id: '7982'
abstract:
- lang: eng
  text: Beyond-intercalation batteries promise a step-change in energy storage compared
    to intercalation-based lithium-ion and sodium-ion batteries. However, only performance
    metrics that include all cell components and operation parameters can tell whether
    a true advance over intercalation batteries has been achieved.
article_number: '17091'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Stefan Alexander
  full_name: Freunberger, Stefan Alexander
  id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
  last_name: Freunberger
  orcid: 0000-0003-2902-5319
citation:
  ama: Freunberger SA. True performance metrics in beyond-intercalation batteries.
    <i>Nature Energy</i>. 2017;2(7). doi:<a href="https://doi.org/10.1038/nenergy.2017.91">10.1038/nenergy.2017.91</a>
  apa: Freunberger, S. A. (2017). True performance metrics in beyond-intercalation
    batteries. <i>Nature Energy</i>. Springer Nature. <a href="https://doi.org/10.1038/nenergy.2017.91">https://doi.org/10.1038/nenergy.2017.91</a>
  chicago: Freunberger, Stefan Alexander. “True Performance Metrics in Beyond-Intercalation
    Batteries.” <i>Nature Energy</i>. Springer Nature, 2017. <a href="https://doi.org/10.1038/nenergy.2017.91">https://doi.org/10.1038/nenergy.2017.91</a>.
  ieee: S. A. Freunberger, “True performance metrics in beyond-intercalation batteries,”
    <i>Nature Energy</i>, vol. 2, no. 7. Springer Nature, 2017.
  ista: Freunberger SA. 2017. True performance metrics in beyond-intercalation batteries.
    Nature Energy. 2(7), 17091.
  mla: Freunberger, Stefan Alexander. “True Performance Metrics in Beyond-Intercalation
    Batteries.” <i>Nature Energy</i>, vol. 2, no. 7, 17091, Springer Nature, 2017,
    doi:<a href="https://doi.org/10.1038/nenergy.2017.91">10.1038/nenergy.2017.91</a>.
  short: S.A. Freunberger, Nature Energy 2 (2017).
date_created: 2020-06-19T08:23:47Z
date_published: 2017-06-05T00:00:00Z
date_updated: 2021-01-12T08:16:20Z
day: '05'
ddc:
- '540'
- '546'
- '541'
doi: 10.1038/nenergy.2017.91
extern: '1'
external_id:
  arxiv:
  - '2002.00712'
file:
- access_level: open_access
  checksum: 2564255b76f5346a32e764dbfd17fa2f
  content_type: application/pdf
  creator: sfreunbe
  date_created: 2020-06-29T13:26:55Z
  date_updated: 2020-07-14T12:48:06Z
  file_id: '8046'
  file_name: NEnergy_Comment_final.pdf
  file_size: 817665
  relation: main_file
file_date_updated: 2020-07-14T12:48:06Z
fulldoi: https://doi.org/10.1038/nenergy.2017.91
has_accepted_license: '1'
intvolume: '         2'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/2002.00712
month: '06'
oa: 1
oa_version: Submitted Version
publication: Nature Energy
publication_identifier:
  issn:
  - 2058-7546
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: True performance metrics in beyond-intercalation batteries
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2017'
...
---
_id: '7986'
article_number: '17036 '
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Nika
  full_name: Mahne, Nika
  last_name: Mahne
- first_name: Bettina
  full_name: Schafzahl, Bettina
  last_name: Schafzahl
- first_name: Christian
  full_name: Leypold, Christian
  last_name: Leypold
- first_name: Mario
  full_name: Leypold, Mario
  last_name: Leypold
- first_name: Sandra
  full_name: Grumm, Sandra
  last_name: Grumm
- first_name: Anita
  full_name: Leitgeb, Anita
  last_name: Leitgeb
- first_name: Gernot A.
  full_name: Strohmeier, Gernot A.
  last_name: Strohmeier
- first_name: Martin
  full_name: Wilkening, Martin
  last_name: Wilkening
- first_name: Olivier
  full_name: Fontaine, Olivier
  last_name: Fontaine
- first_name: Denis
  full_name: Kramer, Denis
  last_name: Kramer
- first_name: Christian
  full_name: Slugovc, Christian
  last_name: Slugovc
- first_name: Sergey M.
  full_name: Borisov, Sergey M.
  last_name: Borisov
- first_name: Stefan Alexander
  full_name: Freunberger, Stefan Alexander
  id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
  last_name: Freunberger
  orcid: 0000-0003-2902-5319
citation:
  ama: Mahne N, Schafzahl B, Leypold C, et al. Singlet oxygen generation as a major
    cause for parasitic reactions during cycling of aprotic lithium–oxygen batteries.
    <i>Nature Energy</i>. 2017;2(5). doi:<a href="https://doi.org/10.1038/nenergy.2017.36">10.1038/nenergy.2017.36</a>
  apa: Mahne, N., Schafzahl, B., Leypold, C., Leypold, M., Grumm, S., Leitgeb, A.,
    … Freunberger, S. A. (2017). Singlet oxygen generation as a major cause for parasitic
    reactions during cycling of aprotic lithium–oxygen batteries. <i>Nature Energy</i>.
    Springer Nature. <a href="https://doi.org/10.1038/nenergy.2017.36">https://doi.org/10.1038/nenergy.2017.36</a>
  chicago: Mahne, Nika, Bettina Schafzahl, Christian Leypold, Mario Leypold, Sandra
    Grumm, Anita Leitgeb, Gernot A. Strohmeier, et al. “Singlet Oxygen Generation
    as a Major Cause for Parasitic Reactions during Cycling of Aprotic Lithium–Oxygen
    Batteries.” <i>Nature Energy</i>. Springer Nature, 2017. <a href="https://doi.org/10.1038/nenergy.2017.36">https://doi.org/10.1038/nenergy.2017.36</a>.
  ieee: N. Mahne <i>et al.</i>, “Singlet oxygen generation as a major cause for parasitic
    reactions during cycling of aprotic lithium–oxygen batteries,” <i>Nature Energy</i>,
    vol. 2, no. 5. Springer Nature, 2017.
  ista: Mahne N, Schafzahl B, Leypold C, Leypold M, Grumm S, Leitgeb A, Strohmeier
    GA, Wilkening M, Fontaine O, Kramer D, Slugovc C, Borisov SM, Freunberger SA.
    2017. Singlet oxygen generation as a major cause for parasitic reactions during
    cycling of aprotic lithium–oxygen batteries. Nature Energy. 2(5), 17036.
  mla: Mahne, Nika, et al. “Singlet Oxygen Generation as a Major Cause for Parasitic
    Reactions during Cycling of Aprotic Lithium–Oxygen Batteries.” <i>Nature Energy</i>,
    vol. 2, no. 5, 17036, Springer Nature, 2017, doi:<a href="https://doi.org/10.1038/nenergy.2017.36">10.1038/nenergy.2017.36</a>.
  short: N. Mahne, B. Schafzahl, C. Leypold, M. Leypold, S. Grumm, A. Leitgeb, G.A.
    Strohmeier, M. Wilkening, O. Fontaine, D. Kramer, C. Slugovc, S.M. Borisov, S.A.
    Freunberger, Nature Energy 2 (2017).
date_created: 2020-06-19T10:42:33Z
date_published: 2017-03-20T00:00:00Z
date_updated: 2021-01-12T08:16:21Z
day: '20'
doi: 10.1038/nenergy.2017.36
extern: '1'
external_id:
  arxiv:
  - '1711.10340'
fulldoi: https://doi.org/10.1038/nenergy.2017.36
intvolume: '         2'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1711.10340
month: '03'
oa: 1
oa_version: Preprint
publication: Nature Energy
publication_identifier:
  issn:
  - 2058-7546
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Singlet oxygen generation as a major cause for parasitic reactions during cycling
  of aprotic lithium–oxygen batteries
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2017'
...
---
_id: '799'
abstract:
- lang: eng
  text: Membrane traffic at the trans-Golgi network (TGN) is crucial for correctly
    distributing various membrane proteins to their destination. Polarly localized
    auxin efflux proteins, including PIN-FORMED1 (PIN1), are dynamically transported
    between the endosomes and the plasma membrane (PM) in the plant cells. The intracellular
    trafficking of PIN1 protein is sensitive to a fungal toxin brefeldin A (BFA),
    which is known to inhibit guanine-nucleotide exchange factors for ADP ribosylation
    factors (ARF GEFs) such as GNOM. However, the molecular details of the BFA-sensitive
    trafficking pathway have not been revealed fully. In a previous study, we have
    identified an Arabidopsis mutant BFA-visualized endocytic trafficking defective
    3 (ben3) which exhibited reduced sensitivity to BFA in terms of BFA-induced intracellular
    PIN1 agglomeration. Here, we show that BEN3 encodes a member of BIG family ARF
    GEFs, BIG2. Fluorescent proteins tagged BEN3/BIG2 co-localized with markers for
    TGN / early endosome (EE). Inspection of conditionally induced de novo synthesized
    PIN1 confirmed that its secretion to the PM is BFA-sensitive and established BEN3/BIG2
    as a crucial component of this BFA action at the level of TGN/EE. Furthermore,
    ben3 mutation alleviated BFA-induced agglomeration of another TGN-localized ARF
    GEF BEN1/MIN7. Taken together our results suggest that BEN3/BIG2 is an ARF GEF
    component, which confers BFA sensitivity to the TGN/EE in Arabidopsis.
article_number: 1801-1811
article_processing_charge: No
author:
- first_name: Saeko
  full_name: Kitakura, Saeko
  last_name: Kitakura
- first_name: Maciek
  full_name: Adamowski, Maciek
  id: 45F536D2-F248-11E8-B48F-1D18A9856A87
  last_name: Adamowski
  orcid: 0000-0001-6463-5257
- first_name: Yuki
  full_name: Matsuura, Yuki
  last_name: Matsuura
- first_name: Luca
  full_name: Santuari, Luca
  last_name: Santuari
- first_name: Hirotaka
  full_name: Kouno, Hirotaka
  last_name: Kouno
- first_name: Kohei
  full_name: Arima, Kohei
  last_name: Arima
- first_name: Christian
  full_name: Hardtke, Christian
  last_name: Hardtke
- first_name: Jirí
  full_name: Friml, Jirí
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
- first_name: Tatsuo
  full_name: Kakimoto, Tatsuo
  last_name: Kakimoto
- first_name: Hirokazu
  full_name: Tanaka, Hirokazu
  last_name: Tanaka
citation:
  ama: Kitakura S, Adamowski M, Matsuura Y, et al. BEN3/BIG2 ARF GEF is involved in
    brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in
    Arabidopsis thaliana. <i>Plant and Cell Physiology</i>. 2017;58(10). doi:<a href="https://doi.org/10.1093/pcp/pcx118">10.1093/pcp/pcx118</a>
  apa: Kitakura, S., Adamowski, M., Matsuura, Y., Santuari, L., Kouno, H., Arima,
    K., … Tanaka, H. (2017). BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive
    trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana.
    <i>Plant and Cell Physiology</i>. Oxford University Press. <a href="https://doi.org/10.1093/pcp/pcx118">https://doi.org/10.1093/pcp/pcx118</a>
  chicago: Kitakura, Saeko, Maciek Adamowski, Yuki Matsuura, Luca Santuari, Hirotaka
    Kouno, Kohei Arima, Christian Hardtke, Jiří Friml, Tatsuo Kakimoto, and Hirokazu
    Tanaka. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive Trafficking at
    the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.” <i>Plant and
    Cell Physiology</i>. Oxford University Press, 2017. <a href="https://doi.org/10.1093/pcp/pcx118">https://doi.org/10.1093/pcp/pcx118</a>.
  ieee: S. Kitakura <i>et al.</i>, “BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive
    trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana,”
    <i>Plant and Cell Physiology</i>, vol. 58, no. 10. Oxford University Press, 2017.
  ista: Kitakura S, Adamowski M, Matsuura Y, Santuari L, Kouno H, Arima K, Hardtke
    C, Friml J, Kakimoto T, Tanaka H. 2017. BEN3/BIG2 ARF GEF is involved in brefeldin
    a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis
    thaliana. Plant and Cell Physiology. 58(10), 1801–1811.
  mla: Kitakura, Saeko, et al. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive
    Trafficking at the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.”
    <i>Plant and Cell Physiology</i>, vol. 58, no. 10, 1801–1811, Oxford University
    Press, 2017, doi:<a href="https://doi.org/10.1093/pcp/pcx118">10.1093/pcp/pcx118</a>.
  short: S. Kitakura, M. Adamowski, Y. Matsuura, L. Santuari, H. Kouno, K. Arima,
    C. Hardtke, J. Friml, T. Kakimoto, H. Tanaka, Plant and Cell Physiology 58 (2017).
date_created: 2018-12-11T11:48:34Z
date_published: 2017-08-21T00:00:00Z
date_updated: 2025-07-10T11:54:55Z
day: '21'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1093/pcp/pcx118
external_id:
  isi:
  - '000413220400019'
  pmid:
  - '29016942'
file:
- access_level: open_access
  checksum: bd3e3a94d55416739cbb19624bb977f8
  content_type: application/pdf
  creator: dernst
  date_created: 2019-04-17T07:52:34Z
  date_updated: 2020-07-14T12:48:06Z
  file_id: '6333'
  file_name: 2017_PlantCellPhysio_Kitakura.pdf
  file_size: 1352913
  relation: main_file
file_date_updated: 2020-07-14T12:48:06Z
fulldoi: https://doi.org/10.1093/pcp/pcx118
has_accepted_license: '1'
intvolume: '        58'
isi: 1
issue: '10'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Plant and Cell Physiology
publication_identifier:
  issn:
  - 0032-0781
publication_status: published
publisher: Oxford University Press
publist_id: '6854'
pubrep_id: '1009'
quality_controlled: '1'
scopus_import: '1'
status: public
title: BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi
  network/early endosome in Arabidopsis thaliana
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 58
year: '2017'
...
---
_id: '800'
abstract:
- lang: eng
  text: Gamma oscillations (30–150 Hz) in neuronal networks are associated with the
    processing and recall of information. We measured local field potentials in the
    dentate gyrus of freely moving mice and found that gamma activity occurs in bursts,
    which are highly heterogeneous in their spatial extensions, ranging from focal
    to global coherent events. Synaptic communication among perisomatic-inhibitory
    interneurons (PIIs) is thought to play an important role in the generation of
    hippocampal gamma patterns. However, how neuronal circuits can generate synchronous
    oscillations at different spatial scales is unknown. We analyzed paired recordings
    in dentate gyrus slices and show that synaptic signaling at interneuron-interneuron
    synapses is distance dependent. Synaptic strength declines whereas the duration
    of inhibitory signals increases with axonal distance among interconnected PIIs.
    Using neuronal network modeling, we show that distance-dependent inhibition generates
    multiple highly synchronous focal gamma bursts allowing the network to process
    complex inputs in parallel in flexibly organized neuronal centers.
article_number: '758'
article_processing_charge: No
author:
- first_name: Michael
  full_name: Strüber, Michael
  last_name: Strüber
- first_name: Jonas
  full_name: Sauer, Jonas
  last_name: Sauer
- 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: Marlene
  full_name: Bartos, Marlene
  last_name: Bartos
citation:
  ama: Strüber M, Sauer J, Jonas PM, Bartos M. Distance-dependent inhibition facilitates
    focality of gamma oscillations in the dentate gyrus. <i>Nature Communications</i>.
    2017;8(1). doi:<a href="https://doi.org/10.1038/s41467-017-00936-3">10.1038/s41467-017-00936-3</a>
  apa: Strüber, M., Sauer, J., Jonas, P. M., &#38; Bartos, M. (2017). Distance-dependent
    inhibition facilitates focality of gamma oscillations in the dentate gyrus. <i>Nature
    Communications</i>. Nature Publishing Group. <a href="https://doi.org/10.1038/s41467-017-00936-3">https://doi.org/10.1038/s41467-017-00936-3</a>
  chicago: Strüber, Michael, Jonas Sauer, Peter M Jonas, and Marlene Bartos. “Distance-Dependent
    Inhibition Facilitates Focality of Gamma Oscillations in the Dentate Gyrus.” <i>Nature
    Communications</i>. Nature Publishing Group, 2017. <a href="https://doi.org/10.1038/s41467-017-00936-3">https://doi.org/10.1038/s41467-017-00936-3</a>.
  ieee: M. Strüber, J. Sauer, P. M. Jonas, and M. Bartos, “Distance-dependent inhibition
    facilitates focality of gamma oscillations in the dentate gyrus,” <i>Nature Communications</i>,
    vol. 8, no. 1. Nature Publishing Group, 2017.
  ista: Strüber M, Sauer J, Jonas PM, Bartos M. 2017. Distance-dependent inhibition
    facilitates focality of gamma oscillations in the dentate gyrus. Nature Communications.
    8(1), 758.
  mla: Strüber, Michael, et al. “Distance-Dependent Inhibition Facilitates Focality
    of Gamma Oscillations in the Dentate Gyrus.” <i>Nature Communications</i>, vol.
    8, no. 1, 758, Nature Publishing Group, 2017, doi:<a href="https://doi.org/10.1038/s41467-017-00936-3">10.1038/s41467-017-00936-3</a>.
  short: M. Strüber, J. Sauer, P.M. Jonas, M. Bartos, Nature Communications 8 (2017).
date_created: 2018-12-11T11:48:34Z
date_published: 2017-10-02T00:00:00Z
date_updated: 2025-07-10T11:54:59Z
day: '02'
ddc:
- '571'
department:
- _id: PeJo
doi: 10.1038/s41467-017-00936-3
ec_funded: 1
external_id:
  isi:
  - '000412053100004'
file:
- access_level: open_access
  checksum: 7e2c7621afd5f802338e92e8619f024d
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:15:17Z
  date_updated: 2020-07-14T12:48:07Z
  file_id: '5135'
  file_name: IST-2017-914-v1+1_s41467-017-00936-3.pdf
  file_size: 4261832
  relation: main_file
file_date_updated: 2020-07-14T12:48:07Z
fulldoi: https://doi.org/10.1038/s41467-017-00936-3
has_accepted_license: '1'
intvolume: '         8'
isi: 1
issue: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '268548'
  name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
publication: Nature Communications
publication_identifier:
  issn:
  - 2041-1723
publication_status: published
publisher: Nature Publishing Group
publist_id: '6853'
pubrep_id: '914'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distance-dependent inhibition facilitates focality of gamma oscillations in
  the dentate gyrus
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '8016'
abstract:
- lang: eng
  text: Long-term modifications of neuronal connections are critical for reliable
    memory storage in the brain. However, their locus of expression—pre- or postsynaptic—is
    highly variable. Here we introduce a theoretical framework in which long-term
    plasticity performs an optimization of the postsynaptic response statistics toward
    a given mean with minimal variance. Consequently, the state of the synapse at
    the time of plasticity induction determines the ratio of pre- and postsynaptic
    modifications. Our theory explains the experimentally observed expression loci
    of the hippocampal and neocortical synaptic potentiation studies we examined.
    Moreover, the theory predicts presynaptic expression of long-term depression,
    consistent with experimental observations. At inhibitory synapses, the theory
    suggests a statistically efficient excitatory-inhibitory balance in which changes
    in inhibitory postsynaptic response statistics specifically target the mean excitation.
    Our results provide a unifying theory for understanding the expression mechanisms
    and functions of long-term synaptic transmission plasticity.
article_processing_charge: No
article_type: original
author:
- first_name: Rui Ponte
  full_name: Costa, Rui Ponte
  last_name: Costa
- first_name: Zahid
  full_name: Padamsey, Zahid
  last_name: Padamsey
- first_name: James A.
  full_name: D’Amour, James A.
  last_name: D’Amour
- first_name: Nigel J.
  full_name: Emptage, Nigel J.
  last_name: Emptage
- first_name: Robert C.
  full_name: Froemke, Robert C.
  last_name: Froemke
- first_name: Tim P
  full_name: Vogels, Tim P
  id: CB6FF8D2-008F-11EA-8E08-2637E6697425
  last_name: Vogels
  orcid: 0000-0003-3295-6181
citation:
  ama: Costa RP, Padamsey Z, D’Amour JA, Emptage NJ, Froemke RC, Vogels TP. Synaptic
    transmission optimization predicts expression loci of long-term plasticity. <i>Neuron</i>.
    2017;96(1):177-189.e7. doi:<a href="https://doi.org/10.1016/j.neuron.2017.09.021">10.1016/j.neuron.2017.09.021</a>
  apa: Costa, R. P., Padamsey, Z., D’Amour, J. A., Emptage, N. J., Froemke, R. C.,
    &#38; Vogels, T. P. (2017). Synaptic transmission optimization predicts expression
    loci of long-term plasticity. <i>Neuron</i>. Elsevier. <a href="https://doi.org/10.1016/j.neuron.2017.09.021">https://doi.org/10.1016/j.neuron.2017.09.021</a>
  chicago: Costa, Rui Ponte, Zahid Padamsey, James A. D’Amour, Nigel J. Emptage, Robert
    C. Froemke, and Tim P Vogels. “Synaptic Transmission Optimization Predicts Expression
    Loci of Long-Term Plasticity.” <i>Neuron</i>. Elsevier, 2017. <a href="https://doi.org/10.1016/j.neuron.2017.09.021">https://doi.org/10.1016/j.neuron.2017.09.021</a>.
  ieee: R. P. Costa, Z. Padamsey, J. A. D’Amour, N. J. Emptage, R. C. Froemke, and
    T. P. Vogels, “Synaptic transmission optimization predicts expression loci of
    long-term plasticity,” <i>Neuron</i>, vol. 96, no. 1. Elsevier, p. 177–189.e7,
    2017.
  ista: Costa RP, Padamsey Z, D’Amour JA, Emptage NJ, Froemke RC, Vogels TP. 2017.
    Synaptic transmission optimization predicts expression loci of long-term plasticity.
    Neuron. 96(1), 177–189.e7.
  mla: Costa, Rui Ponte, et al. “Synaptic Transmission Optimization Predicts Expression
    Loci of Long-Term Plasticity.” <i>Neuron</i>, vol. 96, no. 1, Elsevier, 2017,
    p. 177–189.e7, doi:<a href="https://doi.org/10.1016/j.neuron.2017.09.021">10.1016/j.neuron.2017.09.021</a>.
  short: R.P. Costa, Z. Padamsey, J.A. D’Amour, N.J. Emptage, R.C. Froemke, T.P. Vogels,
    Neuron 96 (2017) 177–189.e7.
date_created: 2020-06-25T12:54:46Z
date_published: 2017-09-27T00:00:00Z
date_updated: 2021-01-12T08:16:32Z
day: '27'
ddc:
- '570'
doi: 10.1016/j.neuron.2017.09.021
extern: '1'
external_id:
  pmid:
  - '28957667'
file:
- access_level: open_access
  checksum: 49fbca2821066c0965bd5678b32b6b48
  content_type: application/pdf
  creator: cziletti
  date_created: 2020-07-09T09:42:49Z
  date_updated: 2020-07-14T12:48:08Z
  file_id: '8103'
  file_name: 2017_Neuron_Costa.pdf
  file_size: 7140149
  relation: main_file
file_date_updated: 2020-07-14T12:48:08Z
fulldoi: https://doi.org/10.1016/j.neuron.2017.09.021
has_accepted_license: '1'
intvolume: '        96'
issue: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 177-189.e7
pmid: 1
publication: Neuron
publication_identifier:
  issn:
  - 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Synaptic transmission optimization predicts expression loci of long-term plasticity
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 96
year: '2017'
...
---
_id: '8017'
abstract:
- lang: eng
  text: nhibitory neurons, although relatively few in number, exert powerful control
    over brain circuits. They stabilize network activity in the face of strong feedback
    excitation and actively engage in computations. Recent studies reveal the importance
    of a precise balance of excitation and inhibition in neural circuits, which often
    requires exquisite fine-tuning of inhibitory connections. We review inhibitory
    synaptic plasticity and its roles in shaping both feedforward and feedback control.
    We discuss the necessity of complex, codependent plasticity mechanisms to build
    nontrivial, functioning networks, and we end by summarizing experimental evidence
    of such interactions.
article_processing_charge: No
article_type: original
author:
- first_name: Guillaume
  full_name: Hennequin, Guillaume
  last_name: Hennequin
- first_name: Everton J.
  full_name: Agnes, Everton J.
  last_name: Agnes
- first_name: Tim P
  full_name: Vogels, Tim P
  id: CB6FF8D2-008F-11EA-8E08-2637E6697425
  last_name: Vogels
  orcid: 0000-0003-3295-6181
citation:
  ama: 'Hennequin G, Agnes EJ, Vogels TP. Inhibitory plasticity: Balance, control,
    and codependence. <i>Annual Review of Neuroscience</i>. 2017;40(1):557-579. doi:<a
    href="https://doi.org/10.1146/annurev-neuro-072116-031005">10.1146/annurev-neuro-072116-031005</a>'
  apa: 'Hennequin, G., Agnes, E. J., &#38; Vogels, T. P. (2017). Inhibitory plasticity:
    Balance, control, and codependence. <i>Annual Review of Neuroscience</i>. Annual
    Reviews. <a href="https://doi.org/10.1146/annurev-neuro-072116-031005">https://doi.org/10.1146/annurev-neuro-072116-031005</a>'
  chicago: 'Hennequin, Guillaume, Everton J. Agnes, and Tim P Vogels. “Inhibitory
    Plasticity: Balance, Control, and Codependence.” <i>Annual Review of Neuroscience</i>.
    Annual Reviews, 2017. <a href="https://doi.org/10.1146/annurev-neuro-072116-031005">https://doi.org/10.1146/annurev-neuro-072116-031005</a>.'
  ieee: 'G. Hennequin, E. J. Agnes, and T. P. Vogels, “Inhibitory plasticity: Balance,
    control, and codependence,” <i>Annual Review of Neuroscience</i>, vol. 40, no.
    1. Annual Reviews, pp. 557–579, 2017.'
  ista: 'Hennequin G, Agnes EJ, Vogels TP. 2017. Inhibitory plasticity: Balance, control,
    and codependence. Annual Review of Neuroscience. 40(1), 557–579.'
  mla: 'Hennequin, Guillaume, et al. “Inhibitory Plasticity: Balance, Control, and
    Codependence.” <i>Annual Review of Neuroscience</i>, vol. 40, no. 1, Annual Reviews,
    2017, pp. 557–79, doi:<a href="https://doi.org/10.1146/annurev-neuro-072116-031005">10.1146/annurev-neuro-072116-031005</a>.'
  short: G. Hennequin, E.J. Agnes, T.P. Vogels, Annual Review of Neuroscience 40 (2017)
    557–579.
date_created: 2020-06-25T12:55:53Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2021-01-12T08:16:32Z
day: '01'
doi: 10.1146/annurev-neuro-072116-031005
extern: '1'
external_id:
  pmid:
  - '28598717'
fulldoi: https://doi.org/10.1146/annurev-neuro-072116-031005
intvolume: '        40'
issue: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 557-579
pmid: 1
publication: Annual Review of Neuroscience
publication_identifier:
  issn:
  - 0147-006X
  - 1545-4126
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
status: public
title: 'Inhibitory plasticity: Balance, control, and codependence'
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 40
year: '2017'
...
---
_id: '8018'
abstract:
- lang: eng
  text: 'Nervous systems use excitatory cell assemblies to encode and represent sensory
    percepts. Similarly, synaptically connected cell assemblies or "engrams" are thought
    to represent memories of past experience. Multiple lines of recent evidence indicate
    that brain systems create and use inhibitory replicas of excitatory representations
    for important cognitive functions. Such matched "inhibitory engrams" can form
    through homeostatic potentiation of inhibition onto postsynaptic cells that show
    increased levels of excitation. Inhibitory engrams can reduce behavioral responses
    to familiar stimuli, thereby resulting in behavioral habituation. In addition,
    by preventing inappropriate activation of excitatory memory engrams, inhibitory
    engrams can make memories quiescent, stored in a latent form that is available
    for context-relevant activation. In neural networks with balanced excitatory and
    inhibitory engrams, the release of innate responses and recall of associative
    memories can occur through focused disinhibition. Understanding mechanisms that
    regulate the formation and expression of inhibitory engrams in vivo may help not
    only to explain key features of cognition but also to provide insight into transdiagnostic
    traits associated with psychiatric conditions such as autism, schizophrenia, and
    posttraumatic stress disorder. '
article_processing_charge: No
article_type: original
author:
- first_name: Helen C.
  full_name: Barron, Helen C.
  last_name: Barron
- first_name: Tim P
  full_name: Vogels, Tim P
  id: CB6FF8D2-008F-11EA-8E08-2637E6697425
  last_name: Vogels
  orcid: 0000-0003-3295-6181
- first_name: Timothy E.
  full_name: Behrens, Timothy E.
  last_name: Behrens
- first_name: Mani
  full_name: Ramaswami, Mani
  last_name: Ramaswami
citation:
  ama: Barron HC, Vogels TP, Behrens TE, Ramaswami M. Inhibitory engrams in perception
    and memory. <i>Proceedings of the National Academy of Sciences</i>. 2017;114(26):6666-6674.
    doi:<a href="https://doi.org/10.1073/pnas.1701812114">10.1073/pnas.1701812114</a>
  apa: Barron, H. C., Vogels, T. P., Behrens, T. E., &#38; Ramaswami, M. (2017). Inhibitory
    engrams in perception and memory. <i>Proceedings of the National Academy of Sciences</i>.
    Proceedings of the National Academy of Sciences. <a href="https://doi.org/10.1073/pnas.1701812114">https://doi.org/10.1073/pnas.1701812114</a>
  chicago: Barron, Helen C., Tim P Vogels, Timothy E. Behrens, and Mani Ramaswami.
    “Inhibitory Engrams in Perception and Memory.” <i>Proceedings of the National
    Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2017.
    <a href="https://doi.org/10.1073/pnas.1701812114">https://doi.org/10.1073/pnas.1701812114</a>.
  ieee: H. C. Barron, T. P. Vogels, T. E. Behrens, and M. Ramaswami, “Inhibitory engrams
    in perception and memory,” <i>Proceedings of the National Academy of Sciences</i>,
    vol. 114, no. 26. Proceedings of the National Academy of Sciences, pp. 6666–6674,
    2017.
  ista: Barron HC, Vogels TP, Behrens TE, Ramaswami M. 2017. Inhibitory engrams in
    perception and memory. Proceedings of the National Academy of Sciences. 114(26),
    6666–6674.
  mla: Barron, Helen C., et al. “Inhibitory Engrams in Perception and Memory.” <i>Proceedings
    of the National Academy of Sciences</i>, vol. 114, no. 26, Proceedings of the
    National Academy of Sciences, 2017, pp. 6666–74, doi:<a href="https://doi.org/10.1073/pnas.1701812114">10.1073/pnas.1701812114</a>.
  short: H.C. Barron, T.P. Vogels, T.E. Behrens, M. Ramaswami, Proceedings of the
    National Academy of Sciences 114 (2017) 6666–6674.
date_created: 2020-06-25T12:56:58Z
date_published: 2017-06-27T00:00:00Z
date_updated: 2021-01-12T08:16:33Z
day: '27'
doi: 10.1073/pnas.1701812114
extern: '1'
external_id:
  pmid:
  - '28611219'
fulldoi: https://doi.org/10.1073/pnas.1701812114
intvolume: '       114'
issue: '26'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5495250/
month: '06'
oa: 1
oa_version: Published Version
page: 6666-6674
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
  eissn:
  - 1091-6490
  issn:
  - 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: Inhibitory engrams in perception and memory
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 114
year: '2017'
...
---
_id: '8019'
abstract:
- lang: eng
  text: Synaptic plasticity is essential for the function of neural systems. It sets
    up initial circuitry and adjusts connection strengths according to the maintenance
    requirements of its host networks. Like all things biological, synaptic plasticity
    must rely on genetic programs to provide the molecular components of its machinery
    to integrate ongoing, often multi-sensory experience without destabilising effects.
    Because of its fundamental importance to healthy behaviour, understanding plasticity
    is thought to hold the key to understanding the brain. There are innumerable ways
    to approach this topic and a complete review of its status quo would be impossible.
    In the current issue we dig into some of the finer points of synaptic plasticity,
    starting small, at the level of genes, and slowly zooming out to synapses, populations
    of synapses, and finally entire systems and brain regions. At each level, we tried
    to represent different perspectives, different systems, and approaches to the
    same questions to give a broad sampling of how synaptic plasticity is being studied.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Tim P
  full_name: Vogels, Tim P
  id: CB6FF8D2-008F-11EA-8E08-2637E6697425
  last_name: Vogels
  orcid: 0000-0003-3295-6181
- first_name: Leslie C
  full_name: Griffith, Leslie C
  last_name: Griffith
citation:
  ama: 'Vogels TP, Griffith LC. Editorial overview: Neurobiology of learning and plasticity
    2017. <i>Current Opinion in Neurobiology</i>. 2017;43:A1-A5. doi:<a href="https://doi.org/10.1016/j.conb.2017.04.002">10.1016/j.conb.2017.04.002</a>'
  apa: 'Vogels, T. P., &#38; Griffith, L. C. (2017). Editorial overview: Neurobiology
    of learning and plasticity 2017. <i>Current Opinion in Neurobiology</i>. Elsevier.
    <a href="https://doi.org/10.1016/j.conb.2017.04.002">https://doi.org/10.1016/j.conb.2017.04.002</a>'
  chicago: 'Vogels, Tim P, and Leslie C Griffith. “Editorial Overview: Neurobiology
    of Learning and Plasticity 2017.” <i>Current Opinion in Neurobiology</i>. Elsevier,
    2017. <a href="https://doi.org/10.1016/j.conb.2017.04.002">https://doi.org/10.1016/j.conb.2017.04.002</a>.'
  ieee: 'T. P. Vogels and L. C. Griffith, “Editorial overview: Neurobiology of learning
    and plasticity 2017,” <i>Current Opinion in Neurobiology</i>, vol. 43. Elsevier,
    pp. A1–A5, 2017.'
  ista: 'Vogels TP, Griffith LC. 2017. Editorial overview: Neurobiology of learning
    and plasticity 2017. Current Opinion in Neurobiology. 43, A1–A5.'
  mla: 'Vogels, Tim P., and Leslie C. Griffith. “Editorial Overview: Neurobiology
    of Learning and Plasticity 2017.” <i>Current Opinion in Neurobiology</i>, vol.
    43, Elsevier, 2017, pp. A1–5, doi:<a href="https://doi.org/10.1016/j.conb.2017.04.002">10.1016/j.conb.2017.04.002</a>.'
  short: T.P. Vogels, L.C. Griffith, Current Opinion in Neurobiology 43 (2017) A1–A5.
date_created: 2020-06-25T13:03:30Z
date_published: 2017-04-17T00:00:00Z
date_updated: 2021-01-12T08:16:33Z
day: '17'
doi: 10.1016/j.conb.2017.04.002
extern: '1'
external_id:
  pmid:
  - '28427877'
fulldoi: https://doi.org/10.1016/j.conb.2017.04.002
intvolume: '        43'
language:
- iso: eng
month: '04'
oa_version: None
page: A1-A5
pmid: 1
publication: Current Opinion in Neurobiology
publication_identifier:
  issn:
  - 0959-4388
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Editorial overview: Neurobiology of learning and plasticity 2017'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2017'
...
---
_id: '803'
abstract:
- lang: eng
  text: Eukaryotic cells store their chromosomes in a single nucleus. This is important
    to maintain genomic integrity, as chromosomes packaged into separate nuclei (micronuclei)
    are prone to massive DNA damage. During mitosis, higher eukaryotes disassemble
    their nucleus and release individualized chromosomes for segregation. How numerous
    chromosomes subsequently reform a single nucleus has remained unclear. Using image-based
    screening of human cells, we identified barrier-to-autointegration factor (BAF)
    as a key factor guiding membranes to form a single nucleus. Unexpectedly, nuclear
    assembly does not require BAF?s association with inner nuclear membrane proteins
    but instead relies on BAF?s ability to bridge distant DNA sites. Live-cell imaging
    and in vitro reconstitution showed that BAF enriches around the mitotic chromosome
    ensemble to induce a densely cross-bridged chromatin layer that is mechanically
    stiff and limits membranes to the surface. Our study reveals that BAF-mediated
    changes in chromosome mechanics underlie nuclear assembly with broad implications
    for proper genome function.
acknowledged_ssus:
- _id: Bio
article_processing_charge: No
author:
- first_name: Matthias
  full_name: Samwer, Matthias
  last_name: Samwer
- first_name: Maximilian
  full_name: Schneider, Maximilian
  last_name: Schneider
- first_name: Rudolf
  full_name: Hoefler, Rudolf
  last_name: Hoefler
- first_name: Philipp S
  full_name: Schmalhorst, Philipp S
  id: 309D50DA-F248-11E8-B48F-1D18A9856A87
  last_name: Schmalhorst
  orcid: 0000-0002-5795-0133
- first_name: Julian
  full_name: Jude, Julian
  last_name: Jude
- first_name: Johannes
  full_name: Zuber, Johannes
  last_name: Zuber
- first_name: Daniel
  full_name: Gerlic, Daniel
  last_name: Gerlic
citation:
  ama: Samwer M, Schneider M, Hoefler R, et al. DNA cross-bridging shapes a single
    nucleus from a set of mitotic chromosomes. <i>Cell</i>. 2017;170(5):956-972. doi:<a
    href="https://doi.org/10.1016/j.cell.2017.07.038">10.1016/j.cell.2017.07.038</a>
  apa: Samwer, M., Schneider, M., Hoefler, R., Schmalhorst, P. S., Jude, J., Zuber,
    J., &#38; Gerlic, D. (2017). DNA cross-bridging shapes a single nucleus from a
    set of mitotic chromosomes. <i>Cell</i>. Cell Press. <a href="https://doi.org/10.1016/j.cell.2017.07.038">https://doi.org/10.1016/j.cell.2017.07.038</a>
  chicago: Samwer, Matthias, Maximilian Schneider, Rudolf Hoefler, Philipp S Schmalhorst,
    Julian Jude, Johannes Zuber, and Daniel Gerlic. “DNA Cross-Bridging Shapes a Single
    Nucleus from a Set of Mitotic Chromosomes.” <i>Cell</i>. Cell Press, 2017. <a
    href="https://doi.org/10.1016/j.cell.2017.07.038">https://doi.org/10.1016/j.cell.2017.07.038</a>.
  ieee: M. Samwer <i>et al.</i>, “DNA cross-bridging shapes a single nucleus from
    a set of mitotic chromosomes,” <i>Cell</i>, vol. 170, no. 5. Cell Press, pp. 956–972,
    2017.
  ista: Samwer M, Schneider M, Hoefler R, Schmalhorst PS, Jude J, Zuber J, Gerlic
    D. 2017. DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes.
    Cell. 170(5), 956–972.
  mla: Samwer, Matthias, et al. “DNA Cross-Bridging Shapes a Single Nucleus from a
    Set of Mitotic Chromosomes.” <i>Cell</i>, vol. 170, no. 5, Cell Press, 2017, pp.
    956–72, doi:<a href="https://doi.org/10.1016/j.cell.2017.07.038">10.1016/j.cell.2017.07.038</a>.
  short: M. Samwer, M. Schneider, R. Hoefler, P.S. Schmalhorst, J. Jude, J. Zuber,
    D. Gerlic, Cell 170 (2017) 956–972.
date_created: 2018-12-11T11:48:35Z
date_published: 2017-08-24T00:00:00Z
date_updated: 2025-07-10T11:55:00Z
day: '24'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1016/j.cell.2017.07.038
external_id:
  isi:
  - '000408372400014'
file:
- access_level: open_access
  checksum: 64897b0c5373f22273f598e4672c60ff
  content_type: application/pdf
  creator: dernst
  date_created: 2019-01-18T13:45:40Z
  date_updated: 2020-07-14T12:48:08Z
  file_id: '5852'
  file_name: 2017_Cell_Samwer.pdf
  file_size: 17666637
  relation: main_file
file_date_updated: 2020-07-14T12:48:08Z
fulldoi: https://doi.org/10.1016/j.cell.2017.07.038
has_accepted_license: '1'
intvolume: '       170'
isi: 1
issue: '5'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 956 - 972
publication: Cell
publication_identifier:
  issn:
  - 0092-8674
publication_status: published
publisher: Cell Press
publist_id: '6848'
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes
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: 170
year: '2017'
...
---
_id: '804'
abstract:
- lang: eng
  text: Polysaccharides (carbohydrates) are key regulators of a large number of cell
    biological processes. However, precise biochemical or genetic manipulation of
    these often complex structures is laborious and hampers experimental structure–function
    studies. Molecular Dynamics (MD) simulations provide a valuable alternative tool
    to generate and test hypotheses on saccharide function. Yet, currently used MD
    force fields often overestimate the aggregation propensity of polysaccharides,
    affecting the usability of those simulations. Here we tested MARTINI, a popular
    coarse-grained (CG) force field for biological macromolecules, for its ability
    to accurately represent molecular forces between saccharides. To this end, we
    calculated a thermodynamic solution property, the second virial coefficient of
    the osmotic pressure (B22). Comparison with light scattering experiments revealed
    a nonphysical aggregation of a prototypical polysaccharide in MARTINI, pointing
    at an imbalance of the nonbonded solute–solute, solute–water, and water–water
    interactions. This finding also applies to smaller oligosaccharides which were
    all found to aggregate in simulations even at moderate concentrations, well below
    their solubility limit. Finally, we explored the influence of the Lennard-Jones
    (LJ) interaction between saccharide molecules and propose a simple scaling of
    the LJ interaction strength that makes MARTINI more reliable for the simulation
    of saccharides.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: P.S.S. was supported by research fellowship 2811/1-1 from the German
  Research Foundation (DFG), and M.S. was supported by EMBO Long Term Fellowship ALTF
  187-2013 and Grant GC65-32 from the  Interdisciplinary Centre for Mathematical and
  Computational Modelling (ICM), University of Warsaw, Poland. The authors thank Antje
  Potthast, Marek Cieplak, Tomasz Włodarski, and Damien Thompson for fruitful discussions
  and the IST Austria Scientific Computing Facility for support.
article_processing_charge: No
arxiv: 1
author:
- first_name: Philipp S
  full_name: Schmalhorst, Philipp S
  id: 309D50DA-F248-11E8-B48F-1D18A9856A87
  last_name: Schmalhorst
  orcid: 0000-0002-5795-0133
- first_name: Felix
  full_name: Deluweit, Felix
  last_name: Deluweit
- first_name: Roger
  full_name: Scherrers, Roger
  last_name: Scherrers
- first_name: Carl-Philipp J
  full_name: Heisenberg, Carl-Philipp J
  id: 39427864-F248-11E8-B48F-1D18A9856A87
  last_name: Heisenberg
  orcid: 0000-0002-0912-4566
- first_name: Mateusz K
  full_name: Sikora, Mateusz K
  id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
  last_name: Sikora
citation:
  ama: Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. Overcoming
    the limitations of the MARTINI force field in simulations of polysaccharides.
    <i>Journal of Chemical Theory and Computation</i>. 2017;13(10):5039-5053. doi:<a
    href="https://doi.org/10.1021/acs.jctc.7b00374">10.1021/acs.jctc.7b00374</a>
  apa: Schmalhorst, P. S., Deluweit, F., Scherrers, R., Heisenberg, C.-P. J., &#38;
    Sikora, M. K. (2017). Overcoming the limitations of the MARTINI force field in
    simulations of polysaccharides. <i>Journal of Chemical Theory and Computation</i>.
    American Chemical Society. <a href="https://doi.org/10.1021/acs.jctc.7b00374">https://doi.org/10.1021/acs.jctc.7b00374</a>
  chicago: Schmalhorst, Philipp S, Felix Deluweit, Roger Scherrers, Carl-Philipp J
    Heisenberg, and Mateusz K Sikora. “Overcoming the Limitations of the MARTINI Force
    Field in Simulations of Polysaccharides.” <i>Journal of Chemical Theory and Computation</i>.
    American Chemical Society, 2017. <a href="https://doi.org/10.1021/acs.jctc.7b00374">https://doi.org/10.1021/acs.jctc.7b00374</a>.
  ieee: P. S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P. J. Heisenberg, and M.
    K. Sikora, “Overcoming the limitations of the MARTINI force field in simulations
    of polysaccharides,” <i>Journal of Chemical Theory and Computation</i>, vol. 13,
    no. 10. American Chemical Society, pp. 5039–5053, 2017.
  ista: Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. 2017.
    Overcoming the limitations of the MARTINI force field in simulations of polysaccharides.
    Journal of Chemical Theory and Computation. 13(10), 5039–5053.
  mla: Schmalhorst, Philipp S., et al. “Overcoming the Limitations of the MARTINI
    Force Field in Simulations of Polysaccharides.” <i>Journal of Chemical Theory
    and Computation</i>, vol. 13, no. 10, American Chemical Society, 2017, pp. 5039–53,
    doi:<a href="https://doi.org/10.1021/acs.jctc.7b00374">10.1021/acs.jctc.7b00374</a>.
  short: P.S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P.J. Heisenberg, M.K. Sikora,
    Journal of Chemical Theory and Computation 13 (2017) 5039–5053.
corr_author: '1'
date_created: 2018-12-11T11:48:35Z
date_published: 2017-10-10T00:00:00Z
date_updated: 2025-06-04T09:49:02Z
day: '10'
department:
- _id: CaHe
doi: 10.1021/acs.jctc.7b00374
external_id:
  arxiv:
  - '1704.03773'
  isi:
  - '000412965700036'
fulldoi: https://doi.org/10.1021/acs.jctc.7b00374
intvolume: '        13'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1704.03773
month: '10'
oa: 1
oa_version: Submitted Version
page: 5039 - 5053
publication: Journal of Chemical Theory and Computation
publication_identifier:
  issn:
  - 1549-9618
publication_status: published
publisher: American Chemical Society
publist_id: '6847'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Overcoming the limitations of the MARTINI force field in simulations of polysaccharides
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2017'
...
---
_id: '805'
abstract:
- lang: eng
  text: During corticogenesis, distinct classes of neurons are born from progenitor
    cells located in the ventricular and subventricular zones, from where they migrate
    towards the pial surface to assemble into highly organized layer-specific circuits.
    However, the precise and coordinated transcriptional network activity defining
    neuronal identity is still not understood. Here, we show that genetic depletion
    of the basic helix-loop-helix (bHLH) transcription factor E2A splice variant E47
    increased the number of Tbr1-positive deep layer and Satb2-positive upper layer
    neurons at E14.5, while depletion of the alternatively spliced E12 variant did
    not affect layer-specific neurogenesis. While ChIP-Seq identified a big overlap
    for E12- and E47-specific binding sites in embryonic NSCs, including sites at
    the cyclin-dependent kinase inhibitor (CDKI) Cdkn1c gene locus, RNA-Seq revealed
    a unique transcriptional regulation by each splice variant. E47 activated the
    expression of the CDKI Cdkn1c through binding to a distal enhancer. Finally, overexpression
    of E47 in embryonic NSCs in vitro impaired neurite outgrowth and E47 overexpression
    in vivo by in utero electroporation disturbed proper layer-specific neurogenesis
    and upregulated p57(KIP2) expression. Overall, this study identified E2A target
    genes in embryonic NSCs and demonstrates that E47 regulates neuronal differentiation
    via p57(KIP2).
article_processing_charge: No
author:
- first_name: Sabrina
  full_name: Pfurr, Sabrina
  last_name: Pfurr
- first_name: Yu
  full_name: Chu, Yu
  last_name: Chu
- first_name: Christian
  full_name: Bohrer, Christian
  last_name: Bohrer
- first_name: Franziska
  full_name: Greulich, Franziska
  last_name: Greulich
- first_name: Robert J
  full_name: Beattie, Robert J
  id: 2E26DF60-F248-11E8-B48F-1D18A9856A87
  last_name: Beattie
  orcid: 0000-0002-8483-8753
- first_name: Könül
  full_name: Mammadzada, Könül
  last_name: Mammadzada
- first_name: Miriam
  full_name: Hils, Miriam
  last_name: Hils
- first_name: Sebastian
  full_name: Arnold, Sebastian
  last_name: Arnold
- first_name: Verdon
  full_name: Taylor, Verdon
  last_name: Taylor
- first_name: Kristina
  full_name: Schachtrup, Kristina
  last_name: Schachtrup
- first_name: N Henriette
  full_name: Uhlenhaut, N Henriette
  last_name: Uhlenhaut
- first_name: Christian
  full_name: Schachtrup, Christian
  last_name: Schachtrup
citation:
  ama: Pfurr S, Chu Y, Bohrer C, et al. The E2A splice variant E47 regulates the differentiation
    of projection neurons via p57(KIP2) during cortical development. <i>Development</i>.
    2017;144:3917-3931. doi:<a href="https://doi.org/10.1242/dev.145698">10.1242/dev.145698</a>
  apa: Pfurr, S., Chu, Y., Bohrer, C., Greulich, F., Beattie, R. J., Mammadzada, K.,
    … Schachtrup, C. (2017). The E2A splice variant E47 regulates the differentiation
    of projection neurons via p57(KIP2) during cortical development. <i>Development</i>.
    Company of Biologists. <a href="https://doi.org/10.1242/dev.145698">https://doi.org/10.1242/dev.145698</a>
  chicago: Pfurr, Sabrina, Yu Chu, Christian Bohrer, Franziska Greulich, Robert J
    Beattie, Könül Mammadzada, Miriam Hils, et al. “The E2A Splice Variant E47 Regulates
    the Differentiation of Projection Neurons via P57(KIP2) during Cortical Development.”
    <i>Development</i>. Company of Biologists, 2017. <a href="https://doi.org/10.1242/dev.145698">https://doi.org/10.1242/dev.145698</a>.
  ieee: S. Pfurr <i>et al.</i>, “The E2A splice variant E47 regulates the differentiation
    of projection neurons via p57(KIP2) during cortical development,” <i>Development</i>,
    vol. 144. Company of Biologists, pp. 3917–3931, 2017.
  ista: Pfurr S, Chu Y, Bohrer C, Greulich F, Beattie RJ, Mammadzada K, Hils M, Arnold
    S, Taylor V, Schachtrup K, Uhlenhaut NH, Schachtrup C. 2017. The E2A splice variant
    E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical
    development. Development. 144, 3917–3931.
  mla: Pfurr, Sabrina, et al. “The E2A Splice Variant E47 Regulates the Differentiation
    of Projection Neurons via P57(KIP2) during Cortical Development.” <i>Development</i>,
    vol. 144, Company of Biologists, 2017, pp. 3917–31, doi:<a href="https://doi.org/10.1242/dev.145698">10.1242/dev.145698</a>.
  short: S. Pfurr, Y. Chu, C. Bohrer, F. Greulich, R.J. Beattie, K. Mammadzada, M.
    Hils, S. Arnold, V. Taylor, K. Schachtrup, N.H. Uhlenhaut, C. Schachtrup, Development
    144 (2017) 3917–3931.
date_created: 2018-12-11T11:48:36Z
date_published: 2017-10-31T00:00:00Z
date_updated: 2023-09-26T16:20:09Z
day: '31'
department:
- _id: SiHi
doi: 10.1242/dev.145698
external_id:
  isi:
  - '000414025600007'
fulldoi: https://doi.org/10.1242/dev.145698
intvolume: '       144'
isi: 1
language:
- iso: eng
month: '10'
oa_version: None
page: 3917 - 3931
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '6846'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The E2A splice variant E47 regulates the differentiation of projection neurons
  via p57(KIP2) during cortical development
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 144
year: '2017'
...
---
_id: '8075'
abstract:
- lang: eng
  text: Ion channel models are the building blocks of computational neuron models.
    Their biological fidelity is therefore crucial for the interpretation of simulations.
    However, the number of published models, and the lack of standardization, make
    the comparison of ion channel models with one another and with experimental data
    difficult. Here, we present a framework for the automated large-scale classification
    of ion channel models. Using annotated metadata and responses to a set of voltage-clamp
    protocols, we assigned 2378 models of voltage- and calcium-gated ion channels
    coded in NEURON to 211 clusters. The IonChannelGenealogy (ICGenealogy) web interface
    provides an interactive resource for the categorization of new and existing models
    and experimental recordings. It enables quantitative comparisons of simulated
    and/or measured ion channel kinetics, and facilitates field-wide standardization
    of experimentally-constrained modeling.
article_number: e22152
article_processing_charge: No
article_type: original
author:
- first_name: William F
  full_name: Podlaski, William F
  last_name: Podlaski
- first_name: Alexander
  full_name: Seeholzer, Alexander
  last_name: Seeholzer
- first_name: Lukas N
  full_name: Groschner, Lukas N
  last_name: Groschner
- first_name: Gero
  full_name: Miesenböck, Gero
  last_name: Miesenböck
- first_name: Rajnish
  full_name: Ranjan, Rajnish
  last_name: Ranjan
- first_name: Tim P
  full_name: Vogels, Tim P
  id: CB6FF8D2-008F-11EA-8E08-2637E6697425
  last_name: Vogels
  orcid: 0000-0003-3295-6181
citation:
  ama: Podlaski WF, Seeholzer A, Groschner LN, Miesenböck G, Ranjan R, Vogels TP.
    Mapping the function of neuronal ion channels in model and experiment. <i>eLife</i>.
    2017;6. doi:<a href="https://doi.org/10.7554/elife.22152">10.7554/elife.22152</a>
  apa: Podlaski, W. F., Seeholzer, A., Groschner, L. N., Miesenböck, G., Ranjan, R.,
    &#38; Vogels, T. P. (2017). Mapping the function of neuronal ion channels in model
    and experiment. <i>ELife</i>. eLife Sciences Publications, Ltd. <a href="https://doi.org/10.7554/elife.22152">https://doi.org/10.7554/elife.22152</a>
  chicago: Podlaski, William F, Alexander Seeholzer, Lukas N Groschner, Gero Miesenböck,
    Rajnish Ranjan, and Tim P Vogels. “Mapping the Function of Neuronal Ion Channels
    in Model and Experiment.” <i>ELife</i>. eLife Sciences Publications, Ltd, 2017.
    <a href="https://doi.org/10.7554/elife.22152">https://doi.org/10.7554/elife.22152</a>.
  ieee: W. F. Podlaski, A. Seeholzer, L. N. Groschner, G. Miesenböck, R. Ranjan, and
    T. P. Vogels, “Mapping the function of neuronal ion channels in model and experiment,”
    <i>eLife</i>, vol. 6. eLife Sciences Publications, Ltd, 2017.
  ista: Podlaski WF, Seeholzer A, Groschner LN, Miesenböck G, Ranjan R, Vogels TP.
    2017. Mapping the function of neuronal ion channels in model and experiment. eLife.
    6, e22152.
  mla: Podlaski, William F., et al. “Mapping the Function of Neuronal Ion Channels
    in Model and Experiment.” <i>ELife</i>, vol. 6, e22152, eLife Sciences Publications,
    Ltd, 2017, doi:<a href="https://doi.org/10.7554/elife.22152">10.7554/elife.22152</a>.
  short: W.F. Podlaski, A. Seeholzer, L.N. Groschner, G. Miesenböck, R. Ranjan, T.P.
    Vogels, ELife 6 (2017).
date_created: 2020-06-30T13:32:18Z
date_published: 2017-03-06T00:00:00Z
date_updated: 2021-01-12T08:16:46Z
day: '06'
ddc:
- '570'
doi: 10.7554/elife.22152
extern: '1'
external_id:
  pmid:
  - '28267430'
file:
- access_level: open_access
  checksum: e5c5a33bcb3ac38ad62df1010ab29040
  content_type: application/pdf
  creator: cziletti
  date_created: 2020-07-16T12:08:40Z
  date_updated: 2020-07-16T12:08:40Z
  file_id: '8124'
  file_name: 2017_elife_Podlaski.pdf
  file_size: 16034505
  relation: main_file
  success: 1
file_date_updated: 2020-07-16T12:08:40Z
fulldoi: https://doi.org/10.7554/elife.22152
has_accepted_license: '1'
intvolume: '         6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
  issn:
  - 2050-084X
publication_status: published
publisher: eLife Sciences Publications, Ltd
quality_controlled: '1'
status: public
title: Mapping the function of neuronal ion channels in model and experiment
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 6
year: '2017'
...
---
_id: '8129'
abstract:
- lang: eng
  text: "Cortical circuits exhibit intricate recurrent architectures that are remarkably
    similar across different brain areas. Such stereotyped structure suggests the
    existence of common computational principles. However, such principles have remained
    largely elusive. Inspired by gated-memory networks, namely long short-term memory
    networks (LSTMs), we introduce a recurrent neural network in which information
    is gated through inhibitory cells that are subtractive (subLSTM). We propose a
    natural mapping of subLSTMs onto known canonical excitatory-inhibitory cortical
    microcircuits. Our empirical evaluation across sequential image classification
    and language modelling tasks shows that subLSTM units can achieve similar performance
    to LSTM units. These results suggest that cortical circuits can be optimised to
    solve complex contextual problems and proposes a novel view on their computational
    function.\r\nOverall our work provides a step towards unifying recurrent networks
    as used in machine learning with their biological counterparts."
article_processing_charge: No
arxiv: 1
author:
- first_name: Rui Ponte
  full_name: Costa, Rui Ponte
  last_name: Costa
- first_name: Yannis M.
  full_name: Assael, Yannis M.
  last_name: Assael
- first_name: Brendan
  full_name: Shillingford, Brendan
  last_name: Shillingford
- first_name: Nando de
  full_name: Freitas, Nando de
  last_name: Freitas
- first_name: Tim P
  full_name: Vogels, Tim P
  id: CB6FF8D2-008F-11EA-8E08-2637E6697425
  last_name: Vogels
  orcid: 0000-0003-3295-6181
citation:
  ama: 'Costa RP, Assael YM, Shillingford B, Freitas N de, Vogels TP. Cortical microcircuits
    as gated-recurrent neural networks. In: <i>Advances in Neural Information Processing
    Systems</i>. Vol 30. Neural Information Processing Systems Foundation; 2017:272-283.'
  apa: 'Costa, R. P., Assael, Y. M., Shillingford, B., Freitas, N. de, &#38; Vogels,
    T. P. (2017). Cortical microcircuits as gated-recurrent neural networks. In <i>Advances
    in Neural Information Processing Systems</i> (Vol. 30, pp. 272–283). Long Beach,
    CA, United States: Neural Information Processing Systems Foundation.'
  chicago: Costa, Rui Ponte, Yannis M. Assael, Brendan Shillingford, Nando de Freitas,
    and Tim P Vogels. “Cortical Microcircuits as Gated-Recurrent Neural Networks.”
    In <i>Advances in Neural Information Processing Systems</i>, 30:272–83. Neural
    Information Processing Systems Foundation, 2017.
  ieee: R. P. Costa, Y. M. Assael, B. Shillingford, N. de Freitas, and T. P. Vogels,
    “Cortical microcircuits as gated-recurrent neural networks,” in <i>Advances in
    Neural Information Processing Systems</i>, Long Beach, CA, United States, 2017,
    vol. 30, pp. 272–283.
  ista: 'Costa RP, Assael YM, Shillingford B, Freitas N de, Vogels TP. 2017. Cortical
    microcircuits as gated-recurrent neural networks. Advances in Neural Information
    Processing Systems. NIPS: Neural Information Processing System vol. 30, 272–283.'
  mla: Costa, Rui Ponte, et al. “Cortical Microcircuits as Gated-Recurrent Neural
    Networks.” <i>Advances in Neural Information Processing Systems</i>, vol. 30,
    Neural Information Processing Systems Foundation, 2017, pp. 272–83.
  short: R.P. Costa, Y.M. Assael, B. Shillingford, N. de Freitas, T.P. Vogels, in:,
    Advances in Neural Information Processing Systems, Neural Information Processing
    Systems Foundation, 2017, pp. 272–283.
conference:
  end_date: 2017-12-09
  location: Long Beach, CA, United States
  name: 'NIPS: Neural Information Processing System'
  start_date: 2017-12-04
date_created: 2020-07-16T19:13:10Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2025-06-26T10:30:43Z
day: '01'
extern: '1'
external_id:
  arxiv:
  - '1711.02448'
intvolume: '        30'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1711.02448
month: '12'
oa: 1
oa_version: Preprint
page: 272-283
publication: Advances in Neural Information Processing Systems
publication_identifier:
  issn:
  - '10495258'
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
status: public
title: Cortical microcircuits as gated-recurrent neural networks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2017'
...
---
_id: '817'
abstract:
- lang: eng
  text: Cryo-electron tomography (cryo-ET) allows cellular ultrastructures and macromolecular
    complexes to be imaged in three-dimensions in their native environments. Cryo-electron
    tomograms are reconstructed from projection images taken at defined tilt-angles.
    In order to recover high-resolution information from cryo-electron tomograms,
    it is necessary to measure and correct for the contrast transfer function (CTF)
    of the microscope. Most commonly, this is performed using protocols that approximate
    the sample as a two-dimensional (2D) plane. This approximation accounts for differences
    in defocus and therefore CTF across the tilted sample. It does not account for
    differences in defocus of objects at different heights within the sample; instead,
    a 3D approach is required. Currently available approaches for 3D-CTF correction
    are computationally expensive and have not been widely implemented. Here we simulate
    the benefits of 3D-CTF correction for high-resolution subtomogram averaging, and
    present a user-friendly, computationally-efficient 3D-CTF correction tool, NovaCTF,
    that is compatible with standard tomogram reconstruction workflows in IMOD. We
    validate the approach on synthetic data and test it using subtomogram averaging
    of real data. Consistent with our simulations, we find that 3D-CTF correction
    allows high-resolution structures to be obtained with much smaller subtomogram
    averaging datasets than are required using 2D-CTF. We also show that using equivalent
    dataset sizes, 3D-CTF correction can be used to obtain higher-resolution structures.
    We present a 3.4. Å resolution structure determined by subtomogram averaging.
author:
- first_name: Beata
  full_name: Turoňová, Beata
  last_name: Turoňová
- first_name: Florian
  full_name: Schur, Florian
  id: 48AD8942-F248-11E8-B48F-1D18A9856A87
  last_name: Schur
  orcid: 0000-0003-4790-8078
- first_name: William
  full_name: Wan, William
  last_name: Wan
- first_name: John
  full_name: Briggs, John
  last_name: Briggs
citation:
  ama: Turoňová B, Schur FK, Wan W, Briggs J. Efficient 3D-CTF correction for cryo-electron
    tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å. <i>Journal
    of Structural Biology</i>. 2017;199(3):187-195. doi:<a href="https://doi.org/10.1016/j.jsb.2017.07.007">10.1016/j.jsb.2017.07.007</a>
  apa: Turoňová, B., Schur, F. K., Wan, W., &#38; Briggs, J. (2017). Efficient 3D-CTF
    correction for cryo-electron tomography using NovaCTF improves subtomogram averaging
    resolution to 3.4Å. <i>Journal of Structural Biology</i>. Academic Press. <a href="https://doi.org/10.1016/j.jsb.2017.07.007">https://doi.org/10.1016/j.jsb.2017.07.007</a>
  chicago: Turoňová, Beata, Florian KM Schur, William Wan, and John Briggs. “Efficient
    3D-CTF Correction for Cryo-Electron Tomography Using NovaCTF Improves Subtomogram
    Averaging Resolution to 3.4Å.” <i>Journal of Structural Biology</i>. Academic
    Press, 2017. <a href="https://doi.org/10.1016/j.jsb.2017.07.007">https://doi.org/10.1016/j.jsb.2017.07.007</a>.
  ieee: B. Turoňová, F. K. Schur, W. Wan, and J. Briggs, “Efficient 3D-CTF correction
    for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution
    to 3.4Å,” <i>Journal of Structural Biology</i>, vol. 199, no. 3. Academic Press,
    pp. 187–195, 2017.
  ista: Turoňová B, Schur FK, Wan W, Briggs J. 2017. Efficient 3D-CTF correction for
    cryo-electron tomography using NovaCTF improves subtomogram averaging resolution
    to 3.4Å. Journal of Structural Biology. 199(3), 187–195.
  mla: Turoňová, Beata, et al. “Efficient 3D-CTF Correction for Cryo-Electron Tomography
    Using NovaCTF Improves Subtomogram Averaging Resolution to 3.4Å.” <i>Journal of
    Structural Biology</i>, vol. 199, no. 3, Academic Press, 2017, pp. 187–95, doi:<a
    href="https://doi.org/10.1016/j.jsb.2017.07.007">10.1016/j.jsb.2017.07.007</a>.
  short: B. Turoňová, F.K. Schur, W. Wan, J. Briggs, Journal of Structural Biology
    199 (2017) 187–195.
date_created: 2018-12-11T11:48:40Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2021-01-12T08:17:16Z
day: '01'
ddc:
- '570'
doi: 10.1016/j.jsb.2017.07.007
extern: '1'
file:
- access_level: open_access
  checksum: 7f2d4bbac767f9acc254d1a4114d181a
  content_type: application/pdf
  creator: kschuh
  date_created: 2019-03-22T09:29:44Z
  date_updated: 2020-07-14T12:48:09Z
  file_id: '6168'
  file_name: 2017_Elsevier_Turonova.pdf
  file_size: 1310009
  relation: main_file
file_date_updated: 2020-07-14T12:48:09Z
fulldoi: https://doi.org/10.1016/j.jsb.2017.07.007
has_accepted_license: '1'
intvolume: '       199'
issue: '3'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 187-195
publication: Journal of Structural Biology
publication_status: published
publisher: Academic Press
publist_id: '6832'
quality_controlled: '1'
status: public
title: Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves
  subtomogram averaging resolution to 3.4Å
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 199
year: '2017'
...
---
OA_place: publisher
_id: '818'
abstract:
- lang: eng
  text: 'Antibiotics have diverse effects on bacteria, including massive changes in
    bacterial gene expression. Whereas the gene expression changes under many antibiotics
    have been measured, the temporal organization of these responses and their dependence
    on the bacterial growth rate are unclear. As described in Chapter 1, we quantified
    the temporal gene expression changes in the bacterium Escherichia coli in response
    to the sudden exposure to antibiotics using a fluorescent reporter library and
    a robotic system. Our data show temporally structured gene expression responses,
    with response times for individual genes ranging from tens of minutes to several
    hours. We observed that many stress response genes were activated in response
    to antibiotics. As certain stress responses cross-protect bacteria from other
    stressors, we then asked whether cellular responses to antibiotics have a similar
    protective role in Chapter 2. Indeed, we found that the trimethoprim-induced acid
    stress response protects bacteria from subsequent acid stress. We combined microfluidics
    with time-lapse imaging to monitor survival, intracellular pH, and acid stress
    response in single cells. This approach revealed that the variable expression
    of the acid resistance operon gadBC strongly correlates with single-cell survival
    time. Cells with higher gadBC expression following trimethoprim maintain higher
    intracellular pH and survive the acid stress longer. Overall, we provide a way
    to identify single-cell cross-protection between antibiotics and environmental
    stressors from temporal gene expression data, and show how antibiotics can increase
    bacterial fitness in changing environments. While gene expression changes to antibiotics
    show a clear temporal structure at the population-level, it is unclear whether
    this clear temporal order is followed by every single cell. Using dual-reporter
    strains described in Chapter 3, we measured gene expression dynamics of promoter
    pairs in the same cells using microfluidics and microscopy. Chapter 4 shows that
    the oxidative stress response and the DNA stress response showed little timing
    variability and a clear temporal order under the antibiotic nitrofurantoin. In
    contrast, the acid stress response under trimethoprim ran independently from all
    other activated response programs including the DNA stress response, which showed
    particularly high timing variability in this stress condition. In summary, this
    approach provides insight into the temporal organization of gene expression programs
    at the single-cell level and suggests dependencies between response programs and
    the underlying variability-introducing mechanisms. Altogether, this work advances
    our understanding of the diverse effects that antibiotics have on bacteria. These
    results were obtained by taking into account gene expression dynamics, which allowed
    us to identify general principles, molecular mechanisms, and dependencies between
    genes. Our findings may have implications for infectious disease treatments, and
    microbial communities in the human body and in nature. '
acknowledgement: 'First of all, I would like to express great gratitude to my PhD
  supervisor Tobias Bollenbach. Through his open and trusting attitude I had the freedom
  to explore different scientific directions during this project, and follow the research
  lines of my interest. I am thankful for constructive and often extensive discussions
  and his support and commitment during the different stages of my PhD. I want to
  thank my committee members, Călin Guet, Terry Hwa and Nassos Typas for their interest
  and their valuable input to this project. Special thanks to Nassos for career guidance,
  and for accepting me in his lab. A big thank you goes to the past, present and affiliated
  members of the Bollenbach group: Guillaume Chevereau, Marjon de Vos, Marta Lukačišinová,
  Veronika Bierbaum, Qi Qin, Marcin Zagórski, Martin Lukačišin, Andreas Angermayr,
  Bor Kavčič, Julia Tischler, Dilay Ayhan, Jaroslav Ferenc, and Georg Rieckh. I enjoyed
  working and discussing with you very much and I will miss our lengthy group meetings,
  our inspiring journal clubs, and our common lunches. Special thanks to Bor for great
  mental and professional support during the hard months of thesis writing, and to
  Marta for very creative times during the beginning of our PhDs. May the ‘Bacterial
  Survival Guide’ decorate the walls of IST forever! A great thanks to my friend and
  collaborator Georg Rieckh for his enthusiasm and for getting so involved in these
  projects, for his endurance and for his company throughout the years. Thanks to
  the FriSBi crowd at IST Austria for interesting meetings and discussions. In particular
  I want to thank Magdalena Steinrück, and Anna Andersson for inspiring exchange,
  and enjoyable time together. Thanks to everybody who contributed to the cover for
  Cell Systems: The constructive input from Tobias Bollenbach, Bor Kavčič, Georg Rieckh,
  Marta Lukačišinová, and Sebastian Nozzi, and the professional implementation by
  the graphic designer Martina Markus from the University of Cologne. Thanks to all
  my office mates in the first floor Bertalanffy building throughout the years: for
  ensuring a pleasant working atmosphere, and for your company! In general, I want
  to thank all the people that make IST such a great environment, with the many possibilities
  to shape our own social and research environment. I want to thank my family for
  all kind of practical support during the years, and my second family in Argentina
  for their enthusiasm. Thanks to my brother Bernhard and my sister Martina for being
  great siblings, and to Helena and Valentin for the joy you brought to my life. My
  deep gratitude goes to Sebastian Nozzi, for constant support, patience, love and
  for believing in me. '
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Karin
  full_name: Mitosch, Karin
  id: 39B66846-F248-11E8-B48F-1D18A9856A87
  last_name: Mitosch
citation:
  ama: Mitosch K. Timing, variability and cross-protection in bacteria – insights
    from dynamic gene expression responses to antibiotics. 2017. doi:<a href="https://doi.org/10.15479/AT:ISTA:th_862">10.15479/AT:ISTA:th_862</a>
  apa: Mitosch, K. (2017). <i>Timing, variability and cross-protection in bacteria
    – insights from dynamic gene expression responses to antibiotics</i>. Institute
    of Science and Technology Austria. <a href="https://doi.org/10.15479/AT:ISTA:th_862">https://doi.org/10.15479/AT:ISTA:th_862</a>
  chicago: Mitosch, Karin. “Timing, Variability and Cross-Protection in Bacteria –
    Insights from Dynamic Gene Expression Responses to Antibiotics.” Institute of
    Science and Technology Austria, 2017. <a href="https://doi.org/10.15479/AT:ISTA:th_862">https://doi.org/10.15479/AT:ISTA:th_862</a>.
  ieee: K. Mitosch, “Timing, variability and cross-protection in bacteria – insights
    from dynamic gene expression responses to antibiotics,” Institute of Science and
    Technology Austria, 2017.
  ista: Mitosch K. 2017. Timing, variability and cross-protection in bacteria – insights
    from dynamic gene expression responses to antibiotics. Institute of Science and
    Technology Austria.
  mla: Mitosch, Karin. <i>Timing, Variability and Cross-Protection in Bacteria – Insights
    from Dynamic Gene Expression Responses to Antibiotics</i>. Institute of Science
    and Technology Austria, 2017, doi:<a href="https://doi.org/10.15479/AT:ISTA:th_862">10.15479/AT:ISTA:th_862</a>.
  short: K. Mitosch, Timing, Variability and Cross-Protection in Bacteria – Insights
    from Dynamic Gene Expression Responses to Antibiotics, Institute of Science and
    Technology Austria, 2017.
corr_author: '1'
date_created: 2018-12-11T11:48:40Z
date_published: 2017-09-27T00:00:00Z
date_updated: 2026-04-08T14:21:57Z
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supervisor:
- first_name: Mark Tobias
  full_name: Bollenbach, Mark Tobias
  id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
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  orcid: 0000-0003-4398-476X
title: Timing, variability and cross-protection in bacteria – insights from dynamic
  gene expression responses to antibiotics
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abstract:
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  text: 'Contagious diseases must transmit from infectious to susceptible hosts in
    order to reproduce. Whilst vectored pathogens can rely on intermediaries to find
    new hosts for them, many infectious pathogens require close contact or direct
    interaction between hosts for transmission. Hence, this means that conspecifics
    are often the main source of infection for most animals and so, in theory, animals
    should avoid conspecifics to reduce their risk of infection. Of course, in reality
    animals must interact with one another, as a bare minimum, to mate. However, being
    social provides many additional benefits and group living has become a taxonomically
    diverse and widespread trait. How then do social animals overcome the issue of
    increased disease? Over the last few decades, the social insects (ants, termites
    and some bees and wasps) have become a model system for studying disease in social
    animals. On paper, a social insect colony should be particularly susceptible to
    disease, given that they often contain thousands of potential hosts that are closely
    related and frequently interact, as well as exhibiting stable environmental conditions
    that encourage microbial growth. Yet, disease outbreaks appear to be rare and
    attempts to eradicate pest species using pathogens have failed time and again.
    Evolutionary biologists investigating this observation have discovered that the
    reduced disease susceptibility in social insects is, in part, due to collectively
    performed disease defences of the workers. These defences act like a “social immune
    system” for the colony, resulting in a per capita decrease in disease, termed
    social immunity. Our understanding of social immunity, and its importance in relation
    to the immunological defences of each insect, continues to grow, but there remain
    many open questions. In this thesis I have studied disease defence in garden ants.
    In the first data chapter, I use the invasive garden ant, Lasius neglectus, to
    investigate how colonies mitigate lethal infections and prevent them from spreading
    systemically. I find that ants have evolved ‘destructive disinfection’ – a behaviour
    that uses endogenously produced acidic poison to kill diseased brood and to prevent
    the pathogen from replicating. In the second experimental chapter, I continue
    to study the use of poison in invasive garden ant colonies, finding that it is
    sprayed prophylactically within the nest. However, this spraying has negative
    effects on developing pupae when they have had their cocoons artificially removed.
    Hence, I suggest that acidic nest sanitation may be maintaining larval cocoon
    spinning in this species. In the next experimental chapter, I investigated how
    colony founding black garden ant queens (Lasius niger) prevent disease when a
    co-foundress dies. I show that ant queens prophylactically perform undertaking
    behaviours, similar to those performed by the workers in mature nests. When a
    co-foundress was infected, these undertaking behaviours improved the survival
    of the healthy queen. In the final data chapter, I explored how immunocompetence
    (measured as antifungal activity) changes as incipient black garden ant colonies
    grow and mature, from the solitary queen phase to colonies with several hundred
    workers. Queen and worker antifungal activity varied throughout this time period,
    but despite social immunity, did not decrease as colonies matured. In addition
    to the above data chapters, this thesis includes two co-authored reviews. In the
    first, we examine the state of the art in the field of social immunity and how
    it might develop in the future. In the second, we identify several challenges
    and open questions in the study of disease defence in animals. We highlight how
    social insects offer a unique model to tackle some of these problems, as disease
    defence can be studied from the cell to the society. '
acknowledgement: "ERC FP7 programme (grant agreement no. 240371)\r\nI have been supremely
  spoilt to work in a lab with such good resources and I must thank the wonderful
  Cremer group technicians, Anna, Barbara, Eva and Florian, for all of their help
  and keeping the lab up and running. You guys will probably be the most missed once
  I realise just how much work you have been saving me! For the same reason, I must
  say a big Dzi ę kuj ę Ci to Wonder Woman Wanda, for her tireless efforts feeding
  my colonies and cranking out thousands of petri dishes and sugar tubes. Again, you
  will be sorely missed now that I will have to take this task on myself. Of course,
  I will be eternally indebted to Prof. Sylvia Cremer for taking me under her wing
  and being a constant source of guidance and inspiration. You have given me the perfect
  balance of independence and supervision. I cannot thank you enough for creating
  such a great working environment and allowing me the freedom to follow my own research
  questions. I have had so many exceptional opportunities – attending and presenting
  at conferences all over the world, inviting me to write the ARE with you, going
  to workshops in Panama and Switzerland, and even organising our own PhD course –
  that I often think I must have had the best PhD in the world. You have taught me
  so much and made me a scientist. I sincerely hope we get the chance to work together
  again in the future. Thank you for everything. I must also thank my PhD Committee,
  Daria Siekhaus and Jacobus “Koos” Boomsma, for being very supportive throughout
  the duration of my PhD. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Christopher
  full_name: Pull, Christopher
  id: 3C7F4840-F248-11E8-B48F-1D18A9856A87
  last_name: Pull
  orcid: 0000-0003-1122-3982
citation:
  ama: Pull C. Disease defence in garden ants. 2017. doi:<a href="https://doi.org/10.15479/AT:ISTA:th_861">10.15479/AT:ISTA:th_861</a>
  apa: Pull, C. (2017). <i>Disease defence in garden ants</i>. Institute of Science
    and Technology Austria. <a href="https://doi.org/10.15479/AT:ISTA:th_861">https://doi.org/10.15479/AT:ISTA:th_861</a>
  chicago: Pull, Christopher. “Disease Defence in Garden Ants.” Institute of Science
    and Technology Austria, 2017. <a href="https://doi.org/10.15479/AT:ISTA:th_861">https://doi.org/10.15479/AT:ISTA:th_861</a>.
  ieee: C. Pull, “Disease defence in garden ants,” Institute of Science and Technology
    Austria, 2017.
  ista: Pull C. 2017. Disease defence in garden ants. Institute of Science and Technology
    Austria.
  mla: Pull, Christopher. <i>Disease Defence in Garden Ants</i>. Institute of Science
    and Technology Austria, 2017, doi:<a href="https://doi.org/10.15479/AT:ISTA:th_861">10.15479/AT:ISTA:th_861</a>.
  short: C. Pull, Disease Defence in Garden Ants, Institute of Science and Technology
    Austria, 2017.
corr_author: '1'
date_created: 2018-12-11T11:48:40Z
date_published: 2017-09-26T00:00:00Z
date_updated: 2026-04-16T10:07:02Z
day: '26'
ddc:
- '576'
- '577'
- '578'
- '579'
- '590'
- '592'
degree_awarded: PhD
department:
- _id: SyCr
doi: 10.15479/AT:ISTA:th_861
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month: '09'
oa: 1
oa_version: Published Version
page: '122'
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supervisor:
- first_name: Sylvia M
  full_name: Cremer, Sylvia M
  id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
  last_name: Cremer
  orcid: 0000-0002-2193-3868
title: Disease defence in garden ants
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...
